diff --git a/licensing/private_license.txt b/licensing/private_license.txt index a9d39041c..bbb8dcf9e 100644 --- a/licensing/private_license.txt +++ b/licensing/private_license.txt @@ -24,7 +24,7 @@ LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic 4. OWNERSHIP OF INTELLECTUAL PROPERTY LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -Copyright 2012-2014 Broad Institute, Inc. +Copyright 2012-2015 Broad Institute, Inc. Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. diff --git a/licensing/protected_license.txt b/licensing/protected_license.txt index a9d39041c..bbb8dcf9e 100644 --- a/licensing/protected_license.txt +++ b/licensing/protected_license.txt @@ -24,7 +24,7 @@ LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic 4. OWNERSHIP OF INTELLECTUAL PROPERTY LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -Copyright 2012-2014 Broad Institute, Inc. +Copyright 2012-2015 Broad Institute, Inc. Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. diff --git a/licensing/public_license.txt b/licensing/public_license.txt index 648ec8fc3..c53c5b34a 100644 --- a/licensing/public_license.txt +++ b/licensing/public_license.txt @@ -1,4 +1,4 @@ -Copyright (c) 2012 The Broad Institute +Copyright 2012-2015 Broad Institute, Inc. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation diff --git a/pom.xml b/pom.xml index da256634c..6490280d1 100644 --- a/pom.xml +++ b/pom.xml @@ -161,6 +161,7 @@ ${gatk.executable.directory}/lib runtime + false diff --git a/protected/gatk-queue-extensions-distribution/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleFindCoveredIntervals.scala b/protected/gatk-queue-extensions-distribution/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleFindCoveredIntervals.scala index 48a393cb6..00b42a871 100644 --- a/protected/gatk-queue-extensions-distribution/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleFindCoveredIntervals.scala +++ b/protected/gatk-queue-extensions-distribution/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleFindCoveredIntervals.scala @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-queue-extensions-distribution/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleHaplotypeCaller.scala b/protected/gatk-queue-extensions-distribution/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleHaplotypeCaller.scala index de7cdd4c6..2f592bcb6 100644 --- a/protected/gatk-queue-extensions-distribution/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleHaplotypeCaller.scala +++ b/protected/gatk-queue-extensions-distribution/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleHaplotypeCaller.scala @@ -1,44 +1,44 @@ /* * By downloading the PROGRAM you agree to the following terms of use: -* +* * BROAD INSTITUTE * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY -* +* * This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). -* +* * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. * NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* +* * 1. DEFINITIONS * 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* +* * 2. LICENSE * 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. * The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. * 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. -* +* * 3. PHONE-HOME FEATURE * LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. -* +* * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* +* * 5. INDEMNIFICATION * LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* +* * 6. NO REPRESENTATIONS OR WARRANTIES * THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. * IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* +* * 7. ASSIGNMENT * This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* +* * 8. MISCELLANEOUS * 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. * 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. diff --git a/protected/gatk-queue-extensions-distribution/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleUnifiedGenotyper.scala b/protected/gatk-queue-extensions-distribution/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleUnifiedGenotyper.scala index 5f4d7dc0b..3120995ec 100644 --- a/protected/gatk-queue-extensions-distribution/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleUnifiedGenotyper.scala +++ b/protected/gatk-queue-extensions-distribution/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleUnifiedGenotyper.scala @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-queue-extensions-distribution/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleUnifiedGenotyperQueueTest.scala b/protected/gatk-queue-extensions-distribution/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleUnifiedGenotyperQueueTest.scala index d49bee6a5..33066ffb0 100644 --- a/protected/gatk-queue-extensions-distribution/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleUnifiedGenotyperQueueTest.scala +++ b/protected/gatk-queue-extensions-distribution/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleUnifiedGenotyperQueueTest.scala @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-queue-extensions-distribution/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/UnmappedExcludedQueueTest.scala b/protected/gatk-queue-extensions-distribution/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/UnmappedExcludedQueueTest.scala index 997f0e9ef..3bb34de38 100644 --- a/protected/gatk-queue-extensions-distribution/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/UnmappedExcludedQueueTest.scala +++ b/protected/gatk-queue-extensions-distribution/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/UnmappedExcludedQueueTest.scala @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/pom.xml b/protected/gatk-tools-protected/pom.xml index 9592586d2..6142872c8 100644 --- a/protected/gatk-tools-protected/pom.xml +++ b/protected/gatk-tools-protected/pom.xml @@ -46,6 +46,11 @@ fastutil + + com.github.broadinstitute + picard + + ${project.groupId} gatk-utils diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/arguments/GenotypeCalculationArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/arguments/GenotypeCalculationArgumentCollection.java index 5974ff3f4..c036ce740 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/arguments/GenotypeCalculationArgumentCollection.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/arguments/GenotypeCalculationArgumentCollection.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -70,22 +70,16 @@ public class GenotypeCalculationArgumentCollection implements Cloneable{ /** * The expected heterozygosity value used to compute prior probability that a locus is non-reference. * - * The default priors are for provided for humans: + * From the heterozygosity we calculate the probability of N samples being hom-ref at a site as 1 - sum_i_2N (hets / i) + * where hets is this case is analogous to the parameter theta from population genetics. See https://en.wikipedia.org/wiki/Coalescent_theory for more details. * - * het = 1e-3 + * Note that heterozygosity as used here is the population genetics concept. (See http://en.wikipedia.org/wiki/Zygosity#Heterozygosity_in_population_genetics. + * We also suggest the book "Population Genetics: A Concise Guide" by John H. Gillespie for further details on the theory.) That is, a hets value of 0.001 + * implies that two randomly chosen chromosomes from the population of organisms would differ from each other at a rate of 1 in 1000 bp. * - * which means that the probability of N samples being hom-ref at a site is: + * The default priors provided for humans (hets = 1e-3) * - * 1 - sum_i_2N (het / i) - * - * Note that heterozygosity as used here is the population genetics concept: - * - * http://en.wikipedia.org/wiki/Zygosity#Heterozygosity_in_population_genetics - * - * That is, a hets value of 0.01 implies that two randomly chosen chromosomes from the population of organisms - * would differ from each other (one being A and the other B) at a rate of 1 in 100 bp. - * - * Note that this quantity has nothing to do with the likelihood of any given sample having a heterozygous genotype, + * Also note that this quantity has nothing to do with the likelihood of any given sample having a heterozygous genotype, * which in the GATK is purely determined by the probability of the observed data P(D | AB) under the model that there * may be a AB het genotype. The posterior probability of this AB genotype would use the het prior, but the GATK * only uses this posterior probability in determining the prob. that a site is polymorphic. So changing the @@ -95,13 +89,13 @@ public class GenotypeCalculationArgumentCollection implements Cloneable{ * The quantity that changes whether the GATK considers the possibility of a het genotype at all is the ploidy, * which determines how many chromosomes each individual in the species carries. */ - @Argument(fullName = "heterozygosity", shortName = "hets", doc = "Heterozygosity value used to compute prior likelihoods for any locus. See the GATKDocs for full details on the meaning of this population genetics concept", required = false) + @Argument(fullName = "heterozygosity", shortName = "hets", doc = "Heterozygosity value used to compute prior likelihoods for any locus", required = false) public Double snpHeterozygosity = HomoSapiensConstants.SNP_HETEROZYGOSITY; /** * This argument informs the prior probability of having an indel at a site. */ - @Argument(fullName = "indel_heterozygosity", shortName = "indelHeterozygosity", doc = "Heterozygosity for indel calling. See the GATKDocs for heterozygosity for full details on the meaning of this population genetics concept", required = false) + @Argument(fullName = "indel_heterozygosity", shortName = "indelHeterozygosity", doc = "Heterozygosity for indel calling", required = false) public double indelHeterozygosity = HomoSapiensConstants.INDEL_HETEROZYGOSITY; /** @@ -135,12 +129,13 @@ public class GenotypeCalculationArgumentCollection implements Cloneable{ * see e.g. Waterson (1975) or Tajima (1996). * This model asserts that the probability of having a population of k variant sites in N chromosomes is proportional to theta/k, for 1=1:N * - * There are instances where using this prior might not be desireable, e.g. for population studies where prior might not be appropriate, + * There are instances where using this prior might not be desirable, e.g. for population studies where prior might not be appropriate, * as for example when the ancestral status of the reference allele is not known. - * By using this argument, user can manually specify priors to be used for calling as a vector for doubles, with the following restriciotns: + * By using this argument, the user can manually specify a list of probabilities for each AC>1 to be used as priors for genotyping, + * with the following restrictions: * a) User must specify 2N values, where N is the number of samples. * b) Only diploid calls supported. - * c) Probability values are specified in double format, in linear space. + * c) Probability values are specified in Double format, in linear space (not log10 space or Phred-scale). * d) No negative values allowed. * e) Values will be added and Pr(AC=0) will be 1-sum, so that they sum up to one. * f) If user-defined values add to more than one, an error will be produced. diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRGatherer.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRGatherer.java index 9ad2282ea..8e663a73b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRGatherer.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRGatherer.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRReadTransformer.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRReadTransformer.java index b524ad08a..9446b578e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRReadTransformer.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRReadTransformer.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -82,7 +82,7 @@ public class BQSRReadTransformer extends ReadTransformer { // Although we could add this check to the apply() method below, it's kind of ugly and inefficient. // The call here would be: RecalUtils.checkForInvalidRecalBams(engine.getSAMFileHeaders(), engine.getArguments().ALLOW_BQSR_ON_REDUCED_BAMS); final BQSRArgumentSet args = engine.getBQSRArgumentSet(); - this.bqsr = new BaseRecalibration(args.getRecalFile(), args.getQuantizationLevels(), args.shouldDisableIndelQuals(), args.getPreserveQscoresLessThan(), args.shouldEmitOriginalQuals(), args.getGlobalQScorePrior()); + this.bqsr = new BaseRecalibration(args.getRecalFile(), args.getQuantizationLevels(), args.shouldDisableIndelQuals(), args.getPreserveQscoresLessThan(), args.shouldEmitOriginalQuals(), args.getGlobalQScorePrior(), args.getStaticQuantizedQuals(), args.getRoundDown()); } final BQSRMode mode = WalkerManager.getWalkerAnnotation(walker, BQSRMode.class); return mode.ApplicationTime(); diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BaseRecalibration.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BaseRecalibration.java index 9095f695e..53fb9c127 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BaseRecalibration.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BaseRecalibration.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -62,6 +62,8 @@ import org.broadinstitute.gatk.utils.recalibration.EventType; import org.broadinstitute.gatk.engine.recalibration.covariates.Covariate; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import java.util.Collections; +import java.util.Iterator; import java.io.File; import java.util.ArrayList; import java.util.List; @@ -86,6 +88,8 @@ public class BaseRecalibration { private final double globalQScorePrior; private final boolean emitOriginalQuals; + private byte[] staticQuantizedMapping = null; + /** * Constructor using a GATK Report file * @@ -93,8 +97,9 @@ public class BaseRecalibration { * @param quantizationLevels number of bins to quantize the quality scores * @param disableIndelQuals if true, do not emit base indel qualities * @param preserveQLessThan preserve quality scores less than this value + * @param staticQuantizedQuals static quantized bins for quality scores */ - public BaseRecalibration(final File RECAL_FILE, final int quantizationLevels, final boolean disableIndelQuals, final int preserveQLessThan, final boolean emitOriginalQuals, final double globalQScorePrior) { + public BaseRecalibration(final File RECAL_FILE, final int quantizationLevels, final boolean disableIndelQuals, final int preserveQLessThan, final boolean emitOriginalQuals, final double globalQScorePrior, final List staticQuantizedQuals, final boolean roundDown) { RecalibrationReport recalibrationReport = new RecalibrationReport(RECAL_FILE); recalibrationTables = recalibrationReport.getRecalibrationTables(); @@ -109,6 +114,15 @@ public class BaseRecalibration { this.preserveQLessThan = preserveQLessThan; this.globalQScorePrior = globalQScorePrior; this.emitOriginalQuals = emitOriginalQuals; + + // staticQuantizedQuals is entirely separate from the dynamic binning that quantizationLevels, and + // staticQuantizedQuals does not make use of quantizationInfo + if(staticQuantizedQuals != null) { + if(staticQuantizedQuals.isEmpty()) { + throw new IllegalStateException("List of static quantized quals is empty."); + } + staticQuantizedMapping = constructStaticQuantizedMapping(staticQuantizedQuals, roundDown); + } } /** @@ -184,7 +198,13 @@ public class BaseRecalibration { // return the quantized version of the recalibrated quality final byte recalibratedQualityScore = quantizationInfo.getQuantizedQuals().get(recalibratedQual); - quals[offset] = recalibratedQualityScore; + // Bin to static quals + if(staticQuantizedMapping != null) { + quals[offset] = staticQuantizedMapping[recalibratedQualityScore]; + } + else { + quals[offset] = recalibratedQualityScore; + } } } } @@ -194,6 +214,67 @@ public class BaseRecalibration { } } + /** + * Constructs an array that maps particular quantized values to a rounded value in staticQuantizedQuals + * + * Rounding is done in probability space. When roundDown is true, we simply round down to the nearest + * available qual in staticQuantizedQuals + * + * @param staticQuantizedQuals the list of qualities to round to + * @param roundDown round down if true, round to nearest (in probability space) otherwise + * @return Array where index representing the quality score to be mapped and the value is the rounded quality score + */ + protected static byte[] constructStaticQuantizedMapping(List staticQuantizedQuals, boolean roundDown) { + // Create array mapping that maps quals to their rounded value. + byte[] mapping = new byte[QualityUtils.MAX_QUAL]; + + Collections.sort(staticQuantizedQuals); + Iterator quantizationIterator = staticQuantizedQuals.iterator(); + + // Fill mapping with one-to-one mappings for values between 0 and MIN_USABLE_Q_SCORE + // This ensures that quals used as special codes will be preserved + for(int i = 0 ; i < QualityUtils.MIN_USABLE_Q_SCORE ; i++) { + mapping[i] = (byte) i; + } + + // If only one staticQuantizedQual is given, fill mappings larger than QualityUtils.MAX_QUAL with that value + if(staticQuantizedQuals.size() == 1) { + int onlyQual = quantizationIterator.next(); + for(int i = QualityUtils.MIN_USABLE_Q_SCORE ; i < QualityUtils.MAX_QUAL ; i++) { + mapping[i] = (byte) onlyQual; + } + return mapping; + } + + int firstQual = QualityUtils.MIN_USABLE_Q_SCORE; + int previousQual = firstQual; + double previousProb = QualityUtils.qualToProb(previousQual); + while(quantizationIterator.hasNext()) { + final int nextQual = quantizationIterator.next(); + final double nextProb = QualityUtils.qualToProb(nextQual); + + for (int i = previousQual ; i < nextQual ; i++) { + if (roundDown) { + mapping[i] = (byte) previousQual; + } else { + final double iProb = QualityUtils.qualToProb(i); + if ((iProb - previousProb) > (nextProb - iProb)) { + mapping[i] = (byte) nextQual; + } else { + mapping[i] = (byte) previousQual; + } + } + } + previousQual = nextQual; + previousProb = nextProb; + } + // Round all quals larger than the largest static qual down to the largest static qual + for(int j = previousQual ; j < QualityUtils.MAX_QUAL ; j++) { + mapping[j] = (byte) previousQual; + } + return mapping; + } + @Ensures("result > 0.0") protected static double hierarchicalBayesianQualityEstimate( final double epsilon, final RecalDatum empiricalQualRG, final RecalDatum empiricalQualQS, final List empiricalQualCovs ) { final double globalDeltaQ = ( empiricalQualRG == null ? 0.0 : empiricalQualRG.getEmpiricalQuality(epsilon) - epsilon ); diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QualQuantizer.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QualQuantizer.java index b01359fca..d9998596d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QualQuantizer.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QualQuantizer.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QuantizationInfo.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QuantizationInfo.java index e054805af..2f2151672 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QuantizationInfo.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QuantizationInfo.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/ReadCovariates.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/ReadCovariates.java index c02dd4881..a21878740 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/ReadCovariates.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/ReadCovariates.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalDatum.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalDatum.java index c92ef1773..43a1d0826 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalDatum.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalDatum.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalDatumNode.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalDatumNode.java index 14b4c762b..d9ad4a7e1 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalDatumNode.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalDatumNode.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalUtils.java index f2f33ee59..c60b1bf1f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalUtils.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalUtils.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationArgumentCollection.java index dcf7ed737..d45ddbef1 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationArgumentCollection.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationArgumentCollection.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -75,18 +75,16 @@ public class RecalibrationArgumentCollection implements Cloneable { /** * This algorithm treats every reference mismatch as an indication of error. However, real genetic variation is expected to mismatch the reference, - * so it is critical that a database of known polymorphic sites is given to the tool in order to skip over those sites. This tool accepts any number of RodBindings (VCF, Bed, etc.) - * for use as this database. For users wishing to exclude an interval list of known variation simply use -XL my.interval.list to skip over processing those sites. - * Please note however that the statistics reported by the tool will not accurately reflected those sites skipped by the -XL argument. + * so it is critical that a database of known polymorphic sites (e.g. dbSNP) is given to the tool in order to mask out those sites. */ - @Input(fullName = "knownSites", shortName = "knownSites", doc = "A database of known polymorphic sites to skip over in the recalibration algorithm", required = false) + @Input(fullName = "knownSites", shortName = "knownSites", doc = "A database of known polymorphic sites", required = false) public List> knownSites = Collections.emptyList(); /** * After the header, data records occur one per line until the end of the file. The first several items on a line are the * values of the individual covariates and will change depending on which covariates were specified at runtime. The last * three items are the data- that is, number of observations for this combination of covariates, number of reference mismatches, - * and the raw empirical quality score calculated by phred-scaling the mismatch rate. Use '/dev/stdout' to print to standard out. + * and the raw empirical quality score calculated by phred-scaling the mismatch rate. */ @Gather(BQSRGatherer.class) @Output(doc = "The output recalibration table file to create", required = true) @@ -107,7 +105,7 @@ public class RecalibrationArgumentCollection implements Cloneable { @Argument(fullName = "covariate", shortName = "cov", doc = "One or more covariates to be used in the recalibration. Can be specified multiple times", required = false) public String[] COVARIATES = null; - /* + /** * The Cycle and Context covariates are standard and are included by default unless this argument is provided. * Note that the ReadGroup and QualityScore covariates are required and cannot be excluded. */ diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReport.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReport.java index a9b401c2b..b9ca005a8 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReport.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReport.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTables.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTables.java index ad227f9bd..70323ad14 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTables.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTables.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ContextCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ContextCovariate.java index f1ef944dc..fa3dc4045 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ContextCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ContextCovariate.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/Covariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/Covariate.java index 4c984c10b..2879efb35 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/Covariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/Covariate.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/CycleCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/CycleCovariate.java index a76a13e4a..23560b627 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/CycleCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/CycleCovariate.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ExperimentalCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ExperimentalCovariate.java index c276f43ec..4cc1d5b98 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ExperimentalCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ExperimentalCovariate.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/QualityScoreCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/QualityScoreCovariate.java index 889e00b9a..6b5243b44 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/QualityScoreCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/QualityScoreCovariate.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ReadGroupCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ReadGroupCovariate.java index 9f4c34463..9fffce30a 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ReadGroupCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ReadGroupCovariate.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatCovariate.java index 64b32d766..7a876db8c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatCovariate.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -113,6 +113,11 @@ public abstract class RepeatCovariate implements ExperimentalCovariate { } + /** + * Please use {@link org.broadinstitute.gatk.utils.variant.TandemRepeatFinder#findMostRelevantTandemRepeatUnitAt(int)} + * @deprecated + */ + @Deprecated public Pair findTandemRepeatUnits(byte[] readBases, int offset) { int maxBW = 0; byte[] bestBWRepeatUnit = new byte[]{readBases[offset]}; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatLengthCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatLengthCovariate.java index fb6aeaf85..96cd80d91 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatLengthCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatLengthCovariate.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitAndLengthCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitAndLengthCovariate.java index 10a7f6672..ff70758b5 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitAndLengthCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitAndLengthCovariate.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitCovariate.java index d961b1460..56da591f2 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitCovariate.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RequiredCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RequiredCovariate.java index 8f2155ff2..a064bd32b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RequiredCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RequiredCovariate.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/StandardCovariate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/StandardCovariate.java index 82e2bd199..9330ae724 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/StandardCovariate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/StandardCovariate.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/package-info.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/package-info.java index 8cc6647b6..8e1822f2a 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/package-info.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/package-info.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/GatherBqsrReports.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/GatherBqsrReports.java new file mode 100644 index 000000000..968ade0e0 --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/GatherBqsrReports.java @@ -0,0 +1,128 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools; + +import htsjdk.samtools.util.IOUtil; +import org.broadinstitute.gatk.engine.recalibration.BQSRGatherer; +import picard.cmdline.CommandLineProgram; +import picard.cmdline.CommandLineProgramProperties; +import picard.cmdline.Option; +import picard.cmdline.StandardOptionDefinitions; + +import java.io.File; +import java.util.List; + +/** + * Gather recalibration reports from parallelized base recalibration runs + * + * This tool is intended to be used to combine recalibration tables from runs of BaseRecalibrator parallelized per-interval. + * The combination is done simply by adding up all observations and errors. + * + *

Usage

+ *

Note that this is a command-line utility that bypasses the GATK engine. As a result, the command-line you must use to + * invoke it is a little different from other GATK tools (see example below), and it does not accept any of the + * classic "CommandLineGATK" arguments.

+ * + *

Input

+ * List of scattered BQSR files + * + *

Output

+ * Combined recalibration table in GATKReport format. + * + *

Command

+ * 
+ *     java -cp GenomeAnalysisTK.jar org.broadinstitute.gatk.tools.GatherBqsrReports \
+ *          -I input.list \
+ *          -O output.grp
+ *
+ * + *

Caveats

+ *
    + *
  • This method DOES NOT recalculate the empirical qualities and quantized qualities. You have to recalculate + * them after combining. The reason for not calculating it is because this function is intended for combining a + * series of recalibration reports, and it only makes sense to calculate the empirical qualities and quantized + * qualities after all the recalibration reports have been combined. This is done to make the tool faster. + *
    • + *
  • The reported empirical quality is recalculated (because it is so simple to do).
    • + *
+ * + */ + +@CommandLineProgramProperties( + usage = "Gathers scattered BQSR recalibration reports into a single file", + usageShort = "Gathers scattered BQSR recalibration reports into a single file" +) +public class GatherBqsrReports extends CommandLineProgram { + @Option(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc="List of scattered BQSR files") + public List INPUT; + + @Option(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc="File to output the gathered file to") + public File OUTPUT; + + public static void main(final String[] args) { + new GatherBqsrReports().instanceMainWithExit(args); + } + + @Override + protected int doWork() { + for (final File report : INPUT) { + IOUtil.assertFileIsReadable(report); + } + + IOUtil.assertFileIsWritable(OUTPUT); + + new BQSRGatherer().gather(INPUT, OUTPUT); + + return 0; + } +} + diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_BaseQualityRankSumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_BaseQualityRankSumTest.java new file mode 100644 index 000000000..dc2183024 --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_BaseQualityRankSumTest.java @@ -0,0 +1,109 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.annotator; + +import htsjdk.variant.vcf.VCFInfoHeaderLine; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AS_StandardAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.ReadUtils; +import org.broadinstitute.gatk.utils.variant.GATKVCFConstants; +import org.broadinstitute.gatk.utils.variant.GATKVCFHeaderLines; + +import java.util.Arrays; +import java.util.List; + + +/** + * Allele-specific rank Sum Test of REF versus ALT base quality scores + * + *

This variant-level annotation compares the base qualities of the data supporting the reference allele with those supporting each alternate allele. To be clear, it does so separately for each alternate allele.

+ * + *

The ideal result is a value close to zero, which indicates there is little to no difference. A negative value indicates that the bases supporting the alternate allele have lower quality scores than those supporting the reference allele. Conversely, a positive value indicates that the bases supporting the alternate allele have higher quality scores than those supporting the reference allele. Finding a statistically significant difference either way suggests that the sequencing process may have been biased or affected by an artifact.

+ * + *

Statistical notes

+ *

The value output for this annotation is the u-based z-approximation from the Mann-Whitney-Wilcoxon Rank Sum Test for base qualities (bases supporting REF vs. bases supporting ALT). See the method document on statistical tests for a more detailed explanation of the ranksum test.

+ * + *

Caveats

+ *
    + *
  • Uninformative reads are not used in these calculations.
    • + *
  • The base quality rank sum test cannot be calculated for sites without a mixture of reads showing both the reference and alternate alleles.
    • + *
+ * + *

Related annotations

+ *
    + *
  • BaseQualityRankSumTest outputs a version of this annotation that includes all alternate alleles in a single calculation.
    • + *
+ * + */ +public class AS_BaseQualityRankSumTest extends AS_RankSumTest implements AS_StandardAnnotation { + @Override + public List getKeyNames() { + return Arrays.asList(GATKVCFConstants.AS_BASE_QUAL_RANK_SUM_KEY); + } + + @Override + public String getRawKeyName() { return GATKVCFConstants.AS_RAW_BASE_QUAL_RANK_SUM_KEY;} + + /** + * Get the element for the given read at the given reference position + * + * @param read the read + * @param refLoc the reference position + * @return a Double representing the element to be used in the rank sum test, or null if it should not be used + */ + @Override + protected Double getElementForRead(final GATKSAMRecord read, final int refLoc) { + return (double) read.getBaseQualities()[ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead(read, refLoc, ReadUtils.ClippingTail.RIGHT_TAIL)]; + } + +} \ No newline at end of file diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_FisherStrand.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_FisherStrand.java new file mode 100644 index 000000000..4166c6bca --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_FisherStrand.java @@ -0,0 +1,154 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.annotator; + +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.*; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.variant.GATKVCFConstants; + +import java.util.Collections; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + + +/** + * Allele-specific strand bias estimated using Fisher's Exact Test + * + * *

Strand bias is a type of sequencing bias in which one DNA strand is favored over the other, which can result in incorrect evaluation of the amount of evidence observed for one allele vs. the other.

+ * + *

The AS_FisherStrand annotation is one of several methods that aims to evaluate whether there is strand bias in the data. It uses Fisher's Exact Test to determine if there is strand bias between forward and reverse strands for the reference or alternate allele, and does so separately for each alternate allele.

+ *

The output is a Phred-scaled p-value. The higher the output value, the more likely there is to be bias. More bias is indicative of false positive calls.

+ * + *

Statistical notes

+ *

See the method document on statistical tests for a more detailed explanation of this application of Fisher's Exact Test.

+ * + *

Caveats

+ *
    + *
  • The FisherStrand test may not be calculated for certain complex indel cases or for multi-allelic sites.
    • + *
  • FisherStrand is best suited for low coverage situations. For testing strand bias in higher coverage situations, see the StrandOddsRatio annotation.
    • + *
+ *

Related annotations

+ *
    + *
  • AS_FisherStrand outputs a version of this annotation that includes all alternate alleles in a single calculation.
    • + *
  • StrandBiasBySample outputs counts of read depth per allele for each strand orientation.
    • + *
  • StrandOddsRatio is an updated form of FisherStrand that uses a symmetric odds ratio calculation.
    • + *
+ * + */ +public class AS_FisherStrand extends AS_StrandBiasTest implements AS_StandardAnnotation { + + @Override + public List getKeyNames() { + return Collections.singletonList(GATKVCFConstants.AS_FISHER_STRAND_KEY); + } + + @Override + protected Map calculateAnnotationFromLikelihoodMap(final Map stratifiedPerReadAlleleLikelihoodMap, + final VariantContext vc) { + // either SNP with no alignment context, or indels: per-read likelihood map needed + final int[][] table = getContingencyTable(stratifiedPerReadAlleleLikelihoodMap, vc, MIN_COUNT); + //logger.info("VC " + vc); + //printTable(table, 0.0); + return pValueAnnotationForBestTable(table, null); + } + + /** + * Create an annotation for the highest (i.e., least significant) p-value of table1 and table2 + * + * @param table1 a contingency table, may be null + * @param table2 a contingency table, may be null + * @return annotation result for FS given tables + */ + private Map pValueAnnotationForBestTable(final int[][] table1, final int[][] table2) { + if ( table2 == null ) + return table1 == null ? null : annotationForOneTable(StrandBiasTableUtils.FisherExactPValueForContingencyTable(table1)); + else if (table1 == null) + return annotationForOneTable(StrandBiasTableUtils.FisherExactPValueForContingencyTable(table2)); + else { // take the one with the best (i.e., least significant pvalue) + double pvalue1 = StrandBiasTableUtils.FisherExactPValueForContingencyTable(table1); + double pvalue2 = StrandBiasTableUtils.FisherExactPValueForContingencyTable(table2); + return annotationForOneTable(Math.max(pvalue1, pvalue2)); + } + } + + /** + * Returns an annotation result given a pValue + * + * @param pValue + * @return a hash map from FS -> phred-scaled pValue + */ + protected Map annotationForOneTable(final double pValue) { + final Object value = String.format("%.3f", QualityUtils.phredScaleErrorRate(Math.max(pValue, MIN_PVALUE))); // prevent INFINITYs + return Collections.singletonMap(getKeyNames().get(0), value); + } + + @Override + protected Map calculateReducedData(AlleleSpecificAnnotationData> combinedData) { + final Map annotationMap = new HashMap<>(); + final Map> perAlleleData = combinedData.getAttributeMap(); + final List refStrandCounts = perAlleleData.get(combinedData.getRefAllele()); + for (final Allele a : perAlleleData.keySet()) { + if(a.equals(combinedData.getRefAllele(),true)) + continue; + final List altStrandCounts = combinedData.getAttribute(a); + final int[][] refAltTable = new int[][] {new int[]{refStrandCounts.get(0),refStrandCounts.get(1)},new int[]{altStrandCounts.get(0),altStrandCounts.get(1)}}; + annotationMap.put(a,QualityUtils.phredScaleErrorRate(Math.max(StrandBiasTableUtils.FisherExactPValueForContingencyTable(refAltTable), MIN_PVALUE))); + } + return annotationMap; + } + + +} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_InbreedingCoeff.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_InbreedingCoeff.java new file mode 100644 index 000000000..3515fe019 --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_InbreedingCoeff.java @@ -0,0 +1,179 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.annotator; + +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFConstants; +import htsjdk.variant.vcf.VCFHeaderLine; +import htsjdk.variant.vcf.VCFInfoHeaderLine; +import org.apache.log4j.Logger; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.walkers.Walker; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AS_StandardAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.variant.GATKVCFConstants; +import org.broadinstitute.gatk.utils.variant.GATKVCFHeaderLines; + +import java.util.*; + +/** + * Allele-specific likelihood-based test for the inbreeding among samples + * + *

This annotation estimates whether there is evidence of inbreeding in a population. The higher the score, the higher the chance that there is inbreeding.

+ * + *

Statistical notes

+ *

The calculation is a continuous generalization of the Hardy-Weinberg test for disequilibrium that works well with limited coverage per sample. The output is the F statistic from running the HW test for disequilibrium with PL values. See the method document on statistical tests for a more detailed explanation of this statistical test.

+ * + *

Caveats

+ *
    + *
  • The inbreeding coefficient can only be calculated for cohorts containing at least 10 founder samples.
    • + *
  • This annotation can take a valid pedigree file to specify founders. If not specified, all samples will be considered as founders.
    • + *
+ * + *

Related annotations

+ *
    + *
  • InbreedingCoeff outputs a version of this annotation that includes all alternate alleles in a single calculation.
    • + *
  • ExcessHet estimates excess heterozygosity in a population of samples.
    • + *
+ * + */ +//TODO: this can't extend InbreedingCoeff because that one is Standard and it would force this to be output all the time; should fix code duplication nonetheless +public class AS_InbreedingCoeff extends InfoFieldAnnotation implements AS_StandardAnnotation { + + private final static Logger logger = Logger.getLogger(InbreedingCoeff.class); + protected static final int MIN_SAMPLES = 10; + private Set founderIds; + private boolean didUniquifiedSampleNameCheck = false; + final private boolean RETURN_ROUNDED = false; + protected HeterozygosityUtils heterozygosityUtils; + + @Override + public void initialize ( AnnotatorCompatible walker, GenomeAnalysisEngine toolkit, Set headerLines ) { + //If available, get the founder IDs and cache them. the IC will only be computed on founders then. + if(founderIds == null && walker != null) { + founderIds = ((Walker) walker).getSampleDB().getFounderIds(); + } + if(walker != null && (((Walker) walker).getSampleDB().getSamples().size() < MIN_SAMPLES || (!founderIds.isEmpty() && founderIds.size() < MIN_SAMPLES))) + logger.warn("Annotation will not be calculated. InbreedingCoeff requires at least " + MIN_SAMPLES + " unrelated samples."); + //intialize a HeterozygosityUtils before annotating for use in unit tests + heterozygosityUtils = new HeterozygosityUtils(RETURN_ROUNDED); + } + + @Override + public List getKeyNames() { return Collections.singletonList(GATKVCFConstants.AS_INBREEDING_COEFFICIENT_KEY); } + + @Override + public List getDescriptions() { return Collections.singletonList(GATKVCFHeaderLines.getInfoLine(getKeyNames().get(0))); } + + @Override + public Map annotate(final RefMetaDataTracker tracker, + final AnnotatorCompatible walker, + final ReferenceContext ref, + final Map stratifiedContexts, + final VariantContext vc, + final Map perReadAlleleLikelihoodMap ) { + + //create a new HeterozygosityUtils to store data for each VariantContext, i.e. each annotate() call + heterozygosityUtils = new HeterozygosityUtils(RETURN_ROUNDED); + + //if none of the "founders" are in the vc samples, assume we uniquified the samples upstream and they are all founders + if (!didUniquifiedSampleNameCheck) { + founderIds = AnnotationUtils.validateFounderIDs(founderIds, vc); + didUniquifiedSampleNameCheck = true; + } + return makeCoeffAnnotation(vc); + } + + protected Map makeCoeffAnnotation(final VariantContext vc) { + final List altAlleles = vc.getAlternateAlleles(); + final List ICvalues = new ArrayList<>(); + + for (final Allele a : altAlleles) { + ICvalues.add(calculateIC(vc, a)); + } + if (heterozygosityUtils.getSampleCount() < MIN_SAMPLES) + return null; + return Collections.singletonMap(getKeyNames().get(0), (Object) AnnotationUtils.encodeValueList(ICvalues, "%.4f")); + } + + protected double calculateIC(final VariantContext vc, final Allele altAllele) { + final int AN = vc.getCalledChrCount(); + final double altAF; + + final double hetCount = heterozygosityUtils.getHetCount(vc, altAllele); + + final double F; + //shortcut to get a value closer to the non-alleleSpecific value for bialleleics + if (vc.isBiallelic()) { + double refAC = heterozygosityUtils.getAlleleCount(vc, vc.getReference()); + double altAC = heterozygosityUtils.getAlleleCount(vc, altAllele); + double refAF = refAC/(altAC+refAC); + altAF = 1 - refAF; + F = 1.0 - (hetCount / (2.0 * refAF * altAF * (double) heterozygosityUtils.getSampleCount())); // inbreeding coefficient + } + else { + //compare number of hets for this allele (and any other second allele) with the expectation based on AFs + //derive the altAF from the likelihoods to account for any accumulation of fractional counts from non-primary likelihoods, + //e.g. for a GQ10 variant, the probability of the call will be ~0.9 and the second best call will be ~0.1 so adding up those 0.1s for het counts can dramatically change the AF compared with integer counts + altAF = heterozygosityUtils.getAlleleCount(vc, altAllele)/ (double) AN; + F = 1.0 - (hetCount / (2.0 * (1 - altAF) * altAF * (double) heterozygosityUtils.getSampleCount())); // inbreeding coefficient + } + + return F; + } +} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_MappingQualityRankSumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_MappingQualityRankSumTest.java new file mode 100644 index 000000000..cc492d193 --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_MappingQualityRankSumTest.java @@ -0,0 +1,104 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.annotator; + +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFInfoHeaderLine; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AS_StandardAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.pileup.PileupElement; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.variant.GATKVCFConstants; +import org.broadinstitute.gatk.utils.variant.GATKVCFHeaderLines; + +import java.util.Arrays; +import java.util.List; +import java.util.Map; + + +/** + * Allele specific Rank Sum Test for mapping qualities of REF versus ALT reads + * + *

This variant-level annotation compares the mapping qualities of the reads supporting the reference allele with those supporting each alternate allele. To be clear, it does so separately for each alternate allele.

+ * + *

The ideal result is a value close to zero, which indicates there is little to no difference. A negative value indicates that the reads supporting the alternate allele have lower mapping quality scores than those supporting the reference allele. Conversely, a positive value indicates that the reads supporting the alternate allele have higher mapping quality scores than those supporting the reference allele.

+ *

Finding a statistically significant difference in quality either way suggests that the sequencing and/or mapping process may have been biased or affected by an artifact. In practice, we only filter out low negative values when evaluating variant quality because the idea is to filter out variants for which the quality of the data supporting the alternate allele is comparatively low. The reverse case, where it is the quality of data supporting the reference allele that is lower (resulting in positive ranksum scores), is not really informative for filtering variants. + * + *

Statistical notes

+ *

The value output for this annotation is the u-based z-approximation from the Mann-Whitney-Wilcoxon Rank Sum Test for mapping qualities (MAPQ of reads supporting REF vs. MAPQ of reads supporting ALT). See the method document on statistical tests for a more detailed explanation of the ranksum test.

+ * + *

Caveats

+ *
  • The mapping quality rank sum test can not be calculated for sites without a mixture of reads showing both the reference and alternate alleles.
    • + *
  • Uninformative reads are not used in these annotations.
    • + *
+ * + *

Related annotations

+ *
    + *
  • MappingQualityRankSumTest outputs a version of this annotation that includes all alternate alleles in a single calculation.
    • + *
  • RMSMappingQuality gives an estimation of the overal read mapping quality supporting a variant call.
    • + *
+ * + */ +public class AS_MappingQualityRankSumTest extends AS_RankSumTest implements AS_StandardAnnotation { + @Override + public List getKeyNames() { return Arrays.asList(GATKVCFConstants.AS_MAP_QUAL_RANK_SUM_KEY); } + + @Override + public String getRawKeyName() { return GATKVCFConstants.AS_RAW_MAP_QUAL_RANK_SUM_KEY;} + + @Override + protected Double getElementForRead(final GATKSAMRecord read, final int refLoc) { + return (double)read.getMappingQuality(); + } +} \ No newline at end of file diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_QualByDepth.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_QualByDepth.java new file mode 100644 index 000000000..4dd30aeae --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_QualByDepth.java @@ -0,0 +1,204 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.annotator; + +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.GenotypesContext; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFInfoHeaderLine; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AS_StandardAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ReducibleAnnotation; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.variant.GATKVCFConstants; +import org.broadinstitute.gatk.utils.variant.GATKVCFHeaderLines; + +import java.util.*; + +/** + * Allele-specific call confidence normalized by depth of sample reads supporting the allele + * + *

This annotation puts the variant confidence QUAL score into perspective by normalizing for the amount of coverage available. Because each read contributes a little to the QUAL score, variants in regions with deep coverage can have artificially inflated QUAL scores, giving the impression that the call is supported by more evidence than it really is. To compensate for this, we normalize the variant confidence by depth, which gives us a more objective picture of how well supported the call is.

+ * + *

Statistical notes

+ *

The QD is the QUAL score normalized by allele depth (AD) for a variant. For a single sample, the HaplotypeCaller calculates the QD by taking QUAL/AD. For multiple samples, HaplotypeCaller and GenotypeGVCFs calculate the QD by taking QUAL/AD of samples with a non hom-ref genotype call. The reason we leave out the samples with a hom-ref call is to not penalize the QUAL for the other samples with the variant call.

+ *

Here is a single-sample example:

+ * 
2	37629	.	C	G	1063.77	.	AC=2;AF=1.00;AN=2;DP=31;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.50;QD=34.32;SOR=2.376	GT:AD:DP:GQ:PL:QSS	1/1:0,31:31:93:1092,93,0:0,960
+

QUAL/AD = 1063.77/31 = 34.32 = QD

+ *

Here is a multi-sample example:

+ * 
10	8046	.	C	T	4107.13	.	AC=1;AF=0.167;AN=6;BaseQRankSum=-3.717;DP=1063;FS=1.616;MLEAC=1;MLEAF=0.167;QD=11.54
+ GT:AD:DP:GQ:PL:QSS	0/0:369,4:373:99:0,1007,12207:10548,98	    0/0:331,1:332:99:0,967,11125:9576,27	    0/1:192,164:356:99:4138,0,5291:5501,4505
+ *

QUAL/AD = 4107.13/356 = 11.54 = QD

+ *

Note that currently, when HaplotypeCaller is run with `-ERC GVCF`, the QD calculation is invoked before AD itself has been calculated, due to a technical constraint. In that case, HaplotypeCaller uses the number of overlapping reads from the haplotype likelihood calculation in place of AD to calculate QD, which generally yields a very similar number. This does not cause any measurable problems, but can cause some confusion since the number may be slightly different than what you would expect to get if you did the calculation manually. For that reason, this behavior will be modified in an upcoming version.

+ * + *

Caveat

+ *

This annotation can only be calculated for sites for which at least one sample was genotyped as carrying a variant allele.

+ * + *

Related annotations

+ *
    + *
  • AS_QualByDepth outputs a version of this annotation that includes all alternate alleles in a single calculation.
    • + *
  • Coverage gives the filtered depth of coverage for each sample and the unfiltered depth across all samples.
    • + *
  • DepthPerAlleleBySample calculates depth of coverage for each allele per sample (AD).
    • + *
+ */ +public class AS_QualByDepth extends InfoFieldAnnotation implements ReducibleAnnotation, AS_StandardAnnotation { + + @Override + public List getKeyNames() { return Arrays.asList(GATKVCFConstants.AS_QUAL_BY_DEPTH_KEY); } + + @Override + public String getRawKeyName() { return GATKVCFConstants.AS_QUAL_KEY; } + + public List getDescriptions() { + //We only have the finalized key name here because the raw key is internal to GenotypeGVCFs and won't get output in any VCF + return Arrays.asList(GATKVCFHeaderLines.getInfoLine(getKeyNames().get(0))); + } + + public Map annotate(final RefMetaDataTracker tracker, + final AnnotatorCompatible walker, + final ReferenceContext ref, + final Map stratifiedContexts, + final VariantContext vc, + final Map perReadAlleleLikelihoodMap ) { + return null; + } + + private List getAlleleDepths(final GenotypesContext genotypes) { + int numAlleles = -1; + for (final Genotype genotype : genotypes) { + if (genotype.hasAD()) { + numAlleles = genotype.getAD().length; + break; + } + } + if (numAlleles == -1) //no genotypes have AD + return null; + Integer[] alleleDepths = new Integer[numAlleles]; + for (int i = 0; i < alleleDepths.length; i++) { + alleleDepths[i] = 0; + } + for (final Genotype genotype : genotypes) { + // we care only about genotypes with variant alleles + if ( !genotype.isHet() && !genotype.isHomVar() ) + continue; + + // if we have the AD values for this sample, let's make sure that the variant depth is greater than 1! + if ( genotype.hasAD() ) { + final int[] AD = genotype.getAD(); + final int totalADdepth = (int) MathUtils.sum(AD); + if ( totalADdepth - AD[0] > 1 ) { + for (int i = 0; i < AD.length; i++) { + alleleDepths[i] += AD[i]; + } + } + } + } + return Arrays.asList(alleleDepths); + } + + @Override + public Map annotateRawData(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc, Map stratifiedPerReadAlleleLikelihoodMap) { + return null; + } + + @Override + public Map combineRawData(List allelesList, List listOfRawData) { + return null; + } + + @Override + public Map finalizeRawData(VariantContext vc, VariantContext originalVC) { + //we need to use the AS_QUAL value that was added to the VC by the GenotypingEngine + if ( !vc.hasAttribute(GATKVCFConstants.AS_QUAL_KEY) ) + return null; + + final GenotypesContext genotypes = vc.getGenotypes(); + if ( genotypes == null || genotypes.isEmpty() ) + return null; + + final List standardDepth = getAlleleDepths(genotypes); + + //Parse the VC's allele-specific qual values + List alleleQualObjList = vc.getAttributeAsList(GATKVCFConstants.AS_QUAL_KEY); + if (alleleQualObjList.size() != vc.getNAlleles() -1) + throw new IllegalStateException("Number of AS_QUAL values doesn't match the number of alternate alleles."); + List alleleQualList = new ArrayList<>(); + for (final Object obj : alleleQualObjList) { + alleleQualList.add(Double.parseDouble(obj.toString())); + } + + // Don't normalize indel length for AS_QD because it will only be called from GenotypeGVCFs, never UG + List QDlist = new ArrayList<>(); + double refDepth = (double)standardDepth.get(0); + for (int i = 0; i < alleleQualList.size(); i++) { + double AS_QD = -10.0 * alleleQualList.get(i) / ((double)standardDepth.get(i+1) + refDepth); //+1 to skip the reference field of the AD, add ref counts to each to match biallelic case + // Hack: see note in the fixTooHighQD method below + AS_QD = QualByDepth.fixTooHighQD(AS_QD); + QDlist.add(AS_QD); + } + + final Map map = new HashMap<>(); + map.put(getKeyNames().get(0), AnnotationUtils.encodeValueList(QDlist, "%.2f")); + return map; + } + + @Override + public void calculateRawData(VariantContext vc, Map pralm, ReducibleAnnotationData rawAnnotations) { + //note that the "raw data" used here is calculated by the GenotypingEngine in GenotypeGVCFs and stored in the AS_QUAL info field + } +} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_RMSAnnotation.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_RMSAnnotation.java new file mode 100644 index 000000000..33930d2a7 --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_RMSAnnotation.java @@ -0,0 +1,192 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.annotator; + +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.GenotypesContext; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFHeaderLine; +import htsjdk.variant.vcf.VCFInfoHeaderLine; +import org.apache.log4j.Logger; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.variant.GATKVCFHeaderLines; + +import java.util.*; + +/** + * Allele-specific implementation of root-mean-squared annotations + */ +public abstract class AS_RMSAnnotation extends RMSAnnotation { + protected final static Logger logger = Logger.getLogger(AS_RMSAnnotation.class); + protected final String splitDelim = "\\|"; //String.split takes a regex, so we need to escape the pipe + protected final String printDelim = "|"; + protected AnnotatorCompatible callingWalker; + + + @Override + public void initialize(final AnnotatorCompatible walker, final GenomeAnalysisEngine toolkit, final Set headerLines) { + if (!AnnotationUtils.walkerSupportsAlleleSpecificAnnotations(walker)) + logger.warn("Allele-specific annotations can only be used with HaplotypeCaller, CombineGVCFs and GenotypeGVCFs -- no data will be output"); + callingWalker = walker; + } + + public List getDescriptions() { + if (AnnotationUtils.walkerRequiresRawData(callingWalker)) + return Arrays.asList(GATKVCFHeaderLines.getInfoLine(getRawKeyName())); + else + return Arrays.asList(GATKVCFHeaderLines.getInfoLine(getKeyNames().get(0))); + } + + //For the raw data here, we're only keeping track of the sum of the squares of our values + //When we go to reduce, we'll use the AD info to get the number of reads + public void calculateRawData(final VariantContext vc, + final Map perReadAlleleLikelihoodMap, + final ReducibleAnnotationData myData) { + + //must use perReadAlleleLikelihoodMap for allele-specific annotations + if (perReadAlleleLikelihoodMap != null) { + if ( perReadAlleleLikelihoodMap.size() == 0 ) + return; + getRMSDataFromPRALM(perReadAlleleLikelihoodMap, myData); + } + else + return; + } + + abstract void getRMSDataFromPRALM(final Map perReadAlleleLikelihoodMap, final ReducibleAnnotationData myData); + + @Override + public Map finalizeRawData(final VariantContext vc, final VariantContext originalVC) { + if (!vc.hasAttribute(getRawKeyName())) + return new HashMap<>(); + final String rawMQdata = vc.getAttributeAsString(getRawKeyName(),null); + if (rawMQdata == null) + return new HashMap<>(); + + final Map annotations = new HashMap<>(); + final ReducibleAnnotationData myData = new AlleleSpecificAnnotationData(originalVC.getAlleles(), rawMQdata); + parseRawDataString(myData); + + final String annotationString = makeFinalizedAnnotationString(vc, myData.getAttributeMap()); + annotations.put(getKeyNames().get(0), annotationString); + return annotations; + } + + @Override + protected void parseRawDataString(final ReducibleAnnotationData myData) { + final String rawDataString = myData.getRawData(); + //get per-allele data by splitting on allele delimiter + final String[] rawDataPerAllele = rawDataString.split(splitDelim); + for (int i=0; i combineRawData(final List vcAlleles, final List annotationList) { + //VC already contains merged alleles from ReferenceConfidenceVariantContextMerger + ReducibleAnnotationData combinedData = new AlleleSpecificAnnotationData(vcAlleles, null); + + for (final ReducibleAnnotationData currentValue : annotationList) { + parseRawDataString(currentValue); + combineAttributeMap(currentValue, combinedData); + + } + final Map annotations = new HashMap<>(); + String annotationString = makeRawAnnotationString(vcAlleles, combinedData.getAttributeMap()); + annotations.put(getRawKeyName(), annotationString); + return annotations; + } + + @Override + public void combineAttributeMap(final ReducibleAnnotationData toAdd, final ReducibleAnnotationData combined) { + //check that alleles match + for (final Allele currentAllele : combined.getAlleles()){ + //combined is initialized with all alleles, but toAdd might have only a subset + if(toAdd.getAttribute(currentAllele) == null) + continue; + if (toAdd.getAttribute(currentAllele) != null && combined.getAttribute(currentAllele) != null) { + combined.putAttribute(currentAllele, (double) combined.getAttribute(currentAllele) + (double) toAdd.getAttribute(currentAllele)); + } + else + combined.putAttribute(currentAllele, toAdd.getAttribute(currentAllele)); + } + } + + protected Map getADcounts(final VariantContext vc) { + final GenotypesContext genotypes = vc.getGenotypes(); + if ( genotypes == null || genotypes.size() == 0 ) { + logger.warn("VC does not have genotypes -- annotations were calculated in wrong order"); + return null; + } + + final Map variantADs = new HashMap<>(); + for(final Allele a : vc.getAlleles()) + variantADs.put(a,0); + + for (final Genotype gt : vc.getGenotypes()) { + if(!gt.hasAD()) { + continue; + } + final int[] ADs = gt.getAD(); + for(int i = 1; i < vc.getNAlleles(); i++) { + variantADs.put(vc.getAlternateAllele(i-1), variantADs.get(vc.getAlternateAllele(i-1))+ADs[i]); //here -1 is to reconcile allele index with alt allele index + } + } + return variantADs; + } +} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_RMSMappingQuality.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_RMSMappingQuality.java new file mode 100644 index 000000000..dc6582997 --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_RMSMappingQuality.java @@ -0,0 +1,152 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.annotator; + +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.*; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.variant.GATKVCFConstants; + +import java.util.*; + + +/** + * Allele-specific Root Mean Square of the mapping quality of reads across all samples. + * + *

This annotation provides an estimation of the mapping quality of reads supporting each alternate allele in a variant call. Depending on the tool it is called from, it produces either raw data (sum of squared MQs) or the calculated root mean square.

+ * + * The raw data is used to accurately calculate the root mean square when combining more than one sample. + * + *

Statistical notes

+ *

The root mean square is equivalent to the mean of the mapping qualities plus the standard deviation of the mapping qualities.

+ * + *

Related annotations

+ * + * + *

Caveat

+ *

Uninformative reads are not used in this annotation.

+ * + *

Related annotations

+ *
    + *
  • RMSMappingQuality outputs a version of this annotation that includes all alternate alleles in a single calculation.
    • + *
  • MappingQualityRankSumTest compares the mapping quality of reads supporting the REF and ALT alleles.
    • + *
+ */ +public class AS_RMSMappingQuality extends AS_RMSAnnotation implements AS_StandardAnnotation, ActiveRegionBasedAnnotation { + + protected final String printFormat = "%.2f"; + + public List getKeyNames() { return Arrays.asList(GATKVCFConstants.AS_RMS_MAPPING_QUALITY_KEY); } + + public String getRawKeyName() { return GATKVCFConstants.AS_RAW_RMS_MAPPING_QUALITY_KEY; } + + public void getRMSDataFromPRALM(Map perReadAlleleLikelihoodMap, ReducibleAnnotationData myData) { + //over all the samples in the Map... + for ( final PerReadAlleleLikelihoodMap perReadLikelihoods : perReadAlleleLikelihoodMap.values() ) { + //for each read... + for ( final Map.Entry> readLikelihoods : perReadLikelihoods.getLikelihoodReadMap().entrySet() ) { + final int mq = readLikelihoods.getKey().getMappingQuality(); + if ( mq != QualityUtils.MAPPING_QUALITY_UNAVAILABLE ) { + if (!PerReadAlleleLikelihoodMap.getMostLikelyAllele(readLikelihoods.getValue()).isInformative()) + continue; + final Allele bestAllele =PerReadAlleleLikelihoodMap.getMostLikelyAllele(readLikelihoods.getValue()).getMostLikelyAllele(); + double currSquareSum = 0; + if (myData.hasAttribute(bestAllele)) + currSquareSum += (double)myData.getAttribute(bestAllele); + myData.putAttribute(bestAllele, currSquareSum + mq * mq); + } + } + } + } + + @Override + public String makeRawAnnotationString(final List vcAlleles, final Map perAlleleValues) { + String annotationString = ""; + for (final Allele current : vcAlleles) { + if (!annotationString.isEmpty()) + annotationString += printDelim; + if(perAlleleValues.get(current) != null) + annotationString += String.format(printFormat,perAlleleValues.get(current)); + else + annotationString += String.format(printFormat, 0.0); + } + return annotationString; + } + + //this just overrides the RMSAnnotation function that's used for UG -- we don't do allele-specific annotations for UG + @Override + public String makeFinalizedAnnotationString(final VariantContext vc, final Map perAlleleData, final Map stratifiedContexts, final Map perReadAlleleLikelihoodMap) { + return makeFinalizedAnnotationString(vc, perAlleleData); + } + + @Override + public String makeFinalizedAnnotationString(final VariantContext vc, final Map perAlleleValues) { + final Map variantADs = getADcounts(vc); + String annotationString = ""; + for (final Allele current : vc.getAlternateAlleles()) { + if (!annotationString.isEmpty()) + annotationString += ","; + if (perAlleleValues.containsKey(current)) + annotationString += String.format(printFormat, Math.sqrt((double) perAlleleValues.get(current) / variantADs.get(current))); + else { + logger.warn("ERROR: VC allele is not found in annotation alleles -- maybe there was trimming?"); + } + } + return annotationString; + } +} \ No newline at end of file diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_RankSumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_RankSumTest.java new file mode 100644 index 000000000..637f4574f --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_RankSumTest.java @@ -0,0 +1,329 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.annotator; + +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFHeaderLine; +import htsjdk.variant.vcf.VCFInfoHeaderLine; +import org.apache.log4j.Logger; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ReducibleAnnotation; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller; +import org.broadinstitute.gatk.tools.walkers.variantutils.CombineGVCFs; +import org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs; +import org.broadinstitute.gatk.utils.MannWhitneyU; +import org.broadinstitute.gatk.utils.collections.Pair; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.exceptions.GATKException; +import org.broadinstitute.gatk.utils.genotyper.MostLikelyAllele; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.variant.GATKVCFHeaderLines; + +import java.util.*; + +/** + * Allele-specific implementation of rank sum test annotations + */ +public abstract class AS_RankSumTest extends RankSumTest implements ReducibleAnnotation { + private final static Logger logger = Logger.getLogger(AS_RMSAnnotation.class); + protected final String splitDelim = "\\|"; //String.split takes a regex, so we need to escape the pipe + protected final String printDelim = "|"; + protected final String reducedDelim = ","; + protected AnnotatorCompatible callingWalker; + + @Override + public void initialize(final AnnotatorCompatible walker, final GenomeAnalysisEngine toolkit, final Set headerLines) { + if (!AnnotationUtils.walkerSupportsAlleleSpecificAnnotations(walker)) + logger.warn("Allele-specific annotations can only be used with HaplotypeCaller, CombineGVCFs and GenotypeGVCFs -- no data will be output"); + callingWalker = walker; + super.initialize(walker, toolkit, headerLines); + } + + public List getDescriptions() { + if (AnnotationUtils.walkerRequiresRawData(callingWalker)) + return Arrays.asList(GATKVCFHeaderLines.getInfoLine(getRawKeyName())); + else + return Arrays.asList(GATKVCFHeaderLines.getInfoLine(getKeyNames().get(0))); + } + + public Map annotateRawData(final RefMetaDataTracker tracker, + final AnnotatorCompatible walker, + final ReferenceContext ref, + final Map stratifiedContexts, + final VariantContext vc, + final Map perReadAlleleLikelihoodMap ) { + + if ( perReadAlleleLikelihoodMap == null) + return new HashMap<>(); + + final Map annotations = new HashMap<>(); + final AlleleSpecificAnnotationData> myData = initializeNewAnnotationData(vc.getAlleles()); + calculateRawData(vc, perReadAlleleLikelihoodMap, myData); + final String annotationString = makeRawAnnotationString(vc.getAlleles(), myData.getAttributeMap()); + annotations.put(getRawKeyName(), annotationString); + return annotations; + } + + protected void parseRawDataString(final ReducibleAnnotationData> myData) { + final String rawDataString = myData.getRawData(); + String rawDataNoBrackets; + final Map> perAlleleValues = new HashMap<>(); + //Initialize maps + for (final Allele current : myData.getAlleles()) { + perAlleleValues.put(current, new CompressedDataList()); + } + //Map gives back list with [] + if (rawDataString.charAt(0) == '[') { + rawDataNoBrackets = rawDataString.substring(1, rawDataString.length() - 1); + } + else { + rawDataNoBrackets = rawDataString; + } + //rawDataPerAllele is the list of values for each allele (each of variable length) + final String[] rawDataPerAllele = rawDataNoBrackets.split(splitDelim); + for (int i=0; i alleleList = perAlleleValues.get(myData.getAlleles().get(i)); + final String[] rawListEntriesAsStringVector = alleleData.split(","); + if (rawListEntriesAsStringVector.length %2 != 0) + throw new GATKException("ERROR: rank sum test raw annotation data must occur in pairs"); + for (int j=0; j combineRawData(final List vcAlleles, final List annotationList) { + //VC already contains merged alleles from ReferenceConfidenceVariantContextMerger + final ReducibleAnnotationData combinedData = initializeNewAnnotationData(vcAlleles); + + for (final ReducibleAnnotationData currentValue : annotationList) { + parseRawDataString(currentValue); + combineAttributeMap(currentValue, combinedData); + + } + final Map annotations = new HashMap<>(); + final String annotationString = makeRawAnnotationString(vcAlleles, combinedData.getAttributeMap()); + annotations.put(getRawKeyName(), annotationString); + return annotations; + } + + protected AlleleSpecificAnnotationData initializeNewAnnotationData(final List vcAlleles) { + Map> perAlleleValues = new HashMap<>(); + for (Allele a : vcAlleles) { + perAlleleValues.put(a, new CompressedDataList()); + } + AlleleSpecificAnnotationData ret = new AlleleSpecificAnnotationData(vcAlleles, perAlleleValues.toString()); + ret.setAttributeMap(perAlleleValues); + return ret; + } + + protected void combineAttributeMap(final ReducibleAnnotationData> toAdd, final ReducibleAnnotationData> combined) { + for (final Allele a : combined.getAlleles()) { + if (toAdd.hasAttribute(a)) { + final CompressedDataList alleleData = combined.getAttribute(a); + alleleData.add(toAdd.getAttribute(a)); + combined.putAttribute(a, alleleData); + } + } + } + + protected String makeRawAnnotationString(final List vcAlleles, final Map> perAlleleValues) { + String annotationString = ""; + for (int i =0; i< vcAlleles.size(); i++) { + if (i!=0) + annotationString += printDelim; + CompressedDataList alleleValues = perAlleleValues.get(vcAlleles.get(i)); + annotationString += alleleValues.toString(); + } + return annotationString; + } + + protected String makeReducedAnnotationString(VariantContext vc, Map perAltRankSumResults) { + String annotationString = ""; + for (final Allele a : vc.getAlternateAlleles()) { + if (!annotationString.isEmpty()) + annotationString += reducedDelim; + if (!perAltRankSumResults.containsKey(a)) + logger.warn("ERROR: VC allele not found in annotation alleles -- maybe there was trimming?"); + else + annotationString += String.format("%.3f", perAltRankSumResults.get(a)); + } + return annotationString; + } + + /** + * + * @param vc -- contains the final set of alleles, possibly subset by GenotypeGVCFs + * @param originalVC -- used to get all the alleles for all gVCFs + * @return + */ + public Map finalizeRawData(final VariantContext vc, final VariantContext originalVC) { + if (!vc.hasAttribute(getRawKeyName())) + return new HashMap<>(); + + final String rawRankSumData = vc.getAttributeAsString(getRawKeyName(),null); + if (rawRankSumData == null) + return new HashMap<>(); + + final Map annotations = new HashMap<>(); + final AlleleSpecificAnnotationData> myData = new AlleleSpecificAnnotationData(originalVC.getAlleles(), rawRankSumData); + parseRawDataString(myData); + + final Map perAltRankSumResults = calculateReducedData(myData.getAttributeMap(), myData.getRefAllele()); + //shortcut for no ref values + if (perAltRankSumResults.isEmpty()) + return annotations; + final String annotationString = makeReducedAnnotationString(vc, perAltRankSumResults); + annotations.put(getKeyNames().get(0), annotationString); + return annotations; + } + + public void calculateRawData(VariantContext vc, Map pralm, ReducibleAnnotationData myData) { + if(pralm == null) + return; + + final Map> perAlleleValues = myData.getAttributeMap(); + for ( final PerReadAlleleLikelihoodMap likelihoodMap : pralm.values() ) { + if ( likelihoodMap != null && !likelihoodMap.isEmpty() ) { + fillQualsFromLikelihoodMap(vc.getAlleles(), vc.getStart(), likelihoodMap, perAlleleValues); + } + } + + } + + private void fillQualsFromLikelihoodMap(final List alleles, + final int refLoc, + final PerReadAlleleLikelihoodMap likelihoodMap, + final Map> perAlleleValues) { + for ( final Map.Entry> el : likelihoodMap.getLikelihoodReadMap().entrySet() ) { + final MostLikelyAllele a = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue()); + if ( ! a.isInformative() ) + continue; // read is non-informative + + final GATKSAMRecord read = el.getKey(); + if ( isUsableRead(read, refLoc) ) { + final Double value = getElementForRead(read, refLoc, a); + if ( value == null ) + continue; + + if(perAlleleValues.containsKey(a.getMostLikelyAllele())) + perAlleleValues.get(a.getMostLikelyAllele()).add(value.intValue()); + } + } + } + + public Map calculateReducedData(final Map> perAlleleValues, final Allele ref) { + final Map perAltRankSumResults = new HashMap<>(); + //shortcut to not try to calculate rank sum if there are no reads that unambiguously support the ref + if (perAlleleValues.get(ref).isEmpty()) + return perAltRankSumResults; + for (final Allele alt : perAlleleValues.keySet()) { + if (alt.equals(ref, false)) + continue; + final MannWhitneyU mannWhitneyU = new MannWhitneyU(useDithering); + //load alts + for (final Number qual : perAlleleValues.get(alt)) { + mannWhitneyU.add(qual, MannWhitneyU.USet.SET1); + } + //load refs + for (final Number qual : perAlleleValues.get(ref)) { + mannWhitneyU.add(qual, MannWhitneyU.USet.SET2); + } + + if (DEBUG) { + System.out.format("%s, REF QUALS:", this.getClass().getName()); + for (final Number qual : perAlleleValues.get(ref)) + System.out.format("%d ", qual); + System.out.println(); + System.out.format("%s, ALT QUALS:", this.getClass().getName()); + for (final Number qual : perAlleleValues.get(alt)) + System.out.format("%d ", qual); + System.out.println(); + + } + // we are testing that set1 (the alt bases) have lower quality scores than set2 (the ref bases) + final Pair testResults = mannWhitneyU.runOneSidedTest(MannWhitneyU.USet.SET1); + perAltRankSumResults.put(alt, testResults.first); + } + return perAltRankSumResults; + } + +} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_ReadPosRankSumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_ReadPosRankSumTest.java new file mode 100644 index 000000000..d125c2fe5 --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_ReadPosRankSumTest.java @@ -0,0 +1,116 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.annotator; + + +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AS_StandardAnnotation; +import org.broadinstitute.gatk.utils.pileup.PileupElement; +import org.broadinstitute.gatk.utils.sam.AlignmentUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.ReadUtils; +import org.broadinstitute.gatk.utils.variant.GATKVCFConstants; + +import java.util.Arrays; +import java.util.List; + +/** + * Allele-specific Rank Sum Test for relative positioning of REF versus ALT allele within reads + * + *

This variant-level annotation tests whether there is evidence of bias in the position of alleles within the reads that support them, between the reference and each alternate allele. To be clear, it does so separately for each alternate allele.

+ * + *

Seeing an allele only near the ends of reads is indicative of error, because that is where sequencers tend to make the most errors. However, some variants located near the edges of sequenced regions will necessarily be covered by the ends of reads, so we can't just set an absolute "minimum distance from end of read" threshold. That is why we use a rank sum test to evaluate whether there is a difference in how well the reference allele and the alternate allele are supported.

+ * + *

The ideal result is a value close to zero, which indicates there is little to no difference in where the alleles are found relative to the ends of reads. A negative value indicates that the alternate allele is found at the ends of reads more often than the reference allele. Conversely, a positive value indicates that the reference allele is found at the ends of reads more often than the alternate allele.

+ * + *

This annotation can be used to evaluate confidence in a variant call and is a recommended covariate for variant recalibration (VQSR). Finding a statistically significant difference in relative position either way suggests that the sequencing process may have been biased or affected by an artifact. In practice, we only filter out low negative values when evaluating variant quality because the idea is to filter out variants for which the quality of the data supporting the alternate allele is comparatively low. The reverse case, where it is the quality of data supporting the reference allele that is lower (resulting in positive ranksum scores), is not really informative for filtering variants.

+ * + *

Statistical notes

+ *

The value output for this annotation is the u-based z-approximation from the Mann-Whitney-Wilcoxon Rank Sum Test for site position within reads (position within reads supporting REF vs. position within reads supporting ALT). See the method document on statistical tests for a more detailed explanation of the ranksum test.

+ * + *

Caveat

+ *
    + *
  • The read position rank sum test can not be calculated for sites without a mixture of reads showing both the reference and alternate alleles.
    • + *
  • Uninformative reads are not used in these annotations.
    • + *
+ * + *

Related annotations

+ *
    + *
  • ReadPosRankRankSumTest outputs a version of this annotation that includes all alternate alleles in a single calculation.
    • + *
+ * + */ +public class AS_ReadPosRankSumTest extends AS_RankSumTest implements AS_StandardAnnotation { + + @Override + public List getKeyNames() { return Arrays.asList(GATKVCFConstants.AS_READ_POS_RANK_SUM_KEY); } + + @Override + public String getRawKeyName() { return GATKVCFConstants.AS_RAW_READ_POS_RANK_SUM_KEY;} + + @Override + protected Double getElementForRead(final GATKSAMRecord read, final int refLoc) { + final int offset = ReadUtils.getReadCoordinateForReferenceCoordinate(read.getSoftStart(), read.getCigar(), refLoc, ReadUtils.ClippingTail.RIGHT_TAIL, true); + if ( offset == ReadUtils.CLIPPING_GOAL_NOT_REACHED ) + return null; + + int readPos = AlignmentUtils.calcAlignmentByteArrayOffset(read.getCigar(), offset, false, 0, 0); + final int numAlignedBases = AlignmentUtils.getNumAlignedBasesCountingSoftClips( read ); + if (readPos > numAlignedBases / 2) + readPos = numAlignedBases - (readPos + 1); + return (double)readPos; + } + + @Override + protected boolean isUsableRead(final GATKSAMRecord read, final int refLoc) { + return super.isUsableRead(read, refLoc) && read.getSoftStart() + read.getCigar().getReadLength() > refLoc; + } +} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_StrandBiasTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_StrandBiasTest.java new file mode 100644 index 000000000..acda6c7ad --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_StrandBiasTest.java @@ -0,0 +1,379 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.annotator; + +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.GenotypesContext; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFHeaderLine; +import htsjdk.variant.vcf.VCFInfoHeaderLine; +import org.apache.log4j.Logger; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ReducibleAnnotation; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.exceptions.GATKException; +import org.broadinstitute.gatk.utils.genotyper.MostLikelyAllele; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.variant.GATKVCFConstants; +import org.broadinstitute.gatk.utils.variant.GATKVCFHeaderLines; + +import java.util.*; + +/** + * Allele-specific implementation of strand bias annotations + */ +public abstract class AS_StrandBiasTest extends StrandBiasTest implements ReducibleAnnotation { + private final static Logger logger = Logger.getLogger(StrandBiasTest.class); + protected final String splitDelim = "\\|"; //String.split takes a regex, so we need to escape the pipe + protected final String printDelim = "|"; + protected final String reducedDelim = ","; + protected AnnotatorCompatible callingWalker; + protected final int MIN_COUNT = 2; + protected static final double MIN_PVALUE = 1E-320; + protected final int FORWARD = 0; + protected final int REVERSE = 1; + protected final ArrayList ZERO_LIST = new ArrayList<>(); + + @Override + public void initialize(final AnnotatorCompatible walker, final GenomeAnalysisEngine toolkit, final Set headerLines) { + if (!AnnotationUtils.walkerSupportsAlleleSpecificAnnotations(walker)) + logger.warn("Allele-specific annotations can only be used with HaplotypeCaller, CombineGVCFs and GenotypeGVCFs -- no data will be output"); + callingWalker = walker; + ZERO_LIST.add(0,0); + ZERO_LIST.add(1,0); + } + + @Override + public List getDescriptions() { + if (AnnotationUtils.walkerRequiresRawData(callingWalker)) + return Arrays.asList(GATKVCFHeaderLines.getInfoLine(getRawKeyName())); + else + return Arrays.asList(GATKVCFHeaderLines.getInfoLine(getKeyNames().get(0))); + } + + @Override + public String getRawKeyName() { return GATKVCFConstants.AS_SB_TABLE_KEY; } + + public Map annotateRawData(final RefMetaDataTracker tracker, + final AnnotatorCompatible walker, + final ReferenceContext ref, + final Map stratifiedContexts, + final VariantContext vc, + final Map perReadAlleleLikelihoodMap ) { + + //for allele-specific annotations we only call from HC and we only use perReadAlleleLikelihoodMap + if ( perReadAlleleLikelihoodMap == null) + return new HashMap<>(); + + // calculate the annotation from the stratified per read likelihood map + // stratifiedPerReadAllelelikelihoodMap can come from HaplotypeCaller call to VariantAnnotatorEngine + else if (perReadAlleleLikelihoodMap != null) { + final HashMap annotations = new HashMap<>(); + final ReducibleAnnotationData> myData = new AlleleSpecificAnnotationData<>(vc.getAlleles(),null); + calculateRawData(vc, perReadAlleleLikelihoodMap, myData); + final Map> perAlleleValues = myData.getAttributeMap(); + final String annotationString = makeRawAnnotationString(vc.getAlleles(), perAlleleValues); + annotations.put(getRawKeyName(), annotationString); + return annotations; + } + else { + // for non-snp variants, we need per-read likelihoods. + // for snps, we can get same result from simple pileup + // for indels that do not have a computed strand bias (SB) or strand bias by sample (SBBS) + return null; + } + } + + protected void parseRawDataString(ReducibleAnnotationData> myData) { + final String rawDataString = myData.getRawData(); + String[] rawDataPerAllele; + String[] rawListEntriesAsStringVector; + Map> perAlleleValues = new HashMap<>(); + //Initialize maps + for (Allele current : myData.getAlleles()) { + perAlleleValues.put(current, new LinkedList()); + } + //rawDataPerAllele is the list of values for each allele (each of variable length) + rawDataPerAllele = rawDataString.split(splitDelim); + for (int i=0; i alleleList = perAlleleValues.get(myData.getAlleles().get(i)); + rawListEntriesAsStringVector = alleleData.split(","); + //Read counts will only ever be integers + for (String s : rawListEntriesAsStringVector) { + if (!s.isEmpty()) + alleleList.add(Integer.parseInt(s.trim())); + } + } + myData.setAttributeMap(perAlleleValues); + } + + @Override + public Map combineRawData(final List vcAlleles, final List annotationList) { + //VC already contains merged alleles from ReferenceConfidenceVariantContextMerger + ReducibleAnnotationData combinedData = new AlleleSpecificAnnotationData(vcAlleles, null); + + for (final ReducibleAnnotationData currentValue : annotationList) { + parseRawDataString(currentValue); + combineAttributeMap(currentValue, combinedData); + } + final Map annotations = new HashMap<>(); + final String annotationString = makeRawAnnotationString(vcAlleles, combinedData.getAttributeMap()); + annotations.put(getRawKeyName(), annotationString); + return annotations; + } + + protected void combineAttributeMap(final ReducibleAnnotationData> toAdd, final ReducibleAnnotationData> combined) { + for (final Allele a : combined.getAlleles()) { + if (toAdd.hasAttribute(a) && toAdd.getAttribute(a) != null) { + if (combined.getAttribute(a) != null) { + combined.getAttribute(a).set(0, (int) combined.getAttribute(a).get(0) + (int) toAdd.getAttribute(a).get(0)); + combined.getAttribute(a).set(1, (int) combined.getAttribute(a).get(1) + (int) toAdd.getAttribute(a).get(1)); + } + else { + List alleleData = new ArrayList<>(); + alleleData.add(0, toAdd.getAttribute(a).get(0)); + alleleData.add(1, toAdd.getAttribute(a).get(1)); + combined.putAttribute(a,alleleData); + } + } + } + } + + protected String makeRawAnnotationString(final List vcAlleles, final Map> perAlleleValues) { + String annotationString = ""; + for (final Allele a : vcAlleles) { + if (!annotationString.isEmpty()) + annotationString += printDelim; + List alleleValues = perAlleleValues.get(a); + if (alleleValues == null) + alleleValues = ZERO_LIST; + annotationString += encode(alleleValues); + } + return annotationString; + } + + protected String encode(List alleleValues) { + String annotationString = ""; + for (int j =0; j < alleleValues.size(); j++) { + annotationString += alleleValues.get(j); + if (j < alleleValues.size()-1) + annotationString += ","; + } + return annotationString; + } + + + + protected String makeReducedAnnotationString(VariantContext vc, Map perAltsStrandCounts) { + String annotationString = ""; + for (Allele a : vc.getAlternateAlleles()) { + if (!annotationString.isEmpty()) + annotationString += reducedDelim; + if (!perAltsStrandCounts.containsKey(a)) + logger.warn("ERROR: VC allele not found in annotation alleles -- maybe there was trimming?"); + else + annotationString += String.format("%.3f", perAltsStrandCounts.get(a)); + } + return annotationString; + } + + /** + * + * @param vc -- contains the final set of alleles, possibly subset by GenotypeGVCFs + * @param originalVC -- used to get all the alleles for all gVCFs + * @return + */ + @Override + public Map finalizeRawData(final VariantContext vc, final VariantContext originalVC) { + Map annotations = new HashMap<>(); + if (!vc.hasAttribute(getRawKeyName())) + return new HashMap<>(); + String rawRankSumData = vc.getAttributeAsString(getRawKeyName(),null); + if (rawRankSumData == null) + return new HashMap<>(); + + AlleleSpecificAnnotationData> myData = new AlleleSpecificAnnotationData<>(originalVC.getAlleles(), rawRankSumData); + parseRawDataString(myData); + + Map perAltRankSumResults = calculateReducedData(myData); + + String annotationString = makeReducedAnnotationString(vc, perAltRankSumResults); + annotations.put(getKeyNames().get(0), annotationString); + return annotations; + } + + @Override + public void calculateRawData(final VariantContext vc, Map pralm, final ReducibleAnnotationData rawAnnotations) { + if(pralm == null) + return; + + getStrandCountsFromLikelihoodMap(vc, pralm, rawAnnotations, MIN_COUNT); + } + + protected abstract Map calculateReducedData(final AlleleSpecificAnnotationData> combinedData ); + + /** + Allocate and fill a 2x2 strand contingency table. In the end, it'll look something like this: + * fw rc + * allele1 # # + * allele2 # # + * @return a 2x2 contingency table + */ + public void getStrandCountsFromLikelihoodMap( final VariantContext vc, + final Map stratifiedPerReadAlleleLikelihoodMap, + final ReducibleAnnotationData perAlleleValues, + final int minCount) { + if( stratifiedPerReadAlleleLikelihoodMap == null ) + return; + if( vc == null ) + return; + + final Allele ref = vc.getReference(); + final List allAlts = vc.getAlternateAlleles(); + + for (final PerReadAlleleLikelihoodMap maps : stratifiedPerReadAlleleLikelihoodMap.values() ) { + final ReducibleAnnotationData> sampleTable = new AlleleSpecificAnnotationData<>(vc.getAlleles(),null); + for (final Map.Entry> el : maps.getLikelihoodReadMap().entrySet()) { + final MostLikelyAllele mostLikelyAllele = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue()); + final GATKSAMRecord read = el.getKey(); + updateTable(mostLikelyAllele.getAlleleIfInformative(), read, ref, allAlts, sampleTable); + } + //for each sample (value in stratified PRALM), only include it if there are >minCount informative reads + if ( passesMinimumThreshold(sampleTable, minCount) ) + combineAttributeMap(sampleTable, perAlleleValues); + } + } + + private void updateTable(final Allele bestAllele, final GATKSAMRecord read, final Allele ref, final List allAlts, final ReducibleAnnotationData> perAlleleValues) { + + final boolean matchesRef = bestAllele.equals(ref, true); + final boolean matchesAnyAlt = allAlts.contains(bestAllele); + + //for uninformative reads + if(bestAllele.isNoCall()) + return; + + //can happen if a read's most likely allele has been removed when --max_alternate_alleles is exceeded + if (!( matchesRef || matchesAnyAlt )) + return; + + final List alleleStrandCounts; + if (perAlleleValues.hasAttribute(bestAllele) && perAlleleValues.getAttribute(bestAllele) != null) + alleleStrandCounts = perAlleleValues.getAttribute(bestAllele); + else { + alleleStrandCounts = new ArrayList<>(); + alleleStrandCounts.add(0,0); + alleleStrandCounts.add(1,0); + } + if (read.isStrandless()) { + // a strandless read counts as observations on both strand, at 50% weight, with a minimum of 1 + // (the 1 is to ensure that a strandless read always counts as an observation on both strands, even + // if the read is only seen once, because it's a merged read or other) + alleleStrandCounts.set(FORWARD, alleleStrandCounts.get(FORWARD)+1); + alleleStrandCounts.set(REVERSE, alleleStrandCounts.get(REVERSE)+1); + } else { + // a normal read with an actual strand + final boolean isFW = !read.getReadNegativeStrandFlag(); + if (isFW) + alleleStrandCounts.set(FORWARD, alleleStrandCounts.get(FORWARD)+1); + else + alleleStrandCounts.set(REVERSE, alleleStrandCounts.get(REVERSE)+1); + } + perAlleleValues.putAttribute(bestAllele, alleleStrandCounts); + } + + /** + * Does this strand data array pass the minimum threshold for inclusion? + * + * @param sampleTable the per-allele fwd/rev read counts for a single sample + * @param minCount The minimum threshold of counts in the array + * @return true if it passes the minimum threshold, false otherwise + */ + protected boolean passesMinimumThreshold(final ReducibleAnnotationData> sampleTable, final int minCount) { + // the read total must be greater than MIN_COUNT + int readTotal = 0; + for (final List alleleValues : sampleTable.getAttributeMap().values()) { + if (alleleValues != null) { + readTotal += alleleValues.get(FORWARD); + readTotal += alleleValues.get(REVERSE); + } + } + return readTotal > minCount; + } + + + @Override + //Allele-specific annotations cannot be called from walkers other than HaplotypeCaller + protected Map calculateAnnotationFromGTfield(final GenotypesContext genotypes){ + return new HashMap<>(); + } + + @Override + //Allele-specific annotations cannot be called from walkers other than HaplotypeCaller + protected Map calculateAnnotationFromStratifiedContexts(final Map stratifiedContexts, + final VariantContext vc){ + return new HashMap<>(); + } + + @Override + //This just calls the non-allele-specific code in StrandBiasTest.java + protected abstract Map calculateAnnotationFromLikelihoodMap(final Map stratifiedPerReadAlleleLikelihoodMap, + final VariantContext vc); + +} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_StrandOddsRatio.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_StrandOddsRatio.java new file mode 100644 index 000000000..9e8124b86 --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_StrandOddsRatio.java @@ -0,0 +1,163 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. 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LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.annotator; + +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.*; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.variant.GATKVCFConstants; + +import java.util.Collections; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + +/** + * Allele-specific strand bias estimated by the Symmetric Odds Ratio test + * + *

Strand bias is a type of sequencing bias in which one DNA strand is favored over the other, which can result in incorrect evaluation of the amount of evidence observed for one allele vs. the other.

+ * + *

The AS_StrandOddsRatio annotation is one of several methods that aims to evaluate whether there is strand bias in the data. It is an updated form of the Fisher Strand Test that is better at taking into account large amounts of data in high coverage situations. It is used to determine if there is strand bias between forward and reverse strands for the reference or alternate allele. It does so separately for each allele. The reported value is ln-scaled.

+ * + *

Statistical notes

+ *

Odds Ratios in the 2x2 contingency table below are

+ * + * $$ R = \frac{X[0][0] * X[1][1]}{X[0][1] * X[1][0]} $$ + * + *

and its inverse:

+ * + * + * + * + * + *
 + strand - strand
REF;X[0][0]X[0][1]
ALT;X[1][0]X[1][1]
+ * + *

The sum R + 1/R is used to detect a difference in strand bias for REF and for ALT (the sum makes it symmetric). A high value is indicative of large difference where one entry is very small compared to the others. A scale factor of refRatio/altRatio where

+ * + * $$ refRatio = \frac{max(X[0][0], X[0][1])}{min(X[0][0], X[0][1} $$ + * + *

and

+ * + * $$ altRatio = \frac{max(X[1][0], X[1][1])}{min(X[1][0], X[1][1]} $$ + * + *

ensures that the annotation value is large only.

+ * + *

See the method document on statistical tests for a more detailed explanation of this statistical test.

+ * + *

Caveat

+ *

+ * The name AS_StrandOddsRatio is not entirely appropriate because the implementation was changed somewhere between the start of development and release of this annotation. Now SOR isn't really an odds ratio anymore. The goal was to separate certain cases of data without penalizing variants that occur at the ends of exons because they tend to only be covered by reads in one direction (depending on which end of the exon they're on), so if a variant has 10 ref reads in the + direction, 1 ref read in the - direction, 9 alt reads in the + direction and 2 alt reads in the - direction, it's actually not strand biased, but the FS score is pretty bad. The implementation that resulted derived in part from empirically testing some read count tables of various sizes with various ratios and deciding from there.

+ * + *

Related annotations

+ *
    + *
  • StrandOddsRatio outputs a version of this annotation that includes all alternate alleles in a single calculation.
    • + *
  • StrandBiasBySample outputs counts of read depth per allele for each strand orientation.
    • + *
  • FisherStrand uses Fisher's Exact Test to evaluate strand bias.
    • + *
+ * + */ +public class AS_StrandOddsRatio extends AS_StrandBiasTest implements AS_StandardAnnotation { + + @Override + public List getKeyNames() { + return Collections.singletonList(GATKVCFConstants.AS_STRAND_ODDS_RATIO_KEY); + } + + @Override + protected Map calculateAnnotationFromLikelihoodMap(Map stratifiedPerReadAlleleLikelihoodMap, + final VariantContext vc){ + // either SNP with no alignment context, or indels: per-read likelihood map needed + final int[][] table = getContingencyTable(stratifiedPerReadAlleleLikelihoodMap, vc, MIN_COUNT); + final double ratio = calculateSOR(table); + return Collections.singletonMap(getKeyNames().get(0), (Object)String.format("%.3f",ratio)); + } + + @Override + protected Map calculateReducedData(AlleleSpecificAnnotationData> combinedData) { + final Map annotationMap = new HashMap<>(); + final Map> perAlleleData = combinedData.getAttributeMap(); + final List refStrandCounts = perAlleleData.get(combinedData.getRefAllele()); + for (final Allele a : perAlleleData.keySet()) { + List altStrandCounts = perAlleleData.get(a); + int[][] refAltTable = new int[][] {new int[]{refStrandCounts.get(0),refStrandCounts.get(1)},new int[]{altStrandCounts.get(0),altStrandCounts.get(1)}}; + annotationMap.put(a,calculateSOR(refAltTable)); + } + return annotationMap; + } + + /** + * Computes the SOR value of a table after augmentation (adding pseudocounts). Based on the symmetric odds ratio but modified to take on + * low values when the reference +/- read count ratio is skewed but the alt count ratio is not. Natural log is taken + * to keep values within roughly the same range as other annotations. + * + * Adding pseudocounts prevent divide-by-zero. + * + * @param originalTable The table before augmentation + * @return the SOR annotation value + */ + final protected double calculateSOR(final int[][] originalTable) { + final double[][] augmentedTable = StrandBiasTableUtils.augmentContingencyTable(originalTable); + + double ratio = 0; + + ratio += (augmentedTable[0][0] / augmentedTable[0][1]) * (augmentedTable[1][1] / augmentedTable[1][0]); + ratio += (augmentedTable[0][1] / augmentedTable[0][0]) * (augmentedTable[1][0] / augmentedTable[1][1]); + + final double refRatio = (Math.min(augmentedTable[0][0], augmentedTable[0][1])/Math.max(augmentedTable[0][0], augmentedTable[0][1])); + final double altRatio = (Math.min(augmentedTable[1][0], augmentedTable[1][1])/Math.max(augmentedTable[1][0], augmentedTable[1][1])); + + ratio = ratio*refRatio/altRatio; + + return Math.log(ratio); + } +} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleCountBySample.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleCountBySample.java index f66390fc1..b83178f3d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleCountBySample.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleCountBySample.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AnnotationUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AnnotationUtils.java index aa736b2d1..81e645a72 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AnnotationUtils.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AnnotationUtils.java @@ -1,44 +1,44 @@ /* * By downloading the PROGRAM you agree to the following terms of use: -* +* * BROAD INSTITUTE * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY -* +* * This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). -* +* * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. * NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* +* * 1. DEFINITIONS * 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* +* * 2. LICENSE * 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. * The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. * 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. -* +* * 3. PHONE-HOME FEATURE * LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. -* +* * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* +* * 5. INDEMNIFICATION * LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* +* * 6. NO REPRESENTATIONS OR WARRANTIES * THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. * IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* +* * 7. ASSIGNMENT * This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* +* * 8. MISCELLANEOUS * 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. * 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. @@ -51,18 +51,64 @@ package org.broadinstitute.gatk.tools.walkers.annotator; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; +import htsjdk.samtools.SAMRecord; import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.VariantContext; +import org.apache.commons.lang.StringUtils; import org.apache.log4j.Logger; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.indels.PairHMMIndelErrorModel; +import org.broadinstitute.gatk.tools.walkers.variantutils.CombineGVCFs; +import org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; + +import java.util.ArrayList; +import java.util.HashSet; +import java.util.List; +import java.util.Set; public class AnnotationUtils { + public static final String ANNOTATION_HC_WARN_MSG = " annotation will not be calculated, must be called from HaplotypeCaller"; + public static final int WARNINGS_LOGGED_SIZE = 3; + + /** + * Helper function to parse the list into the annotation string + * @param valueList the ArrayList returned from StrandBiasBySample.annotate() + * @return the array used by the per-sample Strand Bias annotation + */ + protected static String encodeValueList( final List valueList, final String precisionFormat ) { + List outputList = new ArrayList<>(); + for (Double d : valueList) { + outputList.add(String.format(precisionFormat, d)); + } + return StringUtils.join(outputList, ","); + } + + /** + * Checks if the walker is compatible with allele-specific annotations + */ + public static boolean walkerSupportsAlleleSpecificAnnotations(final AnnotatorCompatible walker) { + return ((walker instanceof HaplotypeCaller) || (walker instanceof CombineGVCFs) || (walker instanceof GenotypeGVCFs)); + } + + /** + * Checks if the walker should get raw annotation data + */ + public static boolean walkerRequiresRawData(final AnnotatorCompatible walker) { + return ((walker instanceof HaplotypeCaller && ((HaplotypeCaller) walker).emitReferenceConfidence()) || walker instanceof CombineGVCFs); + } + /** * Checks if the input data is appropriate * + * @param annotation the input genotype annotation key name(s) * @param walker input walker * @param map input map for each read, holds underlying alleles represented by an aligned read, and corresponding relative likelihood. * @param g input genotype @@ -70,20 +116,38 @@ public class AnnotationUtils { * @param logger logger specific for each caller * * @return true if the walker is a HaplotypeCaller, the likelihood map is non-null and the genotype is non-null and called, false otherwise - * @throws ReviewedGATKException if the size of warningsLogged is less than 4. + * @throws IllegalArgumentException if annotation, walker, g, warningsLogged, or logger are null. + * @throws ReviewedGATKException if the size of warningsLogged is less than 3. */ - public static boolean isAppropriateInput(final AnnotatorCompatible walker, final PerReadAlleleLikelihoodMap map, final Genotype g, final boolean[] warningsLogged, final Logger logger) { + public static boolean isAppropriateInput(final String annotation, final AnnotatorCompatible walker, final PerReadAlleleLikelihoodMap map, final Genotype g, final boolean[] warningsLogged, final Logger logger) { - if ( warningsLogged.length < 4 ){ - throw new ReviewedGATKException("Warnings logged array must have at last 4 elements, but has " + warningsLogged.length); + if ( annotation == null ){ + throw new IllegalArgumentException("The input annotation cannot be null"); + } + + if ( walker == null ) { + throw new IllegalArgumentException("The input walker cannot be null"); + } + + if ( g == null ) { + throw new IllegalArgumentException("The input genotype cannot be null"); + } + + if ( warningsLogged == null ){ + throw new IllegalArgumentException("The input warnings logged cannot be null"); + } + + if ( logger == null ){ + throw new IllegalArgumentException("The input logger cannot be null"); + } + + if ( warningsLogged.length < WARNINGS_LOGGED_SIZE ){ + throw new ReviewedGATKException("Warnings logged array must have at least " + WARNINGS_LOGGED_SIZE + " elements, but has " + warningsLogged.length); } if ( !(walker instanceof HaplotypeCaller) ) { if ( !warningsLogged[0] ) { - if ( walker != null ) - logger.warn("Annotation will not be calculated, must be called from HaplotyepCaller, not " + walker.getClass().getName()); - else - logger.warn("Annotation will not be calculated, must be called from HaplotyepCaller"); + logger.warn(annotation + ANNOTATION_HC_WARN_MSG + ", not " + walker.getClass().getSimpleName()); warningsLogged[0] = true; } return false; @@ -97,22 +161,126 @@ public class AnnotationUtils { return false; } - if ( g == null ){ - if ( !warningsLogged[2] ) { - logger.warn("Annotation will not be calculated, missing genotype"); - warningsLogged[2]= true; - } - return false; - } - if ( !g.isCalled() ){ - if ( !warningsLogged[3] ) { + if ( !warningsLogged[2] ) { logger.warn("Annotation will not be calculated, genotype is not called"); - warningsLogged[3] = true; + warningsLogged[2] = true; } return false; } return true; } + + + //this method is intended to reconcile uniquified sample names + // it comes into play when calling this annotation from GenotypeGVCFs with --uniquifySamples because founderIds + // is derived from the sampleDB, which comes from the input sample names, but vc will have uniquified (i.e. different) + // sample names. Without this check, the founderIds won't be found in the vc and the annotation won't be calculated. + protected static Set validateFounderIDs(final Set founderIds, final VariantContext vc) { + Set vcSamples = new HashSet<>(); + Set returnIDs = founderIds; + vcSamples.addAll(vc.getSampleNames()); + if (!vcSamples.isEmpty()) { + if (founderIds != null) { + vcSamples.removeAll(founderIds); + if (vcSamples.equals(vc.getSampleNames())) + returnIDs = vc.getSampleNames(); + } + } + return returnIDs; + } + + /** + * Get the position of a variant within a read with respect to the closer end, accounting for hard clipped bases and low quality ends + * Used by ReadPosRankSum annotations + * + * @param read a read containing the variant + * @param initialReadPosition the position based on the modified, post-hard-clipped CIGAR + * @return read position + */ + public static int getFinalVariantReadPosition(final GATKSAMRecord read, final int initialReadPosition) { + final int numAlignedBases = getNumAlignedBases(read); + + int readPos = initialReadPosition; + //TODO: this doesn't work for the middle-right position if we index from zero + if (initialReadPosition > numAlignedBases / 2) { + readPos = numAlignedBases - (initialReadPosition + 1); + } + return readPos; + + } + + /** + * + * @param read a read containing the variant + * @return the number of hard clipped and low qual bases at the read start (where start is the leftmost end w.r.t. the reference) + */ + public static int getNumClippedBasesAtStart(final SAMRecord read) { + // check for hard clips (never consider these bases): + final Cigar c = read.getCigar(); + final CigarElement first = c.getCigarElement(0); + + int numStartClippedBases = 0; + if (first.getOperator() == CigarOperator.H) { + numStartClippedBases = first.getLength(); + } + final byte[] unclippedReadBases = read.getReadBases(); + final byte[] unclippedReadQuals = read.getBaseQualities(); + + // Do a stricter base clipping than provided by CIGAR string, since this one may be too conservative, + // and may leave a string of Q2 bases still hanging off the reads. + //TODO: this code may not even get used because HaplotypeCaller already hard clips low quality tails + for (int i = numStartClippedBases; i < unclippedReadBases.length; i++) { + if (unclippedReadQuals[i] < PairHMMIndelErrorModel.BASE_QUAL_THRESHOLD) + numStartClippedBases++; + else + break; + + } + + return numStartClippedBases; + } + + + /** + * + * @param read a read containing the variant + * @return number of non-hard clipped, aligned bases (excluding low quality bases at either end) + */ + //TODO: this is bizarre -- this code counts hard clips, but then subtracts them from the read length, which already doesn't count hard clips + public static int getNumAlignedBases(final GATKSAMRecord read) { + return read.getReadLength() - getNumClippedBasesAtStart(read) - getNumClippedBasesAtEnd(read); + } + + + /** + * + * @param read a read containing the variant + * @return number of hard clipped and low qual bases at the read end (where end is right end w.r.t. the reference) + */ + public static int getNumClippedBasesAtEnd(final GATKSAMRecord read) { + // check for hard clips (never consider these bases): + final Cigar c = read.getCigar(); + CigarElement last = c.getCigarElement(c.numCigarElements() - 1); + + int numEndClippedBases = 0; + if (last.getOperator() == CigarOperator.H) { + numEndClippedBases = last.getLength(); + } + final byte[] unclippedReadBases = read.getReadBases(); + final byte[] unclippedReadQuals = read.getBaseQualities(); + + // Do a stricter base clipping than provided by CIGAR string, since this one may be too conservative, + // and may leave a string of Q2 bases still hanging off the reads. + //TODO: this code may not even get used because HaplotypeCaller already hard clips low quality tails + for (int i = unclippedReadBases.length - numEndClippedBases - 1; i >= 0; i--) { + if (unclippedReadQuals[i] < PairHMMIndelErrorModel.BASE_QUAL_THRESHOLD) + numEndClippedBases++; + else + break; + } + + return numEndClippedBases; + } } diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseCountsBySample.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseCountsBySample.java new file mode 100644 index 000000000..4a94e5183 --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseCountsBySample.java @@ -0,0 +1,153 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.annotator; + +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.GenotypeBuilder; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFFormatHeaderLine; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.GenotypeAnnotation; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.genotyper.MostLikelyAllele; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.variant.GATKVCFConstants; +import org.broadinstitute.gatk.utils.variant.GATKVCFHeaderLines; +import org.broadinstitute.gatk.utils.BaseUtils; + +import java.util.*; + +/** + * Count of A, C, G, T bases for each sample + * + *

This annotation returns the counts of A, C, G, and T bases for each sample, in that order.

+ *

Example:

+ * + * 
BCS=3,0,3,0
+ * + *

+ * This means the number of A bases seen is 3, the number of T bases seen is 0, the number of G bases seen is 3, and the number of T bases seen is 0. + *

+ * + *

+ * BaseCountsBySample is intended to provide insight into the pileup of bases used by HaplotypeCaller in the calling process, which may differ from the pileup + * observed in the original bam file because of the local realignment and additional filtering performed internally by HaplotypeCaller. + *

+ * + *

Caveats

+ *
    + *
  • Can only be requested from HaplotypeCaller, not VariantAnnotator.
    • + *
+ * + *

Related annotations

+ *
    + *
  • BaseCounts counts the percentage of N bases.
    • + *
+ */ + +public class BaseCountsBySample extends GenotypeAnnotation { + + @Override + public void annotate(final RefMetaDataTracker tracker, + final AnnotatorCompatible walker, + final ReferenceContext ref, + final AlignmentContext stratifiedContext, + final VariantContext vc, + final Genotype g, + final GenotypeBuilder gb, + final PerReadAlleleLikelihoodMap alleleLikelihoodMap) { + + if ( alleleLikelihoodMap != null && !alleleLikelihoodMap.isEmpty() ) + gb.attribute(GATKVCFConstants.BASE_COUNTS_BY_SAMPLE_KEY, getBaseCounts(alleleLikelihoodMap, vc)); + } + + @Override + public List getKeyNames() { return Collections.singletonList(GATKVCFConstants.BASE_COUNTS_BY_SAMPLE_KEY); } + + @Override + public List getDescriptions() { + return Collections.singletonList(GATKVCFHeaderLines.getFormatLine(getKeyNames().get(0))); + } + + /** + * Base counts given for the most likely allele + * + * @param perReadAlleleLikelihoodMap for each read, the underlying alleles represented by an aligned read, and corresponding relative likelihood. + * @param vc variant context + * @return count of A, C, G, T bases + * @throws IllegalStateException if alleles in vc are not in perReadAlleleLikelihoodMap + */ + private int[] getBaseCounts(final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap, final VariantContext vc) { + final Set alleles = new HashSet<>(vc.getAlleles()); + + // make sure that there's a meaningful relationship between the alleles in the perReadAlleleLikelihoodMap and our VariantContext + if ( !perReadAlleleLikelihoodMap.getAllelesSet().containsAll(alleles) ) + throw new IllegalStateException("VC alleles " + alleles + " not a strict subset of per read allele map alleles " + perReadAlleleLikelihoodMap.getAllelesSet()); + + final int[] counts = new int[4]; + for ( final Map.Entry> el : perReadAlleleLikelihoodMap.getLikelihoodReadMap().entrySet()) { + final MostLikelyAllele a = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue(), alleles); + if (! a.isInformative() ) continue; // read is non-informative + for (final byte base : el.getKey().getReadBases() ){ + int index = BaseUtils.simpleBaseToBaseIndex(base); + if ( index != -1 ) + counts[index]++; + } + } + + return counts; + } +} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseQualityRankSumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseQualityRankSumTest.java index 7bdc365f1..c61403933 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseQualityRankSumTest.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseQualityRankSumTest.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -65,13 +65,23 @@ import java.util.*; /** * Rank Sum Test of REF versus ALT base quality scores * - *

This variant-level annotation tests compares the base qualities of the data supporting the reference allele with those supporting the alternate allele. The ideal result is a value close to zero, which indicates there is little to no difference. A negative value indicates that the bases supporting the alternate allele have lower quality scores than those supporting the reference allele. Conversely, a positive value indicates that the bases supporting the alternate allele have higher quality scores than those supporting the reference allele. Finding a statistically significant difference either way suggests that the sequencing process may have been biased or affected by an artifact.

+ *

This variant-level annotation compares the base qualities of the data supporting the reference allele with those supporting any alternate allele.

+ * + *

The ideal result is a value close to zero, which indicates there is little to no difference. A negative value indicates that the bases supporting the alternate allele have lower quality scores than those supporting the reference allele. Conversely, a positive value indicates that the bases supporting the alternate allele have higher quality scores than those supporting the reference allele. Finding a statistically significant difference either way suggests that the sequencing process may have been biased or affected by an artifact.

* *

Statistical notes

*

The value output for this annotation is the u-based z-approximation from the Mann-Whitney-Wilcoxon Rank Sum Test for base qualities (bases supporting REF vs. bases supporting ALT). See the method document on statistical tests for a more detailed explanation of the ranksum test.

* - *

Caveat

- *

The base quality rank sum test can not be calculated for sites without a mixture of reads showing both the reference and alternate alleles.

+ *

Caveats

+ *
    + *
  • Uninformative reads are not used in these calculations.
    • + *
  • The base quality rank sum test cannot be calculated for sites without a mixture of reads showing both the reference and alternate alleles.
    • + *
+ * + *

Related annotations

+ * * */ public class BaseQualityRankSumTest extends RankSumTest implements StandardAnnotation { diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ChromosomeCounts.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ChromosomeCounts.java index 6f0bba28e..94a04ddfc 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ChromosomeCounts.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ChromosomeCounts.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -90,6 +90,7 @@ import java.util.*; public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation { private Set founderIds = new HashSet(); + private boolean didUniquifiedSampleNameCheck = false; public Map annotate(final RefMetaDataTracker tracker, final AnnotatorCompatible walker, @@ -99,6 +100,11 @@ public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnn final Map perReadAlleleLikelihoodMap ) { if ( ! vc.hasGenotypes() ) return null; + //if none of the "founders" are in the vc samples, assume we uniquified the samples upstream and they are all founders + if (!didUniquifiedSampleNameCheck) { + checkSampleNames(vc); + didUniquifiedSampleNameCheck = true; + } return VariantContextUtils.calculateChromosomeCounts(vc, new HashMap(), true,founderIds); } @@ -113,4 +119,21 @@ public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnn } public List getDescriptions() { return Arrays.asList(ChromosomeCountConstants.descriptions); } + + //this method is intended to reconcile uniquified sample names + // it comes into play when calling this annotation from GenotypeGVCFs with --uniquifySamples because founderIds + // is derived from the sampleDB, which comes from the input sample names, but vc will have uniquified (i.e. different) + // sample names. Without this check, the founderIds won't be found in the vc and the annotation won't be calculated. + protected void checkSampleNames(final VariantContext vc) { + Set vcSamples = new HashSet<>(); + vcSamples.addAll(vc.getSampleNames()); + if (!vcSamples.isEmpty()) { + if (founderIds!=null) { + vcSamples.retainAll(founderIds); + if (vcSamples.isEmpty()) + founderIds = vc.getSampleNames(); + } + } + } + } \ No newline at end of file diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ClippingRankSumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ClippingRankSumTest.java index 3e70eea57..c05d80b11 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ClippingRankSumTest.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ClippingRankSumTest.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -52,6 +52,7 @@ package org.broadinstitute.gatk.tools.walkers.annotator; import htsjdk.variant.vcf.VCFInfoHeaderLine; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardHCAnnotation; import org.broadinstitute.gatk.utils.sam.AlignmentUtils; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.broadinstitute.gatk.utils.variant.GATKVCFConstants; @@ -71,7 +72,7 @@ import java.util.*; *

The clipping rank sum test cannot be calculated for sites without a mixture of reads showing both the reference and alternate alleles.

* */ -public class ClippingRankSumTest extends RankSumTest { +public class ClippingRankSumTest extends RankSumTest implements StandardHCAnnotation{ @Override public List getKeyNames() { return Arrays.asList(GATKVCFConstants.CLIPPING_RANK_SUM_KEY); } diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/Coverage.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/Coverage.java index f8404800e..bbdd10530 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/Coverage.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/Coverage.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerAlleleBySample.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerAlleleBySample.java index 536f196c4..e5d6942d6 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerAlleleBySample.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerAlleleBySample.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerSampleHC.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerSampleHC.java index 50a640482..339d4fc3e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerSampleHC.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/DepthPerSampleHC.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -51,9 +51,12 @@ package org.broadinstitute.gatk.tools.walkers.annotator; +import org.apache.commons.lang.StringUtils; import org.apache.log4j.Logger; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.GenotypeAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardHCAnnotation; import org.broadinstitute.gatk.utils.contexts.AlignmentContext; import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.utils.genotyper.MostLikelyAllele; @@ -91,10 +94,10 @@ import java.util.*; * * */ -public class DepthPerSampleHC extends GenotypeAnnotation { +public class DepthPerSampleHC extends GenotypeAnnotation implements StandardHCAnnotation{ private final static Logger logger = Logger.getLogger(DepthPerSampleHC.class); private boolean alleleLikelihoodMapSubsetWarningLogged = false; - boolean[] warningsLogged = new boolean[4]; + private final boolean[] warningsLogged = new boolean[AnnotationUtils.WARNINGS_LOGGED_SIZE]; @Override public void annotate(final RefMetaDataTracker tracker, @@ -106,7 +109,7 @@ public class DepthPerSampleHC extends GenotypeAnnotation { final GenotypeBuilder gb, final PerReadAlleleLikelihoodMap alleleLikelihoodMap){ - if ( !AnnotationUtils.isAppropriateInput(walker, alleleLikelihoodMap, g, warningsLogged, logger) ) { + if ( !AnnotationUtils.isAppropriateInput(VCFConstants.DEPTH_KEY , walker, alleleLikelihoodMap, g, warningsLogged, logger) ) { return; } diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ExcessHet.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ExcessHet.java new file mode 100644 index 000000000..274b9ced2 --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ExcessHet.java @@ -0,0 +1,276 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.annotator; + +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.vcf.VCFHeaderLine; +import org.apache.commons.math.stat.StatUtils; +import org.apache.log4j.Logger; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.walkers.Walker; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.MathUtils; +import htsjdk.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.GenotypesContext; +import htsjdk.variant.variantcontext.VariantContext; +import org.broadinstitute.gatk.utils.variant.GATKVCFConstants; +import org.broadinstitute.gatk.utils.variant.GATKVCFHeaderLines; + +import java.util.*; + + +/** + * Phred-scaled p-value for exact test of excess heterozygosity + * + * This annotation estimates excess heterozygosity in a population of samples. It is related to but distinct from InbreedingCoeff, which estimates evidence for inbreeding in a population. ExcessHet scales more reliably to large cohort sizes. + * + *

Statistical notes

+ *

This annotation is a one-sided phred-scaled p-value using an exact test of the Hardy-Weinberg Equilibrium. The null hypothesis is that the number of heterozygotes follows the Hardy-Weinberg Equilibrium. The p-value is the probability of getting the same or more heterozygotes as was observed, given the null hypothesis.

+ *

The implementation used is adapted from Wigginton JE, Cutler DJ, Abecasis GR. A Note on Exact Tests of Hardy-Weinberg Equilibrium. American Journal of Human Genetics. 2005;76(5):887-893.

+ *

The p-value is calculated exactly by using the Levene-Haldane distribution. This implementation also uses a mid-p correction as described by Graffelman, J. & Moreno, V. (2013). The mid p-value in exact tests for Hardy-Weinberg equilibrium. Statistical Applications in Genetics and Molecular Biology, 12(4), pp. 433-448.

+ * + *

Caveats

+ *
    + *
  • The annotation is not accurate for very small p-values. Beyond 1.0E-16 there is no guarantee that the p-value is accurate, just that it is in fact smaller than 1.0E-16.
    • + *
  • For multiallelic sites, all non-reference alleles are treated as a single alternate allele.
    • + *
+ * + *

Related annotations

+ *
    + *
  • InbreedingCoeff estimates whether there is evidence of inbreeding in a population
    • + *
  • AS_InbreedingCoeff outputs an allele-specific version of the InbreedingCoeff annotation.
    • + *
+ * + */ +public class ExcessHet extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation { + private final static Logger logger = Logger.getLogger(ExcessHet.class); + private final double minNeededValue = 1.0E-16; + private Set founderIds; + private final boolean RETURN_ROUNDED = true; + private int sampleCount = -1; + + @Override + public void initialize ( AnnotatorCompatible walker, GenomeAnalysisEngine toolkit, Set headerLines ) { + //If available, get the founder IDs and cache them. The ExcessHet value will only be computed on founders then. + //excessHet respects pedigree files, but doesn't require a minimum number of samples + if(founderIds == null && walker != null) { + founderIds = ((Walker) walker).getSampleDB().getFounderIds(); + } + + } + + @Override + public Map annotate(final RefMetaDataTracker tracker, + final AnnotatorCompatible walker, + final ReferenceContext ref, + final Map stratifiedContexts, + final VariantContext vc, + final Map perReadAlleleLikelihoodMap) { + + return makeEHAnnotation(vc); + } + + protected double calculateEH(final VariantContext vc, final GenotypesContext genotypes) { + HeterozygosityUtils heterozygosityUtils = new HeterozygosityUtils(RETURN_ROUNDED); + final double[] genotypeCountsDoubles = heterozygosityUtils.getGenotypeCountsForRefVsAllAlts(vc, genotypes); + sampleCount = heterozygosityUtils.getSampleCount(); + final int[] genotypeCounts = new int[genotypeCountsDoubles.length]; + for(int i = 0; i < genotypeCountsDoubles.length; i++) { + genotypeCounts[i] = (int)genotypeCountsDoubles[i]; + } + + double pval = exactTest(genotypeCounts); + + //If the actual phredPval would be infinity we will probably still filter out just a very large number + if (pval == 0) { + return Integer.MAX_VALUE; + } + double phredPval = -10.0 * Math.log10(pval); + + return phredPval; + } + + /** + * Note that this method is not accurate for very small p-values. Beyond 1.0E-16 there is no guarantee that the + * p-value is accurate, just that it is in fact smaller than 1.0E-16 (and therefore we should filter it). It would + * be more computationally expensive to calculate accuracy beyond a given threshold. Here we have enough accuracy + * to filter anything below a p-value of 10E-6. + * + * @param genotypeCounts Number of observed genotypes (n_aa, n_ab, n_bb) + * @return Right sided p-value or the probability of getting the observed or higher number of hets given the sample + * size (N) and the observed number of allele a (rareCopies) + */ + protected double exactTest(final int[] genotypeCounts) { + if (genotypeCounts.length != 3) { + throw new IllegalStateException("Input genotype counts must be length 3 for the number of genotypes with {2, 1, 0} ref alleles."); + } + final int REF_INDEX = 0; + final int HET_INDEX = 1; + final int VAR_INDEX = 2; + + final int refCount = genotypeCounts[REF_INDEX]; + final int hetCount = genotypeCounts[HET_INDEX]; + final int homCount = genotypeCounts[VAR_INDEX]; + + if (hetCount < 0 || refCount < 0 || homCount < 0) { + throw new IllegalArgumentException("Genotype counts cannot be less than 0"); + } + + //Split into observed common allele and rare allele + final int obsHomR; + final int obsHomC; + if (refCount < homCount) { + obsHomR = refCount; + obsHomC = homCount; + } else { + obsHomR = homCount; + obsHomC = refCount; + } + + final int rareCopies = 2 * obsHomR + hetCount; + final int N = hetCount + obsHomC + obsHomR; + + //If the probability distribution has only 1 point, then the mid p-value is .5 + if (rareCopies <= 1) { + return .5; + } + + double[] probs = new double[rareCopies + 1]; + + //Find (something close to the) mode for the midpoint + int mid = (int) Math.floor(((double) rareCopies * (2.0 * (double) N - (double) rareCopies)) / (2.0 * (double) N - 1.0)); + if ((mid % 2) != (rareCopies % 2)) { + mid++; + } + + probs[mid] = 1.0; + double mysum = 1.0; + + //Calculate probabilities from midpoint down + int currHets = mid; + int currHomR = (rareCopies - mid) / 2; + int currHomC = N - currHets - currHomR; + + while (currHets >= 2) { + double potentialProb = probs[currHets] * (double) currHets * ((double) currHets - 1.0) / (4.0 * ((double) currHomR + 1.0) * ((double) currHomC + 1.0)); + if (potentialProb < minNeededValue) { + break; + } + + probs[currHets - 2] = potentialProb; + mysum = mysum + probs[currHets - 2]; + + //2 fewer hets means one additional homR and homC each + currHets = currHets - 2; + currHomR = currHomR + 1; + currHomC = currHomC + 1; + } + + //Calculate probabilities from midpoint up + currHets = mid; + currHomR = (rareCopies - mid) / 2; + currHomC = N - currHets - currHomR; + + while (currHets <= rareCopies - 2) { + double potentialProb = probs[currHets] * 4.0 * (double) currHomR * (double) currHomC / (((double) currHets + 2.0) * ((double) currHets + 1.0)); + if (potentialProb < minNeededValue) { + break; + } + + probs[currHets + 2] = potentialProb; + mysum = mysum + probs[currHets + 2]; + + //2 more hets means 1 fewer homR and homC each + currHets = currHets + 2; + currHomR = currHomR - 1; + currHomC = currHomC - 1; + } + + double rightPval = probs[hetCount] / (2.0 * mysum); + //Check if we observed the highest possible number of hets + if (hetCount == rareCopies) { + return rightPval; + } + rightPval = rightPval + StatUtils.sum(Arrays.copyOfRange(probs, hetCount + 1, probs.length)) / mysum; + + return (rightPval); + } + + protected Map makeEHAnnotation(final VariantContext vc) { + final GenotypesContext genotypes = (founderIds == null || founderIds.isEmpty()) ? vc.getGenotypes() : vc.getGenotypes(founderIds); + if (genotypes == null || !vc.isVariant()) + return null; + double EH = calculateEH(vc, genotypes); + if (sampleCount < 1) + return null; + return Collections.singletonMap(getKeyNames().get(0), (Object) String.format("%.4f", EH)); + } + + @Override + public List getKeyNames() { + return Collections.singletonList(GATKVCFConstants.EXCESS_HET_KEY); + } + + @Override + public List getDescriptions() { + return Collections.singletonList(GATKVCFHeaderLines.getInfoLine(getKeyNames().get(0))); + } + +} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FisherStrand.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FisherStrand.java index eb8b17ee4..1a6e4242e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FisherStrand.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FisherStrand.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -51,9 +51,7 @@ package org.broadinstitute.gatk.tools.walkers.annotator; -import cern.jet.math.Arithmetic; import htsjdk.variant.variantcontext.GenotypesContext; -import org.apache.log4j.Logger; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.gatk.utils.contexts.AlignmentContext; @@ -70,7 +68,10 @@ import java.util.*; /** * Strand bias estimated using Fisher's Exact Test * - *

Strand bias is a type of sequencing bias in which one DNA strand is favored over the other, which can result in incorrect evaluation of the amount of evidence observed for one allele vs. the other. The FisherStrand annotation is one of several methods that aims to evaluate whether there is strand bias in the data. It uses Fisher's Exact Test to determine if there is strand bias between forward and reverse strands for the reference or alternate allele.”

+ *

Strand bias is a type of sequencing bias in which one DNA strand is favored over the other, which can result in incorrect evaluation of the amount of evidence observed for one allele vs. the other.

+ * + *

The FisherStrand annotation is one of several methods that aims to evaluate whether there is strand bias in the data. It uses Fisher's Exact Test to determine if there is strand bias between forward and reverse strands for the reference or alternate allele.

+ * *

The output is a Phred-scaled p-value. The higher the output value, the more likely there is to be bias. More bias is indicative of false positive calls.

* *

Statistical notes

@@ -83,6 +84,7 @@ import java.util.*; * *

Related annotations

*
    + *
  • FisherStrand outputs an allele-specific version of this annotation.
    • *
  • StrandBiasBySample outputs counts of read depth per allele for each strand orientation.
    • *
  • StrandOddsRatio is an updated form of FisherStrand that uses a symmetric odds ratio calculation.
    • *
@@ -90,16 +92,25 @@ import java.util.*; */ public class FisherStrand extends StrandBiasTest implements StandardAnnotation, ActiveRegionBasedAnnotation { private final static boolean ENABLE_DEBUGGING = false; - private final static Logger logger = Logger.getLogger(FisherStrand.class); private static final double MIN_PVALUE = 1E-320; private static final int MIN_QUAL_FOR_FILTERED_TEST = 17; private static final int MIN_COUNT = ARRAY_DIM; + @Override + public List getKeyNames() { + return Collections.singletonList(GATKVCFConstants.FISHER_STRAND_KEY); + } + + @Override + public List getDescriptions() { + return Collections.singletonList(GATKVCFHeaderLines.getInfoLine(getKeyNames().get(0))); + } + @Override protected Map calculateAnnotationFromGTfield(final GenotypesContext genotypes){ final int[][] tableFromPerSampleAnnotations = getTableFromSamples( genotypes, MIN_COUNT ); - return ( tableFromPerSampleAnnotations != null )? pValueForBestTable(tableFromPerSampleAnnotations, null) : null; + return ( tableFromPerSampleAnnotations != null )? pValueAnnotationForBestTable(tableFromPerSampleAnnotations, null) : null; } @Override @@ -107,9 +118,11 @@ public class FisherStrand extends StrandBiasTest implements StandardAnnotation, final VariantContext vc){ final int[][] tableNoFiltering = getSNPContingencyTable(stratifiedContexts, vc.getReference(), vc.getAlternateAlleles(), -1, MIN_COUNT); final int[][] tableFiltering = getSNPContingencyTable(stratifiedContexts, vc.getReference(), vc.getAlternateAlleles(), MIN_QUAL_FOR_FILTERED_TEST, MIN_COUNT); - printTable("unfiltered", tableNoFiltering); - printTable("filtered", tableFiltering); - return pValueForBestTable(tableFiltering, tableNoFiltering); + if (ENABLE_DEBUGGING) { + StrandBiasTableUtils.printTable("unfiltered", tableNoFiltering); + StrandBiasTableUtils.printTable("filtered", tableFiltering); + } + return pValueAnnotationForBestTable(tableFiltering, tableNoFiltering); } @Override @@ -119,11 +132,9 @@ public class FisherStrand extends StrandBiasTest implements StandardAnnotation, final int[][] table = getContingencyTable(stratifiedPerReadAlleleLikelihoodMap, vc, MIN_COUNT); //logger.info("VC " + vc); //printTable(table, 0.0); - return pValueForBestTable(table, null); + return pValueAnnotationForBestTable(table, null); } - - /** * Create an annotation for the highest (i.e., least significant) p-value of table1 and table2 * @@ -131,14 +142,14 @@ public class FisherStrand extends StrandBiasTest implements StandardAnnotation, * @param table2 a contingency table, may be null * @return annotation result for FS given tables */ - private Map pValueForBestTable(final int[][] table1, final int[][] table2) { + private Map pValueAnnotationForBestTable(final int[][] table1, final int[][] table2) { if ( table2 == null ) - return table1 == null ? null : annotationForOneTable(pValueForContingencyTable(table1)); + return table1 == null ? null : annotationForOneTable(StrandBiasTableUtils.FisherExactPValueForContingencyTable(table1)); else if (table1 == null) - return annotationForOneTable(pValueForContingencyTable(table2)); + return annotationForOneTable(StrandBiasTableUtils.FisherExactPValueForContingencyTable(table2)); else { // take the one with the best (i.e., least significant pvalue) - double pvalue1 = pValueForContingencyTable(table1); - double pvalue2 = pValueForContingencyTable(table2); + double pvalue1 = StrandBiasTableUtils.FisherExactPValueForContingencyTable(table1); + double pvalue2 = StrandBiasTableUtils.FisherExactPValueForContingencyTable(table2); return annotationForOneTable(Math.max(pvalue1, pvalue2)); } } @@ -153,185 +164,4 @@ public class FisherStrand extends StrandBiasTest implements StandardAnnotation, final Object value = String.format("%.3f", QualityUtils.phredScaleErrorRate(Math.max(pValue, MIN_PVALUE))); // prevent INFINITYs return Collections.singletonMap(getKeyNames().get(0), value); } - - @Override - public List getKeyNames() { - return Collections.singletonList(GATKVCFConstants.FISHER_STRAND_KEY); - } - - @Override - public List getDescriptions() { - return Collections.singletonList(GATKVCFHeaderLines.getInfoLine(getKeyNames().get(0))); - } - - /** - * Helper function to turn the FisherStrand table into the SB annotation array - * @param table the table used by the FisherStrand annotation - * @return the array used by the per-sample Strand Bias annotation - */ - public static List getContingencyArray( final int[][] table ) { - if(table.length != ARRAY_DIM || table[0].length != ARRAY_DIM) { - logger.warn("Expecting a " + ARRAY_DIM + "x" + ARRAY_DIM + " strand bias table."); - return null; - } - - final List list = new ArrayList<>(ARRAY_SIZE); // TODO - if we ever want to do something clever with multi-allelic sites this will need to change - list.add(table[0][0]); - list.add(table[0][1]); - list.add(table[1][0]); - list.add(table[1][1]); - return list; - } - - public static Double pValueForContingencyTable(int[][] originalTable) { - final int[][] normalizedTable = normalizeContingencyTable(originalTable); - - int[][] table = copyContingencyTable(normalizedTable); - - double pCutoff = computePValue(table); - //printTable(table, pCutoff); - - double pValue = pCutoff; - while (rotateTable(table)) { - double pValuePiece = computePValue(table); - - //printTable(table, pValuePiece); - - if (pValuePiece <= pCutoff) { - pValue += pValuePiece; - } - } - - table = copyContingencyTable(normalizedTable); - while (unrotateTable(table)) { - double pValuePiece = computePValue(table); - - //printTable(table, pValuePiece); - - if (pValuePiece <= pCutoff) { - pValue += pValuePiece; - } - } - - //System.out.printf("P-cutoff: %f\n", pCutoff); - //System.out.printf("P-value: %f\n\n", pValue); - - // min is necessary as numerical precision can result in pValue being slightly greater than 1.0 - return Math.min(pValue, 1.0); - } - - // how large do we want the normalized table to be? - private static final double TARGET_TABLE_SIZE = 200.0; - - /** - * Normalize the table so that the entries are not too large. - * Note that this method does NOT necessarily make a copy of the table being passed in! - * - * @param table the original table - * @return a normalized version of the table or the original table if it is already normalized - */ - private static int[][] normalizeContingencyTable(final int[][] table) { - final int sum = table[0][0] + table[0][1] + table[1][0] + table[1][1]; - if ( sum <= TARGET_TABLE_SIZE * 2 ) - return table; - - final double normalizationFactor = (double)sum / TARGET_TABLE_SIZE; - - final int[][] normalized = new int[ARRAY_DIM][ARRAY_DIM]; - for ( int i = 0; i < ARRAY_DIM; i++ ) { - for ( int j = 0; j < ARRAY_DIM; j++ ) - normalized[i][j] = (int)(table[i][j] / normalizationFactor); - } - - return normalized; - } - - private static int [][] copyContingencyTable(int [][] t) { - int[][] c = new int[ARRAY_DIM][ARRAY_DIM]; - - for ( int i = 0; i < ARRAY_DIM; i++ ) - for ( int j = 0; j < ARRAY_DIM; j++ ) - c[i][j] = t[i][j]; - - return c; - } - - - private static void printTable(int[][] table, double pValue) { - logger.info(String.format("%d %d; %d %d : %f", table[0][0], table[0][1], table[1][0], table[1][1], pValue)); - } - - /** - * Printing information to logger.info for debugging purposes - * - * @param name the name of the table - * @param table the table itself - */ - private void printTable(final String name, final int[][] table) { - if ( ENABLE_DEBUGGING ) { - final String pValue = (String)annotationForOneTable(pValueForContingencyTable(table)).get(getKeyNames().get(0)); - logger.info(String.format("FS %s (REF+, REF-, ALT+, ALT-) = (%d, %d, %d, %d) = %s", - name, table[0][0], table[0][1], table[1][0], table[1][1], pValue)); - } - } - - private static boolean rotateTable(int[][] table) { - table[0][0]--; - table[1][0]++; - - table[0][1]++; - table[1][1]--; - - return (table[0][0] >= 0 && table[1][1] >= 0); - } - - private static boolean unrotateTable(int[][] table) { - table[0][0]++; - table[1][0]--; - - table[0][1]--; - table[1][1]++; - - return (table[0][1] >= 0 && table[1][0] >= 0); - } - - private static double computePValue(int[][] table) { - - int[] rowSums = { sumRow(table, 0), sumRow(table, 1) }; - int[] colSums = { sumColumn(table, 0), sumColumn(table, 1) }; - int N = rowSums[0] + rowSums[1]; - - // calculate in log space so we don't die with high numbers - double pCutoff = Arithmetic.logFactorial(rowSums[0]) - + Arithmetic.logFactorial(rowSums[1]) - + Arithmetic.logFactorial(colSums[0]) - + Arithmetic.logFactorial(colSums[1]) - - Arithmetic.logFactorial(table[0][0]) - - Arithmetic.logFactorial(table[0][1]) - - Arithmetic.logFactorial(table[1][0]) - - Arithmetic.logFactorial(table[1][1]) - - Arithmetic.logFactorial(N); - return Math.exp(pCutoff); - } - - private static int sumRow(int[][] table, int column) { - int sum = 0; - for (int r = 0; r < table.length; r++) { - sum += table[r][column]; - } - - return sum; - } - - private static int sumColumn(int[][] table, int row) { - int sum = 0; - for (int c = 0; c < table[row].length; c++) { - sum += table[row][c]; - } - - return sum; - } - - - } diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GCContent.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GCContent.java index 6dc097583..94a1ddb7b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GCContent.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GCContent.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummaries.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummaries.java index 7f01f56db..445a90615 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummaries.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummaries.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HaplotypeScore.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HaplotypeScore.java index 44c38e757..e68696844 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HaplotypeScore.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HaplotypeScore.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HardyWeinberg.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HardyWeinberg.java index 9bf17a721..1762560df 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HardyWeinberg.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HardyWeinberg.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HeterozygosityUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HeterozygosityUtils.java new file mode 100644 index 000000000..ee45f9314 --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HeterozygosityUtils.java @@ -0,0 +1,236 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. 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This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.annotator; + +import htsjdk.variant.variantcontext.*; +import org.broadinstitute.gatk.utils.MathUtils; +import java.util.HashMap; +import java.util.Map; + +/** + * A class containing utility methods used in the calculation of annotations related to cohort heterozygosity, e.g. InbreedingCoefficient and ExcessHet + * Stores sample count to make sure we never have to iterate the genotypes more than once + * Should be reinitialized for each VariantContext + */ +public class HeterozygosityUtils { + + final public static int REF_INDEX = 0; + final public static int HET_INDEX = 1; + final public static int VAR_INDEX = 2; + + protected int sampleCount = -1; + private Map hetCounts; + private Map alleleCounts; + boolean returnRounded = false; + + /** + * Create a new HeterozygosityUtils -- a new class should be instantiated for each VariantContext to store data for that VC + * @param returnRounded round the likelihoods to return integer numbers of counts (as doubles) + */ + protected HeterozygosityUtils(final boolean returnRounded) { + this.returnRounded = returnRounded; + } + + /** + * Get the genotype counts for A/A, A/B, and B/B where A is the reference and B is any alternate allele + * @param vc + * @param genotypes may be subset to just founders if a pedigree file is provided + * @return may be null, otherwise length-3 double[] representing homRef, het, and homVar counts + */ + protected double[] getGenotypeCountsForRefVsAllAlts(final VariantContext vc, final GenotypesContext genotypes) { + if (genotypes == null || !vc.isVariant()) + return null; + + final boolean doMultiallelicMapping = !vc.isBiallelic(); + + int idxAA = 0, idxAB = 1, idxBB = 2; + + double refCount = 0; + double hetCount = 0; + double homCount = 0; + + sampleCount = 0; + for (final Genotype g : genotypes) { + if (g.isCalled() && g.hasLikelihoods() && g.getPloidy() == 2) // only work for diploid samples + sampleCount++; + else + continue; + + //Need to round the likelihoods to deal with small numerical deviations due to normalizing + final double[] normalizedLikelihoodsUnrounded = MathUtils.normalizeFromLog10(g.getLikelihoods().getAsVector()); + double[] normalizedLikelihoods = new double[normalizedLikelihoodsUnrounded.length]; + if (returnRounded) { + for (int i = 0; i < normalizedLikelihoodsUnrounded.length; i++) { + normalizedLikelihoods[i] = Math.round(normalizedLikelihoodsUnrounded[i]); + } + } else { + normalizedLikelihoods = normalizedLikelihoodsUnrounded; + } + + if (doMultiallelicMapping) { + if (g.isHetNonRef()) { + //all likelihoods go to homCount + homCount++; + continue; + } + + if (!g.isHomRef()) { + //get alternate allele for each sample + final Allele a1 = g.getAllele(0); + final Allele a2 = g.getAllele(1); + final int[] idxVector = vc.getGLIndecesOfAlternateAllele(a2.isNonReference() ? a2 : a1); + idxAA = idxVector[0]; + idxAB = idxVector[1]; + idxBB = idxVector[2]; + } + } + + refCount += normalizedLikelihoods[idxAA]; + hetCount += normalizedLikelihoods[idxAB]; + homCount += normalizedLikelihoods[idxBB]; + } + return new double[]{refCount, hetCount, homCount}; + } + + /** + * Get the count of heterozygotes in vc for a specific altAllele (both reference and non-reference hets, e.g. 1/2) + * @param vc + */ + protected void doGenotypeCalculations(final VariantContext vc) { + final GenotypesContext genotypes = vc.getGenotypes(); + if (genotypes == null || !vc.isVariant()) + return; + + final int numAlleles = vc.getNAlleles(); + + sampleCount = 0; + if (hetCounts == null && alleleCounts == null) { + hetCounts = new HashMap<>(); + alleleCounts = new HashMap<>(); + for (final Allele a : vc.getAlleles()) { + if (a.isNonReference()) + hetCounts.put(a, 0.0); + alleleCounts.put(a, 0.0); + } + + int idxAB; + + //for each sample + for (final Genotype g : genotypes) { + if (g.isCalled() && g.hasLikelihoods() && g.getPloidy() == 2) // only work for diploid samples + sampleCount++; + else + continue; + + int altIndex = 0; + for(final Allele a : vc.getAlternateAlleles()) { + //for each alt allele index from 1 to N + altIndex++; + + final double[] normalizedLikelihoodsUnrounded = MathUtils.normalizeFromLog10(g.getLikelihoods().getAsVector()); + double[] normalizedLikelihoods = new double[normalizedLikelihoodsUnrounded.length]; + if (returnRounded) { + for (int i = 0; i < normalizedLikelihoodsUnrounded.length; i++) { + normalizedLikelihoods[i] = Math.round(normalizedLikelihoodsUnrounded[i]); + } + } else { + normalizedLikelihoods = normalizedLikelihoodsUnrounded; + } + //iterate over the other alleles + for (int i = 0; i < numAlleles; i++) { + //only add homozygotes to alleleCounts, not hetCounts + if (i == altIndex) { + final double currentAlleleCounts = alleleCounts.get(a); + alleleCounts.put(a, currentAlleleCounts + 2*normalizedLikelihoods[GenotypeLikelihoods.calculatePLindex(altIndex,altIndex)]); + continue; + } + //pull out the heterozygote PL index, ensuring that the first allele index < second allele index + idxAB = GenotypeLikelihoods.calculatePLindex(Math.min(i,altIndex),Math.max(i,altIndex)); + final double aHetCounts = hetCounts.get(a); + hetCounts.put(a, aHetCounts + normalizedLikelihoods[idxAB]); + final double currentAlleleCounts = alleleCounts.get(a); + //these are guaranteed to be hets + alleleCounts.put(a, currentAlleleCounts + normalizedLikelihoods[idxAB]); + final double refAlleleCounts = alleleCounts.get(vc.getReference()); + alleleCounts.put(vc.getReference(), refAlleleCounts + normalizedLikelihoods[idxAB]); + } + //add in ref/ref likelihood + final double refAlleleCounts = alleleCounts.get(vc.getReference()); + alleleCounts.put(vc.getReference(), refAlleleCounts + 2*normalizedLikelihoods[0]); + } + + } + } + } + + /** + * Get the count of heterozygotes in vc for a specific altAllele (both reference and non-reference hets, e.g. 1/2) + * @param vc + * @param altAllele the alternate allele of interest + * @return number of hets + */ + protected double getHetCount(final VariantContext vc, final Allele altAllele) { + if (hetCounts == null) + doGenotypeCalculations(vc); + return hetCounts.containsKey(altAllele)? hetCounts.get(altAllele) : 0; + } + + protected double getAlleleCount(final VariantContext vc, final Allele allele) { + if (alleleCounts == null) + doGenotypeCalculations(vc); + return alleleCounts.containsKey(allele)? alleleCounts.get(allele) : 0; + } + + protected int getSampleCount() { + return sampleCount; + } +} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HomopolymerRun.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HomopolymerRun.java index 4bc2151fe..85c83fa1f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HomopolymerRun.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HomopolymerRun.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeff.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeff.java index 458a1b696..46a92eb5d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeff.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeff.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -52,19 +52,16 @@ package org.broadinstitute.gatk.tools.walkers.annotator; import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.vcf.VCFHeaderLine; import org.apache.log4j.Logger; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.*; import org.broadinstitute.gatk.utils.contexts.AlignmentContext; import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.engine.walkers.Walker; -import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; -import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.gatk.utils.MathUtils; import htsjdk.variant.vcf.VCFInfoHeaderLine; -import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.GenotypesContext; import htsjdk.variant.variantcontext.VariantContext; import org.broadinstitute.gatk.utils.variant.GATKVCFConstants; @@ -79,24 +76,42 @@ import java.util.*; *

This annotation estimates whether there is evidence of inbreeding in a population. The higher the score, the higher the chance that there is inbreeding.

* *

Statistical notes

- *

The calculation is a continuous generalization of the Hardy-Weinberg test for disequilibrium that works well with limited coverage per sample. The output is a Phred-scaled p-value derived from running the HW test for disequilibrium with PL values. See the method document on statistical tests for a more detailed explanation of this statistical test.

+ *

The calculation is a continuous generalization of the Hardy-Weinberg test for disequilibrium that works well with limited coverage per sample. The output is the F statistic from running the HW test for disequilibrium with PL values. See the method document on statistical tests for a more detailed explanation of this statistical test.

* *

Caveats

*
    - *
  • The Inbreeding Coefficient can only be calculated for cohorts containing at least 10 founder samples.
    • - *
  • This annotation is used in variant recalibration, but may not be appropriate for that purpose if the cohort being analyzed contains many closely related individuals.
    • - *
  • This annotation requires a valid pedigree file.
    • + *
  • The inbreeding coefficient can only be calculated for cohorts containing at least 10 founder samples.
    • + *
  • This annotation is used in variant filtering, but may not be appropriate for that purpose if the cohort being analyzed contains many closely related individuals.
    • + *
  • This annotation can take a valid pedigree file to specify founders.
    • + *
+ * + *

Related annotations

+ *
    + *
  • AS_InbreedingCoeff outputs an allele-specific version of this annotation.
    • + *
  • ExcessHet estimates excess heterozygosity in a population of samples.
    • *
* */ -public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation { +public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation, ReducibleAnnotation { private final static Logger logger = Logger.getLogger(InbreedingCoeff.class); - private static final int MIN_SAMPLES = 10; + protected static final int MIN_SAMPLES = 10; private Set founderIds; - private int sampleCount; - private boolean pedigreeCheckWarningLogged = false; private boolean didUniquifiedSampleNameCheck = false; + protected HeterozygosityUtils heterozygosityUtils; + final private boolean RETURN_ROUNDED = false; + + @Override + public void initialize (final AnnotatorCompatible walker, final GenomeAnalysisEngine toolkit, final Set headerLines ) { + //If available, get the founder IDs and cache them. the IC will only be computed on founders then. + if(founderIds == null && walker != null) { + founderIds = ((Walker) walker).getSampleDB().getFounderIds(); + } + if(walker != null && (((Walker) walker).getSampleDB().getSamples().size() < MIN_SAMPLES || (!founderIds.isEmpty() && founderIds.size() < MIN_SAMPLES))) + logger.warn("Annotation will not be calculated. InbreedingCoeff requires at least " + MIN_SAMPLES + " unrelated samples."); + //intialize a HeterozygosityUtils before annotating for use in unit tests + heterozygosityUtils = new HeterozygosityUtils(RETURN_ROUNDED); + } @Override public Map annotate(final RefMetaDataTracker tracker, @@ -105,78 +120,59 @@ public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnno final Map stratifiedContexts, final VariantContext vc, final Map perReadAlleleLikelihoodMap ) { - //If available, get the founder IDs and cache them. the IC will only be computed on founders then. - if(founderIds == null && walker != null) { - founderIds = ((Walker) walker).getSampleDB().getFounderIds(); - } + + heterozygosityUtils = new HeterozygosityUtils(RETURN_ROUNDED); + //if none of the "founders" are in the vc samples, assume we uniquified the samples upstream and they are all founders if (!didUniquifiedSampleNameCheck) { - checkSampleNames(vc); + founderIds = AnnotationUtils.validateFounderIDs(founderIds, vc); didUniquifiedSampleNameCheck = true; } - if ( founderIds == null || founderIds.isEmpty() ) { - if ( !pedigreeCheckWarningLogged ) { - logger.warn("Annotation will not be calculated, must provide a valid PED file (-ped) from the command line."); - pedigreeCheckWarningLogged = true; - } - return null; - } - else{ - return makeCoeffAnnotation(vc); + return makeCoeffAnnotation(vc); + } + + //Inbreeding coeff doesn't need raw data -- it's calculated from the final genotypes + @Override + public String getRawKeyName() { return null; } + + @Override + public Map annotateRawData(final RefMetaDataTracker tracker, final AnnotatorCompatible walker, final ReferenceContext ref, final Map stratifiedContexts, final VariantContext vc, final Map stratifiedPerReadAlleleLikelihoodMap) { + return null; + } + + @Override + public void calculateRawData(final VariantContext vc, final Map pralm, final ReducibleAnnotationData rawAnnotations) { } + + @Override + public Map combineRawData(final List allelesList, final List listOfRawData) { + return null; + } + + @Override + public Map finalizeRawData(final VariantContext vc, final VariantContext originalVC) { + heterozygosityUtils = new HeterozygosityUtils(RETURN_ROUNDED); + + //if none of the "founders" are in the vc samples, assume we uniquified the samples upstream and they are all founders + if (!didUniquifiedSampleNameCheck) { + founderIds = AnnotationUtils.validateFounderIDs(founderIds, vc); + didUniquifiedSampleNameCheck = true; } + return makeCoeffAnnotation(vc); } protected double calculateIC(final VariantContext vc, final GenotypesContext genotypes) { - final boolean doMultiallelicMapping = !vc.isBiallelic(); - - int idxAA = 0, idxAB = 1, idxBB = 2; - - double refCount = 0.0; - double hetCount = 0.0; - double homCount = 0.0; - sampleCount = 0; // number of samples that have likelihoods - - for ( final Genotype g : genotypes ) { - if ( g.isCalled() && g.hasLikelihoods() && g.getPloidy() == 2) // only work for diploid samples - sampleCount++; - else - continue; - final double[] normalizedLikelihoods = MathUtils.normalizeFromLog10( g.getLikelihoods().getAsVector() ); - if (doMultiallelicMapping) - { - if (g.isHetNonRef()) { - //all likelihoods go to homCount - homCount++; - continue; - } - - //get alternate allele for each sample - final Allele a1 = g.getAllele(0); - final Allele a2 = g.getAllele(1); - if (a2.isNonReference()) { - final int[] idxVector = vc.getGLIndecesOfAlternateAllele(a2); - idxAA = idxVector[0]; - idxAB = idxVector[1]; - idxBB = idxVector[2]; - } - //I expect hets to be reference first, but there are no guarantees (e.g. phasing) - else if (a1.isNonReference()) { - final int[] idxVector = vc.getGLIndecesOfAlternateAllele(a1); - idxAA = idxVector[0]; - idxAB = idxVector[1]; - idxBB = idxVector[2]; - } - } - - refCount += normalizedLikelihoods[idxAA]; - hetCount += normalizedLikelihoods[idxAB]; - homCount += normalizedLikelihoods[idxBB]; + final double[] genotypeCounts = heterozygosityUtils.getGenotypeCountsForRefVsAllAlts(vc, genotypes); //guarantees that sampleCount is set + if (genotypeCounts.length != 3) { + throw new IllegalStateException("Input genotype counts must be length 3 for the number of genotypes with {2, 1, 0} ref alleles."); } + final double refCount = genotypeCounts[HeterozygosityUtils.REF_INDEX]; + final double hetCount = genotypeCounts[HeterozygosityUtils.HET_INDEX]; + final double homCount = genotypeCounts[HeterozygosityUtils.VAR_INDEX]; final double p = ( 2.0 * refCount + hetCount ) / ( 2.0 * (refCount + hetCount + homCount) ); // expected reference allele frequency final double q = 1.0 - p; // expected alternative allele frequency - final double F = 1.0 - ( hetCount / ( 2.0 * p * q * (double) sampleCount) ); // inbreeding coefficient + final double F = 1.0 - ( hetCount / ( 2.0 * p * q * (double) heterozygosityUtils.getSampleCount()) ); // inbreeding coefficient return F; } @@ -185,27 +181,13 @@ public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnno final GenotypesContext genotypes = (founderIds == null || founderIds.isEmpty()) ? vc.getGenotypes() : vc.getGenotypes(founderIds); if (genotypes == null || genotypes.size() < MIN_SAMPLES || !vc.isVariant()) return null; - double F = calculateIC(vc, genotypes); - if (sampleCount < MIN_SAMPLES) + final double F = calculateIC(vc, genotypes); + if (heterozygosityUtils.getSampleCount() < MIN_SAMPLES) return null; return Collections.singletonMap(getKeyNames().get(0), (Object)String.format("%.4f", F)); } - //this method is intended to reconcile uniquified sample names - // it comes into play when calling this annotation from GenotypeGVCFs with --uniquifySamples because founderIds - // is derived from the sampleDB, which comes from the input sample names, but vc will have uniquified (i.e. different) - // sample names. Without this check, the founderIds won't be found in the vc and the annotation won't be calculated. - protected void checkSampleNames(final VariantContext vc) { - Set vcSamples = new HashSet<>(); - vcSamples.addAll(vc.getSampleNames()); - if (!vcSamples.isEmpty()) { - if (founderIds!=null) { - vcSamples.removeAll(founderIds); - if (vcSamples.equals(vc.getSampleNames())) - founderIds = vc.getSampleNames(); - } - } - } + @Override public List getKeyNames() { return Collections.singletonList(GATKVCFConstants.INBREEDING_COEFFICIENT_KEY); } diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LikelihoodRankSumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LikelihoodRankSumTest.java index d18302e25..e05a31f57 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LikelihoodRankSumTest.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LikelihoodRankSumTest.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MVLikelihoodRatio.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MVLikelihoodRatio.java index 1cc87240b..7cfc34b58 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MVLikelihoodRatio.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MVLikelihoodRatio.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityRankSumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityRankSumTest.java index 883c878b6..256b90259 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityRankSumTest.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityRankSumTest.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -70,11 +70,14 @@ import java.util.*; *

Statistical notes

*

The value output for this annotation is the u-based z-approximation from the Mann-Whitney-Wilcoxon Rank Sum Test for mapping qualities (MAPQ of reads supporting REF vs. MAPQ of reads supporting ALT). See the method document on statistical tests for a more detailed explanation of the ranksum test.

* - *

Caveat

- *

The mapping quality rank sum test can not be calculated for sites without a mixture of reads showing both the reference and alternate alleles.

+ *

Caveats

+ *
  • The mapping quality rank sum test can not be calculated for sites without a mixture of reads showing both the reference and alternate alleles.
    • + *
  • Uninformative reads are not used in these annotations.
    • + *
* *

Related annotations

* * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZero.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZero.java index 2b81d45c4..af0d0ceef 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZero.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZero.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/PossibleDeNovo.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/PossibleDeNovo.java index 6471488a5..5208c34ea 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/PossibleDeNovo.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/PossibleDeNovo.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepth.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepth.java index adff9dc33..d1f7cef5e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepth.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepth.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -73,26 +73,26 @@ import htsjdk.variant.variantcontext.VariantContext; import java.util.*; /** - * Variant confidence normalized by unfiltered depth of variant samples + * Variant call confidence normalized by depth of sample reads supporting a variant * *

This annotation puts the variant confidence QUAL score into perspective by normalizing for the amount of coverage available. Because each read contributes a little to the QUAL score, variants in regions with deep coverage can have artificially inflated QUAL scores, giving the impression that the call is supported by more evidence than it really is. To compensate for this, we normalize the variant confidence by depth, which gives us a more objective picture of how well supported the call is.

* *

Statistical notes

*

The QD is the QUAL score normalized by allele depth (AD) for a variant. For a single sample, the HaplotypeCaller calculates the QD by taking QUAL/AD. For multiple samples, HaplotypeCaller and GenotypeGVCFs calculate the QD by taking QUAL/AD of samples with a non hom-ref genotype call. The reason we leave out the samples with a hom-ref call is to not penalize the QUAL for the other samples with the variant call.

- *

Here is a single sample example:

+ *

Here is a single-sample example:

* 
2	37629	.	C	G	1063.77	.	AC=2;AF=1.00;AN=2;DP=31;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.50;QD=34.32;SOR=2.376	GT:AD:DP:GQ:PL:QSS	1/1:0,31:31:93:1092,93,0:0,960

QUAL/AD = 1063.77/31 = 34.32 = QD

- *

Here is a multi-sample example:

+ *

Here is a multi-sample example:

* 
10	8046	.	C	T	4107.13	.	AC=1;AF=0.167;AN=6;BaseQRankSum=-3.717;DP=1063;FS=1.616;MLEAC=1;MLEAF=0.167;QD=11.54
    GT:AD:DP:GQ:PL:QSS	0/0:369,4:373:99:0,1007,12207:10548,98	    0/0:331,1:332:99:0,967,11125:9576,27	    0/1:192,164:356:99:4138,0,5291:5501,4505
*

QUAL/AD = 4107.13/356 = 11.54 = QD

- *

Note that currently, when HaplotypeCaller is run with `-ERC GVCF`, the QD calculation is invoked before AD itself has been calculated, due to a technical constraint. In that case, HaplotypeCaller uses the number of overlapping reads from the haplotype likelihood calculation in place of AD to calculate QD, which generally yields a very similar number. This does not cause any measurable problems, but can cause some confusion since the number may be slightly different than what you would expect to get if you did the calculation manually. For that reason, this behavior will be modified in an upcoming version.

* *

Caveat

*

This annotation can only be calculated for sites for which at least one sample was genotyped as carrying a variant allele.

* *

Related annotations

*
    + *
  • AS_QualByDepth outputs an allele-specific version of this annotation.
    • *
  • Coverage gives the filtered depth of coverage for each sample and the unfiltered depth across all samples.
    • *
  • DepthPerAlleleBySample calculates depth of coverage for each allele per sample (AD).
    • *
@@ -100,6 +100,7 @@ import java.util.*; public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation { // private final static Logger logger = Logger.getLogger(QualByDepth.class); + @Override public Map annotate(final RefMetaDataTracker tracker, final AnnotatorCompatible walker, final ReferenceContext ref, @@ -113,6 +114,25 @@ public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotati if ( genotypes == null || genotypes.size() == 0 ) return null; + final int standardDepth = getDepth(genotypes, stratifiedContexts, perReadAlleleLikelihoodMap); + + if ( standardDepth == 0 ) + return null; + + final double altAlleleLength = GATKVariantContextUtils.getMeanAltAlleleLength(vc); + // Hack: UnifiedGenotyper (but not HaplotypeCaller or GenotypeGVCFs) over-estimates the quality of long indels + // Penalize the QD calculation for UG indels to compensate for this + double QD = -10.0 * vc.getLog10PError() / ((double)standardDepth * indelNormalizationFactor(altAlleleLength, walker instanceof UnifiedGenotyper)); + + // Hack: see note in the fixTooHighQD method below + QD = fixTooHighQD(QD); + + final Map map = new HashMap<>(); + map.put(getKeyNames().get(0), String.format("%.2f", QD)); + return map; + } + + protected int getDepth(final GenotypesContext genotypes, final Map stratifiedContexts, final Map perReadAlleleLikelihoodMap) { int standardDepth = 0; int ADrestrictedDepth = 0; @@ -123,10 +143,6 @@ public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotati continue; // if we have the AD values for this sample, let's make sure that the variant depth is greater than 1! - // TODO -- If we like how this is working and want to apply it to a situation other than the single sample HC pipeline, - // TODO -- then we will need to modify the annotateContext() - and related - routines in the VariantAnnotatorEngine - // TODO -- so that genotype-level annotations are run first (to generate AD on the samples) and then the site-level - // TODO -- annotations must come afterwards (so that QD can use the AD). if ( genotype.hasAD() ) { final int[] AD = genotype.getAD(); final int totalADdepth = (int)MathUtils.sum(AD); @@ -157,20 +173,7 @@ public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotati if ( ADrestrictedDepth > 0 ) standardDepth = ADrestrictedDepth; - if ( standardDepth == 0 ) - return null; - - final double altAlleleLength = GATKVariantContextUtils.getMeanAltAlleleLength(vc); - // Hack: UnifiedGenotyper (but not HaplotypeCaller or GenotypeGVCFs) over-estimates the quality of long indels - // Penalize the QD calculation for UG indels to compensate for this - double QD = -10.0 * vc.getLog10PError() / ((double)standardDepth * indelNormalizationFactor(altAlleleLength, walker instanceof UnifiedGenotyper)); - - // Hack: see note in the fixTooHighQD method below - QD = fixTooHighQD(QD); - - final Map map = new HashMap<>(); - map.put(getKeyNames().get(0), String.format("%.2f", QD)); - return map; + return standardDepth; } /** @@ -178,7 +181,7 @@ public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotati * * @param altAlleleLength the average alternate allele length for the call * @param increaseNormalizationAsLengthIncreases should we apply a normalization factor based on the allele length? - * @return a possitive double + * @return a positive double */ private double indelNormalizationFactor(final double altAlleleLength, final boolean increaseNormalizationAsLengthIncreases) { return ( increaseNormalizationAsLengthIncreases ? Math.max(altAlleleLength / 3.0, 1.0) : 1.0); @@ -190,12 +193,10 @@ public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotati * and VQSR will filter these out. This code looks at the QD value, and if it is above * threshold we map it down to the mean high QD value, with some jittering * - * // TODO -- remove me when HaplotypeCaller bubble caller is live - * * @param QD the raw QD score * @return a QD value */ - private double fixTooHighQD(final double QD) { + protected static double fixTooHighQD(final double QD) { if ( QD < MAX_QD_BEFORE_FIXING ) { return QD; } else { @@ -203,12 +204,14 @@ public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotati } } - private final static double MAX_QD_BEFORE_FIXING = 35; - private final static double IDEAL_HIGH_QD = 30; - private final static double JITTER_SIGMA = 3; + protected final static double MAX_QD_BEFORE_FIXING = 35; + protected final static double IDEAL_HIGH_QD = 30; + protected final static double JITTER_SIGMA = 3; + @Override public List getKeyNames() { return Arrays.asList(GATKVCFConstants.QUAL_BY_DEPTH_KEY); } + @Override public List getDescriptions() { return Arrays.asList(GATKVCFHeaderLines.getInfoLine(getKeyNames().get(0))); } diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RMSAnnotation.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RMSAnnotation.java new file mode 100644 index 000000000..6e50d7192 --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RMSAnnotation.java @@ -0,0 +1,248 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. 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Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.annotator; + +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFConstants; +import htsjdk.variant.vcf.VCFHeaderLine; +import htsjdk.variant.vcf.VCFInfoHeaderLine; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ReducibleAnnotation; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller; +import org.broadinstitute.gatk.tools.walkers.variantutils.CombineGVCFs; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.pileup.PileupElement; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.variant.GATKVCFHeaderLines; + +import java.util.*; + +/** + * Abstract root for all RankSum-based annotations + */ +public abstract class RMSAnnotation extends InfoFieldAnnotation implements ReducibleAnnotation { + protected AnnotatorCompatible callingWalker; + + @Override + public void initialize(final AnnotatorCompatible walker, final GenomeAnalysisEngine toolkit, final Set headerLines) { + callingWalker = walker; + } + + @Override + public List getDescriptions() { + final List headerLines = new ArrayList<>(); + //ideally only HC in GVCF mode would get the raw header line, but that's a little more complicated + if (callingWalker instanceof HaplotypeCaller || callingWalker instanceof CombineGVCFs) + headerLines.add(GATKVCFHeaderLines.getInfoLine(getRawKeyName())); + headerLines.add(GATKVCFHeaderLines.getInfoLine(getKeyNames().get(0))); + return headerLines; + } + + @Override + public Map annotate(final RefMetaDataTracker tracker, + final AnnotatorCompatible walker, + final ReferenceContext ref, + final Map stratifiedContexts, + final VariantContext vc, + final Map perReadAlleleLikelihoodMap ) { + + if ( (stratifiedContexts == null || stratifiedContexts.isEmpty()) && perReadAlleleLikelihoodMap == null) + return null; + + final Map annotations = new HashMap<>(); + final ReducibleAnnotationData myData = new ReducibleAnnotationData<>(null); + calculateRawData(stratifiedContexts, perReadAlleleLikelihoodMap, myData); + final String annotationString = makeFinalizedAnnotationString(vc, myData.getAttributeMap(), stratifiedContexts, perReadAlleleLikelihoodMap); + annotations.put(getKeyNames().get(0), annotationString); + return annotations; + } + + public Map annotateRawData(final RefMetaDataTracker tracker, + final AnnotatorCompatible walker, + final ReferenceContext ref, + final Map stratifiedContexts, + final VariantContext vc, + final Map perReadAlleleLikelihoodMap ) { + + if ( perReadAlleleLikelihoodMap == null) + return new HashMap<>(); + + final Map annotations = new HashMap<>(); + ReducibleAnnotationData myData = new ReducibleAnnotationData<>(null); + calculateRawData(vc, perReadAlleleLikelihoodMap, myData); + String annotationString = makeRawAnnotationString(vc.getAlleles(), myData.getAttributeMap()); + annotations.put(getRawKeyName(), annotationString); + return annotations; + } + + @Override + public Map combineRawData(final List vcAlleles, final List annotationList) { + //VC already contains merged alleles from ReferenceConfidenceVariantContextMerger + ReducibleAnnotationData combinedData = new ReducibleAnnotationData(null); + + for (final ReducibleAnnotationData currentValue : annotationList) { + parseRawDataString(currentValue); + combineAttributeMap(currentValue, combinedData); + + } + final Map annotations = new HashMap<>(); + String annotationString = makeRawAnnotationString(vcAlleles, combinedData.getAttributeMap()); + annotations.put(getRawKeyName(), annotationString); + return annotations; + } + + @Override + public Map finalizeRawData(final VariantContext vc, final VariantContext originalVC) { + if (!vc.hasAttribute(getRawKeyName())) + return new HashMap<>(); + String rawMQdata = vc.getAttributeAsString(getRawKeyName(),null); + if (rawMQdata == null) + return new HashMap<>(); + + ReducibleAnnotationData myData = new ReducibleAnnotationData(rawMQdata); + parseRawDataString(myData); + + String annotationString = makeFinalizedAnnotationString(vc, myData.getAttributeMap()); + return Collections.singletonMap(getKeyNames().get(0), (Object)annotationString); + } + + protected void parseRawDataString(ReducibleAnnotationData myData) { + final String rawDataString = myData.getRawData(); + String[] rawMQdataAsStringVector; + rawMQdataAsStringVector = rawDataString.split(","); + double squareSum = Double.parseDouble(rawMQdataAsStringVector[0]); + myData.putAttribute(Allele.NO_CALL, squareSum); + } + + public void combineAttributeMap(ReducibleAnnotationData toAdd, ReducibleAnnotationData combined) { + if (combined.getAttribute(Allele.NO_CALL) != null) + combined.putAttribute(Allele.NO_CALL, (Double) combined.getAttribute(Allele.NO_CALL) + (Double) toAdd.getAttribute(Allele.NO_CALL)); + else + combined.putAttribute(Allele.NO_CALL, toAdd.getAttribute(Allele.NO_CALL)); + + } + + //Implementations of this method should return a string consisting of the sum of the squared values for the attribute being annotated (or a delimited list of those if allele-specific) + abstract protected String makeRawAnnotationString(List vcAlleles, Map sumOfSquares); + + //Implementations of this method should return a string with the finalized annotation value as will appear in the INFO field + abstract protected String makeFinalizedAnnotationString(VariantContext vc, Map sumOfSquares); + + //Implementations of this method should return a string with the finalized annotation value as will appear in the INFO field + abstract protected String makeFinalizedAnnotationString(VariantContext vc, Map sumOfSquares, Map stratifiedContexts, final Map perReadAlleleLikelihoodMap); + + protected void calculateRawData(final Map stratifiedContexts, + final Map perReadAlleleLikelihoodMap, + final ReducibleAnnotationData myData) { + if (perReadAlleleLikelihoodMap != null) { + calculateRawData((VariantContext) null, perReadAlleleLikelihoodMap, myData); + } + } + + /** + * + * @param vc + * @param perReadAlleleLikelihoodMap + * @param stratifiedContexts + * @return the number of reads at the vc position (-1 if all read data is null) + */ + public int getNumOfReads(final VariantContext vc, + final Map perReadAlleleLikelihoodMap, + final Map stratifiedContexts) { + //don't use the full depth because we don't calculate MQ for reference blocks + int numOfReads = 0; + if(vc.hasAttribute(VCFConstants.DEPTH_KEY)) { + numOfReads += Integer.parseInt(vc.getAttributeAsString(VCFConstants.DEPTH_KEY, "-1")); + if(vc.hasGenotypes()) { + for(Genotype gt : vc.getGenotypes()) { + if(gt.isHomRef() && gt.hasExtendedAttribute("MIN_DP")) //site-level DP contribution will come from MIN_DP for gVCF-called reference variants + numOfReads -= Integer.parseInt(gt.getExtendedAttribute("MIN_DP").toString()); + } + } + return numOfReads; + } + else if (stratifiedContexts != null && !stratifiedContexts.isEmpty()) { + for ( final Map.Entry sample : stratifiedContexts.entrySet() ) { + final AlignmentContext context = sample.getValue(); + for ( final PileupElement p : context.getBasePileup() ) { + int mq = p.getRead().getMappingQuality(); + if ( mq != QualityUtils.MAPPING_QUALITY_UNAVAILABLE ) { + numOfReads++; + } + } + } + return numOfReads; + } + else if (perReadAlleleLikelihoodMap != null && !perReadAlleleLikelihoodMap.isEmpty()) + { + for ( final PerReadAlleleLikelihoodMap perReadLikelihoods : perReadAlleleLikelihoodMap.values() ) { + for ( final GATKSAMRecord read : perReadLikelihoods.getStoredElements() ) { + int mq = read.getMappingQuality(); + if ( mq != QualityUtils.MAPPING_QUALITY_UNAVAILABLE ) { + numOfReads++; + } + } + } + return numOfReads; + } + return -1; + } + +} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RMSMappingQuality.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RMSMappingQuality.java index 038545cf4..fda303cab 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RMSMappingQuality.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RMSMappingQuality.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -51,22 +51,21 @@ package org.broadinstitute.gatk.tools.walkers.annotator; -import org.broadinstitute.gatk.utils.contexts.AlignmentContext; -import org.broadinstitute.gatk.utils.contexts.ReferenceContext; -import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; -import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.gatk.utils.MathUtils; -import org.broadinstitute.gatk.utils.QualityUtils; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.vcf.VCFConstants; import htsjdk.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFStandardHeaderLines; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.*; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller; +import org.broadinstitute.gatk.tools.walkers.variantutils.CombineGVCFs; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.gatk.utils.pileup.PileupElement; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; -import htsjdk.variant.variantcontext.VariantContext; +import org.broadinstitute.gatk.utils.variant.GATKVCFConstants; +import org.broadinstitute.gatk.utils.variant.GATKVCFHeaderLines; import java.util.*; @@ -74,62 +73,106 @@ import java.util.*; /** * Root Mean Square of the mapping quality of reads across all samples. * - *

This annotation provides an estimation of the overall mapping quality of reads supporting a variant call, averaged over all samples in a cohort.

+ *

This annotation provides an estimation of the overall mapping quality of reads supporting a variant call. It produce both raw data (sum of square and num of total reads) and the calculated root mean square.

+ * + * The raw data is used to accurately calculate the root mean square when combining more than one sample. * *

Statistical notes

*

The root mean square is equivalent to the mean of the mapping qualities plus the standard deviation of the mapping qualities.

* + *

Caveat

+ *

Uninformative reads are not used in this annotation.

+ * *

Related annotations

* * */ -public class RMSMappingQuality extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation { +public class RMSMappingQuality extends RMSAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation, ReducibleAnnotation { - public Map annotate(final RefMetaDataTracker tracker, - final AnnotatorCompatible walker, - final ReferenceContext ref, - final Map stratifiedContexts, - final VariantContext vc, - final Map perReadAlleleLikelihoodMap ) { + @Override //this needs an override because MQ is a VCF standard so it's headerline is in a different place + public List getDescriptions() { + final List headerLines = new ArrayList<>(); + //only HC in GVCF mode should get the raw header line + if ((callingWalker instanceof HaplotypeCaller && ((HaplotypeCaller) callingWalker).emitReferenceConfidence()) || callingWalker instanceof CombineGVCFs) + headerLines.add(GATKVCFHeaderLines.getInfoLine(getRawKeyName())); + headerLines.add(VCFStandardHeaderLines.getInfoLine(getKeyNames().get(0))); + return headerLines; + } - final List qualities = new ArrayList<>(); + public List getKeyNames() { return Arrays.asList( + VCFConstants.RMS_MAPPING_QUALITY_KEY); + } + + public String getRawKeyName() { return GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_KEY;} + + @Override + public void calculateRawData(final VariantContext vc, final Map pralm, final ReducibleAnnotationData rawAnnotations) { + Double squareSum = 0.0; + if ( pralm.size() == 0 ) + return; + + for ( final PerReadAlleleLikelihoodMap perReadLikelihoods : pralm.values() ) { + for ( final GATKSAMRecord read : perReadLikelihoods.getStoredElements() ) { + int mq = read.getMappingQuality(); + if ( mq != QualityUtils.MAPPING_QUALITY_UNAVAILABLE ) { + squareSum += mq * mq; + } + } + } + rawAnnotations.putAttribute(Allele.NO_CALL,squareSum); + } + + //this version applies to non-HaplotypeCaller annotators + @Override + protected void calculateRawData(final Map stratifiedContexts, + final Map perReadAlleleLikelihoodMap, + final ReducibleAnnotationData myData) { + + Double squareSum = 0.0; if ( stratifiedContexts != null ) { if ( stratifiedContexts.size() == 0 ) - return null; + return; for ( final Map.Entry sample : stratifiedContexts.entrySet() ) { final AlignmentContext context = sample.getValue(); - for ( final PileupElement p : context.getBasePileup() ) - fillMappingQualitiesFromPileup(p.getRead().getMappingQuality(), qualities); + for ( final PileupElement p : context.getBasePileup() ) { + int mq = p.getRead().getMappingQuality(); + if ( mq != QualityUtils.MAPPING_QUALITY_UNAVAILABLE ) { + squareSum += mq * mq; + } + } } + myData.putAttribute(Allele.NO_CALL,squareSum); } else if (perReadAlleleLikelihoodMap != null) { - if ( perReadAlleleLikelihoodMap.size() == 0 ) - return null; - - for ( final PerReadAlleleLikelihoodMap perReadLikelihoods : perReadAlleleLikelihoodMap.values() ) { - for ( final GATKSAMRecord read : perReadLikelihoods.getStoredElements() ) - fillMappingQualitiesFromPileup(read.getMappingQuality(), qualities); - } - } - else - return null; - - final double rms = MathUtils.rms(qualities); - return Collections.singletonMap(getKeyNames().get(0), (Object)String.format("%.2f", rms)); - } - - private static void fillMappingQualitiesFromPileup(final int mq, final List qualities) { - if ( mq != QualityUtils.MAPPING_QUALITY_UNAVAILABLE ) { - qualities.add(mq); + calculateRawData((VariantContext) null, perReadAlleleLikelihoodMap, myData); } } - public List getKeyNames() { return Arrays.asList(VCFConstants.RMS_MAPPING_QUALITY_KEY); } - - public List getDescriptions() { - return Arrays.asList(VCFStandardHeaderLines.getInfoLine(getKeyNames().get(0))); + @Override + public String makeRawAnnotationString(final List vcAlleles, final Map perAlleleData) { + return String.format("%.2f", perAlleleData.get(Allele.NO_CALL)); } + + @Override + public String makeFinalizedAnnotationString(final VariantContext vc, final Map perAlleleData, final Map stratifiedContexts, final Map perReadAlleleLikelihoodMap) { + if ((stratifiedContexts != null && !stratifiedContexts.isEmpty()) || perReadAlleleLikelihoodMap != null) { + int numOfReads = getNumOfReads(vc, perReadAlleleLikelihoodMap, stratifiedContexts); + return String.format("%.2f", Math.sqrt((double) perAlleleData.get(Allele.NO_CALL) / numOfReads)); + } + else { + return makeFinalizedAnnotationString(vc, perAlleleData); + } + } + + @Override + public String makeFinalizedAnnotationString(final VariantContext vc, final Map perAlleleData) { + int numOfReads = getNumOfReads(vc, null, null); + return String.format("%.2f", Math.sqrt((double)perAlleleData.get(Allele.NO_CALL)/numOfReads)); + } + + } \ No newline at end of file diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumTest.java index c257a05ff..4ed64464b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumTest.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumTest.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -52,12 +52,10 @@ package org.broadinstitute.gatk.tools.walkers.annotator; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.*; import org.broadinstitute.gatk.utils.contexts.AlignmentContext; import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; -import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.gatk.utils.genotyper.MostLikelyAllele; import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.gatk.utils.MannWhitneyU; @@ -76,11 +74,12 @@ import java.util.*; /** - * Abstract root for all RankSum based annotations + * Abstract root for all RankSum-based annotations */ +//TODO: will eventually implement ReducibleAnnotation in order to preserve accuracy for CombineGVCFs and GenotypeGVCFs -- see RMSAnnotation.java for an example of an abstract ReducibleAnnotation public abstract class RankSumTest extends InfoFieldAnnotation implements ActiveRegionBasedAnnotation { static final boolean DEBUG = false; - private boolean useDithering = true; + protected boolean useDithering = true; public Map annotate(final RefMetaDataTracker tracker, final AnnotatorCompatible walker, diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ReadPosRankSumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ReadPosRankSumTest.java index 2c49355f9..09a38952e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ReadPosRankSumTest.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ReadPosRankSumTest.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -51,12 +51,7 @@ package org.broadinstitute.gatk.tools.walkers.annotator; -import htsjdk.samtools.Cigar; -import htsjdk.samtools.CigarElement; -import htsjdk.samtools.CigarOperator; -import htsjdk.samtools.SAMRecord; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.gatk.tools.walkers.indels.PairHMMIndelErrorModel; import htsjdk.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.gatk.utils.pileup.PileupElement; import org.broadinstitute.gatk.utils.sam.AlignmentUtils; @@ -70,7 +65,9 @@ import java.util.*; /** * Rank Sum Test for relative positioning of REF versus ALT alleles within reads * - *

This variant-level annotation tests whether there is evidence of bias in the position of alleles within the reads that support them, between the reference and alternate alleles. Seeing an allele only near the ends of reads is indicative of error, because that is where sequencers tend to make the most errors. However, some variants located near the edges of sequenced regions will necessarily be covered by the ends of reads, so we can't just set an absolute "minimum distance from end of read" threshold. That is why we use a rank sum test to evaluate whether there is a difference in how well the reference allele and the alternate allele are supported.

+ *

This variant-level annotation tests whether there is evidence of bias in the position of alleles within the reads that support them, between the reference and alternate alleles.

+ * + *

Seeing an allele only near the ends of reads is indicative of error, because that is where sequencers tend to make the most errors. However, some variants located near the edges of sequenced regions will necessarily be covered by the ends of reads, so we can't just set an absolute "minimum distance from end of read" threshold. That is why we use a rank sum test to evaluate whether there is a difference in how well the reference allele and the alternate allele are supported.

* *

The ideal result is a value close to zero, which indicates there is little to no difference in where the alleles are found relative to the ends of reads. A negative value indicates that the alternate allele is found at the ends of reads more often than the reference allele. Conversely, a positive value indicates that the reference allele is found at the ends of reads more often than the alternate allele.

* @@ -80,7 +77,15 @@ import java.util.*; *

The value output for this annotation is the u-based z-approximation from the Mann-Whitney-Wilcoxon Rank Sum Test for site position within reads (position within reads supporting REF vs. position within reads supporting ALT). See the method document on statistical tests for a more detailed explanation of the ranksum test.

* *

Caveat

- *

The read position rank sum test can not be calculated for sites without a mixture of reads showing both the reference and alternate alleles.

+ *
    + *
  • The read position rank sum test can not be calculated for sites without a mixture of reads showing both the reference and alternate alleles.
    • + *
  • Uninformative reads are not used in these annotations.
    • + *
+ * + * *

Related annotations

+ * * */ public class ReadPosRankSumTest extends RankSumTest implements StandardAnnotation { @@ -109,7 +114,7 @@ public class ReadPosRankSumTest extends RankSumTest implements StandardAnnotatio @Override protected Double getElementForPileupElement(final PileupElement p) { final int offset = AlignmentUtils.calcAlignmentByteArrayOffset(p.getRead().getCigar(), p, 0, 0); - return (double)getFinalReadPosition(p.getRead(), offset); + return (double)AnnotationUtils.getFinalVariantReadPosition(p.getRead(), offset); } @Override @@ -122,69 +127,5 @@ public class ReadPosRankSumTest extends RankSumTest implements StandardAnnotatio return super.isUsableRead(read, refLoc) && read.getSoftStart() + read.getCigar().getReadLength() > refLoc; } - private int getFinalReadPosition(final GATKSAMRecord read, final int initialReadPosition) { - final int numAlignedBases = getNumAlignedBases(read); - int readPos = initialReadPosition; - if (initialReadPosition > numAlignedBases / 2) { - readPos = numAlignedBases - (initialReadPosition + 1); - } - return readPos; - - } - - private int getNumClippedBasesAtStart(final SAMRecord read) { - // compute total number of clipped bases (soft or hard clipped) - // check for hard clips (never consider these bases): - final Cigar c = read.getCigar(); - final CigarElement first = c.getCigarElement(0); - - int numStartClippedBases = 0; - if (first.getOperator() == CigarOperator.H) { - numStartClippedBases = first.getLength(); - } - final byte[] unclippedReadBases = read.getReadBases(); - final byte[] unclippedReadQuals = read.getBaseQualities(); - - // Do a stricter base clipping than provided by CIGAR string, since this one may be too conservative, - // and may leave a string of Q2 bases still hanging off the reads. - for (int i = numStartClippedBases; i < unclippedReadBases.length; i++) { - if (unclippedReadQuals[i] < PairHMMIndelErrorModel.BASE_QUAL_THRESHOLD) - numStartClippedBases++; - else - break; - - } - - return numStartClippedBases; - } - - private int getNumAlignedBases(final GATKSAMRecord read) { - return read.getReadLength() - getNumClippedBasesAtStart(read) - getNumClippedBasesAtEnd(read); - } - - private int getNumClippedBasesAtEnd(final GATKSAMRecord read) { - // compute total number of clipped bases (soft or hard clipped) - // check for hard clips (never consider these bases): - final Cigar c = read.getCigar(); - CigarElement last = c.getCigarElement(c.numCigarElements() - 1); - - int numEndClippedBases = 0; - if (last.getOperator() == CigarOperator.H) { - numEndClippedBases = last.getLength(); - } - final byte[] unclippedReadBases = read.getReadBases(); - final byte[] unclippedReadQuals = read.getBaseQualities(); - - // Do a stricter base clipping than provided by CIGAR string, since this one may be too conservative, - // and may leave a string of Q2 bases still hanging off the reads. - for (int i = unclippedReadBases.length - numEndClippedBases - 1; i >= 0; i--) { - if (unclippedReadQuals[i] < PairHMMIndelErrorModel.BASE_QUAL_THRESHOLD) - numEndClippedBases++; - else - break; - } - - return numEndClippedBases; - } } diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SampleList.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SampleList.java index c1c226a81..dae9ab9b2 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SampleList.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SampleList.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SpanningDeletions.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SpanningDeletions.java index 1aeb79a6b..1e87377d2 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SpanningDeletions.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SpanningDeletions.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandAlleleCountsBySample.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandAlleleCountsBySample.java index 21632b5eb..902d40ddb 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandAlleleCountsBySample.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandAlleleCountsBySample.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -56,6 +56,7 @@ import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.GenotypeBuilder; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.vcf.VCFFormatHeaderLine; +import org.apache.commons.lang.StringUtils; import org.apache.log4j.Logger; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.GenotypeAnnotation; @@ -105,7 +106,7 @@ import java.util.Map; public class StrandAlleleCountsBySample extends GenotypeAnnotation { private final static Logger logger = Logger.getLogger(StrandAlleleCountsBySample.class); - boolean[] warningsLogged = new boolean[4]; + private final boolean[] warningsLogged = new boolean[AnnotationUtils.WARNINGS_LOGGED_SIZE]; @Override public void annotate(final RefMetaDataTracker tracker, @@ -117,7 +118,7 @@ public class StrandAlleleCountsBySample extends GenotypeAnnotation { final GenotypeBuilder gb, final PerReadAlleleLikelihoodMap alleleLikelihoodMap) { - if ( !AnnotationUtils.isAppropriateInput(walker, alleleLikelihoodMap, g, warningsLogged, logger) ) { + if ( !AnnotationUtils.isAppropriateInput(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, walker, alleleLikelihoodMap, g, warningsLogged, logger) ) { return; } diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasBySample.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasBySample.java index fdfa06241..0f3496015 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasBySample.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasBySample.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -99,7 +99,7 @@ import java.util.*; public class StrandBiasBySample extends GenotypeAnnotation { private final static Logger logger = Logger.getLogger(StrandBiasBySample.class); - boolean[] warningsLogged = new boolean[4]; + private final boolean[] warningsLogged = new boolean[AnnotationUtils.WARNINGS_LOGGED_SIZE]; @Override public void annotate(final RefMetaDataTracker tracker, @@ -110,14 +110,13 @@ public class StrandBiasBySample extends GenotypeAnnotation { final Genotype g, final GenotypeBuilder gb, final PerReadAlleleLikelihoodMap alleleLikelihoodMap) { - - if (!AnnotationUtils.isAppropriateInput(walker, alleleLikelihoodMap, g, warningsLogged, logger)) { + if (!AnnotationUtils.isAppropriateInput(GATKVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY, walker, alleleLikelihoodMap, g, warningsLogged, logger)) { return; } final int[][] table = FisherStrand.getContingencyTable(Collections.singletonMap(g.getSampleName(), alleleLikelihoodMap), vc, 0); - gb.attribute(GATKVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY, FisherStrand.getContingencyArray(table)); + gb.attribute(GATKVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY, StrandBiasTableUtils.getContingencyArray(table)); } @Override diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTableUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTableUtils.java new file mode 100644 index 000000000..563bbe155 --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTableUtils.java @@ -0,0 +1,250 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. 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LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. 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Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. 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This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.annotator; + +import cern.jet.math.Arithmetic; +import org.apache.log4j.Logger; +import org.broadinstitute.gatk.utils.QualityUtils; + +import java.util.ArrayList; +import java.util.List; + +/** + * A class containing many convenience methods used in the strand bias annotation calculations + */ +public class StrandBiasTableUtils { + + private final static Logger logger = Logger.getLogger(StrandBiasTableUtils.class); + + //For now this is only for 2x2 contingency tables + protected static final int ARRAY_DIM = 2; + protected static final int ARRAY_SIZE = ARRAY_DIM * ARRAY_DIM; + private static double MIN_PVALUE = 1E-320; + // how large do we want the normalized table to be? + private static final double TARGET_TABLE_SIZE = 200.0; + private final static double AUGMENTATION_CONSTANT = 1.0; + + /** + * Computes a two-sided p-Value for a Fisher's exact test on the contingency table, after normalizing counts so that the sum does not exceed {@value org.broadinstitute.gatk.tools.walkers.annotator.StrandBiasTableUtils#TARGET_TABLE_SIZE} + * @param originalTable + * @return + */ + public static Double FisherExactPValueForContingencyTable(int[][] originalTable) { + final int[][] normalizedTable = normalizeContingencyTable(originalTable); + + int[][] table = copyContingencyTable(normalizedTable); + + double pCutoff = computePValue(table); + + double pValue = pCutoff; + while (rotateTable(table)) { + double pValuePiece = computePValue(table); + + if (pValuePiece <= pCutoff) { + pValue += pValuePiece; + } + } + + table = copyContingencyTable(normalizedTable); + while (unrotateTable(table)) { + double pValuePiece = computePValue(table); + + if (pValuePiece <= pCutoff) { + pValue += pValuePiece; + } + } + + // min is necessary as numerical precision can result in pValue being slightly greater than 1.0 + return Math.min(pValue, 1.0); + } + + /** + * Helper function to turn the FisherStrand table into the SB annotation array + * @param table the table used by the FisherStrand annotation + * @return the array used by the per-sample Strand Bias annotation + */ + public static List getContingencyArray( final int[][] table ) { + if(table.length != ARRAY_DIM || table[0].length != ARRAY_DIM) { + logger.warn("Expecting a " + ARRAY_DIM + "x" + ARRAY_DIM + " strand bias table."); + return null; + } + + final List list = new ArrayList<>(ARRAY_SIZE); + list.add(table[0][0]); + list.add(table[0][1]); + list.add(table[1][0]); + list.add(table[1][1]); + return list; + } + + /** + * Printing information to logger.info for debugging purposes + * + * @param name the name of the table + * @param table the table itself + */ + public static void printTable(final String name, final int[][] table) { + final String pValue = String.format("%.3f", QualityUtils.phredScaleErrorRate(Math.max(FisherExactPValueForContingencyTable(table), MIN_PVALUE))); + logger.info(String.format("FS %s (REF+, REF-, ALT+, ALT-) = (%d, %d, %d, %d) = %s", + name, table[0][0], table[0][1], table[1][0], table[1][1], pValue)); + } + + /** + * Adds the small value AUGMENTATION_CONSTANT to all the entries of the table. + * + * @param table the table to augment + * @return the augmented table + */ + protected static double[][] augmentContingencyTable(final int[][] table) { + double[][] augmentedTable = new double[ARRAY_DIM][ARRAY_DIM]; + for ( int i = 0; i < ARRAY_DIM; i++ ) { + for ( int j = 0; j < ARRAY_DIM; j++ ) + augmentedTable[i][j] = table[i][j] + AUGMENTATION_CONSTANT; + } + + return augmentedTable; + } + + /** + * Normalize the table so that the entries are not too large. + * Note that this method does NOT necessarily make a copy of the table being passed in! + * + * @param table the original table + * @return a normalized version of the table or the original table if it is already normalized + */ + protected static int[][] normalizeContingencyTable(final int[][] table) { + final int sum = table[0][0] + table[0][1] + table[1][0] + table[1][1]; + if ( sum <= TARGET_TABLE_SIZE * 2 ) + return table; + + final double normalizationFactor = (double)sum / TARGET_TABLE_SIZE; + + final int[][] normalized = new int[ARRAY_DIM][ARRAY_DIM]; + for ( int i = 0; i < ARRAY_DIM; i++ ) { + for ( int j = 0; j < ARRAY_DIM; j++ ) + normalized[i][j] = (int)(table[i][j] / normalizationFactor); + } + + return normalized; + } + + public static int [][] copyContingencyTable(int [][] t) { + int[][] c = new int[ARRAY_DIM][ARRAY_DIM]; + + for ( int i = 0; i < ARRAY_DIM; i++ ) { + //System.arraycopy(t,0,c,0,ARRAY_DIM); + for (int j = 0; j < ARRAY_DIM; j++) { + c[i][j] = t[i][j]; + } + } + + return c; + } + + protected static boolean rotateTable(int[][] table) { + table[0][0]--; + table[1][0]++; + + table[0][1]++; + table[1][1]--; + + return (table[0][0] >= 0 && table[1][1] >= 0); + } + + protected static boolean unrotateTable(int[][] table) { + table[0][0]++; + table[1][0]--; + + table[0][1]--; + table[1][1]++; + + return (table[0][1] >= 0 && table[1][0] >= 0); + } + + protected static double computePValue(int[][] table) { + + int[] rowSums = { sumRow(table, 0), sumRow(table, 1) }; + int[] colSums = { sumColumn(table, 0), sumColumn(table, 1) }; + int N = rowSums[0] + rowSums[1]; + + // calculate in log space for better precision + double pCutoff = Arithmetic.logFactorial(rowSums[0]) + + Arithmetic.logFactorial(rowSums[1]) + + Arithmetic.logFactorial(colSums[0]) + + Arithmetic.logFactorial(colSums[1]) + - Arithmetic.logFactorial(table[0][0]) + - Arithmetic.logFactorial(table[0][1]) + - Arithmetic.logFactorial(table[1][0]) + - Arithmetic.logFactorial(table[1][1]) + - Arithmetic.logFactorial(N); + return Math.exp(pCutoff); + } + + private static int sumRow(int[][] table, int column) { + int sum = 0; + for (int r = 0; r < table.length; r++) { + sum += table[r][column]; + } + + return sum; + } + + private static int sumColumn(int[][] table, int row) { + int sum = 0; + for (int c = 0; c < table[row].length; c++) { + sum += table[row][c]; + } + + return sum; + } + +} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTest.java index 40d8cecf6..ac944b0ec 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTest.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTest.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -58,6 +58,7 @@ import htsjdk.variant.vcf.VCFFormatHeaderLine; import htsjdk.variant.vcf.VCFHeaderLine; import org.apache.log4j.Logger; import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; import org.broadinstitute.gatk.utils.contexts.AlignmentContext; import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; @@ -77,7 +78,8 @@ import java.util.*; /** * Class of tests to detect strand bias. */ -public abstract class StrandBiasTest extends InfoFieldAnnotation { +//TODO: will eventually implement ReducibleAnnotation -- see RMSAnnotation.java for an example of an abstract ReducibleAnnotation +public abstract class StrandBiasTest extends InfoFieldAnnotation implements ActiveRegionBasedAnnotation { private final static Logger logger = Logger.getLogger(StrandBiasTest.class); private static boolean stratifiedPerReadAlleleLikelihoodMapWarningLogged = false; private static boolean inputVariantContextWarningLogged = false; @@ -181,8 +183,16 @@ public abstract class StrandBiasTest extends InfoFieldAnnotation { continue; foundData = true; - final String sbbsString = (String) g.getAnyAttribute(GATKVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY); - final int[] data = encodeSBBS(sbbsString); + int[] data; + if ( g.getAnyAttribute(GATKVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY).getClass().equals(String.class)) { + final String sbbsString = (String) g.getAnyAttribute(GATKVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY); + data = encodeSBBS(sbbsString); + } else if (g.getAnyAttribute(GATKVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY).getClass().equals(ArrayList.class)) { + ArrayList sbbsList = (ArrayList) g.getAnyAttribute(GATKVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY); + data = encodeSBBS(sbbsList); + } else + throw new IllegalArgumentException("Unexpected " + GATKVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY + " type"); + if ( passesMinimumThreshold(data, minCount) ) { for( int index = 0; index < sbArray.length; index++ ) { sbArray[index] += data[index]; @@ -304,7 +314,6 @@ public abstract class StrandBiasTest extends InfoFieldAnnotation { private static void updateTable(final int[] table, final Allele allele, final GATKSAMRecord read, final Allele ref, final List allAlts) { final boolean matchesRef = allele.equals(ref, true); - final boolean matchesAlt = allele.equals(allAlts.get(0), true); final boolean matchesAnyAlt = allAlts.contains(allele); if ( matchesRef || matchesAnyAlt ) { @@ -350,6 +359,20 @@ public abstract class StrandBiasTest extends InfoFieldAnnotation { return array; } + /** + * Helper function to parse the genotype annotation into the SB annotation array + * @param arrayList the ArrayList returned from StrandBiasBySample.annotate() + * @return the array used by the per-sample Strand Bias annotation + */ + private static int[] encodeSBBS( final ArrayList arrayList ) { + final int[] array = new int[ARRAY_SIZE]; + int index = 0; + for ( Integer item : arrayList ) + array[index++] = item.intValue(); + + return array; + } + /** * Helper function to turn the SB annotation array into a contingency table * @param array the array used by the per-sample Strand Bias annotation diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatio.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatio.java index 96913ceb9..653848a0c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatio.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatio.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -66,7 +66,9 @@ import java.util.*; /** * Strand bias estimated by the Symmetric Odds Ratio test * - *

Strand bias is a type of sequencing bias in which one DNA strand is favored over the other, which can result in incorrect evaluation of the amount of evidence observed for one allele vs. the other. The StrandOddsRatio annotation is one of several methods that aims to evaluate whether there is strand bias in the data. It is an updated form of the Fisher Strand Test that is better at taking into account large amounts of data in high coverage situations. It is used to determine if there is strand bias between forward and reverse strands for the reference or alternate allele.

+ *

Strand bias is a type of sequencing bias in which one DNA strand is favored over the other, which can result in incorrect evaluation of the amount of evidence observed for one allele vs. the other.

+ * + *

The StrandOddsRatio annotation is one of several methods that aims to evaluate whether there is strand bias in the data. It is an updated form of the Fisher Strand Test that is better at taking into account large amounts of data in high coverage situations. It is used to determine if there is strand bias between forward and reverse strands for the reference or alternate allele. The reported value is ln-scaled.

* *

Statistical notes

*

Odds Ratios in the 2x2 contingency table below are

@@ -93,15 +95,19 @@ import java.util.*; * *

See the method document on statistical tests for a more detailed explanation of this statistical test.

* + *

Caveat

+ *

+ * The name SOR is not entirely appropriate because the implementation was changed somewhere between the start of development and release of this annotation. Now SOR isn't really an odds ratio anymore. The goal was to separate certain cases of data without penalizing variants that occur at the ends of exons because they tend to only be covered by reads in one direction (depending on which end of the exon they're on), so if a variant has 10 ref reads in the + direction, 1 ref read in the - direction, 9 alt reads in the + direction and 2 alt reads in the - direction, it's actually not strand biased, but the FS score is pretty bad. The implementation that resulted derived in part from empirically testing some read count tables of various sizes with various ratios and deciding from there.

+ * *

Related annotations

* * */ public class StrandOddsRatio extends StrandBiasTest implements StandardAnnotation, ActiveRegionBasedAnnotation { - private final static double AUGMENTATION_CONSTANT = 1.0; private static final int MIN_COUNT = 0; @Override @@ -132,17 +138,17 @@ public class StrandOddsRatio extends StrandBiasTest implements StandardAnnotatio } /** - * Computes the SOR value of a table after augmentation. Based on the symmetric odds ratio but modified to take on + * Computes the SOR value of a table after augmentation (adding pseudocounts). Based on the symmetric odds ratio but modified to take on * low values when the reference +/- read count ratio is skewed but the alt count ratio is not. Natural log is taken * to keep values within roughly the same range as other annotations. * - * Augmentation avoids quotient by zero. + * Adding pseudocounts prevent divide-by-zero. * * @param originalTable The table before augmentation * @return the SOR annotation value */ final protected double calculateSOR(final int[][] originalTable) { - final double[][] augmentedTable = augmentContingencyTable(originalTable); + final double[][] augmentedTable = StrandBiasTableUtils.augmentContingencyTable(originalTable); double ratio = 0; @@ -158,22 +164,6 @@ public class StrandOddsRatio extends StrandBiasTest implements StandardAnnotatio } - /** - * Adds the small value AUGMENTATION_CONSTANT to all the entries of the table. - * - * @param table the table to augment - * @return the augmented table - */ - private static double[][] augmentContingencyTable(final int[][] table) { - double[][] augmentedTable = new double[ARRAY_DIM][ARRAY_DIM]; - for ( int i = 0; i < ARRAY_DIM; i++ ) { - for ( int j = 0; j < ARRAY_DIM; j++ ) - augmentedTable[i][j] = table[i][j] + AUGMENTATION_CONSTANT; - } - - return augmentedTable; - } - /** * Returns an annotation result given a ratio * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TandemRepeatAnnotator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TandemRepeatAnnotator.java index a781d51c7..80ea1ab4c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TandemRepeatAnnotator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TandemRepeatAnnotator.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -76,11 +76,6 @@ import java.util.*; * *

A tandem repeat unit is composed of one or more nucleotides that are repeated multiple times in series. Repetitive sequences are difficult to map to the reference because they are associated with multiple alignment possibilities. Knowing the number of repeat units in a set of tandem repeats tells you the number of different positions the tandem repeat can be placed in. The observation of many tandem repeat units multiplies the number of possible representations that can be made of the region. * - *

Caveat

- *
    - *
  • This annotation is currently not compatible with HaplotypeCaller.
    • - *
- * */ public class TandemRepeatAnnotator extends InfoFieldAnnotation implements StandardUGAnnotation, ActiveRegionBasedAnnotation { private final static Logger logger = Logger.getLogger(TandemRepeatAnnotator.class); diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TransmissionDisequilibriumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TransmissionDisequilibriumTest.java index a96878a0f..2ff64073c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TransmissionDisequilibriumTest.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TransmissionDisequilibriumTest.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantType.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantType.java index c92cac17c..a1191bda9 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantType.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantType.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardHCAnnotation.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardHCAnnotation.java new file mode 100644 index 000000000..65adb6989 --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardHCAnnotation.java @@ -0,0 +1,57 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.annotator.interfaces; + +/** + * Annotations implementing this interface will be default for HaplotypeCaller + */ +public interface StandardHCAnnotation extends AnnotationType {} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariates.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariates.java index cd68e028a..a5419139b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariates.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariates.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -79,7 +79,7 @@ import java.util.Map; * Create plots to visualize base recalibration results * *

- * This tool generates plots for visualizing the quality of a recalibration run. + * This tool generates plots for visualizing the quality of a recalibration run (effected by BaseRecalibrator). *

* *

Input

diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/BaseRecalibrator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/BaseRecalibrator.java index 2c6744f97..0d74a7c4d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/BaseRecalibrator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/BaseRecalibrator.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -86,22 +86,35 @@ import java.util.Arrays; import java.util.List; /** - * Generate base recalibration table to compensate for systematic errors + * Generate base recalibration table to compensate for systematic errors in basecalling confidences * *

- * This tool is designed to work as the first pass in a two-pass processing step. It does a by-locus traversal operating - * only at sites that are not in dbSNP. We assume that all reference mismatches we see are therefore errors and indicative - * of poor base quality. This tool generates tables based on various user-specified covariates (such as read group, - * reported quality score, cycle, and context). Since there is a large amount of data, one can then calculate an empirical - * probability of error given the particular covariates seen at this site, where p(error) = num mismatches / num observations. - * The output file is a table (of the several covariate values, num observations, num mismatches, empirical quality score). - *

- *

- * Note: ReadGroupCovariate and QualityScoreCovariate are required covariates and will be added regardless of whether - * or not they were specified. + * Variant calling algorithms rely heavily on the quality scores assigned to the individual base calls in each sequence + * read. These scores are per-base estimates of error emitted by the sequencing machines. Unfortunately the scores + * produced by the machines are subject to various sources of systematic technical error, leading to over- or + * under-estimated base quality scores in the data. Base quality score recalibration (BQSR) is a process in which we + * apply machine learning to model these errors empirically and adjust the quality scores accordingly. This allows us + * to get more accurate base qualities, which in turn improves the accuracy of our variant calls. + * + * The base recalibration process involves two key steps: first the program builds a model of covariation based on the + * data and a set of known variants (which you can bootstrap if there is none available for your organism), then it + * adjusts the base quality scores in the data based on the model. + * + * There is an optional but highly recommended step that involves building a second model and generating before/after + * plots to visualize the effects of the recalibration process. This is useful for quality control purposes. + * + * This tool performs the first step described above: it builds the model of covariation and produces the recalibration + * table. It operates only at sites that are not in dbSNP; we assume that all reference mismatches we see are therefore + * errors and indicative of poor base quality. This tool generates tables based on various user-specified covariates + * (such as read group, reported quality score, cycle, and context). Assuming we are working with a large amount of data, + * we can then calculate an empirical probability of error given the particular covariates seen at this site, + * where p(error) = num mismatches / num observations. + * + * The output file is a table (of the several covariate values, number of observations, number of mismatches, empirical + * quality score). *

* - *

Input

+ *

Inputs

*

* A BAM file containing data that needs to be recalibrated. *

@@ -131,6 +144,13 @@ import java.util.List; * -knownSites latest_dbsnp.vcf \ * -o recal_data.table * + * + *

Notes

+ *
  • This *base* recalibration process should not be confused with *variant* recalibration, which is a s + * ophisticated filtering technique applied on the variant callset produced in a later step of the analysis workflow.
    • + *
  • ReadGroupCovariate and QualityScoreCovariate are required covariates and will be added regardless of whether + * or not they were specified.
+ * */ @DocumentedGATKFeature(groupName = HelpConstants.DOCS_CAT_DATA, extraDocs = {CommandLineGATK.class}) diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfo.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfo.java index c3914216d..6a2603cef 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfo.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfo.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/RecalibrationEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/RecalibrationEngine.java index aa20c9656..94ee44f3e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/RecalibrationEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/RecalibrationEngine.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/AssignSomaticStatus.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/AssignSomaticStatus.java new file mode 100644 index 000000000..d0e318d8a --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/AssignSomaticStatus.java @@ -0,0 +1,283 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.cancer; + +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.ArgumentCollection; +import org.broadinstitute.gatk.utils.commandline.Output; +import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.walkers.RodWalker; +import org.broadinstitute.gatk.engine.walkers.TreeReducible; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.engine.SampleUtils; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.engine.GATKVCFUtils; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.VariantContextUtils; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.vcf.*; + +import java.util.*; + +/** + * Assigns somatic status to a set of calls + */ +public class AssignSomaticStatus extends RodWalker implements TreeReducible { + @ArgumentCollection + protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); + + @Argument(shortName="n", fullName="normalSample", required=true, doc="The normal sample") + public String normalSample; + + @Argument(shortName="t", fullName="tumorSample", required=true, doc="The tumor sample") + public String tumorSample; + + @Argument(shortName="somaticPriorQ", fullName="somaticPriorQ", required=false, doc="Phred-scaled probability that a site is a somatic mutation") + public byte somaticPriorQ = 60; + + @Argument(shortName="somaticMinLOD", fullName="somaticMinLOD", required=false, doc="Phred-scaled min probability that a site should be called somatic mutation") + public byte somaticMinLOD = 1; + + @Argument(shortName="minimalVCF", fullName="minimalVCF", required=false, doc="If provided, the attributes of the output VCF will only contain the somatic status fields") + public boolean minimalVCF = false; + + @Output + protected VariantContextWriter vcfWriter = null; + + private final String SOMATIC_LOD_TAG_NAME = "SOMATIC_LOD"; + private final String SOMATIC_AC_TAG_NAME = "SOMATIC_AC"; + private final String SOMATIC_NONREF_TAG_NAME = "SOMATIC_NNR"; + + private final Set samples = new HashSet(2); + + /** + * Parse the familial relationship specification, and initialize VCF writer + */ + public void initialize() { + List rodNames = new ArrayList(); + rodNames.add(variantCollection.variants.getName()); + + Map vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames); + Set vcfSamples = SampleUtils.getSampleList(vcfRods, GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE); + + // set up tumor and normal samples + if ( !vcfSamples.contains(normalSample) ) + throw new UserException.BadArgumentValue("--normalSample", "the normal sample " + normalSample + " doesn't match any sample from the input VCF"); + if ( !vcfSamples.contains(tumorSample) ) + throw new UserException.BadArgumentValue("--tumorSample", "the tumor sample " + tumorSample + " doesn't match any sample from the input VCF"); + + logger.info("Normal sample: " + normalSample); + logger.info("Tumor sample: " + tumorSample); + + Set headerLines = new HashSet(); + headerLines.addAll(GATKVCFUtils.getHeaderFields(this.getToolkit())); + headerLines.add(new VCFInfoHeaderLine(VCFConstants.SOMATIC_KEY, 0, VCFHeaderLineType.Flag, "Is this a confidently called somatic mutation")); + headerLines.add(new VCFInfoHeaderLine(SOMATIC_LOD_TAG_NAME, 1, VCFHeaderLineType.Float, "log10 probability that the site is a somatic mutation")); + headerLines.add(new VCFInfoHeaderLine(SOMATIC_AC_TAG_NAME, 1, VCFHeaderLineType.Integer, "Allele count of samples with somatic event")); + headerLines.add(new VCFInfoHeaderLine(SOMATIC_NONREF_TAG_NAME, 1, VCFHeaderLineType.Integer, "Number of samples with somatic event")); + + samples.add(normalSample); + samples.add(tumorSample); + vcfWriter.writeHeader(new VCFHeader(headerLines, samples)); + } + + private double log10pNonRefInSamples(final VariantContext vc, final String sample) { + return log10PLFromSamples(vc, sample, false); + } + + private double log10pRefInSamples(final VariantContext vc, final String sample) { + return log10PLFromSamples(vc, sample, true); + } + + private double log10PLFromSamples(final VariantContext vc, final String sample, boolean calcRefP) { + + Genotype g = vc.getGenotype(sample); + double log10pSample = -1000; + if ( ! g.isNoCall() ) { + final double[] gLikelihoods = MathUtils.normalizeFromLog10(g.getLikelihoods().getAsVector()); + log10pSample = Math.log10(calcRefP ? gLikelihoods[0] : 1 - gLikelihoods[0]); + log10pSample = Double.isInfinite(log10pSample) ? -10000 : log10pSample; + } + return log10pSample; + } + + private int calculateTumorAC(final VariantContext vc) { + int ac = 0; + switch ( vc.getGenotype(tumorSample).getType() ) { + case HET: ac += 1; break; + case HOM_VAR: ac += 2; break; + case NO_CALL: case UNAVAILABLE: case HOM_REF: break; + } + return ac; + } + + private int calculateTumorNNR(final VariantContext vc) { + int nnr = 0; + switch ( vc.getGenotype(tumorSample).getType() ) { + case HET: case HOM_VAR: nnr += 1; break; + case NO_CALL: case UNAVAILABLE: case HOM_REF: break; + } + return nnr; + } + + /** + * P(somatic | D) + * = P(somatic) * P(D | somatic) + * = P(somatic) * P(D | normals are ref) * P(D | tumors are non-ref) + * + * P(! somatic | D) + * = P(! somatic) * P(D | ! somatic) + * = P(! somatic) * + * * ( P(D | normals are non-ref) * P(D | tumors are non-ref) [germline] + * + P(D | normals are ref) * P(D | tumors are ref)) [no-variant at all] + * + * @param vc + * @return + */ + private double calcLog10pSomatic(final VariantContext vc) { + // walk over tumors + double log10pNonRefInTumors = log10pNonRefInSamples(vc, tumorSample); + double log10pRefInTumors = log10pRefInSamples(vc, tumorSample); + + // walk over normals + double log10pNonRefInNormals = log10pNonRefInSamples(vc, normalSample); + double log10pRefInNormals = log10pRefInSamples(vc, normalSample); + + // priors + double log10pSomaticPrior = QualityUtils.qualToErrorProbLog10(somaticPriorQ); + double log10pNotSomaticPrior = Math.log10(1 - QualityUtils.qualToErrorProb(somaticPriorQ)); + + double log10pNotSomaticGermline = log10pNonRefInNormals + log10pNonRefInTumors; + double log10pNotSomaticNoVariant = log10pRefInNormals + log10pRefInTumors; + + double log10pNotSomatic = log10pNotSomaticPrior + MathUtils.log10sumLog10(new double[]{log10pNotSomaticGermline, log10pNotSomaticNoVariant}); + double log10pSomatic = log10pSomaticPrior + log10pNonRefInTumors + log10pRefInNormals; + double lod = log10pSomatic - log10pNotSomatic; + + return Double.isInfinite(lod) ? -10000 : lod; + } + + /** + * For each variant in the file, determine the phasing for the child and replace the child's genotype with the trio's genotype + * + * @param tracker the reference meta-data tracker + * @param ref the reference context + * @param context the alignment context + * @return null + */ + @Override + public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + if (tracker != null) { + for ( VariantContext vc : tracker.getValues(variantCollection.variants, context.getLocation()) ) { + vc = vc.subContextFromSamples(samples); + if ( !vc.isPolymorphicInSamples() ) + continue; + + double log10pSomatic = calcLog10pSomatic(vc); + + // write in the somatic status probability + Map attrs = new HashMap(); // vc.getAttributes()); + if ( ! minimalVCF ) attrs.putAll(vc.getAttributes()); + attrs.put(SOMATIC_LOD_TAG_NAME, log10pSomatic); + if ( log10pSomatic > somaticMinLOD ) { + attrs.put(VCFConstants.SOMATIC_KEY, true); + attrs.put(SOMATIC_NONREF_TAG_NAME, calculateTumorNNR(vc)); + attrs.put(SOMATIC_AC_TAG_NAME, calculateTumorAC(vc)); + + } + final VariantContextBuilder builder = new VariantContextBuilder(vc).attributes(attrs); + VariantContextUtils.calculateChromosomeCounts(builder, false); + VariantContext newvc = builder.make(); + + vcfWriter.add(newvc); + } + + return null; + } + + return null; + } + + /** + * Provide an initial value for reduce computations. + * + * @return Initial value of reduce. + */ + @Override + public Integer reduceInit() { + return null; + } + + /** + * Reduces a single map with the accumulator provided as the ReduceType. + * + * @param value result of the map. + * @param sum accumulator for the reduce. + * @return accumulator with result of the map taken into account. + */ + @Override + public Integer reduce(Integer value, Integer sum) { + return null; + } + + @Override + public Integer treeReduce(Integer sum1, Integer sum2) { + return reduce(sum1, sum2); + } +} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/BaseQualitySumPerAlleleBySample.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/BaseQualitySumPerAlleleBySample.java new file mode 100644 index 000000000..6e2ce6bc0 --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/BaseQualitySumPerAlleleBySample.java @@ -0,0 +1,190 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.cancer; + +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.GenotypeBuilder; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFFormatHeaderLine; +import htsjdk.variant.vcf.VCFHeaderLineCount; +import htsjdk.variant.vcf.VCFHeaderLineType; +import org.apache.log4j.Logger; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.GenotypeAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardSomaticAnnotation; +import org.broadinstitute.gatk.tools.walkers.cancer.m2.MuTect2; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.exceptions.GATKException; +import org.broadinstitute.gatk.utils.genotyper.MostLikelyAllele; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.ReadUtils; +import org.broadinstitute.gatk.utils.variant.GATKVCFConstants; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; +import java.util.Map; + + +/** + * Sum of evidence in reads supporting each allele for each sample + * + *

In the domain of somatic variants, a variant call can be supported by a few high quality reads. The + * BaseQualitySumPerAlleleBySample annotation aims to give the user an estimate of the quality of the evidence supporting + * a variant.

+ * + *

Notes

+ * BaseQualitySumPerAlleleBySample is called and used by MuTect2 for variant filtering. This annotation is applied to SNPs + * and INDELs. Qualities are not literal base qualities, but instead are derived from the per-allele likelihoods derived + * from the assembly engine. + * + *

Caveats

+ *
    + *
  • At this time, BaseQualitySumPerAlleleBySample can only be called from MuTect2
    • + *
+ */ +public class BaseQualitySumPerAlleleBySample extends GenotypeAnnotation implements StandardSomaticAnnotation { + private final static Logger logger = Logger.getLogger(BaseQualitySumPerAlleleBySample.class); + private boolean walkerIdentityCheckWarningLogged = false; + + public List getKeyNames() { return Arrays.asList(GATKVCFConstants.QUALITY_SCORE_SUM_KEY); } + + + public void annotate(final RefMetaDataTracker tracker, + final AnnotatorCompatible walker, + final ReferenceContext ref, + final AlignmentContext stratifiedContext, + final VariantContext vc, + final Genotype g, + final GenotypeBuilder gb, + final PerReadAlleleLikelihoodMap alleleLikelihoodMap) { + + // Can only call from MuTect2 + if ( !(walker instanceof MuTect2) ) { + if ( !walkerIdentityCheckWarningLogged ) { + if ( walker != null ) + logger.warn("Annotation will not be calculated, can only be called from MuTect2, not " + walker.getClass().getName()); + else + logger.warn("Annotation will not be calculated, can only be called from MuTect2"); + walkerIdentityCheckWarningLogged = true; + } + return; + } + + if ( g == null || !g.isCalled() || ( stratifiedContext == null && alleleLikelihoodMap == null) ) + return; + + if (alleleLikelihoodMap != null) { + annotateWithLikelihoods(alleleLikelihoodMap, vc, gb); + } + } + + protected void annotateWithLikelihoods(final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap, final VariantContext vc, final GenotypeBuilder gb) { + final ArrayList refQuals = new ArrayList<>(); + final ArrayList altQuals = new ArrayList<>(); + + // clean up + fillQualsFromLikelihoodMap(vc.getAlleles(), vc.getStart(), perReadAlleleLikelihoodMap, refQuals, altQuals); + double refQualSum = 0; + for(Double d : refQuals) { refQualSum += d; } + + double altQualSum = 0; + for(Double d : altQuals) { altQualSum += d; } + + gb.attribute(GATKVCFConstants.QUALITY_SCORE_SUM_KEY, new Integer[]{ (int) refQualSum, (int) altQualSum}); + } + + public List getDescriptions() { + return Arrays.asList(new VCFFormatHeaderLine(getKeyNames().get(0), VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Sum of base quality scores for each allele")); + } + + // from rank sum test */ + protected void fillQualsFromLikelihoodMap(final List alleles, + final int refLoc, + final PerReadAlleleLikelihoodMap likelihoodMap, + final List refQuals, + final List altQuals) { + for ( final Map.Entry> el : likelihoodMap.getLikelihoodReadMap().entrySet() ) { + final MostLikelyAllele a = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue()); + if ( ! a.isInformative() ) + continue; // read is non-informative + + final GATKSAMRecord read = el.getKey(); + if ( isUsableRead(read) ) { + final Double value = getBaseQualityForRead(read, refLoc); + if ( value == null ) + continue; + + if ( a.getMostLikelyAllele().isReference() ) + refQuals.add(value); + else if ( alleles.contains(a.getMostLikelyAllele()) ) + altQuals.add(value); + } + } + } + + protected boolean isUsableRead(final GATKSAMRecord read) { + return !( read.getMappingQuality() == 0 || + read.getMappingQuality() == QualityUtils.MAPPING_QUALITY_UNAVAILABLE ); + } + + + protected Double getBaseQualityForRead(final GATKSAMRecord read, final int refLoc) { + return (double)read.getBaseQualities()[ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead(read, refLoc, ReadUtils.ClippingTail.RIGHT_TAIL)]; + } + +} \ No newline at end of file diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/OxoGReadCounts.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/OxoGReadCounts.java new file mode 100644 index 000000000..fabfdb167 --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/OxoGReadCounts.java @@ -0,0 +1,197 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.cancer; + +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.GenotypeBuilder; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFFormatHeaderLine; +import htsjdk.variant.vcf.VCFHeaderLineCount; +import htsjdk.variant.vcf.VCFHeaderLineType; +import org.apache.log4j.Logger; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.GenotypeAnnotation; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; +import org.broadinstitute.gatk.tools.walkers.cancer.m2.MuTect2; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.exceptions.GATKException; +import org.broadinstitute.gatk.utils.genotyper.MostLikelyAllele; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.ReadUtils; +import org.broadinstitute.gatk.utils.variant.GATKVCFConstants; +import org.broadinstitute.gatk.utils.variant.GATKVCFHeaderLines; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; +import java.util.Map; + + +/** + * Count of read pairs in the F1R2 and F2R1 configurations supporting the reference and alternate alleles + * + *

This is an annotation that gathers information about the read pair configuration for the reads supporting each + * allele. It can be used along with downstream filtering steps to identify and filter out erroneous variants that occur + * with higher frequency in one read pair orientation.

+ * + *

References

+ *

For more details about the mechanism of oxoG artifact generation, see + * "Discovery and characterization of artefactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation." + * by Costello et al.

+ * + *

Caveats

+ *
    + *
  • At present, this annotation can only be called from MuTect2
    • + *
  • The FOXOG annotation is only calculated for SNPs
    • + *
+ */ +public class OxoGReadCounts extends GenotypeAnnotation { + private final static Logger logger = Logger.getLogger(OxoGReadCounts.class); + private boolean walkerIdentityCheckWarningLogged = false; + Allele refAllele; + Allele altAllele; + + public List getKeyNames() { + return Arrays.asList(GATKVCFConstants.OXOG_ALT_F1R2_KEY, GATKVCFConstants.OXOG_ALT_F2R1_KEY, GATKVCFConstants.OXOG_REF_F1R2_KEY, GATKVCFConstants.OXOG_REF_F2R1_KEY, GATKVCFConstants.OXOG_FRACTION_KEY); + } + + + public void annotate(final RefMetaDataTracker tracker, + final AnnotatorCompatible walker, + final ReferenceContext ref, + final AlignmentContext stratifiedContext, + final VariantContext vc, + final Genotype g, + final GenotypeBuilder gb, + final PerReadAlleleLikelihoodMap alleleLikelihoodMap) { + + // Can only call from MuTect2 + if ( !(walker instanceof MuTect2) ) { + if ( !walkerIdentityCheckWarningLogged ) { + if ( walker != null ) + logger.warn("Annotation will not be calculated, can only be called from MuTect2, not " + walker.getClass().getName()); + else + logger.warn("Annotation will not be calculated, can only be called from MuTect2"); + walkerIdentityCheckWarningLogged = true; + } + return; + } + + if (g == null || !g.isCalled() || (stratifiedContext == null && alleleLikelihoodMap == null)) + return; + + refAllele = vc.getReference(); + altAllele = vc.getAlternateAllele(0); + + if (alleleLikelihoodMap != null) { + annotateWithLikelihoods(alleleLikelihoodMap, vc, gb); + } + } + + protected void annotateWithLikelihoods(final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap, final VariantContext vc, final GenotypeBuilder gb) { + int ALT_F1R2, ALT_F2R1, REF_F1R2, REF_F2R1; + ALT_F1R2 = ALT_F2R1 = REF_F1R2 = REF_F2R1 = 0; + double numerator, denominator; + + for ( final Map.Entry> el : perReadAlleleLikelihoodMap.getLikelihoodReadMap().entrySet() ) { + final MostLikelyAllele a = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue()); + if ( ! a.isInformative() || ! isUsableRead(el.getKey())) + continue; // read is non-informative or MQ0 + if (a.getAlleleIfInformative().equals(refAllele, true) && el.getKey().getReadPairedFlag()) { + if (el.getKey().getReadNegativeStrandFlag() == el.getKey().getFirstOfPairFlag()) + REF_F2R1++; + else + REF_F1R2++; + } + else if (a.getAlleleIfInformative().equals(altAllele,true) && el.getKey().getReadPairedFlag()){ + if (el.getKey().getReadNegativeStrandFlag() == el.getKey().getFirstOfPairFlag()) + ALT_F2R1++; + else + ALT_F1R2++; + } + } + + denominator = ALT_F1R2 + ALT_F2R1; + Double fOxoG = null; + if (vc.isSNP() && denominator > 0) { + if (refAllele.equals(Allele.create((byte) 'C', true)) || refAllele.equals(Allele.create((byte) 'A', true))) + numerator = ALT_F2R1; + else + numerator = ALT_F1R2; + fOxoG = (float) numerator / denominator; + } + + gb.attribute(GATKVCFConstants.OXOG_ALT_F1R2_KEY, new Integer(ALT_F1R2)); + gb.attribute(GATKVCFConstants.OXOG_ALT_F2R1_KEY, new Integer(ALT_F2R1)); + gb.attribute(GATKVCFConstants.OXOG_REF_F1R2_KEY, new Integer(REF_F1R2)); + gb.attribute(GATKVCFConstants.OXOG_REF_F2R1_KEY, new Integer(REF_F2R1)); + gb.attribute(GATKVCFConstants.OXOG_FRACTION_KEY, fOxoG); + } + + public List getDescriptions() { + return Arrays.asList(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.OXOG_ALT_F1R2_KEY), + GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.OXOG_ALT_F2R1_KEY), + GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.OXOG_REF_F1R2_KEY), + GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.OXOG_REF_F2R1_KEY), + GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.OXOG_FRACTION_KEY)); + } + + protected boolean isUsableRead(final GATKSAMRecord read) { + return !( read.getMappingQuality() == 0 || + read.getMappingQuality() == QualityUtils.MAPPING_QUALITY_UNAVAILABLE ); + } +} \ No newline at end of file diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/AnnotatePopulationAFWalker.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/AnnotatePopulationAFWalker.java new file mode 100755 index 000000000..23811a463 --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/AnnotatePopulationAFWalker.java @@ -0,0 +1,186 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.cancer.contamination; + + +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.Input; +import org.broadinstitute.gatk.utils.commandline.Output; +import org.broadinstitute.gatk.utils.commandline.RodBinding; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.samples.Sample; +import org.broadinstitute.gatk.engine.walkers.DataSource; +import org.broadinstitute.gatk.engine.walkers.Requires; +import org.broadinstitute.gatk.engine.walkers.RodWalker; +import org.broadinstitute.gatk.engine.walkers.TreeReducible; +import htsjdk.variant.vcf.VCFHeader; +import htsjdk.variant.vcf.VCFHeaderLine; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; + +import java.util.*; + +/** + * Given a input VCF representing a collection of populations, split the input into each population, and annotate each record with population allele frequencies + */ +// @Requires(DataSource.SAMPLE) <- require the sample data when this works +public class AnnotatePopulationAFWalker extends RodWalker implements TreeReducible { + // control the output + @Output(doc="File to which variants should be written",required=true) + protected VariantContextWriter writer = null; + + // our mapping of population to sample list + private final Map> popMapping = new LinkedHashMap>(); + + @Input(fullName="population", shortName = "pop", doc="the VCF containing large populations of samples", required=true) + public RodBinding pop; + + // either load the lanes into our name list, or the samples, depending on the command line parameters + public void initialize() { + // get the sample information + for (Sample sp: getToolkit().getSampleDB().getSamples()) + if (sp.getOtherPhenotype() != null) { + if (!popMapping.containsKey(sp.getOtherPhenotype())) + popMapping.put(sp.getOtherPhenotype(),new ArrayList()); + popMapping.get(sp.getOtherPhenotype()).add(sp); + } + + // this is a stop-gap until the @Requires tag is working with sample information + if (popMapping.size() == 0) + throw new UserException.BadInput("we require a sample file that contains population information. Please see the wiki about how to supply one"); + + // setup our VCF + // TODO: add code to get the samples from the input VCF, if they set 'preserveGenotypes' above + Set hInfo = new HashSet(); + + VCFHeader vcfHeader = new VCFHeader(hInfo); + writer.writeHeader(vcfHeader); + } + + + // boilerplate code - the standard reduce function for integers + @Override public Integer reduceInit() { return 0; } + @Override public Integer reduce(Integer value, Integer sum) { return(value + sum); } + public Integer treeReduce(Integer lhs, Integer rhs) { return lhs + rhs; } + + @Override + public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + if (tracker == null) return 0; + + // get the variant contexts, and return if we have anything other than one record at this site + Collection vcs = tracker.getValues(pop); + if (vcs.size() != 1) return 0; + VariantContext originalVC = vcs.iterator().next(); + + if (!originalVC.isSNP()) return 0; + VariantContext vc = originalVC; + + // get the list of alleles + List vcAlleles = vc.getAlleles(); + // setup the mapping of allele to population map + Map> popToAlleleFreq = new LinkedHashMap>(); + + // initialize all pops + Map allPopAC = new LinkedHashMap(); + int allPopTotal = 0; + for (Allele a : vcAlleles) allPopAC.put(a,0); + + // find the sub-population allele frequencies, and annotate them + for (Map.Entry> pop : popMapping.entrySet()) { + Map thisPopAC = new LinkedHashMap(); + int total = 0; + for (Allele a : vcAlleles) thisPopAC.put(a,0); + for (Sample s : pop.getValue()) { + Genotype g = vc.getGenotype(s.getID()); + if (g == null) continue; + for (Allele a : vcAlleles) { + int count = a.length(); + + total += count; + thisPopAC.put(a,thisPopAC.get(a) + count); + + allPopTotal += count; + allPopAC.put(a, allPopAC.get(a) + count); + } + } + Map thisPopAF = new LinkedHashMap(); + for (Map.Entry entry : thisPopAC.entrySet()) + thisPopAF.put(entry.getKey(),String.format("%1.5f", (total == 0) ? 0 : (double)entry.getValue()/(double)total)); + popToAlleleFreq.put(pop.getKey(),thisPopAF); + } + + // add the all pops value as well + Map allPopAF = new LinkedHashMap(); + for (Map.Entry entry : allPopAC.entrySet()) + allPopAF.put(entry.getKey(), String.format("%1.5f", (allPopTotal == 0) ? 0 : (double)entry.getValue()/(double)allPopTotal)); + + popToAlleleFreq.put("ALL", allPopAF); + + // add the population af annotations + VariantContextBuilder vcb = new VariantContextBuilder(vc); + Map popToAlleleFreqAsObject = new LinkedHashMap(); + for (Map.Entry> mp : popToAlleleFreq.entrySet()) { + popToAlleleFreqAsObject.put(mp.getKey(),(Object)mp.getValue()); + } + vcb.attributes(popToAlleleFreqAsObject); + writer.add(vc); + return 1; + } + + +} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContEst.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContEst.java new file mode 100755 index 000000000..75e7c9fde --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContEst.java @@ -0,0 +1,729 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.cancer.contamination; + +import htsjdk.samtools.SAMReadGroupRecord; +import htsjdk.samtools.util.StringUtil; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.walkers.*; +import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalculatorProvider; +import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.FixedAFCalculatorProvider; +import org.broadinstitute.gatk.utils.commandline.*; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.sam.SAMReaderID; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedArgumentCollection; +import org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine; +import org.broadinstitute.gatk.tools.walkers.genotyper.VariantCallContext; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.exceptions.GATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; +import htsjdk.variant.variantcontext.*; + +import java.io.*; +import java.util.*; + +/** + * Estimate cross-sample contamination + * + * This tool determine the percent contamination of an input bam by sample, by lane, or in aggregate across all the input reads. + * + *

Usage examples

+ *

These are example commands that show how to run ContEst for typical use cases. Square brackets ("[ ]") + * indicate optional arguments. Note that parameter values and/or resources shown here may not be the latest recommended; see the Best Practices documentation for detailed recommendations.

+ * + *
+ *

Contamination estimation using a VCF containing the normal sample's genotypes (as might be derived from a genotyping array)

+ * 
+ *   java
+ *     -jar GenomeAnalysisTK.jar \
+ *     -T ContEst \
+ *     -R reference.fasta \
+ *     -I tumor.bam \
+ *     --genotypes normalGenotypes.vcf \
+ *     --popFile populationAlleleFrequencies.vcf \
+ *     -L populationSites.interval_list
+ *     [-L targets.interval_list] \
+ *     -isr INTERSECTION \
+ *     -o output.txt
+ *
+ * + *
+ *

Contamination estimation using the normal BAM for genotyping on-the-fly

+ * 
+ *   java
+ *     -jar GenomeAnalysisTK.jar \
+ *     -T ContEst \
+ *     -R reference.fasta \
+ *     -I:eval tumor.bam \
+ *     -I:genotype normal.bam \
+ *     --popFile populationAlleleFrequencies.vcf \
+ *     -L populationSites.interval_list
+ *     [-L targets.interval_list] \
+ *     -isr INTERSECTION \
+ *     -o output.txt
+ *
+ * + *

Output

+ * A text file containing estimated percent contamination, as well as error bars on this estimate. + * + *

Notes

+ * Multiple modes are supported simultaneously, e.g. contamination by sample and readgroup can be computed in the same run. + */ +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} ) +@Allows(value = {DataSource.READS, DataSource.REFERENCE}) +@Requires(value = {DataSource.READS, DataSource.REFERENCE}, referenceMetaData = @RMD(name = "genotypes", type = VariantContext.class)) +@By(DataSource.READS) +public class ContEst extends RodWalker>, ContaminationResults> { + + // ------------------------------------------------------------------------------------------------------------------------------------------------------ + // Some constants we use + // ------------------------------------------------------------------------------------------------------------------------------------------------------ + /** what type of run stats would we like: */ + public enum ContaminationRunType { + SAMPLE, // calculate contamination for each sample + READGROUP, // for each read group + META // for all inputs as a single source + } + // ------------------------------------------------------------------------------------------------------------------------------------------------------ + // inputs + // ------------------------------------------------------------------------------------------------------------------------------------------------------ + + // the genotypes ROD; this contains information about the genotypes from our sample + @Input(fullName="genotypes", shortName = "genotypes", doc="the genotype information for our sample", required=false) + public RodBinding genotypes; + + // the population information; the allele frequencies for each position in known populations + @Input(fullName="popfile", shortName = "pf", doc="the variant file containing information about the population allele frequencies", required=true) + public RodBinding pop; + + // ------------------------------------------------------------------------------------------------------------------------------------------------------ + // outputs and args + // ------------------------------------------------------------------------------------------------------------------------------------------------------ + @Output + PrintStream out; // the general output of the tool + + @Argument(fullName = "min_qscore", required = false, doc = "threshold for minimum base quality score") + public int MIN_QSCORE = 20; + + @Argument(fullName = "min_mapq", required = false, doc = "threshold for minimum mapping quality score") + public int MIN_MAPQ = 20; + + @Argument(fullName = "trim_fraction", doc = "at most, what fraction of sites should be trimmed based on BETA_THRESHOLD", required = false) + public double TRIM_FRACTION = 0.01; + + @Argument(fullName = "beta_threshold", doc = "threshold for p(f>=0.5) to trim", required = false) + public double BETA_THRESHOLD = 0.95; + + @Argument(shortName = "llc", fullName = "lane_level_contamination", doc = "set to META (default), SAMPLE or READGROUP to produce per-bam, per-sample or per-lane estimates", required = false) + private Set laneStats = null; + + @Argument(shortName = "sn", fullName = "sample_name", doc = "The sample name; used to extract the correct genotypes from mutli-sample truth vcfs", required = false) + private String sampleName = "unknown"; + + @Argument(shortName = "pc", fullName = "precision", doc = "the degree of precision to which the contamination tool should estimate (e.g. the bin size)", required = false) + private double precision = 0.1; + + @Argument(shortName = "br", fullName = "base_report", doc = "Where to write a full report about the loci we processed", required = false) + public PrintStream baseReport = null; + + @Argument(shortName = "lf", fullName = "likelihood_file", doc = "write the likelihood values to the specified location", required = false) + public PrintStream likelihoodFile = null; + + @Argument(shortName = "vs", fullName = "verify_sample", doc = "should we verify that the sample name is in the genotypes file?", required = false) + public boolean verifySample = false; + + @Argument(shortName = "mbc", fullName = "minimum_base_count", doc = "what minimum number of bases do we need to see to call contamination in a lane / sample?", required = false) + public Integer minBaseCount = 500; + + @Argument(shortName = "population", fullName = "population", doc = "evaluate contamination for just a single contamination population", required = false) + public String population = "CEU"; + + @Argument(shortName = "gm", fullName = "genotype_mode", doc = "which approach should we take to getting the genotypes (only in array-free mode)", required = false) + public SeqGenotypeMode genotypeMode = SeqGenotypeMode.HARD_THRESHOLD; + + // ------------------------------------------------------------------------------------------------------------------------------------------------------ + // hidden arguments + // ------------------------------------------------------------------------------------------------------------------------------------------------------ + @Hidden + @Argument(fullName = "trim_interval", doc = "progressively trim from 0 to TRIM_FRACTION by this interval", required = false) + public double TRIM_INTERVAL = 0; + + @Hidden + @Argument(fullName = "min_site_depth", required = false, doc = "minimum depth at a site to consider in calculation") + public int MIN_SITE_DEPTH = 0; + + @Hidden + @Argument(fullName = "fixed_epsilon_qscore", required = false, doc = "use a constant epsilon (phred scale) for calculation") + public Byte FIXED_EPSILON = null; + + @Hidden + @Argument(fullName = "min_genotype_depth", required = false, doc = "what minimum depth is required to call a site in seq genotype mode") + public int MIN_GENOTYPE_DEPTH_FOR_SEQ = 50; + + @Hidden + @Argument(fullName = "min_genotype_ratio", required = false, doc = "the ratio of alt to other bases to call a site a hom non-ref variant") + public double MIN_GENOTYPE_RATIO = 0.80; + + @Hidden + @Argument(fullName = "min_genotype_llh", required = false, doc = "the min log likelihood for UG to call a genotype") + public double MIN_UG_LOG_LIKELIHOOD = 5; + // ------------------------------------------------------------------------------------------------------------------------------------------------------ + // global variables to the walker + // ------------------------------------------------------------------------------------------------------------------------------------------------------ + private static final Map alleles = new HashMap(); // the set of alleles we work with + private boolean verifiedSampleName = false; // have we yet verified the sample name? + private final Map contaminationNames = new LinkedHashMap(); // a list, containing the contamination names, be it read groups or bam file names + private static String[] ALL_POPULATIONS = new String[]{"ALL", "CHD", "LWK", "CHB", "CEU", "MXL", "GIH", "MKK", "TSI", "CLM", "GBR", "ASW", "YRI", "IBS", "FIN", "PUR", "JPT", "CHS"}; + private String[] populationsToEvaluate; + + // variables involved in the array-free mode + private boolean useSequencingGenotypes = false; // if false we're using the sequencing geneotypes; otherwise we require array genotypes + public static final String EVAL_BAM_TAG = "eval"; + public static final String GENOTYPE_BAM_TAG = "genotype"; + String evalSample = null; + String genotypeSample = null; + + + // counts for each of the possible combinations + int totalSites = 0; + int countPopulationSites = 0; + int countGenotypeNonHomVar = 0; + int countGenotypeHomVar = 0; + int countPassCoverage = 0; + int countResults = 0; + + public enum SeqGenotypeMode { HARD_THRESHOLD, UNIFIED_GENOTYPER } + // create our list of allele characters for conversion + static { + alleles.put(0,Allele.create((byte) 'A')); + alleles.put(1,Allele.create((byte) 'C')); + alleles.put(2,Allele.create((byte) 'G')); + alleles.put(3,Allele.create((byte) 'T')); + } + + // a bunch of setup to initialize the walker + public void initialize() { + // set the genotypes source - figure out what to do if we're not using arrays + if (genotypes == null || !genotypes.isBound()) { + logger.info("Running in sequencing mode"); + useSequencingGenotypes = true; + // if were not using arrays, we need to figure out what samples are what + for(SAMReaderID id : getToolkit().getReadsDataSource().getReaderIDs()) { + if (id.getTags().getPositionalTags().size() == 0) + throw new UserException.BadInput("BAMs must be tagged with " + GENOTYPE_BAM_TAG + " and " + EVAL_BAM_TAG + " when running in array-free mode. Please see the ContEst documentation for more details"); + + // now sort out what tags go with what bam + for (String tag : id.getTags().getPositionalTags()) { + if (GENOTYPE_BAM_TAG.equalsIgnoreCase(tag)) { + try { + if (getToolkit().getReadsDataSource().getHeader(id).getReadGroups().size() == 0) + throw new RuntimeException("No Read Groups found for Genotyping BAM -- Read Groups are Required in sequencing genotype mode!"); + genotypeSample = getToolkit().getReadsDataSource().getHeader(id).getReadGroups().get(0).getSample(); + } catch (NullPointerException npe) { + throw new UserException.BadInput("Unable to fetch read group from the bam files tagged with " + GENOTYPE_BAM_TAG); + } + } else if (EVAL_BAM_TAG.equalsIgnoreCase(tag)) { + try { + if (getToolkit().getReadsDataSource().getHeader(id).getReadGroups().size() == 0) + throw new RuntimeException("No Read Groups found for Genotyping BAM -- Read Groups are Required in sequencing genotype mode!"); + evalSample = getToolkit().getReadsDataSource().getHeader(id).getReadGroups().get(0).getSample(); + } catch (NullPointerException npe) { + throw new UserException.BadInput("Unable to fetch read group from the bam files tagged with " + EVAL_BAM_TAG); + } + } else { + throw new UserException.BadInput("Unable to process " + tag + " tag, it's not either of the two accepted values: " + GENOTYPE_BAM_TAG + " or " + EVAL_BAM_TAG); + } + } + } + if (evalSample == null || genotypeSample == null) + throw new UserException.BadInput("You must provide both a " + GENOTYPE_BAM_TAG + " tagged bam and a " + EVAL_BAM_TAG + " tagged bam file. Please see the ContEst documentation"); + + } else { + logger.info("Running in array mode"); + } + if (laneStats == null) { + laneStats = new HashSet(); + laneStats.add(ContaminationRunType.META); + } + + for (ContaminationRunType type : laneStats) { + if (type == ContaminationRunType.READGROUP) { + for (SAMReadGroupRecord name : getToolkit().getSAMFileHeader().getReadGroups()) + this.contaminationNames.put(name.getId(),ContaminationRunType.READGROUP); + } else if (type == ContaminationRunType.SAMPLE) { + for (SAMReadGroupRecord name : getToolkit().getSAMFileHeader().getReadGroups()) + this.contaminationNames.put(name.getSample(),ContaminationRunType.SAMPLE); + } else if (type == ContaminationRunType.META) + this.contaminationNames.put("META",ContaminationRunType.META); + else + throw new IllegalArgumentException("Unknown type name " + laneStats); + } + if (baseReport != null) + baseReport.println("lane\tchrom\tposition\trs_id\tref\tfreq_major_allele\tfreq_minor_allele\tgeli_gt\tmaf\tmajor_allele_counts\tminor_allele_counts\ta_counts\tc_counts\tg_counts\tt_counts"); + + this.populationsToEvaluate = (population == null || "EVERY".equals(population)) ? ALL_POPULATIONS : new String[]{population}; + + } + /** + * our map function, which emits a contamination stats for each of the subgroups (lanes, samples, etc) that we encounter + * + * @param tracker the reference meta data tracker, from which we get the array truth data + * @param ref the reference information at this position + * @param context the read context, where we get the alignment data + * @return a mapping of our subgroup name to contamination estimate + */ + @Override + public Map> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + totalSites++; + if (tracker == null) return null; + if (context == null) return null; + + VariantContext popVC = tracker.getFirstValue(pop); + byte referenceBase = ref.getBase(); + if (popVC == null) return null; + countPopulationSites++; + Genotype genotype = getGenotype(tracker,context,ref,useSequencingGenotypes); + + // only use homozygous sites + if (genotype == null || !genotype.isHomVar()) { + countGenotypeNonHomVar++; + return null; + } else { + countGenotypeHomVar++; + } + + + // only use non-reference sites + byte myBase = genotype.getAllele(0).getBases()[0]; + + String rsNumber = ""; + + // our map of contamination results + Map> stats = new HashMap>(); + + // get the base pileup. This is only really required when we have both a genotyping and EVAL_BAM_TAG tagged bams + // becuase we only want contamination estimates drawn from the eval tagged bam + ReadBackedPileup defaultPile; + if (this.useSequencingGenotypes) + defaultPile = context.getBasePileup().getPileupForSample(evalSample); + else + defaultPile = context.getBasePileup(); + + // if we're by-lane, get those stats + for (Map.Entry namePair : contaminationNames.entrySet()) { + ReadBackedPileup pile; + if (namePair.getValue() == ContaminationRunType.READGROUP) + pile = defaultPile.getPileupForReadGroup(namePair.getKey()); + else if (namePair.getValue() == ContaminationRunType.META) + pile = defaultPile; + else if (namePair.getValue() == ContaminationRunType.SAMPLE) + pile = defaultPile.getPileupForSample(namePair.getKey()); + else + throw new IllegalStateException("Unknown state, contamination type = " + laneStats + " is unsupported"); + if (pile != null) { + + ReadBackedPileup filteredPile = + pile.getBaseAndMappingFilteredPileup(MIN_QSCORE, MIN_MAPQ); + + byte[] bases = filteredPile.getBases(); + + // restrict to sites that have greater than our required total depth + if (bases.length < MIN_SITE_DEPTH) { + continue; + } else { + countPassCoverage++; + } + + byte[] quals; + if (FIXED_EPSILON == null) { + quals = filteredPile.getQuals(); + } else { + quals = new byte[bases.length]; + Arrays.fill(quals, FIXED_EPSILON); + } + + Map results = + calcStats(referenceBase, + bases, + quals, + myBase, + rsNumber, + popVC, + baseReport, + context.getLocation(), + precision, + namePair.getKey(), + populationsToEvaluate); + + if (results.size() > 0) { + countResults++; + stats.put(namePair.getKey(), results); + } + } + } + // return our collected stats + return stats; + } + + /** + * get the genotype for the sample at the current position + * @param tracker the reference meta data (RODs) + * @param context the reads + * @param referenceContext the reference information + * @param useSeq are we using sequencing to get our genotypes + * @return a genotype call, which could be null + */ + private Genotype getGenotype(RefMetaDataTracker tracker, AlignmentContext context, ReferenceContext referenceContext, boolean useSeq) { + if (!useSeq) { + Genotype g = getGenotypeFromArray(tracker, this.genotypes,this.verifiedSampleName,this.verifySample,this.sampleName); + if (g != null) this.verifiedSampleName = true; + return g; + } else { + return getGenotypeFromSeq( + context, + referenceContext, + this.alleles, + this.genotypeMode, + this.MIN_GENOTYPE_RATIO, + this.MIN_GENOTYPE_DEPTH_FOR_SEQ, + this.MIN_UG_LOG_LIKELIHOOD, + this.genotypeSample, + this.sampleName, + this.getToolkit()); + } + } + + static Genotype getGenotypeFromSeq(AlignmentContext context, + ReferenceContext referenceContext, + Map alleles, + SeqGenotypeMode genotypeMode, + double minGenotypeRatio, + int minGenotypingDepth, + double minGenotypingLOD, + String genotypingSample, + String sampleName, + GenomeAnalysisEngine toolKit) { + ReadBackedPileup pileup = context.getBasePileup().getPileupForSample(genotypingSample); + if (pileup == null || pileup.isEmpty()) return null; + + // which genotyping mode are we using + if (genotypeMode == SeqGenotypeMode.HARD_THRESHOLD) { + if (sum(pileup.getBaseCounts()) < minGenotypingDepth) return null; + int[] bases = pileup.getBaseCounts(); + int mx = maxPos(bases); + int allGenotypes = sum(bases); + String refBase = String.valueOf((char)referenceContext.getBase()); + if (bases[mx] / (float)allGenotypes >= minGenotypeRatio && !refBase.equals(alleles.get(mx).getBaseString())) { + List al = new ArrayList(); + al.add(alleles.get(mx)); + GenotypeBuilder builder = new GenotypeBuilder(sampleName, al); + return builder.make(); + } + } else if (genotypeMode == SeqGenotypeMode.UNIFIED_GENOTYPER) { + UnifiedArgumentCollection basicUAC = new UnifiedArgumentCollection(); + UnifiedGenotypingEngine engine = new UnifiedGenotypingEngine(basicUAC, FixedAFCalculatorProvider.createThreadSafeProvider(toolKit, basicUAC, logger),toolKit); + AlignmentContext contextSubset = new AlignmentContext(context.getLocation(),pileup,0,true); + List callContexts = engine.calculateLikelihoodsAndGenotypes(null, referenceContext, contextSubset); + if (callContexts != null && callContexts.size() == 1) + for (Genotype g : callContexts.get(0).getGenotypes()){ + if (g.isCalled() && g.isHomVar() && g.getLog10PError() > minGenotypingLOD) + return g; + } + } + else { + throw new GATKException("Unknown genotyping mode, being an enum this really shouldn't be seen ever."); + } + return null; + } + + // utils + private static int sum(int[] a) {int sm = 0; for (int i : a) {sm = sm + i;} return sm;} + private static int maxPos(int[] a) {int mx = 0; for (int i = 0;i < a.length; i++) {if (a[i] > a[mx]) mx = i;} return mx;} + + private static Genotype getGenotypeFromArray(RefMetaDataTracker tracker, RodBinding genotypes, boolean verifiedSampleName, boolean verifySample, String sampleName) { + // get the truthForSample and the hapmap information for this site; if either are null we can't move forward + Collection truths = tracker.getValues(genotypes); + if (truths == null || truths.size() == 0) return null; + + VariantContext truthForSample = truths.iterator().next(); + + // verify that the sample name exists in the input genotype file + if (!verifiedSampleName && verifySample) { + if (!truthForSample.getSampleNames().contains(sampleName)) + throw new UserException.BadInput("The sample name was set to " + sampleName + " but this sample isn't in your genotypes file. Please Verify your sample name"); + verifiedSampleName = true; + } + + GenotypesContext gt = truthForSample.getGenotypes(); + + // if we are supposed to verify the sample name, AND the sample doesn't exist in the genotypes -- skip this site + if (verifySample && !gt.containsSample(sampleName)) return null; + + // if the sample doesn't exist in genotypes AND there is more than one sample in the genotypes file -- skip this site + if (!gt.containsSample(sampleName) && gt.size() != 1) return null; + + // if there is more than one sample in the genotypes file, get it by name. Otherwise just get the sole sample genotype + return gt.size() != 1 ? gt.get(sampleName) : gt.get(0); + } + + + private static class PopulationFrequencyInfo { + private byte majorAllele; + private byte minorAllele; + private double minorAlleleFrequency; + + private PopulationFrequencyInfo(byte majorAllele, byte minorAllele, double minorAlleleFrequency) { + this.majorAllele = majorAllele; + this.minorAllele = minorAllele; + this.minorAlleleFrequency = minorAlleleFrequency; + } + + public byte getMajorAllele() { + return majorAllele; + } + + public byte getMinorAllele() { + return minorAllele; + } + + public double getMinorAlleleFrequency() { + return minorAlleleFrequency; + } + } + + private static PopulationFrequencyInfo parsePopulationFrequencyInfo(VariantContext variantContext, String population) { + PopulationFrequencyInfo info = null; + + List values = (List) variantContext.getAttribute(population); + + if (values != null) { + byte majorAllele = 0; + byte minorAllele = 0; + double maf = -1; + + for (String str : values) { + // strip off the curly braces and trim whitespace + if (str.startsWith("{")) str = str.substring(1, str.length()); + if (str.contains("}")) str = str.substring(0, str.indexOf("}")); + str = str.trim(); + String spl[] = str.split("="); + + byte allele = (byte) spl[0].trim().charAt(0); + double af = Double.valueOf(spl[1].trim()); + + if (af <= 0.5 && minorAllele == 0) { + minorAllele = allele; + maf = af; + } else { + majorAllele = allele; + } + + } + + info = new PopulationFrequencyInfo(majorAllele, minorAllele, maf); + } + return info; + } + + + /** + * Calculate the contamination values per division, be it lane, meta, sample, etc + * @param referenceBase the reference base + * @param bases the bases seen + * @param quals and the bases qual values + * @param myAllele the allele we have (our hom var genotype allele) + * @param rsNumber the dbsnp number if available + * @param popVC the population variant context from hapmap + * @param baseReport if we're writing a base report, write it here + * @param loc our location + * @param precision the percision we're aiming for + * @param lane the lane name information + * @param pops our pops to run over + * @return a mapping of each target population to their estimated contamination + */ + private static Map calcStats(byte referenceBase, + byte[] bases, + byte[] quals, + byte myAllele, + String rsNumber, + VariantContext popVC, + PrintStream baseReport, + GenomeLoc loc, + Double precision, + String lane, + String[] pops) { + int[] alts = new int[4]; + int total = 0; + // get the depth ratio we are aiming for + for (byte base : bases) { + if (base == 'A' || base == 'a') alts[0]++; + if (base == 'C' || base == 'c') alts[1]++; + if (base == 'G' || base == 'g') alts[2]++; + if (base == 'T' || base == 't') alts[3]++; + total++; + } + + Map ret = new HashMap(); + + for (String pop : pops) { + PopulationFrequencyInfo info = parsePopulationFrequencyInfo(popVC, pop); + double alleleFreq = info.getMinorAlleleFrequency(); + if (alleleFreq > 0.5) { + throw new RuntimeException("Minor allele frequency is greater than 0.5, this is an error; we saw AF of " + alleleFreq); + } + + int majorCounts = alts[getBaseIndex(info.getMajorAllele())]; + int minorCounts = alts[getBaseIndex(info.getMinorAllele())]; + int otherCounts = total - majorCounts - minorCounts; + + + // only use sites where this is the minor allele + if (myAllele == info.minorAllele) { + + if (pops.length == 1) { + if (baseReport != null) { + baseReport.print( + StringUtil.join("\t", + lane, + loc.getContig(), + "" + loc.getStart(), + rsNumber, + "" + (char) referenceBase, + "" + (char) info.getMajorAllele(), + "" + (char) info.getMinorAllele(), + "" + (char) info.getMinorAllele() + "" + (char) info.getMinorAllele(), + String.format("%1.4f", alleleFreq), + "" + majorCounts, + "" + minorCounts)); + + for (long cnt : alts) + baseReport.print("\t" + cnt); + baseReport.println(); + } + } + + ContaminationEstimate est = new ContaminationEstimate(precision, alleleFreq, bases, quals, info.getMinorAllele(), info.getMajorAllele(), pop, loc); + ret.put(pop, new ContaminationStats(loc, 1, alleleFreq, minorCounts, majorCounts, otherCounts, alts, est)); + + } + + } + return ret; + } + + private static int getBaseIndex(byte base) { + if (base == 'A' || base == 'a') return 0; + if (base == 'C' || base == 'c') return 1; + if (base == 'G' || base == 'g') return 2; + if (base == 'T' || base == 't') return 3; + return -1; + } + + // create a ContaminationResults to store the run information + @Override + public ContaminationResults reduceInit() { + return new ContaminationResults(precision); + } + + + @Override + public ContaminationResults reduce(Map> value, ContaminationResults sum) { + if (value != null) + sum.add(value); + return sum; + } + + /** + * on traversal done, output all the stats to the appropriate files + * + * @param result the results of our contamination estimate + */ + public void onTraversalDone(ContaminationResults result) { + + // filter out lanes / samples that don't have the minBaseCount + Map> cleanedMap = new HashMap>(); + for (Map.Entry> entry : result.getStats().entrySet()) { + + Map newMap = new HashMap(); + + Map statMap = entry.getValue(); + for (String popKey : statMap.keySet()) { + ContaminationStats stat = statMap.get(popKey); + if (stat.getBasesMatching() + stat.getBasesMismatching() >= minBaseCount) newMap.put(popKey, stat); + } + + + if (newMap.size() > 0) + cleanedMap.put(entry.getKey(), newMap); + else + out.println("Warning: We're throwing out lane " + entry.getKey() + " since it has fewer than " + minBaseCount + + " read bases at genotyped positions"); + } + + // output results at the end, based on the input parameters + result.setStats(cleanedMap); + result.outputReport(precision, out, TRIM_FRACTION, TRIM_INTERVAL, BETA_THRESHOLD); + if (likelihoodFile != null) result.writeCurves(likelihoodFile); + logger.info("Total sites: " + totalSites); + logger.info("Population informed sites: " + countPopulationSites); + logger.info("Non homozygous variant sites: " + countGenotypeNonHomVar); + logger.info("Homozygous variant sites: " + countGenotypeHomVar); + logger.info("Passed coverage: " + countPassCoverage); + logger.info("Results: " + countResults); + } +} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContaminationEstimate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContaminationEstimate.java new file mode 100755 index 000000000..40b70f619 --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContaminationEstimate.java @@ -0,0 +1,234 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; 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DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.cancer.contamination; + + +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.collections.Pair; + +import java.util.Arrays; + +/** + * a class that estimates and stores the contamination values for a site. + */ +class ContaminationEstimate { + private final double precision; // to what precision do we want to run; e.g. if set to 1, we run using 1% increments + private final double[] bins; // the bins representing the discrete contamination levels we're evaluating + private double populationFit = 0.0; + private String popultationName = ""; + + private static double[] precalculatedEpsilon; + + private int arrayAlleleObservations = 0; + private int alternateAlleleObservations = 0; + + // precalculate the 128 values of epsilon that are possible + static { + precalculatedEpsilon = new double[Byte.MAX_VALUE+1]; + + for(int i=0; i <= (int)Byte.MAX_VALUE; i++) { + precalculatedEpsilon[i] = Math.pow(10.0,-1.0*(((double)i)/10.0)); + } + } + + /** + * create the contamination estimate, given: + * @param precision the precision value, to what level are we calculating the contamination + */ + public ContaminationEstimate(double precision, + double maf, + byte[] bases, + byte[] quals, + byte arrayAllele, + byte hapmapAlt, + String popName, + GenomeLoc locus + ) { + // setup the bins to the correct precision + this.precision = precision; + bins = new double[(int)Math.ceil(100/precision)+1]; + if (maf == 0) maf = 0.00001; + + popultationName = popName; + + Arrays.fill(bins,0.0); // just to make sure we don't have any residual values + + // convert the quals + double[] realQuals = new double[quals.length]; + int qIndex = 0; + for (byte qual : quals) {realQuals[qIndex++] = Math.pow(10.0,-1.0*(qual/10.0));} + + // check our inputs + if (maf > 1.0 || maf < 0.0) throw new IllegalArgumentException("Invalid allele Freq: must be between 0 and 1 (inclusive), maf was " + maf + " for population " + popName); + + // calculate the contamination for each bin + int qualOffset = 0; + for (byte base : bases) { + + if (base == arrayAllele) { arrayAlleleObservations++; } + if (base == hapmapAlt) { alternateAlleleObservations++; } + double epsilon = precalculatedEpsilon[quals[qualOffset++]]; + + for (int index = 0; index < bins.length; index++) { + + + double contaminationRate = (1.0 - (double) index / (double) bins.length); + + if (base == arrayAllele) { + bins[index] += Math.log((1.0 - contaminationRate) * (1.0 - epsilon) + + contaminationRate * ((maf) * (1.0 - epsilon) + (1.0 - maf) * (epsilon/3.0))); + populationFit += Math.log(epsilon); + + } else if(hapmapAlt == base) { + bins[index] += Math.log((1.0 - contaminationRate) * (epsilon / 3.0) + + contaminationRate * ((maf) * (epsilon/3.0) + (1.0 - maf) * (1.0 - epsilon))); + + populationFit += Math.log(maf + epsilon); + } + } + } + } + + public double[] getBins() { + return bins; + } + + public void setPopulationFit(double populationFit) { + this.populationFit = populationFit; + } + + public double getPopulationFit() { + return populationFit; + } + + public String getPopultationName() { + return popultationName; + } + + public static class ConfidenceInterval { + + private double start; + private double stop; + private double contamination; + private double maxLikelihood; + double[] newBins; + + public ConfidenceInterval(double bins[], double intervalArea) { + // make a copy of the bins in non-log space + int maxIndex = 0; + for (int x = 0; x < bins.length; x++) if (bins[x] > bins[maxIndex]) maxIndex = x; + newBins = new double[bins.length]; + maxLikelihood = bins[maxIndex]; + + int index = 0; + double total = 0.0; + for (double d : bins) { + newBins[index] = Math.pow(10,(bins[index] - bins[maxIndex])); + total += newBins[index]; + index++; + } + + for (int x = 0; x < newBins.length; x++) { + newBins[x] = newBins[x] / total; + } + double areaUnderCurve = 0; + int leftIndex = maxIndex; + int rightIndex = maxIndex; + while (areaUnderCurve < 0.95) { + + // if the "left" bin is bigger, and can be moved, move it + if (newBins[leftIndex] >= newBins[rightIndex] && leftIndex > 0) { + leftIndex--; + } else { + // otherwise move the right bin if possible + if (rightIndex < bins.length - 1) { + rightIndex++; + } else { + // and if not move the left bin, or die + if (leftIndex > 0) { + leftIndex--; + } else { + throw new RuntimeException("Error trying to compute confidence interval"); + } + } + } + + areaUnderCurve = 0.0; + for (int x = leftIndex; x <= rightIndex; x++) + areaUnderCurve += newBins[x]; + } + start = (bins.length - rightIndex) * (100.0/bins.length); + stop = (bins.length - leftIndex) * (100.0/bins.length); + contamination = (bins.length - maxIndex) * (100.0/bins.length); + } + + public double getStart() { + return start; + } + + public double getStop() { + return stop; + } + + public double getContamination() { + return contamination; + } + + public double getMaxLikelihood() { + return maxLikelihood; + } + + public String toString() { + return contamination + "[" + start + " - " + stop + "] log likelihood = " + maxLikelihood; + } + } +} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContaminationResults.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContaminationResults.java new file mode 100755 index 000000000..fa11db5fc --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContaminationResults.java @@ -0,0 +1,304 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.cancer.contamination; + + +import org.apache.commons.math.MathException; +import org.apache.commons.math.distribution.BetaDistribution; +import org.apache.commons.math.distribution.BetaDistributionImpl; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.Utils; + +import java.io.*; +import java.util.*; + +/** + * our contamination results object; this object aggregates the results of the contamination run over lanes, samples, + * or whatever other divisor we've used on the read data + */ +public class ContaminationResults { + + public static class ContaminationData implements Comparable { + private GenomeLoc site; + private long basesMatching = 0l; + private long basesMismatching = 0l; + private double mismatchFraction = -1d; + private double[] bins; + private double p; + + public long getBasesMatching() { + return basesMatching; + } + + public long getBasesMismatching() { + return basesMismatching; + } + + public double getMismatchFraction() { + return mismatchFraction; + } + + public double[] getBins() { + return bins; + } + + public double getP() { + return p; + } + + public ContaminationData(GenomeLoc site, long basesMatching, long basesMismatching, double[] bins) { + this.site = site; + this.basesMatching = basesMatching; + this.basesMismatching = basesMismatching; + this.bins = bins; + long totalBases = this.basesMatching + this.basesMismatching; + if (totalBases != 0) { + this.mismatchFraction = (double)this.basesMismatching / (double) totalBases; + } + + int a = (int) this.getBasesMismatching() + 1; + int b = (int) this.getBasesMatching() + 1; + BetaDistribution dist = new BetaDistributionImpl(a,b); + try { + this.p = 1.0d - dist.cumulativeProbability(0.5d); + } catch (MathException me) { + throw new RuntimeException("Error! - " + me.toString()); + } + + } + + public int compareTo(ContaminationData other) { + return -Double.compare(this.getP(), other.getP()); + } + + @Override + public String toString() { + return "ContaminationData{" + + "site=" + site + + ", basesMatching=" + basesMatching + + ", basesMismatching=" + basesMismatching + + ", mismatchFraction=" + mismatchFraction + + '}'; + } + } + + + // what precision are we using in our calculations + private final double precision; + + // a map of our contamination targets and their stats + // key: aggregation entity ("META", sample name, or lane name) + // value: ContaminationStats (whcih + private Map> stats = new HashMap>(); + + public ContaminationResults(double precision) { + this.precision = precision; + } + + + Map>> storedData = new HashMap>>(); + + /** + * add to the stats + * + * @param newAggregationStats a mapping of the stat name to their statistics collected + */ + public void add(Map> newAggregationStats) { + + // for each aggregation level + for (String aggregationKey : newAggregationStats.keySet()) { + Map populationContaminationStats = newAggregationStats.get(aggregationKey); + + + // a new way of doing this... store all the data until the end... + if (!storedData.containsKey(aggregationKey)) { storedData.put(aggregationKey, new HashMap>()); } + for (String pop : populationContaminationStats.keySet()) { + ContaminationStats newStats = populationContaminationStats.get(pop); + + // if it exists... just merge it + if (!storedData.get(aggregationKey).containsKey(pop)) { + storedData.get(aggregationKey).put(pop, new ArrayList()); + } + + double[] newData = new double[newStats.getContamination().getBins().length]; + System.arraycopy(newStats.getContamination().getBins(),0,newData,0,newStats.getContamination().getBins().length); + storedData.get(aggregationKey).get(pop).add(new ContaminationData(newStats.getSite(), newStats.getBasesMatching(), newStats.getBasesMismatching(), newData)); + } + + + + // merge the sets + if (stats.containsKey(aggregationKey)) { + + // and for each population + for (String pop : populationContaminationStats.keySet()) { + ContaminationStats newStats = populationContaminationStats.get(pop); + + // if it exists... just merge it + if (stats.get(aggregationKey).containsKey(pop)) { + stats.get(aggregationKey).get(pop).add(newStats); + } else { + stats.get(aggregationKey).put(pop, newStats); + } + } + } else { + stats.put(aggregationKey, populationContaminationStats); + } + } + } + + /** + * output the contamination data, and return the contamination data + * @param out the output source + * @return the contamination value + */ + public void outputReport(double precision, PrintStream out, double fractionToTrim, double trimInterval, double betaThreshold) { + out.println("name\tpopulation\tpopulation_fit\tcontamination\tconfidence_interval_95_width\tconfidence_interval_95_low\tconfidence_interval_95_high\tsites"); + + for (Map.Entry> entry : stats.entrySet()) { + for (ContaminationStats stats : entry.getValue().values()) { + String aggregationLevel = entry.getKey(); + String population = stats.getContamination().getPopultationName(); + + List newStats = storedData.get(aggregationLevel).get(population); + String pm = "%3." + Math.round(Math.log10(1/precision)) +"f"; + + int bins = newStats.iterator().next().getBins().length; + int maxTrim = (int) Math.floor((double)(newStats.size()) * fractionToTrim); + + // sort the collection + Collections.sort(newStats); + + List data = new ArrayList(newStats); + + // trim sites with > 95% p of being > 0.5 f (based on beta distribution) + int trimmed = 0; + for(Iterator i = data.iterator(); trimmed < maxTrim && i.hasNext();) { + ContaminationData x = i.next(); + if (x.getP() >= betaThreshold) { + System.out.println("Trimming " + x.toString() + " with p(f>=0.5) >= " + betaThreshold + " with a value of " + x.getP()); + i.remove(); + trimmed++; + } + } + + double[][] matrix = new double[bins][data.size()]; + + for (int i = 0; i> entry : stats.entrySet()) { + for (ContaminationStats stats : entry.getValue().values()) { + if (!outputBins) { + String[] bins = new String[stats.getContamination().getBins().length]; + for (int index = 0; index < stats.getContamination().getBins().length; index++) + bins[index] = String.valueOf(100.0 * (1 - (double) index / stats.getContamination().getBins().length)); + outputBins = true; + out.print("name,pop,"); + out.println(Utils.join(",",bins)); + } + String[] bins = new String[stats.getContamination().getBins().length]; + int index = 0; + for (double value : stats.getContamination().getBins()) + bins[index++] = String.valueOf(value); + out.print(entry.getKey()+",\""+stats.getContamination().getPopultationName()+"\","); + out.println(Utils.join(",", bins)); + } + } + } + + public Map> getStats() { + return Collections.unmodifiableMap(stats); + } + + public void setStats(Map> stats) { + this.stats = stats; + } +} \ No newline at end of file diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContaminationStats.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContaminationStats.java new file mode 100755 index 000000000..7d60d3ca0 --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContaminationStats.java @@ -0,0 +1,125 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.cancer.contamination; + + +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.omg.PortableInterceptor.SYSTEM_EXCEPTION; + +/** + * a class that tracks our contamination stats; both the estimate of contamination, as well as the number of sites and other + * run-specific data + */ +public class ContaminationStats { + final static int ALLELE_COUNT = 4; + private GenomeLoc site; + private int numberOfSites = 0; + private double sumOfAlleleFrequency = 0.0; + private long basesFor = 0l; + private long basesAgainst = 0l; + private long basesOther = 0l; + private ContaminationEstimate contaminationEstimate; + private final int[] alleleBreakdown; + + public ContaminationStats(GenomeLoc site, int numberOfSites, double sumOfAlleleFrequency, long basesFor, long basesAgainst, long basesOther, int alleleBreakdown[], ContaminationEstimate estimate) { + this.site = site; + this.numberOfSites = numberOfSites; + this.sumOfAlleleFrequency = sumOfAlleleFrequency; + this.basesFor = basesFor; + this.basesAgainst = basesAgainst; + this.contaminationEstimate = estimate; + if (alleleBreakdown.length != ALLELE_COUNT) throw new IllegalArgumentException("Allele breakdown should have length " + ALLELE_COUNT); + this.alleleBreakdown = alleleBreakdown; + } + + public int getNumberOfSites() { + return numberOfSites; + } + + public double getMinorAlleleFrequency() { + return sumOfAlleleFrequency /(double)numberOfSites; + } + + public long getBasesMatching() { + return basesFor; + } + + public long getBasesOther() { + return basesOther; + } + + public long getBasesMismatching() { + return basesAgainst; + } + + public ContaminationEstimate getContamination() { + return this.contaminationEstimate; + } + + public GenomeLoc getSite() { + return site; + } + + public void add(ContaminationStats other) { + if (other == null) return; + this.numberOfSites += other.numberOfSites; + this.sumOfAlleleFrequency += other.sumOfAlleleFrequency; + this.basesOther += other.basesOther; + this.basesFor += other.basesFor; + this.basesAgainst += other.basesAgainst; + for (int x = 0; x < ALLELE_COUNT; x++) this.alleleBreakdown[x] += other.alleleBreakdown[x]; + for (int i = 0; i < this.contaminationEstimate.getBins().length; i++) { + this.contaminationEstimate.getBins()[i] += other.contaminationEstimate.getBins()[i]; + } + this.contaminationEstimate.setPopulationFit(this.contaminationEstimate.getPopulationFit() +other.contaminationEstimate.getPopulationFit()); + } +} \ No newline at end of file diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/Dream_Evaluations.md b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/Dream_Evaluations.md new file mode 100644 index 000000000..dd86aed24 --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/Dream_Evaluations.md @@ -0,0 +1,77 @@ +# Dream Challenge Evaluation + +In order to evaluate the performance of M2, we use two sets of data from the SMC DREAM Challenge. Specifically challenges #3 and #4. + +All scripts referenced here are relative to the current working directory of ``` +/dsde/working/mutect/dream_smc``` + +### Current Performance (Unmasked) +From the output of the evaluation method + +(gsa-unstable 7/13/15, commit:9e93a70) + +|set | subset | type | sensitivity | specificity | accuracy | +|----|--------|------|-------------|-------------|----------| +|SMC 3|chr21|SNP|0.935897435897|0.935897435897|0.935897435897| +|SMC 3|chr21|INDEL|0.904255319149|0.977011494253|0.940633406701| +|SMC 3|wgs|SNP|0.930532709098|0.955188985583|0.94286084734| +|SMC 3|wgs|INDEL|0.902139907396|0.970516962843|0.93632843512| +|SMC 4|chr21|SNP|0.769607843137|0.969135802469|0.869371822803| +|SMC 4|chr21|INDEL|0.771241830065|0.991596638655|0.88141923436| +|SMC 4|wgs|SNP|0.764507007622|0.975374480433|0.869940744028| +|SMC 4|wgs|INDEL|0.768634634353|0.989389679877|0.879012157115| + + + +### How To Run +The SCALA script for running M2 can be found in the gsa-unstable repository under ```private/gatk-tools-private/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2``` + +First, chose the appropriate settings (runnable as environment variables here) +``` +QUEUE_JAR= +OUT_VCF= +GSA_UNSTABLE_HOME= + +# for Dream 3 +NORMAL_BAM=/dsde/working/mutect/dream_smc/bams/synthetic.challenge.set3.normal.bam +TUMOR_BAM=/dsde/working/mutect/dream_smc/bams/synthetic.challenge.set3.tumor.bam + +# for Dream 4 +NORMAL_BAM=/dsde/working/mutect/dream_smc/bams/synthetic.challenge.set4.normal.bam +TUMOR_BAM=/dsde/working/mutect/dream_smc/bams/synthetic.challenge.set4.tumor.bam + +# for WGS +INTERVALS=/dsde/working/mutect/dream_smc/bams/wgs_calling_regions.v1.interval_list + +# for chromosome 21 only +INTERVALS=/dsde/working/mutect/ts/c21_wgs_calling_regions.v1.interval_list + +TEMPDIR=/broad/hptmp/kcibul/mutect +``` + +and then run the following Queue command +``` +java \ + -Djava.io.tmpdir=$TEMPDIR \ + -jar $QUEUE_JAR \ + -S $GSA_UNSTABLE_HOME/private/gatk-tools-private/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/run_M2_dream.scala \ + --job_queue gsa -qsub -jobResReq virtual_free=5G -startFromScratch \ + -sc 200 \ + -normal $NORMAL_BAM \ + -tumor $TUMOR_BAM \ + -L $INTERVALS \ + -o $OUT_VCF \ + -run +``` + +### How To Evaluate + +Run the following +``` +/dsde/working/mutect/dream_smc/dream_eval.pl [3|4] [wgs|21] [SNV|INDEL] input.vcf +``` +where + - [3|4] the dream challenge round + - [wgs|21] evaluate the whole genome, or just a subset (chromosome 21) + - [SNV|INDEL] evaulate SNV (SNPs) or INDELS + diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/M2ArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/M2ArgumentCollection.java new file mode 100644 index 000000000..97ffcf3cf --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/M2ArgumentCollection.java @@ -0,0 +1,117 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.cancer.m2; + +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection; +import org.broadinstitute.gatk.utils.commandline.Advanced; +import org.broadinstitute.gatk.utils.commandline.Argument; + +public class M2ArgumentCollection extends AssemblyBasedCallerArgumentCollection { + @Advanced + @Argument(fullName="m2debug", shortName="m2debug", doc="Print out very verbose M2 debug information", required = false) + public boolean M2_DEBUG = false; + + /** + * Artifact detection mode is used to prepare a panel of normals. This maintains the specified tumor LOD threshold, + * but disables the remaining pragmatic filters. See M2 usage examples for more information. + */ + @Advanced + @Argument(fullName = "artifact_detection_mode", required = false, doc="Enable artifact detection for creating panels of normals") + public boolean ARTIFACT_DETECTION_MODE = false; + + /** + * This is the tumor LOD threshold to output the variant in the VCF, although it may be filtered + */ + @Argument(fullName = "initial_tumor_lod", required = false, doc = "Initial LOD threshold for calling tumor variant") + public double INITIAL_TUMOR_LOD_THRESHOLD = 4.0; + + + @Argument(fullName = "initial_normal_lod", required = false, doc = "Initial LOD threshold for calling normal variant") + public double INITIAL_NORMAL_LOD_THRESHOLD = 0.5; + + /** + * Only variants with tumor LODs exceeding this thresholds can pass filtration + */ + @Argument(fullName = "tumor_lod", required = false, doc = "LOD threshold for calling tumor variant") + public double TUMOR_LOD_THRESHOLD = 6.3; + + /** + * This is a measure of the minimum evidence to show that a variant observed in the tumor is not also present in its normal + */ + @Argument(fullName = "normal_lod", required = false, doc = "LOD threshold for calling normal non-germline") + public double NORMAL_LOD_THRESHOLD = 2.2; + + /** + * The LOD threshold for the normal is typically made more strict if the variant has been seen in dbSNP (i.e. another + * normal sample). We thus require MORE evidence that a variant is NOT seen in this tumor's normal if it has been observed as a germline variant before. + */ + @Argument(fullName = "dbsnp_normal_lod", required = false, doc = "LOD threshold for calling normal non-variant at dbsnp sites") + public double NORMAL_DBSNP_LOD_THRESHOLD = 5.5; + + /** + * This argument is used for the M2 internal "alt_allele_in_normal" filter + **/ + @Argument(fullName = "max_alt_alleles_in_normal_count", required = false, doc="Threshold for maximum alternate allele counts in normal") + public int MAX_ALT_ALLELES_IN_NORMAL_COUNT = 2; + + /** + * This argument is used for the M2 internal "alt_allele_in_normal" filter + */ + @Argument(fullName = "max_alt_alleles_in_normal_qscore_sum", required = false, doc="Threshold for maximum alternate allele quality score sum in normal") + public int MAX_ALT_ALLELES_IN_NORMAL_QSCORE_SUM = 20; + + /** + * This argument is used for the M2 internal "alt_allele_in_normal" filter + */ + @Argument(fullName = "max_alt_allele_in_normal_fraction", required = false, doc="Threshold for maximum alternate allele fraction in normal") + public double MAX_ALT_ALLELE_IN_NORMAL_FRACTION = 0.03; +} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/M2_Contamination_Evaluation.md b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/M2_Contamination_Evaluation.md new file mode 100644 index 000000000..19324dae6 --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/M2_Contamination_Evaluation.md @@ -0,0 +1,157 @@ +# M2 Contamination Correction Evaluation + +In order to evaluate the efficacy of the contamination correction in M2 (adapted from HaplotypeCaller), we created synthetic data consisting of the four intra-run CRSP NA12878 replicates, each contaminated with 1-5% of the HCC-1143 normal. + +### Creating Artificial Contamination Data +``` QUEUE_JAR= + GSA_UNSTABLE_HOME= + BASELINE_BAM=/crsp/picard_aggregation/000007820918/SM-612V3/current/SM-612V3.bam + CONTAMINANT_BAM=/seq/tier3b/picard_aggregation/C970/HCC1143_BL/v1/HCC1143_BL.bam + ``` + +``` +java -jar $QUEUE_JAR \ +-S $GSA_UNSTABLE_HOME/private/gatk-queue-extensions-internal/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/dev/CreateSyntheticContaminationScript.scala \ +-b2 CONTAMINANT_BAM -b1 BASELINE_BAM \ +-f 0.01 -f 0.02 -f 0.03 -f 0.04 -f 0.05 +``` + +Repeat for the other three NA12878 replicates. + + BASELINE_BAM=/crsp/picard_aggregation/000007820818/SM-612V4/current/SM-612V4.bam + + BASELINE_BAM=/crsp/picard_aggregation/000007820718/SM-612V5/current/SM-612V5.bam + + BASELINE_BAM=/crsp/picard_aggregation/000007820618/SM-612V6/current/SM-612V6.bam + +Use ContEst to get the contamination estimate in the data to be passed into M2. (Note that for these data, the ContEst estimate is on the order of 1% higher than the value used to generate the contaminated data.) + + TEMPDIR=/broad/hptmp/$USER + BAM1=HCC1143_BL.small.0.04.contaminated.with.SM-612V3.small.0.96.bam + BAM2=/crsp/picard_aggregation/000007820818/SM-612V4/current/SM-612V4.bam + OUT_TXT=ContEst_0.04HCC1143inNA12878.txt + + java -Djava.io.tmpdir=$TEMPDIR \ + -Xmx512m -jar /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/cga/ContaminationAnalysis/broadinstitute.org/cancer.genome.analysis/00262/107//Queue-1.4-437-g6b8a9e1-svn-35362.jar \ + -S /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/cga/ContaminationAnalysis/broadinstitute.org/cancer.genome.analysis/00262/107//ContaminationPipeline.scala \ + -reference /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta -interval /xchip/cga/reference/hg19/whole_exome_agilent_1.1_refseq_plus_3_boosters_plus_10bp_padding_minus_mito.Homo_sapiens_assembly19.targets.interval_list \ + -out $OUT_TXT \ + -bam $BAM1 -nbam $BAM2 \ + -array /xchip/gcc_data/results2/production/TEENY/BySample/hg19.vcf.txt/TEENY_p_TCGA_302_303_N_GenomeWideSNP_6_F04_1344608.hg19.vcf.txt.store/verstore.00000.TEENY_p_TCGA_302_303_N_GenomeWideSNP_6_F04_1344608.hg19.vcf.txt \ + -pop /xchip/cga/reference/hg19/hg19_population_stratified_af_hapmap_3.3.fixed.vcf -faf true -run -array_interval /xchip/cga/reference/hg19/SNP6.hg19.interval_list + + BAM1=HCC1143_BL.small.0.03.contaminated.with.SM-612V3.small.0.97.bam + BAM2=/crsp/picard_aggregation/000007820818/SM-612V4/current/SM-612V4.bam + OUT_TXT=ContEst_0.03HCC1143inNA12878.txt + + BAM1=HCC1143_BL.small.0.02.contaminated.with.SM-612V3.small.0.98.bam + BAM2=/crsp/picard_aggregation/000007820818/SM-612V4/current/SM-612V4.bam + OUT_TXT=ContEst_0.02HCC1143inNA12878.txt + + BAM1=HCC1143_BL.small.0.01.contaminated.with.SM-612V3.small.0.99.bam + BAM2=/crsp/picard_aggregation/000007820818/SM-612V4/current/SM-612V4.bam + OUT_TXT=ContEst_0.01HCC1143inNA12878.txt + + And so on for the other replicates. + + ContEst estimates for the four replicates at the five contamination levels are as follows: + |Sample|Input Contamination Level|ContEst Estimate| + |------|-------------------------|----------------| + |SM-612V3|0.01|0.016| + |SM-612V3|0.02|0.030| + |SM-612V3|0.03|0.042| + |SM-612V3|0.04|0.055| + |SM-612V3|0.05|0.067| + |SM-612V4|0.01|0.015| + |SM-612V4|0.02|0.028| + |SM-612V4|0.03|0.039| + |SM-612V4|0.04|0.051| + |SM-612V4|0.05|0.063| + |SM-612V5|0.01|0.016| + |SM-612V5|0.02|0.030| + |SM-612V5|0.03|0.042| + |SM-612V5|0.04|0.054| + |SM-612V5|0.05|0.066| + |SM-612V6|0.01|0.015| + |SM-612V6|0.02|0.027| + |SM-612V6|0.03|0.040| + |SM-612V6|0.04|0.051| + |SM-612V6|0.05|0.062| + +###Prepare the inputs for the normal-normal calling script +Create a list of all contamination levels for each replicate + + ls -1 HCC*contam*V3*.bam > HCC1143withNA12878_3.bams.list + ls -1 HCC*contam*V4*.bam > HCC1143withNA12878_4.bams.list + ls -1 HCC*contam*V5*.bam > HCC1143withNA12878_5.bams.list + ls -1 HCC*contam*V6*.bam > HCC1143withNA12878_6.bams.list + +Create a list of the other, uncontaminated normals to call against + + ls -1 /humgen/gsa-hpprojects/NA12878Collection/bams/crsp_ice_validation/SM-612V[^37D].bam > /dsde/working/mutect/laura/contamination/NA12878_not3.list + ls -1 /humgen/gsa-hpprojects/NA12878Collection/bams/crsp_ice_validation/SM-612V[^47D].bam > /dsde/working/mutect/laura/contamination/NA12878_not4.list + ls -1 /humgen/gsa-hpprojects/NA12878Collection/bams/crsp_ice_validation/SM-612V[^57D].bam > /dsde/working/mutect/laura/contamination/NA12878_not5.list + ls -1 /humgen/gsa-hpprojects/NA12878Collection/bams/crsp_ice_validation/SM-612V[^67D].bam > /dsde/working/mutect/laura/contamination/NA12878_not6.list + +###Run the Caller +Run M2 on contaminated bams versus other all other replicates. Run one loop for each contaminated replicate, passing in contamination estimates as given above + + java -jar $QUEUE_JAR -S /dsde/working/mutect/laura/contamination/Qscript_M2_normalNormalLoop.scala -normal /dsde/working/mutect/laura/contamination/NA12878_not3.list -tumor /dsde/working/mutect/laura/contamination/HCC1143withNA12878_3.bams.list -o M2_NA12878run3_ -f 0.016 -f 0.03 -f 0.042 -f 0.055 -f 0.067 + + java -jar $QUEUE_JAR -S /dsde/working/mutect/laura/contamination/Qscript_M2_normalNormalLoop.scala -normal /dsde/working/mutect/laura/contamination/NA12878_not4.list -tumor /dsde/working/mutect/laura/contamination/HCC1143withNA12878_4.bams.list -o M2_NA12878run4_ -f 0.015 -f 0.028 -f 0.039 -f 0.051 -f 0.063 + + java -jar $QUEUE_JAR -S /dsde/working/mutect/laura/contamination/Qscript_M2_normalNormalLoop.scala -normal /dsde/working/mutect/laura/contamination/NA12878_not5.list -tumor /dsde/working/mutect/laura/contamination/HCC1143withNA12878_5.bams.list -o M2_NA12878run5_ -f 0.016 -f 0.030 -f 0.042 -f 0.054 -f 0.066 + + java -jar $QUEUE_JAR -S /dsde/working/mutect/laura/contamination/Qscript_M2_normalNormalLoop.scala -normal /dsde/working/mutect/laura/contamination/NA12878_not6.list -tumor /dsde/working/mutect/laura/contamination/HCC1143withNA12878_6.bams.list -o M2_NA12878run6_ -f 0.015 -f 0.027 -f 0.040 -f 0.051 -f 0.062 + +###Count the False Positives +Pull out passing SNPs not in PON for each contamination level: + + for vcf in M2_NA12878run[0-9]_HCC1143_BL.small.0.01.contaminated.with.SM-612V*.bam.vcf + do + bedtools intersect -a $vcf -b ICE.corrected.bed | grep PASS | awk '{ if ( length($4) + length($5) == 2) print $0 }' | wc -l + done + + for vcf in M2_NA12878run[0-9]_HCC1143_BL.small.0.02.contaminated.with.SM-612V*.bam.vcf + do + bedtools intersect -a $vcf -b ICE.corrected.bed | grep PASS | awk '{ if ( length($4) + length($5) == 2) print $0 }' | wc -l + done + + for vcf in M2_NA12878run[0-9]_HCC1143_BL.small.0.03.contaminated.with.SM-612V*.bam.vcf + do + bedtools intersect -a $vcf -b ICE.corrected.bed | grep PASS | awk '{ if ( length($4) + length($5) == 2) print $0 }' | wc -l + done + + for vcf in M2_NA12878run[0-9]_HCC1143_BL.small.0.04.contaminated.with.SM-612V*.bam.vcf + do + bedtools intersect -a $vcf -b ICE.corrected.bed | grep PASS | awk '{ if ( length($4) + length($5) == 2) print $0 }' | wc -l + done + + for vcf in M2_NA12878run[0-9]_HCC1143_BL.small.0.05.contaminated.with.SM-612V*.bam.vcf + do + bedtools intersect -a $vcf -b ICE.corrected.bed | grep PASS | awk '{ if ( length($4) + length($5) == 2) print $0 }' | wc -l + done + +(I pasted the results from the terminal into Excel because it's just so easy.) + +###Comparison Without Downsampling +To run normal-normal contaminated calling without downsampling, the above /dsde/working/mutect/laura/contamination/Qscript_M2_normalNormalLoop.scala commands can be used, passing in -f 0 for each contamination level instead, e.g.: + + java -jar $QUEUE_JAR -S /dsde/working/mutect/laura/contamination/Qscript_M2_normalNormalLoop.scala -normal /dsde/working/mutect/laura/contamination/NA12878_not3.list -tumor /dsde/working/mutect/laura/contamination/HCC1143withNA12878_3.bams.list -o M2_NA12878run3_noContam_ -f 0.0 -f 0.0 -f 0.0 -f 0.0 -f 0.0 + +###Comparison to M1 +To run normal-normal contaminated calling using M1, run the above Queue commands using a Queue jar containing MuTect and passing in /dsde/working/mutect/laura/contamination/Qscript_M1_normalNormalLoop.scala instead of Qscript_M2_normalNormalLoop.scala, e.g.: + + java -jar $QUEUE_JAR_WITH_M1 -S /dsde/working/mutect/laura/contamination/Qscript_M1_normalNormalLoop.scala -normal /dsde/working/mutect/laura/contamination/NA12878_not3.list -tumor /dsde/working/mutect/laura/contamination/HCC1143withNA12878_3.bams.list -o M1_NA12878run3_ -f 0.016 -f 0.03 -f 0.042 -f 0.055 -f 0.067 + +(The MuTect-containing Queue jar can be built from the gsa-unstable branch ldg_MuTect1.) + +###Latest Results +|M2 SNPs no correction|M2 SNPs with correction|M1 SNPs no correction|M1 SNPs with correction|M2 INDELs no correction|M2 INDELs with correction| +|---------------------|-----------------------|---------------------|-----------------------|-----------------------|-------------------------| +|0%|93|93|181|181|25|25| +|1%|938|258|854|317|68|30| +|2%|2550|464|1941|385|92|21| +|3%|4171|596|3061|515|134|18| +|4%|5513|707|4002|589|162|21| +|5%|6475|794|4854|624|188|29| \ No newline at end of file diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/M2_Panel_Of_Normals_Creation.md b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/M2_Panel_Of_Normals_Creation.md new file mode 100644 index 000000000..72e475b4a --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/M2_Panel_Of_Normals_Creation.md @@ -0,0 +1,35 @@ +# M2 Panel of Normals + +In order to reduce false positives, we use a panel of "normal" (ie non-cancer) samples to filter out both germline events as well as systematic noise. The form of the panel is a VCF file, which is produced via a Queue scripts + +You must supply: +- the reference (defaults to hg19) +- the intervals to evaluate +- the list of BAM files + +### How To Run +The Queue script for producing the PON can be found in the gsa-unstable repository under ```private/gatk-tools-private/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2``` + +First, chose the appropriate settings (runnable as environment variables here) +``` +QUEUE_JAR= +GSA_UNSTABLE_HOME= +TEMPDIR=/broad/hptmp/$USER +``` + +and then run the following Queue command +``` +java \ + -Djava.io.tmpdir=$TEMPDIR \ + -jar $QUEUE_JAR \ + -S $GSA_UNSTABLE_HOME/private/gatk-tools-private/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/run_M2_ICE_NN.scala \ + --job_queue gsa -qsub -jobResReq virtual_free=5G -startFromScratch \ + -sc 50 \ + --allbams \ + --intervals \ + --outputprefix \ + --start_from_scratch --keep_intermediate_outputs \ + -run +``` + +This will produce many VCFs (1 per sample), plus \.genotypes.vcf and \.vcf which are the panel of normals VCF both with and without sample-genotype information. Typically the latter is the one used as input to M2, although either will work. \ No newline at end of file diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2.java new file mode 100644 index 000000000..ec0038bab --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2.java @@ -0,0 +1,1291 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. 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Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.cancer.m2; + +import htsjdk.samtools.SAMFileWriter; +import htsjdk.variant.variantcontext.*; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.vcf.*; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; +import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection; +import org.broadinstitute.gatk.engine.filters.BadMateFilter; +import org.broadinstitute.gatk.engine.io.DirectOutputTracker; +import org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub; +import org.broadinstitute.gatk.engine.iterators.ReadTransformer; +import org.broadinstitute.gatk.engine.walkers.*; +import org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingOutputMode; +import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.FixedAFCalculatorProvider; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.*; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.QualityUtils; +import org.broadinstitute.gatk.utils.activeregion.ActiveRegion; +import org.broadinstitute.gatk.utils.activeregion.ActiveRegionReadState; +import org.broadinstitute.gatk.utils.activeregion.ActivityProfileState; +import org.broadinstitute.gatk.utils.clipping.ReadClipper; +import org.broadinstitute.gatk.utils.commandline.*; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.AlignmentContextUtils; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.downsampling.AlleleBiasedDownsamplingUtils; +import org.broadinstitute.gatk.utils.downsampling.DownsamplingUtils; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.gatk.utils.fragments.FragmentCollection; +import org.broadinstitute.gatk.utils.fragments.FragmentUtils; +import org.broadinstitute.gatk.utils.genotyper.*; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.haplotypeBAMWriter.HaplotypeBAMWriter; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.pairhmm.PairHMM; +import org.broadinstitute.gatk.utils.pileup.PileupElement; +import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.sam.*; +import org.broadinstitute.gatk.utils.variant.GATKVCFConstants; +import org.broadinstitute.gatk.utils.variant.GATKVCFHeaderLines; + +import java.io.FileNotFoundException; +import java.util.*; + +import static java.lang.Math.pow; + +/** + * Call somatic SNPs and indels via local re-assembly of haplotypes + * + *

MuTect2 is a somatic SNP and indel caller that combines the DREAM challenge-winning somatic genotyping engine of the original MuTect (Cibulskis et al., 2013) with the assembly-based machinery of HaplotypeCaller.

+ * + *

The basic operation of MuTect2 proceeds similarly to that of the HaplotypeCaller

+ * + *

Differences from HaplotypeCaller

+ *

While the HaplotypeCaller relies on a ploidy assumption (diploid by default) to inform its genotype likelihood and + * variant quality calculations, MuTect2 allows for a varying allelic fraction for each variant, as is often seen in tumors with purity less + * than 100%, multiple subclones, and/or copy number variation (either local or aneuploidy). MuTect2 also differs from the HaplotypeCaller in that it does apply some hard filters + * to variants before producing output.

+ * + *

Usage examples

+ *

These are example commands that show how to run MuTect2 for typical use cases. Square brackets ("[ ]") + * indicate optional arguments. Note that parameter values shown here may not be the latest recommended; see the + * Best Practices documentation for detailed recommendations.

+ * + *
+ *

Tumor/Normal variant calling

+ * 
+ *   java
+ *     -jar GenomeAnalysisTK.jar \
+ *     -T MuTect2 \
+ *     -R reference.fasta \
+ *     -I:tumor tumor.bam \
+ *     -I:normal normal.bam \
+ *     [--dbsnp dbSNP.vcf] \
+ *     [--cosmic COSMIC.vcf] \
+ *     [-L targets.interval_list] \
+ *     -o output.vcf
+ *
+ * + *

Normal-only calling for panel of normals creation

+ * 
+ *   java
+ *     -jar GenomeAnalysisTK.jar
+ *     -T HaplotypeCaller
+ *     -R reference.fasta
+ *     -I:tumor normal1.bam \
+ *     [--dbsnp dbSNP.vcf] \
+ *     [--cosmic COSMIC.vcf] \
+ *     --artifact_detection_mode \
+ *     [-L targets.interval_list] \
+ *     -o output.normal1.vcf
+ *
+ *
+ * For full PON creation, call each of your normals separately in artifact detection mode. Then use CombineVariants to + * output only sites where a variant was seen in at least two samples: + * 
+ * java -jar GenomeAnalysisTK.jar
+ *     -T CombineVariants
+ *     -R reference.fasta
+ *     -V output.normal1.vcf -V output.normal2.vcf [-V output.normal2.vcf ...] \
+ *     -minN 2 \
+ *     --setKey "null" \
+ *     --filteredAreUncalled \
+ *     --filteredrecordsmergetype KEEP_IF_ANY_UNFILTERED \
+ *     [-L targets.interval_list] \
+ *     -o MuTect2_PON.vcf
+ *
+ * + *

Caveats

+ *
    + *
  • MuTect2 currently only supports the calling of a single tumor-normal pair at a time
    • + *
+ * + */ +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARDISC, extraDocs = {CommandLineGATK.class} ) +@PartitionBy(PartitionType.LOCUS) +@BAQMode(ApplicationTime = ReadTransformer.ApplicationTime.FORBIDDEN) +@ActiveRegionTraversalParameters(extension=100, maxRegion=300) +public class MuTect2 extends ActiveRegionWalker, Integer> implements AnnotatorCompatible, NanoSchedulable { + public static final String BAM_TAG_TUMOR = "tumor"; + public static final String BAM_TAG_NORMAL = "normal"; + + protected Set tumorSAMReaderIDs = new HashSet<>(); + protected Set normalSAMReaderIDs = new HashSet<>(); + protected String tumorSampleName; + protected String normalSampleName; + + protected SampleList samplesList; + protected boolean printTCGAsampleHeader = false; + + // fasta reference reader to supplement the edges of the reference sequence + protected CachingIndexedFastaSequenceFile referenceReader; + + // the assembly engine + protected LocalAssemblyEngine assemblyEngine = null; + + // the likelihoods engine + protected ReadLikelihoodCalculationEngine likelihoodCalculationEngine = null; + + // the genotyping engine + protected HaplotypeCallerGenotypingEngine genotypingEngine = null; + + + private byte MIN_TAIL_QUALITY; + private double log10GlobalReadMismappingRate; + + + + @ArgumentCollection + protected M2ArgumentCollection MTAC = new M2ArgumentCollection(); + + @ArgumentCollection + protected ReadThreadingAssemblerArgumentCollection RTAC = new ReadThreadingAssemblerArgumentCollection(); + + @ArgumentCollection + protected LikelihoodEngineArgumentCollection LEAC = new LikelihoodEngineArgumentCollection(); + + + @Argument(fullName = "debug_read_name", required = false, doc="trace this read name through the calling process") + public String DEBUG_READ_NAME = null; + + @Hidden + @Advanced + @Argument(fullName = "MQ_filtering_level", shortName = "MQthreshold", required = false, doc="Set an alternate MQ threshold for debugging") + final public int MQthreshold = 20; + + + /***************************************/ + // Reference Metadata inputs + /***************************************/ + /** + * MuTect2 has the ability to use COSMIC data in conjunction with dbSNP to adjust the threshold for evidence of a variant + * in the normal. If a variant is present in dbSNP, but not in COSMIC, then more evidence is required from the normal + * sample to prove the variant is not present in germline. + */ + @Input(fullName="cosmic", shortName = "cosmic", doc="VCF file of COSMIC sites", required=false) + public List> cosmicRod = Collections.emptyList(); + + /** + * A panel of normals can be a useful (optional) input to help filter out commonly seen sequencing noise that may appear as low allele-fraction somatic variants. + */ + @Input(fullName="normal_panel", shortName = "PON", doc="VCF file of sites observed in normal", required=false) + public List> normalPanelRod = Collections.emptyList(); + + private HaplotypeBAMWriter haplotypeBAMWriter; + + @Override + public void initialize() { + super.initialize(); + + samplesList = new IndexedSampleList(new ArrayList<>(ReadUtils.getSAMFileSamples(getToolkit().getSAMFileHeader()))); + + // MUTECT: check that we have at least one tumor bam + for(SAMReaderID id : getToolkit().getReadsDataSource().getReaderIDs()) { + if (id.getTags().getPositionalTags().size() == 0) { + throw new RuntimeException("BAMs must be tagged as either 'tumor' or 'normal'"); + } + + // only supports single-sample BAMs (ie first read group is representative) + String bamSampleName = getToolkit().getReadsDataSource().getHeader(id).getReadGroups().get(0).getSample(); + + for(String tag : id.getTags().getPositionalTags()) { + if (BAM_TAG_TUMOR.equalsIgnoreCase(tag)) { + tumorSAMReaderIDs.add(id); + if (tumorSampleName == null) { + tumorSampleName = bamSampleName; + } else { + if (!tumorSampleName.equals(bamSampleName)) { + throw new UserException.BadInput("Found more than one tumor sample name in read data"); + } + } + } else if (BAM_TAG_NORMAL.equalsIgnoreCase(tag)) { + normalSAMReaderIDs.add(id); + if (normalSampleName == null) { + normalSampleName = bamSampleName; + } else { + if (!normalSampleName.equals(bamSampleName)) { + throw new UserException.BadInput("Found more than one normal sample name in read data"); + } + } + } else { + throw new RuntimeException("Unknown BAM tag '" + tag + "' must be either 'tumor' or 'normal'"); + } + } + } + + //If the samples specified are exactly one normal and one tumor, use the TCGA VCF sample header format + if (samplesList.sampleCount() == 2 && normalSampleName != null && tumorSampleName != null && ReadUtils.getSAMFileSamples(getToolkit().getSAMFileHeader()).size() == 2) + printTCGAsampleHeader = true; + + final VariantAnnotatorEngine annotationEngine = initializeVCFOutput(); + + try { + // fasta reference reader to supplement the edges of the reference sequence + referenceReader = new CachingIndexedFastaSequenceFile(getToolkit().getArguments().referenceFile); + } catch( FileNotFoundException e ) { + throw new UserException.CouldNotReadInputFile(getToolkit().getArguments().referenceFile, e); + } + + // create and setup the assembler + assemblyEngine = new ReadThreadingAssembler(RTAC.maxNumHaplotypesInPopulation, RTAC.kmerSizes, RTAC.dontIncreaseKmerSizesForCycles, RTAC.allowNonUniqueKmersInRef, RTAC.numPruningSamples); + + assemblyEngine.setErrorCorrectKmers(RTAC.errorCorrectKmers); + assemblyEngine.setPruneFactor(RTAC.MIN_PRUNE_FACTOR); + assemblyEngine.setDebug(MTAC.DEBUG); + assemblyEngine.setDebugGraphTransformations(RTAC.debugGraphTransformations); + assemblyEngine.setAllowCyclesInKmerGraphToGeneratePaths(RTAC.allowCyclesInKmerGraphToGeneratePaths); + assemblyEngine.setRecoverDanglingBranches(!RTAC.doNotRecoverDanglingBranches); + assemblyEngine.setMinBaseQualityToUseInAssembly(MIN_BASE_QUALTY_SCORE); + + MIN_TAIL_QUALITY = (byte)(MIN_BASE_QUALTY_SCORE - 1); + + if ( RTAC.graphWriter != null ) assemblyEngine.setGraphWriter(RTAC.graphWriter); + + // setup the likelihood calculation engine + if ( LEAC.phredScaledGlobalReadMismappingRate < 0 ) LEAC.phredScaledGlobalReadMismappingRate = -1; + + // configure the global mismapping rate + if ( LEAC.phredScaledGlobalReadMismappingRate < 0 ) { + log10GlobalReadMismappingRate = - Double.MAX_VALUE; + } else { + log10GlobalReadMismappingRate = QualityUtils.qualToErrorProbLog10(LEAC.phredScaledGlobalReadMismappingRate); + logger.info("Using global mismapping rate of " + LEAC.phredScaledGlobalReadMismappingRate + " => " + log10GlobalReadMismappingRate + " in log10 likelihood units"); + } + + //static member function - set number of threads + PairHMM.setNumberOfThreads(getToolkit().getTotalNumberOfThreads()); + // create our likelihood calculation engine + likelihoodCalculationEngine = createLikelihoodCalculationEngine(); + + final MergeVariantsAcrossHaplotypes variantMerger = new MergeVariantsAcrossHaplotypes(); + + final GenomeAnalysisEngine toolkit = getToolkit(); + final GenomeLocParser genomeLocParser = toolkit.getGenomeLocParser(); + + genotypingEngine = new SomaticGenotypingEngine( MTAC, samplesList, genomeLocParser, FixedAFCalculatorProvider.createThreadSafeProvider(getToolkit(), MTAC, logger), !doNotRunPhysicalPhasing, MTAC); + + genotypingEngine.setCrossHaplotypeEventMerger(variantMerger); + genotypingEngine.setAnnotationEngine(annotationEngine); + + + if ( MTAC.bamWriter != null ) { + // we currently do not support multi-threaded BAM writing, so exception out + if ( getToolkit().getTotalNumberOfThreads() > 1 ) + throw new UserException.BadArgumentValue("bamout", "Currently cannot emit a BAM file from the HaplotypeCaller in multi-threaded mode."); + haplotypeBAMWriter = HaplotypeBAMWriter.create(MTAC.bamWriterType, MTAC.bamWriter, getToolkit().getSAMFileHeader()); + } + + // why isn't this a constructor (instead of initialize)? Since the method is package-friendly + trimmer.initialize(getToolkit().getGenomeLocParser(), MTAC.DEBUG, + MTAC.genotypingOutputMode == GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES, false); + + // KCIBUL: what's the right way to set this sensible default for somatic mutation calling from here? + trimmer.snpPadding = 50; + + samplesList = toolkit.getReadSampleList(); + Set sampleSet = SampleListUtils.asSet(samplesList); + + if( MTAC.CONTAMINATION_FRACTION_FILE != null ) + MTAC.setSampleContamination(AlleleBiasedDownsamplingUtils.loadContaminationFile(MTAC.CONTAMINATION_FRACTION_FILE, MTAC.CONTAMINATION_FRACTION, sampleSet, logger)); + + } + + private VariantAnnotatorEngine initializeVCFOutput() { + // initialize the output VCF header + final VariantAnnotatorEngine annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit()); + + Set headerInfo = new HashSet<>(); + + // all annotation fields from VariantAnnotatorEngine + headerInfo.addAll(annotationEngine.getVCFAnnotationDescriptions()); + + // all callers need to add these standard FORMAT field header lines + VCFStandardHeaderLines.addStandardFormatLines(headerInfo, true, + VCFConstants.GENOTYPE_KEY, + VCFConstants.GENOTYPE_ALLELE_DEPTHS, + VCFConstants.GENOTYPE_QUALITY_KEY, + VCFConstants.DEPTH_KEY, + VCFConstants.GENOTYPE_PL_KEY); + + headerInfo.addAll(getM2HeaderLines()); + headerInfo.addAll(getSampleHeaderLines()); + + List outputSampleNames = getOutputSampleNames(); + + vcfWriter.writeHeader(new VCFHeader(headerInfo, outputSampleNames)); + + return annotationEngine; + } + + private Set getM2HeaderLines(){ + Set headerInfo = new HashSet<>(); + headerInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.NORMAL_LOD_KEY)); + headerInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.TUMOR_LOD_KEY)); + headerInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.PANEL_OF_NORMALS_COUNT_KEY)); + headerInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.HAPLOTYPE_COUNT_KEY)); + headerInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.EVENT_COUNT_IN_HAPLOTYPE_KEY)); + headerInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.EVENT_DISTANCE_MIN_KEY)); + headerInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.EVENT_DISTANCE_MAX_KEY)); + + headerInfo.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.ALLELE_FRACTION_KEY)); + + headerInfo.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.STR_CONTRACTION_FILTER_NAME)); + headerInfo.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.PON_FILTER_NAME)); + headerInfo.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.ALT_ALLELE_IN_NORMAL_FILTER_NAME)); + headerInfo.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.MULTI_EVENT_ALT_ALLELE_IN_NORMAL_FILTER_NAME)); + headerInfo.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.HOMOLOGOUS_MAPPING_EVENT_FILTER_NAME)); + headerInfo.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.CLUSTERED_EVENTS_FILTER_NAME)); + headerInfo.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.TUMOR_LOD_FILTER_NAME)); + headerInfo.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.GERMLINE_RISK_FILTER_NAME)); + headerInfo.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.TRIALLELIC_SITE_FILTER_NAME)); + + if ( ! doNotRunPhysicalPhasing ) { + headerInfo.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.HAPLOTYPE_CALLER_PHASING_ID_KEY)); + headerInfo.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.HAPLOTYPE_CALLER_PHASING_GT_KEY)); + } + return headerInfo; + } + + private Set getSampleHeaderLines(){ + Set sampleLines = new HashSet<>(); + if (printTCGAsampleHeader) { + //NOTE: This will only list the first bam file for each tumor/normal sample if there is more than one + Map normalSampleHeaderAttributes = new HashMap<>(); + normalSampleHeaderAttributes.put("ID", "NORMAL"); + normalSampleHeaderAttributes.put("SampleName", normalSampleName); + if (normalSAMReaderIDs.iterator().hasNext() && !getToolkit().getArguments().disableCommandLineInVCF) + normalSampleHeaderAttributes.put("File", normalSAMReaderIDs.iterator().next().getSamFilePath()); + VCFSimpleHeaderLine normalSampleHeader = new VCFSimpleHeaderLine("SAMPLE", normalSampleHeaderAttributes); + Map tumorSampleHeaderAttributes = new HashMap<>(); + tumorSampleHeaderAttributes.put("ID", "TUMOR"); + tumorSampleHeaderAttributes.put("SampleName", tumorSampleName); + if (tumorSAMReaderIDs.iterator().hasNext() && !getToolkit().getArguments().disableCommandLineInVCF) + tumorSampleHeaderAttributes.put("File", tumorSAMReaderIDs.iterator().next().getSamFilePath()); + VCFSimpleHeaderLine tumorSampleHeader = new VCFSimpleHeaderLine("SAMPLE", tumorSampleHeaderAttributes); + + sampleLines.add(normalSampleHeader); + sampleLines.add(tumorSampleHeader); + } + return sampleLines; + } + + private List getOutputSampleNames(){ + if (printTCGAsampleHeader) { + //Already checked for exactly 1 tumor and 1 normal in printTCGAsampleHeader assignment in initialize() + List sampleNamePlaceholders = new ArrayList<>(2); + sampleNamePlaceholders.add("TUMOR"); + sampleNamePlaceholders.add("NORMAL"); + return sampleNamePlaceholders; + } + else { + return SampleListUtils.asList(samplesList); + } + } + + @Override + public ActivityProfileState isActive(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + if( context == null || context.getBasePileup().isEmpty() ) + // if we don't have any data, just abort early + return new ActivityProfileState(ref.getLocus(), 0.0); + + final Map splitContexts = AlignmentContextUtils.splitContextBySampleName(context); + AlignmentContext tumorContext = splitContexts.get(tumorSampleName); + AlignmentContext normalContext = splitContexts.get(normalSampleName); + + // if there are no tumor reads... there is no activity! + if (tumorContext == null) { + return new ActivityProfileState(ref.getLocus(), 0); + } + + // KCIBUL -- this method was inlined and modified from ReferenceConfidenceModel + ReadBackedPileup tumorPileup = tumorContext.getBasePileup().getMappingFilteredPileup(MQthreshold); + final double[] tumorGLs = calcGenotypeLikelihoodsOfRefVsAny(tumorPileup, ref.getBase(), MIN_BASE_QUALTY_SCORE); + final double tumorLod = tumorGLs[1] - tumorGLs[0]; + + // NOTE: do I want to convert to a probability (or just keep this as a LOD score) + + // also at this point, we should throw out noisy sites (hence the nonRefInNormalCheck) but this is non-optimal + double prob = 0; + if (tumorLod > MTAC.INITIAL_TUMOR_LOD_THRESHOLD) { + + // TODO: should we even do this performance optimization? + // in any case, we have to handle the case where there is no normal (and thus no normal context) which is + // different than having a normal but having no reads (where we should not enter the active region) + if (normalSampleName != null && normalContext != null) { + int nonRefInNormal = getCountOfNonRefEvents(normalContext.getBasePileup(), ref.getBase(), MIN_BASE_QUALTY_SCORE); + + final double[] normalGLs = calcGenotypeLikelihoodsOfRefVsAny(normalContext.getBasePileup(), ref.getBase(), MIN_BASE_QUALTY_SCORE, 0.5f); + final double normalLod = normalGLs[0] - normalGLs[1]; + + // TODO: parameterize these + if (normalLod > 1.0 && nonRefInNormal < 4) { + prob = 1; + logger.debug("At " + ref.getLocus().toString() + " tlod: " + tumorLod + " nlod: " + normalLod + " with normal non-ref of " + nonRefInNormal); + } + } else { + prob = 1; + logger.debug("At " + ref.getLocus().toString() + " tlod: " + tumorLod + " and no-normal calling"); + } + + } + + return new ActivityProfileState( ref.getLocus(), prob, ActivityProfileState.Type.NONE, null); + } + + private final static List NO_CALLS = Collections.emptyList(); + @Override + public List map( final ActiveRegion originalActiveRegion, final RefMetaDataTracker metaDataTracker ) { + if ( justDetermineActiveRegions ) + // we're benchmarking ART and/or the active region determination code in the HC, just leave without doing any work + return NO_CALLS; + + if( !originalActiveRegion.isActive() ) + // Not active so nothing to do! + return referenceModelForNoVariation(originalActiveRegion, true); + + // No reads here so nothing to do! + if( originalActiveRegion.size() == 0 ) { return referenceModelForNoVariation(originalActiveRegion, true); } + + logReadInfo(DEBUG_READ_NAME, originalActiveRegion.getReads(), "Present in original active region"); + + // create the assembly using just high quality reads (Q20 or higher). We want to use lower + // quality reads in the PairHMM (and especially in the normal) later, so we can't use a ReadFilter + ActiveRegion assemblyActiveRegion = new ActiveRegion(originalActiveRegion.getLocation(), originalActiveRegion.getSupportingStates(),originalActiveRegion.isActive(), getToolkit().getGenomeLocParser(), originalActiveRegion.getExtension()); + for (GATKSAMRecord rec : originalActiveRegion.getReads()) { + if (rec.getMappingQuality() >= MQthreshold ) { + assemblyActiveRegion.add(rec); + } + } + + logReadInfo(DEBUG_READ_NAME, assemblyActiveRegion.getReads(), "Present in assembly active region"); + + // run the local assembler, getting back a collection of information on how we should proceed + final List givenAlleles = new ArrayList<>(); + final AssemblyResultSet untrimmedAssemblyResult = assembleReads(assemblyActiveRegion, givenAlleles); + + + final TreeSet allVariationEvents = untrimmedAssemblyResult.getVariationEvents(); + // TODO - line bellow might be unecessary : it might be that assemblyResult will always have those alleles anyway + // TODO - so check and remove if that is the case: + allVariationEvents.addAll(givenAlleles); + + final ActiveRegionTrimmer.Result trimmingResult = trimmer.trim(originalActiveRegion,allVariationEvents); + + + // Stop the trimming madness!!! + if (!trimmingResult.isVariationPresent()) + return referenceModelForNoVariation(originalActiveRegion,false); + + logReadInfo(DEBUG_READ_NAME, trimmingResult.getCallableRegion().getReads(), "Present in trimming result"); + + final AssemblyResultSet assemblyResult = + trimmingResult.needsTrimming() ? untrimmedAssemblyResult.trimTo(trimmingResult.getCallableRegion()) : untrimmedAssemblyResult; + +// final AssemblyResultSet assemblyResult = untrimmedAssemblyResult; + + // after talking to Ryan -- they grab the reads out of the assembly (and trim then) to pass into the PairHMM + // because at one point they were trying error correcting of the reads based on the haplotypes.. but that is not + // working out, so it's safe for us just to take the reads +// + final ActiveRegion regionForGenotyping = assemblyResult.getRegionForGenotyping(); + logReadInfo(DEBUG_READ_NAME, regionForGenotyping.getReads(), "Present in region for genotyping"); + +// +// final ActiveRegion regionForGenotyping = trimmingResult.getCallableRegion(); + +// final ActiveRegion regionForGenotyping = originalActiveRegion; + + // filter out reads from genotyping which fail mapping quality based criteria + //TODO - why don't do this before any assembly is done? Why not just once at the beginning of this method + //TODO - on the originalActiveRegion? + //TODO - if you move this up you might have to consider to change referenceModelForNoVariation + //TODO - that does also filter reads. + final Collection filteredReads = filterNonPassingReads(regionForGenotyping); + final Map> perSampleFilteredReadList = splitReadsBySample(filteredReads); + + logReadInfo(DEBUG_READ_NAME, regionForGenotyping.getReads(), "Present in region for genotyping after filtering reads"); + + // abort early if something is out of the acceptable range + // TODO is this ever true at this point??? perhaps GGA. Need to check. + if( ! assemblyResult.isVariationPresent() ) + return referenceModelForNoVariation(originalActiveRegion, false); + + // TODO is this ever true at this point??? perhaps GGA. Need to check. + if( regionForGenotyping.size() == 0 ) { + // no reads remain after filtering so nothing else to do! + return referenceModelForNoVariation(originalActiveRegion, false); + } + + // evaluate each sample's reads against all haplotypes + + final List haplotypes = assemblyResult.getHaplotypeList(); + final Map> reads = splitReadsBySample( regionForGenotyping.getReads() ); + for (List rec : reads.values()) { + logReadInfo(DEBUG_READ_NAME, rec, "Present after splitting assemblyResult by sample"); + } + + final HashMap ARreads_origNormalMQ = new HashMap<>(); + for (GATKSAMRecord read : regionForGenotyping.getReads()) { + ARreads_origNormalMQ.put(read.getReadName(), read.getMappingQuality()); + } + + // modify MAPQ scores in normal to be high so that we don't do any base quality score capping + for(GATKSAMRecord rec : regionForGenotyping.getReads()) { + if (isReadFromNormal(rec)) { + rec.setMappingQuality(60); + } + } + + logger.debug("Computing read likelihoods with " + regionForGenotyping.getReads().size() + " reads against " + haplotypes.size() + " haplotypes across region " + assemblyResult.getRegionForGenotyping().toString()); + + + // Calculate the likelihoods: CPU intensive part. + final ReadLikelihoods readLikelihoods = + likelihoodCalculationEngine.computeReadLikelihoods(assemblyResult,samplesList,reads); + + // Realign reads to their best haplotype. + // KCIBUL: this is new stuff -- review it! + final Map readRealignments = realignReadsToTheirBestHaplotype(readLikelihoods, assemblyResult.getReferenceHaplotype(), assemblyResult.getPaddedReferenceLoc()); + readLikelihoods.changeReads(readRealignments); + + for (GATKSAMRecord rec : readRealignments.keySet()) { + logReadInfo(DEBUG_READ_NAME, rec, "Present after computing read likelihoods"); + } + + // Note: we used to subset down at this point to only the "best" haplotypes in all samples for genotyping, but there + // was a bad interaction between that selection and the marginalization that happens over each event when computing + // GLs. In particular, for samples that are heterozygous non-reference (B/C) the marginalization for B treats the + // haplotype containing C as reference (and vice versa). Now this is fine if all possible haplotypes are included + // in the genotyping, but we lose information if we select down to a few haplotypes. [EB] + + final HaplotypeCallerGenotypingEngine.CalledHaplotypes calledHaplotypes = ((SomaticGenotypingEngine)genotypingEngine).callMutations( + haplotypes, + readLikelihoods, + ARreads_origNormalMQ, + perSampleFilteredReadList, + assemblyResult.getFullReferenceWithPadding(), + assemblyResult.getPaddedReferenceLoc(), + regionForGenotyping.getLocation(), + getToolkit().getGenomeLocParser(), + metaDataTracker, + givenAlleles, false , + tumorSampleName, + normalSampleName, + dbsnp.dbsnp, + cosmicRod, + DEBUG_READ_NAME + ); + + if ( MTAC.bamWriter != null ) { + final Set calledHaplotypeSet = new HashSet<>(calledHaplotypes.getCalledHaplotypes()); + if (MTAC.disableOptimizations) + calledHaplotypeSet.add(assemblyResult.getReferenceHaplotype()); + haplotypeBAMWriter.writeReadsAlignedToHaplotypes( + haplotypes, + assemblyResult.getPaddedReferenceLoc(), + haplotypes, + calledHaplotypeSet, + readLikelihoods); + } + + if( MTAC.DEBUG ) { logger.info("----------------------------------------------------------------------------------"); } + + + List annotatedCalls = new ArrayList<>(); + int eventCount = calledHaplotypes.getCalls().size(); + Integer minEventDistance = null; + Integer maxEventDistance = null; + Integer lastPosition = null; + for (VariantContext vc : calledHaplotypes.getCalls()) { + if (lastPosition == null) { + lastPosition = vc.getStart(); + } else { + int dist = Math.abs(vc.getStart() - lastPosition); + if (maxEventDistance == null || dist > maxEventDistance) { + maxEventDistance = dist; + } + if (minEventDistance == null || dist < minEventDistance) { + minEventDistance = dist; + } + } + } + Map eventDistanceAttributes = new HashMap<>(); + eventDistanceAttributes.put(GATKVCFConstants.EVENT_COUNT_IN_HAPLOTYPE_KEY, eventCount); + eventDistanceAttributes.put(GATKVCFConstants.EVENT_DISTANCE_MIN_KEY, minEventDistance); + eventDistanceAttributes.put(GATKVCFConstants.EVENT_DISTANCE_MAX_KEY, maxEventDistance); + + + // can we do this with the Annotation classes instead? + for (VariantContext originalVC : calledHaplotypes.getCalls()) { + VariantContextBuilder vcb = new VariantContextBuilder(originalVC); + + Map attributes = new HashMap<>(originalVC.getAttributes()); + attributes.putAll(eventDistanceAttributes); + vcb.attributes(attributes); + + Set filters = new HashSet<>(originalVC.getFilters()); + + double tumorLod = originalVC.getAttributeAsDouble(GATKVCFConstants.TUMOR_LOD_KEY, -1); + if (tumorLod < MTAC.TUMOR_LOD_THRESHOLD) { + filters.add(GATKVCFConstants.TUMOR_LOD_FILTER_NAME); + } + + // if we are in artifact detection mode, apply the thresholds for the LOD scores + if (!MTAC.ARTIFACT_DETECTION_MODE) { + filters.addAll(calculateFilters(metaDataTracker, originalVC, eventDistanceAttributes)); + } + + if (filters.size() > 0) { + vcb.filters(filters); + } else { + vcb.passFilters(); + } + + if (printTCGAsampleHeader) { + GenotypesContext genotypesWithBamSampleNames = originalVC.getGenotypes(); + List renamedGenotypes = new ArrayList<>(); + GenotypeBuilder GTbuilder = new GenotypeBuilder(genotypesWithBamSampleNames.get(tumorSampleName)); + GTbuilder.name("TUMOR"); + renamedGenotypes.add(GTbuilder.make()); + GTbuilder = new GenotypeBuilder(genotypesWithBamSampleNames.get(normalSampleName)); + GTbuilder.name("NORMAL"); + renamedGenotypes.add(GTbuilder.make()); + vcb.genotypes(renamedGenotypes); + } + + annotatedCalls.add(vcb.make()); + } + + + + + + + return annotatedCalls; + } + + private Set calculateFilters(RefMetaDataTracker metaDataTracker, VariantContext vc, Map eventDistanceAttributes) { + Set filters = new HashSet<>(); + + Integer eventCount = (Integer) eventDistanceAttributes.get(GATKVCFConstants.EVENT_COUNT_IN_HAPLOTYPE_KEY); + Integer maxEventDistance = (Integer) eventDistanceAttributes.get(GATKVCFConstants.EVENT_DISTANCE_MAX_KEY); + + Collection panelOfNormalsVC = metaDataTracker.getValues(normalPanelRod, + getToolkit().getGenomeLocParser().createGenomeLoc(vc.getChr(), vc.getStart())); + VariantContext ponVc = panelOfNormalsVC.isEmpty()?null:panelOfNormalsVC.iterator().next(); + + if (ponVc != null) { + filters.add(GATKVCFConstants.PON_FILTER_NAME); + } + + // FIXME: how do we sum qscores here? + // FIXME: parameterize thresholds + // && sum of alt likelihood scores > 20 + + // TODO: make the change to have only a single normal sample (but multiple tumors is ok...) + int normalAltCounts = 0; + double normalF = 0; + int normalAltQualityScoreSum = 0; + if (hasNormal()) { + Genotype normalGenotype = vc.getGenotype(normalSampleName); + + // NOTE: how do we get the non-ref depth here? + normalAltCounts = normalGenotype.getAD()[1]; + normalF = (Double) normalGenotype.getExtendedAttribute(GATKVCFConstants.ALLELE_FRACTION_KEY); + + Object qss = normalGenotype.getExtendedAttribute(GATKVCFConstants.QUALITY_SCORE_SUM_KEY); + if (qss != null) { + normalAltQualityScoreSum = (Integer) ((Object[]) qss)[1]; + } else { + logger.error("Null qss at " + vc.getStart()); + } + } + + if ( (normalAltCounts >= MTAC.MAX_ALT_ALLELES_IN_NORMAL_COUNT || normalF >= MTAC.MAX_ALT_ALLELE_IN_NORMAL_FRACTION ) && normalAltQualityScoreSum > MTAC.MAX_ALT_ALLELES_IN_NORMAL_QSCORE_SUM) { + filters.add(GATKVCFConstants.ALT_ALLELE_IN_NORMAL_FILTER_NAME); + } else { + + // NOTE: does normal alt counts presume the normal had all these events in CIS? + if ( eventCount > 1 && normalAltCounts >= 1) { + filters.add(GATKVCFConstants.MULTI_EVENT_ALT_ALLELE_IN_NORMAL_FILTER_NAME); + } else if (eventCount >= 3) { + filters.add(GATKVCFConstants.HOMOLOGOUS_MAPPING_EVENT_FILTER_NAME); + } + + } + + // STR contractions, that is the deletion of one repeat unit of a short repeat (>1bp repeat unit) + // such as ACTACTACT -> ACTACT, are overwhelmingly false positives so we + // hard filter them out by default + if (vc.isIndel()) { + ArrayList rpa = (ArrayList) vc.getAttribute(GATKVCFConstants.REPEATS_PER_ALLELE_KEY); + String ru = vc.getAttributeAsString(GATKVCFConstants.REPEAT_UNIT_KEY, ""); + if (rpa != null && rpa.size() > 1 && ru.length() > 1) { + int refCount = (Integer) rpa.get(0); + int altCount = (Integer) rpa.get(1); + + if (refCount - altCount == 1) { + filters.add(GATKVCFConstants.STR_CONTRACTION_FILTER_NAME); + } + } + } + + // NOTE: what if there is a 3bp indel followed by a snp... we are comparing starts + // so it would be thrown but it's really an adjacent event + if ( eventCount >= 2 && maxEventDistance >= 3) { + filters.add(GATKVCFConstants.CLUSTERED_EVENTS_FILTER_NAME); + } + + return filters; + } + + + private final static byte REF_MODEL_DELETION_QUAL = (byte) 30; + /** + * Calculate the genotype likelihoods for the sample in pileup for being hom-ref contrasted with being ref vs. alt + * + * @param pileup the read backed pileup containing the data we want to evaluate + * @param refBase the reference base at this pileup position + * @param minBaseQual the min base quality for a read in the pileup at the pileup position to be included in the calculation + * @return genotype likelihoods of [AA,AB] + */ + protected double[] calcGenotypeLikelihoodsOfRefVsAny(final ReadBackedPileup pileup, final byte refBase, final byte minBaseQual, final double f) { + final double[] genotypeLikelihoods = new double[2]; + int AA = 0, AB=1; + for( final PileupElement p : pileup ) { + final byte qual = (p.isDeletion() ? REF_MODEL_DELETION_QUAL : p.getQual()); + if( p.isDeletion() || qual > minBaseQual ) { + + // TODO: why not use base qualities here? + //double pobs = QualityUtils.qualToErrorProbLog10(qual); + double pobs = 1.0d - pow(10, (30 / -10.0)); + if( isNonRef(refBase, p)) { + genotypeLikelihoods[AB] += Math.log10(f*pobs + (1-f)*pobs/3.0d); + genotypeLikelihoods[AA] += Math.log10((1-pobs)/3); + } else { + genotypeLikelihoods[AB] += Math.log10(f*(1-pobs)/3.0d + (1-f)*pobs); + genotypeLikelihoods[AA] += Math.log10(pobs); + } + } + } + + return genotypeLikelihoods; + } + + private boolean hasNormal() { + return (normalSampleName != null); + } + + protected int getCountOfNonRefEvents(final ReadBackedPileup pileup, final byte refBase, final byte minBaseQual) { + int i=0; + for( final PileupElement p : pileup ) { + final byte qual = (p.isDeletion() ? REF_MODEL_DELETION_QUAL : p.getQual()); + if( p.isDeletion() || qual > minBaseQual ) { + if( isNonRef(refBase, p)) { + i++; + } + } + } + return i; + } + + protected double[] calcGenotypeLikelihoodsOfRefVsAny(final ReadBackedPileup pileup, final byte refBase, final byte minBaseQual) { + double f = calculateF(pileup, refBase, minBaseQual); + return calcGenotypeLikelihoodsOfRefVsAny(pileup, refBase, minBaseQual, f); + } + + private double calculateF(final ReadBackedPileup pileup, final byte refBase, final byte minBaseQual) { + int refCount = 0, altCount = 0; + for( final PileupElement p : pileup ) { + final byte qual = (p.isDeletion() ? REF_MODEL_DELETION_QUAL : p.getQual()); + + // only consider deletions AND sites of sufficient quality + if( p.isDeletion() || qual > minBaseQual ) { + if( isNonRef(refBase, p)) { + altCount++; + } else { + refCount++; + } + } + } + double f = (double) altCount / ((double) refCount + (double) altCount); + return f; + } + + private boolean isNonRef(byte refBase, PileupElement p) { + return p.getBase() != refBase || p.isDeletion() || p.isBeforeDeletionStart() || p.isAfterDeletionEnd() || p.isBeforeInsertion() || p.isAfterInsertion() || p.isNextToSoftClip(); + } + + int MIN_READ_LENGTH = 30; // private in superclass + + protected Set filterNonPassingReads( final ActiveRegion activeRegion) { + final Set readsToRemove = new LinkedHashSet<>(); + for( final GATKSAMRecord rec : activeRegion.getReads() ) { + + // KCIBUL: only perform read quality filtering on tumor reads... + if (isReadFromNormal(rec)) { + + if( rec.getReadLength() < MIN_READ_LENGTH ) { + readsToRemove.add(rec); + } + + } else { + + + if( rec.getReadLength() < MIN_READ_LENGTH || + rec.getMappingQuality() < MQthreshold || + BadMateFilter.hasBadMate(rec) || + + (keepRG != null && !rec.getReadGroup().getId().equals(keepRG)) ) { + readsToRemove.add(rec); + } + } + } + activeRegion.removeAll(readsToRemove); + return readsToRemove; + } + + private static GATKSAMRecord findReadByName(Collection reads, String name) { + for(GATKSAMRecord read : reads) { + if (name.equals(read.getReadName())) return read; + } + return null; + } + + /** + * Instantiates the appropriate likelihood calculation engine. + * + * @return never {@code null}. + */ + private ReadLikelihoodCalculationEngine createLikelihoodCalculationEngine() { + return new PairHMMLikelihoodCalculationEngine( (byte)LEAC.gcpHMM, LEAC.pairHMM, LEAC.pairHMMSub, LEAC.alwaysLoadVectorLoglessPairHMMLib, log10GlobalReadMismappingRate, LEAC.noFpga, pcrErrorModel ); + } + + /** + * FROM HC + * + * Create an ref model result (ref model or no calls depending on mode) for an active region without any variation + * (not is active, or assembled to just ref) + * + * @param region the region to return a no-variation result + * @param needsToBeFinalized should the region be finalized before computing the ref model (should be false if already done) + * @return a list of variant contexts (can be empty) to emit for this ref region + */ + protected List referenceModelForNoVariation(final ActiveRegion region, final boolean needsToBeFinalized) { + return NO_CALLS; + } + + protected Map> splitReadsBySample( final Collection reads ) { + return HaplotypeCaller.splitReadsBySample(samplesList, reads); + } + + // enable deletions in the pileup + @Override + public boolean includeReadsWithDeletionAtLoci() { return true; } + + // enable non primary and extended reads in the active region + @Override + public EnumSet desiredReadStates() { +// if ( includeUnmappedReads ) +// throw new UserException.BadArgumentValue("includeUnmappedReads", "is not yet functional"); +// else + return EnumSet.of( + ActiveRegionReadState.PRIMARY, + ActiveRegionReadState.NONPRIMARY, + ActiveRegionReadState.EXTENDED); + } + + //--------------------------------------------------------------------------------------------------------------- + // + // reduce + // + //--------------------------------------------------------------------------------------------------------------- + + @Override + public Integer reduceInit() { + return 0; + } + + @Override + public Integer reduce(List callsInRegion, Integer numCalledRegions) { + for( final VariantContext call : callsInRegion ) { + vcfWriter.add( call ); + } + return (callsInRegion.isEmpty() ? 0 : 1) + numCalledRegions; + } + + @Override + public void onTraversalDone(Integer result) { +// if ( SCAC.emitReferenceConfidence == ReferenceConfidenceMode.GVCF ) ((GVCFWriter)vcfWriter).close(false); // GROSS -- engine forces us to close our own VCF writer since we wrapped it +// referenceConfidenceModel.close(); + //TODO remove the need to call close here for debugging, the likelihood output stream should be managed + //TODO (open & close) at the walker, not the engine. + likelihoodCalculationEngine.close(); + logger.info("Ran local assembly on " + result + " active regions"); + } + + + // The following are not used but are required by the AnnotatorCompatible interface + public RodBinding getSnpEffRodBinding() { return null; } + public List> getResourceRodBindings() { return Collections.emptyList(); } + public boolean alwaysAppendDbsnpId() { return false; } + + /** + * rsIDs from this file are used to populate the ID column of the output. Also, the DB INFO flag will be set when appropriate. + * dbSNP overlap is only used to require more evidence of absence in the normal if the variant in question has been seen before in germline. + */ + @ArgumentCollection + protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection(); + public RodBinding getDbsnpRodBinding() { return dbsnp.dbsnp; } + + /** + * If a call overlaps with a record from the provided comp track, the INFO field will be annotated + * as such in the output with the track name (e.g. -comp:FOO will have 'FOO' in the INFO field). + * Records that are filtered in the comp track will be ignored. + * Note that 'dbSNP' has been special-cased (see the --dbsnp argument). + */ + @Advanced + @Input(fullName="comp", shortName = "comp", doc="comparison VCF file", required=false) + public List> comps = Collections.emptyList(); + public List> getCompRodBindings() { return comps; } + + + + /** + * Which annotations to add to the output VCF file. See the VariantAnnotator -list argument to view available annotations. + */ + @Advanced + @Argument(fullName="annotation", shortName="A", doc="One or more specific annotations to apply to variant calls", required=false) +// protected List annotationsToUse = new ArrayList<>(Arrays.asList(new String[]{"ClippingRankSumTest", "DepthPerSampleHC"})); + //protected List annotationsToUse = new ArrayList<>(Arrays.asList(new String[]{"DepthPerAlleleBySample", "BaseQualitySumPerAlleleBySample", "TandemRepeatAnnotator", + // "RMSMappingQuality","MappingQualityRankSumTest","FisherStrand","StrandOddsRatio","ReadPosRankSumTest","QualByDepth", "Coverage"})); + protected List annotationsToUse = new ArrayList<>(Arrays.asList(new String[]{"DepthPerAlleleBySample", "BaseQualitySumPerAlleleBySample", "TandemRepeatAnnotator", "OxoGReadCounts"})); + + /** + * Which annotations to exclude from output in the VCF file. Note that this argument has higher priority than the -A or -G arguments, + * so annotations will be excluded even if they are explicitly included with the other options. + */ + @Advanced + @Argument(fullName="excludeAnnotation", shortName="XA", doc="One or more specific annotations to exclude", required=false) + protected List annotationsToExclude = new ArrayList<>(Arrays.asList(new String[]{"SpanningDeletions"})); + + /** + * Which groups of annotations to add to the output VCF file. See the VariantAnnotator -list argument to view available groups. + */ + @Argument(fullName="group", shortName="G", doc="One or more classes/groups of annotations to apply to variant calls", required=false) + //protected String[] annotationGroupsToUse = { "Standard" }; + protected String[] annotationClassesToUse = { }; + + /** + * A raw, unfiltered, highly sensitive callset in VCF format. + */ + @Output(doc="File to which variants should be written") + protected VariantContextWriter vcfWriter = null; + + /** + * Active region trimmer reference. + */ + @ArgumentCollection + protected ActiveRegionTrimmer trimmer = new ActiveRegionTrimmer(); + + @Hidden + @Argument(fullName="keepRG", shortName="keepRG", doc="Only use read from this read group when making calls (but use all reads to build the assembly)", required = false) + protected String keepRG = null; + + + + + /** + * The minimum confidence needed for a given base for it to be used in variant calling. + */ + @Argument(fullName = "min_base_quality_score", shortName = "mbq", doc = "Minimum base quality required to consider a base for calling", required = false) + public byte MIN_BASE_QUALTY_SCORE = 10; + + + +// PAIR-HMM-Related Goodness + +// public PairHMMLikelihoodCalculationEngine.PCR_ERROR_MODEL pcrErrorModel = PairHMMLikelihoodCalculationEngine.PCR_ERROR_MODEL.CONSERVATIVE; +// public PairHMMLikelihoodCalculationEngine.PCR_ERROR_MODEL pcrErrorModel = PairHMMLikelihoodCalculationEngine.PCR_ERROR_MODEL.AGGRESSIVE; + public PairHMMLikelihoodCalculationEngine.PCR_ERROR_MODEL pcrErrorModel = PairHMMLikelihoodCalculationEngine.PCR_ERROR_MODEL.HOSTILE; + + // Parameters to control read error correction + @Hidden + @Argument(fullName="errorCorrectReads", shortName="errorCorrectReads", doc = "Use an exploratory algorithm to error correct the kmers used during assembly. May cause fundamental problems with the assembly graph itself", required=false) + protected boolean errorCorrectReads = false; + + @Hidden + @Argument(fullName="captureAssemblyFailureBAM", shortName="captureAssemblyFailureBAM", doc="If specified, we will write a BAM called assemblyFailure.bam capturing all of the reads that were in the active region when the assembler failed for any reason", required = false) + protected boolean captureAssemblyFailureBAM = false; + + @Advanced + @Argument(fullName="dontUseSoftClippedBases", shortName="dontUseSoftClippedBases", doc="If specified, we will not analyze soft clipped bases in the reads", required = false) + protected boolean dontUseSoftClippedBases = false; + + @Hidden + @Argument(fullName="justDetermineActiveRegions", shortName="justDetermineActiveRegions", doc = "If specified, the HC won't actually do any assembly or calling, it'll just run the upfront active region determination code. Useful for benchmarking and scalability testing", required=false) + protected boolean justDetermineActiveRegions = false; + + + + + // reference base padding size + private static final int REFERENCE_PADDING = 500; + + private static final byte MIN_TAIL_QUALITY_WITH_ERROR_CORRECTION = 6; + private final static int maxReadsInRegionPerSample = 1000; // TODO -- should be an argument + private final static int minReadsPerAlignmentStart = 5; // TODO -- should be an argument + + + + /** + * High-level function that runs the assembler on the active region reads, + * returning a data structure with the resulting information needed + * for further HC steps + * + * @param activeRegion the region we should assemble + * @param giveAlleles additional alleles we might need to genotype (can be empty) + * @return the AssemblyResult describing how to proceed with genotyping + */ + protected AssemblyResultSet assembleReads(final ActiveRegion activeRegion, final List giveAlleles) { + // Create the reference haplotype which is the bases from the reference that make up the active region + finalizeActiveRegion(activeRegion); // handle overlapping fragments, clip adapter and low qual tails + + final byte[] fullReferenceWithPadding = activeRegion.getActiveRegionReference(referenceReader, REFERENCE_PADDING); + final GenomeLoc paddedReferenceLoc = getPaddedLoc(activeRegion); + final Haplotype referenceHaplotype = createReferenceHaplotype(activeRegion, paddedReferenceLoc); + + // Create ReadErrorCorrector object if requested - will be used within assembly engine. + ReadErrorCorrector readErrorCorrector = null; + if (errorCorrectReads) + readErrorCorrector = new ReadErrorCorrector(RTAC.kmerLengthForReadErrorCorrection, MIN_TAIL_QUALITY_WITH_ERROR_CORRECTION, RTAC.minObservationsForKmerToBeSolid, MTAC.DEBUG, fullReferenceWithPadding); + + try { + final AssemblyResultSet assemblyResultSet = assemblyEngine.runLocalAssembly( activeRegion, referenceHaplotype, fullReferenceWithPadding, paddedReferenceLoc, giveAlleles,readErrorCorrector ); + assemblyResultSet.debugDump(logger); + return assemblyResultSet; + + } catch ( final Exception e ) { + // Capture any exception that might be thrown, and write out the assembly failure BAM if requested + if ( captureAssemblyFailureBAM ) { + final SAMFileWriter writer = SAMFileWriterStub.createSAMFileWriter("assemblyFailure.bam", getToolkit()); + new DirectOutputTracker().addOutput((SAMFileWriterStub) writer); + for ( final GATKSAMRecord read : activeRegion.getReads() ) { + writer.addAlignment(read); + } + writer.close(); + } + throw e; + } + } + + private void finalizeActiveRegion( final ActiveRegion activeRegion ) { + if (activeRegion.isFinalized()) return; + + if( MTAC.DEBUG ) { logger.info("Assembling " + activeRegion.getLocation() + " with " + activeRegion.size() + " reads: (with overlap region = " + activeRegion.getExtendedLoc() + ")"); } + + // Loop through the reads hard clipping the adaptor and low quality tails + final List readsToUse = new ArrayList<>(activeRegion.getReads().size()); + for( final GATKSAMRecord myRead : activeRegion.getReads() ) { + GATKSAMRecord clippedRead; + if (errorCorrectReads) + clippedRead = ReadClipper.hardClipLowQualEnds( myRead, MIN_TAIL_QUALITY_WITH_ERROR_CORRECTION ); + else // default case: clip low qual ends of reads + clippedRead= ReadClipper.hardClipLowQualEnds( myRead, MIN_TAIL_QUALITY ); + + if ( dontUseSoftClippedBases || ! ReadUtils.hasWellDefinedFragmentSize(clippedRead) ) { + // remove soft clips if we cannot reliably clip off adapter sequence or if the user doesn't want to use soft clips at all + clippedRead = ReadClipper.hardClipSoftClippedBases(clippedRead); + } else { + // revert soft clips so that we see the alignment start and end assuming the soft clips are all matches + // TODO -- WARNING -- still possibility that unclipping the soft clips will introduce bases that aren't + // TODO -- truly in the extended region, as the unclipped bases might actually include a deletion + // TODO -- w.r.t. the reference. What really needs to happen is that kmers that occur before the + // TODO -- reference haplotype start must be removed + clippedRead = ReadClipper.revertSoftClippedBases(clippedRead); + } + + clippedRead = ( clippedRead.getReadUnmappedFlag() ? clippedRead : ReadClipper.hardClipAdaptorSequence( clippedRead ) ); + if( !clippedRead.isEmpty() && clippedRead.getCigar().getReadLength() > 0 ) { + clippedRead = ReadClipper.hardClipToRegion(clippedRead, activeRegion.getExtendedLoc().getStart(), activeRegion.getExtendedLoc().getStop()); + if( activeRegion.readOverlapsRegion(clippedRead) && clippedRead.getReadLength() > 0 ) { + //logger.info("Keeping read " + clippedRead + " start " + clippedRead.getAlignmentStart() + " end " + clippedRead.getAlignmentEnd()); + readsToUse.add(clippedRead); + } + } + } + + // TODO -- Performance optimization: we partition the reads by sample 4 times right now; let's unify that code. + + final List downsampledReads = DownsamplingUtils.levelCoverageByPosition(ReadUtils.sortReadsByCoordinate(readsToUse), maxReadsInRegionPerSample, minReadsPerAlignmentStart); + + // handle overlapping read pairs from the same fragment + // KC: commented out as we handle overlapping read pairs in a different way... + //cleanOverlappingReadPairs(downsampledReads, normalSampleNames); + + activeRegion.clearReads(); + activeRegion.addAll(downsampledReads); + activeRegion.setFinalized(true); + } + + private GenomeLoc getPaddedLoc( final ActiveRegion activeRegion ) { + final int padLeft = Math.max(activeRegion.getExtendedLoc().getStart()-REFERENCE_PADDING, 1); + final int padRight = Math.min(activeRegion.getExtendedLoc().getStop()+REFERENCE_PADDING, referenceReader.getSequenceDictionary().getSequence(activeRegion.getExtendedLoc().getContig()).getSequenceLength()); + return getToolkit().getGenomeLocParser().createGenomeLoc(activeRegion.getExtendedLoc().getContig(), padLeft, padRight); + } + + /** + * Helper function to create the reference haplotype out of the active region and a padded loc + * @param activeRegion the active region from which to generate the reference haplotype + * @param paddedReferenceLoc the GenomeLoc which includes padding and shows how big the reference haplotype should be + * @return a non-null haplotype + */ + private Haplotype createReferenceHaplotype(final ActiveRegion activeRegion, final GenomeLoc paddedReferenceLoc) { + return ReferenceConfidenceModel.createReferenceHaplotype(activeRegion, activeRegion.getActiveRegionReference(referenceReader), paddedReferenceLoc); + } + + /** + * Clean up reads/bases that overlap within read pairs + * + * @param reads the list of reads to consider + */ + private void cleanOverlappingReadPairs(final List reads, Set normalSampleNames) { + Map> data = splitReadsBySample(reads); + for ( String sampleName : data.keySet() ) { + final boolean isTumor = !normalSampleNames.contains(sampleName); + final List perSampleReadList = data.get(sampleName); + + final FragmentCollection fragmentCollection = FragmentUtils.create(perSampleReadList); + for ( final List overlappingPair : fragmentCollection.getOverlappingPairs() ) + + // in MuTect -- right now we compare the + FragmentUtils.adjustQualsOfOverlappingPairedFragments(overlappingPair); + + + } + } + + public static void logReadInfo(String readName, Collection records, String message) { + if (readName != null) { + for (GATKSAMRecord rec : records) { + logReadInfo(readName, rec, message); + } + + } + } + + public static void logReadInfo(String readName, GATKSAMRecord rec, String message) { + if (readName != null && rec != null && readName.equals(rec.getReadName())) { + logger.info("Found " + rec.toString() + " - " + message); + } + } + + /** + * Returns a map with the original read as a key and the realigned read as the value. + *

+ * Missing keys or equivalent key and value pairs mean that the read was not realigned. + *

+ * @return never {@code null} + */ + // TODO: migrate from HC -> HCUtils Class and share it! + private Map realignReadsToTheirBestHaplotype(final ReadLikelihoods originalReadLikelihoods, final Haplotype refHaplotype, final GenomeLoc paddedReferenceLoc) { + + final Collection.BestAllele> bestAlleles = originalReadLikelihoods.bestAlleles(); + final Map result = new HashMap<>(bestAlleles.size()); + + for (final ReadLikelihoods.BestAllele bestAllele : bestAlleles) { + final GATKSAMRecord originalRead = bestAllele.read; + final Haplotype bestHaplotype = bestAllele.allele; + final boolean isInformative = bestAllele.isInformative(); + final GATKSAMRecord realignedRead = AlignmentUtils.createReadAlignedToRef(originalRead, bestHaplotype, refHaplotype, paddedReferenceLoc.getStart(), isInformative); + result.put(originalRead,realignedRead); + } + return result; + } + + private boolean isReadFromNormal(GATKSAMRecord rec) { + return normalSampleName != null && normalSampleName.equals(rec.getReadGroup().getSample()); + + } + // KCIBUL: new stuff -- read up on this!! + /** + * As of GATK 3.3, HaplotypeCaller outputs physical (read-based) information (see version 3.3 release notes and documentation for details). This argument disables that behavior. + */ + @Advanced + @Argument(fullName="doNotRunPhysicalPhasing", shortName="doNotRunPhysicalPhasing", doc="Disable physical phasing", required = false) + protected boolean doNotRunPhysicalPhasing = false; + +} + + diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/NA12878_Evaluations.md b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/NA12878_Evaluations.md new file mode 100644 index 000000000..b7d0c58f2 --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/NA12878_Evaluations.md @@ -0,0 +1,81 @@ +# CRSP ICE NA12878 Specificity Evaluation + +In order to evaluate the specificity of M2, we sequenced replicates of NA12878 using ICE (Illumina Content Exomes) all call all pairwise combinations as tumor-normals. By definition, everything called is a false positive. + +The target territory is ```/dsde/working/mutect/crsp_nn/whole_exome_illumina_coding_v1.Homo_sapiens_assembly19.targets.no_empty.interval_list``` + +All scripts referenced here are relative to the current working directory of ``` +/dsde/working/mutect/crsp_nn``` + +### Current M2 Performance + +(gsa-unstable 7/13/15, commit:9e93a70) + +| type | # of false positives | +|------|----------------------| +|SNP|99| +|INDEL|15| + + +TODO: write a simple tool to do this more easily + +To calculate per pair-counts, run: +``` +# for SNPs +for vcf in *.bam.vcf +do + cat $vcf | grep PASS | awk '{ if ( length($4) + length($5) == 2) print $0 }' | wc -l +done + +# for INDELs +for vcf in *.bam.vcf +do + cat $vcf | grep PASS | awk '{ if ( length($4) + length($5) != 2) print $0 }' | wc -l +done +``` + +### Current M1 and Indelocator Performance +For comparison, the M1 & Indelocator calls have been made on this same data set in the Firehose workspace ```CRSP_ICE_NA1878_Production_Analysis``` in the pair set ```NA12878_Replicate_Pairs``` which contains 4 samples and 12 pairwise combinations. + +| type | # of false positives | +|------|----------------------| +|SNP|181| +|INDEL|106| + +These results can be obtained (from a LSF / CGA node running the FuSE daemon) + +``` +SNP: +cat /local/cga-fh/cga/CRSP_ICE_NA1878_Production_Analysis/Pair_Set/NA12878_Replicate_Pairs/Pair/*/jobs/capture/mut/calls/latest/*.call_stats.txt | grep KEEP | wc -l + +INDEL (need to restrict to target territory): +reuse BEDTools +cat /dsde/working/mutect/crsp_nn/whole_exome_illumina_coding_v1.Homo_sapiens_assembly19.targets.no_empty.interval_list | grep -v "@" | awk '{ print $1 "\t" $2-1 "\t" $3 }' > ice.bed +cat /local/cga-fh/cga/CRSP_ICE_NA1878_Production_Analysis/Pair_Set/NA12878_Replicate_Pairs/Pair/*/jobs/capture/indel/maflite/latest/*.full.maf | grep KEEP | cut -f2-4 | awk '{ print $1 "\t" $2-1 "\t" $3 }' > /tmp/indels.bed +bedtools intersect -wa -a /tmp/ice.bed -b /tmp/indels.bed | wc -l +``` + + +### How To Run +The SCALA script for running M2 can be found in the gsa-unstable repository under ```private/gatk-tools-private/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2``` + +First, chose the appropriate settings (runnable as environment variables here) +``` +QUEUE_JAR= +OUT_VCF= +GSA_UNSTABLE_HOME= +TEMPDIR=/broad/hptmp/$USER +``` + +and then run the following Queue command +``` +java \ + -Djava.io.tmpdir=$TEMPDIR \ + -jar $QUEUE_JAR \ + -S $GSA_UNSTABLE_HOME/private/gatk-tools-private/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/run_M2_ICE_NN.scala \ + -sc 50 \ + --job_queue gsa -qsub -jobResReq virtual_free=5G -startFromScratch \ + --allbams /humgen/gsa-hpprojects/NA12878Collection/bams/crsp_ice_validation//NA12878.intra.flowcell.replicate.bam_list \ + -o + -run +``` diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/SomaticGenotypingEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/SomaticGenotypingEngine.java new file mode 100644 index 000000000..2c05ce825 --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/SomaticGenotypingEngine.java @@ -0,0 +1,558 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. 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This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.cancer.m2; + +import com.google.java.contract.Ensures; +import htsjdk.samtools.util.StringUtil; +import htsjdk.variant.variantcontext.*; +import org.apache.log4j.Logger; +import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodsCalculationModel; +import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalculatorProvider; +import org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.commandline.RodBinding; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.genotyper.MostLikelyAllele; +import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods; +import org.broadinstitute.gatk.utils.genotyper.SampleList; +import org.broadinstitute.gatk.utils.haplotype.Haplotype; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.ReadUtils; +import org.broadinstitute.gatk.utils.variant.GATKVCFConstants; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; + +import java.util.*; + +public class SomaticGenotypingEngine extends HaplotypeCallerGenotypingEngine { + + protected M2ArgumentCollection MTAC; + + private final static Logger logger = Logger.getLogger(SomaticGenotypingEngine.class); + + public SomaticGenotypingEngine(final M2ArgumentCollection configuration, final SampleList samples, final GenomeLocParser genomeLocParser, final AFCalculatorProvider afCalculatorProvider, final boolean doPhysicalPhasing, final M2ArgumentCollection MTAC) { + super(configuration, samples, genomeLocParser, afCalculatorProvider, doPhysicalPhasing); + this.MTAC = MTAC; + } + + /** + * Main entry point of class - given a particular set of haplotypes, samples and reference context, compute + * genotype likelihoods and assemble into a list of variant contexts and genomic events ready for calling + * + * The list of samples we're working with is obtained from the readLikelihoods + * + * @param haplotypes Haplotypes to assign likelihoods to + * @param readLikelihoods Map from reads->(haplotypes,likelihoods) + * @param perSampleFilteredReadList Map from sample to reads that were filtered after assembly and before calculating per-read likelihoods. + * @param ref Reference bytes at active region + * @param refLoc Corresponding active region genome location + * @param activeRegionWindow Active window + * @param genomeLocParser GenomeLocParser + * @param activeAllelesToGenotype Alleles to genotype + * @param emitReferenceConfidence whether we should add a <NON_REF> alternative allele to the result variation contexts. + * + * @return A CalledHaplotypes object containing a list of VC's with genotyped events and called haplotypes + * + */ +// @Requires({"refLoc.containsP(activeRegionWindow)", "haplotypes.size() > 0"}) + @Ensures("result != null") + // TODO - can this be refactored? this is hard to follow! + public HaplotypeCallerGenotypingEngine.CalledHaplotypes callMutations ( + final List haplotypes, + //final Map haplotypeReadMap, + final ReadLikelihoods readLikelihoods, + final Map originalNormalReadQualities, + final Map> perSampleFilteredReadList, + final byte[] ref, + final GenomeLoc refLoc, + final GenomeLoc activeRegionWindow, + final GenomeLocParser genomeLocParser, + final RefMetaDataTracker tracker, + final List activeAllelesToGenotype, + final boolean emitReferenceConfidence, + final String tumorSampleName, + final String matchedNormalSampleName, + final RodBinding dbsnpRod, + final List> cosmicRod, + final String DEBUG_READ_NAME + + ) { + + // sanity check input arguments + if (haplotypes == null || haplotypes.isEmpty()) throw new IllegalArgumentException("haplotypes input should be non-empty and non-null, got "+haplotypes); + if (readLikelihoods == null || readLikelihoods.sampleCount() == 0) throw new IllegalArgumentException("readLikelihoods input should be non-empty and non-null, got "+readLikelihoods); + if (ref == null || ref.length == 0 ) throw new IllegalArgumentException("ref bytes input should be non-empty and non-null, got "+ref); + if (refLoc == null || refLoc.size() != ref.length) throw new IllegalArgumentException(" refLoc must be non-null and length must match ref bytes, got "+refLoc); + if (activeRegionWindow == null ) throw new IllegalArgumentException("activeRegionWindow must be non-null, got "+activeRegionWindow); + if (activeAllelesToGenotype == null ) throw new IllegalArgumentException("activeAllelesToGenotype must be non-null, got "+activeAllelesToGenotype); + if (genomeLocParser == null ) throw new IllegalArgumentException("genomeLocParser must be non-null, got "+genomeLocParser); + + + // Somatic Tumor/Normal Sample Handling + verifySamplePresence(tumorSampleName, readLikelihoods.samples()); + final boolean hasNormal = (matchedNormalSampleName != null); + + // update the haplotypes so we're ready to call, getting the ordered list of positions on the reference + // that carry events among the haplotypes + final TreeSet startPosKeySet = decomposeHaplotypesIntoVariantContexts(haplotypes, readLikelihoods, ref, refLoc, activeAllelesToGenotype); + + // Walk along each position in the key set and create each event to be outputted + final Set calledHaplotypes = new HashSet<>(); + final List returnCalls = new ArrayList<>(); + + for( final int loc : startPosKeySet ) { + if( loc >= activeRegionWindow.getStart() && loc <= activeRegionWindow.getStop() ) { // genotyping an event inside this active region + final List eventsAtThisLoc = getVCsAtThisLocation(haplotypes, loc, activeAllelesToGenotype); + + if( eventsAtThisLoc.isEmpty() ) { continue; } + + // Create the event mapping object which maps the original haplotype events to the events present at just this locus + final Map> eventMapper = createEventMapper(loc, eventsAtThisLoc, haplotypes); + + // Sanity check the priority list for mistakes + final List priorityList = makePriorityList(eventsAtThisLoc); + + // Merge the event to find a common reference representation + + VariantContext mergedVC = GATKVariantContextUtils.simpleMerge(eventsAtThisLoc, priorityList, + GATKVariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, + GATKVariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, null, false, false); + + if( mergedVC == null ) { continue; } + + final int numAlts = mergedVC.getNAlleles()-1; + +// final VariantContextBuilder vcb = new VariantContextBuilder(mergedVC); + + final GenotypeLikelihoodsCalculationModel.Model calculationModel = mergedVC.isSNP() + ? GenotypeLikelihoodsCalculationModel.Model.SNP : GenotypeLikelihoodsCalculationModel.Model.INDEL; + + if (emitReferenceConfidence) + mergedVC = addNonRefSymbolicAllele(mergedVC); + + final Map mergeMap = new LinkedHashMap<>(); + mergeMap.put(null, mergedVC.getReference()); // the reference event (null) --> the reference allele + for(int iii = 0; iii < eventsAtThisLoc.size(); iii++) { + mergeMap.put(eventsAtThisLoc.get(iii), mergedVC.getAlternateAllele(iii)); // BUGBUG: This is assuming that the order of alleles is the same as the priority list given to simpleMerge function + } + + final Map> alleleMapper = createAlleleMapper(mergeMap, eventMapper); + + if( configuration.DEBUG && logger != null ) { + if (logger != null) logger.info("Genotyping event at " + loc + " with alleles = " + mergedVC.getAlleles()); + } + + ReadLikelihoods readAlleleLikelihoods = readLikelihoods.marginalize(alleleMapper, genomeLocParser.createPaddedGenomeLoc(genomeLocParser.createGenomeLoc(mergedVC), ALLELE_EXTENSION)); + + //LDG: do we want to do this before or after pulling out overlapping reads? + if (MTAC.isSampleContaminationPresent()) + readAlleleLikelihoods.contaminationDownsampling(MTAC.getSampleContamination()); + + //if (!mergedVC.isBiallelic()) { + // logger.info("[UNSUPPORTED] Detected non-Biallelic VC" + mergedVC.toString()); + // continue; + //} + + // TODO: once tests are passing, refactor to use the new data structure (not the deprecated one) + // handle overlapping fragments + // TODO: CONFIRM WITH GSA IF IT IS OK TO REMOVE READS FROM THE PRALM (should be... they do it in filterPoorlyModeledReads!) + PerReadAlleleLikelihoodMap tumorPRALM = readAlleleLikelihoods.toPerReadAlleleLikelihoodMap(readAlleleLikelihoods.sampleIndex(tumorSampleName)); + filterPRALMForOverlappingReads(tumorPRALM, mergedVC.getReference(), loc, false); + MuTect2.logReadInfo(DEBUG_READ_NAME, tumorPRALM.getLikelihoodReadMap().keySet(), "Present after filtering for overlapping reads"); + // extend to multiple samples + + //handle existence of secondary alts + double[] afs = estimateAlleleFraction(mergedVC, tumorPRALM); + + if( configuration.DEBUG && logger != null ) { + String output = "Calculated allelic fraction at " + loc + " = "; + for (int i = 0; i originalNormalMQs, double[] afs) { + double[] genotypeLikelihoods = new double[mergedVC.getNAlleles()]; + for(Map.Entry> e : tumorPRALM.getLikelihoodReadMap().entrySet()) { + Map m = e.getValue(); + Double refLL = m.get(mergedVC.getReference()); + if (originalNormalMQs.get(e.getKey().getReadName()) != 0) { + genotypeLikelihoods[0] += Math.log10(Math.pow(10, refLL)); + + for (int altInd = 0; altInd < mergedVC.getNAlleles()-1; altInd++) { + Double altLL = m.get(mergedVC.getAlternateAllele(altInd)); + genotypeLikelihoods[altInd+1] += Math.log10(Math.pow(10, refLL) * (1 - afs[altInd]) + Math.pow(10, altLL) * afs[altInd]); + } + } + } + return genotypeLikelihoods; + } + + /** + * Find the allele fractions for each alternate allele + * + * @param vc input VC, for alleles + * @param map read likelihoods + * @return estimated AF for each alt + */ + // FIXME: calculate using the uncertainty rather than this cheap approach + private double[] estimateAlleleFraction(VariantContext vc, PerReadAlleleLikelihoodMap map) { + int[] counts = getRefAltCount(vc, map); + int numAlts = vc.getNAlleles()-1; + double[] afs = new double[numAlts]; + int refCount = counts[0]; + int altCount; + + for(int altInd = 0; altInd < numAlts; altInd++) { + altCount = counts[altInd+1]; + afs[altInd] = (double) altCount / ((double) refCount + (double) altCount); + //logger.info("Counted " + refCount + " ref and " + altCount + " alt " ); + } + + return afs; + } + + /** + * Evalutate the most likely allele for each read, if it is in fact informative + * + * @param mergedVC input VC, for alleles + * @param afMap read likelihoods + * @return an array giving the read counts for the ref and each alt allele + */ + // TODO: ensure there are only two alleles in the VC + private int[] getRefAltCount(VariantContext mergedVC, PerReadAlleleLikelihoodMap afMap) { + int counts[] = new int[mergedVC.getNAlleles()]; + int REF = 0; + + for(Map.Entry> e : afMap.getLikelihoodReadMap().entrySet()) { + Map m = e.getValue(); + Double rl = m.get(mergedVC.getReference()); + for(int altInd=0; altInd= rl) logger.info("Alt found in " + e.getKey().getReadName()); + } + return counts; + } + + + private void logM2Debug(String s) { + if (MTAC.M2_DEBUG) { + logger.info(s); + } + } + + // would have used org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap.getMostLikelyAllele but we have this case where + // there is a read that doesn't overlap the variant site, and thus supports both alleles equally. + private boolean arePairHMMLikelihoodsInformative(double l1, double l2) { + // TODO: should this be parameterized, or simply encoded + double EPSILON = 0.1; + return (Math.abs(l1 - l2) >= EPSILON); + } + + private void filterPRALMForOverlappingReads(PerReadAlleleLikelihoodMap pralm, Allele ref, int location, boolean retainMismatches) { + + Map> m = pralm.getLikelihoodReadMap(); + + + // iterate through the reads, if the name has been seen before we have overlapping (potentially) fragments, so handle them + Map nameToRead = new HashMap<>(); + Set readsToKeep = new HashSet<>(); + + for(GATKSAMRecord rec : m.keySet()) { + // if we haven't seen it... just record the name and add it to the list of reads to keep + GATKSAMRecord existing = nameToRead.get(rec.getReadName()); + if (existing == null) { + nameToRead.put(rec.getReadName(), rec); + readsToKeep.add(rec); + } else { + logM2Debug("Found a paired read for " + rec.getReadName()); + + // NOTE: Can we use FragmentUtils to do all of this processing (to find overlapping pairs?) + // seems like maybe, but it has some requirements about the order of the reads supplied which may be painful to meet + // TODO: CHECK IF THE READS BOTH OVERLAP THE POSITION!!!! + if ( ReadUtils.isInsideRead(existing, location) && ReadUtils.isInsideRead(rec, location) ) { + + MostLikelyAllele existingMLA = pralm.getMostLikelyAllele(pralm.getLikelihoodReadMap().get(existing)); + Allele existingAllele = existingMLA.getMostLikelyAllele(); + + MostLikelyAllele recMLA = pralm.getMostLikelyAllele(pralm.getLikelihoodReadMap().get(rec)); + Allele recAllele = recMLA.getMostLikelyAllele(); + + // if the reads disagree at this position... + if (!existingAllele.equals(recAllele)) { + //... and we're not retaining mismatches, throw them both out + if (!retainMismatches) { + logM2Debug("Discarding read-pair due to disagreement" + rec.getReadName() + " and allele " + existingAllele); + readsToKeep.remove(existing); + + //... and we are retaining mismatches, keep the mismatching one + } else { + if (existingAllele.equals(ref)) { + logM2Debug("Discarding read to keep mismatching " + rec.getReadName() + " and allele " + existingAllele); + readsToKeep.remove(existing); + readsToKeep.add(rec); + } + } + // Otherwise, keep the element with the higher quality score + } else { + logM2Debug("Discarding lower quality read of overlapping pair " + rec.getReadName() + " and allele " + existingAllele); + if (existingMLA.getLog10LikelihoodOfMostLikely() < recMLA.getLog10LikelihoodOfMostLikely()) { + readsToKeep.remove(existing); + readsToKeep.add(rec); + } + } + } else { + // although these are overlapping fragments, they don't overlap at the position in question + // so keep the read + readsToKeep.add(rec); + } + } + + } + + // perhaps moved into PRALM + final Iterator>> it = m.entrySet().iterator(); + while ( it.hasNext() ) { + final Map.Entry> record = it.next(); + if(!readsToKeep.contains(record.getKey())) { + it.remove(); + logM2Debug("Dropping read " + record.getKey() + " due to overlapping read fragment rules"); + } + } + } + + // Move to utility class so we can use one shared with HaplotypeCallerGenotypingEngine + private VariantContext addNonRefSymbolicAllele(final VariantContext mergedVC) { + final VariantContextBuilder vcb = new VariantContextBuilder(mergedVC); + final List originalList = mergedVC.getAlleles(); + final List alleleList = new ArrayList<>(originalList.size() + 1); + alleleList.addAll(mergedVC.getAlleles()); + alleleList.add(GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE); + vcb.alleles(alleleList); + return vcb.make(); + } + +} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/create_M2_pon.scala b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/create_M2_pon.scala new file mode 100644 index 000000000..009eebaca --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/create_M2_pon.scala @@ -0,0 +1,140 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. 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BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.cancer.m2 + +import java.io.File + +import org.broadinstitute.gatk.queue.QScript +import org.broadinstitute.gatk.queue.extensions.gatk._ +import org.broadinstitute.gatk.queue.function.CommandLineFunction +import org.broadinstitute.gatk.queue.util.QScriptUtils +import org.broadinstitute.gatk.utils.commandline.{Input, Output} +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.FilteredRecordMergeType + +import scala.collection.mutable.ListBuffer + +class create_M2_pon extends QScript { + + @Argument(shortName = "bams", required = true, doc = "file of all BAM files") + var allBams: String = "" + + @Argument(shortName = "o", required = true, doc = "Output prefix") + var outputPrefix: String = "" + + @Argument(shortName = "minN", required = false, doc = "minimum number of sample observations to include in PON") + var minN: Int = 2 + + @Argument(doc="Reference fasta file to process with", fullName="reference", shortName="R", required=false) + var reference = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta") + + @Argument(doc="Intervals file to process with", fullName="intervals", shortName="L", required=true) + var intervals : File = "" + + @Argument(shortName = "sc", required = false, doc = "base scatter count") + var scatter: Int = 10 + + + def script() { + val bams = QScriptUtils.createSeqFromFile(allBams) + val genotypesVcf = outputPrefix + ".genotypes.vcf" + val finalVcf = outputPrefix + ".vcf" + + val perSampleVcfs = new ListBuffer[File]() + for (bam <- bams) { + val outputVcf = "sample-vcfs/" + bam.getName + ".vcf" + add( createM2Config(bam, outputVcf)) + perSampleVcfs += outputVcf + } + + val cv = new CombineVariants() + cv.reference_sequence = reference + cv.memoryLimit = 2 + cv.setKey = "null" + cv.minimumN = minN + cv.memoryLimit = 16 + cv.filteredrecordsmergetype = FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED + cv.filteredAreUncalled = true + cv.variant = perSampleVcfs + cv.out = genotypesVcf + + // using this instead of "sites_only" because we want to keep the AC info + val vc = new VcfCutter() + vc.inVcf = genotypesVcf + vc.outVcf = finalVcf + + add (cv, vc) + + } + + + def createM2Config(bam : File, outputVcf : File): org.broadinstitute.gatk.queue.extensions.gatk.MuTect2 = { + val mutect2 = new org.broadinstitute.gatk.queue.extensions.gatk.MuTect2 + + mutect2.reference_sequence = reference + mutect2.artifact_detection_mode = true + mutect2.intervalsString :+= intervals + mutect2.memoryLimit = 2 + mutect2.input_file = List(new TaggedFile(bam, "tumor")) + + mutect2.scatterCount = scatter + mutect2.out = outputVcf + + mutect2 + } +} + +class VcfCutter extends CommandLineFunction { + @Input(doc = "vcf to cut") var inVcf: File = _ + @Output(doc = "output vcf") var outVcf: File = _ + + def commandLine = "cat %s | cut -f1-8 > %s".format(inVcf, outVcf) +} \ No newline at end of file diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/run_M2_ICE_NN.scala b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/run_M2_ICE_NN.scala new file mode 100644 index 000000000..46d31c461 --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/run_M2_ICE_NN.scala @@ -0,0 +1,102 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.queue.qscripts.dev + +import org.broadinstitute.gatk.queue.QScript +import org.broadinstitute.gatk.queue.extensions.gatk._ +import org.broadinstitute.gatk.queue.util.QScriptUtils + +class run_M2_ICE_NN extends QScript { + + @Argument(shortName = "bams", required = true, doc = "file of all BAM files") + var allBams: String = "" + + @Argument(shortName = "o", required = false, doc = "Output prefix") + var outputPrefix: String = "" + + @Argument(shortName = "pon", required = false, doc = "Normal PON") + var panelOfNormals: String = "/dsde/working/mutect/panel_of_normals/panel_of_normals_m2_ice_wgs_territory/m2_406_ice_normals_wgs_calling_regions.vcf"; + + @Argument(shortName = "sc", required = false, doc = "base scatter count") + var scatter: Int = 10 + + + def script() { + val bams = QScriptUtils.createSeqFromFile(allBams) + + for (tumor <- bams) { + for (normal <- bams) { + if (tumor != normal) add( createM2Config(tumor, normal, new File(panelOfNormals), outputPrefix)) + } + } + } + + + def createM2Config(tumorBAM : File, normalBAM : File, panelOfNormals : File, outputPrefix : String): M2 = { + val mutect2 = new MuTect2 + + mutect2.reference_sequence = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta") + mutect2.cosmic :+= new File("/xchip/cga/reference/hg19/hg19_cosmic_v54_120711.vcf") + mutect2.dbsnp = new File("/humgen/gsa-hpprojects/GATK/bundle/current/b37/dbsnp_138.b37.vcf") + mutect2.normal_panel :+= panelOfNormals + + mutect2.intervalsString :+= new File("/dsde/working/mutect/crsp_nn/whole_exome_illumina_coding_v1.Homo_sapiens_assembly19.targets.no_empty.interval_list") + mutect2.memoryLimit = 2 + mutect2.input_file = List(new TaggedFile(normalBAM, "normal"), new TaggedFile(tumorBAM, "tumor")) + + mutect2.scatterCount = scatter + mutect2.out = outputPrefix + tumorBAM.getName + "-vs-" + normalBAM.getName + ".vcf" + + println("Adding " + tumorBAM + " vs " + normalBAM + " as " + mutect2.out) + mutect2 + } +} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/run_M2_dream.scala b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/run_M2_dream.scala new file mode 100644 index 000000000..95b5c0043 --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/run_M2_dream.scala @@ -0,0 +1,89 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.queue.qscripts.dev + +import org.broadinstitute.gatk.queue.QScript +import org.broadinstitute.gatk.queue.extensions.gatk._ + +class run_M2_dream extends QScript { + + @Argument(shortName = "L", required=false, doc = "Intervals file") + var intervalsFile: List[File] = Nil + @Argument(shortName = "normal", required=true, doc = "Normal sample BAM") + var normalBAM: String = "" + @Argument(shortName = "tumor", required=true, doc = "Tumor sample BAM") + var tumorBAM: String = "" + @Argument(shortName = "o", required=true, doc = "Output file") + var outputFile: String = "" + @Argument(shortName = "sc", required=false, doc = "base scatter count") + var scatter: Int = 10 + + + def script() { + + val mutect2 = new MuTect2 + + mutect2.reference_sequence = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta") + mutect2.cosmic :+= new File("/xchip/cga/reference/hg19/hg19_cosmic_v54_120711.vcf") + mutect2.dbsnp = new File("/humgen/gsa-hpprojects/GATK/bundle/current/b37/dbsnp_138.b37.vcf") + mutect2.normal_panel :+= new File("/xchip/cga/reference/hg19/wgs_hg19_125_cancer_blood_normal_panel.vcf") + + mutect2.intervalsString = intervalsFile + mutect2.memoryLimit = 2 + mutect2.input_file = List(new TaggedFile(normalBAM, "normal"), new TaggedFile(tumorBAM, "tumor")) + + mutect2.scatterCount = scatter + mutect2.out = outputFile + add(mutect2) + } + +} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/BaseCoverageDistribution.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/BaseCoverageDistribution.java deleted file mode 100644 index 81c080d17..000000000 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/BaseCoverageDistribution.java +++ /dev/null @@ -1,308 +0,0 @@ -/* -* By downloading the PROGRAM you agree to the following terms of use: -* -* BROAD INSTITUTE -* SOFTWARE LICENSE AGREEMENT -* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY -* -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and -* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. -* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* -* 1. DEFINITIONS -* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* -* 2. LICENSE -* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. -* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. -* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. -* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. -* -* 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. -* -* 4. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. -* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 5. INDEMNIFICATION -* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* -* 6. NO REPRESENTATIONS OR WARRANTIES -* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. -* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* -* 7. ASSIGNMENT -* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* -* 8. MISCELLANEOUS -* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. -* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. -* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. -* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. -* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. -* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. -* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. -*/ - -package org.broadinstitute.gatk.tools.walkers.diagnostics; - -import org.broadinstitute.gatk.utils.commandline.Argument; -import org.broadinstitute.gatk.utils.commandline.Output; -import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.utils.contexts.AlignmentContext; -import org.broadinstitute.gatk.utils.contexts.ReferenceContext; -import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.utils.report.GATKReport; -import org.broadinstitute.gatk.engine.walkers.LocusWalker; -import org.broadinstitute.gatk.utils.GenomeLoc; -import org.broadinstitute.gatk.utils.GenomeLocParser; -import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; -import org.broadinstitute.gatk.utils.help.HelpConstants; - -import java.io.PrintStream; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.LinkedList; -import java.util.Map; - -/** - * Evaluate coverage distribution per base - * - *

- * This tool reports the distribution of coverage per base. It includes reads with deletions in the counts unless - * otherwise specified. Quality filters can be applied before the coverage is calculated. - *

- * - *

Input

- *

- * The BAM file and an optional interval list - *

- * - *

Output

- *

- * A GATK Report with the coverage distribution per base - * - *

- *

Usage example

- * 
- * java -jar GenomeAnalysisTK.jar \
- *   -R reference.fasta \
- *   -T BaseCoverageDistribution \
- *   -I myData.bam \
- *   -L intervals.list \
- *   -fd \
- *   -o report.grp
- *
- * - * @author carneiro - * @since 1/27/13 - */ -@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} ) -public class BaseCoverageDistribution extends LocusWalker, Map>> { - /** - * The name of the file to output the GATK Report table. See the FAQs for more information on the GATK Report format. - */ - @Output(doc = "Output filename") - private PrintStream out; - - /** - * Whether or not a deletion should be counted towards the coverage of a site - */ - @Argument(required = false, shortName="del", fullName = "include_deletions", doc ="Include reads with deletions") - private boolean includeDeletions = true; - - /** - * Whether or not to apply quality filters before calculating coverage distribution. Filtering will use the - * minimum_mapping_quality and minimum_base_quality parameters below. - */ - @Argument(required = false, shortName="fd", fullName = "filtered_distribution", doc ="Apply quality filters") - private boolean calculateFilteredDistribution = false; - - /** - * The minimum mapping quality a read must have to be counted towards the filtered coverage of a site - */ - @Argument(required = false, shortName="mmq", fullName = "minimum_mapping_quality", doc ="Minimum read mapping quality of a read to pass filters") - private byte minMappingQuality = 20; - - /** - * The minimum base quality a base must have to be counted towards the filtered coverage of a site - */ - @Argument(required = false, shortName="mbq", fullName = "minimum_base_quality", doc ="Minimum base quality to pass filters") - private byte minBaseQuality = 17; - - private GenomeLoc previousLocus = null; - private long uncoveredBases = 0L; - private final LinkedList intervalList = new LinkedList(); - - @Override - public boolean includeReadsWithDeletionAtLoci() { - return includeDeletions; - } - - @Override - public void initialize() { - if (getToolkit().getIntervals() != null) - intervalList.addAll(getToolkit().getIntervals()); // if the user provided intervals, keep track of them for uncovered bases calculation - } - - @Override - public ArrayList map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - ArrayList result = new ArrayList(2); - GenomeLoc currentLocus = ref.getLocus(); - tallyUncoveredBases(currentLocus); - previousLocus = currentLocus; - result.add(context.getBasePileup().getReads().size()); // I want the reads instead of the base pileup because I want to count deletions. - if (calculateFilteredDistribution) - result.add(context.getBasePileup().getBaseAndMappingFilteredPileup(minBaseQuality, minMappingQuality).getReads().size()); // filtered pileup - else { - result.add(result.get(0)); // repeat the same value as the unfiltered pileup if filters are not on - } - return result; - } - - @Override - public Map> reduceInit() { - return new HashMap>(10000); - } - - @Override - public Map> reduce(ArrayList value, Map> sum) { - final int unfilteredCoverage = value.get(0); - final int filteredCoverage = value.get(1); - incrementSumArray(sum, unfilteredCoverage, 0); - incrementSumArray(sum, filteredCoverage, 1); - return sum; - } - - @Override - public void onTraversalDone(Map> result) { - tallyUncoveredBasesTillEndOfTraversal(); - GATKReport report; - - if (calculateFilteredDistribution) { - report = GATKReport.newSimpleReport("BaseCoverageDistribution", "Coverage", "Count", "Filtered"); - } else { - report = GATKReport.newSimpleReport("BaseCoverageDistribution", "Coverage", "Count"); - report.addRow(0, uncoveredBases); // preemptively add the uncovered bases row (since they'll never exist in the Map) - } - - for (Map.Entry> entry : result.entrySet()) { - final ArrayList values = entry.getValue(); - final int coverage = entry.getKey(); - if (calculateFilteredDistribution) { - if (coverage == 0) { // special case for the uncovered bases. The filtered pileups may have an entry, but the unfiltered ones won't. - report.addRow(coverage, uncoveredBases, uncoveredBases + values.get(1)); - } else { - report.addRow(coverage, values.get(0), values.get(1)); - } - } else { - report.addRow(coverage, values.get(0)); - } - } - // In case the filtered distribution never had a pileup filtered down to zero coverage, output the overall uncovered bases for both - if (calculateFilteredDistribution && !result.containsKey(0)) { - report.addRow(0, uncoveredBases, uncoveredBases); - } - report.print(out); - } - - /** - * Initializes the ArrayList if needed. Returns the initialized element (or previously initialized) - * this method is used directly by the incrementSumArray. - * - * @param sum the map - * @param coverage the key to the map to extract the array list - * @return if the ArrayList exists, return it. Otherwise, initialize it with 0 counters. - */ - private ArrayList initializeSumArray(final Map> sum, final int coverage) { - ArrayList curr = sum.get(coverage); - if (curr == null) { - curr = new ArrayList(2); - curr.add(0L); // number of bases with this unfiltered coverage - curr.add(0L); // number of bases with this filtered coverage - sum.put(coverage, curr); - } - return curr; - } - - /** - * Increments the counter for the given arrayindex (type of coverage : filtered or unfiltered) initializing if necessary - * - * @param sum the hash - * @param coverage the hash key - * @param arrayIndex which distribution to increment, 0 for unfiltered, 1 for filtered. - */ - private void incrementSumArray(final Map> sum, final int coverage, final int arrayIndex) { - final ArrayList currentTally = initializeSumArray(sum, coverage); - currentTally.set(arrayIndex, currentTally.get(arrayIndex) + 1); - } - - /** - * Counts all the uncovered loci after the end of traversal. - * - * - Modifies the global variable uncoveredBases - * - Uses global variables: intervalList and previousLocus - * - * takes into account that the traversal may have been due over a set of intervals, or over the whole genome. - */ - private void tallyUncoveredBasesTillEndOfTraversal() { - GenomeLocParser parser = getToolkit().getGenomeLocParser(); - GenomeLoc lastLocus; - if (intervalList.isEmpty()) { // whole genome, add up all contigs past previousLocus - final int lastContigIndex = getToolkit().getSAMFileHeader().getSequenceDictionary().size() - 1; - final int lastContigLength = getToolkit().getSAMFileHeader().getSequence(lastContigIndex).getSequenceLength(); - final String lastContigName = getToolkit().getSAMFileHeader().getSequence(lastContigIndex).getSequenceName(); - lastLocus = parser.createGenomeLoc(lastContigName, lastContigIndex, lastContigLength, lastContigLength); - } else { - GenomeLoc lastInterval = intervalList.getLast(); - lastLocus = parser.createGenomeLoc(lastInterval.getContig(), lastInterval.getContigIndex(), lastInterval.getStop(), lastInterval.getStop()); - } - tallyUncoveredBases(lastLocus); - } - - /** - * Counts all the uncovered loci that have been skipped since the last visited locus. This method allows coverage - * tools to run with @By(DataSource.READS) instead of @By(DataSource.REFERENCE), while still accurately calculating - * uncovered bases - * - * //todo -- make this a generic capability of Coverage and DiagnoseTargets - * - * - Modifies the global variable uncoveredBases - * - Uses global variables: intervalList and previousLocus - * - * takes into account that the traversal may have been due over a set of intervals, or over the whole genome. - * - * @param currentLocus the locus we are visiting right now - */ - private void tallyUncoveredBases(GenomeLoc currentLocus) { - long distance = 0; - if (previousLocus == null) { // first base visited - GenomeLocParser parser = getToolkit().getGenomeLocParser(); - if (intervalList.isEmpty()) { // if this is whole genome (no intervals requested), add what we missed. - final GenomeLoc zeroLoc = parser.createGenomeLoc(getToolkit().getSAMFileHeader().getSequence(0).getSequenceName(), 0, 1, 1); - distance += currentLocus.distanceAcrossContigs(zeroLoc, getToolkit().getSAMFileHeader()); - } else { // if we are running on an interval list, add all intervals before the current locus to the uncovered bases counter - while (!intervalList.peek().containsP(currentLocus)) { - GenomeLoc interval = intervalList.removeFirst(); - distance += interval.size(); - } - distance += currentLocus.getStart() - intervalList.peek().getStart(); // now this is the interval that contains the current locus. Discount the bases from the beginning. - } - } else { - final GenomeLoc previousInterval = intervalList.peekFirst(); // peekFirst returns null if interval list is empty (WGS). - distance = currentLocus.distanceAcrossContigs(previousLocus, getToolkit().getSAMFileHeader()) - 1; - if (previousInterval != null && !previousInterval.containsP(currentLocus)) { - intervalList.removeFirst(); // we're done with the previous interval - final GenomeLoc currentInterval = intervalList.peekFirst(); - distance -= currentInterval.distanceAcrossContigs(previousInterval, getToolkit().getSAMFileHeader()) - 1; - } - } - - uncoveredBases += distance; - } -} \ No newline at end of file diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/FindCoveredIntervals.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/FindCoveredIntervals.java index 6f1718430..f9d097dfa 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/FindCoveredIntervals.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/FindCoveredIntervals.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -69,10 +69,13 @@ import org.broadinstitute.gatk.utils.help.HelpConstants; import java.io.PrintStream; /** - * Outputs a list of intervals that are covered above a given threshold + * Outputs a list of intervals that are covered to or above a given threshold * - *

The output list can be used as an interval list for other tools. Note that if the -uncovered argument is given, the - * logic will be inverted and the tool will instead output intervals that fail the coverage threshold.

+ *

The output list can be used as an interval list for other tools. The logic can be inverted using the -uncovered argument argument to instead output intervals that fail the coverage threshold. + *

+ * + *

Application example: find and diagnose low-coverage regions

+ *

Run this toool first with the -uncovered argument to identify regions that have low coverage. Then run DiagnoseTargets on the output intervals to diagnose why they are poorly covered.

* *

Input

*

@@ -90,6 +93,8 @@ import java.io.PrintStream; * -T FindCoveredIntervals \ * -R reference.fasta \ * -I my_file.bam \ + * [-cov 10 \] + * [-uncovered \] * -o output.list * * @@ -157,4 +162,4 @@ public class FindCoveredIntervals extends ActiveRegionWalker { public void onTraversalDone(Long reduce) { logger.info(String.format("Found %d intervals", reduce)); } -} +} \ No newline at end of file diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/AbstractStratification.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/AbstractStratification.java index 1d52c4558..643c7ec2b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/AbstractStratification.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/AbstractStratification.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/CallableStatus.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/CallableStatus.java index ae56cd3e9..9a7f635a5 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/CallableStatus.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/CallableStatus.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java index 56097e625..b14046ec6 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -80,8 +80,7 @@ import java.util.*; * Analyze coverage distribution and validate read mates per interval and per sample * *

- * This tool is useful for diagnosing regions with bad coverage, mapping, or read mate pairs. It analyzes each sample - * independently and aggregates results over intervals of interest. + * This tool is useful for diagnosing regions with bad coverage, mapping, or read mate pairs. It analyzes each sample independently and aggregates results over intervals of interest. Low-coverage regions can be identified by using e.g. FindCoveredIntervals with the -uncovered argument. *

*

Input

*
    diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/IntervalMetric.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/IntervalMetric.java index 71249233d..5cd19038e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/IntervalMetric.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/IntervalMetric.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/IntervalStratification.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/IntervalStratification.java index 4261eee4c..53cdc11da 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/IntervalStratification.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/IntervalStratification.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetric.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetric.java index 20828854a..411fc9e49 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetric.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetric.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricCoverageGap.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricCoverageGap.java index 69b297dc0..b088b2184 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricCoverageGap.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricCoverageGap.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricExcessiveCoverage.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricExcessiveCoverage.java index 33b32df73..33b1f9adc 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricExcessiveCoverage.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricExcessiveCoverage.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricLowCoverage.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricLowCoverage.java index d7f0f01b1..fbfca4146 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricLowCoverage.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricLowCoverage.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricPoorQuality.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricPoorQuality.java index e6aed49b7..5c22a57ea 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricPoorQuality.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusMetricPoorQuality.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusStratification.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusStratification.java index d8af7e846..b20cf8250 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusStratification.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusStratification.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/Metric.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/Metric.java index b5ac8eaf1..6b219c30b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/Metric.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/Metric.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/PluginUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/PluginUtils.java index d7550b389..3d9aaaebd 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/PluginUtils.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/PluginUtils.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetric.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetric.java index 09325b706..b92f727bd 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetric.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetric.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetricBadMates.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetricBadMates.java index dc32b36e8..05e95e105 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetricBadMates.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetricBadMates.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetricNoReads.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetricNoReads.java index dea34836b..0a517bfaa 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetricNoReads.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleMetricNoReads.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleStratification.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleStratification.java index e4c8830f7..1d0d233da 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleStratification.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/SampleStratification.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/ThresHolder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/ThresHolder.java index 7201b29ab..9bb5da08d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/ThresHolder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/ThresHolder.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/Metrics.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/Metrics.java index 53c33c122..490343940 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/Metrics.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/Metrics.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervals.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervals.java index 36cf28696..6674faca6 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervals.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervals.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AFPriorProvider.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AFPriorProvider.java index 6bc7ea732..7e988e69b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AFPriorProvider.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AFPriorProvider.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleLikelihoodMatrixMapper.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleLikelihoodMatrixMapper.java index 54ea7da0a..c14540bb0 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleLikelihoodMatrixMapper.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleLikelihoodMatrixMapper.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/BaseMismatchModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/BaseMismatchModel.java index 3614de7b4..c2722c277 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/BaseMismatchModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/BaseMismatchModel.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ConsensusAlleleCounter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ConsensusAlleleCounter.java index 96f432dc1..90caf37a3 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ConsensusAlleleCounter.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ConsensusAlleleCounter.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/CustomAFPriorProvider.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/CustomAFPriorProvider.java index dd29ee205..caa264a00 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/CustomAFPriorProvider.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/CustomAFPriorProvider.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java index a2ce9a24d..fb2a22e8f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ErrorModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ErrorModel.java index 71587fe3e..1935ebe66 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ErrorModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ErrorModel.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java index 984215df3..1f4202418 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -143,11 +143,11 @@ public abstract class GeneralPloidyGenotypeLikelihoods { * of form int[] -> double (to be more precise, IntArrayWrapper -> Double). * For a given ploidy (chromosome count) and number of alleles, we need a form to iterate deterministically * across all possible allele conformations. - * Problem equivalent to listing in determistic order all possible ways in which N integers will sum to P, + * Problem equivalent to listing in deterministic order all possible ways in which N integers will sum to P, * where N is number of alleles and P is number of chromosomes. * There's an option to list all integers so that sum will be UP to P. * For example, with P=2,N=2, restrictSumTo = 2 iterator will produce - * [2 0 ] [1 1] [ 0 2] + * [2 0] [1 1] [0 2] * * */ @@ -331,7 +331,7 @@ public abstract class GeneralPloidyGenotypeLikelihoods { * @param numChromosomes Ploidy (number of chromosomes describing PL's) * @param originalAlleles List of original alleles * @param allelesToSubset Alleles to subset - * @return Vector of new PL's, ordered accorrding to SumIterator's ordering + * @return Vector of new PL's, ordered according to SumIterator's ordering */ public static double[] subsetToAlleles(final double[] oldLikelihoods, final int numChromosomes, final List originalAlleles, final List allelesToSubset) { @@ -339,14 +339,12 @@ public abstract class GeneralPloidyGenotypeLikelihoods { int newPLSize = GeneralPloidyGenotypeLikelihoods.getNumLikelihoodElements(allelesToSubset.size(), numChromosomes); double[] newPLs = new double[newPLSize]; - int idx = 0; // First fill boolean array stating whether each original allele is present in new mapping final boolean [] allelePresent = new boolean[originalAlleles.size()]; for ( Allele allele : originalAlleles ) allelePresent[idx++] = allelesToSubset.contains(allele); - // compute mapping from old idx to new idx // This might be needed in case new allele set is not ordered in the same way as old set // Example. Original alleles: {T*,C,G,A}. New alleles: {G,C}. Permutation key = [2,1] diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java index 49e49d82d..5c30fc6a0 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java index 3a65a3a9e..cd2986747 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java index c0e2ea95e..10e409309 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java index 6c9a9c7a5..8da146fe2 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java index 93b7524db..bbf3511ac 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCounts.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCounts.java index c7762996d..9c1e72edb 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCounts.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCounts.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculator.java index 9922483cc..c4dc9520b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculator.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculators.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculators.java index 058c744fb..ad5b8a9a9 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculators.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculators.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -317,10 +317,6 @@ public class GenotypeLikelihoodCalculators { public static GenotypeLikelihoodCalculator getInstance(final int ploidy, final int alleleCount) { checkPloidyAndMaximumAllele(ploidy, alleleCount); - if (alleleCount < 0) - throw new IllegalArgumentException("the allele count cannot be negative"); - if (ploidy < 0) - throw new IllegalArgumentException("the ploidy count cannot be negative"); // Non-thread safe (fast) check on tables capacities, // if not enough capacity we expand the tables in a thread-safe manner: diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java index b32f291f9..550817d2b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypePriors.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypePriors.java index 5f4fbb894..2e66ff201 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypePriors.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypePriors.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingData.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingData.java index c73690a84..024f15556 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingData.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingData.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java index 2439e6219..657054953 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -112,10 +112,11 @@ public abstract class GenotypingEngine getAppropriateVCFInfoHeaders() { - Set headerInfo = new HashSet<>(); + final Set headerInfo = new HashSet<>(); if ( configuration.genotypeArgs.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED ) headerInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.NUMBER_OF_DISCOVERED_ALLELES_KEY)); return headerInfo; @@ -191,7 +197,7 @@ public abstract class GenotypingEngine stratifiedContexts, final VariantContext vc, final GenotypeLikelihoodsCalculationModel.Model model, final boolean inheritAttributesFromInputVC, - final Map perReadAlleleLikelihoodMap) { + final Map perReadAlleleLikelihoodMap, + final boolean doAlleleSpecificCalcs) { final boolean limitedContext = tracker == null || refContext == null || rawContext == null || stratifiedContexts == null; // if input VC can't be genotyped, exit with either null VCC or, in case where we need to emit all sites, an empty call @@ -227,7 +234,7 @@ public abstract class GenotypingEngine -0.0 which isn't nice - double log10Confidence = + final double log10Confidence = ! outputAlternativeAlleles.siteIsMonomorphic || configuration.genotypingOutputMode == GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES || configuration.annotateAllSitesWithPLs ? AFresult.getLog10PosteriorOfAFEq0() + 0.0 @@ -238,10 +245,13 @@ public abstract class GenotypingEngine attributes = composeCallAttributes(inheritAttributesFromInputVC, vc, rawContext, stratifiedContexts, tracker, refContext, - outputAlternativeAlleles.alternativeAlleleMLECounts(), outputAlternativeAlleles.siteIsMonomorphic, AFresult, outputAlternativeAlleles.outputAlleles(vc.getReference()),genotypes,model,perReadAlleleLikelihoodMap); + outputAlternativeAlleles.alternativeAlleleMLECounts(), outputAlternativeAlleles.siteIsMonomorphic, AFresult, outputAlternativeAlleles.outputAlleles(vc.getReference()), genotypes, model, perReadAlleleLikelihoodMap, doAlleleSpecificCalcs); builder.attributes(attributes); @@ -334,8 +344,8 @@ public abstract class GenotypingEngine alleles = afcr.getAllelesUsedInGenotyping(); final int alternativeAlleleCount = alleles.size() - 1; - Allele[] outputAlleles = new Allele[alternativeAlleleCount]; - int[] mleCounts = new int[alternativeAlleleCount]; + final Allele[] outputAlleles = new Allele[alternativeAlleleCount]; + final int[] mleCounts = new int[alternativeAlleleCount]; int outputAlleleCount = 0; boolean siteIsMonomorphic = true; for (final Allele alternativeAllele : alleles) { @@ -375,25 +385,6 @@ public abstract class GenotypingEngine= configuration.genotypeArgs.STANDARD_CONFIDENCE_FOR_CALLING); } - /** - * Based in the model used, returns the appropriate heterozygosity argument value. - * @param model genotyping model. - * - * @return a valid heterozygosity in (0,1). - */ - private double getModelTheta(final GenotypeLikelihoodsCalculationModel.Model model) { - switch (model) { - case SNP: - case GENERALPLOIDYSNP: - return configuration.genotypeArgs.snpHeterozygosity; - case INDEL: - case GENERALPLOIDYINDEL: - return configuration.genotypeArgs.indelHeterozygosity; - default: - throw new IllegalArgumentException("Unexpected GenotypeCalculationModel " + model); - } - } - /** * Checks whether the variant context has too many alternative alleles for progress to genotyping the site. @@ -473,7 +464,7 @@ public abstract class GenotypingEngine contexts, double theta, boolean ignoreCoveredSamples, double initialPofRef) { + protected final VariantCallContext estimateReferenceConfidence(VariantContext vc, Map contexts, double log10OfTheta, boolean ignoreCoveredSamples, double initialPofRef) { if ( contexts == null ) return null; @@ -487,7 +478,7 @@ public abstract class GenotypingEngine= configuration.genotypeArgs.STANDARD_CONFIDENCE_FOR_CALLING, false); @@ -504,7 +495,7 @@ public abstract class GenotypingEnginetotal-ploidy(vc) + 1 positions. */ protected final double[] getAlleleFrequencyPriors( final VariantContext vc, final int defaultPloidy, final GenotypeLikelihoodsCalculationModel.Model model ) { - final int totalPloidy = GATKVariantContextUtils.totalPloidy(vc,defaultPloidy); + final int totalPloidy = GATKVariantContextUtils.totalPloidy(vc, defaultPloidy); switch (model) { case SNP: case GENERALPLOIDYSNP: @@ -523,16 +514,13 @@ public abstract class GenotypingEngine= 1) throw new IllegalArgumentException("theta must be greater than 0 and less than 1"); - final double log10PofNonRef = Math.log10(theta / 2.0) + getRefBinomialProbLog10(depth); + protected final double estimateLog10ReferenceConfidenceForOneSample(final int depth, final double log10OfTheta) { + final double log10PofNonRef = log10OfTheta + getRefBinomialProbLog10(depth); return MathUtils.log10OneMinusX(Math.pow(10.0, log10PofNonRef)); } @@ -558,14 +546,19 @@ public abstract class GenotypingEngine inputPriors) { + public static AFPriorProvider composeAlleleFrequencyPriorProvider(final int N, final double heterozygosity, final List inputPriors) { if (!inputPriors.isEmpty()) { // user-specified priors if (inputPriors.size() != N) throw new UserException.BadArgumentValue("inputPrior","Invalid length of inputPrior vector: vector length must be equal to # samples +1 "); + for (final Double prior : inputPriors) { + if (prior <= 0 || prior >= 1) throw new UserException.BadArgumentValue("inputPrior","inputPrior vector values must be greater than 0 and less than 1"); + } return new CustomAFPriorProvider(inputPriors); } else @@ -629,7 +622,8 @@ public abstract class GenotypingEngine composeCallAttributes(final boolean inheritAttributesFromInputVC, final VariantContext vc, final AlignmentContext rawContext, final Map stratifiedContexts, final RefMetaDataTracker tracker, final ReferenceContext refContext, final List alleleCountsofMLE, final boolean bestGuessIsRef, final AFCalculationResult AFresult, final List allAllelesToUse, final GenotypesContext genotypes, - final GenotypeLikelihoodsCalculationModel.Model model, final Map perReadAlleleLikelihoodMap) { + final GenotypeLikelihoodsCalculationModel.Model model, final Map perReadAlleleLikelihoodMap, + final boolean doAlleleSpecificCalcs) { final HashMap attributes = new HashMap<>(); final boolean limitedContext = tracker == null || refContext == null || rawContext == null || stratifiedContexts == null; @@ -651,6 +645,22 @@ public abstract class GenotypingEngine perAlleleQuals = new ArrayList<>(); + //Per-allele quals are not calculated for biallelic sites + if (AFresult.getAllelesUsedInGenotyping().size() > 2) { + for (final Allele a : allAllelesToUse) { + if (a.isNonReference()) + perAlleleQuals.add(AFresult.getLog10PosteriorOfAFEq0ForAllele(a)); + } + } + else { + perAlleleQuals.add(AFresult.getLog10PosteriorOfAFEq0()); + } + + attributes.put(GATKVCFConstants.AS_QUAL_KEY, perAlleleQuals); + } return attributes; } @@ -668,4 +678,50 @@ public abstract class GenotypingEngine 0 is at all plausible. + boolean mapACeq0 = true; + for (int AC = 1; AC < log10Priors.length; AC++) + if (log10Priors[AC] + log10GenotypeLikelihoods[AC] > log10ACeq0Posterior) { + mapACeq0 = false; + break; + } + if (mapACeq0) + return 0.0; + + //TODO bad way to calculate AC > 0 posterior that follows the current behaviour of ExactAFCalculator (StateTracker) + //TODO this is the lousy part... this code just adds up lks and priors of AC != 0 before as if + //TODO Sum(a_i * b_i) is equivalent to Sum(a_i) * Sum(b_i) + //TODO This has to be changed not just here but also in the AFCalculators (StateTracker). + final double log10ACgt0Likelihood = MathUtils.approximateLog10SumLog10(log10GenotypeLikelihoods, 1, log10GenotypeLikelihoods.length); + final double log10ACgt0Prior = MathUtils.approximateLog10SumLog10(log10Priors, 1, log10Priors.length); + final double log10ACgt0Posterior = log10ACgt0Likelihood + log10ACgt0Prior; + final double log10PosteriorNormalizationConstant = MathUtils.approximateLog10SumLog10(log10ACeq0Posterior, log10ACgt0Posterior); + //TODO End of lousy part. + + final double normalizedLog10ACeq0Posterior = log10ACeq0Posterior - log10PosteriorNormalizationConstant; + // This is another condition to return a 0.0 also present in AFCalculator code as well. + if (normalizedLog10ACeq0Posterior >= QualityUtils.qualToErrorProbLog10(configuration.genotypeArgs.STANDARD_CONFIDENCE_FOR_EMITTING)) + return 0.0; + + return 1.0 - Math.pow(10.0, normalizedLog10ACeq0Posterior); + } + } } diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingLikelihoods.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingLikelihoods.java index f06a40b73..d016f19fd 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingLikelihoods.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingLikelihoods.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingModel.java index 4dfb8d312..983c81f07 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingModel.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingOutputMode.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingOutputMode.java index e7669971f..683c74d9b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingOutputMode.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingOutputMode.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/HeterozygosityAFPriorProvider.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/HeterozygosityAFPriorProvider.java index 3466c2a94..187923cc4 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/HeterozygosityAFPriorProvider.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/HeterozygosityAFPriorProvider.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModel.java index dee370eec..79f2725e4 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModel.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java index 7ee4a9aca..a3d6abb07 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModel.java index 1589e8374..a1aa8b66d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModel.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/OutputMode.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/OutputMode.java index c3a2e3b63..d6410fd86 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/OutputMode.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/OutputMode.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/PloidyModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/PloidyModel.java index 1ad1a2241..902b89466 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/PloidyModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/PloidyModel.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/PoolGenotypePriors.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/PoolGenotypePriors.java index eb6b061e3..80da4cb10 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/PoolGenotypePriors.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/PoolGenotypePriors.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ProbabilityVector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ProbabilityVector.java index 3767aa676..7f728db14 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ProbabilityVector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ProbabilityVector.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java index 9f8e88fac..7497a22d0 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollection.java index b2bd306fc..873752bdd 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollection.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollection.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedArgumentCollection.java index 08e13da1b..da04daca7 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedArgumentCollection.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedArgumentCollection.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyper.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyper.java index bfcfd91c2..6a96d4b9f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyper.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyper.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotypingEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotypingEngine.java index b51f96735..b486d6b6c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotypingEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotypingEngine.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -96,6 +96,8 @@ public class UnifiedGenotypingEngine extends GenotypingEngine stratifiedContexts = getFilteredAndStratifiedContexts(refContext, rawContext, model); - return calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model, null); + return calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model, null, false); } /** @@ -293,7 +315,19 @@ public class UnifiedGenotypingEngine extends GenotypingEngine stratifiedContexts, + final VariantContext vc, final GenotypeLikelihoodsCalculationModel.Model model, + final boolean inheritAttributesFromInputVC, + final Map perReadAlleleLikelihoodMap) { + return calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model, inheritAttributesFromInputVC, perReadAlleleLikelihoodMap, false); } public VariantCallContext calculateGenotypes(final RefMetaDataTracker tracker, @@ -328,8 +370,9 @@ public class UnifiedGenotypingEngine extends GenotypingEngine stratifiedContexts, final VariantContext vc, final GenotypeLikelihoodsCalculationModel.Model model, - final Map perReadAlleleLikelihoodMap) { - return calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model, false, perReadAlleleLikelihoodMap); + final Map perReadAlleleLikelihoodMap, + final boolean useAlleleSpecificCalcs) { + return calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model, false, perReadAlleleLikelihoodMap, useAlleleSpecificCalcs); } @Override @@ -342,9 +385,10 @@ public class UnifiedGenotypingEngine extends GenotypingEngine stratifiedContexts, final VariantContext vc, final GenotypeLikelihoodsCalculationModel.Model model, final boolean inheritAttributesFromInputVC, - final Map perReadAlleleLikelihoodMap) { + final Map perReadAlleleLikelihoodMap, + final boolean useAlleleSpecificCalcs) { boolean limitedContext = tracker == null || refContext == null || rawContext == null || stratifiedContexts == null; - final VariantCallContext result = super.calculateGenotypes(tracker,refContext,rawContext,stratifiedContexts,vc,model,inheritAttributesFromInputVC,perReadAlleleLikelihoodMap); + final VariantCallContext result = super.calculateGenotypes(tracker,refContext,rawContext,stratifiedContexts,vc,model,inheritAttributesFromInputVC,perReadAlleleLikelihoodMap, useAlleleSpecificCalcs); if ( verboseWriter != null && !limitedContext ) printVerboseData(refContext.getLocus().toString(), vc, model); return result; @@ -365,9 +409,10 @@ public class UnifiedGenotypingEngine extends GenotypingEngine composeCallAttributes(final boolean inheritAttributesFromInputVC, final VariantContext vc, final AlignmentContext rawContext, final Map stratifiedContexts, final RefMetaDataTracker tracker, final ReferenceContext refContext, final List alleleCountsofMLE, final boolean bestGuessIsRef, final AFCalculationResult AFresult, final List allAllelesToUse, final GenotypesContext genotypes, - final GenotypeLikelihoodsCalculationModel.Model model, final Map perReadAlleleLikelihoodMap) { + final GenotypeLikelihoodsCalculationModel.Model model, final Map perReadAlleleLikelihoodMap, + final boolean useAlleleSpecificCalcs) { final Map result = super.composeCallAttributes(inheritAttributesFromInputVC, vc,rawContext,stratifiedContexts,tracker,refContext,alleleCountsofMLE,bestGuessIsRef, - AFresult,allAllelesToUse,genotypes,model,perReadAlleleLikelihoodMap); + AFresult,allAllelesToUse,genotypes,model,perReadAlleleLikelihoodMap, useAlleleSpecificCalcs); final boolean limitedContext = tracker == null || refContext == null || rawContext == null || stratifiedContexts == null; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/VariantCallContext.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/VariantCallContext.java index c02d0552c..ec9d048f1 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/VariantCallContext.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/VariantCallContext.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculationResult.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculationResult.java index 9e4bd3e09..b1286480c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculationResult.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculationResult.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -102,7 +102,7 @@ public class AFCalculationResult { final Map log10pRefByAllele) { if ( allelesUsedInGenotyping == null || allelesUsedInGenotyping.size() < 1 ) throw new IllegalArgumentException("allelesUsedInGenotyping must be non-null list of at least 1 value " + allelesUsedInGenotyping); if ( alleleCountsOfMLE == null ) throw new IllegalArgumentException("alleleCountsOfMLE cannot be null"); - if ( alleleCountsOfMLE.length != allelesUsedInGenotyping.size() - 1) throw new IllegalArgumentException("alleleCountsOfMLE.length " + alleleCountsOfMLE.length + " != allelesUsedInGenotyping.size() " + allelesUsedInGenotyping.size()); + if ( alleleCountsOfMLE.length != allelesUsedInGenotyping.size() - 1) throw new IllegalArgumentException("alleleCountsOfMLE.length " + alleleCountsOfMLE.length + " != number of alternate alleles used in genotyping " + (allelesUsedInGenotyping.size() - 1)); if ( nEvaluations < 0 ) throw new IllegalArgumentException("nEvaluations must be >= 0 but saw " + nEvaluations); if ( log10LikelihoodsOfAC.length != 2 ) throw new IllegalArgumentException("log10LikelihoodsOfAC must have length equal 2"); if ( log10PriorsOfAC.length != 2 ) throw new IllegalArgumentException("log10PriorsOfAC must have length equal 2"); diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculator.java index 0f243aed9..33c5114e7 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculator.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorFactory.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorFactory.java index a44c2a0c6..68e10f746 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorFactory.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorFactory.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorImplementation.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorImplementation.java index b3c274ef1..f4c188374 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorImplementation.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorImplementation.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -65,7 +65,7 @@ import java.util.Map; */ public enum AFCalculatorImplementation { - /** default implementation */ + /** Fast implementation for multi-allelics (equivalent to {@link #EXACT_REFERENCE} for biallelics sites */ EXACT_INDEPENDENT(IndependentAllelesDiploidExactAFCalculator.class, 2), /** reference implementation of multi-allelic EXACT model. Extremely slow for many alternate alleles */ @@ -75,7 +75,12 @@ public enum AFCalculatorImplementation { EXACT_ORIGINAL(OriginalDiploidExactAFCalculator.class, 2, 2), /** implementation that supports any sample ploidy. Currently not available for the HaplotypeCaller */ - EXACT_GENERAL_PLOIDY(GeneralPloidyExactAFCalculator.class); + EXACT_GENERAL_PLOIDY(GeneralPloidyExactAFCalculator.class), + + /** + * Implementation that implements the {@link #EXACT_INDEPENDENT} for any ploidy. + */ + EXACT_GENERAL_INDEPENDENT(IndependentAllelesExactAFCalculator.class); /** * Special max alt allele count indicating that this maximum is in fact unbound (can be anything). @@ -180,7 +185,7 @@ public enum AFCalculatorImplementation { } /** - * Creates new instance + * Creates new instance. * * @throws IllegalStateException if the instance could not be create due to some exception. The {@link Exception#getCause() cause} will hold a reference to the actual exception. * @return never {@code null}. @@ -205,11 +210,14 @@ public enum AFCalculatorImplementation { final AFCalculatorImplementation preferredValue = preferred == null ? DEFAULT : preferred; if (preferredValue.usableForParams(requiredPloidy,requiredAlternativeAlleleCount)) return preferredValue; - if (EXACT_INDEPENDENT.usableForParams(requiredPloidy,requiredAlternativeAlleleCount)) + else if (EXACT_INDEPENDENT.usableForParams(requiredPloidy,requiredAlternativeAlleleCount)) return EXACT_INDEPENDENT; - if (EXACT_REFERENCE.usableForParams(requiredPloidy,requiredAlternativeAlleleCount)) + else if (EXACT_REFERENCE.usableForParams(requiredPloidy,requiredAlternativeAlleleCount)) return EXACT_REFERENCE; - return EXACT_GENERAL_PLOIDY; + else if (EXACT_GENERAL_INDEPENDENT.usableForParams(requiredPloidy,requiredAlternativeAlleleCount)) + return EXACT_GENERAL_INDEPENDENT; + else + return EXACT_GENERAL_PLOIDY; } /** diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorPerformanceTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorPerformanceTest.java index e97b9ca79..727b1b32d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorPerformanceTest.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorPerformanceTest.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorProvider.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorProvider.java index 5a0e4c1c7..9025c3481 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorProvider.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorProvider.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorTestBuilder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorTestBuilder.java index 108aeb8f6..d5abda74b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorTestBuilder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorTestBuilder.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -52,7 +52,9 @@ package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc; import org.apache.commons.lang.ArrayUtils; +import org.broadinstitute.gatk.tools.walkers.genotyper.AFPriorProvider; import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine; +import org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine; import org.broadinstitute.gatk.utils.MathUtils; import org.broadinstitute.gatk.utils.Utils; import htsjdk.variant.variantcontext.*; @@ -111,6 +113,7 @@ public class AFCalculatorTestBuilder { public double[] makePriors() { final int nPriorValues = 2*nSamples+1; + final double human_theta = 0.001; switch ( priorType ) { case flat: @@ -118,8 +121,9 @@ public class AFCalculatorTestBuilder { //TODO break dependency with human... avoid special reference to this species. case human: - final double[] humanPriors = new double[nPriorValues]; - GenotypingEngine.computeAlleleFrequencyPriors(nPriorValues - 1, humanPriors, 0.001, new ArrayList()); + + final AFPriorProvider log10priorProvider = GenotypingEngine.composeAlleleFrequencyPriorProvider(2*nSamples, human_theta, new ArrayList()); + final double[] humanPriors = log10priorProvider.forTotalPloidy(2*nSamples); return humanPriors; default: throw new RuntimeException("Unexpected type " + priorType); diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ConcurrentAFCalculatorProvider.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ConcurrentAFCalculatorProvider.java index 64c38ca24..ae1e07b96 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ConcurrentAFCalculatorProvider.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ConcurrentAFCalculatorProvider.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/DiploidExactAFCalculator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/DiploidExactAFCalculator.java index 3bdc53f1e..fee15363e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/DiploidExactAFCalculator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/DiploidExactAFCalculator.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactACcounts.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactACcounts.java index 5696b6667..64e0199ee 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactACcounts.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactACcounts.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactACset.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactACset.java index e5879dfa1..402e6b257 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactACset.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactACset.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactAFCalculator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactAFCalculator.java index 3437c6da3..fb1e57f3f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactAFCalculator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactAFCalculator.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -64,6 +64,10 @@ import java.util.*; abstract class ExactAFCalculator extends AFCalculator { protected static final int HOM_REF_INDEX = 0; // AA likelihoods are always first + + // useful so that we don't keep printing out the same warning message + protected static boolean printedWarning = false; + /** * Sorts {@link ExactAFCalculator.LikelihoodSum} instances where those with higher likelihood are first. */ @@ -152,23 +156,29 @@ abstract class ExactAFCalculator extends AFCalculator { if (altAlleleReduction == 0) return vc; - else if (altAlleleReduction != 0) { - logger.warn("this tool is currently set to genotype at most " + maximumAlternativeAlleles - + " alternate alleles in a given context, but the context at " + vc.getChr() + ":" + vc.getStart() - + " has " + (vc.getAlternateAlleles().size()) - + " alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument"); - final List alleles = new ArrayList<>(maximumAlternativeAlleles + 1); - alleles.add(vc.getReference()); - alleles.addAll(reduceScopeAlleles(vc, defaultPloidy, maximumAlternativeAlleles)); - final VariantContextBuilder builder = new VariantContextBuilder(vc); - builder.alleles(alleles); - builder.genotypes(reduceScopeGenotypes(vc, defaultPloidy, alleles)); - if (altAlleleReduction < 0) - throw new IllegalStateException("unexpected: reduction increased the number of alt. alleles!: " + - altAlleleReduction + " " + vc + " " + builder.make()); - return builder.make(); - } else // if (altAlleleReduction < 0) - throw new IllegalStateException("unexpected: reduction increased the number of alt. alleles!: " + - altAlleleReduction + " " + vc); + String message = "this tool is currently set to genotype at most " + maximumAlternativeAlleles + + " alternate alleles in a given context, but the context at " + vc.getContig() + ":" + vc.getStart() + + " has " + (vc.getAlternateAlleles().size()) + + " alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument"; + + if ( !printedWarning ) { + printedWarning = true; + message += ". This warning message is output just once per run and further warnings will be suppressed unless the DEBUG logging level is used."; + logger.warn(message); + } else { + logger.debug(message); + } + + final List alleles = new ArrayList<>(maximumAlternativeAlleles + 1); + alleles.add(vc.getReference()); + alleles.addAll(reduceScopeAlleles(vc, defaultPloidy, maximumAlternativeAlleles)); + final VariantContextBuilder builder = new VariantContextBuilder(vc); + builder.alleles(alleles); + builder.genotypes(reduceScopeGenotypes(vc, defaultPloidy, alleles)); + if (altAlleleReduction < 0) + throw new IllegalStateException("unexpected: reduction increased the number of alt. alleles!: " + - altAlleleReduction + " " + vc + " " + builder.make()); + return builder.make(); } /** diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactCallLogger.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactCallLogger.java index 5927b7561..dee29073b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactCallLogger.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ExactCallLogger.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProvider.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProvider.java index 53bfbcbe6..58f2b8763 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProvider.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProvider.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyExactAFCalculator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyExactAFCalculator.java index e5f205e63..5c5d1eac0 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyExactAFCalculator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyExactAFCalculator.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -59,6 +59,7 @@ import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodCalcula import org.broadinstitute.gatk.utils.MathUtils; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.gatk.utils.variant.GATKVCFConstants; import java.util.*; @@ -66,15 +67,12 @@ public class GeneralPloidyExactAFCalculator extends ExactAFCalculator { static final int MAX_LENGTH_FOR_POOL_PL_LOGGING = 100; // if PL vectors longer than this # of elements, don't log them - - private final static boolean VERBOSE = false; - protected GeneralPloidyExactAFCalculator() { } @Override protected GenotypesContext reduceScopeGenotypes(final VariantContext vc, final int defaultPloidy, final List allelesToUse) { - return subsetAlleles(vc,defaultPloidy,allelesToUse,false); + return subsetAlleles(vc, defaultPloidy, allelesToUse, false); } @Override @@ -229,9 +227,6 @@ public class GeneralPloidyExactAFCalculator extends ExactAFCalculator { // clean up memory indexesToACset.remove(ACset.getACcounts()); - if ( VERBOSE ) - System.out.printf(" *** removing used set=%s%n", ACset.getACcounts()); - } return newPool; } @@ -301,68 +296,6 @@ public class GeneralPloidyExactAFCalculator extends ExactAFCalculator { } -// /** -// * Naive combiner of two multiallelic pools - number of alt alleles must be the same. -// * Math is generalization of biallelic combiner. -// * -// * For vector K representing an allele count conformation, -// * Pr(D | AC = K) = Sum_G Pr(D|AC1 = G) Pr (D|AC2=K-G) * F(G,K) -// * where F(G,K) = choose(m1,[g0 g1 ...])*choose(m2,[...]) / choose(m1+m2,[k1 k2 ...]) -// * @param originalPool First log-likelihood pool GL vector -// * @param yy Second pool GL vector -// * @param ploidy1 Ploidy of first pool (# of chromosomes in it) -// * @param ploidy2 Ploidy of second pool -// * @param numAlleles Number of alleles -// * @param log10AlleleFrequencyPriors Array of biallelic priors -// * @param resultTracker Af calculation result object -// */ -// public static void combineMultiallelicPoolNaively(CombinedPoolLikelihoods originalPool, double[] yy, int ploidy1, int ploidy2, int numAlleles, -// final double[] log10AlleleFrequencyPriors, -// final AFCalcResultTracker resultTracker) { -///* -// final int dim1 = GenotypeLikelihoods.numLikelihoods(numAlleles, ploidy1); -// final int dim2 = GenotypeLikelihoods.numLikelihoods(numAlleles, ploidy2); -// -// if (dim1 != originalPool.getLength() || dim2 != yy.length) -// throw new ReviewedGATKException("BUG: Inconsistent vector length"); -// -// if (ploidy2 == 0) -// return; -// -// final int newPloidy = ploidy1 + ploidy2; -// -// // Say L1(K) = Pr(D|AC1=K) * choose(m1,K) -// // and L2(K) = Pr(D|AC2=K) * choose(m2,K) -// GeneralPloidyGenotypeLikelihoods.SumIterator firstIterator = new GeneralPloidyGenotypeLikelihoods.SumIterator(numAlleles,ploidy1); -// final double[] x = originalPool.getLikelihoodsAsVector(true); -// while(firstIterator.hasNext()) { -// x[firstIterator.getLinearIndex()] += MathUtils.log10MultinomialCoefficient(ploidy1,firstIterator.getCurrentVector()); -// firstIterator.next(); -// } -// -// GeneralPloidyGenotypeLikelihoods.SumIterator secondIterator = new GeneralPloidyGenotypeLikelihoods.SumIterator(numAlleles,ploidy2); -// final double[] y = yy.clone(); -// while(secondIterator.hasNext()) { -// y[secondIterator.getLinearIndex()] += MathUtils.log10MultinomialCoefficient(ploidy2,secondIterator.getCurrentVector()); -// secondIterator.next(); -// } -// -// // initialize output to -log10(choose(m1+m2,[k1 k2...]) -// final int outputDim = GenotypeLikelihoods.numLikelihoods(numAlleles, newPloidy); -// final GeneralPloidyGenotypeLikelihoods.SumIterator outputIterator = new GeneralPloidyGenotypeLikelihoods.SumIterator(numAlleles,newPloidy); -// -// -// // Now, result(K) = logSum_G (L1(G)+L2(K-G)) where G are all possible vectors that sum UP to K -// while(outputIterator.hasNext()) { -// final ExactACset set = new ExactACset(1, new ExactACcounts(outputIterator.getCurrentAltVector())); -// double likelihood = computeLofK(set, x,y, log10AlleleFrequencyPriors, numAlleles, ploidy1, ploidy2, result); -// -// originalPool.add(likelihood, set, outputIterator.getLinearIndex()); -// outputIterator.next(); -// } -//*/ -// } - /** * Compute likelihood of a particular AC conformation and update AFresult object * @param set Set of AC counts to compute @@ -473,79 +406,125 @@ public class GeneralPloidyExactAFCalculator extends ExactAFCalculator { /** * From a given variant context, extract a given subset of alleles, and update genotype context accordingly, - * including updating the PL's, and assign genotypes accordingly + * including updating the PLs, ADs and SACs, and assign genotypes accordingly * @param vc variant context with alleles and genotype likelihoods * @param defaultPloidy ploidy to assume in case that {@code vc} does not contain that information * for a sample. * @param allelesToUse alleles to subset * @param assignGenotypes true: assign hard genotypes, false: leave as no-call - * @return GenotypesContext with new PLs + * @return GenotypesContext with new PLs, SACs and AD. */ + @Override public GenotypesContext subsetAlleles(final VariantContext vc, final int defaultPloidy, final List allelesToUse, final boolean assignGenotypes) { - // the genotypes with PLs - final GenotypesContext oldGTs = vc.getGenotypes(); - // samples - final List sampleIndices = oldGTs.getSampleNamesOrderedByName(); + final GenotypesContext result = GenotypesContext.create(); - // the new genotypes to create - final GenotypesContext newGTs = GenotypesContext.create(); + // Subset genotypes for each sample + for (final Genotype g : vc.getGenotypes()) // If it really needs to process order by sample name do so. + result.add(subsetGenotypeAlleles(g, allelesToUse, vc, defaultPloidy, assignGenotypes)); + return GATKVariantContextUtils.fixADFromSubsettedAlleles(result, vc, allelesToUse); + } + + /** + * From a given genotype, extract a given subset of alleles and update genotype PLs and SACs. + * @param g genotype to subset + * @param allelesToUse alleles to subset + * @param vc variant context with alleles and genotypes + * @param defaultPloidy ploidy to assume in case that {@code vc} does not contain that information for a sample. + * @param assignGenotypes true: assign hard genotypes, false: leave as no-call + * @return Genotypes with new PLs and SACs + */ + private Genotype subsetGenotypeAlleles(final Genotype g, final List allelesToUse, final VariantContext vc, final int defaultPloidy, + boolean assignGenotypes) { + final int ploidy = g.getPloidy() <= 0 ? defaultPloidy : g.getPloidy(); + if (!g.hasLikelihoods()) + return GenotypeBuilder.create(g.getSampleName(),GATKVariantContextUtils.noCallAlleles(ploidy)); + else { + // subset likelihood alleles + final double[] newLikelihoods = subsetLikelihoodAlleles(g, allelesToUse, vc, ploidy); + if (MathUtils.sum(newLikelihoods) > GATKVariantContextUtils.SUM_GL_THRESH_NOCALL) + return GenotypeBuilder.create(g.getSampleName(), GATKVariantContextUtils.noCallAlleles(ploidy)); + else // just now we would care about newSACs + return subsetGenotypeAllelesWithLikelihoods(g, allelesToUse, vc, ploidy, assignGenotypes, newLikelihoods); + } + } + + /** + * From a given genotype, extract a given subset of alleles and return the new PLs + * @param g genotype to subset + * @param allelesToUse alleles to subset + * @param vc variant context with alleles and genotypes + * @param ploidy number of chromosomes + * @return the subsetted PLs + */ + private double[] subsetLikelihoodAlleles(final Genotype g, final List allelesToUse, final VariantContext vc, final int ploidy){ // we need to determine which of the alternate alleles (and hence the likelihoods) to use and carry forward final int numOriginalAltAlleles = vc.getAlternateAlleles().size(); final int numNewAltAlleles = allelesToUse.size() - 1; + // create the new likelihoods array from the alleles we are allowed to use + final double[] originalLikelihoods = g.getLikelihoods().getAsVector(); - // create the new genotypes - for ( int k = 0; k < oldGTs.size(); k++ ) { - final Genotype g = oldGTs.get(sampleIndices.get(k)); - final int declaredPloidy = g.getPloidy(); - final int ploidy = declaredPloidy <= 0 ? defaultPloidy : declaredPloidy; - if ( !g.hasLikelihoods() ) { - newGTs.add(GenotypeBuilder.create(g.getSampleName(),GATKVariantContextUtils.noCallAlleles(ploidy))); - continue; - } - - // create the new likelihoods array from the alleles we are allowed to use - final double[] originalLikelihoods = g.getLikelihoods().getAsVector(); - double[] newLikelihoods; - - // Optimization: if # of new alt alleles = 0 (pure ref call), keep original likelihoods so we skip normalization - // and subsetting - if ( numOriginalAltAlleles == numNewAltAlleles || numNewAltAlleles == 0) { - newLikelihoods = originalLikelihoods; - } else { - newLikelihoods = GeneralPloidyGenotypeLikelihoods.subsetToAlleles(originalLikelihoods, ploidy, vc.getAlleles(), allelesToUse); - - // might need to re-normalize - newLikelihoods = MathUtils.normalizeFromLog10(newLikelihoods, false, true); - } - - // if there is no mass on the (new) likelihoods, then just no-call the sample - if ( MathUtils.sum(newLikelihoods) > GATKVariantContextUtils.SUM_GL_THRESH_NOCALL ) { - newGTs.add(GenotypeBuilder.create(g.getSampleName(), GATKVariantContextUtils.noCallAlleles(ploidy))); - } - else { - final GenotypeBuilder gb = new GenotypeBuilder(g); - - if ( numNewAltAlleles == 0 ) - gb.noPL(); - else - gb.PL(newLikelihoods); - - // if we weren't asked to assign a genotype, then just no-call the sample - if ( !assignGenotypes || MathUtils.sum(newLikelihoods) > GATKVariantContextUtils.SUM_GL_THRESH_NOCALL ) - gb.alleles(GATKVariantContextUtils.noCallAlleles(ploidy)); - else - assignGenotype(gb, newLikelihoods, allelesToUse, ploidy); - newGTs.add(gb.make()); - } + if ( numOriginalAltAlleles != numNewAltAlleles ) { + // might need to re-normalize the new likelihoods + return MathUtils.normalizeFromLog10(GeneralPloidyGenotypeLikelihoods.subsetToAlleles(originalLikelihoods, ploidy, vc.getAlleles(), allelesToUse), + false, true); } + else + return originalLikelihoods; + } - return newGTs; + /** + * From a given genotype, subset the PLs and SACs + * @param g genotype to subset + * @param allelesToUse alleles to subset + * @param vc variant context with alleles and genotypes + * @param ploidy number of chromosomes + * @param assignGenotypes true: assign hard genotypes, false: leave as no-call + * @param newLikelihoods the PL values + * @return genotype with the subsetted PLsL and SACs + */ + private Genotype subsetGenotypeAllelesWithLikelihoods(final Genotype g, final List allelesToUse, final VariantContext vc, int ploidy, + final boolean assignGenotypes, final double[] newLikelihoods) { + final GenotypeBuilder gb = new GenotypeBuilder(g); + + // add likelihoods + gb.PL(newLikelihoods); + + // get and add subsetted SACs + final int[] newSACs = subsetSACAlleles(g, allelesToUse, vc); + if (newSACs != null) + gb.attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, newSACs); + if (assignGenotypes) + assignGenotype(gb, newLikelihoods, allelesToUse, ploidy); + else + gb.alleles(GATKVariantContextUtils.noCallAlleles(ploidy)); + + return gb.make(); + } + + /** + * From a given genotype, extract a given subset of alleles and return the new SACs + * @param g genotype to subset + * @param allelesToUse alleles to subset + * @param vc variant context with alleles and genotypes + * @return the subsetted SACs + */ + private int[] subsetSACAlleles(final Genotype g, final List allelesToUse, final VariantContext vc){ + + if ( !g.hasExtendedAttribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY) ) + return null; + + // we need to determine which of the alternate alleles (and hence the likelihoods) to use and carry forward + final int numOriginalAltAlleles = vc.getAlternateAlleles().size(); + final int numNewAltAlleles = allelesToUse.size() - 1; + final List sacIndexesToUse = numOriginalAltAlleles == numNewAltAlleles ? null : GATKVariantContextUtils.determineSACIndexesToUse(vc, allelesToUse); + + return GATKVariantContextUtils.makeNewSACs(g, sacIndexesToUse); } /** @@ -553,7 +532,7 @@ public class GeneralPloidyExactAFCalculator extends ExactAFCalculator { * * @param newLikelihoods the PL array * @param allelesToUse the list of alleles to choose from (corresponding to the PLs) - * @param numChromosomes Number of chromosomes per pool + * @param numChromosomes Number of chromosomes per pool */ private void assignGenotype(final GenotypeBuilder gb, final double[] newLikelihoods, diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyFailOverAFCalculatorProvider.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyFailOverAFCalculatorProvider.java index 13d9b0e20..bc62af664 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyFailOverAFCalculatorProvider.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyFailOverAFCalculatorProvider.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -81,7 +81,7 @@ public class GeneralPloidyFailOverAFCalculatorProvider extends AFCalculatorProvi preferredImplementation = AFCalculatorImplementation.bestValue(genotypeArgs.samplePloidy,genotypeArgs.MAX_ALTERNATE_ALLELES, null); preferred = preferredImplementation.newInstance(); preferred.setLogger(logger); - failOver = AFCalculatorImplementation.EXACT_GENERAL_PLOIDY.newInstance(); + failOver = AFCalculatorImplementation.EXACT_GENERAL_INDEPENDENT.newInstance(); failOver.setLogger(logger); } diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAlleleAFCalculationResult.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAlleleAFCalculationResult.java new file mode 100644 index 000000000..491c2a2f5 --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAlleleAFCalculationResult.java @@ -0,0 +1,75 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ +package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc; + +import htsjdk.variant.variantcontext.Allele; + +import java.util.List; +import java.util.Map; + +/** + * Trivial subclass that helps with debugging by keeping track of the supporting information for this joint call + */ +class IndependentAlleleAFCalculationResult extends AFCalculationResult { + /** + * List of the supporting bi-allelic AFCalcResults that went into making this multi-allelic joint call + */ + final List supporting; + + IndependentAlleleAFCalculationResult(final int[] alleleCountsOfMLE, final int nEvaluations, + final List allelesUsedInGenotyping, final double[] log10LikelihoodsOfAC, + final double[] log10PriorsOfAC, + final Map log10pRefByAllele, final List supporting) { + super(alleleCountsOfMLE, nEvaluations, allelesUsedInGenotyping, log10LikelihoodsOfAC, + log10PriorsOfAC, log10pRefByAllele); + this.supporting = supporting; + } +} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalculator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalculator.java index 4ca9d7a56..f95c4f648 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalculator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalculator.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -109,22 +109,14 @@ import java.util.*; * XB = AB + BC * BB = BB * - * After each allele has its probability calculated we compute the joint posterior - * as P(D | AF_* == 0) = prod_i P (D | AF_i == 0), after applying the theta^i - * prior for the ith least likely allele. + * The posterior of the site being a variant site is calculated using + * the likelihood of the AF whe all alternatives are collapsed to be zero. */ public class IndependentAllelesDiploidExactAFCalculator extends DiploidExactAFCalculator { - /** - * The min. confidence of an allele to be included in the joint posterior. - */ - private final static double MIN_LOG10_CONFIDENCE_TO_INCLUDE_ALLELE_IN_POSTERIOR = Math.log10(1e-10); - private final static int[] BIALLELIC_NON_INFORMATIVE_PLS = new int[]{0,0,0}; private final static List BIALLELIC_NOCALL = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL); - - /** * Sorts AFCalcResults by their posteriors of AF > 0, so the */ @@ -147,21 +139,6 @@ import java.util.*; biAlleleExactModel = new ReferenceDiploidExactAFCalculator(); } - /** - * Trivial subclass that helps with debugging by keeping track of the supporting information for this joint call - */ - private static class MyAFCalculationResult extends AFCalculationResult { - /** - * List of the supporting bi-allelic AFCalcResults that went into making this multi-allelic joint call - */ - final List supporting; - - private MyAFCalculationResult(int[] alleleCountsOfMLE, int nEvaluations, List allelesUsedInGenotyping, double[] log10LikelihoodsOfAC, double[] log10PriorsOfAC, Map log10pRefByAllele, List supporting) { - super(alleleCountsOfMLE, nEvaluations, allelesUsedInGenotyping, log10LikelihoodsOfAC, log10PriorsOfAC, log10pRefByAllele); - this.supporting = supporting; - } - } - @Override public AFCalculationResult computeLog10PNonRef(final VariantContext vc, final int defaultPloidy, final double[] log10AlleleFrequencyPriors, final StateTracker stateTracker) { @@ -247,21 +224,6 @@ import java.util.*; return results; } - /** - * Helper function to ensure that the computeAlleleIndependentExact is returning reasonable results - */ - private static boolean goodIndependentResult(final VariantContext vc, final List results) { - if ( results.size() != vc.getNAlleles() - 1) return false; - for ( int i = 0; i < results.size(); i++ ) { - if ( results.get(i).getAllelesUsedInGenotyping().size() != 2 ) - return false; - if ( ! results.get(i).getAllelesUsedInGenotyping().contains(vc.getAlternateAllele(i)) ) - return false; - } - - return true; - } - /** * Returns the bi-allelic variant context for each alt allele in vc with bi-allelic likelihoods, in order * @@ -314,65 +276,6 @@ import java.util.*; } } - /** - * Returns a new Genotype with the PLs of the multi-allelic original reduced to a bi-allelic case - * - * This is handled in the following way: - * - * Suppose we have for a A/B/C site the following GLs: - * - * AA AB BB AC BC CC - * - * and we want to get the bi-allelic GLs for X/B, where X is everything not B - * - * XX = AA + AC + CC (since X = A or C) - * XB = AB + BC - * BB = BB - * - * @param original the original multi-allelic genotype - * @param altIndex the index of the alt allele we wish to keep in the bialleic case -- with ref == 0 - * @param nAlts the total number of alt alleles - * @return a new biallelic genotype with appropriate PLs - */ - @Requires({"original.hasLikelihoods()"}) // TODO -- add ploidy == 2 test "original.getPLs() == null || original.getPLs().length == 3"}) - @Ensures({"result.hasLikelihoods()", "result.getPL().length == 3"}) - @Deprecated - protected Genotype combineGLs(final Genotype original, final int altIndex, final int nAlts ) { - if ( original.isNonInformative() ) - return new GenotypeBuilder(original).PL(BIALLELIC_NON_INFORMATIVE_PLS).alleles(BIALLELIC_NOCALL).make(); - - if ( altIndex < 1 || altIndex > nAlts ) throw new IllegalStateException("altIndex must be between 1 and nAlts " + nAlts); - - final double[] normalizedPr = MathUtils.normalizeFromLog10(GenotypeLikelihoods.fromPLs(original.getPL()).getAsVector()); - final double[] biAllelicPr = new double[3]; - - for ( int index = 0; index < normalizedPr.length; index++ ) { - final GenotypeLikelihoods.GenotypeLikelihoodsAllelePair pair = GenotypeLikelihoods.getAllelePair(index); - - if ( pair.alleleIndex1 == altIndex ) { - if ( pair.alleleIndex2 == altIndex ) - // hom-alt case - biAllelicPr[2] = normalizedPr[index]; - else - // het-alt case - biAllelicPr[1] += normalizedPr[index]; - } else { - if ( pair.alleleIndex2 == altIndex ) - // het-alt case - biAllelicPr[1] += normalizedPr[index]; - else - // hom-non-alt - biAllelicPr[0] += normalizedPr[index]; - } - } - - final double[] GLs = new double[3]; - for ( int i = 0; i < GLs.length; i++ ) GLs[i] = Math.log10(biAllelicPr[i]); - - return new GenotypeBuilder(original).PL(GLs).alleles(BIALLELIC_NOCALL).make(); - } - - private static final double PHRED_2_LOG10_COEFF = -.1; /** @@ -504,7 +407,7 @@ import java.util.*; nEvaluations += sortedResultWithThetaNPriors.nEvaluations; } - return new MyAFCalculationResult(alleleCountsOfMLE, nEvaluations, vc.getAlleles(), + return new IndependentAlleleAFCalculationResult(alleleCountsOfMLE, nEvaluations, vc.getAlleles(), // necessary to ensure all values < 0 MathUtils.normalizeFromLog10(new double[] { combinedAltAllelesResult.getLog10LikelihoodOfAFEq0(), combinedAltAllelesResult.getLog10LikelihoodOfAFGT0() }, true), // priors incorporate multiple alt alleles, must be normalized diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesExactAFCalculator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesExactAFCalculator.java new file mode 100644 index 000000000..c1078a919 --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesExactAFCalculator.java @@ -0,0 +1,553 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. 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Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ +package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc; + +import com.google.java.contract.Ensures; +import com.google.java.contract.Requires; +import htsjdk.variant.variantcontext.*; +import org.broadinstitute.gatk.tools.walkers.genotyper.GeneralPloidyGenotypeLikelihoods; +import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeAlleleCounts; +import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodCalculator; +import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodCalculators; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.variant.GATKVCFConstants; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; + +import java.util.*; + +/** + * Independent allele exact AF calculator for any ploidy. + * + *

    + * The method is described in {@link IndependentAllelesDiploidExactAFCalculator} for diploids. + *

    + * + * @author Valentin Ruano-Rubio <valentin@broadinstitute.org> + */ +public class IndependentAllelesExactAFCalculator extends ExactAFCalculator { + + private static final int MAX_LENGTH_FOR_POOL_PL_LOGGING = 100; // if PL vectors longer than this # of elements, don't log them + + /** + * Array that caches the allele list that corresponds to the ith ploidy. + * + *

    + * Each position of the array imakes reference to a list that contains i copies of {@link Allele#NO_CALL}. + *

    + * + *

    + * This array must be queried using {@link #biallelicNoCall(int)}, which will extend the cache + * to larger ploidies if needed. + *

    + */ + private static volatile List[] BIALLELIC_NOCALL = initialBiallelicNoCall(10); + + /** + * Array that caches the allele list that corresponds to the ith ploidy. + * + *

    + * Each position of the array imakes reference to an array that contains + * all-zero likelihoods with the number of genotypes that correspond + * to a biallelic variant with ploidy i. + *

    + * + *

    + * This array must be queried using {@link #biallelicNonInformativePls(int)}, which will extend the cache + * to larger ploidies if needed. + *

    + */ + private static volatile int[][] BIALLELIC_NON_INFORMATIVE_PLS_BY_PLOIDY = initialBiallelicNonInformativePLsByPloidy(10); + + private static final Comparator AFCALC_RESULT_BY_PNONREF_COMPARATOR = new Comparator() { + @Override + @Requires("o1 != null && o1 != null") + public int compare(final AFCalculationResult o1, final AFCalculationResult o2) { + return -1 * Double.compare(o1.getLog10PosteriorOfAFGT0(), o2.getLog10PosteriorOfAFGT0()); + } + }; + + private final ExactAFCalculator biallelicExactAFCalculator; + + protected IndependentAllelesExactAFCalculator(final ExactAFCalculator biallelicExactAFCalculator) { + if (biallelicExactAFCalculator == null) + throw new IllegalArgumentException("the biallelic exact AF calculator cannot be null"); + this.biallelicExactAFCalculator = biallelicExactAFCalculator; + } + + /** + * Creates a new calculator that delegates on {@link GeneralPloidyExactAFCalculator} to run + * the exact model per allele. + * + *

    + * Note: this constructor may be called using reflexion. + *

    + */ + @SuppressWarnings("unused") + protected IndependentAllelesExactAFCalculator() { + this(new GeneralPloidyExactAFCalculator()); + } + + @Override + @Requires("vc != null && likelihoodSums != null") + protected void reduceScopeCalculateLikelihoodSums(final VariantContext vc, final int defaultPloidy, final LikelihoodSum[] likelihoodSums) { + final int numOriginalAltAlleles = likelihoodSums.length; + final GenotypesContext genotypes = vc.getGenotypes(); + for ( final Genotype genotype : genotypes.iterateInSampleNameOrder() ) { + if (!genotype.hasPL()) + continue; + final double[] gls = genotype.getLikelihoods().getAsVector(); + if (MathUtils.sum(gls) >= GATKVariantContextUtils.SUM_GL_THRESH_NOCALL) + continue; + + final int PLindexOfBestGL = MathUtils.maxElementIndex(gls); + + final double bestToHomRefDiffGL = PLindexOfBestGL == PL_INDEX_OF_HOM_REF ? 0.0 : gls[PLindexOfBestGL] - gls[PL_INDEX_OF_HOM_REF]; + final int declaredPloidy = genotype.getPloidy(); + final int ploidy = declaredPloidy <= 0 ? defaultPloidy : declaredPloidy; + + final int[] acCount = GeneralPloidyGenotypeLikelihoods.getAlleleCountFromPLIndex(1 + numOriginalAltAlleles, ploidy, PLindexOfBestGL); + // by convention, first count coming from getAlleleCountFromPLIndex comes from reference allele + for (int k=1; k < acCount.length;k++) + if (acCount[k] > 0 ) + likelihoodSums[k-1].sum += acCount[k] * bestToHomRefDiffGL; + } + } + + @Override + protected GenotypesContext reduceScopeGenotypes(final VariantContext vc, final int defaultPloidy, final List allelesToUse) { + return subsetAlleles(vc,defaultPloidy,allelesToUse,false); + } + + @Override + @Requires("vc != null && log10AlleleFrequencyPriors != null && stateTracker != null") + protected AFCalculationResult computeLog10PNonRef(final VariantContext vc, final int defaultPloidy, final double[] log10AlleleFrequencyPriors, final StateTracker stateTracker) { + final List independentResultTrackers = computeAlleleIndependentExact(vc, defaultPloidy, log10AlleleFrequencyPriors); + + // Paranoia check: + if ( independentResultTrackers.size() <= 1 ) + throw new IllegalStateException("Independent alleles model returned an empty list of results at VC " + vc); + else if ( independentResultTrackers.size() == 2 ) { + // fast path for the very common bi-allelic use case + return independentResultTrackers.get(1); + } else { + final List alternativesOnly = new ArrayList<>(independentResultTrackers.size() - 1); + for (int i = 1; i < independentResultTrackers.size(); i++) + alternativesOnly.add(independentResultTrackers.get(i)); + // we are a multi-allelic, so we need to actually combine the results + final List withMultiAllelicPriors = applyMultiAllelicPriors(alternativesOnly); + return combineIndependentPNonRefs(vc, withMultiAllelicPriors, independentResultTrackers.get(0)); + } + } + + @Requires("conditionalPNonRefResults != null and !conditionalPNonRefResults.empty()") + protected final List applyMultiAllelicPriors(final List conditionalPNonRefResults) { + final ArrayList sorted = new ArrayList(conditionalPNonRefResults); + + // sort the results, so the most likely allele is first + Collections.sort(sorted, AFCALC_RESULT_BY_PNONREF_COMPARATOR); + + double lastPosteriorGt0 = sorted.get(0).getLog10PosteriorOfAFGT0(); + final double log10SingleAllelePriorOfAFGt0 = conditionalPNonRefResults.get(0).getLog10PriorOfAFGT0(); + + for ( int i = 0; i < sorted.size(); i++ ) { + if ( sorted.get(i).getLog10PosteriorOfAFGT0() > lastPosteriorGt0 ) + throw new IllegalStateException("pNonRefResults not sorted: lastPosteriorGt0 " + lastPosteriorGt0 + " but current is " + sorted.get(i).getLog10PosteriorOfAFGT0()); + + final double log10PriorAFGt0 = (i + 1) * log10SingleAllelePriorOfAFGt0; + final double log10PriorAFEq0 = Math.log10(1 - Math.pow(10, log10PriorAFGt0)); + final double[] thetaTONPriors = new double[] { log10PriorAFEq0, log10PriorAFGt0 }; + + // bind pNonRef for allele to the posterior value of the AF > 0 with the new adjusted prior + sorted.set(i, sorted.get(i).withNewPriors(MathUtils.normalizeFromLog10(thetaTONPriors, true))); + } + + return sorted; + } + + /** + * Take the independent estimates of pNonRef for each alt allele and combine them into a single result + * + * Given n independent calculations for each of n alternate alleles create a single + * combined AFCalcResult with: + * + * priors for AF == 0 equal to theta^N for the nth least likely allele + * posteriors that reflect the combined chance that any alleles are segregating and corresponding + * likelihoods + * combined MLEs in the order of the alt alleles in vc + * + * @param sortedResultsWithThetaNPriors the pNonRef result for each allele independently + */ + @Requires("vc != null && sortedResultsWithThetaNPriors != null && combinedAltAllelesResult != null") + protected AFCalculationResult combineIndependentPNonRefs(final VariantContext vc, + final List sortedResultsWithThetaNPriors, + final AFCalculationResult combinedAltAllelesResult) { + + + int nEvaluations = 0; + final int nAltAlleles = sortedResultsWithThetaNPriors.size(); + final int[] alleleCountsOfMLE = new int[nAltAlleles]; + final Map log10pRefByAllele = new HashMap<>(nAltAlleles); + + // the sum of the log10 posteriors for AF == 0 and AF > 0 to determine joint probs + + for ( final AFCalculationResult sortedResultWithThetaNPriors : sortedResultsWithThetaNPriors ) { + final Allele altAllele = sortedResultWithThetaNPriors.getAllelesUsedInGenotyping().get(1); + final int altI = vc.getAlleles().indexOf(altAllele) - 1; + + // MLE of altI allele is simply the MLE of this allele in altAlleles + alleleCountsOfMLE[altI] = sortedResultWithThetaNPriors.getAlleleCountAtMLE(altAllele); + + // bind pNonRef for allele to the posterior value of the AF > 0 with the new adjusted prior + log10pRefByAllele.put(altAllele, sortedResultWithThetaNPriors.getLog10PosteriorOfAFEq0()); + + // trivial -- update the number of evaluations + nEvaluations += sortedResultWithThetaNPriors.nEvaluations; + } + + return new IndependentAlleleAFCalculationResult(alleleCountsOfMLE, nEvaluations, vc.getAlleles(), + // necessary to ensure all values < 0 + MathUtils.normalizeFromLog10(new double[] { combinedAltAllelesResult.getLog10LikelihoodOfAFEq0(), combinedAltAllelesResult.getLog10LikelihoodOfAFGT0() }, true), + // priors incorporate multiple alt alleles, must be normalized + MathUtils.normalizeFromLog10(new double[] { combinedAltAllelesResult.getLog10PriorOfAFEq0(), combinedAltAllelesResult.getLog10PriorOfAFGT0() }, true), + log10pRefByAllele, sortedResultsWithThetaNPriors); + } + + /** + * Compute the conditional exact AFCalcResult for each allele in vc independently, returning + * the result of each, in order of the alt alleles in VC + * + * @param vc the VariantContext we want to analyze, with at least 1 alt allele + * @param log10AlleleFrequencyPriors the priors + * @return a list of the AFCalcResults for each bi-allelic sub context of vc + */ + @Requires({"vc != null", "log10AlleleFrequencyPriors != null"}) + @Ensures("goodIndependentResult(vc, result)") + protected final List computeAlleleIndependentExact(final VariantContext vc, final int defaultPloidy, + final double[] log10AlleleFrequencyPriors) { + final List results = new LinkedList<>(); + + for ( final VariantContext subvc : makeAlleleConditionalContexts(vc, defaultPloidy) ) { + final AFCalculationResult resultTracker = biallelicExactAFCalculator.getLog10PNonRef(subvc, defaultPloidy, vc.getNAlleles() - 1, log10AlleleFrequencyPriors); + results.add(resultTracker); + } + + return results; + } + + /** + * Returns the bi-allelic variant context for each alt allele in vc with bi-allelic likelihoods, in order + * + * @param vc the variant context to split. Must have n.alt.alleles > 1 + * @return a bi-allelic variant context for each alt allele in vc + */ + @Requires({"vc != null", "vc.getNAlleles() > 1"}) + @Ensures("result.size() == vc.getNAlleles() - 1") + protected final List makeAlleleConditionalContexts(final VariantContext vc, final int defaultPloidy) { + final int nAlleles = vc.getNAlleles(); + + // go through the work of ripping up the VC into its biallelic components + final List vcs = new LinkedList<>(); + + for ( int alleleIndex = 0; alleleIndex < nAlleles; alleleIndex++ ) { + vcs.add(biallelicCombinedGLs(vc, defaultPloidy, alleleIndex)); + } + return vcs; + } + + /** + * Create a single bi-allelic variant context from rootVC with alt allele with index altAlleleIndex + * + * @param rootVC the root (potentially multi-allelic) variant context + * @param alleleIndex index of the alt allele, from 0 == reference + * @return a bi-allelic variant context based on rootVC + */ + @Requires({"rootVC.getNAlleles() > 1", "altAlleleIndex < rootVC.getNAlleles()"}) + @Ensures({"result.isBiallelic()"}) + protected final VariantContext biallelicCombinedGLs(final VariantContext rootVC, final int defaultPloidy, final int alleleIndex) { + if ( rootVC.isBiallelic() ) { + return rootVC; + } else { + final int nAlleles = rootVC.getNAlleles(); + final List biallelicGenotypes = new ArrayList<>(rootVC.getNSamples()); + for ( final Genotype g : rootVC.getGenotypes() ) + biallelicGenotypes.add(combineGLs(g, defaultPloidy, alleleIndex, nAlleles)); + + final VariantContextBuilder vcb = new VariantContextBuilder(rootVC); + final Allele allele = alleleIndex == 0 ? rootVC.getReference() : rootVC.getAlternateAllele(alleleIndex - 1); + vcb.alleles(alleleIndex == 0 ? Arrays.asList(allele, GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE) : Arrays.asList(rootVC.getReference(), allele)); + vcb.genotypes(biallelicGenotypes); + return vcb.make(); + } + } + + /** + * Returns a new Genotype with the PLs of the multi-allelic original reduced to a bi-allelic case. + * + *

    Uses the log-sum-exp trick in order to work well with very low PLs

    + * + *

    This is handled in the following way:

    + * + *

    Suppose we have for a A/B/C site the following GLs:

    + * + *

    AA AB BB AC BC CC

    + * + *

    and we want to get the bi-allelic GLs for X/B, where X is everything not B

    + * + *

    XX = AA + AC + CC (since X = A or C)
    + * XB = AB + BC
    + * BB = BB
    + *

    + *

    + * This implementation uses the log-sum-exp trick in order to avoid numeric instability (underflow). + *

    + * + * @param original the original multi-allelic genotype + * @param alleleIndex the index of the alt allele we wish to keep in the bialleic case -- with ref == 0 + * @param numberOfAlleles the total number of alleles (alternatives + the reference). + * @return a new biallelic genotype with appropriate PLs + */ + @Requires({"original.hasLikelihoods() && alleleIndex >= 0"}) + @Ensures({"result.hasLikelihoods()"}) + private Genotype combineGLs(final Genotype original, final int defaultPloidy, final int alleleIndex, final int numberOfAlleles ) { + + final int declaredPloidy = original.getPloidy(); + final int ploidy = declaredPloidy <= 0 ? defaultPloidy : declaredPloidy; + if ( original.isNonInformative() ) + return new GenotypeBuilder(original).PL(biallelicNonInformativePls(ploidy)).alleles(biallelicNoCall(ploidy)).make(); + + final int[] pls = original.getPL(); + + final GenotypeLikelihoodCalculator calculator = GenotypeLikelihoodCalculators.getInstance(ploidy, numberOfAlleles); + final double[] newPLs = new double[ploidy + 1]; + Arrays.fill(newPLs, Double.NEGATIVE_INFINITY); + for (int i = 0; i < pls.length; i++) { + final GenotypeAlleleCounts alleleCounts = calculator.genotypeAlleleCountsAt(i); + final int alleleCount = alleleCounts.alleleCountFor(alleleIndex); + final int newPLIndex = alleleIndex == 0 ? ploidy - alleleCount : alleleCount; + newPLs[newPLIndex] = MathUtils.approximateLog10SumLog10(newPLs[newPLIndex], -.1 * pls[i]); + } + + return new GenotypeBuilder(original).PL(newPLs).alleles(biallelicNoCall(ploidy)).make(); + } + + private static List[] initialBiallelicNoCall(final int initialCapacity) { + final List[] result = new List[initialCapacity + 1]; + for (int i = 0; i < result.length; i++) { + result[i] = GATKVariantContextUtils.noCallAlleles(i); + } + return result; + } + + private static int[][] initialBiallelicNonInformativePLsByPloidy(final int initialCapacity) { + final int[][] result = new int[initialCapacity + 1][]; + for (int i = 0; i < result.length; i++) + result[i] = new int[i]; // { 0, 0, 0 ... 0} is the actual uninformative PL array. + return result; + } + + /** + * Returns a cached array of non-informative PLs (all 0) for a given ploidy. + *

    + * Calling code must never change its elements. + *

    + * @param ploidy the required ploidy. + * @return never {@code null}. + */ + @Requires("ploidy >= 0") + private static int[] biallelicNonInformativePls (final int ploidy) { + if (ploidy >= BIALLELIC_NON_INFORMATIVE_PLS_BY_PLOIDY.length) { + return enlargeIfNecessaryBiallelicNonInformativePlsByPloidyAndGet(ploidy); + } else { + return BIALLELIC_NON_INFORMATIVE_PLS_BY_PLOIDY[ploidy]; + } + } + + /** + * Thread-safe expansion of {@link #BIALLELIC_NON_INFORMATIVE_PLS_BY_PLOIDY}. + * @param ploidy the requested ploidy. + * @return the uninformative likelihoods array for the requested ploidy. + */ + private static synchronized int[] enlargeIfNecessaryBiallelicNonInformativePlsByPloidyAndGet(final int ploidy) { + if (ploidy >= BIALLELIC_NON_INFORMATIVE_PLS_BY_PLOIDY.length) { + final int[][] newValue = Arrays.copyOf(BIALLELIC_NON_INFORMATIVE_PLS_BY_PLOIDY, ploidy * 2); + for (int i = newValue.length - 1; i >= BIALLELIC_NON_INFORMATIVE_PLS_BY_PLOIDY.length; i--) + newValue[i] = new int[i]; // { 0, 0, 0.. } is the actual uninformative PL array. + BIALLELIC_NON_INFORMATIVE_PLS_BY_PLOIDY = newValue; + } + return BIALLELIC_NON_INFORMATIVE_PLS_BY_PLOIDY[ploidy]; + } + + /** + * Returns a cached list of no-call alleles {@link Allele#NO_CALL} that correspond to a given ploidy. + *

    + * Calling code must never change its elements. + *

    + * @param ploidy the required ploidy. + * @return never {@code null}. + */ + private static List biallelicNoCall (final int ploidy) { + if (ploidy >= BIALLELIC_NOCALL.length) { + return enlargeIfNecessaryBiallelicNoCallAndGet(ploidy); + } else { + return BIALLELIC_NOCALL[ploidy]; + } + } + + /** + * Thread-safe expansion of {@link #BIALLELIC_NOCALL}. + * @param ploidy the requested ploidy. + * @return the no-call allele list for the requested ploidy. + */ + private static synchronized List enlargeIfNecessaryBiallelicNoCallAndGet(final int ploidy) { + if (ploidy >= BIALLELIC_NOCALL.length) { + final List[] newValue = Arrays.copyOf(BIALLELIC_NOCALL, ploidy * 2); + for (int i = newValue.length - 1; i >= BIALLELIC_NOCALL.length; i--) + newValue[i] = GATKVariantContextUtils.noCallAlleles(i); + BIALLELIC_NOCALL = newValue; + } + return BIALLELIC_NOCALL[ploidy]; + } + + @Override + @Requires("vc != null && allelesToUse != null") + public GenotypesContext subsetAlleles(VariantContext vc, int defaultPloidy, List allelesToUse, boolean assignGenotypes) { + // the genotypes with PLs + final GenotypesContext oldGTs = vc.getGenotypes(); + + // samples + final List sampleIndices = oldGTs.getSampleNamesOrderedByName(); + + // the new genotypes to create + final GenotypesContext newGTs = GenotypesContext.create(); + + // we need to determine which of the alternate alleles (and hence the likelihoods) to use and carry forward + final int numOriginalAltAlleles = vc.getAlternateAlleles().size(); + final int numNewAltAlleles = allelesToUse.size() - 1; + + + // create the new genotypes + for ( int k = 0; k < oldGTs.size(); k++ ) { + final Genotype g = oldGTs.get(sampleIndices.get(k)); + final int declaredPloidy = g.getPloidy(); + final int ploidy = declaredPloidy <= 0 ? defaultPloidy : declaredPloidy; + if ( !g.hasLikelihoods() ) { + newGTs.add(GenotypeBuilder.create(g.getSampleName(),GATKVariantContextUtils.noCallAlleles(ploidy))); + continue; + } + + // create the new likelihoods array from the alleles we are allowed to use + final double[] originalLikelihoods = g.getLikelihoods().getAsVector(); + double[] newLikelihoods; + + // Optimization: if # of new alt alleles = 0 (pure ref call), keep original likelihoods so we skip normalization + // and subsetting + if ( numOriginalAltAlleles == numNewAltAlleles || numNewAltAlleles == 0) { + newLikelihoods = originalLikelihoods; + } else { + newLikelihoods = GeneralPloidyGenotypeLikelihoods.subsetToAlleles(originalLikelihoods, ploidy, vc.getAlleles(), allelesToUse); + + // might need to re-normalize + newLikelihoods = MathUtils.normalizeFromLog10(newLikelihoods, false, true); + } + + // if there is no mass on the (new) likelihoods, then just no-call the sample + if ( MathUtils.sum(newLikelihoods) > GATKVariantContextUtils.SUM_GL_THRESH_NOCALL ) { + newGTs.add(GenotypeBuilder.create(g.getSampleName(), GATKVariantContextUtils.noCallAlleles(ploidy))); + } + else { + final GenotypeBuilder gb = new GenotypeBuilder(g); + + if ( numNewAltAlleles == 0 ) + gb.noPL(); + else + gb.PL(newLikelihoods); + + // if we weren't asked to assign a genotype, then just no-call the sample + if ( !assignGenotypes || MathUtils.sum(newLikelihoods) > GATKVariantContextUtils.SUM_GL_THRESH_NOCALL ) + gb.alleles(GATKVariantContextUtils.noCallAlleles(ploidy)); + else + assignGenotype(gb, newLikelihoods, allelesToUse, ploidy); + newGTs.add(gb.make()); + } + } + + return GATKVariantContextUtils.fixADFromSubsettedAlleles(newGTs, vc, allelesToUse); + } + + + /** + * Assign genotypes (GTs) to the samples in the Variant Context greedily based on the PLs + * + * @param newLikelihoods the PL array + * @param allelesToUse the list of alleles to choose from (corresponding to the PLs) + * @param numChromosomes Number of chromosomes per pool + */ + private void assignGenotype(final GenotypeBuilder gb, + final double[] newLikelihoods, + final List allelesToUse, + final int numChromosomes) { + final int numNewAltAlleles = allelesToUse.size() - 1; + + // find the genotype with maximum likelihoods + final int PLindex = numNewAltAlleles == 0 ? 0 : MathUtils.maxElementIndex(newLikelihoods); + final GenotypeLikelihoodCalculator calculator = GenotypeLikelihoodCalculators.getInstance(numChromosomes,allelesToUse.size()); + final GenotypeAlleleCounts alleleCounts = calculator.genotypeAlleleCountsAt(PLindex); + + gb.alleles(alleleCounts.asAlleleList(allelesToUse)); + + // remove PLs if necessary + if (newLikelihoods.length > MAX_LENGTH_FOR_POOL_PL_LOGGING) + gb.noPL(); + + if ( numNewAltAlleles > 0 ) + gb.log10PError(GenotypeLikelihoods.getGQLog10FromLikelihoods(PLindex, newLikelihoods)); + } +} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/OriginalDiploidExactAFCalculator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/OriginalDiploidExactAFCalculator.java index 4f61d438d..4f2b1cb35 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/OriginalDiploidExactAFCalculator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/OriginalDiploidExactAFCalculator.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalculator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalculator.java index 05a90fd64..1b6b7aa39 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalculator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalculator.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/StateTracker.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/StateTracker.java index ec858270b..66e9417d5 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/StateTracker.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/StateTracker.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -222,6 +222,7 @@ final class StateTracker { @Requires("allelesUsedInGenotyping != null") protected AFCalculationResult toAFCalculationResult(final double[] log10PriorsByAC) { final int [] subACOfMLE = Arrays.copyOf(alleleCountsOfMLE, allelesUsedInGenotyping.size() - 1); + //TODO bad calculation of normalized log10 ACeq0 and ACgt0 likelihoods, priors and consequently posteriors calculated in AFCalculationResult constructor. final double[] log10Likelihoods = MathUtils.normalizeFromLog10(new double[]{getLog10LikelihoodOfAFzero(), getLog10LikelihoodOfAFNotZero()}, true); final double[] log10Priors = MathUtils.normalizeFromLog10(new double[]{log10PriorsByAC[0], MathUtils.log10sumLog10(log10PriorsByAC, 1)}, true); diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTrimmer.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTrimmer.java index 6a8564b28..4644a779b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTrimmer.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTrimmer.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyBasedCallerArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyBasedCallerArgumentCollection.java index 06f390e71..42432c9ae 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyBasedCallerArgumentCollection.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyBasedCallerArgumentCollection.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -89,11 +89,12 @@ public class AssemblyBasedCallerArgumentCollection extends StandardCallerArgumen } /** - * The assembled haplotypes will be written as BAM to this file if requested. Really for debugging purposes only. - * Note that the output here does not include uninformative reads so that not every input read is emitted to the bam. + * The assembled haplotypes and locally realigned reads will be written as BAM to this file if requested. Really + * for debugging purposes only. Note that the output here does not include uninformative reads so that not every + * input read is emitted to the bam. * - * Turning on this mode may result in serious performance cost for the HC. It's really only appropriate to - * use in specific areas where you want to better understand why the HC is making specific calls. + * Turning on this mode may result in serious performance cost for the caller. It's really only appropriate to + * use in specific areas where you want to better understand why the caller is making specific calls. * * The reads are written out containing an "HC" tag (integer) that encodes which haplotype each read best matches * according to the haplotype caller's likelihood calculation. The use of this tag is primarily intended @@ -101,14 +102,18 @@ public class AssemblyBasedCallerArgumentCollection extends StandardCallerArgumen * easily see which reads go with these haplotype. * * Note that the haplotypes (called or all, depending on mode) are emitted as single reads covering the entire - * active region, coming from read HC and a special read group. + * active region, coming from sample "HC" and a special read group called "ArtificialHaplotype". This will increase the + * pileup depth compared to what would be expected from the reads only, especially in complex regions. * * Note also that only reads that are actually informative about the haplotypes are emitted. By informative we mean * that there's a meaningful difference in the likelihood of the read coming from one haplotype compared to * its next best haplotype. * + * If multiple BAMs are passed as input to the tool (as is common for M2), then they will be combined in the bamout + * output and tagged with the appropriate sample names. + * * The best way to visualize the output of this mode is with IGV. Tell IGV to color the alignments by tag, - * and give it the HC tag, so you can see which reads support each haplotype. Finally, you can tell IGV + * and give it the "HC" tag, so you can see which reads support each haplotype. Finally, you can tell IGV * to group by sample, which will separate the potential haplotypes from the reads. All of this can be seen in * this screenshot * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResult.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResult.java index 291d6da7a..201aa5aa1 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResult.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResult.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResultSet.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResultSet.java index b910ba2f4..c32e814bb 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResultSet.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResultSet.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/EventBlock.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/EventBlock.java index 34536a5fe..4ea2bd579 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/EventBlock.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/EventBlock.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/EventBlockFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/EventBlockFinder.java index b87be5e0f..4fbd027ae 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/EventBlockFinder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/EventBlockFinder.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java index b70765402..88864a3af 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java index 91120f43d..5e3556bda 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java index 4738f01c7..7b4399068 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -108,9 +108,17 @@ import java.io.FileNotFoundException; import java.util.*; /** - * Call SNPs and indels simultaneously via local re-assembly of haplotypes in an active region + * Call germline SNPs and indels via local re-assembly of haplotypes * - *

    The basic operation of the HaplotypeCaller proceeds as follows:

    + *

    The HaplotypeCaller is capable of calling SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region. In other words, whenever the program encounters a region showing signs of variation, it discards the existing mapping information and completely reassembles the reads in that region. This allows the HaplotypeCaller to be more accurate when calling regions that are traditionally difficult to call, for example when they contain different types of variants close to each other. It also makes the HaplotypeCaller much better at calling indels than position-based callers like UnifiedGenotyper.

    + +

    In the so-called GVCF mode used for scalable variant calling in DNA sequence data, HaplotypeCaller runs per-sample to generate an intermediate genomic gVCF (gVCF), which can then be used for joint genotyping of multiple samples in a very efficient way, which enables rapid incremental processing of samples as they roll off the sequencer, as well as scaling to very large cohort sizes (e.g. the 92K exomes of ExAC).

    + +

    In addition, HaplotypeCaller is able to handle non-diploid organisms as well as pooled experiment data. Note however that the algorithms used to calculate variant likelihoods is not well suited to extreme allele frequencies (relative to ploidy) so its use is not recommended for somatic (cancer) variant discovery. For that purpose, use MuTect2 instead.

    + +

    Finally, HaplotypeCaller is also able to correctly handle the splice junctions that make RNAseq a challenge for most variant callers.

    + * + *

    How HaplotypeCaller works

    * *
    *

    1. Define active regions

    @@ -119,7 +127,7 @@ import java.util.*; * evidence for variation.

    * *
    - *

    2. Determine haplotypes by re-assembly of the active region

    + *

    2. Determine haplotypes by assembly of the active region

    * *

    For each ActiveRegion, the program builds a De Bruijn-like graph to reassemble the ActiveRegion, and identifies * what are the possible haplotypes present in the data. The program then realigns each haplotype against the reference @@ -135,7 +143,7 @@ import java.util.*; *
    *

    4. Assign sample genotypes

    * - *

    For each potentially variant site, the program applies Bayes’ rule, using the likelihoods of alleles given the + *

    For each potentially variant site, the program applies Bayes' rule, using the likelihoods of alleles given the * read data to calculate the likelihoods of each genotype per sample given the read data observed for that * sample. The most likely genotype is then assigned to the sample.

    * @@ -159,16 +167,13 @@ import java.util.*; * Best Practices documentation for detailed recommendations.

    * *
    - *

    Single-sample all-sites calling on DNAseq (for `-ERC GVCF` cohort analysis workflow)

    + *

    Single-sample GVCF calling on DNAseq (for `-ERC GVCF` cohort analysis workflow)

    * 
    - *   java
- *     -jar GenomeAnalysisTK.jar
- *     -T HaplotypeCaller
- *     -R reference.fasta
+ *   java -jar GenomeAnalysisTK.jar \
+ *     -R reference.fasta \
+ *     -T HaplotypeCaller \
  *     -I sample1.bam \
  *     --emitRefConfidence GVCF \
- *     --variant_index_type LINEAR \
- *     --variant_index_parameter 128000
  *     [--dbsnp dbSNP.vcf] \
  *     [-L targets.interval_list] \
  *     -o output.raw.snps.indels.g.vcf
@@ -176,10 +181,9 @@ import java.util.*;
  *
  * 
    Variant-only calling on DNAseq
    
  * 
    - *   java
- *     -jar GenomeAnalysisTK.jar
- *     -T HaplotypeCaller
- *     -R reference.fasta
+ *   java -jar GenomeAnalysisTK.jar \
+ *     -R reference.fasta \
+ *     -T HaplotypeCaller \
  *     -I sample1.bam [-I sample2.bam ...] \
  *     [--dbsnp dbSNP.vcf] \
  *     [-stand_call_conf 30] \
@@ -190,10 +194,9 @@ import java.util.*;
  *
  * 
    Variant-only calling on RNAseq
    
  * 
    - *   java
- *     -jar GenomeAnalysisTK.jar
- *     -T HaplotypeCaller
- *     -R reference.fasta
+ *   java -jar GenomeAnalysisTK.jar \
+ *     -R reference.fasta \
+ *     -T HaplotypeCaller \
  *     -I sample1.bam \
  *     [--dbsnp dbSNP.vcf] \
  *     -stand_call_conf 20 \
@@ -210,8 +213,7 @@ import java.util.*;
  *
* *

Special note on ploidy

- *

This tool is able to handle almost any ploidy (except very high ploidies in large pooled experiments); the ploidy - * can be specified using the -ploidy argument for non-diploid organisms.

+ *

This tool is able to handle almost any ploidy (except very high ploidies in large pooled experiments); the ploidy can be specified using the -ploidy argument for non-diploid organisms.

* *

Additional Notes

*
    @@ -290,7 +292,7 @@ public class HaplotypeCaller extends ActiveRegionWalker, In */ @Advanced @Argument(fullName="annotation", shortName="A", doc="One or more specific annotations to apply to variant calls", required=false) - protected List annotationsToUse = new ArrayList<>(Arrays.asList(new String[]{"ClippingRankSumTest", "DepthPerSampleHC"})); + protected List annotationsToUse = new ArrayList<>(); /** * Which annotations to exclude from output in the VCF file. Note that this argument has higher priority than the @@ -302,7 +304,7 @@ public class HaplotypeCaller extends ActiveRegionWalker, In */ @Advanced @Argument(fullName="excludeAnnotation", shortName="XA", doc="One or more specific annotations to exclude", required=false) - protected List annotationsToExclude = new ArrayList<>(Arrays.asList(new String[]{})); + protected List annotationsToExclude = new ArrayList<>(); /** * Which groups of annotations to add to the output VCF file. The single value 'none' removes the default group. See @@ -311,7 +313,7 @@ public class HaplotypeCaller extends ActiveRegionWalker, In * to provide a pedigree file for a pedigree-based annotation) may cause the run to fail. */ @Argument(fullName="group", shortName="G", doc="One or more classes/groups of annotations to apply to variant calls", required=false) - protected String[] annotationClassesToUse = { "Standard" }; + protected List annotationGroupsToUse = new ArrayList<>(Arrays.asList(new String[]{ "Standard", "StandardHCAnnotation" })); @ArgumentCollection private HaplotypeCallerArgumentCollection HCAC = new HaplotypeCallerArgumentCollection(); @@ -480,8 +482,39 @@ public class HaplotypeCaller extends ActiveRegionWalker, In private byte MIN_TAIL_QUALITY; private static final byte MIN_TAIL_QUALITY_WITH_ERROR_CORRECTION = 6; - // the minimum length of a read we'd consider using for genotyping - private final static int MIN_READ_LENGTH = 10; + /** + * Minimum (exclusive) average number of high quality bases per soft-clip to consider that a set of soft-clips is a + * high quality set. + */ + private static final double AVERAGE_HQ_SOFTCLIPS_HQ_BASES_THRESHOLD = 6.0; + + /** + * Maximum-mininum confidence on a variant to exist to consider the position as a potential variant harbouring locus + * when looking for active regions. + */ + private static final double MAXMIN_CONFIDENCE_FOR_CONSIDERING_A_SITE_AS_POSSIBLE_VARIANT_IN_ACTIVE_REGION_DISCOVERY = 4.0; + + /** + * Minimum ploidy assumed when looking for loci that may harbour variation to identify active regions. + *

    + * By default we take the putative ploidy provided by the user, but this turned out to be too insensitive + * for low ploidy, notoriously with haploid samples. Therefore we impose this minimum. + *

    + */ + private static final int MINIMUM_PUTATIVE_PLOIDY_FOR_ACTIVE_REGION_DISCOVERY = 2; + + + /** + * Reads with length lower than this number, after clipping off overhands outside the active region, + * won't be considered for genotyping. + */ + private final static int READ_LENGTH_FILTER_THRESHOLD = 10; + + /** + * Reads with mapping quality lower than this number won't be considered for genotyping, even if they have + * passed earlier filters (e.g. the walkers' own min MQ filter). + */ + private static final int READ_QUALITY_FILTER_THRESHOLD = 20; private SampleList samplesList; @@ -569,14 +602,14 @@ public class HaplotypeCaller extends ActiveRegionWalker, In final UnifiedArgumentCollection simpleUAC = HCAC.cloneTo(UnifiedArgumentCollection.class); simpleUAC.outputMode = OutputMode.EMIT_VARIANTS_ONLY; simpleUAC.genotypingOutputMode = GenotypingOutputMode.DISCOVERY; - simpleUAC.genotypeArgs.STANDARD_CONFIDENCE_FOR_CALLING = Math.min( 4.0, HCAC.genotypeArgs.STANDARD_CONFIDENCE_FOR_CALLING ); // low values used for isActive determination only, default/user-specified values used for actual calling - simpleUAC.genotypeArgs.STANDARD_CONFIDENCE_FOR_EMITTING = Math.min( 4.0, HCAC.genotypeArgs.STANDARD_CONFIDENCE_FOR_EMITTING ); // low values used for isActive determination only, default/user-specified values used for actual calling + simpleUAC.genotypeArgs.STANDARD_CONFIDENCE_FOR_CALLING = Math.min(MAXMIN_CONFIDENCE_FOR_CONSIDERING_A_SITE_AS_POSSIBLE_VARIANT_IN_ACTIVE_REGION_DISCOVERY, HCAC.genotypeArgs.STANDARD_CONFIDENCE_FOR_CALLING ); // low values used for isActive determination only, default/user-specified values used for actual calling + simpleUAC.genotypeArgs.STANDARD_CONFIDENCE_FOR_EMITTING = Math.min(MAXMIN_CONFIDENCE_FOR_CONSIDERING_A_SITE_AS_POSSIBLE_VARIANT_IN_ACTIVE_REGION_DISCOVERY, HCAC.genotypeArgs.STANDARD_CONFIDENCE_FOR_EMITTING ); // low values used for isActive determination only, default/user-specified values used for actual calling simpleUAC.CONTAMINATION_FRACTION = 0.0; simpleUAC.CONTAMINATION_FRACTION_FILE = null; simpleUAC.exactCallsLog = null; // Seems that at least with some test data we can lose genuine haploid variation if we use // UGs engine with ploidy == 1 - simpleUAC.genotypeArgs.samplePloidy = Math.max(2, HCAC.genotypeArgs.samplePloidy); + simpleUAC.genotypeArgs.samplePloidy = Math.max(MINIMUM_PUTATIVE_PLOIDY_FOR_ACTIVE_REGION_DISCOVERY, HCAC.genotypeArgs.samplePloidy); activeRegionEvaluationGenotyperEngine = new UnifiedGenotypingEngine(simpleUAC, FixedAFCalculatorProvider.createThreadSafeProvider(getToolkit(),simpleUAC,logger), toolkit); @@ -592,10 +625,14 @@ public class HaplotypeCaller extends ActiveRegionWalker, In genotypingEngine = new HaplotypeCallerGenotypingEngine(HCAC, samplesList, genomeLocParser, FixedAFCalculatorProvider.createThreadSafeProvider(getToolkit(), HCAC,logger), !doNotRunPhysicalPhasing); // initialize the output VCF header - final VariantAnnotatorEngine annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit()); + final VariantAnnotatorEngine annotationEngine = new VariantAnnotatorEngine(annotationGroupsToUse, annotationsToUse, annotationsToExclude, this, getToolkit()); final Set headerInfo = new HashSet<>(); + //initialize the annotations (this is particularly important to turn off RankSumTest dithering in integration tests) + //do this before we write the header because SnpEff adds to header lines + annotationEngine.invokeAnnotationInitializationMethods(headerInfo); + headerInfo.addAll(genotypingEngine.getAppropriateVCFInfoHeaders()); // all annotation fields from VariantAnnotatorEngine headerInfo.addAll(annotationEngine.getVCFAnnotationDescriptions()); @@ -623,9 +660,6 @@ public class HaplotypeCaller extends ActiveRegionWalker, In vcfWriter.writeHeader(new VCFHeader(headerInfo, sampleSet)); - //now that we have all the VCF headers, initialize the annotations (this is particularly important to turn off RankSumTest dithering in integration tests) - annotationEngine.invokeAnnotationInitializationMethods(headerInfo); - try { // fasta reference reader to supplement the edges of the reference sequence referenceReader = new CachingIndexedFastaSequenceFile(getToolkit().getArguments().referenceFile); @@ -775,15 +809,22 @@ public class HaplotypeCaller extends ActiveRegionWalker, In final String sampleName = sample.getKey(); // The ploidy here is not dictated by the sample but by the simple genotyping-engine used to determine whether regions are active or not. final int activeRegionDetectionHackishSamplePloidy = activeRegionEvaluationGenotyperEngine.getConfiguration().genotypeArgs.samplePloidy; - final double[] genotypeLikelihoods = referenceConfidenceModel.calcGenotypeLikelihoodsOfRefVsAny(sampleName,activeRegionDetectionHackishSamplePloidy,genotypingModel,sample.getValue().getBasePileup(), ref.getBase(), MIN_BASE_QUALTY_SCORE, averageHQSoftClips).genotypeLikelihoods; + final double[] genotypeLikelihoods = referenceConfidenceModel.calcGenotypeLikelihoodsOfRefVsAny(activeRegionDetectionHackishSamplePloidy,sample.getValue().getBasePileup(), ref.getBase(), MIN_BASE_QUALTY_SCORE, averageHQSoftClips).genotypeLikelihoods; genotypes.add( new GenotypeBuilder(sample.getKey()).alleles(noCall).PL(genotypeLikelihoods).make() ); } final List alleles = Arrays.asList(FAKE_REF_ALLELE , FAKE_ALT_ALLELE); - final VariantCallContext vcOut = activeRegionEvaluationGenotyperEngine.calculateGenotypes(new VariantContextBuilder("HCisActive!", context.getContig(), context.getLocation().getStart(), context.getLocation().getStop(), alleles).genotypes(genotypes).make(), GenotypeLikelihoodsCalculationModel.Model.SNP); - final double isActiveProb = vcOut == null ? 0.0 : QualityUtils.qualToProb( vcOut.getPhredScaledQual() ); + final double isActiveProb; - return new ActivityProfileState( ref.getLocus(), isActiveProb, averageHQSoftClips.mean() > 6.0 ? ActivityProfileState.Type.HIGH_QUALITY_SOFT_CLIPS : ActivityProfileState.Type.NONE, averageHQSoftClips.mean() ); + if (genotypes.size() == 1) { + // Faster implementation avoiding the costly and over complicated Exact AFCalculator machinery: + // This is the case when doing GVCF output. + isActiveProb = activeRegionEvaluationGenotyperEngine.calculateSingleSampleRefVsAnyActiveStateProfileValue(genotypes.get(0).getLikelihoods().getAsVector()); + } else { + final VariantCallContext vcOut = activeRegionEvaluationGenotyperEngine.calculateGenotypes(new VariantContextBuilder("HCisActive!", context.getContig(), context.getLocation().getStart(), context.getLocation().getStop(), alleles).genotypes(genotypes).make(), GenotypeLikelihoodsCalculationModel.Model.SNP); + isActiveProb = vcOut == null ? 0.0 : QualityUtils.qualToProb(vcOut.getPhredScaledQual()); + } + return new ActivityProfileState( ref.getLocus(), isActiveProb, averageHQSoftClips.mean() > AVERAGE_HQ_SOFTCLIPS_HQ_BASES_THRESHOLD ? ActivityProfileState.Type.HIGH_QUALITY_SOFT_CLIPS : ActivityProfileState.Type.NONE, averageHQSoftClips.mean() ); } //--------------------------------------------------------------------------------------------------------------- @@ -1138,7 +1179,7 @@ public class HaplotypeCaller extends ActiveRegionWalker, In private Set filterNonPassingReads( final ActiveRegion activeRegion ) { final Set readsToRemove = new LinkedHashSet<>(); for( final GATKSAMRecord rec : activeRegion.getReads() ) { - if( rec.getReadLength() < MIN_READ_LENGTH || rec.getMappingQuality() < 20 || BadMateFilter.hasBadMate(rec) || (keepRG != null && !rec.getReadGroup().getId().equals(keepRG)) ) { + if( rec.getReadLength() < READ_LENGTH_FILTER_THRESHOLD || rec.getMappingQuality() < READ_QUALITY_FILTER_THRESHOLD || BadMateFilter.hasBadMate(rec) || (keepRG != null && !rec.getReadGroup().getId().equals(keepRG)) ) { readsToRemove.add(rec); } } @@ -1173,7 +1214,7 @@ public class HaplotypeCaller extends ActiveRegionWalker, In * * @return true if HC must emit reference confidence. */ - private boolean emitReferenceConfidence() { + public boolean emitReferenceConfidence() { return HCAC.emitReferenceConfidence != ReferenceConfidenceMode.NONE; } diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java index 1a4b4af39..b2210cd25 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java index e1e449409..813a18946 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -274,7 +274,7 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine + * This is the quality assigned to deletion (so without its own base-call quality) pile-up elements, + * when assessing the confidence on the hom-ref call at that site. + *

    + */ + private final static byte REF_MODEL_DELETION_QUAL = 30; + + /** + * Base calls with quality threshold lower than this number won't be considered when assessing the + * confidence on the hom-ref call. + */ + private final static byte BASE_QUAL_THRESHOLD = 6; + + /** + * Only base calls with quality strictly greater than this constant, + * will be considered high quality if they are part of a soft-clip. + */ + private final static byte HQ_BASE_QUALITY_SOFTCLIP_THRESHOLD = 28; /** * Create a new ReferenceConfidenceModel @@ -146,7 +166,6 @@ public class ReferenceConfidenceModel { if ( debuggingWriter != null ) debuggingWriter.close(); } - /** * Calculate the reference confidence for a single sample given the its read data * @@ -205,9 +224,10 @@ public class ReferenceConfidenceModel { results.add(overlappingSite); } else { // otherwise emit a reference confidence variant context + // Assume infinite population on a single sample. final int refOffset = offset + globalRefOffset; final byte refBase = ref[refOffset]; - final RefVsAnyResult homRefCalc = calcGenotypeLikelihoodsOfRefVsAny(sampleName,ploidy,model,pileup, refBase, (byte)6, null); + final RefVsAnyResult homRefCalc = calcGenotypeLikelihoodsOfRefVsAny(ploidy, pileup, refBase, BASE_QUAL_THRESHOLD, null); homRefCalc.capByHomRefLikelihood(); final Allele refAllele = Allele.create(refBase, true); @@ -267,8 +287,27 @@ public class ReferenceConfidenceModel { protected static final int MAX_N_INDEL_INFORMATIVE_READS = 40; // more than this is overkill because GQs are capped at 99 anyway private static final int INITIAL_INDEL_LK_CACHE_PLOIDY_CAPACITY = 20; private static GenotypeLikelihoods[][] indelPLCache = new GenotypeLikelihoods[INITIAL_INDEL_LK_CACHE_PLOIDY_CAPACITY + 1][]; + + /** + * Indel error rate for the indel model used to assess the confidence on the hom-ref call. + */ private static final double INDEL_ERROR_RATE = -4.5; // 10^-4.5 indel errors per bp + /** + * Phred scaled qual value that corresponds to the {@link #INDEL_ERROR_RATE indel error rate}. + */ + private static final byte INDEL_QUAL = (byte) Math.round((INDEL_ERROR_RATE * -10.0)); + + /** + * No indel likelihood (ref allele) used in the indel model to assess the confidence on the hom-ref call. + */ + private static final double NO_INDEL_LIKELIHOOD = QualityUtils.qualToProbLog10(INDEL_QUAL); + + /** + * Indel likelihood (alt. allele) used in the indel model to assess the confidence on the hom-ref call. + */ + private static final double INDEL_LIKELIHOOD = QualityUtils.qualToErrorProbLog10(INDEL_QUAL); + private final GenotypeLikelihoods indelPLCache(final int ploidy, final int nInformativeReads) { return initializeIndelPLCache(ploidy)[nInformativeReads]; } @@ -285,14 +324,11 @@ public class ReferenceConfidenceModel { final GenotypeLikelihoods[] result = new GenotypeLikelihoods[MAX_N_INDEL_INFORMATIVE_READS + 1]; result[0] = GenotypeLikelihoods.fromLog10Likelihoods(new double[ploidy + 1]); for( int nInformativeReads = 1; nInformativeReads <= MAX_N_INDEL_INFORMATIVE_READS; nInformativeReads++ ) { - final byte indelQual = (byte) Math.round((INDEL_ERROR_RATE * -10)); - final double refLikelihood = QualityUtils.qualToProbLog10(indelQual); - final double altLikelihood = QualityUtils.qualToErrorProbLog10(indelQual); double[] PLs = new double[ploidy + 1]; - PLs[0] = nInformativeReads * refLikelihood; + PLs[0] = nInformativeReads * NO_INDEL_LIKELIHOOD; for (int altCount = 1; altCount <= ploidy; altCount++) { - final double refLikelihoodAccum = refLikelihood + MathUtils.Log10Cache.get(ploidy - altCount); - final double altLikelihoodAccum = altLikelihood + MathUtils.Log10Cache.get(altCount); + final double refLikelihoodAccum = NO_INDEL_LIKELIHOOD + MathUtils.Log10Cache.get(ploidy - altCount); + final double altLikelihoodAccum = INDEL_LIKELIHOOD + MathUtils.Log10Cache.get(altCount); PLs[altCount] = nInformativeReads * (MathUtils.approximateLog10SumLog10(refLikelihoodAccum ,altLikelihoodAccum) + denominator); } result[nInformativeReads] = GenotypeLikelihoods.fromLog10Likelihoods(PLs); @@ -304,70 +340,64 @@ public class ReferenceConfidenceModel { /** * Calculate the genotype likelihoods for the sample in pileup for being hom-ref contrasted with being ref vs. alt * - * @param sampleName target sample name. * @param ploidy target sample ploidy. - * @param genotypingModel model to calculate likelihoods and genotypes. * @param pileup the read backed pileup containing the data we want to evaluate * @param refBase the reference base at this pileup position * @param minBaseQual the min base quality for a read in the pileup at the pileup position to be included in the calculation * @param hqSoftClips running average data structure (can be null) to collect information about the number of high quality soft clips * @return a RefVsAnyResult genotype call. */ - public RefVsAnyResult calcGenotypeLikelihoodsOfRefVsAny(final String sampleName, final int ploidy, - final GenotypingModel genotypingModel, - final ReadBackedPileup pileup, final byte refBase, final byte minBaseQual, final MathUtils.RunningAverage hqSoftClips) { - final AlleleList alleleList = new IndexedAlleleList<>(Allele.create(refBase,true), GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE); - // Notice that the sample name is rather irrelevant as this information is never used, just need to be the same in both lines bellow. + public RefVsAnyResult calcGenotypeLikelihoodsOfRefVsAny(final int ploidy, + final ReadBackedPileup pileup, + final byte refBase, + final byte minBaseQual, + final MathUtils.RunningAverage hqSoftClips) { - final int maximumReadCount = pileup.getReads().size(); + final int likelihoodCount = ploidy + 1; + final double log10Ploidy = MathUtils.Log10Cache.get(ploidy); - final List reads = new ArrayList<>(maximumReadCount); - final double[][] likelihoods = new double[2][maximumReadCount]; - final int[] adCounts = new int[2]; - int nextIndex = 0; + final RefVsAnyResult result = new RefVsAnyResult(likelihoodCount); + int readCount = 0; for (final PileupElement p : pileup) { final byte qual = p.isDeletion() ? REF_MODEL_DELETION_QUAL : p.getQual(); if (!p.isDeletion() && qual <= minBaseQual) continue; - final GATKSAMRecord read = p.getRead(); - reads.add(read); - final boolean isAlt = p.getBase() != refBase || p.isDeletion() || p.isBeforeDeletionStart() - || p.isAfterDeletionEnd() || p.isBeforeInsertion() || p.isAfterInsertion() || p.isNextToSoftClip(); - final int bestAllele; - final int worstAllele; - if (isAlt) { - bestAllele = 1; - worstAllele = 0; - } else { - bestAllele = 0; - worstAllele = 1; - } - - likelihoods[bestAllele][nextIndex] = QualityUtils.qualToProbLog10(qual); - likelihoods[worstAllele][nextIndex++] = QualityUtils.qualToErrorProbLog10(qual) + MathUtils.LOG_ONE_THIRD; - adCounts[bestAllele]++; - if (isAlt && hqSoftClips != null && p.isNextToSoftClip()) - hqSoftClips.add(AlignmentUtils.calcNumHighQualitySoftClips(read, (byte) 28)); + readCount++; + calcPileupElementRefVsNonRefLikelihoodAndCount(refBase, likelihoodCount, log10Ploidy, result, p, qual, hqSoftClips); } - - final Map> sampleToReads = Collections.singletonMap(sampleName,reads); - final ReadLikelihoods readLikelihoods = new ReadLikelihoods<>(new IndexedSampleList(sampleName),alleleList,sampleToReads); - final ReadLikelihoods.Matrix sampleLikelihoods = readLikelihoods.sampleMatrix(0); - final int readCount = sampleLikelihoods.readCount(); - for (int i = 0; i < readCount; i++) { - sampleLikelihoods.set(0,i,likelihoods[0][i]); - sampleLikelihoods.set(1,i,likelihoods[1][i]); - } - - final PloidyModel ploidyModel = new HomogeneousPloidyModel(new IndexedSampleList(sampleName),ploidy); - final GenotypingLikelihoods genotypingLikelihoods = genotypingModel.calculateLikelihoods(alleleList, new GenotypingData<>(ploidyModel, readLikelihoods)); - final double[] genotypeLikelihoodArray = genotypingLikelihoods.sampleLikelihoods(0).getAsVector(); - final RefVsAnyResult result = new RefVsAnyResult(genotypeLikelihoodArray.length); - System.arraycopy(genotypeLikelihoodArray,0,result.genotypeLikelihoods,0,genotypeLikelihoodArray.length); - System.arraycopy(adCounts,0,result.AD_Ref_Any,0,2); + final double denominator = readCount * log10Ploidy; + for (int i = 0; i < likelihoodCount; i++) + result.genotypeLikelihoods[i] -= denominator; return result; } + private void calcPileupElementRefVsNonRefLikelihoodAndCount(final byte refBase, final int likelihoodCount, final double log10Ploidy, final RefVsAnyResult result, final PileupElement element, final byte qual, final MathUtils.RunningAverage hqSoftClips) { + final boolean isAlt = element.getBase() != refBase || element.isDeletion() || element.isBeforeDeletionStart() + || element.isAfterDeletionEnd() || element.isBeforeInsertion() || element.isAfterInsertion() || element.isNextToSoftClip(); + final double referenceLikelihood; + final double nonRefLikelihood; + if (isAlt) { + nonRefLikelihood = QualityUtils.qualToProbLog10(qual); + referenceLikelihood = QualityUtils.qualToErrorProbLog10(qual) + MathUtils.LOG_ONE_THIRD; + result.AD_Ref_Any[1]++; + } else { + referenceLikelihood = QualityUtils.qualToProbLog10(qual); + nonRefLikelihood = QualityUtils.qualToErrorProbLog10(qual) + MathUtils.LOG_ONE_THIRD; + result.AD_Ref_Any[0]++; + } + // Homozygous likelihoods don't need the logSum trick. + result.genotypeLikelihoods[0] += referenceLikelihood + log10Ploidy; + result.genotypeLikelihoods[likelihoodCount - 1] += nonRefLikelihood + log10Ploidy; + // Heterozyougs likelihoods need the logSum trick: + for (int i = 1, j = likelihoodCount - 2; i < likelihoodCount - 1; i++, j--) + result.genotypeLikelihoods[i] += + MathUtils.approximateLog10SumLog10( + referenceLikelihood + MathUtils.Log10Cache.get(j), + nonRefLikelihood + MathUtils.Log10Cache.get(i)); + if (isAlt && hqSoftClips != null && element.isNextToSoftClip()) + hqSoftClips.add(AlignmentUtils.calcNumHighQualitySoftClips(element.getRead(), HQ_BASE_QUALITY_SOFTCLIP_THRESHOLD)); + } + /** * Get a list of pileups that span the entire active region span, in order, one for each position */ @@ -491,20 +521,12 @@ public class ReferenceConfidenceModel { // consider each indel size up to max in term, checking if an indel that deletes either the ref bases (deletion // or read bases (insertion) would fit as well as the origin baseline sum of mismatching quality scores for ( int indelSize = 1; indelSize <= maxIndelSize; indelSize++ ) { - for ( final boolean checkInsertion : Arrays.asList(true, false) ) { - final int readI, refI; - if ( checkInsertion ) { - readI = readStart + indelSize; - refI = refStart; - } else { - readI = readStart; - refI = refStart + indelSize; - } - - final int score = sumMismatchingQualities(readBases, readQuals, readI, refBases, refI, baselineMMSum); - if ( score <= baselineMMSum ) - return false; - } + // check insertions: + if (sumMismatchingQualities(readBases, readQuals, readStart + indelSize, refBases, refStart, baselineMMSum) <= baselineMMSum) + return false; + // check deletions: + if (sumMismatchingQualities(readBases, readQuals, readStart, refBases, refStart + indelSize, baselineMMSum) <= baselineMMSum) + return false; } return true; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/AggregatedSubHaplotypeFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/AggregatedSubHaplotypeFinder.java index 04788e25e..fb397963a 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/AggregatedSubHaplotypeFinder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/AggregatedSubHaplotypeFinder.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseEdge.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseEdge.java index a11331502..63cb82174 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseEdge.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseEdge.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraph.java index be049fa3f..973c9ca27 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraph.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraph.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphIterator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphIterator.java index 2c07ff48f..daa9b48f1 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphIterator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphIterator.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseVertex.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseVertex.java index 8d4e4d6d5..5fd4f8fff 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseVertex.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseVertex.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java index 8cbca1aad..03c8c1424 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeBruijnVertex.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeBruijnVertex.java index 658ac42ba..4d436282e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeBruijnVertex.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeBruijnVertex.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeadEndKBestSubHaplotypeFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeadEndKBestSubHaplotypeFinder.java index 9a5b62015..ecb5b4b87 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeadEndKBestSubHaplotypeFinder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeadEndKBestSubHaplotypeFinder.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/EmptyPathHaplotypeFinderNode.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/EmptyPathHaplotypeFinderNode.java index dc086dc68..e0d084c75 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/EmptyPathHaplotypeFinderNode.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/EmptyPathHaplotypeFinderNode.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/GraphUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/GraphUtils.java index 1a8514f23..7dfbb1b0e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/GraphUtils.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/GraphUtils.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotype.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotype.java index 1943765f8..2f9717757 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotype.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotype.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinder.java index 9048046fe..343b6b1c7 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinder.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -90,7 +90,7 @@ public class KBestHaplotypeFinder extends AbstractList implement /** * The top finder. * - *

    If there is only a single source vertex, its finder is the top finder. However whent there + *

    If there is only a single source vertex, its finder is the top finder. However when there * is more than one possible source, we create a composite finder that alternates between individual source vertices * for their best haplotypes.

    */ @@ -472,44 +472,18 @@ public class KBestHaplotypeFinder extends AbstractList implement * The resulting list is sorted by the score with more likely haplotype search results first. *

    * - * @param maxSize maximum number of unique results to return. - * - * @throws IllegalArgumentException if {@code maxSize} is negative. - * - * @return never {@code null}, perhaps an empty list. - */ - public List unique(final int maxSize) { - if (maxSize < 0) throw new IllegalArgumentException("maxSize cannot be negative"); - final int requiredCapacity = Math.min(maxSize,size()); - final Set haplotypes = new HashSet<>(requiredCapacity); - int resultSize = 0; - final List result = new ArrayList<>(requiredCapacity); - for (final KBestHaplotype kbh : this) { - if (haplotypes.add(kbh.haplotype())) { - result.add(kbh); - if (resultSize == maxSize) break; - } - } - return result; - } - - /** - * Returns a unique list of haplotypes solutions. - * - *

    - * The result will not contain more than one haplotype with the same base sequence. The solution of the best - * score is returned. - *

    - *

    - * This makes sense when there are more than one possible path through the graph to create the same haplotype. - *

    - *

    - * The resulting list is sorted by the score with more likely haplotype search results first. - *

    * * @return never {@code null}, perhaps an empty list. */ public List unique() { - return unique(size()); + final int requiredCapacity = size(); + final Set haplotypes = new HashSet<>(requiredCapacity); + final List result = new ArrayList<>(requiredCapacity); + for (final KBestHaplotype kbh : this) { + if (haplotypes.add(kbh.haplotype())) { + result.add(kbh); + } + } + return result; } } diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestSubHaplotypeFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestSubHaplotypeFinder.java index 92ebbe1af..2a2ea9a1d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestSubHaplotypeFinder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestSubHaplotypeFinder.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KmerSearchableGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KmerSearchableGraph.java index 2d208f919..171aa70e6 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KmerSearchableGraph.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KmerSearchableGraph.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/LowWeightChainPruner.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/LowWeightChainPruner.java index c67a973b1..6f6c00b6f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/LowWeightChainPruner.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/LowWeightChainPruner.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -140,10 +140,10 @@ public class LowWeightChainPruner { // must be after since we can add duplicate starts in the above finding algorithm final List> linearChains = new LinkedList<>(); + final PathBuilder builder = new PathBuilder<>(graph, 100); for ( final V chainStart : chainStarts ) { for ( final E outEdge : graph.outgoingEdgesOf(chainStart) ) { - // these chains are composed of the starts + their next vertices - linearChains.add(extendLinearChain(new Path<>(new Path<>(chainStart, graph), outEdge))); + linearChains.add(extendLinearChain(builder.start(chainStart).addEdge(outEdge)).make()); } } @@ -152,28 +152,29 @@ public class LowWeightChainPruner { /** * Extend path while the last vertex has in and out degrees of 1 or 0 - * @param path the path to extend + * @param builder the path builder already started * @return a fully extended linear path */ - protected final Path extendLinearChain(final Path path) { - final V last = path.getLastVertex(); - final Set outEdges = path.getGraph().outgoingEdgesOf(last); - - final int outDegree = outEdges.size(); - final int inDegree = path.getGraph().inDegreeOf(last); - - if ( outDegree != 1 || inDegree > 1 ) { - // out next vertex has multiple outgoing edges, so we are done with the linear path - return path; - } else { - final V next = path.getGraph().getEdgeTarget(outEdges.iterator().next()); - if ( path.containsVertex(next) ) { - // we are done if the path contains a cycle - return path; - } else { - // we now know that last has outdegree == 1, so we keep extending the chain - return extendLinearChain(new Path<>(path, outEdges.iterator().next())); + protected final PathBuilder extendLinearChain(final PathBuilder builder) { + final BaseGraph graph = builder.getGraph(); + V last = builder.lastVertex(); + while (true) { + final Set outEdges = graph.outgoingEdgesOf(last); + final int outDegree = outEdges.size(); + final int inDegree = graph.inDegreeOf(last); + if ( outDegree != 1 || inDegree > 1 ) + break; + else { + final E edge = outEdges.iterator().next(); + final V next = graph.getEdgeTarget(edge); + if (builder.containsVertex(next)) + break; + else { + builder.addEdge(edge); + last = next; + } } } + return builder; } } diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/MultiSampleEdge.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/MultiSampleEdge.java index 067ab49d0..d63d88fb8 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/MultiSampleEdge.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/MultiSampleEdge.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/Path.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/Path.java index 9a94f4c13..1a990e0a1 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/Path.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/Path.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -72,10 +72,7 @@ public class Path { // the last vertex seen in the path protected final T lastVertex; - - // the list of edges comprising the path - private Set edgesAsSet = null; - protected final ArrayList edgesInOrder; + protected final List edgesInOrder; // the scores for the path protected final int totalScore; @@ -94,13 +91,22 @@ public class Path { if ( ! graph.containsVertex(initialVertex) ) throw new IllegalArgumentException("Vertex " + initialVertex + " must be part of graph " + graph); lastVertex = initialVertex; - edgesInOrder = new ArrayList<>(0); + edgesInOrder = Collections.emptyList(); totalScore = 0; this.graph = graph; } + protected Path(final BaseGraph graph, final List edges, final T lastVertex, final int totalScore) { + this.graph = graph; + edgesInOrder = edges; + this.lastVertex = lastVertex; + this.totalScore = totalScore; + } + /** * Convenience constructor for testing that creates a path through vertices in graph + * + * @deprecated use {@link PathBuilder}. */ protected static Path makePath(final List vertices, final BaseGraph graph) { Path path = new Path(vertices.get(0), graph); @@ -119,7 +125,6 @@ public class Path { protected Path(final Path p) { this.edgesInOrder = p.edgesInOrder; this.lastVertex = p.lastVertex; - this.edgesAsSet = p.edgesAsSet; this.totalScore = p.totalScore; this.graph = p.graph; } @@ -178,42 +183,7 @@ public class Path { totalScore = p.totalScore + edge.getMultiplicity(); } - /** - * Get the collection of edges leaving the last vertex of this path - * @return a non-null collection - */ - public Collection getOutgoingEdgesOfLastVertex() { - return getGraph().outgoingEdgesOf(getLastVertex()); - } - - /** - * Does this path contain the given edge - * @param edge the given edge to test - * @return true if the edge is found in this path - */ - public boolean containsEdge( final E edge ) { - if( edge == null ) { throw new IllegalArgumentException("Attempting to test null edge."); } - if ( edgesInOrder.isEmpty() ) return false; - - // initialize contains cache if necessary - if ( edgesAsSet == null ) edgesAsSet = new HashSet(edgesInOrder); - return edgesAsSet.contains(edge); - } - - /** - * Does this path contain the given vertex? - * - * @param v a non-null vertex - * @return true if v occurs within this path, false otherwise - */ - public boolean containsVertex(final T v) { - if ( v == null ) throw new IllegalArgumentException("Vertex cannot be null"); - - // TODO -- warning this is expensive. Need to do vertex caching - return getVertices().contains(v); - } - - /** + /** * Checks whether a given path is a suffix of this path. * * @param other the path to compare against. diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathBuilder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathBuilder.java new file mode 100644 index 000000000..64a60ab3b --- /dev/null +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathBuilder.java @@ -0,0 +1,214 @@ +/* +* By downloading the PROGRAM you agree to the following terms of use: +* +* BROAD INSTITUTE +* SOFTWARE LICENSE AGREEMENT +* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and +* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. +* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: +* +* 1. DEFINITIONS +* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. +* +* 2. LICENSE +* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. +* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. +* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. +* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. +* +* 3. PHONE-HOME FEATURE +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* +* 4. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012-2015 Broad Institute, Inc. +* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 5. INDEMNIFICATION +* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. +* +* 6. NO REPRESENTATIONS OR WARRANTIES +* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. +* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. +* +* 7. ASSIGNMENT +* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. +* +* 8. MISCELLANEOUS +* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. +* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. +* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. +* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. +* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. +* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. +* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +*/ + +package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs; + +import java.util.ArrayList; +import java.util.LinkedHashSet; +import java.util.List; +import java.util.Set; + +/** + * Path builder. + *

    + * Allows the creation of graph path is a efficiently (linear given the length of the path). + *

    + * + * @author Valentin Ruano-Rubio <valentin@broadinstitute.org> + */ +public final class PathBuilder { + + private final BaseGraph graph; + private Set vertices; + + private List edges; + private V lastVertex; + private boolean needToFork; + private final int estimatedPathLength; + private int totalScore; + + /** + * Creates a path builder given the underlying graph and the expected path length. + * + *

    + * The path length estimate does not need to be accurate. + *

    + * @param graph the target graph. + * @param estimatedPathLength the expected path length. + */ + public PathBuilder(final BaseGraph graph, final int estimatedPathLength) { + if (graph == null) throw new IllegalArgumentException("the graph cannot be null"); + if (estimatedPathLength < 0) throw new IllegalArgumentException("the length estimate cannot be null"); + this.estimatedPathLength = estimatedPathLength; + this.graph = graph; + lastVertex = null; + vertices = new LinkedHashSet<>(estimatedPathLength + 1); + edges = new ArrayList<>(estimatedPathLength); + needToFork = false; + totalScore = 0; + } + + /** + * Starts a new path given the first vertex in the path. + * + * + * @param vertex the path start vertex. + * @return this builder. + */ + public PathBuilder start(final V vertex) { + if (vertex == null) throw new IllegalArgumentException("the vertex cannot be null"); + if (!graph.containsVertex(vertex)) throw new IllegalArgumentException("the vertex must belong to the builder graph"); + forkIfNeededAndClear(); + lastVertex = vertex; + vertices.add(vertex); + totalScore = 0; + return this; + } + + /** + * Extends the current path through an edge. + *

    + * The edge provided must have the last vertex in the path as the source vertex. + *

    + * @param extension the extension edge. + * @return this builder. + */ + public PathBuilder addEdge(final E extension) { + if (lastVertex == null) throw new IllegalStateException("the path has not been started"); + if (extension == null) throw new IllegalArgumentException("the input extension edge cannot be null"); + final V source = graph.getEdgeSource(extension); + if (source != lastVertex) throw new IllegalArgumentException("the extension edge source is not the last vertex"); + final V target = graph.getEdgeTarget(extension); + forkIfNeeded(); + vertices.add(target); + edges.add(extension); + totalScore += extension.getMultiplicity(); + lastVertex = target; + return this; + } + + /** + * Create the {@link Path} object that represents the current path. + *

    + * Later changes in the builder won't affect the path returned. + *

    + * + * @return never {@code null}. + */ + public Path make() { + if (lastVertex == null) throw new IllegalStateException("no path was started"); + forkIfNeeded(); + needToFork = true; + return new Path(graph, edges, lastVertex, totalScore); + } + + /** + * Forks the current builder state. + *

    + * After a path is made, we need to clone the collection in the builder if any further edition takes place. + *

    + */ + private void forkIfNeeded() { + if (needToFork) { + vertices = new LinkedHashSet<>(vertices); + edges = new ArrayList<>(edges); + needToFork = false; + } + } + + /** + * + */ + private void forkIfNeededAndClear() { + if (needToFork) { + vertices = new LinkedHashSet<>(Math.max(vertices.size(), estimatedPathLength)); + edges = new ArrayList<>(Math.max(edges.size(), estimatedPathLength)); + lastVertex = null; + totalScore = 0; + needToFork = false; + } else { + vertices.clear(); + edges.clear(); + totalScore = 0; + lastVertex = null; + } + } + + /** + * Returns the underlying graph. + * @return never {@code null}. + */ + public BaseGraph getGraph() { + return graph; + } + + /** + * Returns the last vertex in the path. + * + * @return never {@code null}. + * @throws IllegalStateException if no path was started. + */ + public V lastVertex() { + if (lastVertex == null) throw new IllegalStateException("no path was started"); + return lastVertex; + } + + /** + * Checks whether the current path contains a vertex. + * + * @param vertex the query vertex. + * @return {@code true} iff the current path contains the input vertex. + */ + public boolean containsVertex(final V vertex) { + if (vertex == null) throw new IllegalArgumentException(); + return vertices.contains(vertex); + } +} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RecursiveSubHaplotypeFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RecursiveSubHaplotypeFinder.java index 355897e96..aedfd127f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RecursiveSubHaplotypeFinder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RecursiveSubHaplotypeFinder.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/Route.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/Route.java index 6ba820721..69166699f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/Route.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/Route.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RouteFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RouteFinder.java index 7194a2670..a4e59005b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RouteFinder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RouteFinder.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqGraph.java index e6b4c297a..7c8d45086 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqGraph.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqGraph.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqVertex.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqVertex.java index 85c04fe42..ec5fd5fbe 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqVertex.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqVertex.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedSequenceMerger.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedSequenceMerger.java index 80fdb148d..66452e229 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedSequenceMerger.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedSequenceMerger.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java index 5b5d5bcd9..48cf29ebe 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/TestGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/TestGraph.java index 674a36afb..96040a64d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/TestGraph.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/TestGraph.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/VertexOrder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/VertexOrder.java index eb9055163..27e413cf2 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/VertexOrder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/VertexOrder.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraph.java index 1dd1c4c3e..9ceed6b15 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraph.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraph.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/HaplotypeGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/HaplotypeGraph.java index b5c334e0b..79ceeffb5 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/HaplotypeGraph.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/HaplotypeGraph.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java index fbe4c874c..6053ac550 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java index f9de3173a..8985ede87 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java index 5245a9712..ace1b80a1 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -52,7 +52,6 @@ package org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading; import org.apache.log4j.Logger; -import org.broadinstitute.gatk.tools.walkers.haplotypecaller.KMerCounter; import org.broadinstitute.gatk.tools.walkers.haplotypecaller.Kmer; import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.*; import org.broadinstitute.gatk.utils.BaseUtils; @@ -442,14 +441,17 @@ public class ReadThreadingGraph extends DanglingChainMergingGraph implements Kme */ static protected Collection determineNonUniqueKmers(final SequenceForKmers seqForKmers, final int kmerSize) { // count up occurrences of kmers within each read - final KMerCounter counter = new KMerCounter(kmerSize); + final int stopPosition = seqForKmers.stop - kmerSize; + final Set result = new LinkedHashSet<>(stopPosition + 1); + final Set allKmers = new HashSet<>(stopPosition + 1); for ( int i = 0; i <= stopPosition; i++ ) { final Kmer kmer = new Kmer(seqForKmers.sequence, i, kmerSize); - counter.addKmer(kmer, 1); + if (!allKmers.add(kmer)) { + result.add(kmer); + } } - - return counter.getKmersWithCountsAtLeast(2); + return result; } @Override diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/SequenceForKmers.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/SequenceForKmers.java index 0c9feb746..3ae440b1b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/SequenceForKmers.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/SequenceForKmers.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManager.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManager.java index 4ac4f5739..10c118c31 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManager.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManager.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -279,7 +279,7 @@ public class ConstrainedMateFixingManager { // fix mates, as needed // Since setMateInfo can move reads, we potentially need to remove the mate, and requeue // it to ensure proper sorting - if ( newRead.getReadPairedFlag() && !newRead.getNotPrimaryAlignmentFlag() ) { + if ( isMateFixableRead(newRead) ) { SAMRecordHashObject mate = forMateMatching.get(newRead.getReadName()); if ( mate != null ) { // 1. Frustratingly, Picard's setMateInfo() method unaligns (by setting the reference contig @@ -307,13 +307,9 @@ public class ConstrainedMateFixingManager { reQueueMate = false; } - // we've already seen our mate -- set the mate info and remove it from the map - // Via Nils Homer: - // There will be two SamPairUtil.setMateInfo functions. The default will not update the mate - // cigar tag; in fact, it will remove it if it is present. An alternative SamPairUtil.setMateInfo - // function takes a boolean as an argument ("addMateCigar") and will add/update the mate cigar if - // set to true. This is the one you want to use. - SamPairUtil.setMateInfo(mate.record, newRead, null, true); + // we've already seen our mate -- set the mate info and remove it from the map; + // add/update the mate cigar if appropriate + SamPairUtil.setMateInfo(mate.record, newRead, true); if ( reQueueMate ) waitingReads.add(mate.record); } @@ -364,6 +360,16 @@ public class ConstrainedMateFixingManager { } } + /** + * Is the given read one for which we can fix its mate? + * + * @param read the read + * @return true if we could fix its mate, false otherwise + */ + protected boolean isMateFixableRead(final SAMRecord read) { + return read.getReadPairedFlag() && !read.isSecondaryOrSupplementary(); + } + /** * @param read the read * @return true if the read shouldn't be moved given the constraints of this SAMFileWriter diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/HaplotypeIndelErrorModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/HaplotypeIndelErrorModel.java index f5639a982..1195c9bb5 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/HaplotypeIndelErrorModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/HaplotypeIndelErrorModel.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java index 75df30550..050d174ca 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -130,7 +130,7 @@ import java.util.*; * -T IndelRealigner \ * -R reference.fasta \ * -I input.bam \ - * --known indels.vcf \ + * -known indels.vcf \ * -targetIntervals intervalListFromRTC.intervals \ * -o realignedBam.bam * @@ -394,7 +394,7 @@ public class IndelRealigner extends ReadWalker { throw new RuntimeException("Entropy threshold must be a fraction between 0 and 1"); try { - referenceReader = new CachingIndexedFastaSequenceFile(getToolkit().getArguments().referenceFile); + referenceReader = new CachingIndexedFastaSequenceFile(getToolkit().getArguments().referenceFile, false, true); } catch(FileNotFoundException ex) { throw new UserException.CouldNotReadInputFile(getToolkit().getArguments().referenceFile,ex); diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/LeftAlignIndels.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/LeftAlignIndels.java index a6afa812a..7421311ff 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/LeftAlignIndels.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/LeftAlignIndels.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModel.java index ba9c985db..dd502a354 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModel.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBin.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBin.java index f1b68f3d8..9d9975cea 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBin.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBin.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreator.java index a81af2e5a..a5354831a 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreator.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -51,6 +51,11 @@ package org.broadinstitute.gatk.tools.walkers.indels; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.util.IOUtil; +import htsjdk.samtools.util.Interval; +import htsjdk.samtools.util.IntervalList; +import org.apache.commons.io.FilenameUtils; import org.broadinstitute.gatk.engine.walkers.*; import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.utils.commandline.Input; @@ -61,6 +66,7 @@ import org.broadinstitute.gatk.utils.contexts.AlignmentContext; import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.engine.filters.*; import org.broadinstitute.gatk.engine.iterators.ReadTransformer; +import org.broadinstitute.gatk.utils.exceptions.GATKException; import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.exceptions.UserException; @@ -70,7 +76,9 @@ import org.broadinstitute.gatk.utils.pileup.PileupElement; import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; import htsjdk.variant.variantcontext.VariantContext; -import java.io.PrintStream; +import java.io.BufferedWriter; +import java.io.File; +import java.io.IOException; import java.util.ArrayList; import java.util.Collections; import java.util.List; @@ -143,7 +151,7 @@ public class RealignerTargetCreator extends RodWalker - *
  • DeNovoPrior: Mutation prio; default is 1e-8
    • + *
  • DeNovoPrior: Prior probability of de novo mutations. The default value of 1e-8 is fairly stringent, so if + * you are interested in maximizing sensitivity at the expense of specificity (i.e. are ok with seeing some false + * positives as long as all true positives are detected) you will need to relax this value.
    • *
* *

Output

@@ -138,7 +140,7 @@ import java.util.*; * * */ -@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARDISC, extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} ) public class PhaseByTransmission extends RodWalker, HashMap> { @ArgumentCollection diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingGraph.java index cfd6d5a4c..d2e4f95c2 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingGraph.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingGraph.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingGraphEdge.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingGraphEdge.java index f1955f251..6151e5706 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingGraphEdge.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingGraphEdge.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingRead.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingRead.java index 696c9840f..f68955b40 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingRead.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingRead.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtils.java index 0dc151895..24060876b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtils.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtils.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PreciseNonNegativeDouble.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PreciseNonNegativeDouble.java index a5c121e5e..81d16670a 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PreciseNonNegativeDouble.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PreciseNonNegativeDouble.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasing.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasing.java index ad46e191b..a5d4f38f5 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasing.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasing.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -138,7 +138,7 @@ import static org.broadinstitute.gatk.engine.GATKVCFUtils.getVCFHeadersFromRods; // Filter out all reads with zero mapping quality @ReadFilters({MappingQualityZeroFilter.class}) -@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARDISC, extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} ) public class ReadBackedPhasing extends RodWalker { @Argument(fullName="debug", shortName="debug", doc="If specified, print out very verbose debug information (if -l DEBUG is also specified)", required = false) protected boolean DEBUG = false; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBase.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBase.java index 4df7cda30..416dc538b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBase.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBase.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBasesAtPosition.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBasesAtPosition.java index 98c069b75..1fd05ed0f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBasesAtPosition.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBasesAtPosition.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/SNPallelePair.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/SNPallelePair.java index d91f68b4c..3c38794c3 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/SNPallelePair.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/SNPallelePair.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManager.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManager.java index c1693c95d..809f97214 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManager.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManager.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReads.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReads.java index 4aaaf9c77..ced1e9ce5 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReads.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReads.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariants.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariants.java index d2ad91e97..616b36a4b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariants.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariants.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/GenotypeAndValidate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/GenotypeAndValidate.java index 09346919a..ca3da994c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/GenotypeAndValidate.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/GenotypeAndValidate.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/FrequencyModeSelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/FrequencyModeSelector.java index 3d96ea4e5..b9228f23c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/FrequencyModeSelector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/FrequencyModeSelector.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GLBasedSampleSelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GLBasedSampleSelector.java index cc8611c06..6d2cf5296 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GLBasedSampleSelector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GLBasedSampleSelector.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GTBasedSampleSelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GTBasedSampleSelector.java index 54f4888a3..a7d716c24 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GTBasedSampleSelector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GTBasedSampleSelector.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GenomeEvent.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GenomeEvent.java index 40eb9fc31..78bc3b5f9 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GenomeEvent.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GenomeEvent.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java index 6e4de0860..897ef9a81 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/NullSampleSelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/NullSampleSelector.java index b7f44063f..dc6c1ba58 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/NullSampleSelector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/NullSampleSelector.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/SampleSelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/SampleSelector.java index 470c59157..c2e86faa9 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/SampleSelector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/SampleSelector.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java index 8ec51c3ed..7e459c021 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/ValidationSiteSelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/ValidationSiteSelector.java index 01572780d..c64070cff 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/ValidationSiteSelector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/ValidationSiteSelector.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibration.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibration.java index 2361ca64e..b6ef38ade 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibration.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibration.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/GaussianMixtureModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/GaussianMixtureModel.java index 1eb555f2c..624b6c062 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/GaussianMixtureModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/GaussianMixtureModel.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/MultivariateGaussian.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/MultivariateGaussian.java index 3c8c48a4e..7365340f2 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/MultivariateGaussian.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/MultivariateGaussian.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/TrainingSet.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/TrainingSet.java index 3135a390c..55a26bc42 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/TrainingSet.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/TrainingSet.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/Tranche.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/Tranche.java index c9383758c..f6167e8c4 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/Tranche.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/Tranche.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/TrancheManager.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/TrancheManager.java index 636dd8ece..2290f3c76 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/TrancheManager.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/TrancheManager.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManager.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManager.java index febef6138..cac206083 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManager.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManager.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -84,6 +84,8 @@ public class VariantDataManager { private final VariantRecalibratorArgumentCollection VRAC; protected final static Logger logger = Logger.getLogger(VariantDataManager.class); protected final List trainingSets; + private static final double SAFETY_OFFSET = 0.01; //To use for example as 1/(X + SAFETY_OFFSET) to protect against dividing or taking log of X=0. + private static final double PRECISION = 0.01; //To use mainly with MathUrils.compareDoubles(a,b,PRECISON) public VariantDataManager( final List annotationKeys, final VariantRecalibratorArgumentCollection VRAC ) { this.data = Collections.emptyList(); @@ -334,15 +336,19 @@ public class VariantDataManager { int iii = 0; for( final String key : annotationKeys ) { isNull[iii] = false; - annotations[iii] = decodeAnnotation( key, vc, jitter ); + annotations[iii] = decodeAnnotation( key, vc, jitter, VRAC ); if( Double.isNaN(annotations[iii]) ) { isNull[iii] = true; } iii++; } datum.annotations = annotations; datum.isNull = isNull; } + /** Transforms an interval [xmin, xmax] to (-inf, +inf) **/ + private static double logitTransform( final double x, final double xmin, final double xmax) { + return Math.log((x - xmin)/(xmax - x)); + } - private static double decodeAnnotation( final String annotationKey, final VariantContext vc, final boolean jitter ) { + private static double decodeAnnotation( final String annotationKey, final VariantContext vc, final boolean jitter, final VariantRecalibratorArgumentCollection vrac ) { double value; final double LOG_OF_TWO = 0.6931472; @@ -350,10 +356,20 @@ public class VariantDataManager { try { value = vc.getAttributeAsDouble( annotationKey, Double.NaN ); if( Double.isInfinite(value) ) { value = Double.NaN; } - if( jitter && annotationKey.equalsIgnoreCase("HaplotypeScore") && MathUtils.compareDoubles(value, 0.0, 0.01) == 0 ) { value += 0.01 * Utils.getRandomGenerator().nextGaussian(); } - if( jitter && annotationKey.equalsIgnoreCase("FS") && MathUtils.compareDoubles(value, 0.0, 0.01) == 0 ) { value += 0.01 * Utils.getRandomGenerator().nextGaussian(); } - if( jitter && annotationKey.equalsIgnoreCase("InbreedingCoeff") && MathUtils.compareDoubles(value, 0.0, 0.01) == 0 ) { value += 0.01 * Utils.getRandomGenerator().nextGaussian(); } - if( jitter && annotationKey.equalsIgnoreCase("SOR") && MathUtils.compareDoubles(value, LOG_OF_TWO, 0.01) == 0 ) { value += 0.01 * Utils.getRandomGenerator().nextGaussian(); } //min SOR is 2.0, then we take ln + if( jitter && annotationKey.equalsIgnoreCase("HaplotypeScore") && MathUtils.compareDoubles(value, 0.0, PRECISION) == 0 ) { value += 0.01 * Utils.getRandomGenerator().nextGaussian(); } + if( jitter && annotationKey.equalsIgnoreCase("FS") && MathUtils.compareDoubles(value, 0.0, PRECISION) == 0 ) { value += 0.01 * Utils.getRandomGenerator().nextGaussian(); } + if( jitter && annotationKey.equalsIgnoreCase("InbreedingCoeff") && MathUtils.compareDoubles(value, 0.0, PRECISION) == 0 ) { value += 0.01 * Utils.getRandomGenerator().nextGaussian(); } + if( jitter && annotationKey.equalsIgnoreCase("SOR") && MathUtils.compareDoubles(value, LOG_OF_TWO, PRECISION) == 0 ) { value += 0.01 * Utils.getRandomGenerator().nextGaussian(); } //min SOR is 2.0, then we take ln + if( jitter && annotationKey.equalsIgnoreCase("MQ")) { + if( vrac.MQ_CAP > 0) { + value = logitTransform(value, -SAFETY_OFFSET, vrac.MQ_CAP + SAFETY_OFFSET); + if (MathUtils.compareDoubles(value, logitTransform(vrac.MQ_CAP, -SAFETY_OFFSET, vrac.MQ_CAP + SAFETY_OFFSET), PRECISION) == 0 ) { + value += vrac.MQ_JITTER * Utils.getRandomGenerator().nextGaussian(); + } + } else if( MathUtils.compareDoubles(value, vrac.MQ_CAP, PRECISION) == 0 ) { + value += vrac.MQ_JITTER * Utils.getRandomGenerator().nextGaussian(); + } + } } catch( Exception e ) { value = Double.NaN; // The VQSR works with missing data by marginalizing over the missing dimension when evaluating the Gaussian mixture model } diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDatum.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDatum.java index 3133d4336..8fe785769 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDatum.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDatum.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrator.java index dfbc3dc0a..09a5dc985 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrator.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -141,6 +141,7 @@ import java.util.*; *

Caveats

* *
    + *
  • SNPs and indels must be recalibrated in separate runs (but it is not necessary to separate them into different files). Mixed records are treated as indels.
    • *
  • The values used in the example above are only meant to show how the command lines are composed. * They are not meant to be taken as specific recommendations of values to use in your own work, and they may be * different from the values cited elsewhere in our documentation. For the latest and greatest recommendations on diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java index 577560580..4d11f3ef8 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -77,7 +77,8 @@ public class VariantRecalibratorArgumentCollection { throw new ReviewedGATKException("VariantRecalibrator mode string is unrecognized, input = " + input); } /** - * Use either SNP for recalibrating only SNPs (emitting indels untouched in the output VCF) or INDEL for indels (emitting SNPs untouched in the output VCF). There is also a BOTH option for recalibrating both SNPs and indels simultaneously, but this is meant for testing purposes only and should not be used in actual analyses. + * Use either SNP for recalibrating only SNPs (emitting indels untouched in the output VCF) or INDEL for indels (emitting SNPs untouched in the output VCF). + * There is also a BOTH option for recalibrating both SNPs and indels simultaneously, but this is meant for testing purposes only and should not be used in actual analyses. */ @Argument(fullName = "mode", shortName = "mode", doc = "Recalibration mode to employ", required = true) public VariantRecalibratorArgumentCollection.Mode MODE = VariantRecalibratorArgumentCollection.Mode.SNP; @@ -158,6 +159,41 @@ public class VariantRecalibratorArgumentCollection { @Argument(fullName="badLodCutoff", shortName="badLodCutoff", doc="LOD score cutoff for selecting bad variants", required=false) public double BAD_LOD_CUTOFF = -5.0; + /** + * MQ is capped at a "max" value (60 for bwa-mem) when the alignment is considered perfect. Typically, a huge + * proportion of the reads in a dataset are perfectly mapped, which yields a distribution of MQ values with a + * blob below the max value and a huge peak at the max value. This does not conform to the expectations of the + * Gaussian mixture model of VQSR and has been observed to yield a ROC curve with a jump. + * + * This argument aims to mitigate this problem. Using MQCap = X has 2 effects: (1) MQs are transformed by a scaled + * logit on [0,X] (+ epsilon to avoid division by zero) to make the blob more Gaussian-like and (2) the transformed + * MQ=X are jittered to break the peak into a narrow Gaussian. + * + * Beware that IndelRealigner, if used, adds 10 to MQ for successfully realigned indels. We recommend to either use + * --read-filter ReassignOriginalMQAfterIndelRealignment with HaplotypeCaller or use a MQCap=max+10 to take that + * into account. + * + * If this option is not used, or if MQCap is set to 0, MQ will not be transformed. + */ + @Advanced + @Argument(fullName="MQCapForLogitJitterTransform", shortName = "MQCap", doc="Apply logit transform and jitter to MQ values", required=false) + public int MQ_CAP = 0; + + /** + * The following 2 arguments are hidden because they are only for testing different jitter amounts with and without logit transform. + * Once this will have been tested, and the correct jitter amount chosen (perhaps as a function of the logit range [0,max]) they can be removed. + */ + + @Hidden + @Advanced + @Argument(fullName = "no_MQ_logit", shortName = "NoMQLogit", doc="MQ is by default transformed to log[(MQ_cap + epsilon - MQ)/(MQ + epsilon)] to make it more Gaussian-like. Use this flag to not do that.", required = false) + public boolean NO_MQ_LOGIT = false; + + @Hidden + @Advanced + @Argument(fullName="MQ_jitter", shortName="MQJitt", doc="Amount of jitter (as a factor to a Normal(0,1) noise) to add to the MQ capped values", required = false) + public double MQ_JITTER = 0.05; + ///////////////////////////// // Deprecated Arguments // Keeping them here is meant to provide users with error messages that are more informative than "arg not defined" when they use an argument that has been put out of service diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorEngine.java index c2569d038..ddaf5d400 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorEngine.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriors.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriors.java index 15b0ed0e8..dc9b06354 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriors.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriors.java @@ -25,7 +25,7 @@ * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2014 Broad Institute, Inc. +* Copyright 2012-2015 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -81,7 +81,7 @@ import java.util.*; * *

    * Given a VCF with genotype likelihoods from the HaplotypeCaller, UnifiedGenotyper, or another source which provides - * -unbiased- genotype likelihoods, calculate the posterior genotype state and likelihood given allele frequency + * unbiased genotype likelihoods, calculate the posterior genotype state and likelihood given allele frequency * information from both the samples themselves and input VCFs describing allele frequencies in related populations.

    * *

    The AF field will not be used in this calculation as it does not provide a way to estimate the confidence interval @@ -139,7 +139,8 @@ import java.util.*; * -R reference.fasta \ * -V NA12878.wgs.HC.vcf \ * -supporting 1000G_EUR.genotypes.combined.vcf \ - * -o NA12878.wgs.HC.posteriors.vcf \ + * -o NA12878.wgs.HC.posteriors.vcf + * * *

    Refine the genotypes of a large panel based on the discovered allele frequency

    * 
    @@ -196,7 +197,7 @@ public class CalculateGenotypePosteriors extends RodWalker {
 
     /**
      * Supporting external panels. Allele counts from these panels (taken from AC,AN or MLEAC,AN or raw genotypes) will
-     * be used to inform the frequency distribution underying the genotype priors.
+     * be used to inform the frequency distribution underying the genotype priors. These files must be VCF 4.2 spec or later.
      */
     @Input(fullName="supporting", shortName = "supporting", doc="Other callsets to use in generating genotype posteriors", required=false)
     public List> supportVariants = new ArrayList<>();
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFs.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFs.java
index 50b4c98d2..324e3e1e0 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFs.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFs.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -51,6 +51,9 @@
 
 package org.broadinstitute.gatk.tools.walkers.variantutils;
 
+import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection;
+import org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.gatk.utils.commandline.*;
 import org.broadinstitute.gatk.engine.CommandLineGATK;
 import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
@@ -110,7 +113,38 @@ import java.util.*;
  */
 @DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
 @Reference(window=@Window(start=0,stop=1))
-public class CombineGVCFs extends RodWalker {
+public class CombineGVCFs extends RodWalker implements AnnotatorCompatible {
+
+    /**
+     * Which annotations to recompute for the combined output VCF file.
+     */
+    @Advanced
+    @Argument(fullName="annotation", shortName="A", doc="One or more specific annotations to recompute.  The single value 'none' removes the default annotations", required=false)
+    protected List annotationsToUse = new ArrayList<>(Arrays.asList(new String[]{"AS_RMSMappingQuality"}));
+
+    /**
+     * Which groups of annotations to add to the output VCF file. The single value 'none' removes the default group. See
+     * the VariantAnnotator -list argument to view available groups. Note that this usage is not recommended because
+     * it obscures the specific requirements of individual annotations. Any requirements that are not met (e.g. failing
+     * to provide a pedigree file for a pedigree-based annotation) may cause the run to fail.
+     */
+    @Argument(fullName="group", shortName="G", doc="One or more classes/groups of annotations to apply to variant calls", required=false)
+    protected String[] annotationGroupsToUse = { "Standard" };
+
+
+    /**
+     * The rsIDs from this file are used to populate the ID column of the output.  Also, the DB INFO flag will be set when appropriate. Note that dbSNP is not used in any way for the calculations themselves.
+     */
+    @ArgumentCollection
+    protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
+    public RodBinding getDbsnpRodBinding() { return dbsnp.dbsnp; }
+    public List> getCompRodBindings() { return Collections.emptyList(); }
+    public RodBinding getSnpEffRodBinding() { return null; }
+    public List> getResourceRodBindings() { return Collections.emptyList(); }
+    public boolean alwaysAppendDbsnpId() { return false; }
+
+    // the annotation engine
+    private VariantAnnotatorEngine annotationEngine;
 
     protected final class PositionalState {
         final List VCs;
@@ -177,6 +211,12 @@ public class CombineGVCFs extends RodWalkeremptyList(), this, getToolkit());
+
+        //now that we have all the VCF headers, initialize the annotations (this is particularly important to turn off RankSumTest dithering in integration tests)
+        annotationEngine.invokeAnnotationInitializationMethods(headerLines);
+
         // optimization to prevent mods when we always just want to break bands
         if ( multipleAtWhichToBreakBands == 1 )
             USE_BP_RESOLUTION = true;
@@ -321,7 +361,7 @@ public class CombineGVCFs extends RodWalker annotationsToUse = new ArrayList<>(Arrays.asList(new String[]{"InbreedingCoeff", "FisherStrand", "QualByDepth", "ChromosomeCounts", "StrandOddsRatio"}));
+    protected List annotationsToUse = new ArrayList<>();
+
+    /**
+     * Which groups of annotations to add to the output VCF file. The single value 'none' removes the default group. See
+     * the VariantAnnotator -list argument to view available groups. Note that this usage is not recommended because
+     * it obscures the specific requirements of individual annotations. Any requirements that are not met (e.g. failing
+     * to provide a pedigree file for a pedigree-based annotation) may cause the run to fail.
+     */
+    @Argument(fullName="group", shortName="G", doc="One or more classes/groups of annotations to apply to variant calls", required=false)
+    protected List annotationGroupsToUse = new ArrayList<>(Arrays.asList(new String[]{"Standard"}));
+
 
     /**
      * The rsIDs from this file are used to populate the ID column of the output.  Also, the DB INFO flag will be set when appropriate. Note that dbSNP is not used in any way for the calculations themselves.
@@ -207,11 +218,13 @@ public class GenotypeGVCFs extends RodWalkeremptyList(), this, toolkit);
+        annotationEngine = new VariantAnnotatorEngine(annotationGroupsToUse, annotationsToUse, Collections.emptyList(), this, toolkit);
+
+        // create the genotyping engine
+        boolean doAlleleSpecificGenotyping = annotationsToUse.contains(GATKVCFConstants.AS_QUAL_BY_DEPTH_KEY) || annotationGroupsToUse.contains("AS_Standard");
+                genotypingEngine = new UnifiedGenotypingEngine(createUAC(), samples, toolkit.getGenomeLocParser(), GeneralPloidyFailOverAFCalculatorProvider.createThreadSafeProvider(toolkit, genotypeArgs, logger),
+                toolkit.getArguments().BAQMode, doAlleleSpecificGenotyping);
 
         // take care of the VCF headers
         final Set headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), true);
@@ -230,6 +243,9 @@ public class GenotypeGVCFs extends RodWalker refAlleles = Collections.nCopies(ploidy,VC.getReference());
 
-                //keep 0 depth samples as no-call
-                if (depth > 0) {
+                //keep 0 depth samples and 0 GQ samples as no-call
+                if (depth > 0 && oldGT.hasGQ() && oldGT.getGQ() > 0) {
                     builder.alleles(refAlleles);
                 }
 
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtils.java
index beb2451ee..517ddc3fa 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtils.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtils.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -93,7 +93,10 @@ public class PosteriorLikelihoodsUtils {
             }
 
             //add zero allele counts for any reference alleles not seen in priors (if applicable)
-            totalAlleleCounts.put(vc1.getReference(),totalAlleleCounts.get(vc1.getReference())+numRefSamplesFromMissingResources);
+            int existingRefCounts = 0;
+            if (totalAlleleCounts.containsKey(vc1.getReference()))
+                existingRefCounts += totalAlleleCounts.get(vc1.getReference());
+            totalAlleleCounts.put(vc1.getReference(),existingRefCounts+numRefSamplesFromMissingResources);
         }
 
         // now extract the counts of the alleles present within vc1, and in order
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ReferenceConfidenceVariantContextMerger.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ReferenceConfidenceVariantContextMerger.java
index 1bce6000c..7cc94d4f3 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ReferenceConfidenceVariantContextMerger.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ReferenceConfidenceVariantContextMerger.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -53,12 +53,17 @@ package org.broadinstitute.gatk.tools.walkers.variantutils;
 
 import htsjdk.variant.variantcontext.*;
 import htsjdk.variant.vcf.VCFConstants;
+import org.apache.log4j.Logger;
+import org.broadinstitute.gatk.tools.walkers.annotator.AlleleSpecificAnnotationData;
+import org.broadinstitute.gatk.tools.walkers.annotator.ReducibleAnnotationData;
+import org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine;
 import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodCalculator;
 import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodCalculators;
 import org.broadinstitute.gatk.utils.GenomeLoc;
 import org.broadinstitute.gatk.utils.MathUtils;
 import org.broadinstitute.gatk.utils.Utils;
 import org.broadinstitute.gatk.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.exceptions.GATKException;
 import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.broadinstitute.gatk.utils.variant.GATKVCFConstants;
 import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
@@ -72,6 +77,8 @@ import java.util.*;
  */
 public class ReferenceConfidenceVariantContextMerger {
 
+    private final static Logger logger = Logger.getLogger(ReferenceConfidenceVariantContextMerger.class);
+
     private static Comparable combineAnnotationValues( final List array ) {
         return MathUtils.median(array); // right now we take the median but other options could be explored
     }
@@ -88,10 +95,10 @@ public class ReferenceConfidenceVariantContextMerger {
      * @return new VariantContext representing the merge of all VCs or null if it not relevant
      */
     public static VariantContext merge(final List VCs, final GenomeLoc loc, final Byte refBase, final boolean removeNonRefSymbolicAllele,
-                                       final boolean samplesAreUniquified) {
+                                       final boolean samplesAreUniquified, final VariantAnnotatorEngine annotatorEngine) {
         // this can happen if e.g. you are using a dbSNP file that spans a region with no gVCFs
-        if ( VCs == null || VCs.size() == 0 )
-            return null;
+        if ( VCs == null || VCs.isEmpty() ) {
+            return null; }
 
         // establish the baseline info (sometimes from the first VC)
         final VariantContext first = VCs.get(0);
@@ -99,8 +106,8 @@ public class ReferenceConfidenceVariantContextMerger {
 
         // ref allele
         final Allele refAllele = determineReferenceAlleleGivenReferenceBase(VCs, loc, refBase);
-        if ( refAllele == null )
-            return null;
+        if ( refAllele == null ) {
+            return null; }
 
         // FinalAlleleSet contains the alleles of the new resulting VC
         // Using linked set in order to guarantee a stable order
@@ -111,7 +118,7 @@ public class ReferenceConfidenceVariantContextMerger {
         final Map attributes = new LinkedHashMap<>();
         final Set rsIDs = new LinkedHashSet<>(1); // most of the time there's one id
         int depth = 0;
-        final Map> annotationMap = new LinkedHashMap<>();
+        final Map> annotationMap = new LinkedHashMap<>();
         final GenotypesContext genotypes = GenotypesContext.create();
 
         // In this list we hold the mapping of each variant context alleles.
@@ -134,7 +141,7 @@ public class ReferenceConfidenceVariantContextMerger {
             vcAndNewAllelePairs.add(new Pair<>(vc, isSpanningEvent ? replaceWithNoCallsAndDels(vc) : remapAlleles(vc, refAllele, finalAlleleSet)));
         }
 
-        // Add  and  to the end if at all required in in the output.
+        // Add  and  to the end if at all required in the output.
         if ( sawSpanningDeletion && (sawNonSpanningEvent || !removeNonRefSymbolicAllele) ) finalAlleleSet.add(Allele.SPAN_DEL);
         if (!removeNonRefSymbolicAllele) finalAlleleSet.add(GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE);
 
@@ -155,28 +162,42 @@ public class ReferenceConfidenceVariantContextMerger {
                 }
             }
 
-            if ( loc.getStart() != vc.getStart() )
+            if ( loc.getStart() != vc.getStart() ) {
                 continue;
+            }
 
             // special case ID (just preserve it)
             if ( vc.hasID() ) rsIDs.add(vc.getID());
 
-            // add attributes
-            addReferenceConfidenceAttributes(vc.getAttributes(), annotationMap);
+            // add attributes to annotationMap, store all info field annotations as AlleleSpecificAnnotationData in case they can be parsed that way
+            addReferenceConfidenceAttributes(pair, annotationMap);
         }
 
-        // when combining annotations use the median value from all input VCs which had annotations provided
-        for ( final Map.Entry> p : annotationMap.entrySet() ) {
+        //combine the annotations that are reducible and remove them from annotationMap
+        Map combinedAnnotations = new HashMap<>();
+        if (annotatorEngine != null) {
+            combinedAnnotations = annotatorEngine.combineAnnotations(allelesList, annotationMap);
+        }
+        attributes.putAll(combinedAnnotations);
+
+        // remove stale AC and AF based attributes (including MLEAC and MLEAF lists)
+        //these will be recalculated after genotyping
+        removeStaleAttributesAfterMerge(annotationMap);
+
+        //annotatorEngine.combineAnnotations removed the successfully combined annotations, so now parse those that are left
+        //here we're assuming that things that are left are scalars per sample
+        Map> parsedAnnotationMap = parseRemainingAnnotations(annotationMap);
+
+        // when combining remaining annotations use the median value from all input VCs which had annotations provided
+        for ( final Map.Entry> p : parsedAnnotationMap.entrySet() ) {
             if ( ! p.getValue().isEmpty() ) {
                 attributes.put(p.getKey(), combineAnnotationValues(p.getValue()));
             }
         }
 
-        if ( depth > 0 )
+        if ( depth > 0 ) {
             attributes.put(VCFConstants.DEPTH_KEY, String.valueOf(depth));
-
-        // remove stale AC and AF based attributes
-        removeStaleAttributesAfterMerge(attributes);
+        }
 
         final String ID = rsIDs.isEmpty() ? VCFConstants.EMPTY_ID_FIELD : Utils.join(",", rsIDs);
 
@@ -188,6 +209,39 @@ public class ReferenceConfidenceVariantContextMerger {
         return builder.make();
     }
 
+    /**
+     * parse the annotations that were not identified as reducible annotations and combined by the annotation engine
+     * @param annotationMap the map of info field annotation names and the list of their data from the merged VCs
+     * @return  info field data parsed as ints or doubles
+     */
+    private static Map> parseRemainingAnnotations(final Map> annotationMap) {
+        final Map> parsedAnnotations = new HashMap<>();
+        for (Map.Entry> currentData : annotationMap.entrySet()) {
+            List annotationValues = new ArrayList<>();
+            for (ReducibleAnnotationData value : currentData.getValue()) {
+                try {
+                    final String stringValue = value.getRawData();
+                    if (stringValue.contains(".")) {
+                        annotationValues.add(Double.parseDouble(stringValue));
+                    } else if (Character.isDigit(stringValue.charAt(0))){
+                        annotationValues.add(Integer.parseInt(stringValue));
+                    //TODO: uncomment this to parse dbSNP membership annotation once allele-specific merging for that attribute is added
+                    /*} else if (Character.isLetter(stringValue.charAt(0))) {
+                        if (stringValue.equalsIgnoreCase("true"))
+                            annotationValues.add(true);
+                        else if (stringValue.equalsIgnoreCase("false"))
+                            annotationValues.add(false);*/
+                    }
+
+                } catch (final NumberFormatException e) {
+                    logger.warn("WARNING: remaining (non-reducible) annotations are assumed to be ints or doubles or booleans, but " + value.getRawData() + " doesn't parse and will not be annotated in the final VC.");
+                }
+            }
+            parsedAnnotations.put(currentData.getKey(),annotationValues);
+        }
+        return parsedAnnotations;
+    }
+
     /**
      * @param list  the original alleles list
      * @return a non-null list of non-symbolic alleles
@@ -195,8 +249,9 @@ public class ReferenceConfidenceVariantContextMerger {
     private static List nonSymbolicAlleles(final List list) {
         final List result = new ArrayList<>(list.size());
         for ( final Allele allele : list ) {
-            if ( !allele.isSymbolic() )
+            if ( !allele.isSymbolic() ) {
                 result.add(allele);
+            }
         }
         return result;
     }
@@ -211,8 +266,9 @@ public class ReferenceConfidenceVariantContextMerger {
      */
     private static Allele determineReferenceAlleleGivenReferenceBase(final List VCs, final GenomeLoc loc, final Byte refBase) {
         final Allele refAllele = GATKVariantContextUtils.determineReferenceAllele(VCs, loc);
-        if ( refAllele == null )
-            return ( refBase == null ? null : Allele.create(refBase, true) );
+        if ( refAllele == null ) {
+            return (refBase == null ? null : Allele.create(refBase, true));
+        }
         return refAllele;
     }
 
@@ -221,7 +277,7 @@ public class ReferenceConfidenceVariantContextMerger {
      *
      * @param attributes the attribute map
      */
-    private static void removeStaleAttributesAfterMerge(final Map attributes) {
+    private static void removeStaleAttributesAfterMerge(final Map> attributes) {
         attributes.remove(VCFConstants.ALLELE_COUNT_KEY);
         attributes.remove(VCFConstants.ALLELE_FREQUENCY_KEY);
         attributes.remove(VCFConstants.ALLELE_NUMBER_KEY);
@@ -233,31 +289,35 @@ public class ReferenceConfidenceVariantContextMerger {
     /**
      * Adds attributes to the global map from the new context in a sophisticated manner
      *
-     * @param myAttributes               attributes to add from
+     * @param pair                      VariantContext/Allele list pair from which to get attributes
      * @param annotationMap              map of annotations for combining later
      */
-    private static void addReferenceConfidenceAttributes(final Map myAttributes,
-                                                         final Map> annotationMap) {
+    private static void addReferenceConfidenceAttributes(Pair> pair,
+                                                         final Map> annotationMap) {
+        final Map myAttributes = pair.getFirst().getAttributes(); //these are the info field attributes of the VC in pair
+        final List sampleAlleles = pair.getSecond();
+
         for ( final Map.Entry p : myAttributes.entrySet() ) {
             final String key = p.getKey();
-            final Object value = p.getValue();
+            //allele-specific attributes will always be in list form because they've already been parsed per-allele
+            //non-allele-specific attributes (DP, etc.) will be a list of length 1
+            final List valueList = pair.getFirst().getAttributeAsList(key);
 
-            // add the annotation values to a list for combining later
-            List values = annotationMap.get(key);
-            if( values == null ) {
-                values = new ArrayList<>();
-                annotationMap.put(key, values);
+            // add the existing annotation values to a list for combining later
+            List rawValuesList = annotationMap.get(key);
+            if( rawValuesList == null ) {
+                rawValuesList = new ArrayList<>();
+                annotationMap.put(key, rawValuesList);
             }
-            try {
-                final String stringValue = value.toString();
-                // Branch to avoid unintentional, implicit type conversions that occur with the ? operator.
-                if (stringValue.contains("."))
-                    values.add(Double.parseDouble(stringValue));
-                else
-                    values.add(Integer.parseInt(stringValue));
-            } catch (final NumberFormatException e) {
-                // nothing to do
+            String combinedString = "";
+            for(int i=0; i < valueList.size(); i++) {
+                if (i > 0)
+                    combinedString += ",";
+                combinedString += valueList.get(i);
             }
+            ReducibleAnnotationData pairData = new AlleleSpecificAnnotationData(sampleAlleles, combinedString);
+            rawValuesList.add(pairData);
+            annotationMap.put(key, rawValuesList);
         }
     }
 
@@ -349,46 +409,77 @@ public class ReferenceConfidenceVariantContextMerger {
      * This method assumes that none of the alleles in the VC overlaps with any of the alleles in the set.
      *
      * @param mergedGenotypes       the genotypes context to add to
-     * @param VC                    the Variant Context for the sample
+     * @param vc                    the Variant Context for the sample
      * @param remappedAlleles       the list of remapped alleles for the sample
      * @param targetAlleles         the list of target alleles
      * @param samplesAreUniquified  true if sample names have been uniquified
      */
     private static void mergeRefConfidenceGenotypes(final GenotypesContext mergedGenotypes,
-                                                    final VariantContext VC,
+                                                    final VariantContext vc,
                                                     final List remappedAlleles,
                                                     final List targetAlleles,
                                                     final boolean samplesAreUniquified) {
-        final int maximumPloidy = VC.getMaxPloidy(GATKVariantContextUtils.DEFAULT_PLOIDY);
+        final int maximumPloidy = vc.getMaxPloidy(GATKVariantContextUtils.DEFAULT_PLOIDY);
         // the map is different depending on the ploidy, so in order to keep this method flexible (mixed ploidies)
         // we need to get a map done (lazily inside the loop) for each ploidy, up to the maximum possible.
         final int[][] genotypeIndexMapsByPloidy = new int[maximumPloidy + 1][];
         final int maximumAlleleCount = Math.max(remappedAlleles.size(),targetAlleles.size());
         int[] perSampleIndexesOfRelevantAlleles;
 
-        for ( final Genotype g : VC.getGenotypes() ) {
+        for (final Genotype g : vc.getGenotypes()) {
             final String name;
             if (samplesAreUniquified)
-               name = g.getSampleName() + "." + VC.getSource();
+                name = g.getSampleName() + "." + vc.getSource();
             else
-               name = g.getSampleName();
+                name = g.getSampleName();
             final int ploidy = g.getPloidy();
             final GenotypeBuilder genotypeBuilder = new GenotypeBuilder(g).alleles(GATKVariantContextUtils.noCallAlleles(g.getPloidy()));
             genotypeBuilder.name(name);
-            if (g.hasPL()) {
-                // lazy initialization of the genotype index map by ploidy.
-                perSampleIndexesOfRelevantAlleles = getIndexesOfRelevantAlleles(remappedAlleles, targetAlleles, VC.getStart(), g);
-                final int[] genotypeIndexMapByPloidy = genotypeIndexMapsByPloidy[ploidy] == null
+            final boolean hasPL = g.hasPL();
+            final boolean hasSAC = g.hasExtendedAttribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY);
+            if (hasPL || hasSAC) {
+                perSampleIndexesOfRelevantAlleles = getIndexesOfRelevantAlleles(remappedAlleles, targetAlleles, vc.getStart(), g);
+                if (g.hasPL()) {
+                    // lazy initialization of the genotype index map by ploidy.
+
+                    final int[] genotypeIndexMapByPloidy = genotypeIndexMapsByPloidy[ploidy] == null
                             ? GenotypeLikelihoodCalculators.getInstance(ploidy, maximumAlleleCount).genotypeIndexMap(perSampleIndexesOfRelevantAlleles)
                             : genotypeIndexMapsByPloidy[ploidy];
-                final int[] PLs = generatePL(g, genotypeIndexMapByPloidy);
-                final int[] AD = g.hasAD() ? generateAD(g.getAD(), perSampleIndexesOfRelevantAlleles) : null;
-                genotypeBuilder.PL(PLs).AD(AD);
+                    final int[] PLs = generatePL(g, genotypeIndexMapByPloidy);
+                    final int[] AD = g.hasAD() ? generateAD(g.getAD(), perSampleIndexesOfRelevantAlleles) : null;
+                    genotypeBuilder.PL(PLs).AD(AD);
+                }
+                if (g.hasExtendedAttribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY)) {
+                    final List sacIndexesToUse = adaptToSACIndexes(perSampleIndexesOfRelevantAlleles);
+                    final int[] SACs = GATKVariantContextUtils.makeNewSACs(g, sacIndexesToUse);
+                    genotypeBuilder.attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, SACs);
+                }
             }
             mergedGenotypes.add(genotypeBuilder.make());
         }
     }
 
+    /**
+      * Adapt the relevant alleles to the SAC indexes
+      *
+      * @param perSampleIndexesOfRelevantAlleles
+      * @return SAC indexes
+     */
+    private static List adaptToSACIndexes(final int[] perSampleIndexesOfRelevantAlleles) {
+        if (perSampleIndexesOfRelevantAlleles == null)
+            throw new IllegalArgumentException("The per sample index of relevant alleles must not be null");
+
+        final List sacIndexesToUse = new ArrayList(2 * perSampleIndexesOfRelevantAlleles.length);
+
+        for (int item : perSampleIndexesOfRelevantAlleles) {
+            sacIndexesToUse.add(new Integer(2 * item));
+            sacIndexesToUse.add(new Integer(2 * item + 1));
+        }
+
+        return sacIndexesToUse;
+    }
+
+
     /**
      * Composes a new likelihood array given the original genotype and the genotype index map.
      *
@@ -413,7 +504,7 @@ public class ReferenceConfidenceVariantContextMerger {
 
     /**
      * Determines the allele mapping from myAlleles to the targetAlleles, substituting the generic "" as appropriate.
-     * If the myAlleles set does not contain "" as an allele, it throws an exception.
+     * If the remappedAlleles set does not contain "" as an allele, it throws an exception.
      *
      * @param remappedAlleles   the list of alleles to evaluate
      * @param targetAlleles     the target list of alleles
@@ -423,8 +514,8 @@ public class ReferenceConfidenceVariantContextMerger {
      */
     protected static int[] getIndexesOfRelevantAlleles(final List remappedAlleles, final List targetAlleles, final int position, final Genotype g) {
 
-        if ( remappedAlleles == null || remappedAlleles.size() == 0 ) throw new IllegalArgumentException("The list of input alleles must not be null or empty");
-        if ( targetAlleles == null || targetAlleles.size() == 0 ) throw new IllegalArgumentException("The list of target alleles must not be null or empty");
+        if ( remappedAlleles == null || remappedAlleles.isEmpty()) throw new IllegalArgumentException("The list of input alleles must not be null or empty");
+        if ( targetAlleles == null || targetAlleles.isEmpty() ) throw new IllegalArgumentException("The list of target alleles must not be null or empty");
 
         if ( !remappedAlleles.contains(GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE) )
             throw new UserException("The list of input alleles must contain " + GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE + " as an allele but that is not the case at position " + position + "; please use the Haplotype Caller with gVCF output to generate appropriate records");
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariants.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariants.java
index 134f5e514..069c52177 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariants.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariants.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/SequenceComplexity.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/SequenceComplexity.java
index 666190960..c56cba9af 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/SequenceComplexity.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/SequenceComplexity.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/cancer/TestingReadUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/cancer/TestingReadUtils.java
new file mode 100644
index 000000000..bb8105ec1
--- /dev/null
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/cancer/TestingReadUtils.java
@@ -0,0 +1,110 @@
+/*
+* By downloading the PROGRAM you agree to the following terms of use:
+* 
+* BROAD INSTITUTE
+* SOFTWARE LICENSE AGREEMENT
+* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+* 
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* 
+* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+* 
+* 1. DEFINITIONS
+* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE.
+* 
+* 2. LICENSE
+* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.
+* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+* 
+* 3. PHONE-HOME FEATURE
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* 
+* 4. OWNERSHIP OF INTELLECTUAL PROPERTY
+* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+* Copyright 2012-2015 Broad Institute, Inc.
+* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+* 
+* 5. INDEMNIFICATION
+* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+* 
+* 6. NO REPRESENTATIONS OR WARRANTIES
+* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+* 
+* 7. ASSIGNMENT
+* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+* 
+* 8. MISCELLANEOUS
+* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
+* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.gatk.utils.cancer;
+
+import htsjdk.samtools.SAMFileHeader;
+import htsjdk.samtools.SAMReadGroupRecord;
+import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.gatk.utils.pileup.ReadBackedPileupImpl;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.sam.GATKSAMReadGroupRecord;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: aaron
+ * Date: 2/18/12
+ * Time: 9:33 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class TestingReadUtils {
+    /**
+     * generates an alignment context with the following parameters:
+     * @param totalReads the total number of reads.  total - targetReads with have all 'A' bases
+     * @param targetReads number of reads in the pileup to contain 'T'
+     * @param firstReadGroup the read group for the 'A' reads
+     * @param secondReadGroup the read group for the 'T' reads
+     * @return an alignment context with the reads filled in according to the pattern above.  The pileup will be located at the
+     * first base of the first sequence entry
+     */
+    public static final AlignmentContext generateAlignmentContext(int totalReads, int targetReads, SAMFileHeader header, GenomeLocParser parser, String firstReadGroup, String secondReadGroup) {
+        List reads = new ArrayList();
+
+        // filled with A bases
+        for (int i = 0; i < totalReads - targetReads; i++) {
+            reads.add(addReadGroup(ArtificialSAMUtils.createArtificialRead(header, "Read" + i, 0, 1, 50),firstReadGroup));
+        }
+        byte bases[] = new byte[50];
+        byte quals[] = new byte[50];
+        for (int i = 0; i < 50; i++) {bases[i] = 'T'; quals[i] = 30;}
+        for (int i = totalReads - targetReads; i < totalReads; i++) {
+            reads.add(addReadGroup(ArtificialSAMUtils.createArtificialRead(header, "Read" + i, 0, 1, bases, quals),secondReadGroup));
+        }
+        GenomeLoc loc = parser.createGenomeLoc(header.getSequenceDictionary().getSequence(0).getSequenceName(),1,1);
+        ReadBackedPileup rbp = new ReadBackedPileupImpl(loc, reads, 0);
+        return new AlignmentContext(loc,rbp);
+    }
+
+    public static final GATKSAMRecord addReadGroup(GATKSAMRecord rec, String readGroupName) {
+        GATKSAMReadGroupRecord rgRec = new GATKSAMReadGroupRecord(readGroupName);
+        rgRec.setSample("sample");
+        rec.setReadGroup(rgRec);
+        return rec;
+    }
+    
+}
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/collections/CountSet.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/collections/CountSet.java
index 0d29e0ee6..55c4b43b5 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/collections/CountSet.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/collections/CountSet.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/collections/IntMaxHeap.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/collections/IntMaxHeap.java
index 9484676c2..91b08a61b 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/collections/IntMaxHeap.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/collections/IntMaxHeap.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gga/GenotypingGivenAllelesUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gga/GenotypingGivenAllelesUtils.java
index 134842bcc..c386272e7 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gga/GenotypingGivenAllelesUtils.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gga/GenotypingGivenAllelesUtils.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriter.java
index fd8a98775..3b287a1f1 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriter.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriter.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -341,4 +341,12 @@ public class GVCFWriter implements VariantContextWriter {
             }
         }
     }
+
+    /**
+     * Check the return from PrintStream.checkError() if underlying stream is a java.io.PrintStream
+     * @return false, no error since the underlying stream is not a java.io.PrintStream
+     */
+    public boolean checkError(){
+        return false;
+    }
 }
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/HomRefBlock.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/HomRefBlock.java
index 6e27a5a63..eba6d6771 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/HomRefBlock.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/HomRefBlock.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/AllHaplotypeBAMWriter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/AllHaplotypeBAMWriter.java
index dd756a5aa..9824e08fa 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/AllHaplotypeBAMWriter.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/AllHaplotypeBAMWriter.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java
index 53fcc2e57..97aacb559 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java
index 4edfd4f0f..026a249e7 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/ReadDestination.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/ReadDestination.java
index 567a3635e..f8d8ead57 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/ReadDestination.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/ReadDestination.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/ArrayLoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/ArrayLoglessPairHMM.java
index 18fd5a4fc..a03ea8303 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/ArrayLoglessPairHMM.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/ArrayLoglessPairHMM.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/CnyPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/CnyPairHMM.java
index d01fb9fa7..7beb8b04a 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/CnyPairHMM.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/CnyPairHMM.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/DebugJNILoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/DebugJNILoglessPairHMM.java
index eaaf1798f..0e6f92510 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/DebugJNILoglessPairHMM.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/DebugJNILoglessPairHMM.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/FastLoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/FastLoglessPairHMM.java
index 28add0f64..e27856c40 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/FastLoglessPairHMM.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/FastLoglessPairHMM.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/FlexibleHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/FlexibleHMM.java
index 18ba8e315..654b36e23 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/FlexibleHMM.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/FlexibleHMM.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/JNILoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/JNILoglessPairHMM.java
index 3f4641cd0..a73f20edd 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/JNILoglessPairHMM.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/JNILoglessPairHMM.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/LoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/LoglessPairHMM.java
index 23187b5af..ad9fa20f0 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/LoglessPairHMM.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/LoglessPairHMM.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java
index 63cce9881..368150335 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/sam/ClippedGATKSAMRecord.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/sam/ClippedGATKSAMRecord.java
index 5f6ee422d..40bdb12c6 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/sam/ClippedGATKSAMRecord.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/sam/ClippedGATKSAMRecord.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/variant/TandemRepeatFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/variant/TandemRepeatFinder.java
new file mode 100644
index 000000000..965ef04fc
--- /dev/null
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/variant/TandemRepeatFinder.java
@@ -0,0 +1,271 @@
+/*
+* By downloading the PROGRAM you agree to the following terms of use:
+* 
+* BROAD INSTITUTE
+* SOFTWARE LICENSE AGREEMENT
+* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+* 
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* 
+* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+* 
+* 1. DEFINITIONS
+* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE.
+* 
+* 2. LICENSE
+* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.
+* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+* 
+* 3. PHONE-HOME FEATURE
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* 
+* 4. OWNERSHIP OF INTELLECTUAL PROPERTY
+* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+* Copyright 2012-2015 Broad Institute, Inc.
+* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+* 
+* 5. INDEMNIFICATION
+* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+* 
+* 6. NO REPRESENTATIONS OR WARRANTIES
+* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+* 
+* 7. ASSIGNMENT
+* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+* 
+* 8. MISCELLANEOUS
+* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
+* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.gatk.utils.variant;
+
+import org.broadinstitute.gatk.utils.Utils;
+
+import java.util.Arrays;
+
+/**
+ * Utility to find and quantify tandem repeat units in a byte array.
+ *
+ * 
    
+ *     This class provide a more efficient implementation of deprecated
+ *     {@link GATKVariantContextUtils#findNumberOfRepetitions(byte[], byte[], boolean)}
+ *     and RepeatCovariate which are proven to be inefficient and buggy.
+ * 
    
+ *
+ * 
    
+ *     For now it does not change the logic of those methods in order to preserve current behaviour, but this
+ *     needs to be revisited at some point with the proper re-evaluation.
+ *
+ *     Example.
+ *
+ *     ttcttcttCtgca
+ *
+ *     Where the current offset is in the capital C, will result in the STR unit returned to be TGCA with only one repeat.
+ *     whereas the logical choice is TTC with 3 repeats.
+ *
+ *     And for further proof, a small modification and its effect:
+ *
+ *     ttcttcttCttca
+ *
+ *     Unit T, repeated 2.
+ *
+ *     I would say it should be 4 TTC instead.
+ *
+ *     I think we might well be failing to model the actual PCR artifact appropriately:
+ *
+ *     http://nar.oxfordjournals.org/content/24/14/2807.full
+ *     http://www.ncbi.nlm.nih.gov/pubmed/12560493
+ *
+ * 
    
+ *
+ * @author Valentin Ruano-Rubio <valentin@broadinstitute.org>
+ */
+public final class TandemRepeatFinder {
+
+
+    private final byte[] bases;
+    private final int maxRepeatCount;
+    private final int maxUnitLength;
+
+    public TandemRepeatFinder(final byte[] bases, final int maxUnitLength, final int maxRepeatLength) {
+        if (bases == null) throw new IllegalArgumentException();
+        if (maxRepeatLength < 0) throw new IllegalArgumentException();
+        if (maxUnitLength < 0) throw new IllegalArgumentException();
+        this.maxRepeatCount = maxRepeatLength;
+        this.maxUnitLength = maxUnitLength;
+        this.bases = bases;
+    }
+
+    /**
+     * Calculates the number of repeated units of certain length starting at a position.
+     *
+     * 
    
+     * The repeat unit is determined by the original byte array passed to this tandem repeat finder and the input
+     * offset and length passed to this method based on the following pseudo-code:
+     *
+     * 
    +     *     if (length > 0) {
+     *         unit = bytes[offset .. (offset + length - 1)]
+     *     } else if (length < 0) {
+     *         unit = bytes[offset + length + 1  .. offset]
+     *     } else { // length == 0
+     *         throw IllegalArgumentException() // not allowed.
+     *     }
+     * 
    
+     * 
    
+     *
+     * 
    
+     *     0 will be returned if given the offset and length, part of the unit falls outside the byte array.
+     * 
    
+     * 
    
+     *     Otherwise,
+     *     this method will return the number of repeats (minimum 1 indicating that there is no duplicates) only looking into
+     *     a single direction: if length > 0 forward in the byte array byte[offset .. END],
+     *     if length < 0 then backward in the array byte[0 .. offset].
+     * 
    
+     *
+     * @param offset the offset in the bases byte for which to start
+     * @param length the unit length, a negative indicates a backward unit.
+     * @return the number of repeats.
+     * @throws IllegalArgumentException if {@code length} is 0 or {@code offset} is outside boundaries: (0 .. bases.length - 1)
+     *  where bases is the array passed to this finder at construction.
+     */
+    protected int numberOfRepeats(final int offset, final int length) {
+        if (length == 0) throw new IllegalArgumentException();
+        if (offset < 0 || offset >= bases.length) throw new IllegalArgumentException();
+        int from = offset;
+        int to = offset + length;
+        if (to > bases.length || to < -1) return 0;
+        final int increment = length < 0 ? -1 : 1;
+        final int stop = length < 0? -1 : bases.length;
+        int totalLength = 0;
+        while (to != stop) {
+           if (bases[to] != bases[from]) break;
+           to += increment;
+           from += increment;
+           totalLength++;
+        }
+        return 1 + totalLength / Math.abs(length);
+    }
+
+    public final class Result {
+
+        private final int unitLength;
+        private final int unitOffset;
+        private final int repeatCount;
+
+        private Result(final int unitOffset, final int unitLength, final int repeatCount) {
+            this.unitOffset = unitOffset;
+            this.unitLength = unitLength;
+            this.repeatCount = repeatCount;
+        }
+
+        /**
+         * Returns the repeated unit byte sequence.
+         * @return never {@code null}.
+         */
+        public byte[] getUnit() {
+            return Arrays.copyOfRange(bases,unitOffset, unitOffset + unitLength);
+        }
+
+        /**
+         * Returns the original search bases.
+         *
+         * @return never {@code null}.
+         */
+        public byte[] getBases() {
+            return bases;
+        }
+
+        /**
+         * Returns the unit offset.
+         *
+         * @return 0 to {@link #getBases().length - 1}
+         */
+        public int getUnitOffset() {
+            return unitOffset;
+        }
+
+        /**
+         * Returns the unit length.
+         *
+         * @return 0 to {@link #getBases().length - 1}
+         */
+        public int getUnitLength() {
+            return unitLength;
+        }
+
+        /**
+         * Returns the number of repeats of the unit in the input sequence.
+         * @return 0 or greater.
+         */
+        public int getRepeatCount() {
+            return repeatCount;
+        }
+
+    }
+
+    /**
+     * Re-implements {@link RepeatCovariate#findTandemRepeatUnits(byte[], int)}.
+     *
+     * @param offset search offset.
+     * @return never {@code null}.
+     */
+    public Result findMostRelevantTandemRepeatUnitAt(final int offset) {
+
+        // Notice that this code is not very nice and is rather long but is just a copy of the existing one implemented
+        // in RepeatCovariate, eventually this should be improved.
+
+        // first we look forward for a repeat.
+
+        // first we find the best backward
+        int bestBWRepeatCount = 0;
+        int bestBWOffset = offset;
+        int bestBWLength = 1;
+        for (int str = 1; str <= maxUnitLength; str++) {
+            final int repeatCount = numberOfRepeats(offset, -str);
+            if (repeatCount == 0) {
+                break;
+            } else if ((bestBWRepeatCount = repeatCount) > 1) {
+                bestBWOffset = offset - str + 1;
+                bestBWLength = str;
+                break;
+            }
+        }
+
+        // The best forward:
+        final int bestFWOffset = offset + 1;
+        int bestFWLength = 1;
+        int bestFWRepeatCount = 0;
+        for (int str = 1; str <= maxUnitLength; str++) {
+            final int repeatCount = numberOfRepeats(bestFWOffset, str);
+            if (repeatCount == 0) {
+                break;
+            } else if ((bestFWRepeatCount = repeatCount) > 1) {
+                bestFWLength = str;
+                break;
+            }
+        }
+
+        // And we combine forward and backwards results; if different forward repeat has priority:
+        if (bestFWLength == bestBWLength && Utils.equalRange(bases, bestFWOffset, bases, bestBWOffset, bestFWLength)) {
+            return new Result(bestBWOffset, bestBWLength, Math.min(maxRepeatCount, bestBWRepeatCount + bestFWRepeatCount));
+        }
+          else {
+            final int bestFWBackwardRepeatCount = numberOfRepeats(bestFWOffset + bestFWLength - 1, - bestFWLength) - 1;
+            return new Result(bestFWOffset, bestFWLength, Math.min(maxRepeatCount, bestFWRepeatCount + bestFWBackwardRepeatCount));
+        }
+    }
+}
diff --git a/public/gatk-tools-public/src/main/resources/org/broadinstitute/gatk/tools/walkers/variantrecalibration/plot_Tranches.R b/protected/gatk-tools-protected/src/main/resources/org/broadinstitute/gatk/tools/walkers/variantrecalibration/plot_Tranches.R
old mode 100755
new mode 100644
similarity index 98%
rename from public/gatk-tools-public/src/main/resources/org/broadinstitute/gatk/tools/walkers/variantrecalibration/plot_Tranches.R
rename to protected/gatk-tools-protected/src/main/resources/org/broadinstitute/gatk/tools/walkers/variantrecalibration/plot_Tranches.R
index 4fe59083c..d96add768
--- a/public/gatk-tools-public/src/main/resources/org/broadinstitute/gatk/tools/walkers/variantrecalibration/plot_Tranches.R
+++ b/protected/gatk-tools-protected/src/main/resources/org/broadinstitute/gatk/tools/walkers/variantrecalibration/plot_Tranches.R
@@ -41,7 +41,7 @@ leftShift <- function(x, leftValue = 0) {
 # Tranches plot
 # -----------------------------------------------------------------------------------------------
 data2 = read.table(tranchesFile,sep=",",head=T)
-data2 = data2[order(data2$targetTruthSensitivity, decreasing=T),]
+data2 = data2[order(data2$novelTiTv, decreasing=F),]
 #data2 = data2[order(data2$FDRtranche, decreasing=T),]
 cols = c("cornflowerblue", "cornflowerblue", "darkorange", "darkorange")
 density=c(20, -1, -1, 20)
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LiftoverVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/BaseRecalibrationUnitTest.java
similarity index 76%
rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LiftoverVariantsIntegrationTest.java
rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/BaseRecalibrationUnitTest.java
index c6ae7ea64..218377582 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LiftoverVariantsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/BaseRecalibrationUnitTest.java
@@ -1,44 +1,44 @@
 /*
 * By downloading the PROGRAM you agree to the following terms of use:
-* 
+*
 * BROAD INSTITUTE
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
-* 
+*
 * This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
-* 
+*
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
 * NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
-* 
+*
 * 1. DEFINITIONS
 * 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE.
-* 
+*
 * 2. LICENSE
 * 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.
 * The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
 * 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
-* 
+*
 * 3. PHONE-HOME FEATURE
 * LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
-* 
+*
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
-* 
+*
 * 5. INDEMNIFICATION
 * LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
-* 
+*
 * 6. NO REPRESENTATIONS OR WARRANTIES
 * THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
 * IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
-* 
+*
 * 7. ASSIGNMENT
 * This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
-* 
+*
 * 8. MISCELLANEOUS
 * 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
 * 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
@@ -49,61 +49,68 @@
 * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
 */
 
-package org.broadinstitute.gatk.tools.walkers.variantutils;
+package org.broadinstitute.gatk.engine.recalibration;
 
-import org.broadinstitute.gatk.engine.walkers.WalkerTest;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.QualityUtils;
 import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
+import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.List;
 
-/**
- * Tests LiftoverVariants
- */
-public class LiftoverVariantsIntegrationTest extends WalkerTest {
+public class BaseRecalibrationUnitTest {
 
     @Test
-    public void testb36Tohg19() {
-         WalkerTestSpec spec = new WalkerTestSpec(
-                 "-T LiftoverVariants -o %s -R " + b36KGReference + " --variant " + privateTestDir + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
-                 1,
-                 Arrays.asList("7d5f91fcf419211ae9eca6c66dcec0e6"));
-         executeTest("test b36 to hg19", spec);
+    public void repeatedAndUnorderedFixedQualities() {
+        // Test both repeated quals, and quals that aren't input in order
+        List quantizedQualsOrdered = Arrays.asList(11, 19);
+        List quantizedQualsUnordered = Arrays.asList(19, 11, 19, 19);
+
+        // Unordered and Ordered qmapping should be identical
+        byte[] qmappingUnordered = BaseRecalibration.constructStaticQuantizedMapping(quantizedQualsUnordered, true);
+        byte[] qmappingOrdered = BaseRecalibration.constructStaticQuantizedMapping(quantizedQualsOrdered, true);
+        Assert.assertEquals(qmappingOrdered.length, qmappingUnordered.length);
+        for(int i = 0 ; i < qmappingUnordered.length ; i++) {
+            Assert.assertEquals(qmappingOrdered[i], qmappingUnordered[i]);
+        }
     }
 
     @Test
-    public void testb36Tohg19UnsortedSamples() {
-         WalkerTestSpec spec = new WalkerTestSpec(
-                 "-T LiftoverVariants -o %s -R " + b36KGReference + " --variant " + privateTestDir + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.unsortedSamples.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
-                 1,
-                 Arrays.asList("29dab3555e7f1ee6a60e267b00215a11"));
-         executeTest("test b36 to hg19, unsorted samples", spec);
+    public void nearestVsRoundDown() {
+        List fixedQuantizedQuals = Arrays.asList(10, 20, 30);
+
+        byte[] qmappingRoundDown = BaseRecalibration.constructStaticQuantizedMapping(fixedQuantizedQuals, true);
+        byte[] qmappingRoundNearest = BaseRecalibration.constructStaticQuantizedMapping(fixedQuantizedQuals, false);
+
+        // Depending on rounding strategy, bin 19 should round to 10 or 20
+        Assert.assertEquals(qmappingRoundDown[19], 10);
+        Assert.assertEquals(qmappingRoundNearest[19], 20);
+
+        // Regarless of rounding strategy, bin 21 should always round down to 20
+        Assert.assertEquals(qmappingRoundDown[21], 20);
+        Assert.assertEquals(qmappingRoundNearest[21], 20);
     }
 
     @Test
-    public void testhg18Tohg19Unsorted() {
-         WalkerTestSpec spec = new WalkerTestSpec(
-                 "-T LiftoverVariants -o %s -R " + hg18Reference + " --variant:vcf " + privateTestDir + "liftover_test.vcf -chain " + validationDataLocation + "hg18ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
-                 1,
-                 Arrays.asList("7e7bad0e1890753a01303c09a38ceb8d"));
-         executeTest("test hg18 to hg19, unsorted", spec);
-    }
+    public void onlyOneFixedQualUsed() {
+        // Set all qualities to singleQual value (except for those below MIN_USABLE_Q_SCORE)
+        int singleQual = 10;
+        List fixedQuantizedQuals = Arrays.asList(singleQual);
 
-    @Test
-    public void testLiftoverFilteringOfIndels() {
-        WalkerTestSpec spec = new WalkerTestSpec(
-                "-T FilterLiftedVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "liftover_indel_test.vcf --no_cmdline_in_header",
-                1,
-                Arrays.asList("0909a953291a5e701194668c9b8833ab"));
-        executeTest("test liftover filtering of indels", spec);
-    }
+        byte[] qmapping = BaseRecalibration.constructStaticQuantizedMapping(fixedQuantizedQuals, true);
 
-    @Test
-    public void testLiftoverFailsWithNoOutput() {
-        WalkerTestSpec spec = new WalkerTestSpec(
-                "-T LiftoverVariants -R " + hg18Reference + " --variant:vcf " + privateTestDir + "liftover_test.vcf -chain " + validationDataLocation + "hg18ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
-                0,
-                UserException.class);
-        executeTest("test liftover fails with no output", spec);
+        for(int i = 0 ; i < qmapping.length ; i++) {
+            if(i >= QualityUtils.MIN_USABLE_Q_SCORE) {
+                Assert.assertEquals(qmapping[i], singleQual);
+            }
+            else {
+                // Make sure that all values less than MIN_USABLE_Q_SCORE are preserved
+                Assert.assertEquals(qmapping[i], i);
+            }
+        }
     }
 }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ContextCovariateUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ContextCovariateUnitTest.java
index 25748f70e..1cf60d688 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ContextCovariateUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ContextCovariateUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/CycleCovariateUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/CycleCovariateUnitTest.java
index f40152e94..681f001c1 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/CycleCovariateUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/CycleCovariateUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/QualQuantizerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/QualQuantizerUnitTest.java
index b8d5c5303..c200701f3 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/QualQuantizerUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/QualQuantizerUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ReadCovariatesUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ReadCovariatesUnitTest.java
index f263345e7..8229d2586 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ReadCovariatesUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ReadCovariatesUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ReadGroupCovariateUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ReadGroupCovariateUnitTest.java
index 34548aee3..65ce02cc8 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ReadGroupCovariateUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ReadGroupCovariateUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalDatumUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalDatumUnitTest.java
index 3c9048fae..77cd87a08 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalDatumUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalDatumUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalUtilsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalUtilsUnitTest.java
index 0e95122da..54ed375e0 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalUtilsUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalUtilsUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReportUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReportUnitTest.java
index d16f718be..e6d3d9444 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReportUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReportUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTablesUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTablesUnitTest.java
index f40ef2602..675e10b87 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTablesUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTablesUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTestUtils.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTestUtils.java
index ce374b047..8f29d42c3 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTestUtils.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTestUtils.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RepeatCovariatesUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RepeatCovariatesUnitTest.java
index 66c12a55a..90474319a 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RepeatCovariatesUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RepeatCovariatesUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/WalkerTestIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/WalkerTestIntegrationTest.java
index e2cbcc6a5..d20b08b2f 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/WalkerTestIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/WalkerTestIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_InbreedingCoeffUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_InbreedingCoeffUnitTest.java
new file mode 100644
index 000000000..35be76487
--- /dev/null
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_InbreedingCoeffUnitTest.java
@@ -0,0 +1,250 @@
+/*
+* By downloading the PROGRAM you agree to the following terms of use:
+* 
+* BROAD INSTITUTE
+* SOFTWARE LICENSE AGREEMENT
+* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+* 
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* 
+* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+* 
+* 1. DEFINITIONS
+* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE.
+* 
+* 2. LICENSE
+* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.
+* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+* 
+* 3. PHONE-HOME FEATURE
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* 
+* 4. OWNERSHIP OF INTELLECTUAL PROPERTY
+* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+* Copyright 2012-2015 Broad Institute, Inc.
+* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+* 
+* 5. INDEMNIFICATION
+* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+* 
+* 6. NO REPRESENTATIONS OR WARRANTIES
+* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+* 
+* 7. ASSIGNMENT
+* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+* 
+* 8. MISCELLANEOUS
+* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
+* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.gatk.tools.walkers.annotator;
+
+import htsjdk.variant.variantcontext.*;
+import org.testng.Assert;
+import org.testng.annotations.BeforeSuite;
+import org.testng.annotations.Test;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Set;
+
+/**
+ * Created with IntelliJ IDEA.
+ * User: gauthier
+ * Date: 10/28/2015
+ */
+public class AS_InbreedingCoeffUnitTest {
+    private static double DELTA_PRECISION = 0.001;
+    private Allele Aref, T, C;
+    private int[] hetPLs, homRefPLs;
+
+    @BeforeSuite
+    public void setup() {
+        // alleles
+        Aref = Allele.create("A", true);
+        T = Allele.create("T");
+        C = Allele.create("C");
+
+        // simulating 20 reads with Q30 base qualities
+        hetPLs = new int[] {240, 0, 240};
+        homRefPLs = new int[] {0, 60, 600};
+    }
+
+    private Genotype makeGwithPLs(String sample, Allele a1, Allele a2, double[] pls) {
+        Genotype gt = new GenotypeBuilder(sample, Arrays.asList(a1, a2)).PL(pls).make();
+        if ( pls != null && pls.length > 0 ) {
+            Assert.assertNotNull(gt.getPL());
+            Assert.assertTrue(gt.getPL().length > 0);
+            for ( int i : gt.getPL() ) {
+                Assert.assertTrue(i >= 0);
+            }
+            Assert.assertNotEquals(Arrays.toString(gt.getPL()),"[0]");
+        }
+        return gt;
+    }
+
+    private Genotype makeG(String sample, Allele a1, Allele a2, int... pls) {
+        return new GenotypeBuilder(sample, Arrays.asList(a1, a2)).PL(pls).make();
+    }
+
+    private VariantContext makeVC(String source, List alleles, Genotype... genotypes) {
+        int start = 10;
+        int stop = start; // alleles.contains(ATC) ? start + 3 : start;
+        return new VariantContextBuilder(source, "1", start, stop, alleles)
+                .genotypes(Arrays.asList(genotypes))
+                .filters((String)null)
+                .make();
+    }
+
+    @Test
+    public void testInbreedingCoeffForMultiallelicVC() {
+        //make sure that compound gets (with no ref) don't add to het count
+        VariantContext test1 = makeVC("1",Arrays.asList(Aref,T,C),
+                makeG("s1", Aref, T, 2530, 0, 7099, 366, 3056, 14931),
+                makeG("s2", T, T, 7099, 2530, 0, 7099, 366, 3056),
+                makeG("s3", T, C, 7099, 2530, 7099, 3056, 0, 14931),
+                makeG("s4", Aref, T, 2530, 0, 7099, 366, 3056, 14931),
+                makeG("s5", T, T, 7099, 2530, 0, 7099, 366, 3056),
+                makeG("s6", Aref, T, 2530, 0, 7099, 366, 3056, 14931),
+                makeG("s7", T, T, 7099, 2530, 0, 7099, 366, 3056),
+                makeG("s8", Aref, T, 2530, 0, 7099, 366, 3056, 14931),
+                makeG("s9", T, T, 7099, 2530, 0, 7099, 366, 3056),
+                makeG("s10", Aref, T, 2530, 0, 7099, 366, 3056, 14931));
+
+        final AS_InbreedingCoeff testClass1 = new AS_InbreedingCoeff();
+        testClass1.initialize(null, null, null);
+        final double ICresult1 = testClass1.calculateIC(test1, T);
+        Assert.assertEquals(ICresult1, -0.4285714, DELTA_PRECISION, "Pass");
+        final double ICresult1b = testClass1.calculateIC(test1, C);
+        Assert.assertEquals(ICresult1b, -0.05263, DELTA_PRECISION, "Pass");
+
+        //make sure that hets with different alternate alleles all get counted
+        VariantContext test2 = makeVC("2", Arrays.asList(Aref,T,C),
+                makeG("s1", Aref, C, 4878, 1623, 11297, 0, 7970, 8847),
+                makeG("s2", Aref, T, 2530, 0, 7099, 366, 3056, 14931),
+                makeG("s3", Aref, T, 3382, 0, 6364, 1817, 5867, 12246),
+                makeG("s4", Aref, T, 2488, 0, 9110, 3131, 9374, 12505),
+                makeG("s5", Aref, C, 4530, 2006, 18875, 0, 6847, 23949),
+                makeG("s6", Aref, T, 5325, 0, 18692, 389, 16014, 24570),
+                makeG("s7", Aref, T, 2936, 0, 29743, 499, 21979, 38630),
+                makeG("s8", Aref, T, 6902, 0, 8976, 45, 5844, 9061),
+                makeG("s9", Aref, T, 5732, 0, 10876, 6394, 11408, 17802),
+                makeG("s10", Aref, T, 2780, 0, 25045, 824, 23330, 30939));
+
+        final AS_InbreedingCoeff testClass2 = new AS_InbreedingCoeff();
+        testClass2.initialize(null, null, null);
+        final double ICresult2 = testClass2.calculateIC(test2, T);
+        Assert.assertEquals(ICresult2, -0.666666, DELTA_PRECISION, "Pass");
+        final double ICresult2b = testClass2.calculateIC(test2, C);
+        Assert.assertEquals(ICresult2b, -0.111129, DELTA_PRECISION, "Pass");
+    }
+
+    @Test
+    public void testSingletonVsCommonAllele() {
+
+        final List allGTs = new ArrayList<>();
+        final int numHomRefGTs = 10000;
+        allGTs.add(makeG("het0", Aref, T, hetPLs));
+
+        for ( int i = 0; i < numHomRefGTs; i++ )
+            allGTs.add(makeG("ref" + i, Aref, Aref, homRefPLs));
+
+        int numHetGTs = 1;
+
+        final VariantContext singleton = makeVC("singleton", Arrays.asList(Aref, T), allGTs.toArray(new Genotype[allGTs.size()]));
+        AS_InbreedingCoeff testClass = new AS_InbreedingCoeff();
+        testClass.initialize(null,null,null);
+        final double ICsingleton = testClass.calculateIC(singleton, T);
+
+        final int targetNumHetGTs = 20;
+        for ( int i = numHetGTs; i < targetNumHetGTs; i++ )
+            allGTs.add(makeG("het" + i, Aref, T, hetPLs));
+
+        final VariantContext common = makeVC("common", Arrays.asList(Aref, T), allGTs.toArray(new Genotype[allGTs.size()]));
+        testClass = new AS_InbreedingCoeff();
+        testClass.initialize(null,null,null);
+        final double ICcommon = testClass.calculateIC(common, T);
+
+        Assert.assertTrue(Math.abs(ICsingleton) < Math.abs(ICcommon), String.format("singleton=%f common=%f", ICsingleton, ICcommon));
+    }
+
+    @Test
+    public void testLargeCohorts() {
+
+        final List allGTs = new ArrayList<>();
+        final int numHomRefGTs = 1000000;
+        for ( int i = 0; i < numHomRefGTs; i++ )
+            allGTs.add(makeG("ref" + i, Aref, Aref, homRefPLs));
+
+        allGTs.add(makeG("het0", Aref, T, hetPLs));
+        int numHetGTs = 1;
+
+        final VariantContext singleton = makeVC("singleton", Arrays.asList(Aref, T), allGTs.toArray(new Genotype[allGTs.size()]));
+        AS_InbreedingCoeff testClass = new AS_InbreedingCoeff();
+        testClass.initialize(null,null,null);
+        final double ICsingleton = testClass.calculateIC(singleton, T);
+
+        for ( int i = numHetGTs; i < 100; i++ ) {
+            allGTs.add(makeG("het" + i, Aref, T, hetPLs));
+            numHetGTs++;
+        }
+
+        final VariantContext hundredton = makeVC("hundredton", Arrays.asList(Aref, T), allGTs.toArray(new Genotype[allGTs.size()]));
+        testClass = new AS_InbreedingCoeff();
+        testClass.initialize(null,null,null);
+        final double IChundredton = testClass.calculateIC(hundredton, T);
+
+        Assert.assertTrue(Math.abs(ICsingleton) < Math.abs(IChundredton), String.format("singleton=%f hundredton=%f", ICsingleton, IChundredton));
+
+        for ( int i = numHetGTs; i < numHomRefGTs; i++ )
+            allGTs.add(makeG("het" + i, Aref, T, hetPLs));
+
+        final VariantContext common = makeVC("common", Arrays.asList(Aref, T), allGTs.toArray(new Genotype[allGTs.size()]));
+        testClass = new AS_InbreedingCoeff();
+        testClass.initialize(null,null,null);
+        final double ICcommon = testClass.calculateIC(common, T);
+
+        Assert.assertTrue(Math.abs(IChundredton) < Math.abs(ICcommon), String.format("hundredton=%f common=%f", IChundredton, ICcommon));
+    }
+
+    @Test
+    public void testAllHetsForLargeCohorts() {
+
+        final int numGTs = 1000000;
+
+        final List singletonGTs = new ArrayList<>();
+        for ( int i = 0; i < numGTs; i++ )
+            singletonGTs.add(makeG("ref" + i, Aref, Aref, homRefPLs));
+
+        singletonGTs.add(makeG("het0", Aref, T, hetPLs));
+
+        final VariantContext singleton = makeVC("singleton", Arrays.asList(Aref, T), singletonGTs.toArray(new Genotype[singletonGTs.size()]));
+        AS_InbreedingCoeff testClass = new AS_InbreedingCoeff();
+        testClass.initialize(null, null, null);
+        final double ICsingleton = testClass.calculateIC(singleton, T);
+
+        final List allHetGTs = new ArrayList<>();
+        for ( int i = 0; i < numGTs; i++ )
+            allHetGTs.add(makeG("het" + i, Aref, T, hetPLs));
+
+        final VariantContext allHet = makeVC("allHet", Arrays.asList(Aref, T), allHetGTs.toArray(new Genotype[allHetGTs.size()]));
+        testClass.initialize(null, null, null);
+        final double ICHets = testClass.calculateIC(allHet, T);
+
+        Assert.assertTrue(Math.abs(ICsingleton) < Math.abs(ICHets), String.format("singleton=%f allHets=%f", ICsingleton, ICHets));
+    }
+}
+
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/AnnotationUtilsTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/AnnotationUtilsTest.java
new file mode 100644
index 000000000..671b31989
--- /dev/null
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/AnnotationUtilsTest.java
@@ -0,0 +1,220 @@
+/*
+* By downloading the PROGRAM you agree to the following terms of use:
+* 
+* BROAD INSTITUTE
+* SOFTWARE LICENSE AGREEMENT
+* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+* 
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* 
+* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+* 
+* 1. DEFINITIONS
+* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE.
+* 
+* 2. LICENSE
+* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.
+* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+* 
+* 3. PHONE-HOME FEATURE
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* 
+* 4. OWNERSHIP OF INTELLECTUAL PROPERTY
+* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+* Copyright 2012-2015 Broad Institute, Inc.
+* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+* 
+* 5. INDEMNIFICATION
+* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+* 
+* 6. NO REPRESENTATIONS OR WARRANTIES
+* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+* 
+* 7. ASSIGNMENT
+* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+* 
+* 8. MISCELLANEOUS
+* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
+* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.gatk.tools.walkers.annotator;
+
+import htsjdk.samtools.Cigar;
+import htsjdk.samtools.CigarElement;
+import htsjdk.samtools.CigarOperator;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
+import org.testng.annotations.BeforeClass;
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.ArrayList;
+import java.util.LinkedList;
+import java.util.List;
+
+public class AnnotationUtilsTest {
+
+    //Basic aligned read
+    private GATKSAMRecord allMatch;
+
+    //Read with insertion and deletion
+    private GATKSAMRecord twoIndels;
+
+    //Read with soft clips at start
+    private GATKSAMRecord softClipStart;
+
+    //Read with hard clips at start
+    private GATKSAMRecord hardClipStart;
+
+    //Read with low quality tail
+    private GATKSAMRecord lowQualTail;
+
+    //Read with low quality tail, partially soft clipped
+    private GATKSAMRecord lowQualClippedTail;
+
+    //Read with low quality bases at start
+    private GATKSAMRecord lowQualStart;
+
+    //Read with low quality bases, partially soft clipped at both ends
+    private GATKSAMRecord lowQualBothEnds;
+
+    @BeforeClass
+    public void init() {
+        List cigarElements_allMatch = new LinkedList<>();
+        cigarElements_allMatch.add(new CigarElement(151, CigarOperator.M));
+        allMatch = ArtificialSAMUtils.createArtificialRead(new Cigar(cigarElements_allMatch));
+
+        List cigarElements_2indels = new LinkedList<>();
+        cigarElements_2indels.add(new CigarElement(66, CigarOperator.M));
+        cigarElements_2indels.add(new CigarElement(10, CigarOperator.I));
+        cigarElements_2indels.add(new CigarElement(7, CigarOperator.M));
+        cigarElements_2indels.add(new CigarElement(10, CigarOperator.D));
+        cigarElements_2indels.add(new CigarElement(68, CigarOperator.M));
+        twoIndels = ArtificialSAMUtils.createArtificialRead(new Cigar(cigarElements_2indels));
+
+        List cigarElements_softClipStart = new LinkedList<>();
+        cigarElements_softClipStart.add(new CigarElement(17, CigarOperator.S));
+        cigarElements_softClipStart.add(new CigarElement(134, CigarOperator.M));
+        softClipStart = ArtificialSAMUtils.createArtificialRead(new Cigar(cigarElements_softClipStart));
+
+        List cigarElements_hardClipStart = new LinkedList<>();
+        cigarElements_hardClipStart.add(new CigarElement(17, CigarOperator.H));
+        cigarElements_hardClipStart.add(new CigarElement(134, CigarOperator.M));
+        hardClipStart = ArtificialSAMUtils.createArtificialRead(new Cigar(cigarElements_hardClipStart));
+
+
+        final byte [] bases_lowQualTail = {'A', 'C', 'T', 'G', 'A', 'A', 'A', 'A', 'A', 'A'};
+        final byte [] quals_lowQualTail = {30, 15, 25, 30, 2, 2, 2, 2, 2, 2};
+        lowQualTail = ArtificialSAMUtils.createArtificialRead(bases_lowQualTail, quals_lowQualTail, "10M");
+
+        final byte [] bases_lowQualClippedTail = {'A', 'C', 'T', 'G', 'A', 'A', 'A', 'A', 'A', 'A'};
+        final byte [] quals_lowQualClippedTail = {30, 15, 25, 30, 2, 2, 2, 2, 2, 2};
+        lowQualClippedTail = ArtificialSAMUtils.createArtificialRead(bases_lowQualClippedTail, quals_lowQualClippedTail, "8M2S");
+
+        final byte [] bases_lowQualStart = {'A', 'A', 'A', 'A', 'A', 'A', 'A', 'C', 'T', 'G'};
+        final byte [] quals_lowQualStart = {2, 2, 2, 2, 2, 2, 30, 15, 25, 30};
+        lowQualStart = ArtificialSAMUtils.createArtificialRead(bases_lowQualStart, quals_lowQualStart, "10M");
+
+        final byte [] bases_lowQualBothEnds = {'A', 'A', 'A', 'A', 'A', 'A', 'G', 'C', 'T', 'G', 'A', 'A', 'A', 'A', 'A', 'A'};
+        final byte [] quals_lowQualBothEnds = { 2, 2, 2, 2, 2, 2, 30, 15, 25, 30, 2, 2, 2, 2, 2, 2};
+        lowQualBothEnds = ArtificialSAMUtils.createArtificialRead(bases_lowQualBothEnds, quals_lowQualBothEnds, "2S12M2S");
+
+    }
+
+    @DataProvider(name = "makeGetFinalVariantReadPositionTestReads")
+    public Object[][] makeFinalPosTestReads() {
+        final List tests = new ArrayList<>();
+        tests.add(new Object[] {allMatch, 10, 10});
+        tests.add(new Object[] {allMatch, 140, 10});
+        tests.add(new Object[] {twoIndels, 10, 10});
+        tests.add(new Object[] {twoIndels, 140, 10});
+        tests.add(new Object[] {hardClipStart, 20, 20});
+        tests.add(new Object[] {hardClipStart, 110, 6});  //this is what the code produces as-is
+        tests.add(new Object[] {softClipStart, 10, 10});
+        tests.add(new Object[] {softClipStart, 140, 10});
+        tests.add(new Object[] {lowQualTail, 3, 0});
+        tests.add(new Object[] {lowQualTail, 2, 2});
+        tests.add(new Object[] {lowQualClippedTail, 3, 0});
+        tests.add(new Object[] {lowQualClippedTail, 2, 2});
+        tests.add(new Object[] {lowQualStart, 7, -4});   //this is what the code produces as-is, but should be 1
+        tests.add(new Object[] {lowQualStart, 8, -5}); //this is what the code produces as-is, but should be 1
+        tests.add(new Object[] {lowQualBothEnds, 7, -4});   //this is what the code produces as-is, but should be 1
+        tests.add(new Object[] {lowQualBothEnds, 8, -5});    //this is what the code produces as-is, but should be 1
+        return tests.toArray(new Object[][]{});
+    }
+
+    @Test(dataProvider = "makeGetFinalVariantReadPositionTestReads")
+    public void testGetFinalVariantReadPosition(GATKSAMRecord read, int variantPosition, int expected) throws Exception {
+        Assert.assertEquals(AnnotationUtils.getFinalVariantReadPosition(read, variantPosition), expected);
+    }
+
+    @DataProvider(name = "getNumClippedBasesAtStartTestReads")
+    public Object[][] numClipStart() {
+        final List tests = new ArrayList<>();
+        tests.add(new Object[] {allMatch, 0});
+        tests.add(new Object[] {twoIndels, 0});
+        tests.add(new Object[] {softClipStart, 0});
+        tests.add(new Object[] {hardClipStart, 17});
+        tests.add(new Object[] {lowQualTail, 0});
+        tests.add(new Object[] {lowQualClippedTail, 0});
+        tests.add(new Object[] {lowQualStart, 6});
+        tests.add(new Object[] {lowQualBothEnds, 6});
+        return tests.toArray(new Object[][]{});
+    }
+
+    @Test(dataProvider = "getNumClippedBasesAtStartTestReads")
+    public void testGetNumClippedBasesAtStart(GATKSAMRecord read, int expected) throws Exception {
+        Assert.assertEquals(AnnotationUtils.getNumClippedBasesAtStart(read),expected);
+    }
+
+    @DataProvider(name = "getNumAlignedBasesTestReads")
+    public Object[][] numAligned() {
+        final List tests = new ArrayList<>();
+        tests.add(new Object[] {allMatch, 151});
+        tests.add(new Object[] {twoIndels, 151});
+        tests.add(new Object[] {softClipStart, 151});
+        tests.add(new Object[] {hardClipStart, 117});  //This is what the code produces, but it's wrong
+        tests.add(new Object[] {lowQualTail, 4});
+        tests.add(new Object[] {lowQualClippedTail, 4});
+        tests.add(new Object[] {lowQualStart, 4});
+        tests.add(new Object[] {lowQualBothEnds, 4});
+        return tests.toArray(new Object[][]{});
+    }
+
+    @Test(dataProvider = "getNumAlignedBasesTestReads")
+    public void testGetNumAlignedBases(GATKSAMRecord read, int expected) throws Exception {
+        Assert.assertEquals(AnnotationUtils.getNumAlignedBases(read),expected);
+    }
+
+    @DataProvider(name = "getNumClippedBasesAtEndTestReads")
+    public Object[][] numClipEnd() {
+        final List tests = new ArrayList<>();
+        tests.add(new Object[] {allMatch, 0});
+        tests.add(new Object[] {twoIndels, 0});
+        tests.add(new Object[] {softClipStart, 0});
+        tests.add(new Object[] {hardClipStart, 0});
+        tests.add(new Object[] {lowQualTail, 6});
+        tests.add(new Object[] {lowQualClippedTail, 6});
+        tests.add(new Object[] {lowQualStart, 0});
+        tests.add(new Object[] {lowQualBothEnds, 6});
+        return tests.toArray(new Object[][]{});
+    }
+
+    @Test(dataProvider = "getNumClippedBasesAtEndTestReads")
+    public void testGetNumClippedBasesAtEnd(GATKSAMRecord read, int expected) throws Exception {
+        Assert.assertEquals(AnnotationUtils.getNumClippedBasesAtEnd(read), expected);
+    }
+}
\ No newline at end of file
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/ExcessHetUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/ExcessHetUnitTest.java
new file mode 100644
index 000000000..8b5194485
--- /dev/null
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/ExcessHetUnitTest.java
@@ -0,0 +1,248 @@
+/*
+* By downloading the PROGRAM you agree to the following terms of use:
+* 
+* BROAD INSTITUTE
+* SOFTWARE LICENSE AGREEMENT
+* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+* 
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* 
+* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+* 
+* 1. DEFINITIONS
+* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE.
+* 
+* 2. LICENSE
+* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.
+* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+* 
+* 3. PHONE-HOME FEATURE
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* 
+* 4. OWNERSHIP OF INTELLECTUAL PROPERTY
+* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+* Copyright 2012-2015 Broad Institute, Inc.
+* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+* 
+* 5. INDEMNIFICATION
+* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+* 
+* 6. NO REPRESENTATIONS OR WARRANTIES
+* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+* 
+* 7. ASSIGNMENT
+* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+* 
+* 8. MISCELLANEOUS
+* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
+* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.gatk.tools.walkers.annotator;
+
+import htsjdk.variant.variantcontext.*;
+import org.testng.Assert;
+import org.testng.annotations.BeforeSuite;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+/**
+ * Created with IntelliJ IDEA.
+ * User: mshand
+ * Date: 9/3/15
+ */
+public class ExcessHetUnitTest {
+    private static double DELTA_PRECISION = .001;
+    private Allele Aref, T, C;
+    private int[] hetPLs, homRefPLs;
+
+    @BeforeSuite
+    public void setup() {
+        // alleles
+        Aref = Allele.create("A", true);
+        T = Allele.create("T");
+        C = Allele.create("C");
+
+        // simulating 20 reads with Q30 base qualities
+        hetPLs = new int[]{240, 0, 240};
+        homRefPLs = new int[]{0, 60, 600};
+    }
+
+    private Genotype makeGwithPLs(String sample, Allele a1, Allele a2, double[] pls) {
+        Genotype gt = new GenotypeBuilder(sample, Arrays.asList(a1, a2)).PL(pls).make();
+        if (pls != null && pls.length > 0) {
+            Assert.assertNotNull(gt.getPL());
+            Assert.assertTrue(gt.getPL().length > 0);
+            for (int i : gt.getPL()) {
+                Assert.assertTrue(i >= 0);
+            }
+            Assert.assertNotEquals(Arrays.toString(gt.getPL()), "[0]");
+        }
+        return gt;
+    }
+
+    private Genotype makeG(String sample, Allele a1, Allele a2, int... pls) {
+        return new GenotypeBuilder(sample, Arrays.asList(a1, a2)).PL(pls).make();
+    }
+
+    private VariantContext makeVC(String source, List alleles, Genotype... genotypes) {
+        int start = 10;
+        int stop = start; // alleles.contains(ATC) ? start + 3 : start;
+        return new VariantContextBuilder(source, "1", start, stop, alleles)
+                .genotypes(Arrays.asList(genotypes))
+                .filters((String) null)
+                .make();
+    }
+
+    @Test
+    public void testExcessHetForMultiallelicVC() {
+        //make sure that compound gets (with no ref) don't add to het count
+        VariantContext test1 = makeVC("1", Arrays.asList(Aref, T, C),
+                makeG("s1", Aref, T, 2530, 0, 7099, 366, 3056, 14931),
+                makeG("s2", T, T, 7099, 2530, 0, 7099, 366, 3056),
+                makeG("s3", T, C, 7099, 2530, 7099, 3056, 0, 14931),
+                makeG("s4", Aref, T, 2530, 0, 7099, 366, 3056, 14931),
+                makeG("s5", T, T, 7099, 2530, 0, 7099, 366, 3056),
+                makeG("s6", Aref, T, 2530, 0, 7099, 366, 3056, 14931),
+                makeG("s7", T, T, 7099, 2530, 0, 7099, 366, 3056),
+                makeG("s8", Aref, T, 2530, 0, 7099, 366, 3056, 14931),
+                makeG("s9", T, T, 7099, 2530, 0, 7099, 366, 3056),
+                makeG("s10", Aref, T, 2530, 0, 7099, 366, 3056, 14931));
+
+        final double EHresult1 = new ExcessHet().calculateEH(test1, test1.getGenotypes());
+        Assert.assertEquals(EHresult1, 5.85, DELTA_PRECISION, "Pass");
+
+        //make sure that hets with different alternate alleles all get counted
+        VariantContext test2 = makeVC("2", Arrays.asList(Aref, T, C),
+                makeG("s1", Aref, C, 4878, 1623, 11297, 0, 7970, 8847),
+                makeG("s2", Aref, T, 2530, 0, 7099, 366, 3056, 14931),
+                makeG("s3", Aref, T, 3382, 0, 6364, 1817, 5867, 12246),
+                makeG("s4", Aref, T, 2488, 0, 9110, 3131, 9374, 12505),
+                makeG("s5", Aref, C, 4530, 2006, 18875, 0, 6847, 23949),
+                makeG("s6", Aref, T, 5325, 0, 18692, 389, 16014, 24570),
+                makeG("s7", Aref, T, 2936, 0, 29743, 499, 21979, 38630),
+                makeG("s8", Aref, T, 6902, 0, 8976, 45, 5844, 9061),
+                makeG("s9", Aref, T, 5732, 0, 10876, 6394, 11408, 17802),
+                makeG("s10", Aref, T, 2780, 0, 25045, 824, 23330, 30939));
+
+        final double EHresult2 = new ExcessHet().calculateEH(test2, test2.getGenotypes());
+        Assert.assertEquals(EHresult2, 25.573, DELTA_PRECISION, "Pass");
+    }
+
+    @Test
+    public void testSingletonVsCommonAllele() {
+
+        final List allGTs = new ArrayList<>();
+        final int numHomRefGTs = 10000;
+        for (int i = 0; i < numHomRefGTs; i++)
+            allGTs.add(makeG("ref" + i, Aref, Aref, homRefPLs));
+
+        allGTs.add(makeG("het0", Aref, T, hetPLs));
+        int numHetGTs = 1;
+
+        final VariantContext singleton = makeVC("singleton", Arrays.asList(Aref, T), allGTs.toArray(new Genotype[allGTs.size()]));
+        final double EHsingleton = new ExcessHet().calculateEH(singleton, singleton.getGenotypes());
+
+        final int targetNumHetGTs = 20;
+        for (int i = numHetGTs; i < targetNumHetGTs; i++)
+            allGTs.add(makeG("het" + i, Aref, T, hetPLs));
+
+        final VariantContext common = makeVC("common", Arrays.asList(Aref, T), allGTs.toArray(new Genotype[allGTs.size()]));
+        final double EHcommon = new ExcessHet().calculateEH(common, common.getGenotypes());
+
+        Assert.assertTrue(Math.abs(EHsingleton) < Math.abs(EHcommon), String.format("singleton=%f common=%f", EHsingleton, EHcommon));
+    }
+
+    @Test
+    public void testLargeCohorts() {
+
+        final List allGTs = new ArrayList<>();
+        final int numHomRefGTs = 1000000;
+        for (int i = 0; i < numHomRefGTs; i++)
+            allGTs.add(makeG("ref" + i, Aref, Aref, homRefPLs));
+
+        allGTs.add(makeG("het0", Aref, T, hetPLs));
+        int numHetGTs = 1;
+
+        final VariantContext singleton = makeVC("singleton", Arrays.asList(Aref, T), allGTs.toArray(new Genotype[allGTs.size()]));
+        final double EHsingleton = new ExcessHet().calculateEH(singleton, singleton.getGenotypes());
+
+        for (int i = numHetGTs; i < 100; i++) {
+            allGTs.add(makeG("het" + i, Aref, T, hetPLs));
+            numHetGTs++;
+        }
+
+        final VariantContext hundredton = makeVC("hundredton", Arrays.asList(Aref, T), allGTs.toArray(new Genotype[allGTs.size()]));
+        final double EHhundredton = new ExcessHet().calculateEH(hundredton, hundredton.getGenotypes());
+
+        Assert.assertTrue(Math.abs(EHsingleton) < Math.abs(EHhundredton), String.format("singleton=%f hundredton=%f", EHsingleton, EHhundredton));
+
+        for (int i = numHetGTs; i < numHomRefGTs; i++)
+            allGTs.add(makeG("het" + i, Aref, T, hetPLs));
+
+        final VariantContext common = makeVC("common", Arrays.asList(Aref, T), allGTs.toArray(new Genotype[allGTs.size()]));
+        final double EHcommon = new ExcessHet().calculateEH(common, common.getGenotypes());
+
+        Assert.assertTrue(Math.abs(EHhundredton) < Math.abs(EHcommon), String.format("hundredton=%f common=%f", EHhundredton, EHcommon));
+    }
+
+    @Test
+    public void testAllHetsForLargeCohorts() {
+
+        final int numGTs = 1000000;
+
+        final List singletonGTs = new ArrayList<>();
+        for (int i = 0; i < numGTs; i++)
+            singletonGTs.add(makeG("ref" + i, Aref, Aref, homRefPLs));
+
+        singletonGTs.add(makeG("het0", Aref, T, hetPLs));
+
+        final VariantContext singleton = makeVC("singleton", Arrays.asList(Aref, T), singletonGTs.toArray(new Genotype[singletonGTs.size()]));
+        final double EHsingleton = new ExcessHet().calculateEH(singleton, singleton.getGenotypes());
+
+        final List allHetGTs = new ArrayList<>();
+        for (int i = 0; i < numGTs; i++)
+            allHetGTs.add(makeG("het" + i, Aref, T, hetPLs));
+
+        final VariantContext allHet = makeVC("allHet", Arrays.asList(Aref, T), allHetGTs.toArray(new Genotype[allHetGTs.size()]));
+        final double EHHets = new ExcessHet().calculateEH(allHet, allHet.getGenotypes());
+
+        Assert.assertTrue(Math.abs(EHsingleton) < Math.abs(EHHets), String.format("singleton=%f allHets=%f", EHsingleton, EHHets));
+    }
+
+    @DataProvider(name = "smallSets")
+    public Object[][] counts() {
+        return new Object[][]{
+                {1, 0, 0, .5},
+                {1, 1, 0, .5},
+                {1, 1, 1, .7},
+                {4, 0, 0, .114},
+                {2, 1, 1, .571},
+                {0, 2, 2, .957},
+                {1, 1, 40, .982},
+                {3, 0, 39, .482},
+        };
+    }
+
+
+    @Test(dataProvider = "smallSets")
+    public void smallSets(int hetCount, int homrefCount, int homvarCount, double expected) {
+        double actual = new ExcessHet().exactTest(new int[]{homrefCount, hetCount, homvarCount});
+        Assert.assertEquals(actual, expected, DELTA_PRECISION, "Pass");
+    }
+}
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummariesUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummariesUnitTest.java
index dd18b9d08..b2f758cd9 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummariesUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummariesUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeffUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeffUnitTest.java
index 888d761af..f23079bfe 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeffUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeffUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -59,6 +59,7 @@ import org.testng.annotations.Test;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
+import java.util.Set;
 
 /**
  * Created with IntelliJ IDEA.
@@ -102,41 +103,48 @@ public class InbreedingCoeffUnitTest {
     private VariantContext makeVC(String source, List alleles, Genotype... genotypes) {
         int start = 10;
         int stop = start; // alleles.contains(ATC) ? start + 3 : start;
-        return new VariantContextBuilder(source, "1", start, stop, alleles).genotypes(Arrays.asList(genotypes)).filters(null).make();
+        return new VariantContextBuilder(source, "1", start, stop, alleles)
+                .genotypes(Arrays.asList(genotypes))
+                .filters((String)null)
+                .make();
     }
 
     @Test
     public void testInbreedingCoeffForMultiallelicVC() {
         //make sure that compound gets (with no ref) don't add to het count
         VariantContext test1 = makeVC("1",Arrays.asList(Aref,T,C),
-                makeG("s1",Aref,T,2530,0,7099,366,3056,14931),
-                makeG("s2",T,T,7099,2530,0,7099,366,3056,14931),
-                makeG("s3",T,C,7099,2530,7099,3056,0,14931),
-                makeG("s4",Aref,T,2530,0,7099,366,3056,14931),
-                makeG("s5",T,T,7099,2530,0,7099,366,3056,14931),
-                makeG("s6",Aref,T,2530,0,7099,366,3056,14931),
-                makeG("s7",T,T,7099,2530,0,7099,366,3056,14931),
-                makeG("s8",Aref,T,2530,0,7099,366,3056,14931),
-                makeG("s9",T,T,7099,2530,0,7099,366,3056,14931),
-                makeG("s10",Aref,T,2530,0,7099,366,3056,14931));
+                makeG("s1", Aref, T, 2530, 0, 7099, 366, 3056, 14931),
+                makeG("s2", T, T, 7099, 2530, 0, 7099, 366, 3056),
+                makeG("s3", T, C, 7099, 2530, 7099, 3056, 0, 14931),
+                makeG("s4", Aref, T, 2530, 0, 7099, 366, 3056, 14931),
+                makeG("s5", T, T, 7099, 2530, 0, 7099, 366, 3056),
+                makeG("s6", Aref, T, 2530, 0, 7099, 366, 3056, 14931),
+                makeG("s7", T, T, 7099, 2530, 0, 7099, 366, 3056),
+                makeG("s8", Aref, T, 2530, 0, 7099, 366, 3056, 14931),
+                makeG("s9", T, T, 7099, 2530, 0, 7099, 366, 3056),
+                makeG("s10", Aref, T, 2530, 0, 7099, 366, 3056, 14931));
 
-        final double ICresult1 = new InbreedingCoeff().calculateIC(test1, test1.getGenotypes());
+        InbreedingCoeff testClass = new InbreedingCoeff();
+        //Since we're calling this from outside the AnnotationEngine, the InbreedingCoeff has to be initialized so it can store genotype counts
+        testClass.initialize(null, null, null);
+        final double ICresult1 = testClass.calculateIC(test1, test1.getGenotypes());
         Assert.assertEquals(ICresult1, -0.3333333, DELTA_PRECISION, "Pass");
 
         //make sure that hets with different alternate alleles all get counted
         VariantContext test2 = makeVC("2", Arrays.asList(Aref,T,C),
-            makeG("s1",Aref,C,4878,1623,11297,0,7970,8847),
-            makeG("s2",Aref,T,2530,0,7099,366,3056,14931),
-            makeG("s3",Aref,T,3382,0,6364,1817,5867,12246),
-            makeG("s4",Aref,T,2488,0,9110,3131,9374,12505),
-            makeG("s5",Aref,C,4530,2006,18875,0,6847,23949),
-            makeG("s6",Aref,T,5325,0,18692,389,16014,24570),
-            makeG("s7",Aref,T,2936,0,29743,499,21979,38630),
-            makeG("s8",Aref,T,6902,0,8976,45,5844,9061),
-            makeG("s9",Aref,T,5732,0,10876,6394,11408,17802),
-            makeG("s10",Aref,T,2780,0,25045,824,23330,30939));
+                makeG("s1", Aref, C, 4878, 1623, 11297, 0, 7970, 8847),
+                makeG("s2", Aref, T, 2530, 0, 7099, 366, 3056, 14931),
+                makeG("s3", Aref, T, 3382, 0, 6364, 1817, 5867, 12246),
+                makeG("s4", Aref, T, 2488, 0, 9110, 3131, 9374, 12505),
+                makeG("s5", Aref, C, 4530, 2006, 18875, 0, 6847, 23949),
+                makeG("s6", Aref, T, 5325, 0, 18692, 389, 16014, 24570),
+                makeG("s7", Aref, T, 2936, 0, 29743, 499, 21979, 38630),
+                makeG("s8", Aref, T, 6902, 0, 8976, 45, 5844, 9061),
+                makeG("s9", Aref, T, 5732, 0, 10876, 6394, 11408, 17802),
+                makeG("s10", Aref, T, 2780, 0, 25045, 824, 23330, 30939));
 
-        final double ICresult2 = new InbreedingCoeff().calculateIC(test2, test2.getGenotypes());
+        testClass.initialize(null, null, null);
+        final double ICresult2 = testClass.calculateIC(test2, test2.getGenotypes());
         Assert.assertEquals(ICresult2, -1.0, DELTA_PRECISION, "Pass");
     }
 
@@ -152,14 +160,17 @@ public class InbreedingCoeffUnitTest {
         int numHetGTs = 1;
 
         final VariantContext singleton = makeVC("singleton", Arrays.asList(Aref, T), allGTs.toArray(new Genotype[allGTs.size()]));
-        final double ICsingleton = new InbreedingCoeff().calculateIC(singleton, singleton.getGenotypes());
+        InbreedingCoeff testClass = new InbreedingCoeff();
+        testClass.initialize(null, null, null);
+        final double ICsingleton = testClass.calculateIC(singleton, singleton.getGenotypes());
 
         final int targetNumHetGTs = 20;
         for ( int i = numHetGTs; i < targetNumHetGTs; i++ )
             allGTs.add(makeG("het" + i, Aref, T, hetPLs));
 
         final VariantContext common = makeVC("common", Arrays.asList(Aref, T), allGTs.toArray(new Genotype[allGTs.size()]));
-        final double ICcommon = new InbreedingCoeff().calculateIC(common, common.getGenotypes());
+        testClass.initialize(null, null, null);
+        final double ICcommon = testClass.calculateIC(common, common.getGenotypes());
 
         Assert.assertTrue(Math.abs(ICsingleton) < Math.abs(ICcommon), String.format("singleton=%f common=%f", ICsingleton, ICcommon));
     }
@@ -176,7 +187,9 @@ public class InbreedingCoeffUnitTest {
         int numHetGTs = 1;
 
         final VariantContext singleton = makeVC("singleton", Arrays.asList(Aref, T), allGTs.toArray(new Genotype[allGTs.size()]));
-        final double ICsingleton = new InbreedingCoeff().calculateIC(singleton, singleton.getGenotypes());
+        InbreedingCoeff testClass = new InbreedingCoeff();
+        testClass.initialize(null, null, null);
+        final double ICsingleton = testClass.calculateIC(singleton, singleton.getGenotypes());
 
         for ( int i = numHetGTs; i < 100; i++ ) {
             allGTs.add(makeG("het" + i, Aref, T, hetPLs));
@@ -184,7 +197,8 @@ public class InbreedingCoeffUnitTest {
         }
 
         final VariantContext hundredton = makeVC("hundredton", Arrays.asList(Aref, T), allGTs.toArray(new Genotype[allGTs.size()]));
-        final double IChundredton = new InbreedingCoeff().calculateIC(hundredton, hundredton.getGenotypes());
+        testClass.initialize(null, null, null);
+        final double IChundredton = testClass.calculateIC(hundredton, hundredton.getGenotypes());
 
         Assert.assertTrue(Math.abs(ICsingleton) < Math.abs(IChundredton), String.format("singleton=%f hundredton=%f", ICsingleton, IChundredton));
 
@@ -192,7 +206,8 @@ public class InbreedingCoeffUnitTest {
             allGTs.add(makeG("het" + i, Aref, T, hetPLs));
 
         final VariantContext common = makeVC("common", Arrays.asList(Aref, T), allGTs.toArray(new Genotype[allGTs.size()]));
-        final double ICcommon = new InbreedingCoeff().calculateIC(common, common.getGenotypes());
+        testClass.initialize(null, null, null);
+        final double ICcommon = testClass.calculateIC(common, common.getGenotypes());
 
         Assert.assertTrue(Math.abs(IChundredton) < Math.abs(ICcommon), String.format("hundredton=%f common=%f", IChundredton, ICcommon));
     }
@@ -209,14 +224,17 @@ public class InbreedingCoeffUnitTest {
         singletonGTs.add(makeG("het0", Aref, T, hetPLs));
 
         final VariantContext singleton = makeVC("singleton", Arrays.asList(Aref, T), singletonGTs.toArray(new Genotype[singletonGTs.size()]));
-        final double ICsingleton = new InbreedingCoeff().calculateIC(singleton, singleton.getGenotypes());
+        InbreedingCoeff testClass = new InbreedingCoeff();
+        testClass.initialize(null, null, null);
+        final double ICsingleton = testClass.calculateIC(singleton, singleton.getGenotypes());
 
         final List allHetGTs = new ArrayList<>();
         for ( int i = 0; i < numGTs; i++ )
             allHetGTs.add(makeG("het" + i, Aref, T, hetPLs));
 
         final VariantContext allHet = makeVC("allHet", Arrays.asList(Aref, T), allHetGTs.toArray(new Genotype[allHetGTs.size()]));
-        final double ICHets = new InbreedingCoeff().calculateIC(allHet, allHet.getGenotypes());
+        testClass.initialize(null, null, null);
+        final double ICHets = testClass.calculateIC(allHet, allHet.getGenotypes());
 
         Assert.assertTrue(Math.abs(ICsingleton) < Math.abs(ICHets), String.format("singleton=%f allHets=%f", ICsingleton, ICHets));
     }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepthUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepthUnitTest.java
index cbc429837..a3259dd14 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepthUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepthUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumUnitTest.java
index 5242414d7..5bacc7450 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUnitTest.java
index 4fa913cdc..7cc76a199 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTableUtilsTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTableUtilsTest.java
new file mode 100644
index 000000000..440f14aac
--- /dev/null
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTableUtilsTest.java
@@ -0,0 +1,127 @@
+/*
+* By downloading the PROGRAM you agree to the following terms of use:
+* 
+* BROAD INSTITUTE
+* SOFTWARE LICENSE AGREEMENT
+* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+* 
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* 
+* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+* 
+* 1. DEFINITIONS
+* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE.
+* 
+* 2. LICENSE
+* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.
+* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+* 
+* 3. PHONE-HOME FEATURE
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* 
+* 4. OWNERSHIP OF INTELLECTUAL PROPERTY
+* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+* Copyright 2012-2015 Broad Institute, Inc.
+* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+* 
+* 5. INDEMNIFICATION
+* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+* 
+* 6. NO REPRESENTATIONS OR WARRANTIES
+* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+* 
+* 7. ASSIGNMENT
+* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+* 
+* 8. MISCELLANEOUS
+* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
+* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.gatk.tools.walkers.annotator;
+
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class StrandBiasTableUtilsTest {
+    private static final double DELTA_PRECISION = 10e-7;
+
+    @DataProvider(name = "UsingTable")
+    public Object[][] makeUsingTable() {
+
+                        /* NOTE: the expected P values were computed in R as follows
+             fisher = function(v) {
+                return(fisher.test(matrix(v, nrow=2, ncol=2))$p.value)
+             }
+        */
+        //> fisher(c(2068, 6796, 1133, 0))
+
+        final List tests = new ArrayList<>();
+        tests.add(new Object[]{0, 0, 0, 0, 1.0});
+        tests.add(new Object[]{100000, 100000, 100000, 100000, 1.0});
+        tests.add(new Object[]{1, 2, 3, 4, 1.0});
+        tests.add(new Object[]{0, 0, 100000, 100000, 1.0});
+        tests.add(new Object[]{100000, 100000, 100000, 0, 0.0});             //below R's or Java's precision
+
+        tests.add(new Object[]{200000, 100000, 1, 2, 1.0});                   //differs from GATK4 implementation
+        tests.add(new Object[]{100, 100, 100, 0, 3.730187e-23});
+        tests.add(new Object[]{13736, 9047, 41, 1433, 1.232E-4});              //differs from GATK4 implementation
+        tests.add(new Object[]{66, 14, 64, 4, 0.0688244});
+        tests.add(new Object[]{351169, 306836, 153739, 2379, 0.0});              //below R's or Java's precision
+        tests.add(new Object[]{116449, 131216, 289, 16957, 0.0026801});               //differs from GATK4 implementation
+        tests.add(new Object[]{137, 159, 9, 23, 0.10752410});                     //differs from GATK4 implementation
+        tests.add(new Object[]{129, 90, 21, 20, 0.6450772});                       //differs from GATK4 implementation
+        tests.add(new Object[]{14054, 9160, 16, 7827, 0.0});             //below R's or Java's precision
+        tests.add(new Object[]{32803, 9184, 32117, 3283, 0.0289540});              //differs from GATK4 implementation
+        tests.add(new Object[]{2068, 6796, 1133, 0, 0.0});             //below R's or Java's precision
+
+        return tests.toArray(new Object[][]{});
+    }
+
+    @Test(dataProvider = "UsingTable")
+    public void testPValueForContingencyTable(final int refpos, final int refneg, final int altpos, final int altneg, double expectedPvalue) throws Exception {
+        final int[][] contingencyTable = new int[2][2];
+        contingencyTable[0][0] = refpos;
+        contingencyTable[0][1] = refneg;
+        contingencyTable[1][0] = altpos;
+        contingencyTable[1][1] = altneg;
+        final double pvalue = StrandBiasTableUtils.FisherExactPValueForContingencyTable(contingencyTable);
+        Assert.assertEquals(pvalue, expectedPvalue, DELTA_PRECISION, "Pvalues");
+    }
+
+    @Test
+    public void testGetContingencyArray() throws Exception {
+        final int[][] t = new int[2][2];
+        t[0][0] = 1; t[0][1] = 2; t[1][0] = 3; t[1][1] = 4;
+        final List tList = StrandBiasTableUtils.getContingencyArray(t);
+        final List truthList = new ArrayList();
+        truthList.add(1); truthList.add(2); truthList.add(3); truthList.add(4);
+        Assert.assertEquals(tList, truthList);
+    }
+
+    @Test
+    public void testCopyContingencyTable() throws Exception {
+        final int[][] t = new int[2][2];
+        t[0][0] = 1; t[0][1] = 2; t[1][0] = 3; t[1][1] = 4;
+        final int[][] t2 = StrandBiasTableUtils.copyContingencyTable(t);
+        Assert.assertTrue(t[0][0] == t2[0][0]);
+        Assert.assertTrue(t[1][0] == t2[1][0]);
+        Assert.assertTrue(t[0][1] == t2[0][1]);
+        Assert.assertTrue(t[1][1] == t2[1][1]);
+    }
+}
\ No newline at end of file
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatioUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatioUnitTest.java
index e7398c393..4be0bbebf 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatioUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatioUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java
index 333175938..515888a09 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -74,7 +74,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
 
     final static String REF = b37KGReference;
     final static String CEUTRIO_BAM = validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam";
-    final static String standardAnnotations = " -G Standard -G StandardUG ";
+    final static String STANDARD_ANNOTATIONS = " -G Standard -G StandardUG ";
 
     public static String baseTestString() {
         return "-T VariantAnnotator -R " + b36KGReference + " --no_cmdline_in_header -o %s";
@@ -84,7 +84,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsNotAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("360610e4990860bb5c45249b8ac31e5b"));
+                Arrays.asList("b65bf866457f000926b76d0f9d40065e"));
         executeTest("test file has annotations, not asking for annotations, #1", spec);
     }
 
@@ -92,23 +92,23 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsNotAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --variant " + privateTestDir + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("d69a3c92a0e8f44e09e7377e3eaed4e8"));
+                Arrays.asList("8e830da0bf34f1dc91bbc2fa64b8a518"));
         executeTest("test file has annotations, not asking for annotations, #2", spec);
     }
 
     @Test
     public void testHasAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + standardAnnotations + "--variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("92eb47332dd9d7ee7fbe3120dc39c594"));
+                baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
+                Arrays.asList("d6cd81fc2f483f29d44fbb27d1772841"));
         executeTest("test file has annotations, asking for annotations, #1", spec);
     }
 
     @Test
     public void testHasAnnotsAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + standardAnnotations + "--variant " + privateTestDir + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("c367bf7cebd7b26305f8d4736788aec8"));
+                baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
+                Arrays.asList("300836de4e2c8424734d2ee0ca4261c1"));
         executeTest("test file has annotations, asking for annotations, #2", spec);
     }
 
@@ -116,7 +116,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsNotAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("540a9be8a8cb85b0f675fea1184bf78c"));
+                Arrays.asList("58793dec36f8aec2cd8894898ece7c4e"));
         executeTest("test file doesn't have annotations, not asking for annotations, #1", spec);
     }
 
@@ -126,51 +126,51 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
         // they don't get reordered.  It's a good test of the genotype ordering system.
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --variant " + privateTestDir + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("f900e65b65ff0f9d9eb0891ef9b28c73"));
+                Arrays.asList("27745920cc780b04e8f5acba79f868ca"));
         executeTest("test file doesn't have annotations, not asking for annotations, #2", spec);
     }
 
     @Test
     public void testNoAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + standardAnnotations + "--variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("098dcad8d90d90391755a0191c9db59c"));
+                baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
+                Arrays.asList("192f393da4e28aecf16112562e65083a"));
         executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
     }
 
     @Test
     public void testNoAnnotsAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + standardAnnotations + "--variant " + privateTestDir + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("f3bbfbc179d2e1bae49890f1e9dfde34"));
+                baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
+                Arrays.asList("52baff55535f7c87545a7818052a2d5c"));
         executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
     }
 
     @Test
     public void testExcludeAnnotations() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + standardAnnotations + "-XA FisherStrand -XA ReadPosRankSumTest --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("7267450fc4d002f75a24ca17278e0950"));
+                baseTestString() + STANDARD_ANNOTATIONS + "-XA FisherStrand -XA ReadPosRankSumTest --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
+                Arrays.asList("334915d90fa92ee9fa07d4647912ceac"));
         executeTest("test exclude annotations", spec);
     }
 
     @Test
     public void testAskingStrandAlleleCountsBySample() throws IOException{
-        String logFileName = new String("testAskingStrandAlleleCountsBySample.log");
+        File logFile = createTempFile("testAskingStrandAlleleCountsBySample.log", ".tmp");
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000 -A StrandAlleleCountsBySample -log " + logFileName, 1,
-                Arrays.asList("0c0c4a219cb487598fb1fbb77db71eca"));
+                baseTestString() + " --variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000 "
+                        + "-A StrandAlleleCountsBySample -log " + logFile.getAbsolutePath(), 1,
+                Arrays.asList("5c0fe344544a887acbb5cd83083d303b"));
         executeTest("test file has annotations, adding StrandAlleleCountsBySample annotation", spec);
 
-        File file = new File(logFileName);
-        Assert.assertTrue(FileUtils.readFileToString(file).contains("Annotation will not be calculated, must be called from HaplotyepCaller"));
+        Assert.assertTrue(FileUtils.readFileToString(logFile).contains(AnnotationUtils.ANNOTATION_HC_WARN_MSG));
     }
 
     @Test
     public void testAskingGCContent() throws IOException{
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000 -A GCContent", 1,
-                Arrays.asList("02f634fd978cf2a66738704581508569"));
+                Arrays.asList("82238b65dbd085baaec68be2975a9bf8"));
         final File outputVCF = executeTest("test file has annotations, adding GCContent annotation", spec).getFirst().get(0);
         final VCFCodec codec = new VCFCodec();
         final VCFHeader header = (VCFHeader) codec.readActualHeader(codec.makeSourceFromStream(new FileInputStream(outputVCF)));
@@ -182,48 +182,48 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testOverwritingHeader() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + standardAnnotations + "--variant " + privateTestDir + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
-                Arrays.asList("18592c72d83ee84e1326acb999518c38"));
+                baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
+                Arrays.asList("ab84654ac412a0aaaec99e86e357f0fd"));
         executeTest("test overwriting header", spec);
     }
 
     @Test
     public void testNoReads() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + standardAnnotations + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
-                Arrays.asList("6de950b381d2d92b21bab6144e8f0714"));
+                baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
+                Arrays.asList("489a09a8531d9c8ef683ad8cc81db3e8"));
         executeTest("not passing it any reads", spec);
     }
 
     @Test
     public void testDBTagWithDbsnp() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --dbsnp " + b36dbSNP129 + standardAnnotations + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
-                Arrays.asList("e0bd85747c87ea4df6ef67f593cbacbf"));
+                baseTestString() + " --dbsnp " + b36dbSNP129 + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
+                Arrays.asList("a7af6774ea1f7622d999cae1b7f8ea32"));
         executeTest("getting DB tag with dbSNP", spec);
     }
 
     @Test
     public void testMultipleIdsWithDbsnp() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --alwaysAppendDbsnpId --dbsnp " + b36dbSNP129 + standardAnnotations + "--variant " + privateTestDir + "vcfexample3withIDs.vcf -L " + privateTestDir + "vcfexample3withIDs.vcf", 1,
-                Arrays.asList("194a942f17104292192fb564a3c96610"));
+                baseTestString() + " --alwaysAppendDbsnpId --dbsnp " + b36dbSNP129 + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3withIDs.vcf -L " + privateTestDir + "vcfexample3withIDs.vcf", 1,
+                Arrays.asList("de8cfffe3b61b7c8832096a399e9d954"));
         executeTest("adding multiple IDs with dbSNP", spec);
     }
 
     @Test
     public void testDBTagWithHapMap() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --comp:H3 " + privateTestDir + "fakeHM3.vcf" + standardAnnotations + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
-                Arrays.asList("9e41ae733a76632b40eda38e3cef909d"));
+                baseTestString() + " --comp:H3 " + privateTestDir + "fakeHM3.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
+                Arrays.asList("25443af7099f7de184b8dcdfb659f62e"));
         executeTest("getting DB tag with HM3", spec);
     }
 
     @Test
     public void testDBTagWithTwoComps() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --comp:H3 " + privateTestDir + "fakeHM3.vcf --comp:foo " + privateTestDir + "fakeHM3.vcf " + standardAnnotations + " --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
-                Arrays.asList("7b718bae0444f1896a6e86da80531218"));
+                baseTestString() + " --comp:H3 " + privateTestDir + "fakeHM3.vcf --comp:foo " + privateTestDir + "fakeHM3.vcf " + STANDARD_ANNOTATIONS + " --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
+                Arrays.asList("ea9b10d2b82a7846c01a017f6f3bb57e"));
         executeTest("getting DB tag with 2 comps", spec);
     }
 
@@ -231,37 +231,54 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoQuals() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --variant " + privateTestDir + "noQual.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L " + privateTestDir + "noQual.vcf -A QualByDepth", 1,
-                Arrays.asList("aea983adc01cd059193538cc30adc17d"));
+                Arrays.asList("b6321f3ce7a60d083be64d5ec9a54c1b"));
         executeTest("test file doesn't have QUALs", spec);
     }
 
     @Test
     public void testUsingExpression() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf" + standardAnnotations + "--variant " + privateTestDir + "vcfexample3empty.vcf -E foo.AF -L " + privateTestDir + "vcfexample3empty.vcf", 1,
-                Arrays.asList("0bed7b4f6ed0556c5e7d398353a9fa91"));
+                baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -E foo.AF -L " + privateTestDir + "vcfexample3empty.vcf", 1,
+                Arrays.asList("f26d1f849cceca0ab115737f8db670ae"));
         executeTest("using expression", spec);
     }
 
+    @Test
+    public void testUsingExpressionAlleleMisMatch() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString() + " --resourceAlleleConcordance --resource:foo " + privateTestDir + "targetAnnotations.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty-mod.vcf -E foo.AF -L " + privateTestDir + "vcfexample3empty-mod.vcf", 1,
+                Arrays.asList("6f288c4b672ac3a22cb2385981f51d75"));
+        executeTest("using expression allele mismatch", spec);
+    }
+
     @Test
     public void testUsingExpressionMultiAllele() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations-multiAllele.vcf" + standardAnnotations + "--variant " + privateTestDir + "vcfexample3empty-multiAllele.vcf -E foo.AF -E foo.AC -L " + privateTestDir + "vcfexample3empty-multiAllele.vcf", 1,
-                Arrays.asList("195cf0f5b1aa5c7d00a0595dcca02f4c"));
+                baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations-multiAllele.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty-multiAllele.vcf -E foo.AF -E foo.AC -L " + privateTestDir + "vcfexample3empty-multiAllele.vcf", 1,
+                Arrays.asList("af92a439f092f45da10adac0f9c8fc8f"));
         executeTest("using expression with multi-alleles", spec);
     }
 
+    @Test
+    public void testFilterInExpression(){
+        /* The order of filters in the output seems platform-dependent. May need to change htsjdk to make the order consistent across platforms. [Sato] */
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString() + " --resource:foo " + privateTestDir + "annotationResourceWithFilter.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty-multiAllele.vcf -E foo.FILTER -L " + privateTestDir + "vcfexample3empty-multiAllele.vcf", 1,
+                Arrays.asList("77bc144fd432b8886ab19ed20bfb9396"));
+        executeTest("annotate a vcf with the FILTER field of another vcf", spec);
+    }
+
     @Test
     public void testUsingExpressionWithID() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf" + standardAnnotations + "--variant " + privateTestDir + "vcfexample3empty.vcf -E foo.ID -L " + privateTestDir + "vcfexample3empty.vcf", 1,
-                Arrays.asList("b3fe9d3bdb18ca2629543f849a7d27ed"));
+                baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -E foo.ID -L " + privateTestDir + "vcfexample3empty.vcf", 1,
+                Arrays.asList("58a86fe8a34c92127eb33e36107941dd"));
         executeTest("using expression with ID", spec);
     }
 
     @Test
     public void testTabixAnnotationsAndParallelism() {
-        final String MD5 = "99938d1e197b8f10c408cac490a00a62";
+        final String MD5 = "c5beea399dadbba66a7fc46036eeafe5";
         for ( String file : Arrays.asList("CEU.exon.2010_03.sites.vcf", "CEU.exon.2010_03.sites.vcf.gz")) {
             WalkerTestSpec spec = new WalkerTestSpec(
                     baseTestString() + " -A HomopolymerRun --variant:vcf " + validationDataLocation + file + " -L " + validationDataLocation + "CEU.exon.2010_03.sites.vcf --no_cmdline_in_header", 1,
@@ -283,7 +300,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
             validationDataLocation + "1kg_exomes_unfiltered.AFR.unfiltered.vcf --snpEffFile  " + validationDataLocation +
             "snpEff2.0.5.AFR.unfiltered.vcf -L 1:1-1,500,000 -L 2:232,325,429",
             1,
-            Arrays.asList("d9291845ce5a8576898d293a829a05b7")
+            Arrays.asList("6618f3ae9dc6d4ce6ebd4eb8f9495103")
         );
         executeTest("Testing SnpEff annotations", spec);
     }
@@ -296,7 +313,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
             "--snpEffFile  " + privateTestDir + "snpEff_unsupported_version_gatk_mode.vcf " +
             "-L 1:10001292-10012424",
             1,
-            Arrays.asList("7352cf23a4d45d3d2bb34ab44a4100ae")
+            Arrays.asList("7533645a3791ce30d7407f789e1ffbb0")
         );
         executeTest("Testing SnpEff annotations (unsupported version, GATK mode)", spec);
     }
@@ -309,14 +326,14 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
             "--snpEffFile  " + privateTestDir + "snpEff_unsupported_version_no_gatk_mode.vcf " +
             "-L 1:10001292-10012424",
             1,
-            Arrays.asList("87cbf53c65ef4498b721f901f87f0161")
+            Arrays.asList("0e201a91a2b2b130debcd5dd7d9328ab")
         );
         executeTest("Testing SnpEff annotations (unsupported version, no GATK mode)", spec);
     }
 
     @Test(enabled = true)
     public void testTDTAnnotation() {
-        final String MD5 = "427dfdc665359b67eff210f909ebf8a2";
+        final String MD5 = "9532ca341b52be650b35e32d7c765030";
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantAnnotator -R " + b37KGReference + " -A TransmissionDisequilibriumTest --variant:vcf " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf" +
                         " -L " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + privateTestDir + "ug.random50000.family.ped -o %s", 1,
@@ -327,7 +344,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
 
     @Test(enabled = true)
     public void testChromosomeCountsPed() {
-        final String MD5 = "6b5cbedf4a8b3385edf128d81c8a46f2";
+        final String MD5 = "4ab0b4245ba2c5c62424775879f51379";
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantAnnotator -R " + b37KGReference + " -A ChromosomeCounts --variant:vcf " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf" +
                         " -L " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + privateTestDir + "ug.random50000.family.ped -o %s", 1,
@@ -337,7 +354,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
 
     @Test(enabled = true)
     public void testInbreedingCoeffPed() {
-        final String MD5 = "159a771c1deaeffb786097e106943893";
+        final String MD5 = "914e6882f01bae43f1d6ba1b0023cf91";
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantAnnotator -R " + b37KGReference + " -A InbreedingCoeff --variant:vcf " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf" +
                         " -L " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + privateTestDir + "ug.random50000.family.ped -o %s", 1,
@@ -347,7 +364,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
 
     @Test(enabled = true)
     public void testAlleleTrimming() {
-        final String MD5 = "5f4b8dcbd4ec3b773486945e5b38e7f3";
+        final String MD5 = "90f9ee6c34c0820435dce7a0d63b4c1e";
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantAnnotator -R " + b37KGReference + " -A InbreedingCoeff --variant:vcf " + privateTestDir + "alleleTrim.vcf.gz" +
                         " -L 1:26608870-26608875 -no_cmdline_in_header --resource:exac " + privateTestDir +  "exacAlleleTrim.vcf.gz  -E exac.AC_Adj" +
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotatorUnitTest.java
index d403dc6fa..d356c629d 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotatorUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotatorUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java
index 116e2efde..dcbe80446 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRGathererUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRGathererUnitTest.java
index ca10b9a1a..3daffaa3e 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRGathererUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRGathererUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java
index e3bfde076..2c362acd2 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -52,6 +52,8 @@
 package org.broadinstitute.gatk.tools.walkers.bqsr;
 
 import org.broadinstitute.gatk.engine.walkers.WalkerTest;
+import org.broadinstitute.gatk.utils.commandline.ArgumentException;
+import org.broadinstitute.gatk.utils.exceptions.GATKException;
 import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
@@ -118,7 +120,7 @@ public class BQSRIntegrationTest extends WalkerTest {
                 {new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", "", "0b5a8e259e997e4c7b5836d4c28e6f4d")},
                 {new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-10,200,000", "", "281682124584ab384f23359934df0c3b")},
                 {new BQSRTest(b36KGReference, validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.1RG.bam", "1:10,000,000-10,200,000", "", "0a92fdff5fd26227c29d34eda5a32f49")},
-                {new BQSRTest(b36KGReference, validationDataLocation + "originalQuals.1kg.chr1.1-1K.1RG.bam", "1:1-1,000", " -OQ", "90d8c24077e8ae9a0037a9aad5f09e31")},
+                {new BQSRTest(hg18Reference, privateTestDir + "originalQuals.1kg.chr1.1-1K.1RG.bam", "chr1:1-1,000", " -OQ", "90d8c24077e8ae9a0037a9aad5f09e31")},
                 {new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-20,000,000", " --solid_recal_mode REMOVE_REF_BIAS", "c41ef02c640ef1fed4bfc03b9b33b616")},
                 {new BQSRTest(b36KGReference, privateTestDir + "NA19240.chr1.BFAST.SOLID.hasCSNoCall.bam", "1:50,000-80,000", " --solid_nocall_strategy LEAVE_READ_UNRECALIBRATED", "b577cd1d529425f66db49620db09fdca")},
                 {new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:anyNameABCD,VCF " + privateTestDir + "vcfexample3.vcf", "0b5a8e259e997e4c7b5836d4c28e6f4d")},
@@ -196,12 +198,13 @@ public class BQSRIntegrationTest extends WalkerTest {
     public Object[][] createPRTestData() {
         List tests = new ArrayList();
 
-        tests.add(new Object[]{1, new PRTest(" -qq -1", "ce09e16466151bb37305dbfd5dc88f35")});
-        tests.add(new Object[]{1, new PRTest(" -qq 6", "2d12f3d48b1797ea0671e28a435527fe")});
-        tests.add(new Object[]{1, new PRTest(" -DIQ", "f3dbf3ae2725f1e7aa8ae61a09beac51")});
-
+        tests.add(new Object[]{1, new PRTest(" -qq -1", "8a38828e3b14ce067614d4248e3ea95a")});
+        tests.add(new Object[]{1, new PRTest(" -qq 6", "e4f23250b2c87f0d68d042cc3d2ec1d3")});
+        tests.add(new Object[]{1, new PRTest(" -DIQ", "2dfa45f004d3a371fd290ed67fbdf573")});
+        tests.add(new Object[]{1, new PRTest(" --useOriginalQualities -SQQ 10 -SQQ 20 -SQQ 30", "4882354d9e603f9bbe7c9591bba0a573")});
+        tests.add(new Object[]{1, new PRTest(" --useOriginalQualities -SQQ 10 -SQQ 20 -SQQ 30 -RDQ", "6ffdfc4593e83f7c234b6249412433af")});
         for ( final int nct : Arrays.asList(1, 2, 4) ) {
-            tests.add(new Object[]{nct, new PRTest("", "0746ae12c106a8af0b3b01f22e9efcba")});
+            tests.add(new Object[]{nct, new PRTest("", "6451093cadfc14d7359617b2a7ea6db8")});
         }
 
         return tests.toArray(new Object[][]{});
@@ -264,4 +267,36 @@ public class BQSRIntegrationTest extends WalkerTest {
                 UserException.class);
         executeTest("testPRFailWithBadPL", spec);
     }
+
+    @Test
+    public void testPRWithConflictingArguments_qqAndSQQ() {
+        // -qq and -SQQ shouldn't be able to be run in the same command
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                " -T PrintReads" +
+                        " -R " + hg18Reference +
+                        " -I " + HiSeqBam +
+                        " -L " + HiSeqInterval +
+                        " -qq 4 -SQQ 9" +
+                        " -BQSR " + privateTestDir + "HiSeq.1mb.1RG.highMaxCycle.table" +
+                        " -o /dev/null",
+                0,
+                ArgumentException.class);
+        executeTest("testPRWithConflictingArguments_qqAndSQQ", spec);
+    }
+
+    @Test
+    public void testPRWithConflictingArguments_qlAndSQQ() {
+        // Arguments -SQQ and -ql conflict and should throw an exception
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                " -T PrintReads" +
+                        " -R " + hg18Reference +
+                        " -I " + HiSeqBam +
+                        " -L " + HiSeqInterval +
+                        " -SQQ 4 -ql 4 " +
+                        " -BQSR " + privateTestDir + "HiSeq.1mb.1RG.lowMaxCycle.table" +
+                        " -o /dev/null",
+                0,
+                ArgumentException.class);
+        executeTest("testPRWithConflictingArguments_qlAndSQQ", spec);
+    }
 }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfoUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfoUnitTest.java
index 3b4243831..2adaec781 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfoUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfoUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/BaseQualitySumPerAlleleBySampleUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/BaseQualitySumPerAlleleBySampleUnitTest.java
new file mode 100644
index 000000000..f507c8b47
--- /dev/null
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/BaseQualitySumPerAlleleBySampleUnitTest.java
@@ -0,0 +1,80 @@
+/*
+* By downloading the PROGRAM you agree to the following terms of use:
+* 
+* BROAD INSTITUTE
+* SOFTWARE LICENSE AGREEMENT
+* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+* 
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* 
+* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+* 
+* 1. DEFINITIONS
+* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE.
+* 
+* 2. LICENSE
+* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.
+* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+* 
+* 3. PHONE-HOME FEATURE
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* 
+* 4. OWNERSHIP OF INTELLECTUAL PROPERTY
+* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+* Copyright 2012-2015 Broad Institute, Inc.
+* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+* 
+* 5. INDEMNIFICATION
+* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+* 
+* 6. NO REPRESENTATIONS OR WARRANTIES
+* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+* 
+* 7. ASSIGNMENT
+* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+* 
+* 8. MISCELLANEOUS
+* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
+* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.gatk.tools.walkers.cancer;
+
+import htsjdk.samtools.SAMFileHeader;
+import org.broadinstitute.gatk.utils.QualityUtils;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+public class BaseQualitySumPerAlleleBySampleUnitTest {
+    @Test
+    public void BasicTest() {
+        BaseQualitySumPerAlleleBySample a = new BaseQualitySumPerAlleleBySample();
+
+        final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(5, 1, 10000);
+        final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 1, 76);
+
+        read.setMappingQuality(60);
+        Assert.assertTrue(a.isUsableRead(read));
+
+        read.setMappingQuality(0);
+        Assert.assertFalse(a.isUsableRead(read));
+
+        read.setMappingQuality(QualityUtils.MAPPING_QUALITY_UNAVAILABLE);
+        Assert.assertFalse(a.isUsableRead(read));
+
+    }
+    
+}
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/beagle/BeagleIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContEstIntegrationTest.java
similarity index 75%
rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/beagle/BeagleIntegrationTest.java
rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContEstIntegrationTest.java
index 30ae63869..ac1edfaa9 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/beagle/BeagleIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContEstIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -49,61 +49,55 @@
 * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
 */
 
-package org.broadinstitute.gatk.tools.walkers.beagle;
+package org.broadinstitute.gatk.tools.walkers.cancer.contamination;
 
 import org.broadinstitute.gatk.engine.walkers.WalkerTest;
 import org.testng.annotations.Test;
 
 import java.util.Arrays;
- 
-public class BeagleIntegrationTest extends WalkerTest {
+import java.util.Collections;
+import java.util.List;
 
-    private static final String beagleValidationDataLocation = privateTestDir + "/Beagle/";
-    @Test
-    public void testBeagleOutput() {
-        WalkerTestSpec spec = new WalkerTestSpec(
-                "-T BeagleOutputToVCF -R " + hg19Reference + " " +
-                        "--variant:VCF3 " + beagleValidationDataLocation + "inttestbgl.input.vcf " +
-                        "--beagleR2:BEAGLE " + beagleValidationDataLocation + "inttestbgl.r2 " +
-                        "--beagleProbs:BEAGLE " + beagleValidationDataLocation + "inttestbgl.gprobs " +
-                        "--beaglePhased:BEAGLE " + beagleValidationDataLocation + "inttestbgl.phased " +
-                        "-o %s --no_cmdline_in_header -U LENIENT_VCF_PROCESSING", 1, Arrays.asList("1c4f2fed1d452368fa4dfe3e209ebb57"));
-        spec.disableShadowBCF();
-        executeTest("test BeagleOutputToVCF", spec);
-    }
-   
-    @Test
-    public void testBeagleInput() {
-        WalkerTestSpec spec = new WalkerTestSpec(
-                "-T ProduceBeagleInput -R " + hg19Reference + " " +
-                        "--variant:VCF3 " + beagleValidationDataLocation + "inttestbgl.input.vcf " +
-                         "-o %s -U LENIENT_VCF_PROCESSING", 1, Arrays.asList("f301b089d21da259873f04bdc468835d"));
-        spec.disableShadowBCF();
-        executeTest("test BeagleInput", spec);
+/**
+ * Test ContEst with and without a "genotyping array" VCF
+ *
+ * @author gauthier
+ */
+public class ContEstIntegrationTest extends WalkerTest {
+    public static final String DREAMBamsDirectory = new String("/dsde/working/mutect/dream_smc/bams/");
+    public static final String ContaminatedBamsDirectory = new String("/dsde/working/mutect/contamination/bams/");
+    public static final String NormalBamsDirectory = new String("/humgen/gsa-hpprojects/NA12878Collection/bams/crsp_ice_validation/");
+    public static final String ICEexomeIntervals = new String("/seq/references/HybSelOligos/HybSelOligos/whole_exome_illumina_coding_v1/whole_exome_illumina_coding_v1.Homo_sapiens_assembly19.targets.interval_list");
+
+    @Test(enabled = true)
+    public void testWithArray() {
+        List md5sums = Arrays.asList("d41d8cd98f00b204e9800998ecf8427e");
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T ContEst" +
+                " -I " + DREAMBamsDirectory + "synthetic.challenge.set4.tumor.bam" +
+                " -R " + b37KGReference +
+                " --popfile " + validationDataLocation + "cancer/hg19_population_stratified_af_hapmap_3.3.fixed.vcf" +
+                " --genotypes " + validationDataLocation + "cancer/Dream.set3.tumorGTs.vcf" +
+                " -L " + validationDataLocation + "cancer/SNP6.hg19.interval_list" +
+                " -L " + ICEexomeIntervals +
+                " -L 1" +
+                " -isr INTERSECTION",md5sums);
+        executeTest("testWithArray",spec);
     }
 
-    @Test
-    public void testBeagleInput2() {
-        WalkerTestSpec spec = new WalkerTestSpec(
-                "-T ProduceBeagleInput --variant:VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/NA12878_HSQ_chr22_14-16m.vcf "+
-                        "--validation:VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/NA12878_OMNI_chr22_14-16m.vcf "+
-                        "-L 22:14000000-16000000 -o %s -bvcf %s -bs 0.8 -U LENIENT_VCF_PROCESSING -valp 0.98 -R /humgen/1kg/reference/human_g1k_v37.fasta --no_cmdline_in_header ",2,
-                Arrays.asList("660986891b30cdc937e0f2a3a5743faa","4b6417f892ccfe5c63b8a60cb0ef3740"));
-        spec.disableShadowBCF();
-        executeTest("test BeagleInputWithBootstrap",spec);
+    @Test(enabled = true)
+    public void testArrayFree(){
+        List md5sums = Arrays.asList("d41d8cd98f00b204e9800998ecf8427e");
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T ContEst" +
+                        " -I:eval " + ContaminatedBamsDirectory + "HCC1143_BL.small.0.05.contaminated.with.SM-612V3.small.0.95.bam" +
+                        " -I:genotype " + NormalBamsDirectory + "SM-612V4.bam" +
+                        " -R " + b37KGReference +
+                        " --popfile " + validationDataLocation + "hg19_population_stratified_af_hapmap_3.3.fixed.vcf" +
+                        " -L " + validationDataLocation + "SNP6.hg19.interval_list" +
+                        " -L " + ICEexomeIntervals +
+                        " -L 1" +
+                        " -isr INTERSECTION",md5sums);
+        executeTest("testArrayFree",spec);
     }
-
-    @Test
-    public void testBeagleOutput2() {
-        WalkerTestSpec spec = new WalkerTestSpec(
-                "-T BeagleOutputToVCF -R "+hg19Reference+" "+
-                "--variant:VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.vcf "+
-                "--beagleR2:beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.r2 "+
-                "--beagleProbs:beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.gprobs.bgl "+
-                "--beaglePhased:beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.phased.bgl "+
-                "-L 20:1-70000 -o %s --no_cmdline_in_header -U LENIENT_VCF_PROCESSING",1,Arrays.asList("e036636fcd6a748ede4a70ea47941d47"));
-        spec.disableShadowBCF();
-        executeTest("testBeagleChangesSitesToRef",spec);
-    }
-
 }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContEstUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContEstUnitTest.java
new file mode 100644
index 000000000..9b8990a08
--- /dev/null
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContEstUnitTest.java
@@ -0,0 +1,134 @@
+/*
+* By downloading the PROGRAM you agree to the following terms of use:
+* 
+* BROAD INSTITUTE
+* SOFTWARE LICENSE AGREEMENT
+* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+* 
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* 
+* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+* 
+* 1. DEFINITIONS
+* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE.
+* 
+* 2. LICENSE
+* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.
+* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+* 
+* 3. PHONE-HOME FEATURE
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* 
+* 4. OWNERSHIP OF INTELLECTUAL PROPERTY
+* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+* Copyright 2012-2015 Broad Institute, Inc.
+* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+* 
+* 5. INDEMNIFICATION
+* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+* 
+* 6. NO REPRESENTATIONS OR WARRANTIES
+* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+* 
+* 7. ASSIGNMENT
+* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+* 
+* 8. MISCELLANEOUS
+* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
+* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.gatk.tools.walkers.cancer.contamination;
+
+import htsjdk.samtools.SAMFileHeader;
+import org.broadinstitute.gatk.utils.cancer.TestingReadUtils;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
+import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
+import htsjdk.variant.variantcontext.Allele;
+import htsjdk.variant.variantcontext.Genotype;
+import org.testng.annotations.Test;
+
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+
+import static org.testng.AssertJUnit.assertTrue;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: aaron
+ * Date: 2/18/12
+ * Time: 4:05 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class ContEstUnitTest extends BaseTest {
+    SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1,1,2000);
+    GenomeLocParser parser = new GenomeLocParser(header.getSequenceDictionary());
+    private static final Map alleles = new HashMap();
+    String primaryRG = new String("genotype");
+    static {
+        alleles.put(0,Allele.create((byte) 'A'));
+        alleles.put(1,Allele.create((byte) 'C'));
+        alleles.put(2,Allele.create((byte) 'G'));
+        alleles.put(3,Allele.create((byte) 'T'));
+    }
+    @Test
+    public void testGettingGenotypes() {
+        // test that we can get a
+        Genotype g = testContaminationGenotype(20,80,0.8);
+        assertTrue(g.isHomVar());
+        assertTrue("T".equals(g.getGenotypeString()));
+
+        g = testContaminationGenotype(19,81,0.8);
+        assertTrue(g.isHomVar());
+        assertTrue("T".equals(g.getGenotypeString()));
+
+        g = testContaminationGenotype(21,79,0.8);
+        assertTrue(g == null);
+    }
+
+    private Genotype testContaminationGenotype(int aBases, int tBases, double minGenotypeRatio) {
+        // setup all the parameters
+        AlignmentContext context = TestingReadUtils.generateAlignmentContext(aBases + tBases, tBases, header, parser, primaryRG, primaryRG);
+        GenomeLoc loc = parser.createGenomeLoc(header.getSequenceDictionary().getSequence(0).getSequenceName(),1,1);
+        ReferenceContext referenceContext = new ReferenceContext(parser,loc,(byte)'A');
+        ContEst.SeqGenotypeMode genotypeMode = ContEst.SeqGenotypeMode.HARD_THRESHOLD;
+        int minGenotypingDepth = 50;
+        double minGenotypingLOD = 5;
+        Map> bamReadGroupMapping = new HashMap>();
+        HashSet brgm = new HashSet();
+        brgm.add(primaryRG);
+
+        bamReadGroupMapping.put(ContEst.GENOTYPE_BAM_TAG,brgm);
+        String sampleName = "sample";
+        GenomeAnalysisEngine toolKit = null;
+        return ContEst.getGenotypeFromSeq(context,
+                referenceContext,
+                alleles,
+                genotypeMode,
+                minGenotypeRatio,
+                minGenotypingDepth,
+                minGenotypingLOD,
+                sampleName,
+                sampleName,
+                toolKit);
+    }
+
+
+}
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2IntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2IntegrationTest.java
new file mode 100644
index 000000000..f9b18d4b9
--- /dev/null
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2IntegrationTest.java
@@ -0,0 +1,124 @@
+/*
+* By downloading the PROGRAM you agree to the following terms of use:
+* 
+* BROAD INSTITUTE
+* SOFTWARE LICENSE AGREEMENT
+* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+* 
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* 
+* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+* 
+* 1. DEFINITIONS
+* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE.
+* 
+* 2. LICENSE
+* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.
+* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+* 
+* 3. PHONE-HOME FEATURE
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* 
+* 4. OWNERSHIP OF INTELLECTUAL PROPERTY
+* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+* Copyright 2012-2015 Broad Institute, Inc.
+* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+* 
+* 5. INDEMNIFICATION
+* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+* 
+* 6. NO REPRESENTATIONS OR WARRANTIES
+* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+* 
+* 7. ASSIGNMENT
+* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+* 
+* 8. MISCELLANEOUS
+* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
+* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.gatk.tools.walkers.cancer.m2;
+
+import org.broadinstitute.gatk.engine.walkers.WalkerTest;
+import org.testng.annotations.Test;
+
+import java.util.*;
+
+public class MuTect2IntegrationTest extends WalkerTest {
+    final static String REF = hg19Reference;
+
+    final static String CCLE_MICRO_TUMOR_BAM = privateTestDir + "HCC1143.cghub.ccle.micro.bam";
+    final static String CCLE_MICRO_NORMAL_BAM = privateTestDir + "HCC1143_BL.cghub.ccle.micro.bam";
+    final static String CCLE_MICRO_INTERVALS_FILE = privateTestDir + "HCC1143.cghub.ccle.micro.intervals";
+
+    final static String DBSNP=b37dbSNP132;
+    final static String COSMIC="/xchip/cga/reference/hg19/hg19_cosmic_v54_120711.vcf";
+    final static String PON="/xchip/cga/reference/hg19/refseq_exome_10bp_hg19_300_1kg_normal_panel.vcf";
+
+    final static String DREAM3_TUMOR_BAM = validationDataLocation + "cancer/dream3.integrationtest.tumor.bam";
+    final static String DREAM3_NORMAL_BAM = validationDataLocation + "cancer/dream3.integrationtest.normal.bam";
+    final static String DREAM3_TP_INTERVALS_FILE = privateTestDir + "m2_dream3.tp.intervals";
+    final static String DREAM3_FP_INTERVALS_FILE = privateTestDir + "m2_dream3.fp.intervals";
+
+
+
+    private void M2Test(String tumorBam, String normalBam, String intervals, String args, String md5) {
+                final String base = String.format(
+                "-T MuTect2 --no_cmdline_in_header -dt NONE --disableDithering -alwaysloadVectorHMM -pairHMM LOGLESS_CACHING -ip 50 -R %s --dbsnp %s --cosmic %s --normal_panel %s -I:tumor %s -I:normal %s -L %s",
+                REF, DBSNP, COSMIC, PON, tumorBam, normalBam, intervals) +
+                " -o %s ";
+
+        final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
+
+        // TODO: do we want to enable this and why?  It explodes with
+        // java.lang.RuntimeException: java.lang.ClassCastException: java.lang.Double cannot be cast to java.lang.String
+        //    at htsjdk.variant.variantcontext.writer.BCF2FieldEncoder$StringOrCharacter.javaStringToBCF2String(BCF2FieldEncoder.java:312)
+        spec.disableShadowBCF();
+        executeTest("testM2: args=" + args, spec);
+    }
+
+    @Test
+    public void testMicroRegression() {
+        M2Test(CCLE_MICRO_TUMOR_BAM, CCLE_MICRO_NORMAL_BAM, CCLE_MICRO_INTERVALS_FILE, "", "617054c6d056cad7448a463cb8d04a55");
+    }
+
+    /**
+     * Tests all the True Positive sites in the DREAM 3 data set.  We don't necessarily call
+     * all of these (e.g. we have some FNs) but it's the full set of things we want to be able
+     * to call, and not regress
+     */
+    @Test
+    public void testTruePositivesDream3() {
+        M2Test(DREAM3_TUMOR_BAM, DREAM3_NORMAL_BAM, DREAM3_TP_INTERVALS_FILE, "", "f856432679e43445d2939772be4326cf");
+    }
+
+    /**
+     * Tests a number of False Positive calls from the DREAM 3 data set.  Some of them are not rejected
+     * (e.g. we have some FPs!) but most are rejected.
+     */
+    @Test
+    public void testFalsePositivesDream3() {
+        M2Test(DREAM3_TUMOR_BAM, DREAM3_NORMAL_BAM, DREAM3_FP_INTERVALS_FILE, "", "11357aa543e7c6b2725cd330adba23a0");
+    }
+
+    /*
+     * Test that contamination downsampling reduces tumor LOD, rejects more variants
+     */
+    @Test
+    public void testContaminationCorrection() {
+        M2Test(CCLE_MICRO_TUMOR_BAM, CCLE_MICRO_NORMAL_BAM, CCLE_MICRO_INTERVALS_FILE, "-contamination 0.1", "d7947ddf0240fe06a44621312831f44c");
+    }
+
+}
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/how_to_make_dream3_bams.txt b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/how_to_make_dream3_bams.txt
new file mode 100644
index 000000000..e10ab75ca
--- /dev/null
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/how_to_make_dream3_bams.txt
@@ -0,0 +1,24 @@
+# intervals file (m2_dream3.intervals) was created by merging the following data sets:
+#     1. all M2 calls (including failures) from chr21 on the full DREAM 3 challenge data set, after being called 
+#        realigned by BWA-MEM.  This is to capture FP, TN and some TP
+#     2. all TP events from the DREAM 3 truth data for chr21
+#
+# Then the following command was run to produce the subsetted BAMs
+
+cat m2_dream3.tp.intervals m2_dream3.fp.intervals > m2_dream3.intervals
+
+export GATK_JAR=/humgen/gsa-hpprojects/GATK/bin/current/GenomeAnalysisTK.jar
+export REF=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta 
+
+java -jar $GATK_JAR -T PrintReads -R $REF -ip 250 -L m2_dream3.intervals \
+-I /cga/tcga-gsc/benchmark/data/realignments/synthetic.challenge.set3.tumor/IS3.snv.indel.sv.bam \
+-o dream3.integrationtest.tumor.bam
+
+
+java -jar $GATK_JAR -T PrintReads -R $REF -ip 250 -L m2_dream3.intervals \
+-I /cga/tcga-gsc/benchmark/data/realignments/synthetic.challenge.set3.normal/G15512.prenormal.sorted.bam \
+-o dream3.integrationtest.normal.bam
+
+mv *.bam /humgen/gsa-hpprojects/GATK/data/Validation_Data/cancer
+mv *.bai /humgen/gsa-hpprojects/GATK/data/Validation_Data/cancer
+
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java
index e78b3d3fc..e754c3aaf 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java
index 9a1e6d799..b65fbc1fd 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java
index 8b5e42109..6b1911448 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -71,11 +71,11 @@ public class DiagnoseTargetsIntegrationTest extends WalkerTest {
 
     @Test(enabled = true)
     public void testSingleSample() {
-        DTTest("testSingleSample ", "-I " + singleSample + " -max 75", "5cad1b8e3bf5582842bbeadbc173e8aa");
+        DTTest("testSingleSample ", "-I " + singleSample + " -max 75", "13bfe41ef083d2716e07d35223916a4e");
     }
 
     @Test(enabled = true)
     public void testMultiSample() {
-        DTTest("testMultiSample ", "-I " + multiSample, "c2a11ad34104fd5e4e65bdf049abe5e7");
+        DTTest("testMultiSample ", "-I " + multiSample, "64b4fa6cf4c4d16e822289990ee88240");
     }
 }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusStatisticsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusStatisticsUnitTest.java
index 6a08859a4..5fd8e8562 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusStatisticsUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusStatisticsUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java
index 0fbd950f6..8604e05ea 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceIntegrationTest.java
index 6d1c4b0e3..de63ed550 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -59,24 +59,89 @@ import java.util.Arrays;
 
 public class FastaAlternateReferenceIntegrationTest extends WalkerTest {
 
+    private static String CONTIGUOUS_INTERVAL_SAME_CONTIG_MD5 = "e1f4b93f9071d158d94dc4fb25e07702";
+    private static String CONTIGUOUS_INTERVAL_DIFF_CONTIG_MD5 = "dfca4e0b0fe0cb18596ec51af541a69e";
+
     @Test
     public void testReferenceOnly() {
 
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T FastaReferenceMaker -R " + b36KGReference + " -L 1:10,000,100-10,000,500 -L 1:10,100,000-10,101,000 -L 1:10,900,000-10,900,001 -o %s",
                  1,
-                 Arrays.asList("328d2d52cedfdc52da7d1abff487633d"));
+                 Arrays.asList("75d4d352a9ce4fae22fd7924a42c800a"));
         executeTest("test FastaReference", spec);
     }
 
     @Test
-    public void testIndelsAndSnpMask() {
+    public void testReferenceOnlyContiguousSameContig() {
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T FastaReferenceMaker -R " + b36KGReference + " -L 1:10,000,100-10,000,200 -L 1:10,000,201-10,000,301 -o %s",
+                1,
+                Arrays.asList(CONTIGUOUS_INTERVAL_SAME_CONTIG_MD5));
+        executeTest("test FastaReference with contiguous intervals, same contig", spec);
+    }
+
+    @Test
+    public void testReferenceOnlyContiguousDiffContigs() {
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T FastaReferenceMaker -R " + b36KGReference + " -L 1:10,000,100-10,000,200 -L 2:10,000,201-10,000,301 -o %s",
+                1,
+                Arrays.asList(CONTIGUOUS_INTERVAL_DIFF_CONTIG_MD5));
+        executeTest("test FastaReference with contiguous intervals, different contigs", spec);
+    }
+
+    @Test
+    public void testAlternateReferenceContiguousSameContig() {
+        // Show that FastaAlternateReferenceMaker behaves the same as FastaReferenceMaker across contiguous intervals on the same contig.
+        // Note that there are variant locations in this interval.
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -V " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -L 1:10,000,100-10,000,200 -L 1:10,000,201-10,000,301 -o %s",
+                1,
+                Arrays.asList(CONTIGUOUS_INTERVAL_SAME_CONTIG_MD5));
+        executeTest("test Alternate FastaReference with contiguous intervals, same contig", spec);
+    }
+
+    @Test
+    public void testAlternateReferenceContiguousDiffContigs() {
+        // Show that FastaAlternateReferenceMaker behaves the same as FastaReferenceMaker across contiguous intervals on different contigs.
+        // Note that there are variant locations in this interval.
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -V " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -L 1:10,000,100-10,000,200 -L 2:10,000,201-10,000,301 -o %s",
+                1,
+                Arrays.asList(CONTIGUOUS_INTERVAL_DIFF_CONTIG_MD5));
+        executeTest("test Alternate FastaReference with contiguous intervals, different contigs", spec);
+    }
+
+    @Test
+    public void testSnpMask() {
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -V " + b36dbSNP129 + " --snpmask:vcf " + b36dbSNP129 + " -L 1:10,271,272-10,271,302 -o %s",
+                1,
+                Arrays.asList("01a0dffc62fc940c97e29276457f1ff0"));
+        executeTest("test snp mask", spec);
+    }
+
+    @Test
+    public void testSnpMaskPriority() {
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -V " + b36dbSNP129 + " --snpmaskPriority --snpmask:vcf " + b36dbSNP129 + " -L 1:10,271,272-10,271,302 -o %s",
+                1,
+                Arrays.asList("0950493e5038f7d588034ce4dd21292a"));
+        executeTest("test snp mask priority", spec);
+    }
+
+    @Test
+         public void testIndelsAndSnpMask() {
 
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -V " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 --snpmask:vcf " + b36dbSNP129 + " -L 1:10,075,000-10,075,380 -L 1:10,093,447-10,093,847 -L 1:10,271,252-10,271,452 -o %s",
-                 1,
-                 Arrays.asList("ef481be9962e21d09847b8a1d4a4ff65"));
-        executeTest("test indels", spec);
+                1,
+                Arrays.asList("375efb2feb017f01339f680fdffac6cd"));
+        executeTest("test indels and snp mask", spec);
     }
 
     @Test
@@ -85,7 +150,7 @@ public class FastaAlternateReferenceIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -V " + GATKDataLocation + "dbsnp_129_b36.vcf -L 1:10,023,400-10,023,500 -L 1:10,029,200-10,029,500 -o %s",
                  1,
-                 Arrays.asList("8b6cd2e20c381f9819aab2d270f5e641"));
+                 Arrays.asList("81e30f0ab92684c496343c8ea51a393e"));
         executeTest("test SNPs", spec);
     }
 
@@ -108,7 +173,7 @@ public class FastaAlternateReferenceIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T FastaAlternateReferenceMaker -R " + b37KGReference + " --use_IUPAC_sample NA12878 -V " + privateTestDir + "NA12878.WGS.b37.chr20.firstMB.vcf -L 20:61050-66380 -o %s",
                 1,
-                Arrays.asList("5feb2a576ff2ed1745a007eaa36448b3"));
+                Arrays.asList("8fd887bca9f3949f2c23c3565f7dcc1b"));
         executeTest("test iupac", spec);
     }
 }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationIntegrationTest.java
index 6c139b2e9..973b6a875 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -68,7 +68,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testNoAction() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("a890cd298298e22bc04a2e5a20b71170"));
+                Arrays.asList("42a73683f2064a73d4b21a06c208205b"));
         executeTest("test no action", spec);
     }
 
@@ -76,7 +76,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testClusteredSnps() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -window 10 --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("f46b2fe2dbe6a423b5cfb10d74a4966d"));
+                Arrays.asList("5e5c03487b0b89169dafad327d8afd4a"));
         executeTest("test clustered SNPs", spec);
     }
 
@@ -84,7 +84,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testMask1() {
         WalkerTestSpec spec1 = new WalkerTestSpec(
                 baseTestString() + " -maskName foo --mask " + privateTestDir + "vcfexample2.vcf --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("86dbbf62a0623b2dc5e8969c26d8cb28"));
+                Arrays.asList("a286b5919ff373f454d24374a115c696"));
         executeTest("test mask all", spec1);
     }
 
@@ -92,7 +92,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testMask2() {
         WalkerTestSpec spec2 = new WalkerTestSpec(
                 baseTestString() + " -maskName foo --mask:VCF " + privateTestDir + "vcfMask.vcf --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("2fb33fccda1eafeea7a2f8f9219baa39"));
+                Arrays.asList("c05349a096f6c4919ed24b293f40ffa8"));
         executeTest("test mask some", spec2);
     }
 
@@ -100,7 +100,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testMask3() {
         WalkerTestSpec spec3 = new WalkerTestSpec(
                 baseTestString() + " -maskName foo -maskExtend 10 --mask:VCF " + privateTestDir + "vcfMask.vcf --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("4351e00bd9d821e37cded5a86100c973"));
+                Arrays.asList("e45e4a287072cb6d4ec7596344fd0579"));
         executeTest("test mask extend", spec3);
     }
 
@@ -108,7 +108,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testMaskReversed() {
         WalkerTestSpec spec3 = new WalkerTestSpec(
                 baseTestString() + " -maskName outsideGoodSites -filterNotInMask --mask:BED " + privateTestDir + "goodMask.bed --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("e65d27c13953fc3a77dcad27a4357786"));
+                Arrays.asList("35428e4348a11abc260a1d40049bdefd"));
         executeTest("test filter sites not in mask", spec3);
     }
 
@@ -124,7 +124,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testFilter1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("2f056b50a41c8e6ba7645ff4c777966d"));
+                Arrays.asList("d7a9a49ed19bc0452595c293915a1480"));
         executeTest("test filter #1", spec);
     }
 
@@ -132,7 +132,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testFilter2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("b2a8c1a5d99505be79c03120e9d75f2f"));
+                Arrays.asList("0c0fddb0eb6f9d3f74556332cd498079"));
         executeTest("test filter #2", spec);
     }
 
@@ -140,7 +140,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testFilterWithSeparateNames() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --filterName ABF -filter 'AlleleBalance < 0.7' --filterName FSF -filter 'FisherStrand == 1.4' --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("e350d9789bbdf334c1677506590d0798"));
+                Arrays.asList("45f90fd349d76b386fce4b9075d16b7e"));
         executeTest("test filter with separate names #2", spec);
     }
 
@@ -148,7 +148,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testInvertFilter() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --filterName ABF -filter 'AlleleBalance < 0.7' --filterName FSF -filter 'FisherStrand == 1.4' --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000 --invertFilterExpression", 1,
-                Arrays.asList("d478fd6bcf0884133fe2a47adf4cd765"));
+                Arrays.asList("c88c845108a26bebfeb09c420671c06f"));
         executeTest("test inversion of selection of filter with separate names #2", spec);
     }
 
@@ -156,7 +156,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testInvertJexlFilter() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --filterName ABF -filter 'AlleleBalance >= 0.7' --filterName FSF -filter 'FisherStrand != 1.4' --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("6fa6cd89bfc8b6b4dfc3da25eb36d08b")); // Differs from testInvertFilter() because their VCF header FILTER description uses the -filter argument. Their filter statuses are identical.
+                Arrays.asList("f5e03e4584f9b1d82f9d430543f06bd6")); // Differs from testInvertFilter() because their VCF header FILTER description uses the -filter argument. Their filter statuses are identical.
         executeTest("test inversion of selection of filter via JEXL with separate names #2", spec);
     }
 
@@ -164,7 +164,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testGenotypeFilters1() {
         WalkerTestSpec spec1 = new WalkerTestSpec(
                 baseTestString() + " -G_filter 'GQ == 0.60' -G_filterName foo --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("060e9e7b6faf8b2f7b3291594eb6b39c"));
+                Arrays.asList("ced70cfb4e6681a3aa0633cd0510ada0"));
         executeTest("test genotype filter #1", spec1);
     }
 
@@ -172,7 +172,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testGenotypeFilters2() {
         WalkerTestSpec spec2 = new WalkerTestSpec(
                 baseTestString() + " -G_filter 'isHomVar == 1' -G_filterName foo --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("00f90028a8c0d56772c47f039816b585"));
+                Arrays.asList("837b6a3ce3fad3bd77ec3e870c4d2f10"));
         executeTest("test genotype filter #2", spec2);
     }
 
@@ -180,7 +180,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testDeletions() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --filterExpression 'QUAL < 100' --filterName foo --variant:VCF " + privateTestDir + "twoDeletions.vcf", 1,
-                Arrays.asList("8077eb3bab5ff98f12085eb04176fdc9"));
+                Arrays.asList("32ed1e11fde63a57c1dfb7f83f5344f0"));
         executeTest("test deletions", spec);
     }
 
@@ -189,7 +189,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
             "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
                     + " --filterExpression 'FS > 60.0' --filterName SNP_FS -V " + privateTestDir + "unfilteredForFiltering.vcf", 1,
-                Arrays.asList("8ed32a2272bab8043a255362335395ef"));
+                Arrays.asList("0febd66699fcd7f521377d1d0d0016fb"));
         executeTest("testUnfilteredBecomesFilteredAndPass", spec);
     }
 
@@ -198,7 +198,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
                         + " --filterExpression 'DP < 8' --filterName lowDP -V " + privateTestDir + "filteringDepthInFormat.vcf", 1,
-                Arrays.asList("a01f7cce53ea556c9741aa60b6124c41"));
+                Arrays.asList("c3eff7d167e1bfca5726a6e475e6b3ec"));
         executeTest("testFilteringDPfromINFO", spec);
     }
 
@@ -207,7 +207,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
                         + " --genotypeFilterExpression 'DP < 8' --genotypeFilterName lowDP -V " + privateTestDir + "filteringDepthInFormat.vcf", 1,
-                Arrays.asList("e10485c7c33d9211d0c1294fd7858476"));
+                Arrays.asList("260dd9d7e35737fe695b241b7a5a52a2"));
         executeTest("testFilteringDPfromFORMAT", spec);
     }
 
@@ -216,7 +216,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
                         + " --genotypeFilterExpression 'DP < 8' --genotypeFilterName highDP -V " + privateTestDir + "filteringDepthInFormat.vcf --invertGenotypeFilterExpression", 1,
-                Arrays.asList("d2664870e7145eb73a2295766482c823"));
+                Arrays.asList("907527b89d3f819cc3f6f88f51fcaaf6"));
         executeTest("testInvertGenotypeFilterExpression", spec);
     }
 
@@ -225,7 +225,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
                         + " --genotypeFilterExpression 'DP >= 8' --genotypeFilterName highDP -V " + privateTestDir + "filteringDepthInFormat.vcf", 1,
-                Arrays.asList("8ddd8f3b5ee351c4ab79cb186b1d45ba")); // Differs from testInvertFilter because FILTER description uses the -genotypeFilterExpression argument
+                Arrays.asList("d79b2e5a7502a6d6e902bc40d74cc826")); // Differs from testInvertFilter because FILTER description uses the -genotypeFilterExpression argument
         executeTest("testInvertJexlGenotypeFilterExpression", spec);
     }
 
@@ -234,7 +234,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
                         + " --genotypeFilterExpression 'DP < 8' --genotypeFilterName lowDP -V " + privateTestDir + "filteringDepthInFormat.vcf --setFilteredGtToNocall", 1,
-                Arrays.asList("9ff801dd726eb4fc562b278ccc6854b1"));
+                Arrays.asList("454d265ee8b425284ed7fca8ca4774be"));
         executeTest("testSetFilteredGtoNocall", spec);
     }
 
@@ -245,7 +245,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants --setFilteredGtToNocall -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("81b99386a64a8f2b857a7ef2bca5856e")
+                Arrays.asList("7771f07a9997296852ab367fac2c7a6c")
         );
 
         spec.disableShadowBCF();
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUnitTester.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUnitTester.java
index 585bb2f8d..32080e3c4 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUnitTester.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUnitTester.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUtilsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUtilsUnitTest.java
index 7c3a85d53..367d1810c 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUtilsUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUtilsUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ArtificialReadPileupTestProvider.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ArtificialReadPileupTestProvider.java
index d65770d7b..d163ccae5 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ArtificialReadPileupTestProvider.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ArtificialReadPileupTestProvider.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java
index 830f3681d..44bf0acc3 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCountsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCountsUnitTest.java
index 3ee0a79ed..545ead5e9 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCountsUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCountsUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculatorUnitTest.java
index d3a0864da..65d56cc2a 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculatorUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculatorUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingDataUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingDataUnitTest.java
index a96302d0a..b185db532 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingDataUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingDataUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HeterogeneousPloidyModel.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HeterogeneousPloidyModel.java
index e918602da..2d10c6a66 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HeterogeneousPloidyModel.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HeterogeneousPloidyModel.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModelUnitTest.java
index 1b5d97994..d5a26fee0 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModelUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModelUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java
index 778b38093..d3e681e84 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedAlleleListUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedAlleleListUnitTest.java
index 151a2325f..de44779b9 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedAlleleListUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedAlleleListUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedSampleListUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedSampleListUnitTest.java
index 098c39c66..f9e4ad05f 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedSampleListUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedSampleListUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModelUnitTest.java
index 70fdf5245..464e94ab8 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModelUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModelUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/NanoSchedulerIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/NanoSchedulerIntegrationTest.java
index bae62b6c5..40f5370a6 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/NanoSchedulerIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/NanoSchedulerIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -70,7 +70,7 @@ public class NanoSchedulerIntegrationTest extends WalkerTest {
 
         for ( final int nt : Arrays.asList(1, 2) )
             for ( final int nct : Arrays.asList(1, 2) ) {
-                tests.add(new Object[]{ "BOTH",  "18418ddc2bdbe20c38ece6dd18535be7", nt, nct });
+                tests.add(new Object[]{ "BOTH",  "52f590f6b37a1b3b12042ae917738965", nt, nct });
             }
 
         return tests.toArray(new Object[][]{});
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTest.java
index 32ad71f4b..1a795edd8 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTester.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTester.java
index 0aededd99..a894d26bc 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTester.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTester.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUnitTester.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUnitTester.java
index c79acccbc..e3ef6e58b 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUnitTester.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUnitTester.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUtilsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUtilsUnitTest.java
index 4575e62c1..659832d10 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUtilsUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUtilsUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollectionUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollectionUnitTest.java
index 4781488a9..6c24cb1e1 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollectionUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollectionUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java
index 4d7b1568b..61cb79428 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -99,12 +99,13 @@ public class UnifiedGenotyperEngineUnitTest extends BaseTest {
         final List tests = new ArrayList<>();
 
         // this functionality can be adapted to provide input data for whatever you might want in your data
+        //Note that this copies code from GenotypingEngine::estimateLog10ReferenceConfidenceForOneSample to provide expected values
         final double p = Math.log10(0.5);
-        for ( final double theta : Arrays.asList(0.1, 0.01, 0.001) ) {
+        for ( final double log10ofTheta : Arrays.asList(0.0, -1.0, -2.0, -3.0) ) {
             for ( final int depth : Arrays.asList(0, 1, 2, 10, 100, 1000, 10000) ) {
-                final double log10PofNonRef = Math.log10(theta / 2.0) + MathUtils.log10BinomialProbability(depth, 0, p);
+                final double log10PofNonRef = log10ofTheta + MathUtils.log10BinomialProbability(depth, 0, p);
                 final double log10POfRef = MathUtils.log10OneMinusX(Math.pow(10.0, log10PofNonRef));
-                tests.add(new Object[]{depth, theta, log10POfRef});
+                tests.add(new Object[]{depth, log10ofTheta, log10POfRef});
             }
         }
 
@@ -112,8 +113,8 @@ public class UnifiedGenotyperEngineUnitTest extends BaseTest {
     }
 
     @Test(dataProvider = "ReferenceQualityCalculation")
-    public void testReferenceQualityCalculation(final int depth, final double theta, final double expected) {
-        final double ref = getEngine().estimateLog10ReferenceConfidenceForOneSample(depth, theta);
+    public void testReferenceQualityCalculation(final int depth, final double log10ofTheta, final double expected) {
+        final double ref = getEngine().estimateLog10ReferenceConfidenceForOneSample(depth, log10ofTheta);
         Assert.assertTrue(MathUtils.goodLog10Probability(ref), "Reference calculation wasn't a well formed log10 prob " + ref);
         Assert.assertEquals(ref, expected, TOLERANCE, "Failed reference confidence for single sample");
     }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java
index a3458305b..a1de74780 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -69,21 +69,25 @@ public class UnifiedGenotyperGeneralPloidySuite1IntegrationTest extends WalkerTe
 
     @Test(enabled = true)
     public void testSNP_ACS_Pools() {
-        executor.PC_LSV_Test_short("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 6 -out_mode EMIT_ALL_CONFIDENT_SITES", "LSV_SNP_ACS", "SNP", "fa4f5e31d1f45193aa3a9b2a9a931ffd");
+        executor.PC_LSV_Test_short("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 6 -out_mode EMIT_ALL_CONFIDENT_SITES", "LSV_SNP_ACS", "SNP", "bf6012b6e7dec2d44b2bcb402c98c95e");
     }
 
     @Test(enabled = true)
     public void testBOTH_GGA_Pools() {
-        executor.PC_LSV_Test(String.format("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_BOTH_GGA", "BOTH", "972c8db4b1cc971bd714fd9c1a72b65a");
+        executor.PC_LSV_Test(String.format("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_BOTH_GGA", "BOTH", "217d9108c3014261dbe8befa383a2226");
     }
 
     @Test(enabled = true)
     public void testINDEL_GGA_Pools() {
-        executor.PC_LSV_Test(String.format("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_INDEL_GGA", "INDEL", "8096ec08219205af56bd4ea762412f7c");
+        executor.PC_LSV_Test(String.format("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_INDEL_GGA", "INDEL", "6a7f00e7f26cbc1891f40c9ed8b6579b");
     }
 
     @Test(enabled = true)
     public void testINDEL_maxAltAlleles2_ploidy1_Pools_noRef() {
-        executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "6007e0735aa5a680da92396345824077");
+        //TODO interesting case in where the faster but approxiate allele independent Exact AC approach causes an additional allele to pop up!.
+        //TODO the old MD5 is kept for the record.
+        //TODO this should be revisit once we get into addressing inaccuracies by the independent allele approach.
+//        executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "b5ff7530827f4b9039a58bdc8a3560d2");
+        executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "c0271a4c281991a86490c1955456af26");
     }
 }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java
index a2f2262fa..2fb2d11c5 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -63,16 +63,16 @@ public class UnifiedGenotyperGeneralPloidySuite2IntegrationTest extends WalkerTe
 
     @Test(enabled = true)
     public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() {
-        executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","fdcdfbed14fb7d703cd991ee7d2821a6");
+        executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","c445bcd828c540c009bc8fc9f48916bc");
     }
 
     @Test(enabled = true)
     public void testMT_SNP_DISCOVERY_sp4() {
-        executor.PC_MT_Test(CEUTRIO_BAM, "-A AlleleCountBySample -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","7d533bea2ad3a151a1ec80e658e5756b");
+        executor.PC_MT_Test(CEUTRIO_BAM, "-A AlleleCountBySample -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","8d8c7926ca9c68251c41eb03b8efaba2");
     }
 
     @Test(enabled = true)
     public void testMT_SNP_GGA_sp10() {
-        executor.PC_MT_Test(CEUTRIO_BAM, String.format("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "39ce89507ceb66ee7ae99ed68d50042d");
+        executor.PC_MT_Test(CEUTRIO_BAM, String.format("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "34242c0ae59b0645fb6df5c322e92f01");
     }
 }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidyTestExecutor.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidyTestExecutor.java
index 7eb913997..9930d80ac 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidyTestExecutor.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidyTestExecutor.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
index 8475cbd18..f4e03043b 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -78,7 +78,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 1:10,000,000-10,500,000",
                 1,
-                Arrays.asList("8e0ba82e36df60fd0122818d0227041b"));
+                Arrays.asList("b132da42e1017c8825d84a06cf79a1e9"));
         executeTest(String.format("test indel caller in SLX"), spec);
     }
 
@@ -92,7 +92,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
                         " -minIndelCnt 1" +
                         " -L 1:10,000,000-10,100,000",
                 1,
-                Arrays.asList("02ed507c8c1d289b6c0092899b1b839e"));
+                Arrays.asList("23e32822d81f198ee52676f24ef74343"));
 
         executeTest(String.format("test indel caller in SLX with low min allele count"), spec);
     }
@@ -105,7 +105,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 1:10,000,000-10,500,000",
                 1,
-                Arrays.asList("2b87723c03c46987dc3ee6d82f893c23"));
+                Arrays.asList("93580986b871890a4fc86ebf98877efa"));
 
         executeTest(String.format("test indel calling, multiple technologies"), spec);
     }
@@ -115,7 +115,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
                         "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
-                Arrays.asList("1bd415ee64fa01039e7b623fbd2ae838"));
+                Arrays.asList("4da9878ee36d0fb387d5a58631383ffa"));
         executeTest("test MultiSample Pilot2 indels with alleles passed in", spec);
     }
 
@@ -125,7 +125,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
                 baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
                         + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
                         "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
-                Arrays.asList("4833c9b471cab8ce5bc5747f8cb1548d"));
+                Arrays.asList("9ab4f5306438b5a64cb2cb90020b7b82"));
         executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec);
     }
 
@@ -140,7 +140,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
                 baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation +
                         "low_coverage_CEU.chr1.10k-11k.bam -o %s -L " + result.get(0).getAbsolutePath(), 1,
-                Arrays.asList("781d305993aedcc1a4c199a5c63ac54c"));
+                Arrays.asList("6de8d740908e22b46785d5eba6278eb2"));
         executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
     }
 
@@ -150,7 +150,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommandIndelsb37 + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + privateTestDir + vcf + " -I " + validationDataLocation +
                         "NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam -o %s -L " + validationDataLocation + vcf, 1,
-                Arrays.asList("0bc38748e786259e7fd4e199ccdd7287"));
+                Arrays.asList("6e8319e65fef1059c2092c05e6916257"));
         executeTest("test GENOTYPE_GIVEN_ALLELES with no evidence in reads", spec);
     }
 
@@ -162,7 +162,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 20:10,000,000-10,100,000",
                 1,
-                Arrays.asList("0313e91607166767b7f1b1d6fcdf9263"));
+                Arrays.asList("745eb3eefa93aca72f724aab4734c7ef"));
 
         executeTest(String.format("test UG with base indel quality scores"), spec);
     }
@@ -181,7 +181,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
     public void testMinIndelFraction0() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 assessMinIndelFraction + " -minIndelFrac 0.0", 1,
-                Arrays.asList("003243a8cc024cb297f86cc84de91be5"));
+                Arrays.asList("56673c166ba25f625d026e593d5cc667"));
         executeTest("test minIndelFraction 0.0", spec);
     }
 
@@ -189,7 +189,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
     public void testMinIndelFraction25() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 assessMinIndelFraction + " -minIndelFrac 0.25", 1,
-                Arrays.asList("d9fcd63e9eed692850eb49e124176648"));
+                Arrays.asList("2ce1754313561b9cb134152b8f98bf43"));
         executeTest("test minIndelFraction 0.25", spec);
     }
 
@@ -197,7 +197,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
     public void testMinIndelFraction100() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 assessMinIndelFraction + " -minIndelFrac 1", 1,
-                Arrays.asList("49821450356b4b398f3bcb688e13af36"));
+                Arrays.asList("c7f190f7cea34a7f9c931cd8de110a48"));
         executeTest("test minIndelFraction 1.0", spec);
     }
 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
index de8ac514c..44a5ab268 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -86,7 +86,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMinBaseQualityScore() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --min_base_quality_score 26", 1,
-                Arrays.asList("a36d082235ad30bd343f6c0538b32d0b"));
+                Arrays.asList("21369e50334d2b77b0e638e47e1b8c64"));
         executeTest("test min_base_quality_score 26", spec);
     }
 
@@ -94,7 +94,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testSLOD() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper --disableDithering -R " + b36KGReference + " --computeSLOD --no_cmdline_in_header -glm BOTH --dbsnp " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
-                Arrays.asList("4b80c1ef04831113f1911bf4a33a2931"));
+                Arrays.asList("e58d9a5758c5b11f86558608260d93d5"));
         executeTest("test SLOD", spec);
     }
 
@@ -102,7 +102,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testNDA() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommand + " --annotateNDA -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
-                Arrays.asList("c5a649ae11f5e45817d9877a97e0195d"));
+                Arrays.asList("fc8cdf9eeb475773303809c077f83c65"));
         executeTest("test NDA", spec);
     }
 
@@ -110,7 +110,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testCompTrack() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper --disableDithering -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -comp:FOO " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
-                Arrays.asList("55c9e4ec4d1795b395b70bafc423c243"));
+                Arrays.asList("c98294d321bde3e1e3c4fcee3e88d6d9"));
         executeTest("test using comp track", spec);
     }
 
@@ -124,17 +124,17 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
     @Test
     public void testOutputParameterSitesOnly() {
-        testOutputParameters("-sites_only", "fc1d87645f2dc5e7a9355753df6e6acb");
+        testOutputParameters("-sites_only", "5b8938ed55a2b7ae8a52056c9130367b");
     }
 
     @Test
     public void testOutputParameterAllConfident() {
-        testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "406f48975e5232df4444416c2a570225");
+        testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "f353b36db7305f47963446220e39debe");
     }
 
     @Test
     public void testOutputParameterAllSites() {
-        testOutputParameters("--output_mode EMIT_ALL_SITES", "0899ffd439d9f4f61aad574f4a74b3de");
+        testOutputParameters("--output_mode EMIT_ALL_SITES", "364aec53db79d20698fe0d088828736f");
     }
 
     private void testOutputParameters(final String args, final String md5) {
@@ -148,7 +148,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testConfidence() {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1,
-                Arrays.asList("6039ce16c722d9b133a1f76534c98a69"));
+                Arrays.asList("ec59b34bedf40d70850ab5ffe42bbddd"));
         executeTest("test confidence 1", spec1);
     }
 
@@ -156,7 +156,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testNoPrior() {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 -inputPrior 0.33333 -inputPrior 0.33333", 1,
-                Arrays.asList("ef478aae219a84a8a81b9c65fc24b67a"));
+                Arrays.asList("7e8a51e658debdaadbcf17761ed011da"));
         executeTest("test no prior 1", spec1);
 
     }
@@ -165,7 +165,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testUserPrior() {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 -inputPrior 0.001 -inputPrior 0.495", 1,
-                Arrays.asList("ba1531d124436d2522c0a6335f57813b"));
+                Arrays.asList("b3514f5b3510b6667fd2c85ecc529de7"));
         executeTest("test user prior 1", spec1);
 
     }
@@ -174,7 +174,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void emitPLsAtAllSites() {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --output_mode EMIT_ALL_SITES -allSitePLs", 1,
-                Arrays.asList("38588b2aea153ae4a087a0804ada1e95"));
+                Arrays.asList("6fd14930acb08f0dd9749a8c4d7df831"));
         // GDA: TODO: BCF encoder/decoder doesn't seem to support non-standard values in genotype fields. IE even if there is a field defined in FORMAT and in the header the BCF2 encoder will still fail
         spec1.disableShadowBCF();
 
@@ -190,12 +190,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
     @Test
     public void testHeterozyosity1() {
-        testHeterozosity( 0.01, "a89a1805344f71f299a50103a25d2117" );
+        testHeterozosity( 0.01, "815f01ef28bf576beb5528ac6fdd5248" );
     }
 
     @Test
     public void testHeterozyosity2() {
-        testHeterozosity( 1.0 / 1850, "8fbf7fd8685e34f37d7c8e08d673a471" );
+        testHeterozosity( 1.0 / 1850, "8dd14ba8ef6314a99921849b2544b8c6" );
     }
 
     private void testHeterozosity(final double arg, final String md5) {
@@ -238,7 +238,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
         // Note that we need to turn off any randomization for this to work, so no downsampling and no annotations
 
-        String md5 = "1f3fad09a63269c36e871e7ee04ebfaa";
+        String md5 = "398d3ad38834fea8961ab6f46a21dc4b";
         final String myCommand = "-T UnifiedGenotyper --disableDithering -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -minIndelFrac 0.0 --dbsnp " + b36dbSNP129;
 
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
@@ -274,7 +274,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 1:10,000,000-10,100,000",
                 1,
-                Arrays.asList("051810b8e584a8c4718ea4d95551c768"));
+                Arrays.asList("34980dbce4fcd2aa21c46ea0e1897422"));
 
         executeTest(String.format("test multiple technologies"), spec);
     }
@@ -293,7 +293,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -L 1:10,000,000-10,100,000" +
                         " -baq CALCULATE_AS_NECESSARY",
                 1,
-                Arrays.asList("7b90d6ff043bf9fafbbb80a451261cdc"));
+                Arrays.asList("5f02a7449305b26aab3ff994dfb53fda"));
 
         executeTest(String.format("test calling with BAQ"), spec);
     }
@@ -310,7 +310,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                 baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000 " +
                 "-A SnpEff",
                 1,
-                Arrays.asList("037ce3364668ee6527fba80c4f4bff95"));
+                Arrays.asList("b61c0dece2d77544f9313c24191e0089"));
+
         executeTest("testSnpEffAnnotationRequestedWithoutRodBinding", spec);
     }
 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java
index 1a19b5e91..98f9cad32 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java
index b97d108c7..b652f1047 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -70,7 +70,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
     public void testMultiSamplePilot1() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
-                Arrays.asList("b43bf9147e30cc68068a91a5e8405767"));
+                Arrays.asList("0f9eff0ad2f8cb8e277922bd037825f7"));
         executeTest("test MultiSample Pilot1", spec);
     }
 
@@ -78,7 +78,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
     public void testWithAllelesPassedIn1() {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
-                Arrays.asList("ce804ffdc146414f354bc9040ffffa87"));
+                Arrays.asList("196979c91f84c01fb5d89e73339c09fa"));
         executeTest("test MultiSample Pilot2 with alleles passed in", spec1);
     }
 
@@ -86,7 +86,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
     public void testWithAllelesPassedIn2() {
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
-                Arrays.asList("5d9bc104f1507433944176b58d75bbcf"));
+                Arrays.asList("391c4e1437a3fa5c99584b466a56d7bb"));
         executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2);
     }
 
@@ -94,7 +94,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
     public void testSingleSamplePilot2() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1,
-                Arrays.asList("a4c7464ff35e5ca7291935abc71f0614"));
+                Arrays.asList("41b1d92cdea4581f7843b714345547d6"));
         executeTest("test SingleSample Pilot2", spec);
     }
 
@@ -102,7 +102,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
     public void testMultipleSNPAlleles() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1,
-                Arrays.asList("837847b512c8f60d7c572dd6a80239d8"));
+                Arrays.asList("4ae7c090dfb85f6286f1187a746def58"));
         executeTest("test Multiple SNP alleles", spec);
     }
 
@@ -110,7 +110,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
     public void testBadRead() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH -I " + privateTestDir + "badRead.test.bam -o %s -L 1:22753424-22753464", 1,
-                Arrays.asList("2b3056f62f2da84c318e8809d8b3dd1a"));
+                Arrays.asList("67dbab7d307d02b3d879eca8bd15a573"));
         executeTest("test bad read", spec);
     }
 
@@ -118,7 +118,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
     public void testReverseTrim() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1,
-                Arrays.asList("0fc44ff26d3f913e7012b000a4de9682"));
+                Arrays.asList("5c2c49bb5e276df933b2d264e9d4a327"));
         executeTest("test reverse trim", spec);
     }
 
@@ -126,7 +126,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
     public void testMismatchedPLs() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1,
-                Arrays.asList("0dba3bc42c0eb43fea205d528739e9da"));
+                Arrays.asList("ed5f90897c9a348e4f861eff8992b4e2"));
         executeTest("test mismatched PLs", spec);
     }
 }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculationUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculationUnitTest.java
index 7cddf67ea..eba969d90 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculationUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculationUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -53,6 +53,7 @@ package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc;
 
 import htsjdk.variant.variantcontext.*;
 import org.apache.commons.lang.ArrayUtils;
+import org.broadinstitute.gatk.tools.walkers.genotyper.AFPriorProvider;
 import org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine;
 import org.broadinstitute.gatk.utils.BaseTest;
 import org.broadinstitute.gatk.utils.MathUtils;
@@ -197,10 +198,14 @@ public class AFCalculationUnitTest extends BaseTest {
         for ( final int nSamples : Arrays.asList(1, 2, 3, 4) ) {
             List calcs = createAFCalculators(Arrays.asList(AFCalculatorImplementation.values()), MAX_ALT_ALLELES, PLOIDY);
 
+            //number of entries in the priors array, one for AC=[0,2*nSamples]
             final int nPriorValues = 2*nSamples+1;
+            //total number of chromosomes in our samples -- here we're assuming diploid
+            final int totalPloidy = 2*nSamples;
+            final double theta = 0.001;
             final double[] flatPriors = MathUtils.normalizeFromLog10(new double[nPriorValues], true);  // flat priors
-            final double[] humanPriors = new double[nPriorValues];
-            UnifiedGenotypingEngine.computeAlleleFrequencyPriors(nPriorValues - 1, humanPriors, 0.001, new ArrayList());
+            final AFPriorProvider log10priorProvider = UnifiedGenotypingEngine.composeAlleleFrequencyPriorProvider(totalPloidy, theta, new ArrayList());
+            final double[] humanPriors = log10priorProvider.forTotalPloidy(totalPloidy);
 
             for ( final double[] priors : Arrays.asList(flatPriors, humanPriors) ) { // , humanPriors) ) {
                 for ( AFCalculator model : calcs ) {
@@ -609,16 +614,16 @@ public class AFCalculationUnitTest extends BaseTest {
             final Genotype AB = makePL(Arrays.asList(A,C), REF_PL, 0, 10000);
 
             final double[] flatPriors = new double[]{0.0,0.0,0.0};
-            final double[] noPriors = new double[3];
             // test that function computeAlleleFrequency correctly operates when the flat prior option is set
             // computeAlleleFrequencyPriors takes linear priors
             final ArrayList inputPrior = new ArrayList();
             inputPrior.add(1.0/3);
             inputPrior.add(1.0/3);
-            UnifiedGenotypingEngine.computeAlleleFrequencyPriors(2, noPriors, 0.0, inputPrior);
+            final AFPriorProvider log10priorProvider = UnifiedGenotypingEngine.composeAlleleFrequencyPriorProvider(2, 0.0, inputPrior);
+            final double[] noPriors = log10priorProvider.forTotalPloidy(2);
 
             GetGLsTest cfgFlatPrior = new GetGLsTest(model, 1, Arrays.asList(AB), flatPriors, "flatPrior");
-            GetGLsTest cfgNoPrior = new GetGLsTest(model, 1, Arrays.asList(AB), flatPriors, "noPrior");
+            GetGLsTest cfgNoPrior = new GetGLsTest(model, 1, Arrays.asList(AB), noPriors, "noPrior");
             final AFCalculationResult resultTrackerFlat = cfgFlatPrior.execute();
             final AFCalculationResult resultTrackerNoPrior = cfgNoPrior.execute();
 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorPerformanceUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorPerformanceUnitTest.java
index b7427a181..c3e6936b7 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorPerformanceUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorPerformanceUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorResultUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorResultUnitTest.java
index 9a869a5cc..f414311b5 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorResultUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorResultUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProviderUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProviderUnitTest.java
index 9fddd1722..0ded6f8ca 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProviderUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProviderUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java
index ef0a46027..d5f0b7625 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyFailOverAFCalculatorProviderUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyFailOverAFCalculatorProviderUnitTest.java
index e97be921a..a43d330a6 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyFailOverAFCalculatorProviderUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyFailOverAFCalculatorProviderUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -88,7 +88,7 @@ public class GeneralPloidyFailOverAFCalculatorProviderUnitTest {
                     Assert.assertNotNull(failOver);
                     final AFCalculatorImplementation failOverImplementation = AFCalculatorImplementation.fromCalculatorClass(failOver.getClass());
                     Assert.assertTrue(failOverImplementation.usableForParams(PLOIDIES[i],MAX_ALT_ALLELES[j]));
-                    Assert.assertEquals(failOverImplementation, AFCalculatorImplementation.EXACT_GENERAL_PLOIDY);
+                    Assert.assertEquals(failOverImplementation, AFCalculatorImplementation.EXACT_GENERAL_INDEPENDENT);
                 }
             }
         }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalculatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalculatorUnitTest.java
index 1f588ff0f..aa2c3976f 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalculatorUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalculatorUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AFPriorProviderUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AFPriorProviderUnitTest.java
index 366b90bb7..8844eb783 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AFPriorProviderUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AFPriorProviderUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSet.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSet.java
index 3a12ee99c..cce9708bd 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSet.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSet.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java
index 3f0cb94f3..11921ee3b 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResultSetUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResultSetUnitTest.java
index b1174e22a..908198cbb 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResultSetUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResultSetUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/Civar.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/Civar.java
index 8771866ff..6d34f7693 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/Civar.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/Civar.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/CivarUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/CivarUnitTest.java
index cbaea15c6..607bdc985 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/CivarUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/CivarUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/FastLoglessPairHMMUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/FastLoglessPairHMMUnitTest.java
index 8773bbc63..fc6efae37 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/FastLoglessPairHMMUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/FastLoglessPairHMMUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java
index c46a2a2de..2ba09aa9f 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeBaseComparatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeBaseComparatorUnitTest.java
index dfd91ab24..336775aac 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeBaseComparatorUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeBaseComparatorUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
index 136b656f2..f14fda293 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -72,7 +72,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
 
     @Test
     public void testHaplotypeCallerMultiSampleComplex1() {
-        HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "070729585401dda47838911928ffbd2f");
+        HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "066f1ce9e9826bcfedf6cd80bc560ab8");
     }
 
     private void HCTestSymbolicVariants(String bam, String args, String md5) {
@@ -84,7 +84,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
     // TODO -- need a better symbolic allele test
     @Test
     public void testHaplotypeCallerSingleSampleSymbolic() {
-        HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "2bddd2bf5427142bf2235daa8589efee");
+        HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "8a83ab27177f0b7adf50031f061f9cd7");
     }
 
     private void HCTestComplexGGA(String bam, String args, String md5) {
@@ -96,13 +96,13 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
     @Test
     public void testHaplotypeCallerMultiSampleGGAComplex() {
         HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538",
-                "64421f715e0258defc9efcfef56bdaab");
+                "2a5de432f04198737732064206c7d63d");
     }
 
     @Test
     public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
         HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
-                "d2306f6ecfcee9340423ba251e0736a3");
+                "afaa41101f492d37f57bb18cc638c6bc");
     }
 
     private void HCTestComplexConsensusMode(String bam, String args, String md5) {
@@ -114,7 +114,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
     @Test
     public void testHaplotypeCallerMultiSampleConsensusModeComplex() {
         HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538 -L 20:133041-133161 -L 20:300207-300337",
-                "22c4135a87be18940ff622ea7ff9cabc");
+                "d42ba795fe346d8372cae3c00c9c2f23");
     }
 
 }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
index 6f5634b56..20b089630 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -75,12 +75,16 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
         final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
 
         // this functionality can be adapted to provide input data for whatever you might want in your data
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "3e440b1b755a21d7bd3ecb093af8f43e"});
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "ebe078a1e209a5b231aeeba6deebcb8a"});
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "2ad9b5d87416c466292c2b97480e1f5c"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "6ca1e6cb78157273a4a96ba00e6d4713"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "8645c191ca5dbbae8dcb1389717f985a"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "9606db453f9e8beae27669afcea288a1"});
+        //TODO the latest independent exact AC calculation for haploids causes a clear variant to be lost here.
+        //TODO this might need to be addressed at some point.
+        //TODO the following test is commented out for the record
+        //tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "7f09c261950bf86e435edfa69ed2ec71"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "02300a1f64e085cc0f4420d8160743c1"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "f71ea433b1334a2d146cc6ad76b46d98"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "daddb5349c34e9190f0563e220894748"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "03e5815cc351f1ec2feed89d2aed8268"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "5d5cca382bdf6987b2aef87918ed374c"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "532888aff96c356397a21ef790636818"});
 
         return tests.toArray(new Object[][]{});
     }
@@ -94,13 +98,13 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
         final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
 
         // this functionality can be adapted to provide input data for whatever you might want in your data
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "92c7415dd1a5793161032d839b88fc28"});
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "b90d7c900ff4a8b5e58d6bd4ad64d750"});
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "8a1dcc091cb28e1fbbc86a1de85dfd4c"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "7e84e4562d8df6e593e58f017f697355"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "307ce5ada7c68e2f08664937bafa6281"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "cfe629c5a3be3b6524258ad1f9145488"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "12fbfffa4bb2b8d520f8021a40b37d19"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "a5ea6d4052bbf9e8bba9011bc6f0d203"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "31da2254620f4a9c34ccf7c311cc133f"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "c95f52fe395392331dc3102902d54408"});
 
-        final String NA12878bandedResolutionMD5 = "d51df38ad52cf2b0ecbce362e60fb24e";
+        final String NA12878bandedResolutionMD5 = "fbe6099d138a069a65e4713bcae1e873";
         tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, NA12878bandedResolutionMD5});
         tests.add(new Object[]{NA12878_WEx + " -I " + privateTestDir + "NA20313.highCoverageRegion.bam -sn NA12878",
                 ReferenceConfidenceMode.GVCF, WExIntervals, NA12878bandedResolutionMD5});
@@ -117,12 +121,12 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
         final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
 
         // this functionality can be adapted to provide input data for whatever you might want in your data
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "f441aab92b07591281fa44748b7bd71e"});
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "d54d7988552a13de90977ba06b094b74"});
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "c3c12414059390f3d6e3e533502c1869"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "91164cf1247f5b187ad133b280aa1fd2"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "b5c1b79550a8d8bb479895e2be38d945"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "79e913ab2ddf19b3cae75f2da9394239"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "5088d6cf80a6da7c769f97b1ab44c745"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "0895f09731d0ef89ec131c9f75aafe70"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "195017f498d3508e6eee492eb00da97b"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "4f8e3e249509a24da21d5dd8e3594f92"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "ef96f5295b048ef31f5ba82d078a44a2"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "cd809158689ddbbfd18a4eaae016f9a0"});
 
         return tests.toArray(new Object[][]{});
     }
@@ -135,12 +139,12 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
         final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
 
         // this functionality can be adapted to provide input data for whatever you might want in your data
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "081d943a092b7ad71d1f1fa6ec191ace"});
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "93f95c7a51741f8e527f1308ffd91052"});
-        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "1f2e5b5c06cb6d1196315c4308421f6d"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "3d8f4f849df0b9cddb1ec61279e91a83"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "1fbe1435b860400ecae3115141453c9a"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "fe9e1992cc28b798dd3ee66aaba726aa"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "bb85582fcc2ce45407640fa8a70421ab"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "e01603c5d4c3142978a91b8cd6a98618"});
+        tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "b9e471935b960a7dba3eb2b13939ccaf"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "c724ecdaea7eab5a6239ff4daaa6e034"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "194d27bd2321ff1a8b895a4e9a8d2938"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "4a3dfcfc2f5d27b75725346d63e0b83a"});
 
         return tests.toArray(new Object[][]{});
     }
@@ -266,7 +270,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
     public void testWrongGVCFNonVariantRecordOrderBugFix() {
         final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
                 HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, WRONG_GVCF_RECORD_ORDER_BUGFIX_BAM, WRONG_GVCF_RECORD_ORDER_BUGFIX_INTERVALS, GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
-        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("7fa0578150ea8ef333cb141f78cf4a5a"));
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("9b3b232ceeb109f2624826ea20825a82"));
         spec.disableShadowBCF();
         executeTest("testMissingGVCFIndexingStrategyException", spec);
     }
@@ -283,7 +287,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
     public void testNoCallGVCFMissingPLsBugFix() {
         final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
                 HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, NOCALL_GVCF_BUGFIX_BAM, NOCALL_GVCF_BUGFIX_INTERVALS, GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
-        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("befa4bf150099b3faf44130a6c9cdbb9"));
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("c5a017f1cbd60219506be76f30fc4468"));
         spec.disableShadowBCF();
         executeTest("testNoCallGVCFMissingPLsBugFix", spec);
     }
@@ -312,4 +316,13 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
         executeTest(" testGeneralPloidyArrayIndexBug2Fix", spec);
     }
 
+    @Test
+    public void testAlleleSpecificAnnotations() {
+        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -G Standard -G AS_Standard --disableDithering",
+                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", "20:10433000-10437000", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("716db262a288eb2a477df3f1957372c7"));
+        spec.disableShadowBCF();
+        executeTest(" testAlleleSpecificAnnotations", spec);
+    }
+
 }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngineUnitTest.java
index b9c005554..c07ff16cb 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngineUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngineUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index 0b6bfd201..4ac07e377 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -96,87 +96,87 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerMultiSample() throws IOException {
-        HCTest(CEUTRIO_BAM, "", "e8a73b950d027239b780757d898c7334");
+        HCTest(CEUTRIO_BAM, "", "bdc5a942a7df2d4c61388ecc74a163cf");
     }
 
     @Test
     public void testHaplotypeCallerSingleSample() throws IOException {
 
-        HCTest(NA12878_BAM, "", "c741efeb6f3e412c4e707da3cabee621");
+        HCTest(NA12878_BAM, "", "5941f88fa1372eb598880a4711ac08de");
     }
 
     @Test
     public void testHaplotypeCallerMultiSampleHaploid() throws IOException {
-        HCTest(CEUTRIO_BAM, "-ploidy 1", "5bfcfdea258a3dafa04a99dd2b000c87");
+        HCTest(CEUTRIO_BAM, "-ploidy 1", "4c32640204a11fe46a23d97b1012bca2");
     }
 
     @Test
     public void testHaplotypeCallerSingleSampleHaploid() throws IOException {
-        HCTest(NA12878_BAM, "-ploidy 1", "304d2ade384406342655fdfd445576a3");
+        HCTest(NA12878_BAM, "-ploidy 1", "e09c5fd862f86f69289d847e3b293e19");
     }
 
     @Test
     public void testHaplotypeCallerSingleSampleTetraploid() throws IOException {
-        HCTest(NA12878_BAM, "-ploidy 4", "1d7aee93f3f2e331fcfa8f765467c66c");
+        HCTest(NA12878_BAM, "-ploidy 4", "bbae9f77683591200b2034d5461e6425");
     }
 
     @Test
     public void testHaplotypeCallerMinBaseQuality() throws IOException {
-        HCTest(NA12878_BAM, "-mbq 15", "c741efeb6f3e412c4e707da3cabee621");
+        HCTest(NA12878_BAM, "-mbq 15", "5941f88fa1372eb598880a4711ac08de");
     }
 
     @Test
     public void testHaplotypeCallerMinBaseQualityHaploid() throws IOException {
-        HCTest(NA12878_BAM, "-mbq 15 -ploidy 1", "304d2ade384406342655fdfd445576a3");
+        HCTest(NA12878_BAM, "-mbq 15 -ploidy 1", "e09c5fd862f86f69289d847e3b293e19");
     }
 
     @Test
     public void testHaplotypeCallerMinBaseQualityTetraploid() throws IOException {
-        HCTest(NA12878_BAM, "-mbq 15 -ploidy 4", "1d7aee93f3f2e331fcfa8f765467c66c");
+        HCTest(NA12878_BAM, "-mbq 15 -ploidy 4", "bbae9f77683591200b2034d5461e6425");
     }
 
     @Test
     public void testHaplotypeCallerGraphBasedSingleSample() throws IOException {
-        HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "ffd2363d2f7afd694b8e9b23c51b0cea");
+        HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "9a4ba54146449914b1fbaed5465b692e");
     }
 
     @Test
     public void testHaplotypeCallerGraphBasedMultiSampleHaploid() throws IOException {
-        HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased -ploidy 1", "ab1630552bcc0a46431b3f6b7bd50bb5");
+        HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased -ploidy 1", "5333e3ff4d7fc53624eab801250be4f0");
     }
 
     @Test
     public void testHaplotypeCallerGraphBasedMultiSample() throws IOException {
-        HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "31a21023efaf6f030478e5542ec652fe");
+        HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "e9759bf254b7b4d06e4a68c94a417cf1");
     }
 
     @Test
     public void testHaplotypeCallerSingleSampleWithDbsnp() throws IOException {
-        HCTest(NA12878_BAM, "-D " + b37dbSNP132, "1c91ca0c8c04cbce1ace3e9884efd458");
+        HCTest(NA12878_BAM, "-D " + b37dbSNP132, "7466c4d9ce6a1d23bcb428fc9f446843");
     }
 
     @Test
     public void testHaplotypeCallerMultiSampleGGA() throws IOException {
         HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf" +
                 " -isr INTERSECTION -L " + GGA_INTERVALS_FILE,
-                "2944a830504b4e0b87bb8babc8ea39ae");
+                "c2fe156912e59626c0393b9b47c9419e");
     }
 
     @Test
     public void testHaplotypeCallerMultiSampleGGAHaploid() throws IOException {
         HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -ploidy 1 -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf -isr INTERSECTION -L 20:10080000-10100000",
-                "b4da788ff173453d915a807149d9ab5d");
+                "49f737983375c740361daa2d48ed0249");
     }
 
     @Test
     public void testHaplotypeCallerMultiSampleGGATetraploid() throws IOException {
         HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -ploidy 4 -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf -isr INTERSECTION -L 20:10080000-10100000",
-                "7a3a8a81c3f984d74e6e3e35f5e62aa3");
+                "6ba0fa930899f70fee9a7b1161508f93");
     }
 
     @Test
     public void testHaplotypeCallerInsertionOnEdgeOfContig() throws IOException {
-        HCTest(CEUTRIO_MT_TEST_BAM, "-L MT:1-10", "60e578f65ab2be60f31ee8395845607a");
+        HCTest(CEUTRIO_MT_TEST_BAM, "-L MT:1-10", "da1f6b9a7e5913910531b00f3b35ce06");
     }
 
     private void HCTestIndelQualityScores(String bam, String args, String md5) {
@@ -187,7 +187,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerSingleSampleIndelQualityScores() {
-        HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "60df4797f86c1454c0eb76c5eaf2ad38");
+        HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "22028b104dd60b23a399e5e3a877a1fb");
     }
 
     private void HCTestNearbySmallIntervals(String bam, String args, String md5) {
@@ -224,7 +224,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerNearbySmallIntervals() {
-        HCTestNearbySmallIntervals(NA12878_BAM, "", "7af25494bf2b05cc838ebf7055407c30");
+        HCTestNearbySmallIntervals(NA12878_BAM, "", "6e55de7bf49ecdc71f6d4c9565a19853");
     }
 
     // This problem bam came from a user on the forum and it spotted a problem where the ReadClipper
@@ -234,14 +234,14 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void HCTestProblematicReadsModifiedInActiveRegions() {
         final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3 -L 4:49139026-49139965";
-        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("3f01b3be2004f784a0fddc9e63aeba2a"));
+        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("f8774326a268f7d394b333818d15d05c"));
         executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
     }
 
     @Test
     public void HCTestStructuralIndels() {
         final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
-        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("1ca9a141cb65c6070a93d5a2c55a9b3b"));
+        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("034c6b151dfde537d5843f70880bf8a4"));
         executeTest("HCTestStructuralIndels: ", spec);
     }
 
@@ -281,7 +281,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void testLeftAlignmentBamOutBugFix() {
         final String base = String.format("-T HaplotypeCaller -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, LEFT_ALIGNMENT_BAMOUT_TEST_INPUT)
                 + " --no_cmdline_in_header -bamout %s -o /dev/null -L 1:11740000-11740700 --allowNonUniqueKmersInRef";
-        final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("c19f0e62f90794661f5927c360d50998"));
+        final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("c1840293b4565ce1cef393c6a0d5fc9a"));
         executeTest("LeftAlignmentBamOutBugFix", spec);
     }
 
@@ -296,7 +296,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void HCTestDBSNPAnnotationWGS() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub " +  HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1,
-                Arrays.asList("e894e9f50112edad270f36f78e76a8e3"));
+                Arrays.asList("ab816ff6facc08acb19c55bd6e828f02"));
         executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
     }
 
@@ -305,7 +305,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub " +  HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,100,000-11,000,000 -D " + b37dbSNP132
                         + " -L " + hg19Intervals + " -isr INTERSECTION", 1,
-                Arrays.asList("9e384f2bd2eb7a6d5ee1685ab5e75501"));
+                Arrays.asList("fd1a539e14902f6957eb939aac1412f0"));
         executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec);
     }
 
@@ -313,7 +313,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void HCTestDBSNPAnnotationWGSGraphBased() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -pairHMMSub " +  HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1,
-                Arrays.asList("801a3af44153deee939370dcaaa110ab"));
+                Arrays.asList("1810c35e8298dff4aa1b7b04fb5f4962"));
         executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
     }
 
@@ -322,7 +322,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -pairHMMSub " +  HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-11,000,000 -D " + b37dbSNP132
                         + " -L " + hg19Intervals + " -isr INTERSECTION", 1,
-                Arrays.asList("efac9fd7e7a92e3f130e7db9cbff4a45"));
+                Arrays.asList("8a06a53388d73ec667b353379f3b351e"));
         executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec);
     }
 
@@ -345,7 +345,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void HCTestAggressivePcrIndelModelWGS() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T HaplotypeCaller --disableDithering --pcr_indel_model AGGRESSIVE -pairHMMSub " + HMM_SUB_IMPLEMENTATION +  " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,270,000-10,300,000", 1,
-                Arrays.asList("c851be534595a2547a8ebf81f1b923d1"));
+                Arrays.asList("be71ab16d55437cbe3005ea3b93cece6"));
         executeTest("HC calling with aggressive indel error modeling on WGS intervals", spec);
     }
 
@@ -353,7 +353,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void HCTestConservativePcrIndelModelWGS() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T HaplotypeCaller --disableDithering --pcr_indel_model CONSERVATIVE -pairHMMSub " + HMM_SUB_IMPLEMENTATION +  " " + ALWAYS_LOAD_VECTOR_HMM  + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,270,000-10,300,000", 1,
-                Arrays.asList("95a3f339a15b1398cfc9f9e933999ea9"));
+                Arrays.asList("8a5185d0a9400c8b3f4b12da65181c4b"));
         executeTest("HC calling with conservative indel error modeling on WGS intervals", spec);
     }
 
@@ -373,7 +373,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void testLackSensitivityDueToBadHaplotypeSelectionFix() {
         final String commandLine = String.format("-T HaplotypeCaller -pairHMMSub %s %s -R %s -I %s -L %s --no_cmdline_in_header --maxNumHaplotypesInPopulation 16",
                 HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReferenceWithDecoy, privateTestDir + "hc-lack-sensitivity.bam", privateTestDir + "hc-lack-sensitivity.interval_list");
-        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("e6bc4d979ae90c35809a2030ad709b5e"));
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("02ec3090c4a6359fa10e6d8b30e1d5a2"));
         spec.disableShadowBCF();
         executeTest("testLackSensitivityDueToBadHaplotypeSelectionFix", spec);
     }
@@ -382,7 +382,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void testMissingKeyAlternativeHaplotypesBugFix() {
         final String commandLine = String.format("-T HaplotypeCaller -pairHMMSub %s %s -R %s -I %s -L %s --no_cmdline_in_header ",
                 HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReferenceWithDecoy, privateTestDir + "lost-alt-key-hap.bam", privateTestDir + "lost-alt-key-hap.interval_list");
-        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("e8ef8b17a7561dd056805c15baec285e"));
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("13c9f094b9c54960dc2fd3a1815a2645"));
         spec.disableShadowBCF();
         executeTest("testMissingKeyAlternativeHaplotypesBugFix", spec);
     }
@@ -405,7 +405,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
         // but please make sure that both outputs get the same variant,
         // alleles all with DBSNP ids
         // We test here that change in active region size does not have an effect in placement of indels.
-        final String md5 = "df27ceb13e6cda2c97cacd23608c2f7f";
+        final String md5 = "6121d05f96eca3b1dbe3a881d968b6c5";
         final WalkerTestSpec shortSpec = new WalkerTestSpec(commandLineShortInterval + " -o %s",Arrays.asList(md5));
         executeTest("testDifferentIndelLocationsDueToSWExactDoubleComparisonsFix::shortInterval",shortSpec);
         final WalkerTestSpec longSpec = new WalkerTestSpec(commandLineLongInterval + " -o %s",Arrays.asList(md5));
@@ -452,14 +452,19 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
                                 " -R " + REF +
                                 " -I " + NA12878_BAM +
                                 " -L " + INTERVALS_FILE +
-				" --mergeVariantsViaLD " +
+				                " --mergeVariantsViaLD " +
                                 " -o %s",
                         1, UserException.DeprecatedArgument.class));
     }
 
     @Test
     public void testHaplotypeCallerTandemRepeatAnnotator() throws IOException{
-        HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A TandemRepeatAnnotator -XA MappingQualityZero -XA SpanningDeletions", "481787c9275ab9f2e2b53025805472b7");
+        HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A TandemRepeatAnnotator -XA MappingQualityZero -XA SpanningDeletions", "03738462e7f0b6f149f40b790a3a7261");
+    }
+
+    @Test
+    public void testHBaseCountsBySample() throws IOException{
+        HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A BaseCountsBySample", "8739d92898113436666f1cff3bc39bc5");
     }
 }
 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java
index f5894b84f..76c7cfc3e 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java
index ed3413364..ec2be4041 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -69,7 +69,7 @@ public class HaplotypeCallerParallelIntegrationTest extends WalkerTest {
         List tests = new ArrayList<>();
 
         for ( final int nct : Arrays.asList(1, 2, 4) ) {
-            tests.add(new Object[]{nct, "8bcf149228e8845915733d6fd889a141"});
+            tests.add(new Object[]{nct, "07f969acede5e0ad7e1e94f4383af2a9"});
         }
 
         return tests.toArray(new Object[][]{});
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculatorUnitTest.java
index 2ef8b7332..8eae1588d 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculatorUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculatorUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeScoreComparatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeScoreComparatorUnitTest.java
index b137c3c20..69138bd65 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeScoreComparatorUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeScoreComparatorUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeSizeAndBaseComparatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeSizeAndBaseComparatorUnitTest.java
index 593b3a833..ffc3ed72f 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeSizeAndBaseComparatorUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeSizeAndBaseComparatorUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KMerCounterCaseFixUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KMerCounterCaseFixUnitTest.java
index 3609af77a..d84483615 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KMerCounterCaseFixUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KMerCounterCaseFixUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerUnitTest.java
index 55a3106a5..b5fa37df9 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMergerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMergerUnitTest.java
index 826666d43..4819c7f21 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMergerUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMergerUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java
index 3e73bd024..08dc468da 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java
index 40e3aa30e..963a7da61 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMProbabilityBugIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMProbabilityBugIntegrationTest.java
index 4ec4c4cbf..a07e815a6 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMProbabilityBugIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMProbabilityBugIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadErrorCorrectorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadErrorCorrectorUnitTest.java
index e82c84b22..d230ed7b6 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadErrorCorrectorUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadErrorCorrectorUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java
index 119cf45fd..b240e5ffb 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java
index 078177f4a..8973eb9ba 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseEdgeUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseEdgeUnitTest.java
index b8310e024..dad8d8e2d 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseEdgeUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseEdgeUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java
index edaf56ee3..61d568d57 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseVertexUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseVertexUnitTest.java
index ec4238d10..e633ca39c 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseVertexUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseVertexUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixMergerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixMergerUnitTest.java
index a1baa298e..5c73ce2fe 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixMergerUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixMergerUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixSplitterUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixSplitterUnitTest.java
index 314ba5c02..b94cc75cf 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixSplitterUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixSplitterUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeBruijnVertexUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeBruijnVertexUnitTest.java
index 19105eeed..8a9cedfb3 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeBruijnVertexUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeBruijnVertexUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/GraphUtilsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/GraphUtilsUnitTest.java
index 68a298f0c..b2a530d6c 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/GraphUtilsUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/GraphUtilsUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/HaplotypeGraphUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/HaplotypeGraphUnitTest.java
index 9255ef96d..1f28f6b97 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/HaplotypeGraphUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/HaplotypeGraphUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinderUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinderUnitTest.java
index 33d091953..60065ea92 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinderUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinderUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/LowWeightChainPrunerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/LowWeightChainPrunerUnitTest.java
index facf6a08e..c0093c275 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/LowWeightChainPrunerUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/LowWeightChainPrunerUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/MultiSampleEdgeUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/MultiSampleEdgeUnitTest.java
index c929d2c0b..caeafd16e 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/MultiSampleEdgeUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/MultiSampleEdgeUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathBuilderUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathBuilderUnitTest.java
new file mode 100644
index 000000000..a0675e428
--- /dev/null
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathBuilderUnitTest.java
@@ -0,0 +1,136 @@
+/*
+* By downloading the PROGRAM you agree to the following terms of use:
+* 
+* BROAD INSTITUTE
+* SOFTWARE LICENSE AGREEMENT
+* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+* 
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* 
+* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+* 
+* 1. DEFINITIONS
+* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE.
+* 
+* 2. LICENSE
+* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.
+* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+* 
+* 3. PHONE-HOME FEATURE
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* 
+* 4. OWNERSHIP OF INTELLECTUAL PROPERTY
+* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+* Copyright 2012-2015 Broad Institute, Inc.
+* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+* 
+* 5. INDEMNIFICATION
+* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+* 
+* 6. NO REPRESENTATIONS OR WARRANTIES
+* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+* 
+* 7. ASSIGNMENT
+* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+* 
+* 8. MISCELLANEOUS
+* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
+* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs;
+
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+/**
+ * Unit tests for {@link PathBuilder}
+ *
+ * @author Valentin Ruano-Rubio <valentin@broadinstitute.org>
+ */
+public class PathBuilderUnitTest {
+
+    private static final SeqGraph TEST_GRAPH;
+
+    static {
+        TEST_GRAPH = new SeqGraph(3);
+        final SeqVertex head = new SeqVertex("AAA");
+        final SeqVertex allele1 = new SeqVertex("A");
+        final SeqVertex allele2 = new SeqVertex("T");
+        final SeqVertex tail = new SeqVertex("TTT");
+        TEST_GRAPH.addVertices(head, allele1, allele2, tail);
+        TEST_GRAPH.addEdge(head, allele1, new BaseEdge(true, 10));
+        TEST_GRAPH.addEdge(head, allele2, new BaseEdge(false, 20));
+        TEST_GRAPH.addEdge(allele1, tail, new BaseEdge(true, 30));
+        TEST_GRAPH.addEdge(allele2, tail, new BaseEdge(false, 40));
+    }
+
+    @Test
+    public void testPathBuilderCreationAndGetGraph() {
+        final PathBuilder builder = new PathBuilder<>(TEST_GRAPH, 3);
+        Assert.assertSame(builder.getGraph(), TEST_GRAPH);
+        try {
+            builder.lastVertex();
+        } catch (final IllegalStateException ex) {
+            // expected exception because we have not started a path yet.
+        }
+    }
+
+    @Test(dependsOnMethods = "testPathBuilderCreationAndGetGraph")
+    public void testStartAndLastVertex() {
+        final PathBuilder builder = new PathBuilder<>(TEST_GRAPH, 3);
+        final SeqVertex start = TEST_GRAPH.getReferenceSourceVertex();
+        Assert.assertSame(builder.start(start), builder);
+        Assert.assertSame(builder.lastVertex(), start);
+    }
+
+    @Test(dependsOnMethods = "testStartAndLastVertex")
+    public void testReferencePathCreation() {
+        final PathBuilder builder = new PathBuilder<>(TEST_GRAPH, 3);
+        final SeqVertex start = TEST_GRAPH.getReferenceSourceVertex();
+        final Set verticesSoFar = new HashSet<>();
+        builder.start(start);
+        verticesSoFar.add(start);
+        SeqVertex last = start;
+        int score = 0;
+        final List edgeList = new ArrayList<>();
+        while (true) {
+            final SeqVertex next = TEST_GRAPH.getNextReferenceVertex(last);
+            if (next == null)
+                break;
+            final BaseEdge edge = TEST_GRAPH.getEdge(last, next);
+            score += edge.getMultiplicity();
+            edgeList.add(edge);
+            Assert.assertSame(builder.addEdge(edge), builder);
+            last = next;
+            verticesSoFar.add(next);
+            Assert.assertEquals(builder.lastVertex(), last);
+            for (final SeqVertex v: verticesSoFar)
+                Assert.assertTrue(builder.containsVertex(v));
+            for (final SeqVertex v: TEST_GRAPH.vertexSet())
+                if (!verticesSoFar.contains(v))
+                    Assert.assertFalse(builder.containsVertex(v));
+        }
+        final Path path = builder.make();
+        Assert.assertNotNull(path);
+        Assert.assertEquals(path.totalScore, score);
+        Assert.assertEquals(path.edgesInOrder,edgeList);
+    }
+
+}
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathUnitTest.java
index 951272633..cbec4b9b2 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RouteUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RouteUnitTest.java
index a39a73f63..8f7513be7 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RouteUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RouteUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java
index 60796c4dc..9fb138613 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqVertexUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqVertexUnitTest.java
index 89e9a8543..2086234c7 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqVertexUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqVertexUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitterUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitterUnitTest.java
index 8c80b7839..8fa4f4ae8 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitterUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitterUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraphUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraphUnitTest.java
index 1e4bc4f9d..ade84cbf6 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraphUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraphUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssemblerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssemblerUnitTest.java
index f51838369..cacf2ba2a 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssemblerUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssemblerUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java
index 13891ed92..83a00412a 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/SequenceForKmersUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/SequenceForKmersUnitTest.java
index 955857b04..c17b8d1b4 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/SequenceForKmersUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/SequenceForKmersUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManagerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManagerUnitTest.java
index 4f5453fdb..1ef0db5d4 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManagerUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManagerUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -52,7 +52,9 @@
 package org.broadinstitute.gatk.tools.walkers.indels;
 
 import htsjdk.samtools.SAMFileHeader;
+import htsjdk.samtools.SAMFileWriter;
 import htsjdk.samtools.SAMRecord;
+import htsjdk.samtools.util.ProgressLoggerInterface;
 import org.broadinstitute.gatk.utils.BaseTest;
 import org.broadinstitute.gatk.utils.GenomeLocParser;
 import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
@@ -61,6 +63,7 @@ import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import java.util.ArrayList;
 import java.util.List;
 
 
@@ -136,4 +139,60 @@ public class ConstrainedMateFixingManagerUnitTest extends BaseTest {
 
         Assert.assertTrue(manager.forMateMatching.containsKey("foo"));
     }
+
+    @Test
+    public void testSupplementaryAlignmentsDoNotCauseBadMateFixing() {
+        final List properReads = ArtificialSAMUtils.createPair(header, "foo", 1, 1000, 2000, true, false);
+        final GATKSAMRecord read1 = properReads.get(0);
+        read1.setFlags(99);   // first in pair, negative strand
+
+        final GATKSAMRecord read2 = properReads.get(1);
+        read2.setFlags(161);   // second in pair, mate negative strand
+
+        final GATKSAMRecord read2Supp = new GATKSAMRecord(read2);
+        read2Supp.setReadName("foo");
+        read2Supp.setFlags(2209);   // second in pair, mate negative strand, supplementary
+        read2Supp.setAlignmentStart(100);
+        read2Supp.setMateAlignmentStart(1000);
+
+        final DummyWriter writer = new DummyWriter();
+        final ConstrainedMateFixingManager manager = new ConstrainedMateFixingManager(writer, genomeLocParser, 10000, 200, 10000);
+        manager.addRead(read2Supp, false, false);
+        manager.addRead(read1, false, false);
+        manager.addRead(read2, false, false);
+        manager.close(); // "write" the reads to our dummy writer
+
+        // check to make sure that none of the mate locations were changed, which is the problem brought to us by a user
+        for ( final SAMRecord read : writer.reads ) {
+            final int start = read.getAlignmentStart();
+            switch (start) {
+                case 100:
+                    Assert.assertEquals(read.getMateAlignmentStart(), 1000);
+                    break;
+                case 1000:
+                    Assert.assertEquals(read.getMateAlignmentStart(), 2000);
+                    break;
+                case 2000:
+                    Assert.assertEquals(read.getMateAlignmentStart(), 1000);
+                    break;
+                default:
+                    Assert.assertTrue(false, "We saw a read located at the wrong position");
+            }
+        }
+    }
+
+    private class DummyWriter implements SAMFileWriter {
+
+        public List reads;
+
+        public DummyWriter() { reads = new ArrayList<>(10); }
+
+        public void addAlignment(final SAMRecord alignment) { reads.add(alignment);}
+
+        public SAMFileHeader getFileHeader() { return null; }
+
+        public void setProgressLogger(final ProgressLoggerInterface progress) {}
+
+        public void close() {}
+    }
 }
\ No newline at end of file
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerIntegrationTest.java
index c08420fa2..b8703447a 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -66,8 +66,8 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
     private static final String knownIndels = validationDataLocation + "indelRealignerTest.pilot1.ceu.vcf";
     private static final String baseCommandPrefix = "-T IndelRealigner -noPG -R " + b36KGReference + " -I " + mainTestBam + " -targetIntervals " + mainTestIntervals + " -compress 0 -L 20:49,500-55,500 ";
     private static final String baseCommand = baseCommandPrefix + "-o %s ";
-    private static final String base_md5 = "458588d68c8ea7e54443ea722604b265";
-    private static final String base_md5_with_SW_or_VCF = "d5ed91bd5b2023c69078a0fc00268d3c";
+    private static final String base_md5 = "ab7407d2299d9ba73449cea376eeb9c4";
+    private static final String base_md5_with_SW_or_VCF = "fa57bd96b83038ac6a70e58e11bf5364";
 
     @Test
     public void testDefaults() {
@@ -90,7 +90,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
         WalkerTestSpec spec1 = new WalkerTestSpec(
                 baseCommand + "--consensusDeterminationModel KNOWNS_ONLY -known " + knownIndels,
                 1,
-                Arrays.asList("a1b9396f4d5b65f7ae6e0062daf363a3"));
+                Arrays.asList("c42b6f3e1270e43cce2b6f75b6a38f30"));
         executeTest("realigner known indels only from VCF", spec1);
     }
 
@@ -107,7 +107,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
     public void testLods() {
         HashMap e = new HashMap();
         e.put("-LOD 60", base_md5);
-        e.put( "-LOD 1 --consensusDeterminationModel USE_SW",  "dea9bd14323b33348d9cf28e256415f2" );
+        e.put( "-LOD 1 --consensusDeterminationModel USE_SW",  "0c4597e48b4e194de32ebe494704ea6b" );
 
         for ( Map.Entry entry : e.entrySet() ) {
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@@ -123,7 +123,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T IndelRealigner -noPG -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10,000,000-11,000,000 -targetIntervals " + validationDataLocation + "indelRealignerTest.NA12878.chrom1.intervals -compress 0 -o %s",
                 1,
-                Arrays.asList("b91c0bf803247f703dc1cb6ccdc4f18f"));
+                Arrays.asList("19e6859b9ef09c7e0a79a19626908b17"));
         executeTest("realigner long run", spec);
     }
 
@@ -132,7 +132,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseCommand + "--noOriginalAlignmentTags --consensusDeterminationModel USE_SW",
                 1,
-                Arrays.asList("041e2254f271261fb46dc3878cf638f6"));
+                Arrays.asList("8f5684359d7b26acaacfa657ef395a0c"));
         executeTest("realigner no output tags", spec);
     }
 
@@ -154,7 +154,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
     @Test
     public void testMaxReadsInMemory() {
         HashMap e = new HashMap();
-        e.put("--maxReadsInMemory 10000", "0108cd5950f1a4eb90209c3dca8f9e11");
+        e.put("--maxReadsInMemory 10000", "236c64f2da0047534b44444d9d699378");
         e.put( "--maxReadsInMemory 40000", base_md5 );
 
         for ( Map.Entry entry : e.entrySet() ) {
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerLargeScaleTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerLargeScaleTest.java
index 165e611a4..4dc1b23e4 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerLargeScaleTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerLargeScaleTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerUnitTest.java
index ec5b681a8..a706d3182 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModelUnitTest.java
index 91fa5ed46..ce78b68f6 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModelUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModelUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBinUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBinUnitTest.java
index 7fac51266..97e658a5d 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBinUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBinUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorIntegrationTest.java
index ff1ebe32a..23881d330 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -51,45 +51,60 @@
 
 package org.broadinstitute.gatk.tools.walkers.indels;
 
+import htsjdk.samtools.reference.ReferenceSequenceFile;
+import htsjdk.samtools.util.Interval;
+import htsjdk.samtools.util.IntervalList;
 import org.broadinstitute.gatk.engine.walkers.WalkerTest;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.broadinstitute.gatk.utils.GenomeLoc;
+import org.broadinstitute.gatk.utils.GenomeLocParser;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.interval.IntervalUtils;
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
 
 public class RealignerTargetCreatorIntegrationTest extends WalkerTest {
 
-    @Test
-    public void testIntervals1() {
-        String md5 = "3f0b63a393104d0c4158c7d1538153b8";
-
-        WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
-                "-T RealignerTargetCreator -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam --mismatchFraction 0.15 -L 1:10,000,000-10,050,000 -o %s",
-                 1,
-                 Arrays.asList(md5));
-        executeTest("test standard nt=1", spec1);
-
-        WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
-                "-nt 4 -T RealignerTargetCreator -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam --mismatchFraction 0.15 -L 1:10,000,000-10,050,000 -o %s",
-                 1,
-                 Arrays.asList(md5));
-        executeTest("test standard nt=4", spec2);
+    @DataProvider(name = "intervals1")
+    public Object[][] intervals1() {
+        String arguments = "-T RealignerTargetCreator -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam --mismatchFraction 0.15 -L 1:10,000,000-10,050,000";
+        return new Object[][]{
+                {"test standard nt=1", arguments},
+                {"test standard nt=4", "-nt 4 " + arguments}
+        };
     }
 
-    @Test
-    public void testIntervals2() {
+    @DataProvider(name = "intervals2")
+    public Object[][] intervals2() {
+        String arguments = "-T RealignerTargetCreator --known " + b36dbSNP129 + " -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,200,000";
+        return new Object[][]{
+                {"test with dbsnp nt=1", arguments},
+                {"test with dbsnp nt=4", "-nt 4 " + arguments}
+        };
+    }
+
+    @Test(dataProvider = "intervals1")
+    public void testIntervals1(String testName, String arguments) {
+        String md5 = "3f0b63a393104d0c4158c7d1538153b8";
+
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(arguments + " -o %s", 1, Arrays.asList(md5));
+        executeTest(testName, spec);
+    }
+
+    @Test(dataProvider = "intervals2")
+    public void testIntervals2(String testName, String arguments) {
         String md5 = "d073237694175c75d37bd4f40b8c64db";
 
-        WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
-                "-T RealignerTargetCreator --known " + b36dbSNP129 + " -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,200,000 -o %s",
-                 1,
-                 Arrays.asList(md5));
-        executeTest("test with dbsnp nt=1", spec1);
-
-        WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
-                "-nt 4 -T RealignerTargetCreator --known " + b36dbSNP129 + " -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,200,000 -o %s",
-                 1,
-                 Arrays.asList(md5));
-        executeTest("test with dbsnp nt=4", spec2);
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(arguments + " -o %s", 1, Arrays.asList(md5));
+        executeTest(testName, spec);
     }
 
     @Test
@@ -110,4 +125,35 @@ public class RealignerTargetCreatorIntegrationTest extends WalkerTest {
                 Arrays.asList(""));
         executeTest("test bad cigar string string does not fail", spec);
     }
+
+    @Test(dataProvider = "intervals1")
+    public void testTargetListAgainstIntervalList(String testName, String arguments) throws IOException {
+        final List md5 = Collections.emptyList();
+        final File targetListFile = createTempFile("RTCTest", ".targets");
+        final File intervalListFile = createTempFile("RTCTest", ".interval_list");
+
+        WalkerTest.WalkerTestSpec targetListSpec = new WalkerTest.WalkerTestSpec(arguments, 1, md5);
+        WalkerTest.WalkerTestSpec intervalListSpec = new WalkerTest.WalkerTestSpec(arguments, 1, md5);
+
+        targetListSpec.setOutputFileLocation(targetListFile);
+        intervalListSpec.setOutputFileLocation(intervalListFile);
+
+        executeTest(testName + " (compare target-list and interval-list output)", targetListSpec);
+        executeTest(testName + " (compare target-list and interval-list output)", intervalListSpec);
+
+        final ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(BaseTest.hg19Reference));
+        final GenomeLocParser hg19GenomeLocParser = new GenomeLocParser(seq);
+        final List targetList = IntervalUtils.intervalFileToList(hg19GenomeLocParser,
+                targetListFile.getAbsolutePath());
+        final List targetListResult = new ArrayList<>();
+        for ( GenomeLoc target : targetList ) {
+            targetListResult.add(new Interval(target.getContig(), target.getStart(), target.getStop()));
+        }
+
+        final List intervalListResult = IntervalList.fromFile(intervalListFile).getIntervals();
+
+        Assert.assertFalse(targetListResult.isEmpty());
+        Assert.assertFalse(intervalListResult.isEmpty());
+        Assert.assertEquals(targetListResult, intervalListResult);
+    }
 }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorLargeScaleTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorLargeScaleTest.java
index 39d38aebc..4d2a628e4 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorLargeScaleTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorLargeScaleTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmissionIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmissionIntegrationTest.java
index 3bc03f539..f6cc5399b 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmissionIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmissionIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -88,7 +88,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 2,
-                Arrays.asList("af979bcb353edda8dee2127605c71daf","1ea9994f937012e8de599ec7bcd62a0e")
+                Arrays.asList("af979bcb353edda8dee2127605c71daf","3934b5de598024496a5de0ec35bde5b0")
         );
         executeTest("testTrueNegativeMV", spec);
     }
@@ -107,7 +107,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 2,
-                Arrays.asList("1dc36ff8d1d5f5d2c1c1bf21517263bf","547fdfef393f3045a96d245ef6af8acb")
+                Arrays.asList("1dc36ff8d1d5f5d2c1c1bf21517263bf","3260c4f7fda274aeb081744718cca829")
         );
         executeTest("testTruePositiveMV", spec);
     }
@@ -126,7 +126,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 2,
-                Arrays.asList("ae60f2db6102ca1f4e93cd18d0634d7a","9529e2bf214d72e792d93fbea22a3b91")
+                Arrays.asList("ae60f2db6102ca1f4e93cd18d0634d7a","14158702ed830ae022db69cbce83b3ed")
         );
         executeTest("testFalsePositiveMV", spec);
     }
@@ -145,7 +145,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 2,
-                Arrays.asList("590ee56e745984296f73e4277277eac7","8c157d79dd00063d2932f0d2b96f53d8")
+                Arrays.asList("590ee56e745984296f73e4277277eac7","a0940a778e2e3b5454f99a54b40820ce")
         );
         executeTest("testSpecialCases", spec);
     }
@@ -167,7 +167,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 2,
-                Arrays.asList("78158d738917b8f0b7a736a1739b2cc5","343e418850ae4a687ebef2acd55fcb07")
+                Arrays.asList("78158d738917b8f0b7a736a1739b2cc5","3a45b5179dc32cb68f500ff78ef966a6")
         );
         executeTest("testPriorOption", spec);
     }
@@ -187,7 +187,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("9529e2bf214d72e792d93fbea22a3b91")
+                Arrays.asList("14158702ed830ae022db69cbce83b3ed")
         );
         executeTest("testMVFileOption", spec);
     }
@@ -208,7 +208,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
                         "-fatherAlleleFirst"
                 ),
                 2,
-                Arrays.asList("dc6afb769b55e6038677fa590b2b2e89","52ffa82428e63ade22ea37b72ae58492")
+                Arrays.asList("dc6afb769b55e6038677fa590b2b2e89","c534df2b637d07bed96e3cd644b31554")
         );
         executeTest("testFatherAlleleFirst", spec);
     }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtilsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtilsUnitTest.java
index 740f2759c..08be802f2 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtilsUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtilsUnitTest.java
@@ -1,44 +1,44 @@
 /*
 * By downloading the PROGRAM you agree to the following terms of use:
-*
+* 
 * BROAD INSTITUTE
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
-*
+* 
 * This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
-*
+* 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
 * NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
-*
+* 
 * 1. DEFINITIONS
 * 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE.
-*
+* 
 * 2. LICENSE
 * 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.
 * The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
 * 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
-*
+* 
 * 3. PHONE-HOME FEATURE
 * LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
-*
+* 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
-*
+* 
 * 5. INDEMNIFICATION
 * LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
-*
+* 
 * 6. NO REPRESENTATIONS OR WARRANTIES
 * THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
 * IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
-*
+* 
 * 7. ASSIGNMENT
 * This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
-*
+* 
 * 8. MISCELLANEOUS
 * 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
 * 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasingIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasingIntegrationTest.java
index 8933314c8..094163ea7 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasingIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasingIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -77,7 +77,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
                         + " -L chr20:332341-382503",
                 1,
-                Arrays.asList("1bb034bd54421fe4884e3142ed92d47e"));
+                Arrays.asList("fd9810d1984fce38a78683124b6be933"));
         executeTest("MAX 10 het sites [TEST ONE]; require PQ >= 10", spec);
     }
 
@@ -87,7 +87,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
                         + " -L chr20:1232503-1332503",
                 1,
-                Arrays.asList("c12954252d4c8659b5ecf7517b277496"));
+                Arrays.asList("27c0e81c71f599685f6bdc433652645d"));
         executeTest("MAX 10 het sites [TEST TWO]; require PQ >= 10", spec);
     }
 
@@ -97,7 +97,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 2, 30)
                         + " -L chr20:332341-382503",
                 1,
-                Arrays.asList("0b945e30504d04e9c6fa659ca5c25ed5"));
+                Arrays.asList("ca2556135efef75f04a0692afbce85bd"));
         executeTest("MAX 2 het sites [TEST THREE]; require PQ >= 30", spec);
     }
 
@@ -107,7 +107,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 5, 100)
                         + " -L chr20:332341-382503",
                 1,
-                Arrays.asList("e9e8ef92d694ca71f29737fba26282f5"));
+                Arrays.asList("46507837790c71b4f8cba4f1551987a7"));
         executeTest("MAX 5 het sites [TEST FOUR]; require PQ >= 100", spec);
     }
 
@@ -117,7 +117,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 1000, 7, 10)
                         + " -L chr20:332341-482503",
                 1,
-                Arrays.asList("b9c9347c760a06db635952bf4920fb48"));
+                Arrays.asList("30a61a4853b1df1b6afb0a42fb01ca00"));
         executeTest("MAX 7 het sites [TEST FIVE]; require PQ >= 10; cacheWindow = 1000", spec);
     }
 
@@ -127,7 +127,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
                         + " -L chr20:652810-681757",
                 1,
-                Arrays.asList("02c3a903842aa035ae379f16bc3d64ae"));
+                Arrays.asList("acfcca2d271c3403dc42a16e0494f11b"));
         executeTest("MAX 10 het sites [TEST SIX]; require PQ >= 10; cacheWindow = 20000; has inconsistent sites", spec);
     }
 
@@ -137,7 +137,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "CEU.trio.2010_03.genotypes.hg18.vcf", 20000, 10, 10)
                         + " -L chr20:332341-802503",
                 1,
-                Arrays.asList("ac41d1aa9c9a67c07d894f485c29c574"));
+                Arrays.asList("504e9af1f767db3d9da9bb6665daabcb"));
         executeTest("Use trio-phased VCF, adding read-backed phasing information in HP tag (as is now standard for RBP) [TEST SEVEN]", spec);
     }
 
@@ -152,7 +152,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 " -o %s" +
                 " --no_cmdline_in_header",
                 1,
-                Arrays.asList("59ee67d657ee955477bca94d07014ac3"));
+                Arrays.asList("d7797171d9ca4e173fab6b5af1e6d539"));
         executeTest("Do not merge unphased SNPs", spec);
     }
 }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManagerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManagerUnitTest.java
index c511e5994..7e707479f 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManagerUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManagerUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsIntegrationTest.java
index c615315a9..afaaf7036 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -87,7 +87,7 @@ public class SplitNCigarReadsIntegrationTest extends WalkerTest {
     public void testSplitsWithOverhangs() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T SplitNCigarReads -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -o %s --no_pg_tag -U ALLOW_N_CIGAR_READS", 1,
-                Arrays.asList("2832abc680c6b5a0219702ad5bf22f01"));
+                Arrays.asList("72fbeb2043f005e1698e21563f0625a9"));
         executeTest("test splits with overhangs", spec);
     }
 
@@ -95,7 +95,7 @@ public class SplitNCigarReadsIntegrationTest extends WalkerTest {
     public void testSplitsFixNDN() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T SplitNCigarReads -R " + b37KGReference + " -I " + privateTestDir + "splitNCigarReadsSnippet.bam -o %s --no_pg_tag -U ALLOW_N_CIGAR_READS -fixNDN", 1,
-                Arrays.asList("4ee1c1a64847e2b2f660a3a86f9d7e32"));
+                Arrays.asList("add7012d5e814d6cfd32f6cac1eb8ce3"));
         executeTest("test fix NDN", spec);
     }
 
@@ -103,7 +103,7 @@ public class SplitNCigarReadsIntegrationTest extends WalkerTest {
     public void testSplitsWithOverhangsNotClipping() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T SplitNCigarReads --doNotFixOverhangs -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -o %s --no_pg_tag -U ALLOW_N_CIGAR_READS", 1,
-                Arrays.asList("59783610006bf7a1ccae57ee2016123b"));
+                Arrays.asList("6a55ac0a945e010bf03e1dd8f7749417"));
         executeTest("test splits with overhangs not clipping", spec);
     }
 
@@ -111,7 +111,7 @@ public class SplitNCigarReadsIntegrationTest extends WalkerTest {
     public void testSplitsWithOverhangs0Mismatches() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T SplitNCigarReads --maxMismatchesInOverhang 0 -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -o %s --no_pg_tag -U ALLOW_N_CIGAR_READS", 1,
-                Arrays.asList("7547a5fc41ebfd1bbe62ce854b37b6ef"));
+                Arrays.asList("8a577047955ff9edca3caf1f6e545d3e"));
         executeTest("test splits with overhangs 0 mismatches", spec);
     }
 
@@ -119,7 +119,7 @@ public class SplitNCigarReadsIntegrationTest extends WalkerTest {
     public void testSplitsWithOverhangs5BasesInOverhang() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T SplitNCigarReads --maxBasesInOverhang 5 -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -o %s --no_pg_tag -U ALLOW_N_CIGAR_READS", 1,
-                Arrays.asList("f222eb02b003c08d4a606ab1bcb7931b"));
+                Arrays.asList("bdd822868b88063cf50c6336ed1a5e64"));
         executeTest("test splits with overhangs 5 bases in overhang", spec);
     }
 }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsUnitTest.java
index f92afc6f2..f5b4264dd 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java
index d4eb17c29..984e06eee 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -64,7 +64,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forSimulation.vcf -o %s",
                  1,
-                 Arrays.asList("dd9e17a9c268578e903ecd4ca0a4a335"));
+                 Arrays.asList("d929369b9095420a8aaff2595ec2f80a"));
         executeTest("testVariants", spec);
     }
 
@@ -74,7 +74,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-RL 70 -T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forSimulation.vcf -o %s",
                  1,
-                 Arrays.asList("d7388376ffd4d3826d48a5be0be70632"));
+                 Arrays.asList("bbc65e4f8bd3a1656616476a1e190ecf"));
         executeTest("testReadLength", spec);
     }
 
@@ -84,7 +84,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-ER 40 -T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forSimulation.vcf -o %s",
                  1,
-                 Arrays.asList("6c9bf583f4b2708d6b82f54516474b7b"));
+                 Arrays.asList("cb0e4b11bbd1b5a154ad6c99541cd017"));
         executeTest("testErrorRate", spec);
     }
 
@@ -94,7 +94,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-RGPL SOLID -T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forSimulation.vcf -o %s",
                 1,
-                Arrays.asList("26db391f223ead74d786006a502029d8"));
+                Arrays.asList("2b5c6cda9a434c9e25e5da5599eeae51"));
         executeTest("testPlatformTag", spec);
     }
 
@@ -105,7 +105,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SimulateReadsForVariants --no_pg_tag --useAFAsAlleleFraction -DP 100 -R " + b37KGReference + " -V " + publicTestDir + "forAlleleFractionSimulation.vcf -o %s",
                 1,
-                Arrays.asList("3425c807525dff71310d1517e00a4f7e"));
+                Arrays.asList("1ae2c354718b470e30b44d5e59cb9944"));
         executeTest("testAlleleFraction", spec);
 
     }
@@ -116,7 +116,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forLongInsert.vcf -o %s",
                 1,
-                Arrays.asList("bb412c1fc8f95523dd2fc623d53dbeec"));
+                Arrays.asList("5c069bff8efb988660c7f6d28a3117fc"));
         executeTest("testLongInsertFailure", spec);
     }
 
@@ -126,7 +126,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-RL 269 -T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forLongInsert.vcf -o %s",
                 1,
-                Arrays.asList("9236320c470cd8d6759c21b79206f63f"));
+                Arrays.asList("0657f6a692d22b5e2b7f5832710042e4"));
         executeTest("testLongInsertSuccess", spec);
     }
 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/validation/ValidationSiteSelectorIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/validation/ValidationSiteSelectorIntegrationTest.java
index cbe3408de..247f3ca16 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/validation/ValidationSiteSelectorIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/validation/ValidationSiteSelectorIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -84,7 +84,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(sampleNone + freqUnif + "--variant " + testfile),
                 1,
-                Arrays.asList("19fe0e3297bfd502911608490222a2fd")
+                Arrays.asList("d52bc5a7d99916ddda2d281694a733e2")
         );
 
         executeTest("testNoSampleSelectionFreqUniform--" + testfile, spec);
@@ -96,7 +96,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(sampleNone + freqAF + "--variant " + testfile),
                 1,
-                Arrays.asList("91a7f3bf452241040646e61ee6ab1a23")
+                Arrays.asList("a509bacf1920bd080fc8a9026d187bf7")
         );
 
         executeTest("testNoSampleSelectionFreqAF--" + testfile, spec);
@@ -108,7 +108,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(sampleGT + freqUnif + "--variant " + testfile),
                 1,
-                Arrays.asList("faae3baf1feb76877fcb81c01b5d44f3")
+                Arrays.asList("dcb50e6c733b791bb79720a418d5683f")
         );
 
         executeTest("testPolyGTFreqUniform--" + testfile, spec);
@@ -120,7 +120,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(sampleGT + freqAF + "--variant " + testfile),
                 1,
-                Arrays.asList("d2ba4e3e76f87e2c1a12d82e7a3dc595")
+                Arrays.asList("c8a3892a8074d0ee5050119cc239fb76")
         );
 
         executeTest("testPolyGTFreqAF--" + testfile, spec);
@@ -132,7 +132,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(sampleGL + freqAF + "--variant " + testfile),
                 1,
-                Arrays.asList("d2ba4e3e76f87e2c1a12d82e7a3dc595")
+                Arrays.asList("c8a3892a8074d0ee5050119cc239fb76")
         );
 
         executeTest("testPolyGLFreqAF--" + testfile, spec);
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalIntegrationTest.java
index 1c79501fa..88bd7a4cd 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -335,7 +335,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                 " --eval " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
                 " --comp:comp_genotypes " + privateTestDir + "yri.trio.gatk.ug.head.vcf";
         WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
-                1, Arrays.asList("4b9dcbce0717285e3c0c736c1bed744c"));
+                1, Arrays.asList("eaa3708d9db22fca0844a652bb73b82f"));
         executeTestParallel("testSelect1", spec);
     }
 
@@ -350,6 +350,17 @@ public class VariantEvalIntegrationTest extends WalkerTest {
         executeTestParallel("testVEMendelianViolationEvaluator" + vcfFile, spec);
     }
 
+    @Test
+    public void testMVEvalFamilyStrat() {
+        String vcfFile = "/PhaseByTransmission/PhaseByTransmission.IntegrationTest.TP.vcf";
+        String pedFile = "/PhaseByTransmission/PhaseByTransmission.IntegrationTest.goodFamilies.ped";
+
+        WalkerTestSpec spec = new WalkerTestSpec("-R "+b37KGReference+ " -T VariantEval -ped " + privateTestDir + pedFile + " -eval " + privateTestDir + vcfFile + " -noEV -noST -ST Family -EV MendelianViolationEvaluator -o %s",
+                1,
+                Arrays.asList("d599d3e6b308ac06b2c2e003cf596328"));
+        executeTestParallel("testMVEvalFamilyStrat", spec);
+    }
+
 
     private static String withSelect(String cmd, String select, String name) {
         return String.format("%s -select '%s' -selectName %s", cmd, select, name);
@@ -377,7 +388,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                            " --dbsnp " + b37dbSNP132 +
                            " --eval:evalBI " + variantEvalTestDataRoot + "ALL.20100201.chr20.bi.sites.vcf" +
                            " -noST -ST Novelty -o %s";
-        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("112bb3221688acad83f29542bfb33151"));
+        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("fe9dcf4933a645f55be1cb0e33497e49"));
         executeTestParallel("testEvalTrackWithoutGenotypes",spec);
     }
 
@@ -404,7 +415,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                 " --eval:evalBI " + variantEvalTestDataRoot + "ALL.20100201.chr20.bi.sites.vcf" +
                 " --eval:evalBC " + variantEvalTestDataRoot + "ALL.20100201.chr20.bc.sites.vcf" +
                 " -noST -ST Novelty -o %s";
-        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("81dcdde458c1ebb9aa35289ea8f12bc8"));
+        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("8dfdec264fcff9472bdee7d223fdb3ca"));
         executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
     }
 
@@ -586,7 +597,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                                         "-o %s"
                                 ),
                                 1,
-                                Arrays.asList("f8460af997436a5ce4407fefb0e2724d")
+                                Arrays.asList("af317f1ea1b80e5d4bc4f2d8523ef73d")
                               );
         executeTest("testModernVCFWithLargeIndels", spec);
     }
@@ -690,4 +701,22 @@ public class VariantEvalIntegrationTest extends WalkerTest {
         tests.add(new Object[]{"genotypes/genotypes", evalGenotypes, compGenotypes, "73790b530595fcbd467a88475ea9717f"});
         return tests.toArray(new Object[][]{});
     }
+
+
+    @Test
+    public void testPrintMissingComp() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                buildCommandLine(
+                        "-T VariantEval",
+                        "-R " + b37KGReference,
+                        "-eval " + privateTestDir + "validationReportEval.noGenotypes.vcf",
+                        "--comp " + privateTestDir + "validationReportComp.noGenotypes.vcf",
+                        "-L 20",
+                        "-EV PrintMissingComp"
+                ),
+                0,
+                Arrays.asList("d41d8cd98f00b204e9800998ecf8427e")); // sato: make sure it doesn't throw a null pointer exception.
+        executeTest("testPrintMissingComp", spec);
+
+    }
 }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalWalkerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalWalkerUnitTest.java
index 964d6c151..11b34a0c0 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalWalkerUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalWalkerUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -140,7 +140,7 @@ public class VariantEvalWalkerUnitTest extends BaseTest {
         }
 
         @Override
-        public List getRelevantStates(final ReferenceContext ref, final RefMetaDataTracker tracker, final VariantContext comp, final String compName, final VariantContext eval, final String evalName, final String sampleName) {
+        public List getRelevantStates(final ReferenceContext ref, final RefMetaDataTracker tracker, final VariantContext comp, final String compName, final VariantContext eval, final String evalName, final String sampleName, final String familyName) {
             int i = Integer.valueOf(evalName); // a terrible hack, but we can now provide accessible states
             List states = new ArrayList();
             for ( int state : integers )
@@ -180,12 +180,12 @@ public class VariantEvalWalkerUnitTest extends BaseTest {
         final RefMetaDataTracker tracker = new RefMetaDataTracker();
         final ReferenceContext ref = null;
         final VariantContext comp = null;
-        final String compName = null, sampleName = null;
+        final String compName = null, sampleName = null, familyName = null;
 
         // increment eval counts for each stratification of divisors of i from from 1...maxI
         for ( int i = 1; i <= cfg.maxI; i++ ) {
             final String evalName = String.valueOf(i); // terrible hack to stratify by divisor
-            for ( EvaluationContext nec : VEwalker.getEvaluationContexts(tracker, ref, eval, evalName, comp, compName, sampleName) ) {
+            for ( EvaluationContext nec : VEwalker.getEvaluationContexts(tracker, ref, eval, evalName, comp, compName, sampleName, familyName) ) {
                 synchronized (nec) {
                     nec.apply(tracker, ref, null, comp, eval);
                 }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java
index 724f5e129..a01355e65 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java
index a3f2f9eac..e4b1dc4eb 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManagerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManagerUnitTest.java
index 14b13e23c..f5b92941e 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManagerUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManagerUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java
index 872f5f399..103d25b67 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
index 473ab8cd4..926fab004 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -94,14 +94,14 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
 
     VRTest lowPass = new VRTest(validationDataLocation + "phase1.projectConsensus.chr20.raw.snps.vcf",
             "41e2d951a17de433fe378bb3d9ec75d4",  // tranches
-            "19c77724f08d90896914d3d348807399",  // recal file
-            "c6a186a1a9271f5de35f1e5aeb8749a6"); // cut VCF
+            "3fe87e69c6a613addb7eff5449e86aa1",  // recal file
+            "78b8f1934d77341df2f6a9fdbd30fa74"); // cut VCF
 
     VRTest lowPassPlusExomes = new VRTest(validationDataLocation + "phase1.projectConsensus.chr20.raw.snps.vcf",
             validationDataLocation + "1kg_exomes_unfiltered.AFR.unfiltered.vcf",
             "ce4bfc6619147fe7ce1f8331bbeb86ce",  // tranches
-            "b7cad6a0bbbf0330e0ac712a80c3144f",  // recal file
-            "bee399765991636461599565c9634bcf"); // cut VCF
+            "5a298554e9175961f63506c4e42ea78b",  // recal file
+            "f284c0cbb00407cc5273c6f1a871513e"); // cut VCF
 
     @DataProvider(name = "VRTest")
     public Object[][] createData1() {
@@ -196,8 +196,8 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
 
     VRTest bcfTest = new VRTest(privateTestDir + "vqsr.bcf_test.snps.unfiltered.bcf",
             "3ad7f55fb3b072f373cbce0b32b66df4",  // tranches
-            "e91a5b25ea1eefdcff488e0326028b51",  // recal file
-            "e6a0c5173d8c8fbd08afdc5e5e7d3a78"); // cut VCF
+            "73489f9365e4884b2dd89477350a7fe0",  // recal file
+            "0bd2067f831e5388b790e7bb7f45d98f"); // cut VCF
 
     @DataProvider(name = "VRBCFTest")
     public Object[][] createVRBCFTest() {
@@ -251,14 +251,14 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
     VRTest indelUnfiltered = new VRTest(
             validationDataLocation + "combined.phase1.chr20.raw.indels.unfiltered.sites.vcf", // all FILTERs as .
             "9a331328370889168a7aa3a625f73620",  // tranches
-            "689c7853fe2e63216da3b0d47e27740e",  // recal file
-            "4147373ec8e0aba7ace3658677007990"); // cut VCF
+            "d8f68f41c8fbdff84f909f4de4a67476",  // recal file
+            "ca376c261dc041faa4dfa31e53fed1e2"); // cut VCF
 
     VRTest indelFiltered = new VRTest(
             validationDataLocation + "combined.phase1.chr20.raw.indels.filtered.sites.vcf", // all FILTERs as PASS
             "9a331328370889168a7aa3a625f73620",  // tranches
-            "689c7853fe2e63216da3b0d47e27740e",  // recal file
-            "8dd8ea31e419f68d80422b34b14e24e4"); // cut VCF
+            "d8f68f41c8fbdff84f909f4de4a67476",  // recal file
+            "c968a943ef24520de6ed15c830ab5ac4"); // cut VCF
 
     @DataProvider(name = "VRIndelTest")
     public Object[][] createTestVariantRecalibratorIndel() {
@@ -316,7 +316,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -tranchesFile " + privateTestDir + "VQSR.mixedTest.tranches" +
                         " -recalFile " + privateTestDir + "VQSR.mixedTest.recal",
-                Arrays.asList("cd42484985179c7f549e652f0f6a94d0"));
+                Arrays.asList("41d5c363bd311677ae1fcf98f4a18487"));
         final List outputFiles = executeTest("testApplyRecalibrationSnpAndIndelTogether", spec).getFirst();
         setPDFsForDeletion(outputFiles);
     }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java
index 7f860f343..346566720 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -74,7 +74,7 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest {
                         " -L 20:10,000,000-10,001,432" +
                         " -V " + validationDataLocation + "1000G.phase3.broad.withGenotypes.chr20.1MB.vcf",
                 1,
-                Arrays.asList("afe5c06ef62612e4c663a3f8e9f5cd60"));
+                Arrays.asList("3e60ca3e04fecf5d6004c08d6f7503ca"));
         executeTest("testUsingDiscoveredAF", spec);
     }
 
@@ -89,7 +89,7 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest {
                         " -L 20:10,000,000-10,001,432" +
                         " -V " + validationDataLocation + "1000G.phase3.broad.withGenotypes.chr20.1MB.vcf",
                 1,
-                Arrays.asList("de153b79fd1c0e1c1f769ec4a9fb01e0"));
+                Arrays.asList("1cca249ebc2599c7f24210d4f3204049"));
         executeTest("testMissingPriors", spec);
     }
 
@@ -103,7 +103,7 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest {
                         " -V " + validationDataLocation + "NA12878.Jan2013.haplotypeCaller.subset.indels.vcf" +
                         " -supporting " + validationDataLocation + "1000G.phase3.broad.withGenotypes.chr20.1MB.vcf",
                 1,
-                Arrays.asList("7876c43e9fc13723bd890b8adc5d053d"));
+                Arrays.asList("cc59ceb6dab620a353edf03ef14090f1"));
         executeTest("testInputINDELs", spec);
     }
 
@@ -117,7 +117,7 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest {
                         " -V " + CEUtrioTest +
                         " -supporting " + CEUtrioPopPriorsTest,
                 1,
-                Arrays.asList("781f85f56dac9074c96ace31b09e0f59"));
+                Arrays.asList("c7d35ce5f3675528fc484baa1c5df7b4"));
         executeTest("testFamilyPriors", spec);
     }
 
@@ -131,7 +131,7 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest {
                         " -V " + getThreeMemberNonTrioTest +
                         " -skipPop",
                 1,
-                Arrays.asList("abfa4332bce9aba911ad2eba34ee9924"));
+                Arrays.asList("c523b99da1f7e0c0ea4090b916ae7379"));
         executeTest("testFamilyPriors", spec);
     }
 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java
index 8ac40aa74..080c8da02 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -100,7 +100,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "tetraploid-gvcf-3.vcf" +
                         " -L " + privateTestDir + "tetraploid-gvcfs.intervals",
                 1,
-                Arrays.asList("7b3153135e4f8e1d137d3f4beb46f182"));
+                Arrays.asList("f3538bcaf27f5e8b036d4c1f8734e4c2"));
         executeTest("combineSingleSamplePipelineGVCF", spec);
     }
 
@@ -112,7 +112,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "diploid-gvcf-3.vcf" +
                         " -L " + privateTestDir + "tetraploid-gvcfs.intervals",
                 1,
-                Arrays.asList("4f546634213ece6f08ec9258620b92bb"));
+                Arrays.asList("32cd060d6662bdc835f70a848d48fb0e"));
         executeTest("combineSingleSamplePipelineGVCF", spec);
     }
 
@@ -190,7 +190,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
     @Test
     public void testMD5s() throws Exception {
         final String cmd = baseTestString(" -L 1:69485-69791");
-        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("b7c753452ab0c05f9cee538e420b87fa"));
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("82fa951ce741451267dbf30335e0f71d"));
         spec.disableShadowBCF();
         executeTest("testMD5s", spec);
     }
@@ -198,7 +198,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
     @Test
     public void testBasepairResolutionOutput() throws Exception {
         final String cmd = baseTestString(" -L 1:69485-69791 --convertToBasePairResolution");
-        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("bb6420ead95da4c72e76ca4bf5860ef0"));
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("8e1bfa842d53f86d46b2166574c0c66c"));
         spec.disableShadowBCF();
         executeTest("testBasepairResolutionOutput", spec);
     }
@@ -206,7 +206,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
     @Test
     public void testBreakBlocks() throws Exception {
         final String cmd = baseTestString(" -L 1:69485-69791 --breakBandsAtMultiplesOf 5");
-        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("dd31182124c4b78a8a03edb1e0cf618b"));
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("76d78f83c7db247ce12087d6118dc5df"));
         spec.disableShadowBCF();
         executeTest("testBreakBlocks", spec);
     }
@@ -217,7 +217,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
                 "-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                         " -V " + privateTestDir + "spanningDel.1.g.vcf -V " + privateTestDir + "spanningDel.2.g.vcf",
                 1,
-                Arrays.asList("58984edf9a3a92c9fc97039b97755861"));
+                Arrays.asList("cb46cb8fd6506ab3e80bd50f9231643c"));
         spec.disableShadowBCF();
         executeTest("testSpanningDeletions", spec);
     }
@@ -228,7 +228,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
                 "-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                         " -V " + privateTestDir + "spanningDel.many.g.vcf",
                 1,
-                Arrays.asList("5c88e10211def13ba847c29d0fe9e191"));
+                Arrays.asList("5aeb14d64b9103b62d053aeb6158e5de"));
         spec.disableShadowBCF();
         executeTest("testMultipleSpanningDeletionsForOneSample", spec);
     }
@@ -239,7 +239,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
                 "-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                         " -V " + privateTestDir + "spanningDel.many.haploid.g.vcf",
                 1,
-                Arrays.asList("76fc5f6b949ac0b893061828af800bf8"));
+                Arrays.asList("3fca32a67922bf30f72fe066fe7159fe"));
         spec.disableShadowBCF();
         executeTest("testMultipleSpanningDeletionsForOneSampleHaploid", spec);
     }
@@ -250,7 +250,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
                 "-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                         " -V " + privateTestDir + "spanningDel.many.tetraploid.g.vcf",
                 1,
-                Arrays.asList("0ec79471550ec5e30540f68cb0651b14"));
+                Arrays.asList("6891eaaef2991d7f967c7876fd2e4f5c"));
         spec.disableShadowBCF();
         executeTest("testMultipleSpanningDeletionsForOneSampleTetraploid", spec);
     }
@@ -259,7 +259,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
     public void testWrongReferenceBaseBugFix() throws Exception {
         final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -V " + (privateTestDir + "combine-gvcf-wrong-ref-input1.vcf"
                 + " -V " + (privateTestDir + "combine-gvcf-wrong-ref-input2.vcf") + " -o %s --no_cmdline_in_header");
-        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("c0fdba537399cf28b28771963e2c5174"));
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("224c3d6e06f7ce4bdb55411b2e376577"));
         spec.disableShadowBCF();
         executeTest("testWrongReferenceBaseBugFix",spec);
 
@@ -268,8 +268,17 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
     @Test
     public void testBasepairResolutionInput() throws Exception {
         final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -V " + privateTestDir + "gvcf.basepairResolution.vcf";
-        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("6aeb88ca94cb5223f26175da72b985f2"));
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("d3244d99e9423b45099a220f19fac516"));
         spec.disableShadowBCF();
         executeTest("testBasepairResolutionInput", spec);
     }
+
+    @Test
+    public void testAlleleSpecificAnnotations() throws Exception {
+        final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard -V "
+                + privateTestDir + "NA12878.AS.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.chr20snippet.g.vcf";
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("cbb2571eeb95e661acee8f9e1d1cbfbd"));
+        spec.disableShadowBCF();
+        executeTest("testAlleleSpecificAnnotations", spec);
+    }
 }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java
index b6d05eefb..cc5bcbbff 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -132,30 +132,30 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
          cvExecuteTest("combine PLs 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec, true);
     }
 
-    @Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "6469fce8a5cd5a0f77e5ac5d9e9e192b", " -U LENIENT_VCF_PROCESSING"); }
-    @Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "a4cedaa83d54e34cafc3ac4b80acf5b4", " -setKey foo -U LENIENT_VCF_PROCESSING"); }
-    @Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "ac58a5fde17661e2a19004ca954d9781", " -setKey null -U LENIENT_VCF_PROCESSING"); }
-    @Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "67a8076e30b4bca0ea5acdc9cd26a4e0"); } // official project VCF files in tabix format
+    @Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "e3dbdfa14aefb2f6bd1213287d34a2e5", " -U LENIENT_VCF_PROCESSING"); }
+    @Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "d727fab83b4265859c4a902f6e66ac3d", " -setKey foo -U LENIENT_VCF_PROCESSING"); }
+    @Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "42fc3d2c68415a61ff15e594a63d9349", " -setKey null -U LENIENT_VCF_PROCESSING"); }
+    @Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "a3994d6145bb3813950939238db4c592"); } // official project VCF files in tabix format
 
-    @Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "909c6dc74eeb5ab86f8e74073eb0c1d6"); }
-    @Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "381875b3280ba56eef0152e56f64f68d"); }
+    @Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "e7fd959312e2aff0b4231963ee690aec"); }
+    @Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "23439a1f0108b57a14e18efe9482cc88"); }
 
-    @Test public void combineWithPLs() { combinePLs("combine.3.vcf", "combine.4.vcf", "f0ce3fb83d4ad9ba402d7cb11cd000c3"); }
+    @Test public void combineWithPLs() { combinePLs("combine.3.vcf", "combine.4.vcf", "27aa46cdb022be3959e7240a0d7ac794"); }
 
-    @Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "4efdf983918db822e4ac13d911509576"); } // official project VCF files in tabix format
-    @Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "848d4408ee953053d2307cefebc6bd6d"); } // official project VCF files in tabix format
-    @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "629656bfef7713c23f3a593523503b2f"); }
+    @Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "9bdda937754e1407183406808f560723"); } // official project VCF files in tabix format
+    @Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "6344953a82a422115bd647ec1d696b94"); } // official project VCF files in tabix format
+    @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "c4b995405872b22ded76c0a9e183c52d"); }
 
-    @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "e54d0dcf14f90d5c8e58b45191dd0219"); }
+    @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "f9d1d7e6246f0ce9e493357d5b320323"); }
 
     @Test public void uniqueSNPs() {
         // parallelism must be disabled because the input VCF is malformed (DB=0) and parallelism actually fixes this which breaks the md5s
         //both of these files have the YRI trio and merging of duplicate samples without priority must be specified with UNSORTED merge type
-        combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", " -genotypeMergeOptions UNSORTED", "e5ea6ac3905bd9eeea1a2ef5d2cb5af7", true);
+        combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", " -genotypeMergeOptions UNSORTED", "5aece78046bfb7d6ee8dc4d551542e3a", true);
     }
 
-    @Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "def52bcd3942bbe39cd7ebe845c4f206"); }
-    @Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "5f61145949180bf2a0cd342d8e064860"); }
+    @Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "0897efcc0046bd94760315838d4d0fa5"); }
+    @Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "8b12b09a6ec4e3fde2352bbf82637f1e"); }
 
     @Test public void threeWayWithRefs() {
         WalkerTestSpec spec = new WalkerTestSpec(
@@ -169,7 +169,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
                         " -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" +
                         " -genotypeMergeOptions UNIQUIFY -L 1"),
                 1,
-                Arrays.asList("58e6281df108c361e99673a501ee4749"));
+                Arrays.asList("8f8ba6d671f67386883c11873df3cf95"));
         cvExecuteTest("threeWayWithRefs", spec, true);
     }
 
@@ -186,17 +186,17 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
         cvExecuteTest("combineComplexSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec, true);
     }
 
-    @Test public void complexTestFull() { combineComplexSites("", "9d989053826ffe5bef7c4e05ac51bcca"); }
-    @Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "4f38d9fd30a7ae83e2a7dec265a28772"); }
-    @Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "46bbbbb8fc9ae6467a4f8fe35b8d7d14"); }
-    @Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "46bbbbb8fc9ae6467a4f8fe35b8d7d14"); }
+    @Test public void complexTestFull() { combineComplexSites("", "3a702773e31674b14a1073d455f6f1ce"); }
+    @Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "cabad0e328f1c967d44aaf2085da5dcf"); }
+    @Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "31f6f62664cc5891e9a8e228dbb6278d"); }
+    @Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "31f6f62664cc5891e9a8e228dbb6278d"); }
 
     @Test
     public void combineDBSNPDuplicateSites() {
          WalkerTestSpec spec = new WalkerTestSpec(
                  "-T CombineVariants --no_cmdline_in_header -L 1:902000-903000 -o %s -R " + b37KGReference + " -V:v1 " + b37dbSNP132,
                  1,
-                 Arrays.asList("aa926eae333208dc1f41fe69dc95d7a6"));
+                 Arrays.asList("b0d4b86702b44fc4faa527c34adf6239"));
          cvExecuteTest("combineDBSNPDuplicateSites:", spec, true);
     }
 
@@ -207,7 +207,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
                         + " -R " + b37KGReference
                         + " -V " + privateTestDir + "combineVariantsLeavesRecordsUnfiltered.vcf",
                 1,
-                Arrays.asList("f8c014d0af7e014475a2a448dc1f9cef"));
+                Arrays.asList("11aab642395645589e48edee1fb179e2"));
         cvExecuteTest("combineLeavesUnfilteredRecordsUnfiltered: ", spec, false);
     }
 
@@ -229,7 +229,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
         // Just checking that this does not fail, hence no output files and MD5
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T CombineVariants --no_cmdline_in_header -o %s "
-                        + " -R " + hg19RefereneWithChrPrefixInChromosomeNames
+                        + " -R " + hg19ReferenceWithChrPrefixInChromosomeNames
                         + " -V " + privateTestDir + "WES-chr1.DEL.vcf"
                         + " -V " + privateTestDir + "WGS-chr1.DEL.vcf"
                         + " -genotypeMergeOptions UNIQUIFY",
@@ -237,4 +237,18 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
                 Arrays.asList(""));
         executeTest("combineSymbolicVariants: ", spec);
     }
-}
\ No newline at end of file
+
+    @Test
+    public void combineSpanningDels() {
+        // Just checking that this does not fail, hence no output files and MD5
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T CombineVariants --no_cmdline_in_header -o %s "
+                        + " -R " + b37KGReference
+                        + " -V " + privateTestDir + "test.spanningdel.combine.1.vcf "
+                        + " -V " + privateTestDir + "test.spanningdel.combine.2.vcf "
+                        + " -genotypeMergeOptions UNIQUIFY",
+                0,
+                Arrays.asList(""));
+        executeTest("combineSpanningDels: ", spec);
+    }
+}
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsUnitTest.java
index d3a145be6..1df099b00 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetricsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetricsUnitTest.java
index c7043bad9..f0b6d33da 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetricsUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetricsUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordanceIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordanceIntegrationTest.java
index 32603d084..eb9f56899 100755
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordanceIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordanceIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
index 73f410786..bcaf889b8 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -56,15 +56,18 @@ import htsjdk.tribble.readers.PositionalBufferedStream;
 import htsjdk.variant.variantcontext.Genotype;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.vcf.VCFCodec;
+import org.apache.commons.io.FileUtils;
 import org.broadinstitute.gatk.engine.walkers.WalkerTest;
+import org.broadinstitute.gatk.tools.walkers.annotator.AnnotationUtils;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
-import java.util.Arrays;
 import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 
 public class GenotypeGVCFsIntegrationTest extends WalkerTest {
@@ -82,17 +85,21 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -V " + privateTestDir + "testUpdatePGT.vcf", b37KGReference),
                 1,
-                Arrays.asList("23ff3e22262929138ca1f00fc111cadf"));
+                Arrays.asList("beebc536d20d69a45c6f56fbb041c9bc"));
         executeTest("testUpdatePGT", spec);
     }
 
     @Test(enabled = true)
-    public void testUpdatePGTStrandAlleleCountsBySample() {
+    public void testUpdatePGTStrandAlleleCountsBySample() throws IOException{
+        final String logFileName = new String("testUpdatePGTStrandAlleleCountsBySample.log");
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString(" -V " + privateTestDir + "testUpdatePGT.vcf -A StrandAlleleCountsBySample", b37KGReference),
+                baseTestString(" -V " + privateTestDir + "testUpdatePGT.vcf -A StrandAlleleCountsBySample -log " + logFileName, b37KGReference),
                 1,
-                Arrays.asList("88fa4a021e4aac9a0e48bd54b2949ece"));
-        executeTest("testUpdatePGT, adding StrandAlleleCountsBySample annotation", spec);
+                Arrays.asList("527d513874a787821daf54b8fc8a33e3"));
+        executeTest("testUpdatePGTStrandAlleleCountsBySample", spec);
+
+        File file = new File(logFileName);
+        Assert.assertTrue(FileUtils.readFileToString(file).contains(AnnotationUtils.ANNOTATION_HC_WARN_MSG));
     }
 
     @Test(enabled = true)
@@ -103,7 +110,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
                         " -L 20:10,000,000-20,000,000", b37KGReference),
                 1,
-                Arrays.asList("06b4e2589c5b903f7c51ae9968bebe77"));
+                Arrays.asList("63bdb33fe44b6589adc5c36b0ea740b2"));
         executeTest("combineSingleSamplePipelineGVCF", spec);
     }
 
@@ -115,7 +122,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "tetraploid-gvcf-3.vcf" +
                         " -L " + privateTestDir + "tetraploid-gvcfs.intervals", b37KGReference),
                 1,
-                Arrays.asList("599394c205c1d6641b9bebabbd29e13c"));
+                Arrays.asList("3708b0d993a683e8c7421f60d7123cf4"));
         executeTest("combineSingleSamplePipelineGVCF", spec);
     }
 
@@ -127,7 +134,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "diploid-gvcf-3.vcf" +
                         " -L " + privateTestDir + "tetraploid-gvcfs.intervals", b37KGReference),
                 1,
-                Arrays.asList("f7d5344a85e6d7fc2437d4253b424cb0"));
+                Arrays.asList("7d7a65ea549fcd30553766ad4333f9e2"));
         executeTest("combineSingleSamplePipelineGVCF", spec);
     }
 
@@ -139,7 +146,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
                         " --includeNonVariantSites -L 20:10,030,000-10,033,000 -L 20:10,386,000-10,386,500", b37KGReference),
                 1,
-                Arrays.asList("c9e4d1e52ee1f3a5233f1fb100f24d5e"));
+                Arrays.asList("8b338d065806f7c7eea67f56a1f6009e"));
         executeTest("combineSingleSamplePipelineGVCF_includeNonVariants", spec);
     }
 
@@ -152,7 +159,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
                         " -L 20:10,000,000-20,000,000", b37KGReference),
                 1,
-                Arrays.asList("aa19980b9a525afed43e98c821114ae5"));
+                Arrays.asList("2d4e6a3193c493514576a758e891b951"));
         executeTest("combineSingleSamplePipelineGVCFHierarchical", spec);
     }
 
@@ -164,7 +171,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
                         " -L 20:10,000,000-11,000,000 --dbsnp " + b37dbSNP132, b37KGReference),
                 1,
-                Arrays.asList("f23c9d62542a69b5cbf0e9f89fdd235d"));
+                Arrays.asList("7693207e925359df331e64664c5b8763"));
         executeTest("combineSingleSamplePipelineGVCF_addDbsnp", spec);
     }
 
@@ -174,7 +181,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                 "-T GenotypeGVCFs --no_cmdline_in_header -L 1:69485-69791 -o %s -R " + b37KGReference +
                 " -V " + privateTestDir + "gvcfExample1.vcf",
                 1,
-                Arrays.asList("d602d9e5d336798e4ccb52d2b5f91677"));
+                Arrays.asList("84ad9c6e7582dbcc693deacdeff5984a"));
         executeTest("testJustOneSample", spec);
     }
 
@@ -185,14 +192,14 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V " + privateTestDir + "gvcfExample1.vcf" +
                         " -V " + privateTestDir + "gvcfExample2.vcf",
                 1,
-                Arrays.asList("6c6d6ef90386eb6c6ed649379aac0c13"));
+                Arrays.asList("54b76f721811c9c7958e849c40b8d4e2"));
         executeTest("testSamplesWithDifferentLs", spec);
     }
 
     @Test(enabled = true)
     public void testNoPLsException() {
         // Test with input files with (1) 0/0 and (2) ./.
-        final String md5 = "d04b32cf2fa97d303ff7fdc779a653d4";
+        final String md5 = "276159213ddaaf82cd0e640cc7a77fc4";
         WalkerTestSpec spec1 = new WalkerTestSpec(
                 "-T GenotypeGVCFs --no_cmdline_in_header -L 1:1115550-1115551 -o %s -R " + hg19Reference +
                         " --variant " + privateTestDir + "combined_genotype_gvcf_exception.vcf",
@@ -212,7 +219,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseBPResolutionString("-nda"),
                 1,
-                Arrays.asList("7132a43d93a9855d03b27b4b0381194c"));
+                Arrays.asList("3c9c84b78e7d3b358c8cb7e29a2d302b"));
         executeTest("testNDA", spec);
     }
 
@@ -221,7 +228,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseBPResolutionString("-maxAltAlleles 1"),
                 1,
-                Arrays.asList("07844593a4e1ff1110ef8c1de42cc290"));
+                Arrays.asList("87ed70b8f910b662aa67e8ed1b2ed174"));
         executeTest("testMaxAltAlleles", spec);
     }
 
@@ -230,7 +237,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseBPResolutionString("-stand_call_conf 300 -stand_emit_conf 100"),
                 1,
-                Arrays.asList("56caad762b26479ba5e2cc99222b9030"));
+                Arrays.asList("1d98fb542a39090db3a8f89ae232e1e5"));
         executeTest("testStandardConf", spec);
     }
 
@@ -246,20 +253,16 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         "-variant_index_parameter 128000 -A StrandAlleleCountsBySample",
                 1, Arrays.asList("")
         );
-        specHaplotypeCaller.disableShadowBCF(); //TODO: Remove when BaseTest.assertAttributesEquals() works with SC
+        specHaplotypeCaller.disableShadowBCF(); //TODO: Remove when BaseTest.assertAttributesEquals() works with SAC
         final File gVCF = executeTest("testStrandAlleleCountsBySampleHaplotypeCaller", specHaplotypeCaller).getFirst().get(0);
-        List gVCFList = getAttributeValues(gVCF, new String("SAC"));
 
         //Use gVCF from HaplotypeCaller
         final WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -V " + gVCF.getAbsolutePath(), b37KGReference),
                 1,
-                Arrays.asList(""));
-        final File outputVCF = executeTest("testStrandAlleleCountsBySample", spec).getFirst().get(0);
-        List outputVCFList = getAttributeValues(outputVCF, new String("SAC"));
-
-        // All of the SAC values in the VCF were derived from the gVCF
-        Assert.assertTrue(gVCFList.containsAll(outputVCFList));
+                Arrays.asList("eeff965cd79c0b7085c7d4d7ecf82b68"));
+        spec.disableShadowBCF();  //TODO: Remove when BaseTest.assertAttributesEquals() works with SAC
+        executeTest("testStrandAlleleCountsBySample", spec);
     }
 
     @Test
@@ -274,7 +277,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V:combined2 " + privateTestDir + "combine.single.sample.pipeline.combined.vcf" +
                         " --uniquifySamples", b37KGReference),
                 1,
-                Arrays.asList("ba36b36145e038e3cb004adf11bce96c"));
+                Arrays.asList("b73f5bf5646695ca019d84d44c74c819"));
         executeTest("testUniquifiedSamples", spec);
 
     }
@@ -446,7 +449,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
     }
 
 
-    private static final String simpleSpanningDeletionsMD5 = "1cf4ea1da40306741ec4b9a5fe1568b9";
+    private static final String simpleSpanningDeletionsMD5 = "85c14341171548997e4503f7b5a9253f";
 
     @Test(enabled = true)
     public void testSpanningDeletionsMD5() {
@@ -476,7 +479,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                 "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                         " -V " + privateTestDir + "spanningDel.1.g.vcf -V " + privateTestDir + "spanningDel.2.g.vcf -V " + privateTestDir + "spanningDel.3.g.vcf",
                 1,
-                Arrays.asList("0aa7ceae6af1dc4fda6732e978ace864"));
+                Arrays.asList("6c5761ffb7a0c5252f3f5048d52f500e"));
         spec.disableShadowBCF();
         executeTest("testMultipleSpanningDeletionsMD5", spec);
     }
@@ -487,7 +490,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                 "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                         " -V " + privateTestDir + "spanningDel.delOnly.g.vcf",
                 1,
-                Arrays.asList("02cca337e097b86c5471929036ad4b64"));
+                Arrays.asList("c8414446dbac9a3639bfc2f347cc2c1d"));
         spec.disableShadowBCF();
         executeTest("testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles", spec);
     }
@@ -498,7 +501,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                 "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
                         " -V " + privateTestDir + "spanningDel.depr.delOnly.g.vcf",
                 1,
-                Arrays.asList("46169d08f93e5ff57856c7b64717314b"));
+                Arrays.asList("d1d8c3db65905b4ef79f960f9565ca94"));
         spec.disableShadowBCF();
         executeTest("testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles", spec);
     }
@@ -514,4 +517,89 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
         spec.disableShadowBCF();
         executeTest("testGenotypingSpanningDeletionOverSpan", spec);
     }
+
+    @Test(enabled = true)
+    public void testBadADPropagationHaploidBugTest() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
+                        " -V " + privateTestDir + "ad-bug-input.vcf",
+                1,
+                Arrays.asList("a8dcb9024e3701449ec2a1fe75e0d057"));
+        spec.disableShadowBCF();
+        executeTest("testBadADPropagationHaploidBugTest", spec);
+    }
+
+    @Test(enabled = true)
+    public void testSAC() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
+                        " -V " + privateTestDir + "261_S01_raw_variants_gvcf.vcf",
+                1,
+                Arrays.asList("01a9eee63801d46de8fcf1d6f80f8359"));
+        spec.disableShadowBCF();
+        executeTest("testSAC", spec);
+    }
+
+    @Test(enabled = true)
+    public void testSACMultisampleTetraploid() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
+                        " -V " + privateTestDir + "tetraploid-multisample-sac.g.vcf",
+                1,
+                Arrays.asList("8c79a16f6a524d49ff402b8c0b39b396"));
+        spec.disableShadowBCF();
+        executeTest("testSACMultisampleTetraploid", spec);
+    }
+
+    @Test(enabled = true)
+    public void testSetZeroRGQsToNoCall() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString(" -V " + privateTestDir + "set.zero.RGQs.no.call.sample1.g.vcf" +
+                        " -V " + privateTestDir + "set.zero.RGQs.no.call.sample2.g.vcf" +
+                        " -L chr16:1279274-1279874 -allSites", hg19ReferenceWithChrPrefixInChromosomeNames),
+                1,
+                Arrays.asList("75f6402da0f6b8b4e69c847fe8b5179a"));
+        executeTest("testSetZeroRGQsToNoCall", spec);
+    }
+
+    @Test
+         public void testAlleleSpecificAnnotations() {
+        final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V "
+                + privateTestDir + "NA12878.AS.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.chr20snippet.g.vcf";
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("35daaea8dea591d35ca99854c8d36e5f"));
+        spec.disableShadowBCF();
+        executeTest("testAlleleSpecificAnnotations", spec);
+    }
+
+    @Test
+    //make sure none of the assumptions about things being merged as lists break the single-sample case
+    //This test file also doesn't have raw data, so test to make sure that doesn't make GenotypeGVCFs crash and burn
+    //Note that AS_InbreedingCoeff and InbreedingCoeff may still differ for bialleleic sites for low number of samples because allele frequencies are derived differently
+    public void testAlleleSpecificAnnotations_oneSample() {
+        final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V "
+                + privateTestDir + "NA12878.AS.chr20snippet.g.vcf";
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("b6026b2a2d2da39f181a4905b2225dad"));
+        spec.disableShadowBCF();
+        executeTest("testAlleleSpecificAnnotations_oneSample", spec);
+    }
+
+    @Test
+    //do at least 10 samples so InbreedingCoeff and AS_InbreedingCoeff are output
+    public void testAlleleSpecificAnnotations_elevenSamples() {
+        final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V "
+                + privateTestDir + "multiSamples.g.vcf";
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("84b5723c9c8eeb5549aaceb4fd4053b5"));
+        spec.disableShadowBCF();
+        executeTest("testAlleleSpecificAnnotations_elevenSamples", spec);
+    }
+
+    @Test
+    public void testFractionInformativeReads() {
+        final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -G AS_Standard -o %s --no_cmdline_in_header -A FractionInformativeReads --disableDithering -V "
+                + privateTestDir + "NA12878.AS.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.chr20snippet.g.vcf";
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("794cfec86a8bee1f6955766b5a98b950"));
+        spec.disableShadowBCF();
+        executeTest("testAlleleSpecificAnnotations", spec);
+    }
+
 }
\ No newline at end of file
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java
index aa117ef9f..4b5d9979f 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -51,9 +51,14 @@
 
 package org.broadinstitute.gatk.tools.walkers.variantutils;
 
+import org.apache.commons.io.FileUtils;
+import org.apache.log4j.Level;
 import org.broadinstitute.gatk.engine.walkers.WalkerTest;
+import org.testng.Assert;
 import org.testng.annotations.Test;
 
+import java.io.File;
+import java.io.IOException;
 import java.util.Arrays;
 
 /**
@@ -66,17 +71,83 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest {
          WalkerTestSpec spec = new WalkerTestSpec(
                  "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "forLeftAlignVariantsTest.vcf --no_cmdline_in_header",
                  1,
-                 Arrays.asList("bcf05f56adbb32a47b6d6b27b327d5c2"));
+                 Arrays.asList("5d82f53b036d9a0fca170e5be68d5ab2"));
          executeTest("test left alignment", spec);
     }
 
     @Test
-    public void testLeftAlignmentWithTrimmingAndMultialleliecs() {
+    public void testLeftAlignmentLongAllelesError() throws IOException {
+
+        // Need to see log INFO messages
+        Level level = logger.getLevel();
+        logger.setLevel(Level.INFO);
+
+        File logFile = createTempFile("testLargeReferenceAlleleError.log", ".tmp");
+        String logFileName = logFile.getAbsolutePath();
+
         WalkerTestSpec spec = new WalkerTestSpec(
-                "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "forHardLeftAlignVariantsTest.vcf --no_cmdline_in_header -trim -split",
+                "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "longAlleles.vcf --no_cmdline_in_header -log " + logFileName,
                 1,
-                Arrays.asList("d12468cf08cfd14354f781d5f42b279f"));
-        executeTest("test left alignment with trimming and hard multiple alleles", spec);
+                Arrays.asList("136f88a5bd07a022a3404089359cb8ee"));
+        executeTest("test left alignment with long alleles with an error", spec);
+
+        // Make sure the "reference allele too long" message is in the log
+        Assert.assertTrue(FileUtils.readFileToString(logFile).contains(ValidateVariants.REFERENCE_ALLELE_TOO_LONG_MSG));
+
+        // Set the log level back
+        logger.setLevel(level);
+    }
+
+    @Test
+    public void testLeftAlignmentLongAllelesFix() throws IOException {
+
+        // Need to see log INFO messages
+        Level level = logger.getLevel();
+        logger.setLevel(Level.INFO);
+
+        File logFile = createTempFile("testLargeReferenceAlleleError.log", ".tmp");
+        String logFileName = logFile.getAbsolutePath();
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir +
+                        "longAlleles.vcf --no_cmdline_in_header --reference_window_stop 208 -log " + logFileName,
+                1,
+                Arrays.asList("c4ca5520ee499da171053059e3717b2f"));
+        executeTest("test left alignment with long alleles fix", spec);
+
+        // Make sure the "reference allele too long" message is in the log
+        Assert.assertFalse(FileUtils.readFileToString(logFile).contains(ValidateVariants.REFERENCE_ALLELE_TOO_LONG_MSG));
+
+        // Set the log level back
+        logger.setLevel(level);
+    }
+
+    @Test
+    public void testLeftAlignmentDontTrim() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "forLeftAlignVariantsTest.vcf --dontTrimAlleles --no_cmdline_in_header",
+                1,
+                Arrays.asList("dd238fe14b4a495a489907c1e021221e"));
+        executeTest("test left alignment, don't trim", spec);
+    }
+
+    @Test
+    public void testLeftAlignmentWithMultialleliecs() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "forHardLeftAlignVariantsTest.vcf --no_cmdline_in_header -split",
+                1,
+                Arrays.asList("534bea653d4a0e59e74f4107c1768558"));
+        executeTest("test left alignment with hard multiple alleles", spec);
+
+    }
+
+    @Test
+    public void testLeftAlignmentDontTrimWithMultialleliecs() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "forHardLeftAlignVariantsTest.vcf --dontTrimAlleles --no_cmdline_in_header -split",
+                1,
+                Arrays.asList("189b8136ee62b54bf7b227e99c892440"));
+        executeTest("test left alignment with hard multiple alleles, don't trim", spec);
 
     }
 }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java
index b9cfc0949..440582438 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java
index e24623998..9b78c08aa 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -134,7 +134,7 @@ public class PosteriorLikelihoodsUtilsUnitTest extends BaseTest {
     private VariantContext makeVC(String source, List alleles, Genotype... genotypes) {
         int start = 10;
         int stop = start; // alleles.contains(ATC) ? start + 3 : start;
-        return new VariantContextBuilder(source, "1", start, stop, alleles).genotypes(Arrays.asList(genotypes)).filters(null).make();
+        return new VariantContextBuilder(source, "1", start, stop, alleles).genotypes(Arrays.asList(genotypes)).filters((String)null).make();
     }
 
     @Test
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariantsIntegrationTest.java
index e8afa6250..b7adf675d 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariantsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariantsIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -66,7 +66,7 @@ public class RegenotypeVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T RegenotypeVariants -R " + b36KGReference + " --variant " + testFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("46ff472fc7ef6734ad01170028d5924a")
+                Arrays.asList("88118ebd39d6576aa1171082d8f37cd8")
         );
 
         executeTest("testRegenotype--" + testFile, spec);
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java
index dce5ff522..64636d182 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -52,6 +52,7 @@
 package org.broadinstitute.gatk.tools.walkers.variantutils;
 
 import org.broadinstitute.gatk.engine.walkers.WalkerTest;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
@@ -64,10 +65,10 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         return "-T SelectVariants -R " + b36KGReference + " -L 1 -o %s --no_cmdline_in_header" + args;
     }
 
-    private static final String SAMPLE_EXCLUSION_MD5 = "eea22fbf1e490e59389a663c3d6a6537";
-    private static final String INVERT_SELECTION_MD5 = "831bc0a5a723b0681a910d668ff3757b";
-    private static final String MAX_FILTERED_GT_SELECTION_MD5 = "0365de1bbf7c037be00badace0a74d02";
-    private static final String MIN_FILTERED_GT_SELECTION_MD5 = "fcee8c8caa0696a6675961bb12664878";
+    private static final String SAMPLE_EXCLUSION_MD5 = "2e52f21e7dcc67151a51630807a4eef2";
+    private static final String INVERT_SELECTION_MD5 = "26d192b868746ab14133f145ae812e7c";
+    private static final String MAX_FILTERED_GT_SELECTION_MD5 = "f83ac0deb7a8b022d6d40a85627a71ec";
+    private static final String MIN_FILTERED_GT_SELECTION_MD5 = "346620b7a5d66dabf89d3f42d6e27db7";
 
     @Test
     public void testDiscordanceNoSampleSpecified() {
@@ -78,7 +79,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
                         + b37hapmapGenotypes + " -disc " + testFile
                         + " -o %s --no_cmdline_in_header -U LENIENT_VCF_PROCESSING",
                 1,
-                Arrays.asList("954415f84996d27b07d00855e96d33a2")
+                Arrays.asList("9e08f761d2ba9a2bae9c279701aabc70")
         );
         spec.disableShadowBCF();
 
@@ -92,7 +93,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -sn A -sn B -sn C --variant " + testfile),
                 1,
-                Arrays.asList("125d1c9fa111cd38dfa2ff3900f16b57")
+                Arrays.asList("792962a5cc830e86dfc89caffbda1707")
         );
 
         executeTest("testRepeatedLineSelection--" + testfile, spec);
@@ -107,7 +108,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
                         + b37hapmapGenotypes + " -disc " + testFile
                         + " -o %s --no_cmdline_in_header -U LENIENT_VCF_PROCESSING",
                 1,
-                Arrays.asList("ca1b5226eaeaffb78d4abd9d2ee10c43")
+                Arrays.asList("c9aa80cabf036a268a032a61d398cdd5")
         );
         spec.disableShadowBCF();
 
@@ -122,7 +123,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile),
                 1,
-                Arrays.asList("4386fbb258dcef4437495a37f5a83c53")
+                Arrays.asList("8090c349d12549b437a80e29c285fdd5")
         );
         spec.disableShadowBCF();
         executeTest("testComplexSelection--" + testfile, spec);
@@ -136,7 +137,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" --ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES -sn A -se '[CDH]' -sn Z -sn T -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile),
                 1,
-                Arrays.asList("4386fbb258dcef4437495a37f5a83c53")
+                Arrays.asList("8090c349d12549b437a80e29c285fdd5")
         );
         spec.disableShadowBCF();
         executeTest("testComplexSelectionWithNonExistingSamples--" + testfile, spec);
@@ -149,7 +150,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -env -ef -select 'foo!=0||DP>0' --variant " + testfile),
                 1,
-                Arrays.asList("44e77cea624cfff2b8acc3a4b30485cb")    // should yield empty vcf because the foo!=0 will yield complete expression false
+                Arrays.asList("e7ec1f2c8077d07b54721e68b603d42c")    // should yield empty vcf because the foo!=0 will yield complete expression false
         );
         spec.disableShadowBCF();
         executeTest("testNonExistingSelection--" + testfile, spec);
@@ -166,7 +167,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -L 1:1-1000000 -o %s --no_cmdline_in_header -xl_sn A -xl_sf " + samplesFile + " --variant " + testfile,
                 1,
-                Arrays.asList("1f5c72951a35667c4bdf1be153787e27")
+                Arrays.asList("30aabc865634bf887cad0c02cdcde042")
         );
         spec.disableShadowBCF();
 
@@ -184,7 +185,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -L 1:1-1000000 -o %s --no_cmdline_in_header -xl_sf " + samplesFile + " --variant " + testfile,
                 1,
-                Arrays.asList("875d7e00ac8081e87ab9fb1b20c83677")
+                Arrays.asList("1afba8d53094bdef63db1e39d52be5aa")
         );
         spec.disableShadowBCF();
 
@@ -252,7 +253,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
                         + b37hapmapGenotypes + " --variant " + testFile
                         + " -o %s --no_cmdline_in_header -U LENIENT_VCF_PROCESSING",
                 1,
-                Arrays.asList("946e7f2e0ae08dc0e931c1634360fc46")
+                Arrays.asList("24114c01b81fc0052ee36523ccd1d338")
         );
         spec.disableShadowBCF();
 
@@ -269,7 +270,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -restrictAllelesTo MULTIALLELIC -selectType MIXED --variant " + testFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("2c50ab2ae96fae40bfc2b8398fc5e54e")
+                Arrays.asList("41dda9f4b9ec9f9b0f3593b2cbd82cd5")
         );
 
         executeTest("testVariantTypeSelection--" + testFile, spec);
@@ -285,7 +286,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -selectType INDEL --variant " + testFile + " -o %s --no_cmdline_in_header --maxIndelSize 2",
                 1,
-                Arrays.asList("2c50ab2ae96fae40bfc2b8398fc5e54e")
+                Arrays.asList("41dda9f4b9ec9f9b0f3593b2cbd82cd5")
         );
 
         executeTest("testMaxIndelLengthSelection--" + testFile, spec);
@@ -301,7 +302,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -selectType INDEL --variant " + testFile + " -o %s --no_cmdline_in_header --minIndelSize 2",
                 1,
-                Arrays.asList("fa5f3eb4f0fc5cedc93e6c519c0c8bcb")
+                Arrays.asList("ed9dc00d0551630a2eed9e81a2a357d3")
         );
 
         executeTest("testMinIndelLengthSelection--" + testFile, spec);
@@ -314,7 +315,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant:dbsnp " + testFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("a554459c9ccafb9812ff6d8c06c11726")
+                Arrays.asList("86d97e682b2dccff75d079f3b5d17f4b")
         );
 
         executeTest("testUsingDbsnpName--" + testFile, spec);
@@ -327,7 +328,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("a554459c9ccafb9812ff6d8c06c11726")
+                Arrays.asList("86d97e682b2dccff75d079f3b5d17f4b")
         );
 
         executeTest("testRemoveMLE--" + testFile, spec);
@@ -340,7 +341,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants --keepOriginalAC -R " + b36KGReference + " -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("ad7e8b25e431a3229a78cec063876559")
+                Arrays.asList("6f26cf5a7fd20682e1de193e5bb5f61f")
         );
 
         executeTest("testKeepOriginalAC--" + testFile, spec);
@@ -353,7 +354,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants --keepOriginalAC -env -trimAlternates -R " + b36KGReference + " -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("4695c99d96490ed4e5b1568c5b52dea6")
+                Arrays.asList("e0ac2b37387048bf51ac2914bdd2e178")
         );
 
         executeTest("testKeepOriginalACAndENV--" + testFile, spec);
@@ -366,7 +367,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants --keepOriginalDP -R " + b37KGReference + " -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("e897097a47aee5516dc4f1c0b9d69037")
+                Arrays.asList("ce5168e2eadee2550188892b1ea444be")
         );
 
         executeTest("testKeepOriginalDP--" + testFile, spec);
@@ -379,7 +380,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -select 'KG_FREQ < 0.5' --variant " + testFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("44f7c47395ca5b2afef5313f592c8cea")
+                Arrays.asList("bfbfefbd4a84b093ee0b63eab8cc1be9")
         );
 
         executeTest("testMultipleRecordsAtOnePosition--" + testFile, spec);
@@ -392,7 +393,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b37KGReference + " --variant " + testFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("ef3c5f75074a5dd2b2cd2715856a2542")
+                Arrays.asList("cc33eb41a821d9aebdfb99d309854db0")
         );
 
         executeTest("testNoGTs--" + testFile, spec);
@@ -405,7 +406,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b37KGReference + " -o %s --no_cmdline_in_header -sf " + samplesFile + " --excludeNonVariants -trimAlternates --variant " + testfile,
                 1,
-                Arrays.asList("69862fb97e8e895fe65c7abb14b03cee")
+                Arrays.asList("b86340de516d6c37cc3a2eeb3bfb4821")
         );
         executeTest("test select from multi allelic with excludeNonVariants --" + testfile, spec);
     }
@@ -417,7 +418,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
                 "-T SelectVariants -R " + b37KGReference + " -o %s --no_cmdline_in_header " +
                         "-sn SAMPLE-CC -sn SAMPLE-CT -sn SAMPLE-CA --excludeNonVariants --variant " + testfile,
                 1,
-                Arrays.asList("8fe7cdca8638461909262cb0769b2527")
+                Arrays.asList("7807bb2bf8c70963f65a97f30c8deb39")
         );
         executeTest("test multi allelic annotation ordering --" + testfile, spec);
     }
@@ -468,19 +469,19 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         final String testFile = privateTestDir + "forHardLeftAlignVariantsTest.vcf";
         final String cmd = "-T SelectVariants -R " + b37KGReference + " -sn NA12878 -env -trimAlternates "
                 + "-V " + testFile + " -o %s --no_cmdline_in_header";
-        WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("9df942000eb18b12d9008c7d9b5c4178"));
+        WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("354cd7aa25791465d0f4c7d53b81a3a3"));
         executeTest("testAlleleTrimming", spec);
     }
 
     @DataProvider(name="unusedAlleleTrimmingProvider")
     public Object[][] unusedAlleleTrimmingProvider() {
         return new Object[][] {
-                { privateTestDir+"forHardLeftAlignVariantsTest.vcf", "-trimAlternates", "9df942000eb18b12d9008c7d9b5c4178"},
-                { privateTestDir+"forHardLeftAlignVariantsTest.vcf", "", "981b757e3dc6bf3864ac7e493cf9d30d"},
-                { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT", "8ded359dd87fd498ff38736ea0fa4c28"},
-                { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env", "a7e7288dcd779cfac6983069de45b79c"},
-                { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -trimAlternates", "2e726d06a8d317199e8dda74691948a3"},
-                { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env -trimAlternates", "1e5585f86c347da271a79fbfc61ac849"}
+                { privateTestDir+"forHardLeftAlignVariantsTest.vcf", "-trimAlternates", "354cd7aa25791465d0f4c7d53b81a3a3"},
+                { privateTestDir+"forHardLeftAlignVariantsTest.vcf", "", "5e81af1825aa207b0a352f5eeb5db700"},
+                { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT", "339cca608ff18a355abc629bca448043"},
+                { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env", "3e8e2ebbc576ceee717a7ce80e23dd35"},
+                { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -trimAlternates", "8650d66b2199a4f8ce0acc660b2091cd"},
+                { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env -trimAlternates", "14538e17d5aca22c655c42e130f8cebc"}
         };
     }
 
@@ -603,7 +604,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -IDs " + idFile + " --variant " + testFile),
                 1,
-                Arrays.asList("2c50ab2ae96fae40bfc2b8398fc5e54e")
+                Arrays.asList("c6632b63617162455f02670174a2322a")
         );
         spec.disableShadowBCF();
         executeTest("testKeepSelectionID--" + testFile, spec);
@@ -611,6 +612,8 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
 
     /**
      * Test excluding variants with IDs
+     * Also tests --forceValidOutput flag, which changes the GQ from floats to ints to match
+     * header spec.
      */
     @Test
     public void testExcludeSelectionID() {
@@ -618,9 +621,9 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         String idFile = privateTestDir + "complexExample1.vcf.id";
 
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString(" -xlIDs " + idFile + " --variant " + testFile),
+                baseTestString(" -xlIDs " + idFile + " --variant " + testFile + " --forceValidOutput"),
                 1,
-                Arrays.asList("77514a81233e1bbc0f5e47b0fb76a89a")
+                Arrays.asList("613826acb415f05bf288536701a87855")
         );
         spec.disableShadowBCF();
         executeTest("testExcludeSelectionID--" + testFile, spec);
@@ -636,7 +639,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -xlSelectType SNP --variant " + testFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("fa5f3eb4f0fc5cedc93e6c519c0c8bcb")
+                Arrays.asList("ed9dc00d0551630a2eed9e81a2a357d3")
         );
 
         executeTest("testExcludeSelectionType--" + testFile, spec);
@@ -650,7 +653,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R "+b37KGReference + " -mv -mvq 0 --variant  " + testFile + " -ped " + pedFile + " -o %s  --no_cmdline_in_header",
                 1,
-                Arrays.asList("406243096074a417d2aa103bd3d13e01"));
+                Arrays.asList("f7fe7cbc84b3f2dfadcc40e19eeeb1f9"));
 
         executeTest("testMendelianViolationSelection--" + testFile, spec);
     }
@@ -663,9 +666,9 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R "+b37KGReference + " -mv -mvq 0 -invMv --variant  " + testFile + " -ped " + pedFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("35921fb2dedca0ead83027a66b725794"));
+                Arrays.asList("865418a69ee57be4432f248c027e6aff"));
 
-        executeTest("testMendelianViolationSelection--" + testFile, spec);
+        executeTest("testInvertMendelianViolationSelection--" + testFile, spec);
     }
 
     @Test
@@ -727,10 +730,45 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants --setFilteredGtToNocall -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("81b99386a64a8f2b857a7ef2bca5856e")
+                Arrays.asList("7771f07a9997296852ab367fac2c7a6c")
         );
 
         spec.disableShadowBCF();
         executeTest("testSetFilteredGtoNocall--" + testfile, spec);
     }
+    @Test
+    public void testSACSimpleDiploid() {
+        String testfile = privateTestDir + "261_S01_raw_variants_gvcf.vcf";
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T SelectVariants -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header -trimAlternates",
+                1,
+                Arrays.asList("c9d297e7758bf5681270029401cc97c2"));
+        spec.disableShadowBCF();
+        executeTest("testSACSimpleDiploid", spec);
+    }
+
+    @Test
+    public void testSACDiploid() {
+        String testfile = privateTestDir + "diploid-multisample-sac.g.vcf";
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T SelectVariants -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header -sn NA12891 -trimAlternates",
+                1,
+                Arrays.asList("7aecb079b16448f0377b6b03069b2994"));
+        spec.disableShadowBCF();
+        executeTest("testSACDiploid", spec);
+    }
+
+    @Test
+    public void testSACNonDiploid() {
+        String testfile = privateTestDir + "tetraploid-multisample-sac.g.vcf";
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T SelectVariants -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header -sn NA12891 -trimAlternates",
+                1,
+                ReviewedGATKException.class);
+        spec.disableShadowBCF();
+        executeTest("testSACNonDiploid", spec);
+    }
 }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsParallelIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsParallelIntegrationTest.java
index 8116b6b11..a6b020e41 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsParallelIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsParallelIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -90,17 +90,17 @@ public class SelectVariantsParallelIntegrationTest extends WalkerTest {
                 String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";
                 String samplesFile = validationDataLocation + "SelectVariants.samples.txt";
                 String args = " -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile;
-                new ParallelSelectTestProvider(b36KGReference, args, "4386fbb258dcef4437495a37f5a83c53", nt);
+                new ParallelSelectTestProvider(b36KGReference, args, "8090c349d12549b437a80e29c285fdd5", nt);
             }
             { // new tests on b37 using testdir VCF
                 final String testfile = privateTestDir + "NA12878.hg19.example1.vcf";
                 final String args = "-select 'DP > 30' -V " + testfile;
-                new ParallelSelectTestProvider(b37KGReference, args, "c64b45a14d41b1e5cddbe036b47e7519", nt);
+                new ParallelSelectTestProvider(b37KGReference, args, "b899cebdd30e6641437489b746301797", nt);
             }
             { // AD and PL decoding race condition
                 final String testfile = privateTestDir + "race_condition.vcf";
                 final String args = "-env -trimAlternates -sn SAMPLE -L 1:1-10,000,000 -V " + testfile;
-                new ParallelSelectTestProvider(b37KGReference, args, "e86c6eb105ecdd3ff026999ffc692821", nt);
+                new ParallelSelectTestProvider(b37KGReference, args, "ace613ed2e4929f448d30d85110d6ced", nt);
             }
         }
 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFStreamingIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFStreamingIntegrationTest.java
index 33b04a175..aa61d2c7e 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFStreamingIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFStreamingIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -87,7 +87,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
                     " --no_cmdline_in_header " +
                     " -o %s",
             1,
-            Arrays.asList("283f434b3efbebb8e10ed6347f97d104")
+            Arrays.asList("f9f6418698f967ba7ca451ac1fb4cc8d")
         );
 
         executeTest("testSimpleVCFStreaming", spec);
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariantsIntegrationTest.java
index 2721b5d47..7d2f2d0c6 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariantsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariantsIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -51,20 +51,25 @@
 
 package org.broadinstitute.gatk.tools.walkers.variantutils;
 
+import org.apache.commons.io.FileUtils;
+import org.apache.log4j.Level;
 import org.broadinstitute.gatk.engine.walkers.WalkerTest;
 import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.testng.Assert;
 import org.testng.annotations.Test;
 
+import java.io.File;
+import java.io.IOException;
 import java.util.Arrays;
 
 public class ValidateVariantsIntegrationTest extends WalkerTest {
 
-    protected static final String emptyMd5 = "d41d8cd98f00b204e9800998ecf8427e";
-    protected static final String defaultRegion = "1:10001292-10001303";
+    protected static final String EMPTY_MD5 = "d41d8cd98f00b204e9800998ecf8427e";
+    protected static final String DEFAULT_REGION = "1:10001292-10001303";
 
 
     public static String baseTestString(final String file, String type) {
-        return baseTestString(file,type,defaultRegion,b36KGReference);
+        return baseTestString(file,type,DEFAULT_REGION,b36KGReference);
     }
 
     public static String baseTestString(String file, String type, String region, String reference) {
@@ -88,7 +93,7 @@ public class ValidateVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString("validationExampleGood.vcf", "ALL"),
                 0,
-                Arrays.asList(emptyMd5)
+                Arrays.asList(EMPTY_MD5)
         );
 
         executeTest("test good file", spec);
@@ -175,7 +180,7 @@ public class ValidateVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString("validationExampleBad.vcf", "-ALL"),
                 0,
-                Arrays.asList(emptyMd5)
+                Arrays.asList(EMPTY_MD5)
         );
 
         executeTest("test no validation", spec);
@@ -184,18 +189,27 @@ public class ValidateVariantsIntegrationTest extends WalkerTest {
     @Test
     public void testComplexEvents() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString("complexEvents.vcf", "ALL"),
+                baseTestString("complexEvents.vcf", "ALL", DEFAULT_REGION, b37KGReference),
                 0,
-                Arrays.asList(emptyMd5)
+                Arrays.asList(EMPTY_MD5)
         );
 
         executeTest("test validating complex events", spec);
     }
 
+    @Test(description = "Checks out of order header contigs")
+    public void testOutOfOrderHeaderContigsError() {
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString("complexEvents-outOfOrder.vcf", "ALL", DEFAULT_REGION, b37KGReference),
+                0, UserException.LexicographicallySortedSequenceDictionary.class);
+        executeTest("test out of order header contigs error", spec);
+    }
+
     @Test(description = "Fixes '''bug''' reported in story https://www.pivotaltracker.com/story/show/68725164")
     public void testUnusedAlleleFix() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString("validationUnusedAllelesBugFix.vcf","-ALLELES","1:1-739000",b37KGReference),0,Arrays.asList(emptyMd5));
+                baseTestString("validationUnusedAllelesBugFix.vcf","-ALLELES","1:1-739000",b37KGReference),0,Arrays.asList(EMPTY_MD5));
         executeTest("test unused allele bug fix", spec);
     }
 
@@ -205,4 +219,76 @@ public class ValidateVariantsIntegrationTest extends WalkerTest {
                 baseTestString("validationUnusedAllelesBugFix.vcf","ALLELES","1:1-739000",b37KGReference),0, UserException.FailsStrictValidation.class);
         executeTest("test unused allele bug fix", spec);
     }
+
+    @Test(description = "Checks '''bug''' reported in issue https://github.com/broadinstitute/gsa-unstable/issues/963")
+    public void testLargeReferenceAlleleError() throws IOException {
+        // Need to see log INFO messages
+        Level level = logger.getLevel();
+        logger.setLevel(Level.INFO);
+
+        File logFile = createTempFile("testLargeReferenceAlleleError.log", ".tmp");
+        String logFileName = logFile.getAbsolutePath();
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString("longAlleles.vcf", "ALL", "1", b37KGReference) + " -log " + logFileName,
+                0, Arrays.asList(EMPTY_MD5));
+        executeTest("test long reference allele bug error", spec);
+
+        // Make sure the "reference allele too long" message is in the log
+        Assert.assertTrue(FileUtils.readFileToString(logFile).contains(ValidateVariants.REFERENCE_ALLELE_TOO_LONG_MSG));
+        
+        // Set the log level back
+        logger.setLevel(level);
+    }
+
+    @Test(description = "Checks '''bug''' is fixed, reported in issue https://github.com/broadinstitute/gsa-unstable/issues/963")
+    public void testLargeReferenceAlleleFix() throws IOException {
+        // Need to see log INFO messages
+        Level level = logger.getLevel();
+        logger.setLevel(Level.INFO);
+
+        File logFile = createTempFile("testLargeReferenceAllele.log", ".tmp");
+        String logFileName = logFile.getAbsolutePath();
+
+        // expand window for the large reference allele
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString("longAlleles.vcf","ALL","1",b37KGReference) + " --reference_window_stop 208 -log " + logFileName,
+                0, Arrays.asList(EMPTY_MD5));
+        executeTest("test long reference allele bug fix", spec);
+
+        // Make sure the "reference allele too long" message is not in the log
+        Assert.assertFalse(FileUtils.readFileToString(logFile).contains(ValidateVariants.REFERENCE_ALLELE_TOO_LONG_MSG));
+
+        // All of the validation tests have passed since UserException.FailsStrictValidation is not thrown.
+
+        // Set the log level back
+        logger.setLevel(level);
+    }
+
+    @Test(description = "Checks '''issue''' reported in issue https://github.com/broadinstitute/gsa-unstable/issues/964")
+    public void testWrongContigHeaderLengthError()  {
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString("longAlleles-wrongLength.vcf", "ALL", "1", b37KGReference),
+                0, UserException.IncompatibleSequenceDictionaries.class);
+        executeTest("test wrong header contig length error", spec);
+    }
+
+    @Test
+    public void testAllowWrongContigHeaderLengthDictIncompat()  {
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString("longAlleles-wrongLength.vcf", "ALL", "1", b37KGReference) + "  --reference_window_stop 208 -U ALLOW_SEQ_DICT_INCOMPATIBILITY ",
+                0, Arrays.asList(EMPTY_MD5));
+        executeTest("test to allow wrong header contig length, not checking dictionary incompatibility", spec);
+    }
+
+    @Test
+    public void testAllowWrongContigHeaderLength()  {
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString("longAlleles-wrongLength.vcf", "ALL", "1", b37KGReference) + "  --reference_window_stop 208 -U ",
+                0, Arrays.asList(EMPTY_MD5));
+        executeTest("test to allow wrong header contig length, no compatibility checks", spec);
+    }
 }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantContextMergerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantContextMergerUnitTest.java
index 642733d8f..a2b1b3f8b 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantContextMergerUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantContextMergerUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -52,6 +52,8 @@
 package org.broadinstitute.gatk.tools.walkers.variantutils;
 
 import htsjdk.variant.variantcontext.*;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine;
 import org.broadinstitute.gatk.utils.*;
 import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
@@ -65,6 +67,7 @@ import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 
 /**
@@ -103,7 +106,7 @@ public class VariantContextMergerUnitTest  extends BaseTest {
     @Test(dataProvider = "referenceConfidenceMergeData")
     public void testReferenceConfidenceMerge(final String testID, final List toMerge, final GenomeLoc loc,
                                              final boolean returnSiteEvenIfMonomorphic, final boolean uniquifySamples, final VariantContext expectedResult) {
-        final VariantContext result = ReferenceConfidenceVariantContextMerger.merge(toMerge, loc, returnSiteEvenIfMonomorphic ? (byte) 'A' : null, true, uniquifySamples);
+        final VariantContext result = ReferenceConfidenceVariantContextMerger.merge(toMerge, loc, returnSiteEvenIfMonomorphic ? (byte) 'A' : null, true, uniquifySamples, null);
         if ( result == null ) {
             Assert.assertTrue(expectedResult == null);
             return;
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantUtils.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantUtils.java
new file mode 100644
index 000000000..269527c4d
--- /dev/null
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantUtils.java
@@ -0,0 +1,99 @@
+/*
+* By downloading the PROGRAM you agree to the following terms of use:
+* 
+* BROAD INSTITUTE
+* SOFTWARE LICENSE AGREEMENT
+* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
+* 
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* 
+* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
+* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
+* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
+* 
+* 1. DEFINITIONS
+* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE.
+* 
+* 2. LICENSE
+* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation.
+* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
+* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
+* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
+* 
+* 3. PHONE-HOME FEATURE
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* 
+* 4. OWNERSHIP OF INTELLECTUAL PROPERTY
+* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
+* Copyright 2012-2015 Broad Institute, Inc.
+* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
+* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
+* 
+* 5. INDEMNIFICATION
+* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
+* 
+* 6. NO REPRESENTATIONS OR WARRANTIES
+* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
+* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+* 
+* 7. ASSIGNMENT
+* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
+* 
+* 8. MISCELLANEOUS
+* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
+* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
+* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
+* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
+* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
+* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
+* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
+*/
+
+package org.broadinstitute.gatk.tools.walkers.variantutils;
+
+import htsjdk.tribble.readers.LineIterator;
+import htsjdk.tribble.readers.PositionalBufferedStream;
+import htsjdk.variant.variantcontext.Genotype;
+import htsjdk.variant.variantcontext.VariantContext;
+import htsjdk.variant.vcf.VCFCodec;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+public class VariantUtils {
+
+    /**
+     * Returns a list of attribute values from a VCF file
+     *
+     * @param vcfFile VCF file
+     * @param attributeName attribute name
+     *
+     * @throws IOException if the file does not exist or can not be opened
+     *
+     * @return list of attribute values
+     */
+    public static List getAttributeValues(final File vcfFile, final String attributeName) throws IOException {
+        final VCFCodec codec = new VCFCodec();
+        final FileInputStream s = new FileInputStream(vcfFile);
+        final LineIterator lineIteratorVCF = codec.makeSourceFromStream(new PositionalBufferedStream(s));
+        codec.readHeader(lineIteratorVCF);
+
+        List attributeValues = new ArrayList();
+        while (lineIteratorVCF.hasNext()) {
+            final String line = lineIteratorVCF.next();
+            final VariantContext vc = codec.decode(line);
+
+            for (final Genotype g : vc.getGenotypes()) {
+                if (g.hasExtendedAttribute(attributeName)) {
+                    attributeValues.add((String) g.getExtendedAttribute(attributeName));
+                }
+            }
+        }
+
+        s.close();
+        return attributeValues;
+    }
+}
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/BaseCoverageDistributionIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantUtilsUnitTest.java
similarity index 79%
rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/BaseCoverageDistributionIntegrationTest.java
rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantUtilsUnitTest.java
index dd2f3bd55..2e1035209 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/BaseCoverageDistributionIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantUtilsUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -49,47 +49,26 @@
 * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
 */
 
-package org.broadinstitute.gatk.tools.walkers.diagnostics;
+package org.broadinstitute.gatk.tools.walkers.variantutils;
 
-import org.broadinstitute.gatk.engine.walkers.WalkerTest;
-import org.testng.annotations.DataProvider;
+import org.broadinstitute.gatk.engine.GATKVCFUtils;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.testng.Assert;
 import org.testng.annotations.Test;
 
+import java.io.File;
+import java.io.IOException;
 import java.util.Arrays;
+import java.util.List;
 
-/**
- * @author Mauricio Carneiro
- * @since 2/6/13
- */
-public class BaseCoverageDistributionIntegrationTest extends WalkerTest {
-    final static String REF = hg18Reference;
-    final String bam = validationDataLocation + "small_bam_for_countloci.withRG.bam";
+public class VariantUtilsUnitTest extends BaseTest {
 
-    @DataProvider(name = "BasicArguments")
-    public Object[][] basicArgumentsDataProvider() {
-        return new Object[][] {
-                // Tests simple counting on one interval with everything in the same contig including tallying of uncovered bases.
-                {"testSingleInterval ", "-L chr1:90000-100000", "45368696dc008d1a07fb2b05fbafd1f4"},
-                // Tests specially the tallying of uncovered bases across multiple intervals. Makes sure it's only adding the bases present in the intervals requested.
-                {"testMultipleIntervals ", "-L chr1:10-20 -L chr1:40-100 -L chr1:10,000-11,000 -L chr1:40,000-60,000 -L chr1:76,000-99,000 ", "45dafe59e5e54451b88c914d6ecbddc6"},
-                // Tests adding the entire genome around every covered base as uncovered. Especially tests the tally in the beginning and end of the run, adding up all chromosomes not visited (this test file only has reads on chr1).
-                {"testNoIntervals ", "", "c399f780f0b7da6be2614d837c368d1c"},
-
-                // the following three tests are equivalent but now include the filtered distribution option. These tests are aimed at the filtered distribution output.
-                {"testFilteredSingleInterval ", "-fd -L chr1:90000-100000", "7017cf191bf54e85111972a882e1d5fa"},
-                {"testFilteredMultipleIntervals ", "-fd -L chr1:10-20 -L chr1:40-100 -L chr1:10,000-11,000 -L chr1:40,000-60,000 -L chr1:76,000-99,000 ", "75d11cc02210676d6c19939fb0b9ab2e"},
-                {"testFilteredNoIntervals ", "-fd ", "e7abfa6c7be493de4557a64f66688148"},
-        };
+    @Test
+    public void testgetAttributeValues() throws IOException {
+        String pathname = privateTestDir + "261_S01_raw_variants_gvcf.vcf";
+        String attributeName = "SAC";
+        File vcfFile = new File(pathname);
+        List attributeValues = VariantUtils.getAttributeValues(vcfFile, attributeName);
+        Assert.assertEquals(attributeValues, Arrays.asList("33,43,25,23,0,0,0,0"));
     }
-
-    @Test(dataProvider = "BasicArguments", enabled = true)
-    private void BaseCoverageDistributionTest(String testName, String args, String md5) {
-        String base = String.format("-T BaseCoverageDistribution -R %s -I %s ", REF, bam) + " -o %s ";
-        WalkerTestSpec spec = new WalkerTestSpec(base + args, Arrays.asList(md5));
-        executeTest(testName, spec);
-    }
-
-
-
-
 }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitivesIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitivesIntegrationTest.java
index 874cfa928..dae526d31 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitivesIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitivesIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -66,7 +66,7 @@ public class VariantsToAllelicPrimitivesIntegrationTest extends WalkerTest {
          WalkerTestSpec spec = new WalkerTestSpec(
                  "-T VariantsToAllelicPrimitives -o %s -R " + b37KGReference + " -V " + privateTestDir + "vcfWithMNPs.vcf --no_cmdline_in_header",
                  1,
-                 Arrays.asList("c5333d2e352312bdb7c5182ca3009594"));
+                 Arrays.asList("db9929eef707d7dff0aef576f49e4a0d"));
          executeTest("test MNPs To SNPs", spec);
     }
 }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java
index 387c26021..61ef9991c 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTableIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTableIntegrationTest.java
index fd7cf737a..8d4474473 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTableIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTableIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCFIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCFIntegrationTest.java
index ff9b45b98..81cc0f26e 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCFIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCFIntegrationTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -70,7 +70,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
     @Test
     public void testVariantsToVCFUsingGeliInput() {
         List md5 = new ArrayList();
-        md5.add("22373883afa2221b5a4f75a50f30f26b");
+        md5.add("c73bcc3658b4a4d8bd9d794069d41dbd");
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +
@@ -88,7 +88,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
     @Test
     public void testGenotypesToVCFUsingGeliInput() {
         List md5 = new ArrayList();
-        md5.add("738eb66dbc400dcd1786cd9e49902e8c");
+        md5.add("a1771924b58dd633620114ef0f462acb");
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +
@@ -106,7 +106,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
     @Test
     public void testGenotypesToVCFUsingHapMapInput() {
         List md5 = new ArrayList();
-        md5.add("67656672acc264156f5a3e01e5cac61a");
+        md5.add("970157c9e15c53a6e50faaad41227487");
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +
@@ -123,7 +123,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
     @Test
     public void testGenotypesToVCFUsingVCFInput() {
         List md5 = new ArrayList();
-        md5.add("21084d32ce7ac5df3cee1730bfaaf71c");
+        md5.add("975830cb2bff58c7df426bbf09a08244");
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/ContigComparatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/ContigComparatorUnitTest.java
index 77d61eb5c..1509655cf 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/ContigComparatorUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/ContigComparatorUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/RandomDNA.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/RandomDNA.java
index 64ff70c24..49477f01d 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/RandomDNA.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/RandomDNA.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -62,8 +62,7 @@ import java.util.Random;
  *
  * @author Valentin Ruano-Rubio <valentin@broadinstitute.org>
  */
-public class
-        RandomDNA {
+public class RandomDNA {
 
     private Random random;
 
@@ -127,6 +126,22 @@ public class
         }
     }
 
+    /**
+     * Returns a single random base.
+     * @return any of 'A', 'C', 'G' or 'T'.
+     */
+    public byte nextBase() {
+        final int index = random.nextInt(4);
+        switch (index) {
+            case 0: return 'A';
+            case 1: return 'C';
+            case 2: return 'G';
+            case 3: return 'T';
+            default:
+                throw new IllegalStateException("this cannot be happening!!!");
+        }
+    }
+
     /**
      * Returns a random RNA sequence of bases.
      * @param size the length of the sequence.
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/CountSetUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/CountSetUnitTest.java
index f56e970a4..b7a76d1c8 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/CountSetUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/CountSetUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IndexedSetUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IndexedSetUnitTest.java
index 2dafcb70d..36acb38e7 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IndexedSetUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IndexedSetUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IntMaxHeapUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IntMaxHeapUnitTest.java
index aeab35ad4..d62c00a12 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IntMaxHeapUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IntMaxHeapUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffEngineUnitTest.java
index e00ac7e8e..d4056f927 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffEngineUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffEngineUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffNodeUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffNodeUnitTest.java
index 38252223a..e65fe4b27 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffNodeUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffNodeUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffableReaderUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffableReaderUnitTest.java
index e20ba1625..620b0f190 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffableReaderUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffableReaderUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DifferenceUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DifferenceUnitTest.java
index cee923476..e55b51a24 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DifferenceUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DifferenceUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotypeUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotypeUnitTest.java
index 502f4d1c3..360955cb2 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotypeUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotypeUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAlleleUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAlleleUnitTest.java
index bb816b11d..13972ae90 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAlleleUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAlleleUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java
index c62586753..5fddfdd1d 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriterUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriterUnitTest.java
index 28fe83d6c..9f2f0f398 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriterUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriterUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -90,6 +90,10 @@ public class GVCFWriterUnitTest extends BaseTest {
         public void add(VariantContext vc) {
             emitted.add(vc);
         }
+
+        public boolean checkError(){
+            return false;
+        }
     }
 
     private MockWriter mockWriter;
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/gvcf/HomRefBlockUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/gvcf/HomRefBlockUnitTest.java
index 88b5b6bbc..7b1f5c756 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/gvcf/HomRefBlockUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/gvcf/HomRefBlockUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java
index e2f703e01..93a5393de 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/CnyPairHMMUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/CnyPairHMMUnitTest.java
index 8e6958f9d..4393d134c 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/CnyPairHMMUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/CnyPairHMMUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMEmpiricalBenchmark.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMEmpiricalBenchmark.java
index 456daf365..fe6042771 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMEmpiricalBenchmark.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMEmpiricalBenchmark.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModelUnitTest.java
index 3d4865e38..3181b43c0 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModelUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModelUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMSyntheticBenchmark.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMSyntheticBenchmark.java
index 34ac9d983..21bd5670d 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMSyntheticBenchmark.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMSyntheticBenchmark.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMTestData.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMTestData.java
index 0fba905f7..aefd8dff2 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMTestData.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMTestData.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMUnitTest.java
index 1c34405b0..8cef47ea1 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentUnitTest.java
index 7ec12397b..e499d6139 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentUnitTest.java
@@ -25,7 +25,7 @@
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2014 Broad Institute, Inc.
+* Copyright 2012-2015 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/public/VectorPairHMM/src/main/c++/Sandbox.java b/public/VectorPairHMM/src/main/c++/Sandbox.java
index ae8497ea7..99c91d23b 100644
--- a/public/VectorPairHMM/src/main/c++/Sandbox.java
+++ b/public/VectorPairHMM/src/main/c++/Sandbox.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/external-example/src/main/java/org/mycompany/app/MyExampleWalker.java b/public/external-example/src/main/java/org/mycompany/app/MyExampleWalker.java
index 8dedbdd59..c6188df7d 100644
--- a/public/external-example/src/main/java/org/mycompany/app/MyExampleWalker.java
+++ b/public/external-example/src/main/java/org/mycompany/app/MyExampleWalker.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/external-example/src/test/java/org/mycompany/app/MyExampleWalkerIntegrationTest.java b/public/external-example/src/test/java/org/mycompany/app/MyExampleWalkerIntegrationTest.java
index c3461f23e..9f866bf08 100644
--- a/public/external-example/src/test/java/org/mycompany/app/MyExampleWalkerIntegrationTest.java
+++ b/public/external-example/src/test/java/org/mycompany/app/MyExampleWalkerIntegrationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/external-example/src/test/java/org/mycompany/app/MyExampleWalkerUnitTest.java b/public/external-example/src/test/java/org/mycompany/app/MyExampleWalkerUnitTest.java
index 56335f1f0..3c8ca6c81 100644
--- a/public/external-example/src/test/java/org/mycompany/app/MyExampleWalkerUnitTest.java
+++ b/public/external-example/src/test/java/org/mycompany/app/MyExampleWalkerUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineExecutable.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineExecutable.java
index a2bb4afd9..ceb2eda3d 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineExecutable.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineExecutable.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java
index 328960390..9f6c16edc 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GATKVCFUtils.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GATKVCFUtils.java
index 4d05d824e..c1daca1e7 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GATKVCFUtils.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GATKVCFUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java
index 3117d3c57..be2bf610a 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -642,7 +642,7 @@ public class GenomeAnalysisEngine {
         // If reads are present, assume that accessing the reads is always the dominant factor and shard based on that supposition.
         if(!readsDataSource.isEmpty()) {
             if(!readsDataSource.hasIndex() && !exclusions.contains(ValidationExclusion.TYPE.ALLOW_UNINDEXED_BAM))
-                throw new UserException.CommandLineException("Cannot process the provided BAM file(s) because they were not indexed.  The GATK does offer limited processing of unindexed BAMs in --unsafe mode, but this GATK feature is currently unsupported.");
+                throw new UserException.CommandLineException("Cannot process the provided BAM/CRAM file(s) because they were not indexed.  The GATK does offer limited processing of unindexed BAM/CRAMs in --unsafe mode, but this feature is unsupported -- use it at your own risk!");
             if(!readsDataSource.hasIndex() && intervals != null && !argCollection.allowIntervalsWithUnindexedBAM)
                 throw new UserException.CommandLineException("Cannot perform interval processing when reads are present but no index is available.");
 
@@ -886,8 +886,8 @@ public class GenomeAnalysisEngine {
             // Compile a set of sequence names that exist in the BAM files.
             SAMSequenceDictionary readsDictionary = reads.getHeader().getSequenceDictionary();
 
-            if (readsDictionary.size() == 0) {
-                logger.info("Reads file is unmapped.  Skipping validation against reference.");
+            if (readsDictionary.isEmpty()) {
+                logger.info("Reads file is unmapped. Skipping validation against reference.");
                 return;
             }
 
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/ReadMetrics.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/ReadMetrics.java
index 0f00bd668..f391b45f5 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/ReadMetrics.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/ReadMetrics.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/ReadProperties.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/ReadProperties.java
index 0f6aee60c..5e4a3559d 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/ReadProperties.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/ReadProperties.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/SampleUtils.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/SampleUtils.java
index eb98e0bb4..838a4ae24 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/SampleUtils.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/SampleUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/WalkerManager.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/WalkerManager.java
index 0660cb015..c0008c32f 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/WalkerManager.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/WalkerManager.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/Aligner.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/Aligner.java
index e9622c931..eb403c610 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/Aligner.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/Aligner.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/Alignment.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/Alignment.java
index 02bc06fa0..2b2c6b12a 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/Alignment.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/Alignment.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAAligner.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAAligner.java
index 2668b8ce7..d9924c70d 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAAligner.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAAligner.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAConfiguration.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAConfiguration.java
index b533a0d33..54e63e4cc 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAConfiguration.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAConfiguration.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWTFiles.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWTFiles.java
index 16cc4adac..f5a337bfa 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWTFiles.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWTFiles.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignerTestHarness.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignerTestHarness.java
index 91e41e5b3..50981a355 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignerTestHarness.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignerTestHarness.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentMatchSequence.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentMatchSequence.java
index f1148c6c2..f3ba0e4fe 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentMatchSequence.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentMatchSequence.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentState.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentState.java
index f4ba1bb9e..4331b9667 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentState.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentState.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAAlignment.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAAlignment.java
index 88ef4a557..34be0f885 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAAlignment.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAAlignment.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAJavaAligner.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAJavaAligner.java
index 09a5b4584..40dfc030b 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAJavaAligner.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAJavaAligner.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/LowerBound.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/LowerBound.java
index e5e292bd8..04e165e28 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/LowerBound.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/LowerBound.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/package-info.java
index 5a6d70d21..0daa83e79 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/package-info.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/package-info.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/AMBWriter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/AMBWriter.java
index b090bab0e..90e6b97d1 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/AMBWriter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/AMBWriter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/ANNWriter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/ANNWriter.java
index 123b3ca1f..7619d4102 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/ANNWriter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/ANNWriter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWT.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWT.java
index 7d0c43b4a..dedb71d48 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWT.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWT.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTReader.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTReader.java
index 9b28e2a42..956f1e9bb 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTReader.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTReader.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTSupplementaryFileGenerator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTSupplementaryFileGenerator.java
index e60a78bd4..551cf1a7e 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTSupplementaryFileGenerator.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTSupplementaryFileGenerator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTWriter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTWriter.java
index 4f2a15945..636412dbd 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTWriter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTWriter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Bases.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Bases.java
index d0cd84994..d6fa7bd70 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Bases.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Bases.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Counts.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Counts.java
index c6684b5ad..66ff7e392 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Counts.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Counts.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/CreateBWTFromReference.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/CreateBWTFromReference.java
index baa5ebefc..b9775b274 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/CreateBWTFromReference.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/CreateBWTFromReference.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SequenceBlock.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SequenceBlock.java
index 555e7ccb4..f4d13024e 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SequenceBlock.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SequenceBlock.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArray.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArray.java
index d1edfe5cb..f052ee3c7 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArray.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArray.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayReader.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayReader.java
index dc8cdc0c1..9bc95e173 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayReader.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayReader.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayWriter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayWriter.java
index df152b90a..b98da8cee 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayWriter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayWriter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedInputStream.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedInputStream.java
index 727a378d6..f94c351a7 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedInputStream.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedInputStream.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedOutputStream.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedOutputStream.java
index b3dbba893..e14ce625b 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedOutputStream.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedOutputStream.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/CreatePACFromReference.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/CreatePACFromReference.java
index fac3d92ff..057342c50 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/CreatePACFromReference.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/CreatePACFromReference.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/PackUtils.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/PackUtils.java
index e60780a64..4b64c03a6 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/PackUtils.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/PackUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedInputStream.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedInputStream.java
index 060050047..5eed18d5e 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedInputStream.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedInputStream.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedOutputStream.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedOutputStream.java
index 44c462b89..b9d94b640 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedOutputStream.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedOutputStream.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/DbsnpArgumentCollection.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/DbsnpArgumentCollection.java
index 05ebffa07..39247f5b4 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/DbsnpArgumentCollection.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/DbsnpArgumentCollection.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java
index 4fec3e240..0601034df 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -50,21 +50,24 @@ import java.util.concurrent.TimeUnit;
  */
 public class GATKArgumentCollection {
 
+    // the default value of the stop of the expanded window
+    public static final int DEFAULT_REFERENCE_WINDOW_STOP = 0;
+
     /** the constructor */
     public GATKArgumentCollection() {
     }
 
     // parameters and their defaults
     /**
-     * An input file containing sequence data mapped to a reference, in SAM or BAM format, or a text file containing a
-     * list of input files (with extension .list). Note that the GATK requires an accompanying index for each SAM or
-     * BAM file. Please see our online documentation for more details on input formatting requirements.
+     * An input file containing sequence data mapped to a reference, in BAM or CRAM format, or a text file containing a
+     * list of input files (with extension .list). Note that the GATK requires an accompanying .bai index for each BAM
+     * or CRAM file. Please see our online documentation for more details on input formatting requirements.
      */
-    @Input(fullName = "input_file", shortName = "I", doc = "Input file containing sequence data (SAM or BAM)", required = false)
+    @Input(fullName = "input_file", shortName = "I", doc = "Input file containing sequence data (BAM or CRAM)", required = false)
     public List samFiles = new ArrayList<>();
 
     @Advanced
-    @Argument(fullName = "showFullBamList",doc="Emit a log entry (level INFO) containing the full list of sequence data files to be included in the analysis (including files inside .bam.list files).")
+    @Argument(fullName = "showFullBamList",doc="Emit a log entry (level INFO) containing the full list of sequence data files to be included in the analysis (including files inside .bam.list or .cram.list files).")
     public Boolean showFullBamList = false;
 
     @Advanced
@@ -278,8 +281,8 @@ public class GATKArgumentCollection {
     public boolean FIX_MISENCODED_QUALS = false;
     /**
      * This flag tells GATK to ignore warnings when encountering base qualities that are too high and that seemingly
-     * indicate a problem with the base quality encoding of the BAM file. You should only use this if you really know
-     * what you are doing; otherwise you could seriously mess up your data and ruin your analysis.
+     * indicate a problem with the base quality encoding of the BAM or CRAM file. You should only use this if you really
+     * know what you are doing; otherwise you could seriously mess up your data and ruin your analysis.
      */
     @Argument(fullName = "allow_potentially_misencoded_quality_scores", shortName="allowPotentiallyMisencodedQuals", doc="Ignore warnings about base quality score encoding", required = false)
     public boolean ALLOW_POTENTIALLY_MISENCODED_QUALS = false;
@@ -320,7 +323,8 @@ public class GATKArgumentCollection {
     /**
      * Enables on-the-fly recalibrate of base qualities, intended primarily for use with BaseRecalibrator and PrintReads
      * (see Best Practices workflow documentation). The covariates tables are produced by the BaseRecalibrator tool.
-     * Please be aware that you should only run recalibration with the covariates file created on the same input bam(s).
+     * Please be aware that you should only run recalibration with the covariates file created on the same input BAM(s)
+     * or CRAM(s).
      */
     @Input(fullName="BQSR", shortName="BQSR", required=false, doc="Input covariates table file for on-the-fly base quality score recalibration")
     public File BQSR_RECAL_FILE = null;
@@ -332,10 +336,27 @@ public class GATKArgumentCollection {
      * Any value greater than zero will be used to recalculate the quantization using that many levels.
      * Negative values mean that we should quantize using the recalibration report's quantization level.
      */
-    @Advanced
     @Argument(fullName="quantize_quals", shortName = "qq", doc = "Quantize quality scores to a given number of levels (with -BQSR)", required=false)
     public int quantizationLevels = 0;
 
+    /**
+     * Static quantized quals are entirely separate from the quantize_qual option which uses dynamic binning.
+     * The two types of binning should not be used together.
+     */
+    @Advanced
+    @Argument(fullName="static_quantized_quals", shortName = "SQQ", doc = "Use static quantized quality scores to a given number of levels (with -BQSR)", required=false,  exclusiveOf = "quantize_quals", minValue = QualityUtils.MIN_USABLE_Q_SCORE, maxValue = QualityUtils.MAX_QUAL)
+    public List staticQuantizationQuals = null;
+
+    /**
+     * Round down quantized only works with the static_quantized_quals option, and should not be used with
+     * the dynamic binning option provided by quantize_quals.  When roundDown = false, rounding is done in
+     * probability space to the nearest bin.  When roundDown = true, the value is rounded to the nearest bin
+     * that is smaller than the current bin.
+     */
+    @Hidden
+    @Argument(fullName="round_down_quantized", shortName = "RDQ", doc = "Round quals down to nearest quantized qual", required=false, exclusiveOf="quantize_quals")
+    public boolean roundDown = false;
+
     /**
      * Turns off printing of the base insertion and base deletion tags when using the -BQSR argument. Only the base substitution qualities will be produced.
      */
@@ -343,14 +364,14 @@ public class GATKArgumentCollection {
     public boolean disableIndelQuals = false;
 
     /**
-     * By default, the OQ tag in not emitted when using the -BQSR argument. Use this flag to include OQ tags in the output BAM file.
+     * By default, the OQ tag in not emitted when using the -BQSR argument. Use this flag to include OQ tags in the output BAM or CRAM file.
      * Note that this may results in significant file size increase.
      */
     @Argument(fullName="emit_original_quals", shortName = "EOQ", doc = "Emit the OQ tag with the original base qualities (with -BQSR)", required=false)
     public boolean emitOriginalQuals = false;
 
     /**
-     * This flag tells GATK not to modify quality scores less than this value. Instead they will be written out unmodified in the recalibrated BAM file.
+     * This flag tells GATK not to modify quality scores less than this value. Instead they will be written out unmodified in the recalibrated BAM or CRAM file.
      * In general it's unsafe to change qualities scores below < 6, since base callers use these values to indicate random or bad bases.
      * For example, Illumina writes Q2 bases when the machine has really gone wrong. This would be fine in and of itself,
      * but when you select a subset of these reads based on their ability to align to the reference and their dinucleotide effect,
@@ -379,7 +400,7 @@ public class GATKArgumentCollection {
     @Argument(fullName = "validation_strictness", shortName = "S", doc = "How strict should we be with validation", required = false)
     public ValidationStringency strictnessLevel = ValidationStringency.SILENT;
     /**
-     * Some tools keep program records in the SAM header by default. Use this argument to override that behavior and discard program records for the SAM header.
+     * Some tools keep program records in the SAM header by default. Use this argument to override that behavior and discard program records for the SAM header. Does not work on CRAM files.
      */
     @Argument(fullName = "remove_program_records", shortName = "rpr", doc = "Remove program records from the SAM header", required = false)
     public boolean removeProgramRecords = false;
@@ -390,12 +411,12 @@ public class GATKArgumentCollection {
     public boolean keepProgramRecords = false;
 
     /**
-     * On-the-fly sample renaming works only with single-sample BAM and VCF files. Each line of the mapping file must
-     * contain the absolute path to a BAM or VCF file, followed by whitespace, followed by the new sample name for that
-     * BAM or VCF file. The sample name may contain non-tab whitespace, but leading or trailing whitespace will be 
-     * ignored. The engine will verify at runtime that each BAM/VCF targeted for sample renaming has only a single 
-     * sample specified in its header (though, in the case of BAM files, there may be multiple read groups for that 
-     * sample).
+     * On-the-fly sample renaming works only with single-sample BAM, CRAM, and VCF files. Each line of the mapping file
+     * must contain the absolute path to a BAM, CRAM, or VCF file, followed by whitespace, followed by the new sample
+     * name for that BAM, CRAM, or VCF file. The sample name may contain non-tab whitespace, but leading or trailing
+     * whitespace will be ignored. The engine will verify at runtime that each BAM/CRAM/VCF targeted for sample
+     * renaming has only a single sample specified in its header (though, in the case of BAM/CRAM files, there may be
+     * multiple read groups for that sample).
      */
     @Advanced
     @Argument(fullName = "sample_rename_mapping_file", shortName = "sample_rename_mapping_file", doc = "Rename sample IDs on-the-fly at runtime using the provided mapping file", required = false)
@@ -453,12 +474,12 @@ public class GATKArgumentCollection {
 
     @Advanced
     @Argument(fullName = "simplifyBAM", shortName = "simplifyBAM",
-              doc = "If provided, output BAM files will be simplified to include just key reads for downstream variation discovery analyses (removing duplicates, PF-, non-primary reads), as well stripping all extended tags from the kept reads except the read group identifier",
+              doc = "If provided, output BAM/CRAM files will be simplified to include just key reads for downstream variation discovery analyses (removing duplicates, PF-, non-primary reads), as well stripping all extended tags from the kept reads except the read group identifier",
               required = false)
     public boolean simplifyBAM = false;
 
     @Advanced
-    @Argument(fullName = "disable_bam_indexing", doc = "Turn off on-the-fly creation of indices for output BAM files.",
+    @Argument(fullName = "disable_bam_indexing", doc = "Turn off on-the-fly creation of indices for output BAM/CRAM files.",
             required = false)
     public boolean disableBAMIndexing = false;
 
@@ -488,7 +509,7 @@ public class GATKArgumentCollection {
     @Argument(fullName="num_cpu_threads_per_data_thread", shortName = "nct", doc="Number of CPU threads to allocate per data thread", required = false, minValue = 1)
     public int numberOfCPUThreadsPerDataThread = 1;
 
-    @Argument(fullName="num_io_threads", shortName = "nit", doc="Number of given threads to allocate to IO", required = false, minValue = 0)
+    @Argument(fullName="num_io_threads", shortName = "nit", doc="Number of given threads to allocate to BAM IO", required = false, minValue = 0)
     @Hidden
     public int numberOfIOThreads = 0;
 
@@ -500,7 +521,8 @@ public class GATKArgumentCollection {
     @Argument(fullName = "monitorThreadEfficiency", shortName = "mte", doc = "Enable threading efficiency monitoring", required = false)
     public Boolean monitorThreadEfficiency = false;
 
-    @Argument(fullName = "num_bam_file_handles", shortName = "bfh", doc="Total number of BAM file handles to keep open simultaneously", required=false, minValue = 1)
+    @Argument(fullName = "num_bam_file_handles", shortName = "bfh", doc="When using IO threads, total number of BAM file handles to keep open simultaneously", required=false, minValue = 1)
+    @Hidden
     public Integer numberOfBAMFileHandles = null;
     /**
      * This will filter out read groups matching : (e.g. SM:sample1) or a .txt file containing the filter strings one per line.
@@ -598,7 +620,7 @@ public class GATKArgumentCollection {
     /**
      * NO INTEGRATION TESTS are available.  Use at your own risk.
      */
-    @Argument(fullName="allow_intervals_with_unindexed_bam",doc="Allow interval processing with an unsupported BAM",required=false)
+    @Argument(fullName="allow_intervals_with_unindexed_bam",doc="Allow interval processing with an unsupported BAM/CRAM",required=false)
     @Hidden
     public boolean allowIntervalsWithUnindexedBAM = false;
 
@@ -642,5 +664,17 @@ public class GATKArgumentCollection {
     @Argument(fullName="variant_index_parameter",shortName = "variant_index_parameter",doc="Parameter to pass to the VCF/BCF IndexCreator",required=false)
     @Advanced
     public int variant_index_parameter = GATKVCFUtils.DEFAULT_INDEX_PARAMETER;
+
+    // --------------------------------------------------------------------------------------------------------------
+    //
+    // Window arguments
+    //
+    // -------------------------------------------------------------------------------------------------------------
+    /**
+     * Stop of the expanded window for which the reference context should be provided, relative to the locus.
+     */
+    @Argument(fullName = "reference_window_stop", shortName = "ref_win_stop", doc = "Reference window stop", minValue = 0, required = false)
+    @Advanced
+    public int reference_window_stop = DEFAULT_REFERENCE_WINDOW_STOP;
 }
 
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/StandardVariantContextInputArgumentCollection.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/StandardVariantContextInputArgumentCollection.java
index 331029f52..ff8da29db 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/StandardVariantContextInputArgumentCollection.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/StandardVariantContextInputArgumentCollection.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/crypt/CryptUtils.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/crypt/CryptUtils.java
index cbbbe47e1..d7696d6ca 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/crypt/CryptUtils.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/crypt/CryptUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/crypt/GATKKey.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/crypt/GATKKey.java
index 42a88b9d0..3260476eb 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/crypt/GATKKey.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/crypt/GATKKey.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/package-info.java
index 680da25bb..71a1af2a1 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/package-info.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/package-info.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusView.java
index 4bcecbcad..865a72b7b 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusView.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusView.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusView.java
index 777e23cb8..6d961a370 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusView.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusView.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalOverlappingRODsFromStream.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalOverlappingRODsFromStream.java
index 1525c381a..1eb58a1d0 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalOverlappingRODsFromStream.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalOverlappingRODsFromStream.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedView.java
index 4dfc31d86..659a2c7ed 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedView.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedView.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/InvalidPositionException.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/InvalidPositionException.java
index 997435d84..b00d1c664 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/InvalidPositionException.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/InvalidPositionException.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceView.java
index d4278c9b2..ede909e92 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceView.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceView.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -26,6 +26,7 @@
 package org.broadinstitute.gatk.engine.datasources.providers;
 
 import htsjdk.samtools.reference.ReferenceSequence;
+import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection;
 import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
 import org.broadinstitute.gatk.engine.walkers.Reference;
 import org.broadinstitute.gatk.engine.walkers.Walker;
@@ -74,7 +75,7 @@ public class LocusReferenceView extends ReferenceView {
 
 
     /**
-     * Start of the expanded window for which the reference context should be provided,
+     * Stop of the expanded window for which the reference context should be provided,
      * relative to the locus in question.
      */
     private final int windowStop;
@@ -99,10 +100,11 @@ public class LocusReferenceView extends ReferenceView {
 
     /**
      * Create a new locus reference view.
+     * @param walker input walker
      * @param provider source for locus data.
      */
     public LocusReferenceView( Walker walker, LocusShardDataProvider provider ) {
-        super( provider );
+        super(provider);
         initializeBounds(provider);
 
         // Retrieve information about the window being accessed.
@@ -113,11 +115,22 @@ public class LocusReferenceView extends ReferenceView {
             if( window.stop() < 0 ) throw new ReviewedGATKException( "Reference window ends before current locus" );
 
             windowStart = window.start();
-            windowStop = window.stop();
+
+            if ( walker.getArguments() == null ){
+                windowStop = window.stop();
+            } else {
+                // Use reference arguments if set, otherwise use the annotation
+                windowStop = walker.getArguments().reference_window_stop != GATKArgumentCollection.DEFAULT_REFERENCE_WINDOW_STOP ?
+                        walker.getArguments().reference_window_stop : window.stop();
+            }
         }
         else {
             windowStart = 0;
-            windowStop = 0;
+            if ( walker.getArguments() == null ){
+                windowStop = 0;
+            } else {
+                windowStop = walker.getArguments().reference_window_stop;
+            }
         }
 
         if(bounds != null) {
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusShardDataProvider.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusShardDataProvider.java
index 7dc589da7..bcb148b92 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusShardDataProvider.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusShardDataProvider.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusView.java
index 11437cf2c..78262b560 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusView.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/LocusView.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ManagingReferenceOrderedView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ManagingReferenceOrderedView.java
index 17e8c4290..bb5fcdd92 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ManagingReferenceOrderedView.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ManagingReferenceOrderedView.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RODMetaDataContainer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RODMetaDataContainer.java
index 197abd49a..419898581 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RODMetaDataContainer.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RODMetaDataContainer.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadBasedReferenceOrderedView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadBasedReferenceOrderedView.java
index dea8acf5f..ae555c3ee 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadBasedReferenceOrderedView.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadBasedReferenceOrderedView.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceView.java
index c7b2575be..6687ee658 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceView.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceView.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadShardDataProvider.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadShardDataProvider.java
index f9629f5c8..541787f49 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadShardDataProvider.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadShardDataProvider.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadView.java
index ec879fdfd..5c6bf31e4 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadView.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReadView.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedView.java
index 3be983d4a..93a2e0aec 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedView.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedView.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceView.java
index 2eade15e2..870d5bafa 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceView.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceView.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RodLocusView.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RodLocusView.java
index 297ccbedd..269cb6f0a 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RodLocusView.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/RodLocusView.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProvider.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProvider.java
index a36bee579..99ad5a577 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProvider.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProvider.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/View.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/View.java
index f628bb47c..1611778d9 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/View.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/View.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/package-info.java
index bc8a60251..db2aabe1c 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/package-info.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/providers/package-info.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancer.java
index efe6336ad..cc3fcd185 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancer.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancer.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMAccessPlan.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMAccessPlan.java
index 178d440bf..259c77b3c 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMAccessPlan.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMAccessPlan.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMSchedule.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMSchedule.java
index aca33e411..71db6022c 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMSchedule.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMSchedule.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMScheduler.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMScheduler.java
index f916bc185..047477905 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMScheduler.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BAMScheduler.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BGZFBlockLoadingDispatcher.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BGZFBlockLoadingDispatcher.java
index cc1d9e9a4..acb931130 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BGZFBlockLoadingDispatcher.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BGZFBlockLoadingDispatcher.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockInputStream.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockInputStream.java
index 125d4f731..84c55e434 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockInputStream.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockInputStream.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockLoader.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockLoader.java
index 09a0cab2a..b26297d02 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockLoader.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/BlockLoader.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FileHandleCache.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FileHandleCache.java
index 7f6653888..1765b7b78 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FileHandleCache.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FileHandleCache.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointer.java
index 4ea4aabf9..78b6eab68 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointer.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointer.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndex.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndex.java
index 3b94e438a..b1d54d2b1 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndex.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndex.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -25,12 +25,10 @@
 
 package org.broadinstitute.gatk.engine.datasources.reads;
 
-import htsjdk.samtools.Bin;
-import htsjdk.samtools.GATKBin;
-import htsjdk.samtools.GATKChunk;
-import htsjdk.samtools.LinearIndex;
+import htsjdk.samtools.*;
 import htsjdk.samtools.seekablestream.SeekableBufferedStream;
 import htsjdk.samtools.seekablestream.SeekableFileStream;
+import htsjdk.samtools.seekablestream.SeekableStream;
 import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 import org.broadinstitute.gatk.utils.exceptions.UserException;
 
@@ -70,10 +68,11 @@ public class GATKBAMIndex {
      */
     public static final int MAX_BINS = 37450;   // =(8^6-1)/7+1
 
+    private final SAMSequenceDictionary sequenceDictionary;
     private final File mFile;
 
     //TODO: figure out a good value for this buffer size
-    private final int BUFFERED_STREAM_BUFFER_SIZE = 8192;
+    private static final int BUFFERED_STREAM_BUFFER_SIZE = 8192;
 
     /**
      * Number of sequences stored in this index.
@@ -86,11 +85,14 @@ public class GATKBAMIndex {
     private final long[] sequenceStartCache;
 
     private SeekableFileStream fileStream;
+    private SeekableStream baiStream;
     private SeekableBufferedStream bufferedStream;
     private long fileLength;
 
-    public GATKBAMIndex(final File file) {
+    public GATKBAMIndex(final File file, final SAMSequenceDictionary sequenceDictionary) {
         mFile = file;
+        this.sequenceDictionary = sequenceDictionary;
+
         // Open the file stream.
         openIndexFile();
 
@@ -127,12 +129,12 @@ public class GATKBAMIndex {
         skipToSequence(referenceSequence);
 
         int binCount = readInteger();
-        List bins = new ArrayList();
+        List bins = new ArrayList<>();
         for (int binNumber = 0; binNumber < binCount; binNumber++) {
             final int indexBin = readInteger();
             final int nChunks = readInteger();
 
-            List chunks = new ArrayList(nChunks);
+            List chunks = new ArrayList<>(nChunks);
             long[] rawChunkData = readLongs(nChunks*2);
             for (int ci = 0; ci < nChunks; ci++) {
                 final long chunkBegin = rawChunkData[ci*2];
@@ -289,7 +291,8 @@ public class GATKBAMIndex {
             final int nBins = readInteger();
             // System.out.println("# nBins: " + nBins);
             for (int j = 0; j < nBins; j++) {
-                final int bin = readInteger();
+                /* final int bin = */
+                readInteger();
                 final int nChunks = readInteger();
                 // System.out.println("# bin[" + j + "] = " + bin + ", nChunks = " + nChunks);
                 skipBytes(16 * nChunks);
@@ -308,7 +311,8 @@ public class GATKBAMIndex {
     private void openIndexFile() {
         try {
             fileStream = new SeekableFileStream(mFile);
-            bufferedStream = new SeekableBufferedStream(fileStream,BUFFERED_STREAM_BUFFER_SIZE);
+            baiStream = SamIndexes.asBaiSeekableStreamOrNull(fileStream, sequenceDictionary);
+            bufferedStream = new SeekableBufferedStream(baiStream, BUFFERED_STREAM_BUFFER_SIZE);
             fileLength=bufferedStream.length();
         }
         catch (IOException exc) {
@@ -319,6 +323,7 @@ public class GATKBAMIndex {
     private void closeIndexFile() {
         try {
             bufferedStream.close();
+            baiStream.close();
             fileStream.close();
             fileLength = -1;
         }
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexData.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexData.java
index f1d6203d6..80d5ba0ce 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexData.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexData.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIterator.java
index c272e0acd..f992cf111 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIterator.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIterator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalSharder.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalSharder.java
index e355c7ee2..fd5b73be7 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalSharder.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalSharder.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShard.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShard.java
index 4714df9b7..d84aa5dd8 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShard.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShard.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShardBalancer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShardBalancer.java
index 6fb4d48ed..cf4286d35 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShardBalancer.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/LocusShardBalancer.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShard.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShard.java
index d8ae3bf55..399e4bc73 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShard.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShard.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancer.java
index 4a27219e4..5b52c8f29 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancer.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancer.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSource.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSource.java
index 79b853e6b..c97201b09 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSource.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSource.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -28,6 +28,7 @@ package org.broadinstitute.gatk.engine.datasources.reads;
 import htsjdk.samtools.MergingSamRecordIterator;
 import htsjdk.samtools.SamFileHeaderMerger;
 import htsjdk.samtools.*;
+import htsjdk.samtools.reference.ReferenceSequenceFileFactory;
 import htsjdk.samtools.util.CloseableIterator;
 import htsjdk.samtools.util.CloserUtil;
 import htsjdk.samtools.util.RuntimeIOException;
@@ -372,10 +373,19 @@ public class SAMDataSource {
             originalToMergedReadGroupMappings.put(id,mappingToMerged);
         }
 
+        final SAMSequenceDictionary samSequenceDictionary;
+        if (referenceFile == null) {
+            samSequenceDictionary = mergedHeader.getSequenceDictionary();
+        } else {
+            samSequenceDictionary = ReferenceSequenceFileFactory.
+                    getReferenceSequenceFile(referenceFile).
+                    getSequenceDictionary();
+        }
+
         for(SAMReaderID id: readerIDs) {
             File indexFile = findIndexFile(id.getSamFile());
             if(indexFile != null)
-                bamIndices.put(id,new GATKBAMIndex(indexFile));
+                bamIndices.put(id,new GATKBAMIndex(indexFile, samSequenceDictionary));
         }
 
         resourcePool.releaseReaders(readers);
@@ -497,20 +507,13 @@ public class SAMDataSource {
      * @return True if all readers that require an index for SAMFileSpan creation have an index.
      */
     public boolean hasIndex() {
-        for (final SAMReaderID readerID: readerIDs)
-            if (isSAMFileSpanSupported(readerID))
-                if (!hasIndex(readerID))
-                    return false;
+        for (final SAMReaderID readerID: readerIDs) {
+            if (!hasIndex(readerID)) {
+                return false;
+            }
+        }
         return true;
     }
-    /**
-     * Returns true if the reader can use file spans.
-     * @return true if file spans are supported.
-     */
-    private boolean isSAMFileSpanSupported(final SAMReaderID readerID) {
-        // example: https://github.com/samtools/htsjdk/blob/ee4308ede60962f3ab4275473ac384724b471149/src/java/htsjdk/samtools/BAMFileReader.java#L341
-        return readerID.getSamFile().getName().toLowerCase().endsWith(SamReader.Type.BAM_TYPE.fileExtension());
-    }
 
     /**
      * Returns true if the reader caches its SAMFileHeader for each iterator.
@@ -579,16 +582,7 @@ public class SAMDataSource {
         SAMReaders readers = resourcePool.getAvailableReaders();
 
         for ( SAMReaderID id: getReaderIDs() ) {
-            GATKBAMFileSpan span;
-            try {
-                span = new GATKBAMFileSpan(readers.getReader(id).indexing().getFilePointerSpanningReads());
-            } catch (RuntimeException e) {
-                if ("Not implemented.".equals(e.getMessage())) { https://github.com/samtools/htsjdk/blob/035d4319643657d715e93c53c13fe4a1f64e0188/src/java/htsjdk/samtools/CRAMFileReader.java#L197
-                    span = new GATKBAMFileSpan(new GATKChunk(0, Long.MAX_VALUE));
-                } else {
-                    throw e;
-                }
-            }
+            final GATKBAMFileSpan span = new GATKBAMFileSpan(readers.getReader(id).indexing().getFilePointerSpanningReads());
             initialPositions.put(id, span);
         }
 
@@ -636,16 +630,7 @@ public class SAMDataSource {
                 }
                 else {
                     final SamReader reader = readers.getReader(id);
-                    try {
-                        iterator = ((SamReader.Indexing)reader).iterator(shard.getFileSpans().get(id));
-                    } catch (RuntimeException re) {
-                        if ("Not implemented.".equals(re.getMessage())) { // https://github.com/samtools/htsjdk/blob/429f2a8585d9c98a3efd4cedc5188b60b1e66ac5/src/java/htsjdk/samtools/CRAMFileReader.java#L192
-                            // No way to jump into the file span. Query the whole file.
-                            iterator = readers.getReader(id).iterator();
-                        } else {
-                            throw re;
-                        }
-                    }
+                    iterator = ((SamReader.Indexing)reader).iterator(shard.getFileSpans().get(id));
                 }
             } catch ( RuntimeException e ) { // we need to catch RuntimeExceptions here because the Picard code is throwing them (among SAMFormatExceptions) sometimes
                 throw new UserException.MalformedBAM(id.getSamFile(), e.getMessage());
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/Shard.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/Shard.java
index eb9ec480a..a8f46fabb 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/Shard.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/Shard.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ShardBalancer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ShardBalancer.java
index 237a38021..fee842db9 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ShardBalancer.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/ShardBalancer.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/package-info.java
index f3506f22c..399737b5a 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/package-info.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/package-info.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMFileStat.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMFileStat.java
index 95e0341fc..69ba13ce9 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMFileStat.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMFileStat.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMTagRenamer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMTagRenamer.java
index bde44a08c..5c601ef45 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMTagRenamer.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMTagRenamer.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/FindLargeShards.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/FindLargeShards.java
index b6869f0b9..5aaba79c0 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/FindLargeShards.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/FindLargeShards.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBAMRegion.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBAMRegion.java
index b0842e161..95454122e 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBAMRegion.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBAMRegion.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBGZFBounds.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBGZFBounds.java
index 807e0380d..01299aec1 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBGZFBounds.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBGZFBounds.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/UnzipSingleBlock.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/UnzipSingleBlock.java
index d65b779e5..399ea3803 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/UnzipSingleBlock.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/UnzipSingleBlock.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/package-info.java
index 65a909a21..e50a770c8 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/package-info.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/package-info.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSource.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSource.java
index 6b7bf2187..21d1c7c2f 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSource.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSource.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/package-info.java
index 581d213dd..77bea8969 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/package-info.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reference/package-info.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/DataStreamSegment.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/DataStreamSegment.java
index 2543c42b7..c12933c85 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/DataStreamSegment.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/DataStreamSegment.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/EntireStream.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/EntireStream.java
index eba5b534e..389f2c6fa 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/EntireStream.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/EntireStream.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/MappedStreamSegment.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/MappedStreamSegment.java
index 0344ff032..c4904818d 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/MappedStreamSegment.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/MappedStreamSegment.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPool.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPool.java
index 6920ba242..3ed14bb9f 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPool.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPool.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataSource.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataSource.java
index e90cb8047..1dd8e8fb9 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataSource.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataSource.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ResourcePool.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ResourcePool.java
index 7d6e9c010..213ab28a6 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ResourcePool.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/ResourcePool.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/package-info.java
index 41b7e53b7..402087d7c 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/package-info.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/rmd/package-info.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/Accumulator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/Accumulator.java
index 9276331e1..8d166e1c8 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/Accumulator.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/Accumulator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroScheduler.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroScheduler.java
index f7e3dbcda..0f01f76ce 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroScheduler.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroScheduler.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroSchedulerMBean.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroSchedulerMBean.java
index 30e03c6a8..b0fd074a6 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroSchedulerMBean.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/HierarchicalMicroSchedulerMBean.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/LinearMicroScheduler.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/LinearMicroScheduler.java
index fc68b9c7a..04516da45 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/LinearMicroScheduler.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/LinearMicroScheduler.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/MicroScheduler.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/MicroScheduler.java
index f9660a94a..27e0859ff 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/MicroScheduler.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/MicroScheduler.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/MicroSchedulerMBean.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/MicroSchedulerMBean.java
index 772fe01dd..06fcfef5e 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/MicroSchedulerMBean.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/MicroSchedulerMBean.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/OutputMergeTask.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/OutputMergeTask.java
index 4e5ef9ff0..846657ab3 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/OutputMergeTask.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/OutputMergeTask.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/ReduceTree.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/ReduceTree.java
index e02b846b7..b1ab50b41 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/ReduceTree.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/ReduceTree.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/ShardTraverser.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/ShardTraverser.java
index 443fdf7e7..5753b0fbb 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/ShardTraverser.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/ShardTraverser.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/TreeReducer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/TreeReducer.java
index 270b06f33..67a5fabbd 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/TreeReducer.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/TreeReducer.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/WindowMaker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/WindowMaker.java
index 496178d88..e2f870d55 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/WindowMaker.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/WindowMaker.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/package-info.java
index c0d6e9dcc..400f02881 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/package-info.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/executive/package-info.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BAQReadTransformer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BAQReadTransformer.java
index f0e889a63..c3ff6ae16 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BAQReadTransformer.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BAQReadTransformer.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BadCigarFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BadCigarFilter.java
index 0b7d1a905..d4f6cb8a8 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BadCigarFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BadCigarFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BadMateFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BadMateFilter.java
index 562e50ea9..317322da9 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BadMateFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/BadMateFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/CountingFilteringIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/CountingFilteringIterator.java
index 8717f1ff3..de49247a7 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/CountingFilteringIterator.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/CountingFilteringIterator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/DisableableReadFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/DisableableReadFilter.java
index 9c44be3de..2898ca1cf 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/DisableableReadFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/DisableableReadFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/DuplicateReadFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/DuplicateReadFilter.java
index 310f1dee3..bb1d7e82b 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/DuplicateReadFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/DuplicateReadFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/FailsVendorQualityCheckFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/FailsVendorQualityCheckFilter.java
index fc5cdcb53..1834be5ee 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/FailsVendorQualityCheckFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/FailsVendorQualityCheckFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/FilterManager.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/FilterManager.java
index 90d8a3fd8..b0dcae564 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/FilterManager.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/FilterManager.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/LibraryReadFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/LibraryReadFilter.java
index d6e78a616..e56dc27b4 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/LibraryReadFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/LibraryReadFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilter.java
index 05c6f564e..4e267167e 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityFilter.java
index 58ec76660..85dda8ece 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityUnavailableFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityUnavailableFilter.java
index ff1542e41..f006a3ccf 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityUnavailableFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityUnavailableFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityZeroFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityZeroFilter.java
index b0d40c074..46f044b69 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityZeroFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MappingQualityZeroFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MateSameStrandFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MateSameStrandFilter.java
index 20dda5427..a8a02dafa 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MateSameStrandFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MateSameStrandFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MaxInsertSizeFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MaxInsertSizeFilter.java
index c7b512f2b..0407d8591 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MaxInsertSizeFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MaxInsertSizeFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MissingReadGroupFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MissingReadGroupFilter.java
index 0a7a2cdbf..7acc34e7f 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MissingReadGroupFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/MissingReadGroupFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformer.java
index e01827723..aa449a105 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformer.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformer.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NoOriginalQualityScoresFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NoOriginalQualityScoresFilter.java
index 4e8a1dc2b..482a54117 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NoOriginalQualityScoresFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NoOriginalQualityScoresFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NotPrimaryAlignmentFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NotPrimaryAlignmentFilter.java
index 55a697d3e..841a139e2 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NotPrimaryAlignmentFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/NotPrimaryAlignmentFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/OverclippedReadFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/OverclippedReadFilter.java
index 07c7bfc8e..fe96f9fb9 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/OverclippedReadFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/OverclippedReadFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -40,8 +40,8 @@ import org.broadinstitute.gatk.utils.exceptions.UserException;
  *     This filter is intended to filter out reads that are potentially from foreign organisms.
  *     From experience with sequencing of human DNA we have found cases of contamination by bacterial
  *     organisms; the symptoms of such contamination are a class of reads with only a small number
- *     of aligned bases and additionally many soft-clipped bases on both ends.  This filter is intended
- *     to remove such reads.
+ *     of aligned bases and additionally many soft-clipped bases.  This filter is intended
+ *     to remove such reads. Consecutive soft-clipped blocks are treated as a single block
  * 
    
  *
  */
@@ -50,25 +50,31 @@ public class OverclippedReadFilter extends ReadFilter {
     @Argument(fullName = "filter_is_too_short_value", shortName = "filterTooShort", doc = "Value for which reads with less than this number of aligned bases is considered too short", required = false)
     int tooShort = 30;
 
+    @Argument(fullName = "do_not_require_softclips_both_ends", shortName = "NoRequireSCBothEnds", doc = "Allow a read to be filtered out based on having only 1 soft-clipped block. By default, both ends must have a soft-clipped block, setting this flag requires only 1 soft-clipped block.", required = false)
+    Boolean doNotRequireSoftclipsOnBothEnds = false;
+
 
     public boolean filterOut(final SAMRecord read) {
-        boolean sawLeadingSoftclip = false;
-        boolean sawAlignedBase = false;
         int alignedLength = 0;
+        int softClipBlocks = 0;
+        int minSoftClipBlocks = doNotRequireSoftclipsOnBothEnds ? 1 : 2;
+        CigarOperator lastOperator = null;
 
         for ( final CigarElement element : read.getCigar().getCigarElements() ) {
             if ( element.getOperator() == CigarOperator.S ) {
-                if ( sawAlignedBase )  // if this is true then we must also have seen a leading soft-clip
-                    return (alignedLength < tooShort);
-                sawLeadingSoftclip = true;
+                //Treat consecutive S blocks as a single one
+                if(lastOperator != CigarOperator.S){
+                    softClipBlocks += 1;
+                }
+
             } else if ( element.getOperator().consumesReadBases() ) {   // M, I, X, and EQ (S was already accounted for above)
-                if ( !sawLeadingSoftclip )
-                    return false;
-                sawAlignedBase = true;
                 alignedLength += element.getLength();
             }
+            lastOperator = element.getOperator();
         }
 
-        return false;
+        return(alignedLength < tooShort && softClipBlocks >= minSoftClipBlocks);
+
     }
+
 }
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/Platform454Filter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/Platform454Filter.java
index f1b375835..22822dd3a 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/Platform454Filter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/Platform454Filter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformFilter.java
index 7ca07d35d..8c7fcc630 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilter.java
index b0e0bbebb..c00d52124 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilter.java
@@ -1,28 +1,28 @@
-/*
-* Copyright (c) 2012 The Broad Institute
-* 
-* Permission is hereby granted, free of charge, to any person
-* obtaining a copy of this software and associated documentation
-* files (the "Software"), to deal in the Software without
-* restriction, including without limitation the rights to use,
-* copy, modify, merge, publish, distribute, sublicense, and/or sell
-* copies of the Software, and to permit persons to whom the
-* Software is furnished to do so, subject to the following
-* conditions:
-* 
-* The above copyright notice and this permission notice shall be
-* included in all copies or substantial portions of the Software.
-* 
-* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
-* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-*/
-
+/*
+* Copyright 2012-2015 Broad Institute, Inc.
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
 package org.broadinstitute.gatk.engine.filters;
 
 import htsjdk.samtools.SAMReadGroupRecord;
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilterHelper.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilterHelper.java
index 428806d6a..d92ffe73c 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilterHelper.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/PlatformUnitFilterHelper.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadFilter.java
index a2102a838..1720fdc76 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilter.java
index 9f815cf72..7c57b0d60 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadLengthFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadLengthFilter.java
index f9a6fab57..b0fc108e6 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadLengthFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadLengthFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadNameFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadNameFilter.java
index cdee7e14b..94548ab3a 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadNameFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadNameFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadStrandFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadStrandFilter.java
index 292803d1c..6cfcdac8a 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadStrandFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReadStrandFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignMappingQualityFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignMappingQualityFilter.java
index 89be38db7..dffd8662e 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignMappingQualityFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignMappingQualityFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignOneMappingQualityFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignOneMappingQualityFilter.java
index 2ff1d5a4e..0a4eeaf8e 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignOneMappingQualityFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/ReassignOneMappingQualityFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/SampleFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/SampleFilter.java
index ab63e1e00..df582abb5 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/SampleFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/SampleFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/SingleReadGroupFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/SingleReadGroupFilter.java
index 58cf9183d..b5f7e4418 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/SingleReadGroupFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/SingleReadGroupFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/UnmappedReadFilter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/UnmappedReadFilter.java
index d5f8d30ff..e448068cd 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/UnmappedReadFilter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/UnmappedReadFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/package-info.java
index 7e36ffbdf..c5ba1d96e 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/package-info.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/package-info.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/BySampleSAMFileWriter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/BySampleSAMFileWriter.java
index 6dd8833b8..15b6f2dff 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/BySampleSAMFileWriter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/BySampleSAMFileWriter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/DirectOutputTracker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/DirectOutputTracker.java
index 96c9cb24d..d5c6695ab 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/DirectOutputTracker.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/DirectOutputTracker.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/FastqFileWriter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/FastqFileWriter.java
index 772c327bd..ec9b5ee2b 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/FastqFileWriter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/FastqFileWriter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/NWaySAMFileWriter.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/NWaySAMFileWriter.java
index 74ed19d3e..87a8b6629 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/NWaySAMFileWriter.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/NWaySAMFileWriter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/OutputTracker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/OutputTracker.java
index d5925900c..693d70954 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/OutputTracker.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/OutputTracker.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/ThreadGroupOutputTracker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/ThreadGroupOutputTracker.java
index fdb5fd2cb..70a94a65f 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/ThreadGroupOutputTracker.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/ThreadGroupOutputTracker.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/OutputStreamStorage.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/OutputStreamStorage.java
index ac348a2ab..7ed538b4d 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/OutputStreamStorage.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/OutputStreamStorage.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/SAMFileWriterStorage.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/SAMFileWriterStorage.java
index 68943f887..108b1f0e7 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/SAMFileWriterStorage.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/SAMFileWriterStorage.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -75,12 +75,10 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage writers;
 
@@ -175,6 +185,14 @@ public class VariantContextWriterStorage implements Storage, Var
         setWriteFullFormatField(argumentCollection.neverTrimVCFFormatField);
     }
 
+    @Override
     public void writeHeader(VCFHeader header) {
         vcfHeader = header;
 
@@ -274,6 +275,7 @@ public class VariantContextWriterStub implements Stub, Var
     /**
      * @{inheritDoc}
      */
+    @Override
     public void close() {
         outputTracker.getStorage(this).close();
     }
@@ -300,4 +302,12 @@ public class VariantContextWriterStub implements Stub, Var
                 getOutputFile() != null && // that are going to disk
                 engine.getArguments().generateShadowBCF; // and we actually want to do it
     }
+
+    /**
+     * Check the return from PrintStream.checkError() if underlying stream for a java.io.PrintStream
+     * @return true if PrintStream.checkError() returned true, false otherwise
+     */
+    public boolean checkError(){
+        return genotypeStream.checkError();
+    }
 }
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIterator.java
index ecce811f9..7ab11e3e5 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIterator.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIterator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/GenomeLocusIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/GenomeLocusIterator.java
index c76a07e36..3a21d5a32 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/GenomeLocusIterator.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/GenomeLocusIterator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/IterableIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/IterableIterator.java
index bf8b69741..7ef375b93 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/IterableIterator.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/IterableIterator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/MalformedBAMErrorReformatingIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/MalformedBAMErrorReformatingIterator.java
index d3a6bdc4b..d04ddaa4e 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/MalformedBAMErrorReformatingIterator.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/MalformedBAMErrorReformatingIterator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityReadTransformer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityReadTransformer.java
index ea2e081c7..f7c408004 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityReadTransformer.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityReadTransformer.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/NullSAMIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/NullSAMIterator.java
index ca53fcf1d..743847e59 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/NullSAMIterator.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/NullSAMIterator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/PeekingIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/PeekingIterator.java
index f46fb0cce..8db59fbe2 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/PeekingIterator.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/PeekingIterator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/PositionTrackingIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/PositionTrackingIterator.java
index a79d592f7..dfeb73921 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/PositionTrackingIterator.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/PositionTrackingIterator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/RNAReadTransformer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/RNAReadTransformer.java
index 4cc2a82be..2b92758e0 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/RNAReadTransformer.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/RNAReadTransformer.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIterator.java
index 7a3ca935f..223c2faec 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIterator.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIterator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformer.java
index b7db50594..575aebfe5 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformer.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformer.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformersMode.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformersMode.java
index 3fa18c496..fc7e77364 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformersMode.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformersMode.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformingIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformingIterator.java
index ed5c4b3b9..e3d676b47 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformingIterator.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/ReadTransformingIterator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIterator.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIterator.java
index 8721779bf..6c0004c71 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIterator.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIterator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/package-info.java
index 338789022..e450d451c 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/package-info.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/iterators/package-info.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/package-info.java
index bd34a1792..51722e707 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/package-info.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/package-info.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReport.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReport.java
index 3bd174442..d81c27088 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReport.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReport.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportException.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportException.java
index 4de344eb6..46158825b 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportException.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportException.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRArgumentSet.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRArgumentSet.java
index 497eafe68..491451103 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRArgumentSet.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRArgumentSet.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -28,11 +28,14 @@ package org.broadinstitute.gatk.engine.recalibration;
 import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection;
 
 import java.io.File;
+import java.util.List;
 
 public class BQSRArgumentSet {
     // declare public, STL-style for easier and more efficient access:
     private File BQSR_RECAL_FILE;
     private int quantizationLevels;
+    private List staticQuantizedQuals;
+    private boolean roundDown;
     private boolean disableIndelQuals;
     private boolean emitOriginalQuals;
     private int PRESERVE_QSCORES_LESS_THAN;
@@ -41,6 +44,8 @@ public class BQSRArgumentSet {
     public BQSRArgumentSet(final GATKArgumentCollection args) {
         this.BQSR_RECAL_FILE = args.BQSR_RECAL_FILE;
         this.quantizationLevels = args.quantizationLevels;
+        this.staticQuantizedQuals = args.staticQuantizationQuals;
+        this.roundDown = args.roundDown;
         this.disableIndelQuals = args.disableIndelQuals;
         this.emitOriginalQuals = args.emitOriginalQuals;
         this.PRESERVE_QSCORES_LESS_THAN = args.PRESERVE_QSCORES_LESS_THAN;
@@ -51,6 +56,10 @@ public class BQSRArgumentSet {
 
     public int getQuantizationLevels() { return quantizationLevels; }
 
+    public List getStaticQuantizedQuals() {return staticQuantizedQuals; }
+
+    public boolean getRoundDown() {return roundDown; }
+
     public boolean shouldDisableIndelQuals() { return disableIndelQuals; }
 
     public boolean shouldEmitOriginalQuals() { return emitOriginalQuals; }
@@ -67,6 +76,12 @@ public class BQSRArgumentSet {
         this.quantizationLevels = quantizationLevels;
     }
 
+    public void setStaticQuantizedQuals(final List staticQuantizedQuals) { this.staticQuantizedQuals = staticQuantizedQuals; }
+
+    public void setRoundDown(final boolean roundDown) {
+        this.roundDown = roundDown;
+    }
+
     public void setDisableIndelQuals(final boolean disableIndelQuals) {
         this.disableIndelQuals = disableIndelQuals;
     }
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRMode.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRMode.java
index de6500e19..13e97f810 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRMode.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRMode.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/resourcemanagement/ThreadAllocation.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/resourcemanagement/ThreadAllocation.java
index 034413520..867647625 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/resourcemanagement/ThreadAllocation.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/resourcemanagement/ThreadAllocation.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Affection.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Affection.java
index 0e5833b99..2dac6e111 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Affection.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Affection.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Gender.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Gender.java
index 0f26bc630..fd721edbc 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Gender.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Gender.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/MendelianViolation.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/MendelianViolation.java
index a37eb8d88..0e37cb4bb 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/MendelianViolation.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/MendelianViolation.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/PedReader.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/PedReader.java
index 8946d2808..0bbc3c8a9 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/PedReader.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/PedReader.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/PedigreeValidationType.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/PedigreeValidationType.java
index 14fefd2be..1a373e114 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/PedigreeValidationType.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/PedigreeValidationType.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Sample.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Sample.java
index 0d60c39a1..41cc0b229 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Sample.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Sample.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -234,7 +234,9 @@ public class Sample implements Comparable { // implements java.io.Serial
                 return o1; // keep o1, since it's a real value
             else {
                 // both o1 and o2 have a value
-                if ( o1 == o2 )
+                if ( o1 instanceof String && o1.equals(o2) )
+                    return o1;
+                else if ( o1 == o2 )
                     return o1;
                 else
                     throw new UserException("Inconsistent values detected for " + name + " for field " + field + " value1 " + o1 + " value2 " + o2);
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDB.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDB.java
index 141f01b3a..c0502da06 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDB.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDB.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDBBuilder.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDBBuilder.java
index 2744bec61..2b5427f76 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDBBuilder.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/SampleDBBuilder.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Trio.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Trio.java
index b5a698b9a..3bbf7bfb6 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Trio.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/samples/Trio.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/ArtificialReadsTraversal.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/ArtificialReadsTraversal.java
index ac34b7594..91ba863ea 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/ArtificialReadsTraversal.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/ArtificialReadsTraversal.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCache.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCache.java
index f84824a59..858a557fd 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCache.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCache.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraversalEngine.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraversalEngine.java
index 25abafd2d..3671ded82 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraversalEngine.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraversalEngine.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegions.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegions.java
index b3a0603f4..9eb732cc3 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegions.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegions.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicates.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicates.java
index a8c88aace..41738a09f 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicates.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicates.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseLociNano.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseLociNano.java
index 1c16c0e19..0c2676b5a 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseLociNano.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseLociNano.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadPairs.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadPairs.java
index c68e10908..4387436fe 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadPairs.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadPairs.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsNano.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsNano.java
index e392041f0..ccc81599a 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsNano.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsNano.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/package-info.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/package-info.java
index 72d10994d..b203e39c3 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/package-info.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/package-info.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionTraversalParameters.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionTraversalParameters.java
index bcae8ecdc..f017cfb27 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionTraversalParameters.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionTraversalParameters.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionWalker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionWalker.java
index eb964c826..3e92ff73b 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionWalker.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionWalker.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Allows.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Allows.java
index 7188fd01c..ef2251e50 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Allows.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Allows.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Attribution.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Attribution.java
index ded2941f3..613b6b2e4 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Attribution.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Attribution.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/BAQMode.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/BAQMode.java
index 931381efb..8a500c180 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/BAQMode.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/BAQMode.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/By.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/By.java
index 3962c98e0..903f5bd13 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/By.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/By.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DataSource.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DataSource.java
index fab984084..e6deb7635 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DataSource.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DataSource.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DisabledReadFilters.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DisabledReadFilters.java
index ccf09fd40..5708e2664 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DisabledReadFilters.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DisabledReadFilters.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Downsample.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Downsample.java
index f85123ab6..19929988c 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Downsample.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Downsample.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DuplicateWalker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DuplicateWalker.java
index 42398ec33..46691e44a 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DuplicateWalker.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/DuplicateWalker.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/FailMethod.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/FailMethod.java
index 3f8862975..a2d12dc46 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/FailMethod.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/FailMethod.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/LocusWalker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/LocusWalker.java
index 3c6268de3..66f34b3a0 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/LocusWalker.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/LocusWalker.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/NanoSchedulable.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/NanoSchedulable.java
index 5852b77cf..329aaaca3 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/NanoSchedulable.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/NanoSchedulable.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionBy.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionBy.java
index 200614e50..5078d4ea7 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionBy.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionBy.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionType.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionType.java
index 2c738e109..eb6b6040b 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionType.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/PartitionType.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RMD.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RMD.java
index a2ee8d0bd..8a221cb35 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RMD.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RMD.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadFilters.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadFilters.java
index eac57155e..3438232bc 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadFilters.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadFilters.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadPairWalker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadPairWalker.java
index 67eae69ac..9b8e3be01 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadPairWalker.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadPairWalker.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadWalker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadWalker.java
index 8c59bc8eb..81731315a 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadWalker.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ReadWalker.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RefWalker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RefWalker.java
index 90c10c50a..0535acaff 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RefWalker.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RefWalker.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Reference.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Reference.java
index 3598cf505..c3cee866f 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Reference.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Reference.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RemoveProgramRecords.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RemoveProgramRecords.java
index ad945f277..8f6f5e3c1 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RemoveProgramRecords.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RemoveProgramRecords.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Requires.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Requires.java
index 5a16a6767..9dec898aa 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Requires.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Requires.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RodWalker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RodWalker.java
index 88a1eaacf..ef94e7e2d 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RodWalker.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/RodWalker.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/TreeReducible.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/TreeReducible.java
index c170f3d19..a0411484a 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/TreeReducible.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/TreeReducible.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Walker.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Walker.java
index 88c4ff388..9d08422eb 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Walker.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Walker.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -40,6 +40,7 @@ import org.broadinstitute.gatk.utils.baq.BAQ;
 import org.broadinstitute.gatk.utils.collections.Pair;
 import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.gatk.engine.recalibration.BQSRMode;
+import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection;
 
 import java.util.List;
 
@@ -85,18 +86,49 @@ public abstract class Walker {
     /**
      * Gets the master sequence dictionary for this walker
      * @link GenomeAnalysisEngine.getMasterSequenceDictionary
-     * @return
+     * @return the master sequence dictionary or null if no genome analysis toolkit.
      */
     protected SAMSequenceDictionary getMasterSequenceDictionary() {
-        return getToolkit().getMasterSequenceDictionary();
+        if ( toolkit == null )
+            return null;
+        else
+            return toolkit.getMasterSequenceDictionary();
     }
 
+    /**
+     * Gets the GATK argument collection
+     * @link GenomeAnalysisEngine.getArguments
+     * @return the GATK argument collection or null if no genome analysis toolkit.
+     */
+    public GATKArgumentCollection getArguments(){
+        if ( toolkit == null )
+            return null;
+        else
+            return toolkit.getArguments();
+    }
+
+    /**
+     * Gets the GATK samples database
+     * @link GenomeAnalysisEngine.getSampleDB
+     * @return the GATK samples database or null if no genome analysis toolkit.
+     */
     public SampleDB getSampleDB() {
-        return getToolkit().getSampleDB();
+        if ( toolkit == null )
+            return null;
+        else
+            return toolkit.getSampleDB();
     }
 
+    /**
+     * Gets a sample from the GATK samples database
+     * @param id the sample ID
+     * @return the sample from the GATK samples database or null if no genome analysis toolkit or samples database.
+     */
     protected Sample getSample(final String id) {
-        return getToolkit().getSampleDB().getSample(id);
+        if ( getSampleDB() == null )
+            return null;
+        else
+            return getSampleDB().getSample(id);
     }
 
     /**
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/WalkerName.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/WalkerName.java
index 9e02bf182..2c8dca90b 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/WalkerName.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/WalkerName.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Window.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Window.java
index 66205b93f..f613607c6 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Window.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/Window.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/CommandLineGATKUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/CommandLineGATKUnitTest.java
index dc3e99653..a5ddd0654 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/CommandLineGATKUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/CommandLineGATKUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java
index fb498412a..9f5d88114 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -324,12 +324,12 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
 
     @Test()
     public void testDefaultBaseQualities20() {
-        executeTest("testDefaultBaseQualities20", testDefaultBaseQualities(20, "7d254a9d0ec59c66ee3e137f56f4c78f"));
+        executeTest("testDefaultBaseQualities20", testDefaultBaseQualities(20, "90a450f74554bbd2cc3a9e0f9de68e26"));
     }
 
     @Test()
     public void testDefaultBaseQualities30() {
-        executeTest("testDefaultBaseQualities30", testDefaultBaseQualities(30, "0f50def6cbbbd8ccd4739e2b3998e503"));
+        executeTest("testDefaultBaseQualities30", testDefaultBaseQualities(30, "ec11db4173ce3b8e43997f00dab5ae26"));
     }
 
     @Test(expectedExceptions = Exception.class)
@@ -731,12 +731,12 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
 
     @Test
     public void testSAMWriterFeatures() {
-        testBAMFeatures("-compress 0", "bb4b55b1f80423970bb9384cbf0d8793");
-        testBAMFeatures("-compress 9", "b85ee1636d62e1bb8ed65a245c307167");
-        testBAMFeatures("-simplifyBAM", "38f9c30a27dfbc085a2ff52a1617d579");
+        testBAMFeatures("-compress 0", "49228d4f5b14c4cfed4a09372eb71139");
+        testBAMFeatures("-compress 9", "bc61a1b2b53a2ec7c63b533fa2f8701b");
+        testBAMFeatures("-simplifyBAM", "a1127bab46674b165496b79bb9fa7964");
 
         //Validate MD5
-        final String expectedMD5 = "6627b9ea33293a0083983feb94948c1d";
+        final String expectedMD5 = "c58b9114fc15b53655f2c03c819c29fd";
         final File md5Target = testBAMFeatures("--generate_md5", expectedMD5);
         final File md5File = new File(md5Target.getAbsoluteFile() + ".md5");
         md5File.deleteOnExit();
@@ -758,8 +758,8 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
     @DataProvider(name = "vcfFeaturesData")
     public Object[][] getVCFFeaturesData() {
         return new Object[][]{
-                {"--sites_only", "94bf1f2c0946e933515e4322323a5716"},
-                {"--bcf", "03f2d6988f54a332da48803c78f9c4b3"}
+                {"--sites_only", "6ef742ee6d9bcbc7b23f928c0e8a1d0e"},
+                {"--bcf", "285549ca1a719a09fa95cfa129520621"}
         };
     }
 
@@ -775,8 +775,8 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
     @DataProvider(name = "vcfFormatHandlingData")
     public Object[][] getVCFFormatHandlingData() {
         return new Object[][]{
-                {true, "95b6262efbd40b6b72f44f808f3e4c45"},
-                {false, "333232e08b8cdd3303309e438c44277f"}
+                {true, "870f39e19ec89c8a09f7eca0f5c4bcb9"},
+                {false, "baf9a1755d3b4e0ed25b03233e99ca91"}
         };
     }
 
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/GATKVCFUtilsUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/GATKVCFUtilsUnitTest.java
index 3881eb719..439c7e5ab 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/GATKVCFUtilsUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/GATKVCFUtilsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngineUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngineUnitTest.java
index 424083a11..79fdb9253 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngineUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngineUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/InstantiableWalker.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/InstantiableWalker.java
index 4c6e35d0c..7258e4d86 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/InstantiableWalker.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/InstantiableWalker.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/MaxRuntimeIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/MaxRuntimeIntegrationTest.java
index 2d48487e4..9ae72597b 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/MaxRuntimeIntegrationTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/MaxRuntimeIntegrationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/ReadMetricsUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/ReadMetricsUnitTest.java
index 50c7f8222..6a1c3407d 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/ReadMetricsUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/ReadMetricsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/SampleUtilsUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/SampleUtilsUnitTest.java
index 7de5f0dbf..972816ca6 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/SampleUtilsUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/SampleUtilsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/UninstantiableWalker.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/UninstantiableWalker.java
index 11a3c3d6d..32fcee33d 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/UninstantiableWalker.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/UninstantiableWalker.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/WalkerManagerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/WalkerManagerUnitTest.java
index 0a940ef22..5173dcb89 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/WalkerManagerUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/WalkerManagerUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/CramIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/CramIntegrationTest.java
index 644b5ed1c..31565a69c 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/CramIntegrationTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/CramIntegrationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -26,10 +26,11 @@
 package org.broadinstitute.gatk.engine.arguments;
 
 import org.broadinstitute.gatk.engine.walkers.WalkerTest;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
-import java.util.Arrays;
+import java.util.Collections;
 
 /**
  * Test the GATK core CRAM parsing mechanism.
@@ -38,28 +39,25 @@ public class CramIntegrationTest extends WalkerTest {
     @DataProvider(name="cramData")
     public Object[][] getCRAMData() {
         return new Object[][] {
-                {"PrintReads", "exampleBAM.bam", "", "cram", "fc6e3919a8a34266c89ef66e97ceaba9"},
-                //{"PrintReads", "exampleCRAM.cram", "", "cram", "026ebc00c2a8f9832e37f1a6a0f53521"}, https://github.com/samtools/htsjdk/issues/148
-                {"PrintReads", "exampleCRAM.cram", "", "bam", "99e5f740b43594a5b8e5bc1a007719e0"},
-                {"PrintReads", "exampleCRAM-noindex.cram", "", "bam", "99e5f740b43594a5b8e5bc1a007719e0"},
-                {"PrintReads", "exampleCRAM.cram", " -L chr1:200", "bam", "072435e8272411c31b2234f851706384"},
-                {"PrintReads", "exampleCRAM-noindex.cram", " -L chr1:200", "bam", "072435e8272411c31b2234f851706384"},
+                {"PrintReads", "exampleBAM.bam", "", "cram", "97470174cd313a4d200b2a96ffd73e99"},
+                {"PrintReads", "exampleCRAM.cram", "", "cram", "424c725c4ffe7215e358ecf5abd5e5e8"},
+                {"PrintReads", "exampleCRAM.cram", "", "bam", "247805098718dd74b8a871796424d359"},
+                {"PrintReads", "exampleCRAM.cram", " -L chr1:200", "bam", "a5b26631cd89f86f6184bcac7bc9c9ca"},
                 {"CountLoci", "exampleCRAM.cram", "", "txt", "ade93df31a6150321c1067e749cae9be"},
-                {"CountLoci", "exampleCRAM-noindex.cram", "", "txt", "ade93df31a6150321c1067e749cae9be"},
                 {"CountLoci", "exampleCRAM.cram", " -L chr1:200", "txt", "b026324c6904b2a9cb4b88d6d61c81d1"},
-                {"CountLoci", "exampleCRAM-noindex.cram", " -L chr1:200", "txt", "b026324c6904b2a9cb4b88d6d61c81d1"},
                 {"CountReads", "exampleCRAM.cram", "", "txt", "4fbafd6948b6529caa2b78e476359875"},
-                {"CountReads", "exampleCRAM-noindex.cram", "", "txt", "4fbafd6948b6529caa2b78e476359875"},
                 {"CountReads", "exampleCRAM.cram", " -L chr1:200", "txt", "b026324c6904b2a9cb4b88d6d61c81d1"},
-                {"CountReads", "exampleCRAM-noindex.cram", " -L chr1:200", "txt", "b026324c6904b2a9cb4b88d6d61c81d1"},
-                {"PrintReads", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "bam", "9598062587ad8d2ec596a8ecb19be979"},
+                {"PrintReads", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "bam", "24dbd14b60220461f47ec5517962cb7f"},
                 {"CountLoci", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "txt", "26ab0db90d72e28ad0ba1e22ee510510"},
                 {"CountReads", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "txt", "6d7fce9fee471194aa8b5b6e47267f03"},
+                {"PrintReads", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "bam", "84bee5063d8fa0d07e7c3ff7e825ae3a"},
+                {"CountLoci", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "txt", "26ab0db90d72e28ad0ba1e22ee510510"},
+                {"CountReads", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "txt", "6d7fce9fee471194aa8b5b6e47267f03"},
         };
     }
 
     @Test(dataProvider = "cramData")
-    public void testCRAM(String walker, String input, String args, String ext, String md5) {
+    public void testCram(String walker, String input, String args, String ext, String md5) {
         WalkerTestSpec spec = new WalkerTestSpec(
                 " -T Test" + walker + "Walker" +
                     " -I " + publicTestDir + input +
@@ -67,8 +65,26 @@ public class CramIntegrationTest extends WalkerTest {
                     args +
                     " -o %s",
                 1, // just one output file
-                Arrays.asList(ext),
-                Arrays.asList(md5));
-        executeTest(String.format("testCRAM %s %s -> %s: %s", walker, input, ext, args), spec);
+                Collections.singletonList(ext),
+                Collections.singletonList(md5));
+        executeTest(String.format("testCram %s %s -> %s: %s", walker, input, ext, args), spec);
+    }
+
+    @DataProvider(name = "cramNoIndexData")
+    public Object[][] getCramNoIndexData() {
+        return new Object[][]{
+                {"exampleCRAM-nobai-nocrai.cram"},
+        };
+    }
+
+    @Test(dataProvider = "cramNoIndexData")
+    public void testCramNoIndex(String input) {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                " -T TestPrintReadsWalker" +
+                        " -I " + publicTestDir + input +
+                        " -R " + exampleFASTA,
+                0,
+                UserException.class);
+        executeTest(String.format("testCramNoIndex %s", input), spec);
     }
 }
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java
index 1229ecfff..6de2f969e 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -29,7 +29,6 @@ import org.broadinstitute.gatk.engine.walkers.WalkerTest;
 import org.testng.annotations.Test;
 
 import java.io.File;
-import java.util.Arrays;
 import java.util.Collections;
 
 /**
@@ -45,25 +44,10 @@ public class IntervalIntegrationTest extends WalkerTest {
                         " -R " + hg18Reference +
                         " -o %s",
                         1, // just one output file
-                        Arrays.asList(md5));
+                        Collections.singletonList(md5));
         executeTest("testAllIntervalsImplicit",spec);
     }
 
-// '-L all' is no longer supported
-//    @Test(enabled = true)
-//    public void testAllExplicitIntervalParsing() {
-//        String md5 = "7821db9e14d4f8e07029ff1959cd5a99";
-//        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-//                "-T TestCountLociWalker" +
-//                        " -I " + validationDataLocation + "OV-0930.normal.chunk.bam" +
-//                        " -R " + hg18Reference +
-//                        " -L all" +
-//                        " -o %s",
-//                        1, // just one output file
-//                        Arrays.asList(md5));
-//        executeTest("testAllIntervalsExplicit",spec);
-//    }
-
     @Test
     public void testUnmappedReadInclusion() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@@ -78,12 +62,38 @@ public class IntervalIntegrationTest extends WalkerTest {
         // our base file
         File baseOutputFile = createTempFile("testUnmappedReadInclusion",".bam");
         spec.setOutputFileLocation(baseOutputFile);
-        spec.addAuxFile("95e98192e5b90cf80eaa87a4ace263da",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
+        spec.addAuxFile("c66bb2c3c5382e2acff09b2b359562bb",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
         spec.addAuxFile("fadcdf88597b9609c5f2a17f4c6eb455", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai"));
 
         executeTest("testUnmappedReadInclusion",spec);
     }
 
+    @Test
+    public void testMultipleIntervalInclusionOnCRAM() {
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T TestPrintReadsWalker" +
+                        " -I " + validationDataLocation + "MV1994.cram" +
+                        " -R " + validationDataLocation + "Escherichia_coli_K12_MG1655.fasta" +
+                        " -L Escherichia_coli_K12:11000" +
+                        " -L Escherichia_coli_K12:12000" +
+                        " -L Escherichia_coli_K12:13000" +
+                        " -L Escherichia_coli_K12:14000" +
+                        " -L Escherichia_coli_K12:15000" +
+                        " -L Escherichia_coli_K12:16000" +
+                        " -L Escherichia_coli_K12:17000" +
+                        " -L unmapped",
+                0, // two output files
+                Collections.emptyList());
+
+        // our base file
+        File baseOutputFile = createTempFile("testUnmappedReadInclusion", ".cram");
+        spec.setOutputFileLocation(baseOutputFile);
+        spec.addAuxFile("0f11cc035455cd68fb388e33aaf5feff", createTempFileFromBase(baseOutputFile.getAbsolutePath()));
+        spec.addAuxFile("ebbe6e311b6bb240554ec96ed9809216", createTempFileFromBase(baseOutputFile.getAbsolutePath() + ".bai"));
+
+        executeTest("testUnmappedReadInclusionCRAM", spec);
+    }
+
     @Test
     public void testMixedMappedAndUnmapped() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@@ -99,7 +109,7 @@ public class IntervalIntegrationTest extends WalkerTest {
         // our base file
         File baseOutputFile = createTempFile("testUnmappedReadInclusion",".bam");
         spec.setOutputFileLocation(baseOutputFile);
-        spec.addAuxFile("3944b5a6bfc06277ed3afb928a20d588",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
+        spec.addAuxFile("c64cff3ed376bc8f2977078dbdac4518",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
         spec.addAuxFile("fa90ff91ac0cc689c71a3460a3530b8b", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai"));
 
         executeTest("testUnmappedReadInclusion",spec);
@@ -136,7 +146,7 @@ public class IntervalIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L " + validationDataLocation + "intervalTest.1.vcf",
                         1, // just one output file
-                        Arrays.asList(md5));
+                        Collections.singletonList(md5));
         executeTest("testIntervalParsingFromFile", spec);
     }
 
@@ -151,7 +161,7 @@ public class IntervalIntegrationTest extends WalkerTest {
                         " -L " + validationDataLocation + "intervalTest.1.vcf" +
                         " -L " + validationDataLocation + "intervalTest.2.vcf",
                         1, // just one output file
-                        Arrays.asList(md5));
+                        Collections.singletonList(md5));
         executeTest("testIntervalMergingFromFiles", spec);
     }
 
@@ -166,7 +176,7 @@ public class IntervalIntegrationTest extends WalkerTest {
                         " -L " + validationDataLocation + "intervalTest.1.vcf" +
                         " -XL " + validationDataLocation + "intervalTest.2.vcf",
                         1, // just one output file
-                        Arrays.asList(md5));
+                        Collections.singletonList(md5));
         executeTest("testIntervalExclusionsFromFiles", spec);
     }
 
@@ -181,7 +191,7 @@ public class IntervalIntegrationTest extends WalkerTest {
                         " -L " + validationDataLocation + "intervalTest.1.vcf" +
                         " -L chr1:1677524-1677528",
                         1, // just one output file
-                        Arrays.asList(md5));
+                        Collections.singletonList(md5));
         executeTest("testMixedIntervalMerging", spec);
     }
 
@@ -195,7 +205,7 @@ public class IntervalIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L " + validationDataLocation + "intervalTest.bed",
                         1, // just one output file
-                        Arrays.asList(md5));
+                        Collections.singletonList(md5));
         executeTest("testBed", spec);
     }
 
@@ -209,7 +219,7 @@ public class IntervalIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L " + validationDataLocation + "intervalTest.3.vcf",
                 1, // just one output file
-                Arrays.asList(md5));
+                Collections.singletonList(md5));
         executeTest("testComplexVCF", spec);
     }
 
@@ -224,7 +234,7 @@ public class IntervalIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L " + validationDataLocation + "intervalTest.3.vcf",
                 1, // just one output file
-                Arrays.asList(md5));
+                Collections.singletonList(md5));
         executeTest("testComplexVCFWithPadding", spec);
     }
 
@@ -239,7 +249,7 @@ public class IntervalIntegrationTest extends WalkerTest {
                         " -L " + validationDataLocation + "intervalTest.1.vcf" +
                         " -XL " + validationDataLocation + "intervalTest.3.vcf",
                         1, // just one output file
-                        Arrays.asList(md5));
+                        Collections.singletonList(md5));
         executeTest("testMergingWithComplexVCF", spec);
     }
 
@@ -253,7 +263,7 @@ public class IntervalIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L " + validationDataLocation + "intervalTest.empty.vcf",
                         1, // just one output file
-                        Arrays.asList(md5));
+                        Collections.singletonList(md5));
         executeTest("testEmptyVCFWarning", spec);
     }
 
@@ -268,7 +278,7 @@ public class IntervalIntegrationTest extends WalkerTest {
                         " -L " + validationDataLocation + "intervalTest.1.vcf" +
                         " -XL " + validationDataLocation + "intervalTest.1.vcf",
                         1, // just one output file
-                        Arrays.asList(md5));
+                        Collections.singletonList(md5));
         executeTest("testIncludeExcludeIsTheSame", spec);
     }
 
@@ -282,7 +292,7 @@ public class IntervalIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L " + privateTestDir + "symbolic_alleles_1.vcf",
                 1, // just one output file
-                Arrays.asList(md5));
+                Collections.singletonList(md5));
         executeTest("testSymbolicAlleles", spec);
     }
 
@@ -298,7 +308,7 @@ public class IntervalIntegrationTest extends WalkerTest {
                 " -isr INTERSECTION" +
                 " -o %s",
                 1, // just one output file
-                Arrays.asList(md5));
+                Collections.singletonList(md5));
         executeTest("testIntersectionOfLexicographicallySortedIntervals", spec);
     }
 }
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/InvalidArgumentIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/InvalidArgumentIntegrationTest.java
index ca9682747..985c3444a 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/InvalidArgumentIntegrationTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/InvalidArgumentIntegrationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/LoggingIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/LoggingIntegrationTest.java
index 73c177688..abb5fb61d 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/LoggingIntegrationTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/LoggingIntegrationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/CryptUtilsUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/CryptUtilsUnitTest.java
index beac3ace8..51d4c2434 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/CryptUtilsUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/CryptUtilsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyIntegrationTest.java
index 350ba7b75..2d2ce2bd3 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyIntegrationTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyIntegrationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -38,7 +38,7 @@ public class GATKKeyIntegrationTest extends WalkerTest {
     public static final String BASE_COMMAND = String.format("-T TestPrintReadsWalker -R %s -I %s -o %%s",
                                                             publicTestDir + "exampleFASTA.fasta",
                                                             publicTestDir + "exampleBAM.bam");
-    public static final String MD5_UPON_SUCCESSFUL_RUN = "e7b4a5b62f9d4badef1cd07040011b2b";
+    public static final String MD5_UPON_SUCCESSFUL_RUN = "462656ec9632f8c21ee534d35093c3f8";
 
 
     private void runGATKKeyTest ( String testName, String etArg, String keyArg, Class expectedException, String md5 ) {
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyUnitTest.java
index 89ef0b26e..2d1579501 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusViewUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusViewUnitTest.java
index 99d7559c4..02751f664 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusViewUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/AllLocusViewUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusViewUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusViewUnitTest.java
index 6665b7481..2c45ebc8c 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusViewUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/CoveredLocusViewUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedViewUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedViewUnitTest.java
index 791046a77..27936b5fe 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedViewUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/IntervalReferenceOrderedViewUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceViewUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceViewUnitTest.java
index 3f620f900..4115b97b1 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceViewUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceViewUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusViewTemplate.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusViewTemplate.java
index 72f2bb1ee..fc7857d84 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusViewTemplate.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/LocusViewTemplate.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceViewUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceViewUnitTest.java
index 8bf4f4103..342c9ca14 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceViewUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReadReferenceViewUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedViewUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedViewUnitTest.java
index dbc2f5518..ec26ba2b4 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedViewUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceOrderedViewUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceViewTemplate.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceViewTemplate.java
index bffd23da1..68ecabc10 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceViewTemplate.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ReferenceViewTemplate.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProviderUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProviderUnitTest.java
index 251eec49a..3ada2445f 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProviderUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/providers/ShardDataProviderUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancerUnitTest.java
index 258e61b49..afa700116 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancerUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ActiveRegionShardBalancerUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/DownsamplerBenchmark.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/DownsamplerBenchmark.java
index 7df9bc2cb..553ca998f 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/DownsamplerBenchmark.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/DownsamplerBenchmark.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointerUnitTest.java
index a54237bfb..7c016c3fa 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointerUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/FilePointerUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexUnitTest.java
index 289a10cf1..13f356959 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKBAMIndexUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -52,14 +52,19 @@ public class GATKBAMIndexUnitTest extends BaseTest {
      */
     private GATKBAMIndex bamIndex;
 
-    
+    /**
+     * Sequences.
+     */
+    private SAMSequenceDictionary sequenceDictionary;
+
+
     @BeforeClass
     public void init() throws FileNotFoundException {
         SAMFileReader reader = new SAMFileReader(bamFile);
-        SAMSequenceDictionary sequenceDictionary = reader.getFileHeader().getSequenceDictionary();
+        this.sequenceDictionary = reader.getFileHeader().getSequenceDictionary();
         reader.close();
         
-        bamIndex = new GATKBAMIndex(bamIndexFile);
+        bamIndex = new GATKBAMIndex(bamIndexFile, sequenceDictionary);
     }
 
     @Test
@@ -95,13 +100,13 @@ public class GATKBAMIndexUnitTest extends BaseTest {
 
     @Test( expectedExceptions = UserException.MalformedFile.class )
     public void testDetectTruncatedBamIndexWordBoundary() {
-        GATKBAMIndex index = new GATKBAMIndex(new File(privateTestDir + "truncated_at_word_boundary.bai"));
+        GATKBAMIndex index = new GATKBAMIndex(new File(privateTestDir + "truncated_at_word_boundary.bai"), sequenceDictionary);
         index.readReferenceSequence(0);
     }
 
     @Test( expectedExceptions = UserException.MalformedFile.class )
     public void testDetectTruncatedBamIndexNonWordBoundary() {
-        GATKBAMIndex index = new GATKBAMIndex(new File(privateTestDir + "truncated_at_non_word_boundary.bai"));
+        GATKBAMIndex index = new GATKBAMIndex(new File(privateTestDir + "truncated_at_non_word_boundary.bai"), sequenceDictionary);
         index.readReferenceSequence(0);
     }
 
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKWalkerBenchmark.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKWalkerBenchmark.java
index aa66d6636..1a42dd067 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKWalkerBenchmark.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/GATKWalkerBenchmark.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIteratorUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIteratorUnitTest.java
index 90ac7549e..817fcc112 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIteratorUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/IntervalOverlapFilteringIteratorUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/MockLocusShard.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/MockLocusShard.java
index bed203b3d..d006fcaba 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/MockLocusShard.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/MockLocusShard.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/PicardBaselineBenchmark.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/PicardBaselineBenchmark.java
index f96a35a79..90c75598e 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/PicardBaselineBenchmark.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/PicardBaselineBenchmark.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadProcessingBenchmark.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadProcessingBenchmark.java
index 71fc81aeb..a8973e16b 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadProcessingBenchmark.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadProcessingBenchmark.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancerUnitTest.java
index c4f6159a1..20a99f754 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancerUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancerUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSourceUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSourceUnitTest.java
index 8be72a22c..16f43f98e 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSourceUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSourceUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderIDUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderIDUnitTest.java
index c975fb166..b8bf0eadb 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderIDUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMReaderIDUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SeekableBufferedStreamUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SeekableBufferedStreamUnitTest.java
index c67cadb8d..201d9c41d 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SeekableBufferedStreamUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SeekableBufferedStreamUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/TheoreticalMinimaBenchmark.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/TheoreticalMinimaBenchmark.java
index aa66f179f..039ca4d5e 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/TheoreticalMinimaBenchmark.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/TheoreticalMinimaBenchmark.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSourceIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSourceIntegrationTest.java
index a544d716a..36cbb58bf 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSourceIntegrationTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/reference/ReferenceDataSourceIntegrationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java
index a77c0961c..15bc5b731 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java
index 514b85737..0f6f9e384 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingIntegrationTest.java
index c98243adc..8dac72faa 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingIntegrationTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingIntegrationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIteratorUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIteratorUnitTest.java
index 27804c6d1..4fbb02a92 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIteratorUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/DownsamplingReadsIteratorUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerUnitTest.java
index 8e3ac5f49..af7e5716c 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/FractionalDownsamplerUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsamplerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsamplerUnitTest.java
index 74a936782..e3f2fee1a 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsamplerUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/LevelingDownsamplerUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java
index fdc8587ba..219307802 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/PositionallyDownsampledArtificialSingleSampleReadStreamAnalyzer.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/PositionallyDownsampledArtificialSingleSampleReadStreamAnalyzer.java
index b8a57e791..d23fb1b7c 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/PositionallyDownsampledArtificialSingleSampleReadStreamAnalyzer.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/PositionallyDownsampledArtificialSingleSampleReadStreamAnalyzer.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerUnitTest.java
index 88a1c5d5c..87e2ac868 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/ReservoirDownsamplerUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerUnitTest.java
index c22a3eaed..47a1179b2 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/downsampling/SimplePositionalDownsamplerUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/executive/ReduceTreeUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/executive/ReduceTreeUnitTest.java
index 50f21a62e..44432cfac 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/executive/ReduceTreeUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/executive/ReduceTreeUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/AllowNCigarMalformedReadFilterUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/AllowNCigarMalformedReadFilterUnitTest.java
index d3fb18896..c0e48a974 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/AllowNCigarMalformedReadFilterUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/AllowNCigarMalformedReadFilterUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/BadCigarFilterUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/BadCigarFilterUnitTest.java
index f774af092..109c64c72 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/BadCigarFilterUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/BadCigarFilterUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/BadReadGroupsIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/BadReadGroupsIntegrationTest.java
index f4232067d..9f21233aa 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/BadReadGroupsIntegrationTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/BadReadGroupsIntegrationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -35,7 +35,7 @@ public class BadReadGroupsIntegrationTest extends WalkerTest {
     @Test
     public void testMissingReadGroup() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T TestPrintReadsWalker -R " + b36KGReference + " -I " + privateTestDir + "missingReadGroup.bam -o /dev/null",
+                "-T TestPrintReadsWalker -R " + hg18Reference + " -I " + privateTestDir + "missingReadGroup.bam -o /dev/null",
                 0,
                 UserException.ReadMissingReadGroup.class);
         executeTest("test Missing Read Group", spec);
@@ -44,7 +44,7 @@ public class BadReadGroupsIntegrationTest extends WalkerTest {
     @Test
     public void testUndefinedReadGroup() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T TestPrintReadsWalker -R " + b36KGReference + " -I " + privateTestDir + "undefinedReadGroup.bam -o /dev/null",
+                "-T TestPrintReadsWalker -R " + hg18Reference + " -I " + privateTestDir + "undefinedReadGroup.bam -o /dev/null",
                 0,
                 UserException.ReadHasUndefinedReadGroup.class);
         executeTest("test Undefined Read Group", spec);
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilterUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilterUnitTest.java
index 405610011..aec599099 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilterUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/MalformedReadFilterUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformerUnitTest.java
index beb4123fe..6a35f0b3e 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformerUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/NDNCigarReadTransformerUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/OverclippedReadFilterUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/OverclippedReadFilterUnitTest.java
index 3400b61e9..2e28ef0da 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/OverclippedReadFilterUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/OverclippedReadFilterUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -42,11 +42,12 @@ import java.util.*;
 public class OverclippedReadFilterUnitTest extends ReadFilterTest {
 
     @Test(enabled = true, dataProvider= "OverclippedDataProvider")
-    public void testOverclippedFilter(final String cigarString, final boolean expectedResult) {
+    public void testOverclippedFilter(final String cigarString, boolean doNotRequireSoftclipsOnBothEnds, final boolean expectedResult) {
 
-       final OverclippedReadFilter filter = new OverclippedReadFilter();
-       final SAMRecord read = buildSAMRecord(cigarString);
-       Assert.assertEquals(filter.filterOut(read), expectedResult, cigarString);
+        final OverclippedReadFilter filter = new OverclippedReadFilter();
+        filter.doNotRequireSoftclipsOnBothEnds = doNotRequireSoftclipsOnBothEnds;
+        final SAMRecord read = buildSAMRecord(cigarString);
+        Assert.assertEquals(filter.filterOut(read), expectedResult, cigarString);
     }
 
     private SAMRecord buildSAMRecord(final String cigarString) {
@@ -58,20 +59,47 @@ public class OverclippedReadFilterUnitTest extends ReadFilterTest {
     public Iterator overclippedDataProvider() {
         final List result = new LinkedList();
 
-        result.add(new Object[] { "1S10M1S", true });
-        result.add(new Object[] { "1S10X1S", true });
-        result.add(new Object[] { "1H1S10M1S1H", true });
-        result.add(new Object[] { "1S40M1S", false });
-        result.add(new Object[] { "1S40X1S", false });
-        result.add(new Object[] { "1H10M1S", false });
-        result.add(new Object[] { "1S10M1H", false });
-        result.add(new Object[] { "10M1S", false });
-        result.add(new Object[] { "1S10M", false });
-        result.add(new Object[] { "1S10M10D10M1S", true });
-        result.add(new Object[] { "1S1M40I1S", false });
-        result.add(new Object[] { "1S10I1S", true });
-        result.add(new Object[] { "1S40I1S", false });
+        result.add(new Object[] { "1S10M1S", false, true });
+        result.add(new Object[] { "1S10X1S", false, true });
+        result.add(new Object[] { "1H1S10M1S1H", false, true });
+        result.add(new Object[] { "1S40M1S", false, false});
+        result.add(new Object[] { "1S40X1S", false, false });
+        result.add(new Object[] { "1H10M1S", false, false});
+        result.add(new Object[] { "1S10M1H", false, false});
+
+        result.add(new Object[] { "10M1S", false, false});
+        result.add(new Object[] { "1S10M", false, false});
+
+        result.add(new Object[] { "10M1S", true, true});
+        result.add(new Object[] { "1S10M", true, true});
+
+        result.add(new Object[] { "1S10M10D10M1S", false, true });
+        result.add(new Object[] { "1S1M40I1S", false, false });
+
+        result.add(new Object[] { "1S10I1S", false, true });
+        result.add(new Object[] { "1S40I1S", false, false });
+        result.add(new Object[] { "1S40I1S", true, false });
+
+        result.add(new Object[] { "25S40I25M", true, false });
+
+        //Read is too short once soft-clipping removed
+        result.add(new Object[] { "25S25M", true, true });
+        result.add(new Object[] { "25S25X", true, true });
+        result.add(new Object[] { "25S25H", true, true });
+        result.add(new Object[] { "25S25H", false, false });
+
+        result.add(new Object[] { "25S25M25S", false, true });
+        result.add(new Object[] { "25M25S", true, true });
+        result.add(new Object[] { "25S25M", true, true });
+
+        result.add(new Object[] { "25S35S", true, true });
+
+        //Read long enough even with soft clipping removed
+        result.add(new Object[] { "25S35M25S", true, false });
+        result.add(new Object[] { "35M25S", true, false });
+        result.add(new Object[] { "25S35M", true, false });
 
         return result.iterator();
     }
+
 }
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/ReadFilterTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/ReadFilterTest.java
index d997f3758..9c3e3904d 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/ReadFilterTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/ReadFilterTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilterUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilterUnitTest.java
index 3a0fc6ebd..8f11220ac 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilterUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/ReadGroupBlackListFilterUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/UnsafeMalformedReadFilterUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/UnsafeMalformedReadFilterUnitTest.java
index 343ad656e..38b1cb7c2 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/UnsafeMalformedReadFilterUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/UnsafeMalformedReadFilterUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/io/OutputTrackerUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/io/OutputTrackerUnitTest.java
index 479e19ebe..1e00065a4 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/io/OutputTrackerUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/io/OutputTrackerUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/io/stubs/ArgumentTypeDescriptorUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/io/stubs/ArgumentTypeDescriptorUnitTest.java
index 60e529281..ecffcfc55 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/io/stubs/ArgumentTypeDescriptorUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/io/stubs/ArgumentTypeDescriptorUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIteratorUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIteratorUnitTest.java
index b295e1230..3c5d84cf0 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIteratorUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/BoundedReadIteratorUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapterUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapterUnitTest.java
index fc7465de3..9f2589d70 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapterUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/GATKSAMIteratorAdapterUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityUnitTest.java
index 994de2b28..d743d0021 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIteratorUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIteratorUnitTest.java
index c12bb1551..a931bcb18 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIteratorUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/ReadFormattingIteratorUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIteratorUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIteratorUnitTest.java
index c7e7d05d5..4e3c20590 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIteratorUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/iterators/VerifyingSamIteratorUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportUnitTest.java
index 3042e3082..bcfb60c38 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/phonehome/GATKRunReportUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/PedReaderUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/PedReaderUnitTest.java
index cd6014bcd..b059f8d50 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/PedReaderUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/PedReaderUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/SampleDBUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/SampleDBUnitTest.java
index fc934ef06..d6d1ed216 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/SampleDBUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/SampleDBUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -117,6 +117,9 @@ public class SampleDBUnitTest extends BaseTest {
     private static final String testPEDStringInconsistentGender =
             "fam1 kid 0   0   2 2";
 
+    private static final String testPEDStringConsistent =
+            "fam1 kid dad   mom   1 2";
+
     private static final Set testPEDSamplesAsSet =
             new HashSet(testPEDSamples);
 
@@ -128,20 +131,20 @@ public class SampleDBUnitTest extends BaseTest {
 
     @Test()
     public void loadPEDFile() {
-        builder.addSamplesFromPedigreeFiles(Arrays.asList(testPED));
-        SampleDB db = builder.getFinalSampleDB();
+        final SampleDB db = builder.addSamplesFromPedigreeFiles(Arrays.asList(testPED))
+                                   .getFinalSampleDB();
         Assert.assertEquals(testPEDSamplesAsSet, db.getSamples());
     }
 
     @Test()
     public void loadPEDString() {
-        builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDString));
-        SampleDB db = builder.getFinalSampleDB();
+        final SampleDB db = builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDString))
+                             .getFinalSampleDB();
         Assert.assertEquals(testPEDSamplesAsSet, db.getSamples());
     }
 
     private static final void addSAMHeader() {
-        SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 10);
+        final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 10);
         ArtificialSAMUtils.createEnumeratedReadGroups(header, Arrays.asList("1", "2", "3"),
                 Arrays.asList("kid", "mom", "dad"));
         builder.addSamplesFromSAMHeader(header);
@@ -150,66 +153,84 @@ public class SampleDBUnitTest extends BaseTest {
     @Test()
     public void loadSAMHeader() {
         addSAMHeader();
-        SampleDB db = builder.getFinalSampleDB();
+        final SampleDB db = builder.getFinalSampleDB();
         Assert.assertEquals(testSAMSamples, db.getSamples());
     }
 
     @Test()
     public void loadSAMHeaderPlusPED() {
         addSAMHeader();
-        builder.addSamplesFromPedigreeFiles(Arrays.asList(testPED));
-        SampleDB db = builder.getFinalSampleDB();
+        final SampleDB db = builder.addSamplesFromPedigreeFiles(Arrays.asList(testPED))
+                                   .getFinalSampleDB();
         Assert.assertEquals(testPEDSamples, db.getSamples());
     }
 
     @Test()
     public void loadDuplicateData() {
-        builder.addSamplesFromPedigreeFiles(Arrays.asList(testPED));
-        builder.addSamplesFromPedigreeFiles(Arrays.asList(testPED));
-        SampleDB db = builder.getFinalSampleDB();
+        final SampleDB db = builder.addSamplesFromPedigreeFiles(Arrays.asList(testPED))
+                                   .addSamplesFromPedigreeFiles(Arrays.asList(testPED))
+                                   .getFinalSampleDB();
         Assert.assertEquals(testPEDSamples, db.getSamples());
     }
 
     @Test(expectedExceptions = UserException.class)
     public void loadNonExistentFile() {
-        builder.addSamplesFromPedigreeFiles(Arrays.asList(new File("non-existence-file.txt")));
-        SampleDB db = builder.getFinalSampleDB();
+        final SampleDB db = builder.addSamplesFromPedigreeFiles(Arrays.asList(new File("non-existence-file.txt")))
+                           .getFinalSampleDB();
         Assert.assertEquals(testSAMSamples, db.getSamples());
     }
 
     @Test(expectedExceptions = UserException.class)
     public void loadInconsistentData() {
-        builder = new SampleDBBuilder(PedigreeValidationType.STRICT);
-        builder.addSamplesFromPedigreeFiles(Arrays.asList(testPED));
-        builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDStringInconsistentGender));
+        builder = new SampleDBBuilder(PedigreeValidationType.STRICT)
+                      .addSamplesFromPedigreeFiles(Arrays.asList(testPED))
+                      .addSamplesFromPedigreeStrings(Arrays.asList(testPEDStringInconsistentGender));
         builder.getFinalSampleDB();
     }
 
+    @Test
+    public void loadConsistentData() {
+        // build a temporary DB and get the resulting sample to use for test result comparison
+        final Sample baseKidSample = new SampleDBBuilder(PedigreeValidationType.STRICT)
+                                        .addSamplesFromPedigreeStrings(Arrays.asList(testPEDStringConsistent))
+                                        .getFinalSampleDB()
+                                        .getSample("kid");
+
+        // build a sample DB and then merge in the consistent test string
+        final SampleDB finalDB = new SampleDBBuilder(PedigreeValidationType.STRICT)
+                                     .addSamplesFromPedigreeFiles(Arrays.asList(testPED))
+                                     .addSamplesFromPedigreeStrings(Arrays.asList(testPEDStringConsistent))
+                                     .getFinalSampleDB();
+
+        Assert.assertEquals(finalDB.getSamples().size(), 3);
+        Assert.assertTrue(finalDB.getSample("kid").equals(baseKidSample));
+    }
+
     @Test(expectedExceptions = UserException.class)
     public void sampleInSAMHeaderNotInSamplesDB() {
         addSAMHeader();
-        builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDStringInconsistentGender));
-        builder.getFinalSampleDB();
+        builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDStringInconsistentGender))
+               .getFinalSampleDB();
     }
 
     @Test()
     public void getFamilyIDs() {
-        builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDMultipleFamilies));
-        SampleDB db = builder.getFinalSampleDB();
+        final SampleDB db = builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDMultipleFamilies))
+                                   .getFinalSampleDB();
         Assert.assertEquals(db.getFamilyIDs(), new TreeSet(Arrays.asList("fam1", "fam2", "fam3")));
     }
 
     @Test()
     public void getFamily() {
-        builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDMultipleFamilies));
-        SampleDB db = builder.getFinalSampleDB();
+        final SampleDB db = builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDMultipleFamilies))
+                                   .getFinalSampleDB();
         Assert.assertEquals(db.getFamily("fam1"), testPEDSamplesAsSet);
     }
 
     @Test()
     public void getFamilies(){
-        builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDMultipleFamilies));
-        SampleDB db = builder.getFinalSampleDB();
+        final SampleDB db = builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDMultipleFamilies))
+                                   .getFinalSampleDB();
         Assert.assertEquals(db.getFamilies(),testGetFamilies);
         Assert.assertEquals(db.getFamilies(null),testGetFamilies);
         Assert.assertEquals(db.getFamilies(testGetPartialFamiliesIds),testGetPartialFamilies);
@@ -218,8 +239,8 @@ public class SampleDBUnitTest extends BaseTest {
     @Test()
     public void testGetChildrenWithParents()
     {
-        builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDMultipleFamilies2));
-        SampleDB db = builder.getFinalSampleDB();
+        final SampleDB db = builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDMultipleFamilies2))
+                                   .getFinalSampleDB();
         Assert.assertEquals(db.getChildrenWithParents(), testKidsWithParentsFamilies2);
         Assert.assertEquals(db.getChildrenWithParents(false), testKidsWithParentsFamilies2);
         Assert.assertEquals(db.getChildrenWithParents(true), new HashSet(Arrays.asList(new Sample("kid", "fam1", "dad", "mom", Gender.MALE,   Affection.AFFECTED))));
@@ -227,16 +248,16 @@ public class SampleDBUnitTest extends BaseTest {
 
     @Test()
     public void testGetFounderIds(){
-        builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDMultipleFamilies2));
-        SampleDB db = builder.getFinalSampleDB();
+        final SampleDB db = builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDMultipleFamilies2))
+                                   .getFinalSampleDB();
         Assert.assertEquals(db.getFounderIds(), new HashSet(Arrays.asList("dad","mom","dad2","mom2","dad4")));
     }
 
     @Test()
     public void loadFamilyIDs() {
-        builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDMultipleFamilies));
-        SampleDB db = builder.getFinalSampleDB();
-        Map> families = db.getFamilies();
+        final SampleDB db = builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDMultipleFamilies))
+                                   .getFinalSampleDB();
+        final Map> families = db.getFamilies();
         Assert.assertEquals(families.size(), 3);
         Assert.assertEquals(families.keySet(), new TreeSet(Arrays.asList("fam1", "fam2", "fam3")));
 
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/SampleUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/SampleUnitTest.java
index b1b09db01..4e63d5dbe 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/SampleUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/samples/SampleUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/DummyActiveRegionWalker.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/DummyActiveRegionWalker.java
index b32a3db63..e17ff3e73 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/DummyActiveRegionWalker.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/DummyActiveRegionWalker.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCacheUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCacheUnitTest.java
index 75c669c1d..88421abc0 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCacheUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TAROrderedReadCacheUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegionsUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegionsUnitTest.java
index 5b710a10d..c69774b7b 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegionsUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegionsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicatesUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicatesUnitTest.java
index a332be127..10f6801f3 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicatesUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseDuplicatesUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsUnitTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsUnitTest.java
index a03802635..099d9e20c 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsUnitTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseReadsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestCountLociWalker.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestCountLociWalker.java
index 8b7a8d758..8bf453300 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestCountLociWalker.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestCountLociWalker.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestCountReadsWalker.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestCountReadsWalker.java
index cc0162fc1..7362c4d3c 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestCountReadsWalker.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestCountReadsWalker.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestErrorThrowingWalker.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestErrorThrowingWalker.java
index 00774f7b7..d5308a375 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestErrorThrowingWalker.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestErrorThrowingWalker.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestPrintReadsWalker.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestPrintReadsWalker.java
index bbf653ac1..e3c852eae 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestPrintReadsWalker.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestPrintReadsWalker.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestPrintVariantsWalker.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestPrintVariantsWalker.java
index 8af514693..89d630d9f 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestPrintVariantsWalker.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/TestPrintVariantsWalker.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java
index ff6b1242f..e19f6c8dd 100644
--- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java
+++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/walkers/WalkerTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentDefinitionField.java b/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentDefinitionField.java
index 1a6cda658..849d994ae 100644
--- a/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentDefinitionField.java
+++ b/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentDefinitionField.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentField.java b/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentField.java
index 9c93efd5d..d4e0aea36 100644
--- a/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentField.java
+++ b/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentField.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/GATKExtensionsGenerator.java b/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/GATKExtensionsGenerator.java
index 3b7f7db17..90adfc206 100644
--- a/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/GATKExtensionsGenerator.java
+++ b/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/GATKExtensionsGenerator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ReadFilterField.java b/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ReadFilterField.java
index b23f1aafa..581aef077 100644
--- a/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ReadFilterField.java
+++ b/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ReadFilterField.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/CNV/ONLY_GENOTYPE_xhmmCNVpipeline.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/CNV/ONLY_GENOTYPE_xhmmCNVpipeline.scala
index 83379787f..c2ff1c4b6 100644
--- a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/CNV/ONLY_GENOTYPE_xhmmCNVpipeline.scala
+++ b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/CNV/ONLY_GENOTYPE_xhmmCNVpipeline.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/CNV/xhmmCNVpipeline.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/CNV/xhmmCNVpipeline.scala
index d031f5d4d..fd7698f09 100644
--- a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/CNV/xhmmCNVpipeline.scala
+++ b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/CNV/xhmmCNVpipeline.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/GATKResourcesBundle.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/GATKResourcesBundle.scala
index ccc0cb56a..ef6baffbb 100644
--- a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/GATKResourcesBundle.scala
+++ b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/GATKResourcesBundle.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCountLoci.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCountLoci.scala
index e988a42a5..0900b369f 100644
--- a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCountLoci.scala
+++ b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCountLoci.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCountReads.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCountReads.scala
index 55711c026..65da43863 100644
--- a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCountReads.scala
+++ b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCountReads.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCustomWalker.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCustomWalker.scala
index e38ba3ef7..9826494f7 100644
--- a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCustomWalker.scala
+++ b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleCustomWalker.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExamplePrintReads.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExamplePrintReads.scala
index f3c4bf382..8d300f988 100644
--- a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExamplePrintReads.scala
+++ b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExamplePrintReads.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleReadFilter.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleReadFilter.scala
index f736406d1..20798a38e 100644
--- a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleReadFilter.scala
+++ b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleReadFilter.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleRetryMemoryLimit.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleRetryMemoryLimit.scala
index 71e009469..34a25562e 100644
--- a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleRetryMemoryLimit.scala
+++ b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExampleRetryMemoryLimit.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/HelloWorld.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/HelloWorld.scala
index c095169b7..7564da943 100644
--- a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/HelloWorld.scala
+++ b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/HelloWorld.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/ChunkVCF.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/ChunkVCF.scala
index ab687c020..2cf5b765c 100644
--- a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/ChunkVCF.scala
+++ b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/ChunkVCF.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/Vcf2Table.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/Vcf2Table.scala
index eb57d2e5f..aaa071d28 100755
--- a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/Vcf2Table.scala
+++ b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/Vcf2Table.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/VcfToPed.scala b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/VcfToPed.scala
index 962d495d3..85bb70f0c 100644
--- a/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/VcfToPed.scala
+++ b/public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/lib/VcfToPed.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/cancer/MuTect.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/cancer/MuTect.scala
index f116af51a..d8ade79a5 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/cancer/MuTect.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/cancer/MuTect.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/BamGatherFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/BamGatherFunction.scala
index 53885109e..e502bb701 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/BamGatherFunction.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/BamGatherFunction.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/CatVariantsGatherer.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/CatVariantsGatherer.scala
index fd91e5352..e111e1984 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/CatVariantsGatherer.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/CatVariantsGatherer.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/ContigScatterFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/ContigScatterFunction.scala
index e1da454f5..d7d79bc27 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/ContigScatterFunction.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/ContigScatterFunction.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/DistributedScatterFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/DistributedScatterFunction.scala
index f4ad99390..49d51ef69 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/DistributedScatterFunction.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/DistributedScatterFunction.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/DoC/package.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/DoC/package.scala
index fc999d04a..4df0ac7cb 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/DoC/package.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/DoC/package.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKIntervals.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKIntervals.scala
index c1d71e281..72e73956e 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKIntervals.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKIntervals.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKScatterFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKScatterFunction.scala
index 12fea171b..afe465563 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKScatterFunction.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKScatterFunction.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/IntervalScatterFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/IntervalScatterFunction.scala
index 99454d459..8fd76224d 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/IntervalScatterFunction.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/IntervalScatterFunction.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/LocusScatterFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/LocusScatterFunction.scala
index 5d71d3585..7983f56e2 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/LocusScatterFunction.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/LocusScatterFunction.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/ReadScatterFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/ReadScatterFunction.scala
index 01e9eed2d..4a7deeac1 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/ReadScatterFunction.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/ReadScatterFunction.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/TaggedFile.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/TaggedFile.scala
index e1612091f..967a00d5a 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/TaggedFile.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/TaggedFile.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/VcfGatherFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/VcfGatherFunction.scala
index 68664c34b..6ba815b8e 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/VcfGatherFunction.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/VcfGatherFunction.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/WriteFlankingIntervalsFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/WriteFlankingIntervalsFunction.scala
index 290eff973..0f89fe38e 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/WriteFlankingIntervalsFunction.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/WriteFlankingIntervalsFunction.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/XHMM/package.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/XHMM/package.scala
index 36fcdc74d..153cf4b95 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/XHMM/package.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/gatk/XHMM/package.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/AddOrReplaceReadGroups.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/AddOrReplaceReadGroups.scala
index 6b70d2f58..e02863f20 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/AddOrReplaceReadGroups.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/AddOrReplaceReadGroups.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CalculateHsMetrics.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CalculateHsMetrics.scala
index 68c4ca730..fb6e4d538 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CalculateHsMetrics.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CalculateHsMetrics.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -58,11 +58,15 @@ class CalculateHsMetrics extends org.broadinstitute.gatk.queue.function.JavaComm
   @Argument(doc="The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE, LIBRARY, READ_GROUP} This option may be specified 0 or more times.", shortName = "level", fullName = "metric_accumulation_level", required = false)
   var level: Seq[picard.analysis.MetricAccumulationLevel] = Seq(MetricAccumulationLevel.SAMPLE)
 
+  @Argument(doc="Optional file to output per-target coverage", shortName = "coverage", fullName = "per_target_coverage", required = false)
+  var perTargetCoverage: File = _
+
   override def inputBams = input
   override def outputFile = output
   override def commandLine = super.commandLine +
     required("BAIT_INTERVALS=" + baits) +
     required("TARGET_INTERVALS=" + targets) +
     required("REFERENCE_SEQUENCE=" + reference) +
-    repeat("METRIC_ACCUMULATION_LEVEL=", level, spaceSeparated=false, escape=true, format="%s")
+    repeat("METRIC_ACCUMULATION_LEVEL=", level, spaceSeparated=false, escape=true, format="%s") +
+    optional("PER_TARGET_COVERAGE=", perTargetCoverage, spaceSeparated = false)
 }
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CollectGcBiasMetrics.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CollectGcBiasMetrics.scala
index f0d2300c4..f36d14afd 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CollectGcBiasMetrics.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CollectGcBiasMetrics.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CollectMultipleMetrics.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CollectMultipleMetrics.scala
index 15073668a..022179b1d 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CollectMultipleMetrics.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CollectMultipleMetrics.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CollectWgsMetrics.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CollectWgsMetrics.scala
new file mode 100644
index 000000000..923ce0005
--- /dev/null
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CollectWgsMetrics.scala
@@ -0,0 +1,70 @@
+/*
+* Copyright 2012-2015 Broad Institute, Inc.
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.gatk.queue.extensions.picard
+
+import org.broadinstitute.gatk.utils.commandline.{Argument, Output, Input}
+import java.io.File
+
+class CollectWgsMetrics extends org.broadinstitute.gatk.queue.function.JavaCommandLineFunction with PicardMetricsFunction {
+  analysisName = "CollectWgsMetrics"
+  javaMainClass = "picard.analysis.CollectWgsMetrics"
+
+  @Input(doc = "The input SAM or BAM files to analyze", shortName = "i", fullName = "input_bam_files", required = true)
+  var input: Seq[File] = Nil
+
+  @Output(doc = "The output file to write statistics to", shortName = "o", fullName = "output_file", required = true)
+  var output: File = _
+
+  @Argument(doc = "Reference file", shortName = "r", fullName = "reference", required = true)
+  var reference: File = _
+
+  @Argument(doc = "Minimum mapping quality for a read to contribute coverage.", shortName = "mq", fullName = "minimum_mapping_quality", required = false)
+  var mq: Integer = _
+
+  @Argument(doc = "Minimum base quality for a base to contribute coverage.", shortName = "q", fullName = "minimum_base_quality", required = false)
+  var q: Integer = _
+
+  @Argument(doc = "Treat bases with coverage exceeding this value as if they had coverage at this value.", shortName = "cap", fullName = "coverage_cap", required = false)
+  var cap: Integer = _
+
+  @Argument(doc = "For debugging purposes, stop after processing this many genomic bases.", fullName = "stop_after", required = false)
+  var stopAfter: Long = _
+
+  @Argument(doc = "Determines whether to include the base quality histogram in the metrics file.", fullName = "include_bq_histogram", required = false)
+  var includeBQHistogram: Boolean = _
+
+  override def inputBams = input
+
+  override def outputFile = output
+
+  override def commandLine = super.commandLine +
+    required("REFERENCE_SEQUENCE=" + reference) +
+    optional("MQ=", mq, spaceSeparated = false) +
+    optional("Q=", q, spaceSeparated = false) +
+    optional("CAP=", cap, spaceSeparated = false) +
+    optional("STOP_AFTER=", stopAfter, spaceSeparated = false) +
+    optional("INCLUDE_BQ_HISTOGRAM=", includeBQHistogram, spaceSeparated = false)
+}
\ No newline at end of file
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/FastqToSam.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/FastqToSam.scala
index 44e10af86..24b88b185 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/FastqToSam.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/FastqToSam.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/MarkDuplicates.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/MarkDuplicates.scala
index fe7739093..94b88c81d 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/MarkDuplicates.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/MarkDuplicates.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/MergeSamFiles.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/MergeSamFiles.scala
index 1b25a8e6c..e0d07b245 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/MergeSamFiles.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/MergeSamFiles.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/PicardBamFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/PicardBamFunction.scala
index 80a60c502..2be93f04e 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/PicardBamFunction.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/PicardBamFunction.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/PicardMetricsFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/PicardMetricsFunction.scala
index b9885a969..2b0ef1a72 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/PicardMetricsFunction.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/PicardMetricsFunction.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/ReorderSam.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/ReorderSam.scala
index 1813694a3..482a6b57f 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/ReorderSam.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/ReorderSam.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/RevertSam.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/RevertSam.scala
index 2012b543e..d79ed96d6 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/RevertSam.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/RevertSam.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/SamToFastq.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/SamToFastq.scala
index e5624fcd6..7a65d5e9e 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/SamToFastq.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/SamToFastq.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/SortSam.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/SortSam.scala
index 847ed9238..663186e0c 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/SortSam.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/SortSam.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/ValidateSamFile.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/ValidateSamFile.scala
index e9ad0970f..11f51356e 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/ValidateSamFile.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/ValidateSamFile.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsCommandLineFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsCommandLineFunction.scala
index a7e603074..54400a01e 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsCommandLineFunction.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsCommandLineFunction.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsIndexFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsIndexFunction.scala
index cb55c06fb..86a5a12e2 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsIndexFunction.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsIndexFunction.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsMergeFunction.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsMergeFunction.scala
index 4d7c0c6fd..a3a60b629 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsMergeFunction.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/samtools/SamtoolsMergeFunction.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/snpeff/SnpEff.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/snpeff/SnpEff.scala
index ae316bcc2..fb8b8b8ee 100644
--- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/snpeff/SnpEff.scala
+++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/snpeff/SnpEff.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKIntervalsUnitTest.scala b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKIntervalsUnitTest.scala
index f2ec8a929..bc7f85c6f 100644
--- a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKIntervalsUnitTest.scala
+++ b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/extensions/gatk/GATKIntervalsUnitTest.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/extensions/gatk/QueueFeaturesQueueTest.scala b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/extensions/gatk/QueueFeaturesQueueTest.scala
index f1db69e1c..010382233 100644
--- a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/extensions/gatk/QueueFeaturesQueueTest.scala
+++ b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/extensions/gatk/QueueFeaturesQueueTest.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -43,7 +43,7 @@ class QueueFeaturesQueueTest {
       " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
       " -I " + BaseTest.publicTestDir + "exampleBAM_with_unmapped.bam",
       " -out " + testOut).mkString
-    spec.fileMD5s += testOut -> "c7f086293509b1c506f7a25b13754637"
+    spec.fileMD5s += testOut -> "3134a6c732d7f235373095586bc7d470"
     QueueTest.executeTest(spec)
 
     //Second case: When intervals are explicitly provided, unmapped reads should not be included
@@ -56,7 +56,7 @@ class QueueFeaturesQueueTest {
       " -I " + BaseTest.publicTestDir + "exampleBAM_with_unmapped.bam",
       " -L chr1",
       " -out " + testOut2).mkString
-    spec2.fileMD5s += testOut2 -> "44bda07e3421a79c56213900ad3f7d7c"
+    spec2.fileMD5s += testOut2 -> "aa33e589879c4baf6a470d22da76d885"
     QueueTest.executeTest(spec2)
   }
 
diff --git a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleCountLociQueueTest.scala b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleCountLociQueueTest.scala
index f6cc7465f..5e3474098 100644
--- a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleCountLociQueueTest.scala
+++ b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleCountLociQueueTest.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleCountReadsQueueTest.scala b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleCountReadsQueueTest.scala
index e79ea8a9f..189a88c21 100644
--- a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleCountReadsQueueTest.scala
+++ b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleCountReadsQueueTest.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExamplePrintReadsQueueTest.scala b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExamplePrintReadsQueueTest.scala
index fcaf0d7cf..4829db78c 100644
--- a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExamplePrintReadsQueueTest.scala
+++ b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExamplePrintReadsQueueTest.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleReadFilterQueueTest.scala b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleReadFilterQueueTest.scala
index af701740e..39b74dcf0 100644
--- a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleReadFilterQueueTest.scala
+++ b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleReadFilterQueueTest.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleRetryMemoryLimitQueueTest.scala b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleRetryMemoryLimitQueueTest.scala
index dddccaa83..46f630b57 100644
--- a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleRetryMemoryLimitQueueTest.scala
+++ b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleRetryMemoryLimitQueueTest.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/HelloWorldQueueTest.scala b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/HelloWorldQueueTest.scala
index cef77f961..1e51d75e2 100644
--- a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/HelloWorldQueueTest.scala
+++ b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/HelloWorldQueueTest.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -149,4 +149,23 @@ class HelloWorldQueueTest {
     spec.expectedFilePaths = Seq("pipelineLogDir/HelloWorld-1.out")
     QueueTest.executeTest(spec)
   }
+
+  @Test(timeOut=36000000)
+  def testHelloWorldParallelShell() {
+    val spec = new QueueTestSpec
+    spec.name = "HelloWorldWithLogDirectory"
+    spec.args = "-S " + QueueTest.publicQScriptsPackageDir + "examples/HelloWorld.scala"
+    spec.jobRunners = Seq("ParallelShell")
+    QueueTest.executeTest(spec)
+  }
+
+  @Test(timeOut=36000000)
+  def testHelloWorldParallelShellMaxConcurrentRun() {
+    val spec = new QueueTestSpec
+    spec.name = "HelloWorldWithLogDirectory"
+    spec.args = "-S " + QueueTest.publicQScriptsPackageDir + "examples/HelloWorld.scala" +
+      " -maxConcurrentRun 10"
+    spec.jobRunners = Seq("ParallelShell")
+    QueueTest.executeTest(spec)
+  }
 }
diff --git a/public/gatk-queue/src/main/java/org/broadinstitute/gatk/queue/QueueVersion.java b/public/gatk-queue/src/main/java/org/broadinstitute/gatk/queue/QueueVersion.java
index e5e9dcb08..f3d5a7db5 100644
--- a/public/gatk-queue/src/main/java/org/broadinstitute/gatk/queue/QueueVersion.java
+++ b/public/gatk-queue/src/main/java/org/broadinstitute/gatk/queue/QueueVersion.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/java/org/broadinstitute/gatk/queue/package-info.java b/public/gatk-queue/src/main/java/org/broadinstitute/gatk/queue/package-info.java
index 755b69683..24722a083 100644
--- a/public/gatk-queue/src/main/java/org/broadinstitute/gatk/queue/package-info.java
+++ b/public/gatk-queue/src/main/java/org/broadinstitute/gatk/queue/package-info.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QCommandLine.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QCommandLine.scala
index 843743e48..7994ae9a5 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QCommandLine.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QCommandLine.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QCommandPlugin.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QCommandPlugin.scala
index 6df8b3c36..1e22d7ed9 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QCommandPlugin.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QCommandPlugin.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QException.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QException.scala
index 1ae41e950..80ffe558a 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QException.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QException.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QScript.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QScript.scala
index f01044539..541da93c9 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QScript.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QScript.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -82,8 +82,7 @@ trait QScript extends Logging with PrimitiveOptionConversions with StringFileCon
    * @param newExtension New extension to append.
    * @return new File with the new extension in the current directory.
    */
-  protected def swapExt(file: File, oldExtension: String, newExtension: String) =
-    new File(file.getName.stripSuffix(oldExtension) + newExtension)
+  protected def swapExt(file: File, oldExtension: String, newExtension: String) = QScriptUtils.swapExt(file, oldExtension, newExtension)
 
   /**
    * Exchanges the extension on a file.
@@ -93,8 +92,7 @@ trait QScript extends Logging with PrimitiveOptionConversions with StringFileCon
    * @param newExtension New extension to append.
    * @return new File with the new extension in dir.
    */
-  protected def swapExt(dir: File, file: File, oldExtension: String, newExtension: String) =
-    new File(dir, file.getName.stripSuffix(oldExtension) + newExtension)
+  protected def swapExt(dir: File, file: File, oldExtension: String, newExtension: String) = QScriptUtils.swapExt(dir, file, oldExtension, newExtension)
 
   /**
    * Adds one or more command line functions to be run.
@@ -181,4 +179,5 @@ object QScript {
   def resetAddOrder() {
     addOrder = 0
   }
+
 }
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QScriptManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QScriptManager.scala
index 8df12c25f..8ffee1e08 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QScriptManager.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QScriptManager.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QSettings.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QSettings.scala
index 7574518ef..b95e158bd 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QSettings.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/QSettings.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLineJobManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLineJobManager.scala
index a3b004ce6..ab1fcbb43 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLineJobManager.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLineJobManager.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLineJobRunner.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLineJobRunner.scala
index e5c2594b5..941126f35 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLineJobRunner.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLineJobRunner.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLinePluginManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLinePluginManager.scala
index 3931c5f0c..37c50d09a 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLinePluginManager.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/CommandLinePluginManager.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/FunctionEdge.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/FunctionEdge.scala
index 1b02f5dde..9a567c60d 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/FunctionEdge.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/FunctionEdge.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/InProcessJobManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/InProcessJobManager.scala
index aa7d06955..351b50c8a 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/InProcessJobManager.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/InProcessJobManager.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/InProcessRunner.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/InProcessRunner.scala
index bb8896d48..b65a695d3 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/InProcessRunner.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/InProcessRunner.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobManager.scala
index e8fb1f08d..16bc39c06 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobManager.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobManager.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobRunInfo.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobRunInfo.scala
index 20a536e91..26713290c 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobRunInfo.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobRunInfo.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobRunner.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobRunner.scala
index d7e4868e7..eca27e914 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobRunner.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/JobRunner.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/MappingEdge.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/MappingEdge.scala
index af5160216..e2b22561b 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/MappingEdge.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/MappingEdge.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QEdge.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QEdge.scala
index d3f2f4ba6..6718dbb3b 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QEdge.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QEdge.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QGraph.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QGraph.scala
index 31cdef904..a34b9e6f9 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QGraph.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QGraph.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -434,7 +434,20 @@ class QGraph extends Logging {
         var doneJobs = Set.empty[FunctionEdge]
         var failedJobs = Set.empty[FunctionEdge]
 
-        while (running && readyJobs.size > 0 && !readyRunningCheck(lastRunningCheck)) {
+        def startJobs: Boolean = {
+
+          def canRunMoreConcurrentJobs: Boolean =
+            if(settings.maximumNumberOfConcurrentJobs.isDefined)
+              runningJobs.size + startedJobs.size < settings.maximumNumberOfConcurrentJobs.get
+            else
+              true
+
+          running && readyJobs.size > 0 &&
+            !readyRunningCheck(lastRunningCheck) &&
+            canRunMoreConcurrentJobs
+        }
+
+        while (startJobs) {
           val edge = readyJobs.head
           edge.runner = newRunner(edge.function)
           edge.start()
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QGraphSettings.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QGraphSettings.scala
index 1345e79ba..bc068682b 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QGraphSettings.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QGraphSettings.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -28,7 +28,7 @@ package org.broadinstitute.gatk.queue.engine
 import java.io.File
 import org.broadinstitute.gatk.queue.QSettings
 import org.broadinstitute.gatk.queue.util.{EmailSettings, SystemUtils}
-import org.broadinstitute.gatk.utils.commandline.{Advanced, ArgumentCollection, Argument}
+import org.broadinstitute.gatk.utils.commandline.{ClassType, Advanced, ArgumentCollection, Argument}
 
 /**
  * Command line options for a QGraph.
@@ -80,6 +80,11 @@ class QGraphSettings {
   @Argument(fullName="disableJobReport", shortName="disableJobReport", doc="If provided, we will not create a job report", required=false)
   var disableJobReport: Boolean = false
 
+  @Advanced
+  @ClassType(classOf[Int])
+  @Argument(fullName="maximumNumberOfJobsToRunConcurrently", shortName="maxConcurrentRun", doc="The maximum number of jobs to start at any given time. (Default is no limit)", required=false)
+  var maximumNumberOfConcurrentJobs: Option[Int] = None
+
   @ArgumentCollection
   val emailSettings = new EmailSettings
 
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QNode.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QNode.scala
index 5751a723d..82d22c22a 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QNode.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QNode.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QStatusMessenger.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QStatusMessenger.scala
index 14e40821b..912d3782b 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QStatusMessenger.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/QStatusMessenger.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/RunnerStatus.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/RunnerStatus.scala
index 93c9fde91..5d5ac04e5 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/RunnerStatus.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/RunnerStatus.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/drmaa/DrmaaJobManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/drmaa/DrmaaJobManager.scala
index 02cf34e85..fedf091ed 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/drmaa/DrmaaJobManager.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/drmaa/DrmaaJobManager.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/drmaa/DrmaaJobRunner.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/drmaa/DrmaaJobRunner.scala
index aa19bfa26..ea4fafee7 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/drmaa/DrmaaJobRunner.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/drmaa/DrmaaJobRunner.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/gridengine/GridEngineJobManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/gridengine/GridEngineJobManager.scala
index eb60cb324..7b8e5231a 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/gridengine/GridEngineJobManager.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/gridengine/GridEngineJobManager.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/gridengine/GridEngineJobRunner.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/gridengine/GridEngineJobRunner.scala
index 8ddda6c97..b5b0121c0 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/gridengine/GridEngineJobRunner.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/gridengine/GridEngineJobRunner.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/lsf/Lsf706JobManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/lsf/Lsf706JobManager.scala
index dbe25366a..0b5a5ce49 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/lsf/Lsf706JobManager.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/lsf/Lsf706JobManager.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/lsf/Lsf706JobRunner.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/lsf/Lsf706JobRunner.scala
index eeb82a333..d35c9c0c9 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/lsf/Lsf706JobRunner.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/lsf/Lsf706JobRunner.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/parallelshell/ParallelShellJobManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/parallelshell/ParallelShellJobManager.scala
new file mode 100644
index 000000000..c200538c6
--- /dev/null
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/parallelshell/ParallelShellJobManager.scala
@@ -0,0 +1,70 @@
+/*
+* Copyright 2012-2015 Broad Institute, Inc.
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.gatk.queue.engine.parallelshell
+
+import org.broadinstitute.gatk.queue.function.CommandLineFunction
+import org.broadinstitute.gatk.queue.engine.CommandLineJobManager
+
+/**
+ * Runs multiple jobs locally without blocking.
+ * Use this with care as it might not be the most efficient way to run things.
+ * However, for some scenarios, such as running multiple single threaded
+ * programs concurrently it can be quite useful.
+ * 
+ * All this code is based on the normal shell runner in GATK Queue and all 
+ * credits for everything except the concurrency part goes to the GATK team.
+ * 
+ * @author Johan Dahlberg
+ *
+ */
+class ParallelShellJobManager extends CommandLineJobManager[ParallelShellJobRunner] {
+
+  def runnerType = classOf[ParallelShellJobRunner]
+
+  /**
+   * Create new ParallelShellJobRunner
+   * @param function Function for the runner.
+   * @return a new ParallelShellJobRunner instance
+   */
+  def create(function: CommandLineFunction) =
+    new ParallelShellJobRunner(function)
+
+  /**
+   * Update the status of the specified jobrunners.
+   * @param runners Runners to update.
+   * @return runners which were updated.
+   */
+  override def updateStatus(
+    runners: Set[ParallelShellJobRunner]): Set[ParallelShellJobRunner] =
+    runners.filter { runner => runner.updateJobStatus() }
+
+  /**
+   * Stop the specified runners.
+   * @param runners Runners to stop.
+   */
+  override def tryStop(runners: Set[ParallelShellJobRunner]) =
+    runners.foreach(_.tryStop())
+}
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/parallelshell/ParallelShellJobRunner.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/parallelshell/ParallelShellJobRunner.scala
new file mode 100644
index 000000000..8afb80a25
--- /dev/null
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/parallelshell/ParallelShellJobRunner.scala
@@ -0,0 +1,151 @@
+/*
+* Copyright 2012-2015 Broad Institute, Inc.
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.gatk.queue.engine.parallelshell
+
+import org.broadinstitute.gatk.queue.function.CommandLineFunction
+import org.broadinstitute.gatk.queue.engine.{ RunnerStatus, CommandLineJobRunner }
+import java.util.Date
+import org.broadinstitute.gatk.utils.Utils
+import org.broadinstitute.gatk.utils.runtime.{ ProcessSettings, OutputStreamSettings }
+import scala.concurrent._
+import ExecutionContext.Implicits.global
+import scala.util.{ Success, Failure }
+import org.broadinstitute.gatk.queue.util.Logging
+
+/**
+ * Runs multiple jobs locally without blocking.
+ * Use this with care as it might not be the most efficient way to run things.
+ * However, for some scenarios, such as running multiple single threaded
+ * programs concurrently it can be quite useful.
+ *
+ * All this code is based on the normal shell runner in GATK Queue and all
+ * credits for everything except the concurrency part goes to the GATK team.
+ *
+ * @author Johan Dahlberg - 20150611
+ *
+ * @param function Command to run.
+ */
+class ParallelShellJobRunner(val function: CommandLineFunction) extends CommandLineJobRunner with Logging {
+
+  // Controller on the thread that started the job
+  val controller: ThreadSafeProcessController = new ThreadSafeProcessController()
+
+  // Once the application exits this promise will be fulfilled.
+  val finalExitStatus = Promise[Int]()
+
+  /**
+   * Runs the function on the local shell.
+   */
+  def start() {
+    val commandLine = Array("sh", jobScript.getAbsolutePath)
+    val stdoutSettings = new OutputStreamSettings
+    val stderrSettings = new OutputStreamSettings
+    val mergeError = function.jobErrorFile == null
+
+    stdoutSettings.setOutputFile(function.jobOutputFile, true)
+    if (function.jobErrorFile != null)
+      stderrSettings.setOutputFile(function.jobErrorFile, true)
+
+    if (logger.isDebugEnabled) {
+      stdoutSettings.printStandard(true)
+      stderrSettings.printStandard(true)
+    }
+
+    val processSettings = new ProcessSettings(
+      commandLine, mergeError, function.commandDirectory, null,
+      null, stdoutSettings, stderrSettings)
+
+    updateJobRun(processSettings)
+
+    getRunInfo.startTime = new Date()
+    getRunInfo.exechosts = Utils.resolveHostname()
+    updateStatus(RunnerStatus.RUNNING)
+
+    // Run the command line process in a future.
+    val executedFuture =
+      future { controller.exec(processSettings) }
+
+    // Register a callback on the completion of the future, making sure that
+    // the status of the job is updated accordingly. 
+    executedFuture.onComplete {
+      case Success(exitStatus) =>
+        logger.debug(commandLine.mkString(" ") + " :: Got return on exit status in future: " + exitStatus)
+        finalExitStatus.success(exitStatus)
+        getRunInfo.doneTime = new Date()
+        exitStatusUpdateJobRunnerStatus(exitStatus)
+      case Failure(throwable) =>
+        logger.debug(
+          "Failed in return from run with: " +
+            throwable.getClass.getCanonicalName + " :: " +
+            throwable.getMessage)
+        finalExitStatus.failure(throwable)
+        getRunInfo.doneTime = new Date()
+        updateStatus(RunnerStatus.FAILED)
+    }
+  }
+
+  /**
+   * Possibly invoked from a shutdown thread, find and
+   * stop the controller from the originating thread
+   */
+  def tryStop() = {
+    try {
+      controller.tryDestroy()
+    } catch {
+      case e: Exception =>
+        logger.error("Unable to kill shell job: " + function.description, e)
+    }
+  }
+
+  /**
+   * Update the status of the runner based on the exit status
+   * of the process.
+   */
+  def exitStatusUpdateJobRunnerStatus(exitStatus: Int): Unit = {
+    exitStatus match {
+      case 0 => updateStatus(RunnerStatus.DONE)
+      case _ => updateStatus(RunnerStatus.FAILED)
+    }
+  }
+
+  /**
+   * Attempts to get the status of a job by looking at if the finalExitStatus
+   * promise has completed or not.
+   * @return if the jobRunner has updated it's status or not.
+   */
+  def updateJobStatus(): Boolean = {
+    if (finalExitStatus.isCompleted) {
+      val completedExitStatus = finalExitStatus.future.value.get.get
+      exitStatusUpdateJobRunnerStatus(completedExitStatus)
+      true
+    } else {
+      // Make sure the status is update here, otherwise Queue will think
+      // it's lots control over the job and kill it after 5 minutes.
+      updateStatus(status)
+      false
+    }
+  }
+}
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/parallelshell/ThreadSafeProcessController.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/parallelshell/ThreadSafeProcessController.scala
new file mode 100644
index 000000000..4bf3f994c
--- /dev/null
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/parallelshell/ThreadSafeProcessController.scala
@@ -0,0 +1,106 @@
+/*
+* Copyright 2012-2015 Broad Institute, Inc.
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.gatk.queue.engine.parallelshell
+
+import java.io.PrintWriter
+
+import org.broadinstitute.gatk.queue.util.Logging
+import org.broadinstitute.gatk.utils.runtime.ProcessSettings
+import scala.sys.process._
+
+/**
+ *
+ */
+class ThreadSafeProcessController extends Logging {
+
+  private var process: Option[Process] = None
+
+  /**
+   * Construct a process logger writing the stdout and stderr of the
+   * process controlled by this instance to the files specified in
+   * the provided ProcessSettings instance.
+   * @param processSettings specifiying which files to write to
+   * @return a process logger which can be used by the `scala.sys.process`
+   */
+  private def getProcessLogger(processSettings: ProcessSettings): ProcessLogger = {
+
+    val (stdOutFile, stdErrFile) = {
+
+      val stdOutFile = processSettings.getStdoutSettings.getOutputFile
+
+      if(processSettings.getStderrSettings.getOutputFile != null) {
+        val stdErrFile = processSettings.getStderrSettings.getOutputFile
+        (stdOutFile, stdErrFile)
+      } else {
+        (stdOutFile, stdOutFile)
+      }
+
+    }
+
+    val stdOutPrintWriter = new PrintWriter(stdOutFile)
+    val stdErrPrintWriter = new PrintWriter(stdErrFile)
+
+    def printToWriter(printWriter: PrintWriter)(line: String): Unit = {
+      printWriter.println(line)
+      printWriter.flush()
+    }
+
+    val stringStdOutPrinterFunc = printToWriter(stdOutPrintWriter) _
+    val stringStdErrPrinterFunc = printToWriter(stdErrPrintWriter) _
+
+    val processLogger = ProcessLogger(
+      stringStdOutPrinterFunc,
+      stringStdErrPrinterFunc
+      )
+
+    processLogger
+  }
+
+  /**
+   * Execute the process specified in process settings
+   * @param processSettings specifying the commandline to run.
+   * @return the exit status of the process.
+   */
+  def exec(processSettings: ProcessSettings): Int = {
+
+    val commandLine: ProcessBuilder = processSettings.getCommand.mkString(" ")
+    logger.debug("Trying to start process: " + commandLine)
+    process = Some(commandLine.run(getProcessLogger(processSettings)))
+    process.get.exitValue()
+
+  }
+
+  /**
+   * Attempt to destroy the underlying process.
+   */
+  def tryDestroy(): Unit = {
+    logger.debug("Trying to kill process")
+    process.getOrElse {
+      throw new IllegalStateException("Tried to kill unstarted job.")
+    }.destroy()
+  }
+
+}
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/pbsengine/PbsEngineJobManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/pbsengine/PbsEngineJobManager.scala
index fb68231d2..31dfabec2 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/pbsengine/PbsEngineJobManager.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/pbsengine/PbsEngineJobManager.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/pbsengine/PbsEngineJobRunner.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/pbsengine/PbsEngineJobRunner.scala
index 092152f3b..5fa0d5bd6 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/pbsengine/PbsEngineJobRunner.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/pbsengine/PbsEngineJobRunner.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/shell/ShellJobManager.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/shell/ShellJobManager.scala
index 5645590e2..e97f69edd 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/shell/ShellJobManager.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/shell/ShellJobManager.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/shell/ShellJobRunner.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/shell/ShellJobRunner.scala
index 327be225e..191867609 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/shell/ShellJobRunner.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/engine/shell/ShellJobRunner.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/CommandLineFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/CommandLineFunction.scala
index e1cb7d037..998d4e564 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/CommandLineFunction.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/CommandLineFunction.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/InProcessFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/InProcessFunction.scala
index 5525eeb91..a7d1363ba 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/InProcessFunction.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/InProcessFunction.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/JavaCommandLineFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/JavaCommandLineFunction.scala
index 80027a02d..61aa43375 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/JavaCommandLineFunction.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/JavaCommandLineFunction.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/ListWriterFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/ListWriterFunction.scala
index c7450b1c0..33aa1f463 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/ListWriterFunction.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/ListWriterFunction.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/QFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/QFunction.scala
index f7e26718e..358b8c3f1 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/QFunction.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/QFunction.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/RetryMemoryLimit.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/RetryMemoryLimit.scala
index 9202c2aa2..1799c9a03 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/RetryMemoryLimit.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/RetryMemoryLimit.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/CloneFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/CloneFunction.scala
index ccc9dcfbe..5eb581a8b 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/CloneFunction.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/CloneFunction.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ConcatenateLogsFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ConcatenateLogsFunction.scala
index b97cee157..35429c702 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ConcatenateLogsFunction.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ConcatenateLogsFunction.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/GatherFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/GatherFunction.scala
index 704426524..a94e86d2a 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/GatherFunction.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/GatherFunction.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/GathererFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/GathererFunction.scala
index 4fcc19f90..f5604522a 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/GathererFunction.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/GathererFunction.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ScatterFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ScatterFunction.scala
index 29f8c41c1..e115667ec 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ScatterFunction.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ScatterFunction.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ScatterGatherableFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ScatterGatherableFunction.scala
index 50ad3cf9a..6bb865bc2 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ScatterGatherableFunction.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/ScatterGatherableFunction.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/SimpleTextGatherFunction.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/SimpleTextGatherFunction.scala
index 2c6aa58d2..306872377 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/SimpleTextGatherFunction.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/function/scattergather/SimpleTextGatherFunction.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/clf/vcf/VCFExtractIntervals.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/clf/vcf/VCFExtractIntervals.scala
index e3b936f0b..4910e1df6 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/clf/vcf/VCFExtractIntervals.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/clf/vcf/VCFExtractIntervals.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/clf/vcf/VCFExtractSamples.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/clf/vcf/VCFExtractSamples.scala
index 799061abc..cd15b519d 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/clf/vcf/VCFExtractSamples.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/clf/vcf/VCFExtractSamples.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/SortByRef.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/SortByRef.scala
index 0ee38e99b..6131f1684 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/SortByRef.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/SortByRef.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractIntervals.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractIntervals.scala
index 8abcf5bc0..1cba5f21f 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractIntervals.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractIntervals.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractSamples.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractSamples.scala
index 99571e9f2..f2cc999eb 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractSamples.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractSamples.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractSites.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractSites.scala
index 5bd25bf55..31b43c2c8 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractSites.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFExtractSites.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFSimpleMerge.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFSimpleMerge.scala
index b3093c8f2..3c4e02577 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFSimpleMerge.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/library/ipf/vcf/VCFSimpleMerge.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ClassFieldCache.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ClassFieldCache.scala
index 82b8ca572..27758454b 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ClassFieldCache.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ClassFieldCache.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/CollectionUtils.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/CollectionUtils.scala
index 5c0be04a0..e77ef47d8 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/CollectionUtils.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/CollectionUtils.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/EmailMessage.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/EmailMessage.scala
index e38183af6..e8d2f22f2 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/EmailMessage.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/EmailMessage.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/EmailSettings.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/EmailSettings.scala
index d31541060..8ab5a1397 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/EmailSettings.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/EmailSettings.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/Logging.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/Logging.scala
index 3a83a2f50..a9b12d172 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/Logging.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/Logging.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/PrimitiveOptionConversions.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/PrimitiveOptionConversions.scala
index edaf80229..66a7242a5 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/PrimitiveOptionConversions.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/PrimitiveOptionConversions.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QJobReport.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QJobReport.scala
index ddc11eb34..fd86d4d11 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QJobReport.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QJobReport.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QJobsReporter.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QJobsReporter.scala
index 082062364..7b6dde65a 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QJobsReporter.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QJobsReporter.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QScriptUtils.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QScriptUtils.scala
index 3fbce2292..5627a46c1 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QScriptUtils.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/QScriptUtils.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -41,6 +41,27 @@ import collection.JavaConversions._
 
 object QScriptUtils {
 
+  /**
+   * Exchanges the extension on a file.
+   * @param file File to look for the extension.
+   * @param oldExtension Old extension to strip off, if present.
+   * @param newExtension New extension to append.
+   * @return new File with the new extension in the current directory.
+   */
+  def swapExt(file: File, oldExtension: String, newExtension: String) =
+    new File(file.getName.stripSuffix(oldExtension) + newExtension)
+
+  /**
+   * Exchanges the extension on a file.
+   * @param dir New directory for the file.
+   * @param file File to look for the extension.
+   * @param oldExtension Old extension to strip off, if present.
+   * @param newExtension New extension to append.
+   * @return new File with the new extension in dir.
+   */
+  def swapExt(dir: File, file: File, oldExtension: String, newExtension: String) =
+    new File(dir, file.getName.stripSuffix(oldExtension) + newExtension)
+
   /**
    * Takes a bam list file and produces a scala sequence with each file allowing the bam list
    * to have empty lines and comment lines (lines starting with #).
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ReflectionUtils.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ReflectionUtils.scala
index d172e976a..c13f08833 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ReflectionUtils.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ReflectionUtils.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RemoteFile.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RemoteFile.scala
index 141081385..5ae4f7691 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RemoteFile.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RemoteFile.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RemoteFileConverter.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RemoteFileConverter.scala
index b38b27a5a..8f984f4cb 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RemoteFileConverter.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RemoteFileConverter.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/Retry.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/Retry.scala
index 8d1c1cfca..4f23f59d4 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/Retry.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/Retry.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RetryException.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RetryException.scala
index ffd69cc7f..eb0d96bde 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RetryException.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/RetryException.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ScalaCompoundArgumentTypeDescriptor.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ScalaCompoundArgumentTypeDescriptor.scala
index 80ab0683b..c6cf39c57 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ScalaCompoundArgumentTypeDescriptor.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ScalaCompoundArgumentTypeDescriptor.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ShellUtils.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ShellUtils.scala
index 02d767a6d..ff23690ad 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ShellUtils.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/ShellUtils.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/StringFileConversions.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/StringFileConversions.scala
index ee21380ee..f6e59317a 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/StringFileConversions.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/StringFileConversions.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/SystemUtils.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/SystemUtils.scala
index cf8537224..440c15574 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/SystemUtils.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/SystemUtils.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/TextFormatUtils.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/TextFormatUtils.scala
index c776dd531..cea1b7722 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/TextFormatUtils.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/TextFormatUtils.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/VCF_BAM_utilities.scala b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/VCF_BAM_utilities.scala
index 9de4b288f..f722f66fb 100644
--- a/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/VCF_BAM_utilities.scala
+++ b/public/gatk-queue/src/main/scala/org/broadinstitute/gatk/queue/util/VCF_BAM_utilities.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/function/CommandLineFunctionUnitTest.scala b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/function/CommandLineFunctionUnitTest.scala
index 351fb71e0..ab7ca2878 100644
--- a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/function/CommandLineFunctionUnitTest.scala
+++ b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/function/CommandLineFunctionUnitTest.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTest.scala b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTest.scala
index 024fcb6f1..ed1c1c77f 100644
--- a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTest.scala
+++ b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTest.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -53,7 +53,7 @@ object QueueTest extends BaseTest with Logging {
   /**
    * All the job runners configured to run QueueTests at The Broad.
    */
-  final val allJobRunners = Seq("GridEngine", "Shell")
+  final val allJobRunners = Seq("GridEngine", "Shell", "ParallelShell")
 
   /**
    * The default job runners to run.
diff --git a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTestEvalSpec.scala b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTestEvalSpec.scala
index 764449cff..e0df4d9b5 100644
--- a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTestEvalSpec.scala
+++ b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTestEvalSpec.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTestSpec.scala b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTestSpec.scala
index 4fdcb08da..ac1802e42 100644
--- a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTestSpec.scala
+++ b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTestSpec.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/ShellUtilsUnitTest.scala b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/ShellUtilsUnitTest.scala
index 944cc851a..3f3acb56c 100644
--- a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/ShellUtilsUnitTest.scala
+++ b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/ShellUtilsUnitTest.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/StringFileConversionsUnitTest.scala b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/StringFileConversionsUnitTest.scala
index 160e04036..090ba8622 100644
--- a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/StringFileConversionsUnitTest.scala
+++ b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/StringFileConversionsUnitTest.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/SystemUtilsUnitTest.scala b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/SystemUtilsUnitTest.scala
index 2fd78e363..e0950ceee 100644
--- a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/SystemUtilsUnitTest.scala
+++ b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/util/SystemUtilsUnitTest.scala
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-root/pom.xml b/public/gatk-root/pom.xml
index 206f655b1..9f1c9d464 100644
--- a/public/gatk-root/pom.xml
+++ b/public/gatk-root/pom.xml
@@ -44,8 +44,8 @@
         org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.gatk.utils.TestNGTestTransformer,org.broadinstitute.gatk.utils.GATKTextReporter,org.uncommons.reportng.HTMLReporter
 
         
-        1.134
-        1.133
+        1.141
+        1.141
     
 
     
@@ -64,7 +64,7 @@
             
                 com.google.code.cofoja
                 cofoja
-                1.0-r139
+                1.2-20140817
             
             
                 com.github.samtools
@@ -718,6 +718,17 @@
             GATK Public Local Repository
             file:${gatk.basedir}/public/repo
         
+        
+            
+                false
+            
+            
+                true
+            
+            broad.artifactory.snapshots
+            Broad Institute Artifactory SNAPSHOTs
+            https://artifactory.broadinstitute.org/artifactory/libs-snapshot
+        
     
 
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java
index 391b0202f..f11e01d20 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -25,6 +25,7 @@
 
 package org.broadinstitute.gatk.tools;
 
+import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.samtools.reference.ReferenceSequenceFile;
 import htsjdk.samtools.reference.ReferenceSequenceFileFactory;
 import org.apache.log4j.BasicConfigurator;
@@ -47,6 +48,7 @@ import htsjdk.variant.vcf.VCFCodec;
 import htsjdk.variant.vcf.VCFHeader;
 import org.broadinstitute.gatk.utils.exceptions.UserException;
 import htsjdk.variant.variantcontext.VariantContext;
+import htsjdk.variant.variantcontext.VariantContextComparator;
 import htsjdk.variant.variantcontext.writer.Options;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
 import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory;
@@ -228,9 +230,9 @@ public class CatVariants extends CommandLineProgram {
 
         variant = parseVariantList(variant);
 
-        Comparator> positionComparator = new PositionComparator();
+        Comparator> positionComparator = new PositionComparator(ref.getSequenceDictionary());
 
-        Queue> priorityQueue;
+        Queue> priorityQueue;
         if (assumeSorted)
             priorityQueue = new LinkedList<>();
         else
@@ -244,7 +246,7 @@ public class CatVariants extends CommandLineProgram {
                 return 1;
 
             if (assumeSorted){
-                priorityQueue.add(new Pair<>(0,file));
+                priorityQueue.add(new Pair(null,file));
             }
             else{
                 if (!file.exists()) {
@@ -257,9 +259,8 @@ public class CatVariants extends CommandLineProgram {
                     continue;
                 }
                 VariantContext vc = it.next();
-                int firstPosition = vc.getStart();
                 reader.close();
-                priorityQueue.add(new Pair<>(firstPosition,file));
+                priorityQueue.add(new Pair<>(vc,file));
             }
         }
 
@@ -318,15 +319,19 @@ public class CatVariants extends CommandLineProgram {
         }
     }
 
-    private static class PositionComparator implements Comparator> {
+    private static class PositionComparator implements Comparator> {
+    	
+    	VariantContextComparator comp;
+    	
+    	public PositionComparator(final SAMSequenceDictionary dict){
+    		comp = new VariantContextComparator(dict);
+    	}
 
         @Override
-        public int compare(Pair p1, Pair p2) {
-            int startPositionP1 = p1.getFirst();
-            int startPositionP2 = p2.getFirst();
-            if (startPositionP1  == startPositionP2)
-                return 0;
-            return startPositionP1 < startPositionP2 ? -1 : 1 ;
+        public int compare(final Pair p1, final Pair p2) {
+            final VariantContext startPositionP1 = p1.getFirst();
+            final VariantContext startPositionP2 = p2.getFirst();
+            return comp.compare(startPositionP1, startPositionP2);
         }
     }
 }
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/ListAnnotations.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/ListAnnotations.java
deleted file mode 100644
index 4bc91d6e3..000000000
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/ListAnnotations.java
+++ /dev/null
@@ -1,85 +0,0 @@
-/*
-* Copyright (c) 2012 The Broad Institute
-* 
-* Permission is hereby granted, free of charge, to any person
-* obtaining a copy of this software and associated documentation
-* files (the "Software"), to deal in the Software without
-* restriction, including without limitation the rights to use,
-* copy, modify, merge, publish, distribute, sublicense, and/or sell
-* copies of the Software, and to permit persons to whom the
-* Software is furnished to do so, subject to the following
-* conditions:
-* 
-* The above copyright notice and this permission notice shall be
-* included in all copies or substantial portions of the Software.
-* 
-* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
-* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-*/
-
-package org.broadinstitute.gatk.tools;
-
-import org.broadinstitute.gatk.utils.commandline.CommandLineProgram;
-import org.broadinstitute.gatk.utils.exceptions.UserException;
-import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotationHelpUtils;
-import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.gatk.utils.help.HelpConstants;
-
-/**
- * Utility program to print a list of available annotations
- *
- * 
    This is a very simple utility tool that retrieves available annotations for use with tools such as
- * UnifiedGenotyper, HaplotypeCaller and VariantAnnotator.
    
- *
- * 
    Important note
    
- * 
    This is a command-line utility that bypasses the GATK engine. As a result, the command-line you must use to
- * invoke it is a little different from other GATK tools (see usage below), and it does not accept any of the
- * classic "CommandLineGATK" arguments.
    
- *
- * 
    Usage
    
- * 
    java -cp GenomeAnalysisTK.jar org.broadinstitute.gatk.tools.ListAnnotations
    
- *
- * @author vdauwera
- * @since 3/14/13
- */
-@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_HELPUTILS )
-public class ListAnnotations extends CommandLineProgram {
-
-    /*
-     * Print usage information
-     *
-     * TODO: would be more convenient if we could just call the program by name instead of the full classpath
-     */
-    private static void printUsage() {
-        System.err.println("Usage: java -cp dist/GenomeAnalysisTK.jar org.broadinstitute.gatk.tools.ListAnnotations");
-        System.err.println("    Prints a list of available annotations and exits.");
-    }
-
-    // TODO: override CommandLineProgram bit that offers version, logging etc arguments. We don't need that stuff here and it makes the doc confusing.
-
-    @Override
-    protected int execute() throws Exception {
-
-        AnnotationHelpUtils.listAnnotations();
-        return 0;
-    }
-
-    public static void main(String[] args){
-        try {
-            ListAnnotations instance = new ListAnnotations();
-            start(instance, args);
-            System.exit(CommandLineProgram.result);
-        } catch ( UserException e ) {
-            printUsage();
-            exitSystemWithUserError(e);
-        } catch ( Exception e ) {
-            exitSystemWithError(e);
-        }
-    }
-}
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalance.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalance.java
index 5de5d6656..ccb4be7f8 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalance.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalance.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalanceBySample.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalanceBySample.java
index 1c99fa8fc..fb7300809 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalanceBySample.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalanceBySample.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleSpecificAnnotationData.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleSpecificAnnotationData.java
new file mode 100644
index 000000000..df3944214
--- /dev/null
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleSpecificAnnotationData.java
@@ -0,0 +1,96 @@
+/*
+* Copyright 2012-2015 Broad Institute, Inc.
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.gatk.tools.walkers.annotator;
+
+import htsjdk.variant.variantcontext.Allele;
+import org.broadinstitute.gatk.utils.exceptions.GATKException;
+
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * A class to encapsulate the raw data for allele-specific classes compatible with the ReducibleAnnotation interface
+ * @param  the type of raw data to be stored for later annotation calculation
+ */
+public class AlleleSpecificAnnotationData extends ReducibleAnnotationData{
+    final private List alleleList;
+    private Allele refAllele;
+
+    public AlleleSpecificAnnotationData(final List inputAlleles, final String inputData) {
+        super(inputData);
+        attributeMap = new HashMap<>();
+        for(final Allele a : inputAlleles) {
+            attributeMap.put(a, null);
+        }
+        alleleList = inputAlleles;
+        for(Allele a : alleleList) {
+            if(a.isReference()) {
+                refAllele = a;
+            }
+        }
+    }
+
+    @Override
+    public List getAlleles() {return Collections.unmodifiableList(alleleList);}
+
+    /**
+     * Get the reference allele for this allele-specific data.
+     * (Used in cases where annotations compare some attribute of the alt alleles to that of the reference.)
+     * @return  the reference allele for this data
+     */
+    public Allele getRefAllele() {return refAllele;}
+
+    public void setAttributeMap(Map inputMap) {
+        super.setAttributeMap(inputMap);
+        checkRefAlleles();
+    }
+
+    private void checkRefAlleles() {
+        boolean foundRef = false;
+        for (Allele a : alleleList) {
+            if (a.isReference()) {
+                if (foundRef)
+                    throw new GATKException("ERROR: multiple reference alleles found in annotation data\n");
+                foundRef = true;
+            }
+        }
+        if (!foundRef)
+            throw new GATKException("ERROR: no reference alleles found in annotation data\n");
+    }
+
+    public String makeRawAnnotationString(String printDelim) {
+        String annotationString = "";
+        for (final Allele current : alleleList) {
+            if (!annotationString.isEmpty())
+                annotationString += printDelim;
+            if(attributeMap.get(current) != null)
+                annotationString += attributeMap.get(current).toString();
+        }
+        return annotationString.replaceAll("[\\[\\]\\s]", "");
+    }
+}
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseCounts.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseCounts.java
index a01c945ac..66ea8dff6 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseCounts.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseCounts.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/CompressedDataList.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/CompressedDataList.java
new file mode 100644
index 000000000..a89859fa3
--- /dev/null
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/CompressedDataList.java
@@ -0,0 +1,117 @@
+/*
+* Copyright 2012-2015 Broad Institute, Inc.
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.gatk.tools.walkers.annotator;
+
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Map;
+
+/**
+ * A class to represent data as a list of  pairs.  For example, the list 2,2,2,2,2,2,3,4,4,4,5,5
+ * would be compressed as 2,6,3,1,4,3,5,2. The compressed list should be sorted in ascending order by value.
+ *
+ * Created by gauthier on 9/25/15.
+ */
+public class CompressedDataList  implements Iterable {
+    protected Map valueCounts = new HashMap<>();
+
+    public Map getValueCounts(){
+        return valueCounts;
+    }
+
+    public boolean isEmpty(){
+        return valueCounts.isEmpty();
+    }
+
+    @Override
+    public Iterator iterator(){
+        Iterator it = new Iterator() {
+            private Iterator keySetIterator = valueCounts.keySet().iterator();
+            private T currentKey = valueCounts.isEmpty() ? null : keySetIterator.next();
+            private int currentValueIndex = 0;
+            private int currentValueSize = valueCounts.isEmpty() ? 0 : valueCounts.get(currentKey);
+
+            @Override
+            public boolean hasNext() {
+                return !valueCounts.isEmpty() && (keySetIterator.hasNext() || currentValueIndex < currentValueSize);
+            }
+
+            @Override
+            public T next() {
+                T retKey = currentKey;
+                currentValueIndex++;
+                if(currentValueIndex==currentValueSize){
+                    if(keySetIterator.hasNext()) {
+                        currentKey = keySetIterator.next();
+                        currentValueIndex = 0;
+                        currentValueSize = valueCounts.get(currentKey);
+                    }
+                }
+                return retKey;
+            }
+
+            @Override
+            public void remove() {
+                throw new UnsupportedOperationException();
+            }
+        };
+        return it;
+    }
+
+    @Override
+    public String toString(){
+        String str = "";
+        Object[] keys = valueCounts.keySet().toArray();
+        Arrays.sort(keys);
+        for (Object i: keys){
+            if(!str.isEmpty())
+                str+=",";
+            str+=(i+","+valueCounts.get(i));
+        }
+        return str;
+    }
+
+    public void add(final T val){
+        add(val, 1);
+    }
+
+    public void add(final T val, final int count){
+        if(valueCounts.containsKey(val)){
+            valueCounts.put(val, valueCounts.get(val)+count);
+        }
+        else
+            valueCounts.put(val, count);
+
+    }
+
+    public void add(final CompressedDataList obj){
+        for(Map.Entry pair : obj.getValueCounts().entrySet()){
+            this.add(pair.getKey(),pair.getValue());
+        }
+    }
+
+}
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FractionInformativeReads.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FractionInformativeReads.java
new file mode 100644
index 000000000..747e0fc23
--- /dev/null
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FractionInformativeReads.java
@@ -0,0 +1,115 @@
+/*
+* Copyright 2012-2015 Broad Institute, Inc.
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.gatk.tools.walkers.annotator;
+
+import htsjdk.variant.variantcontext.Allele;
+import htsjdk.variant.variantcontext.Genotype;
+import htsjdk.variant.variantcontext.VariantContext;
+import htsjdk.variant.vcf.VCFConstants;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ReducibleAnnotation;
+import org.broadinstitute.gatk.utils.MathUtils;
+import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
+import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
+import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.utils.variant.GATKVCFConstants;
+
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * The fraction of reads that were deemed "informative" by the HaplotypeCaller over the entire cohort
+ *
+ * 
    The FractionInformativeReads annotation produces a single fraction for each site: sum(AD)/sum(DP). The sum in the numerator
+ * is over all the samples in the cohort and all the alleles in each sample. The sum in the denominator is over all the samples.
+ *
+ *
+ * 
    Caveats
    
+ * 
      
+ *     
    • This annotation is generated by HaplotypeCaller or GenotypeGVCFs (it will not work when called from VariantAnnotator).
      • 
+ * 
    
+ *
+ * 
    Related annotations
    
+ * 
      
+ *     
    • DepthPerAlleleBySample displays the number of reads supporting each allele, without calculating the fraction.
      • 
+ * 
    
+ */
+
+public class FractionInformativeReads extends InfoFieldAnnotation implements ReducibleAnnotation {
+    @Override
+    public String getRawKeyName() {
+        return null;
+    }
+
+    @Override
+    public List getKeyNames() {
+        return Collections.singletonList(GATKVCFConstants.FRACTION_INFORMATIVE_READS_KEY);
+    }
+
+    @Override
+    public Map annotateRawData(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc, Map stratifiedPerReadAlleleLikelihoodMap) {
+        return null;
+    }
+
+    @Override
+    public Map combineRawData(List allelesList, List listOfRawData) {
+        return null;
+    }
+
+    @Override
+    public Map finalizeRawData(VariantContext vc, VariantContext originalVC) {
+
+        int totalAD = 0;
+        for (final Genotype gt : vc.getGenotypes()){
+            if(gt != null) {
+                if(gt.hasAD()) {
+                    totalAD += MathUtils.sum(gt.getAD());
+                    continue;
+                }
+                // this is needed since the finalizing of HOM_REF genotypes comes after the finalizing of annotations. so the AD field is null at this point.
+                // TODO: this will become unneeded if the above statement is false in which case it can be safely removed.
+                if(gt.hasExtendedAttribute(GATKVCFConstants.MIN_DP_FORMAT_KEY)) {
+                    totalAD += Integer.parseInt((String) gt.getExtendedAttribute(GATKVCFConstants.MIN_DP_FORMAT_KEY));
+                }
+            }
+        }
+        final int depth =  vc.getAttributeAsInt(VCFConstants.DEPTH_KEY, 0);
+        return Collections.singletonMap(GATKVCFConstants.FRACTION_INFORMATIVE_READS_KEY, (Object) (depth != 0 ? totalAD / (double) depth : 0));
+    }
+
+    @Override
+    public void calculateRawData(VariantContext vc, Map pralm, ReducibleAnnotationData rawAnnotations) {
+
+    }
+
+    @Override
+    public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc, Map stratifiedPerReadAlleleLikelihoodMap) {
+        return null;
+    }
+}
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LowMQ.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LowMQ.java
index 1d4b7a002..34c58683f 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LowMQ.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LowMQ.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZeroBySample.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZeroBySample.java
index 728fa3fa3..be3b40194 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZeroBySample.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZeroBySample.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/NBaseCount.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/NBaseCount.java
index 465fa285f..b4cafa8f7 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/NBaseCount.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/NBaseCount.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ReducibleAnnotationData.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ReducibleAnnotationData.java
new file mode 100644
index 000000000..0c18bb187
--- /dev/null
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ReducibleAnnotationData.java
@@ -0,0 +1,105 @@
+/*
+* Copyright 2012-2015 Broad Institute, Inc.
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.gatk.tools.walkers.annotator;
+
+import htsjdk.variant.variantcontext.Allele;
+
+import java.util.*;
+
+/**
+ * A class to encapsulate the raw data for classes compatible with the ReducibleAnnotation interface
+ */
+public class ReducibleAnnotationData {
+    protected String rawData;
+    protected Map attributeMap;
+
+    /**
+     * Create a new ReducibleAnnotationData using the raw data string from a VCF
+     * @param inputData the raw data as read in from a VCF
+     */
+    public ReducibleAnnotationData(final String inputData) {
+        rawData = inputData; attributeMap = new HashMap<>();
+        attributeMap.put(Allele.NO_CALL, null);
+    }
+
+    /**
+     *
+     * @return the string of raw data as represented in the VCF
+     */
+    public String getRawData() {return rawData;}
+
+    /**
+     * Note: parent class ReducibleAnnotationData is non-allele specific and stores all values with the no-call allele
+     * @return the list of alleles for which we have raw annotation data
+     */
+    public List getAlleles() {
+        List ret = new ArrayList();
+        ret.addAll(attributeMap.keySet());
+        return ret;
+    }
+
+    /**
+     *
+     * @param key   the allele of interest
+     * @return  do we have data for the allele of interest?
+     */
+    public boolean hasAttribute(Allele key) {
+        return attributeMap.containsKey(key);
+    }
+
+    /**
+     *
+     * @param key the allele of interest
+     * @return  data for the allele of interest
+     */
+    public T getAttribute(Allele key) {
+        return attributeMap.get(key);
+    }
+
+    /**
+     *
+     * @param key   the allele of interest
+     * @param value raw data corresponding to the allele of interest
+     */
+    public void putAttribute(Allele key, T value) {
+        attributeMap.put(key, value);
+    }
+
+    /**
+     * Assign all of the per-allele raw data at once
+     * @param inputMap  the pre-calculated per-allele data
+     */
+    public void setAttributeMap(Map inputMap) {
+        attributeMap = inputMap;
+    }
+
+    /**
+     * Get the stored raw per-allele data
+     * @return
+     */
+    public Map getAttributeMap() {return Collections.unmodifiableMap(attributeMap);}
+
+}
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEff.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEff.java
index 9da3de861..ceb353bdc 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEff.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEff.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUtil.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUtil.java
index c82a013b6..adb2c4ab4 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUtil.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUtil.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotator.java
index c748f75ce..ca386e8d8 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotator.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -53,7 +53,7 @@ import java.util.*;
  * Annotate variant calls with context information
  *
  * 
    
- * This tool is designed to annotate variant calls based on their context (ass opposed to functional annotation).
+ * This tool is designed to annotate variant calls based on their context (as opposed to functional annotation).
  * Various annotation modules are available; see the
  * documentation
  * for a complete list.
@@ -68,7 +68,10 @@ import java.util.*;
  * An annotated VCF.
  * 
    
  *
- * 
    Usage example
    
+ * 
    Usage examples
    
+ * 
    
+ *
+ * 
    Annotate a VCF with dbSNP IDs and depth of coverage for each sample
    
  * 
      * java -jar GenomeAnalysisTK.jar \
  *   -R reference.fasta \
@@ -81,6 +84,32 @@ import java.util.*;
  *   --dbsnp dbsnp.vcf
  * 
    
  *
+ * 
    Annotate a VCF with allele frequency by an external resource. Annotation will only occur if there is allele concordance between the resource and the input VCF 
    
+ * 
    + * java -jar GenomeAnalysisTK.jar \
+ *   -R reference.fasta \
+ *   -T VariantAnnotator \
+ *   -I input.bam \
+ *   -o output.vcf \
+ *   -V input.vcf \
+ *   -L input.vcf \
+ *   --resource:foo resource.vcf
+ *   -E foo.AF
+ *   --resourceAlleleConcordance
+ * 
    
+ *
+ * 
    Annotate with AF and FILTER fields from an external resource 
    
+ * 
    + * java -jar GenomeAnalysisTK.jar \
+ *   -R reference.fasta \
+ *   -T VariantAnnotator \
+ *   -o output.vcf \
+ *   --resource:foo resource.vcf \
+ *   --expression foo.AF \
+ *   --expression foo.FILTER \
+ *   -V input.vcf \
+ * 
    
+ *
  */
 @DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
 @Requires(value={})
@@ -95,9 +124,9 @@ public class VariantAnnotator extends RodWalker implements Ann
 
     /**
      * The INFO field will be annotated with information on the most biologically significant effect
-     * listed in the SnpEff output file for each variant.
+     * listed for each variant in the SnpEff file.
      */
-    @Input(fullName="snpEffFile", shortName = "snpEffFile", doc="A SnpEff output file from which to add annotations", required=false)
+    @Input(fullName="snpEffFile", shortName = "snpEffFile", doc="SnpEff file from which to get annotations", required=false)
     public RodBinding snpEffFile;
     public RodBinding getSnpEffRodBinding() { return snpEffFile; }
 
@@ -114,7 +143,7 @@ public class VariantAnnotator extends RodWalker implements Ann
       * Records that are filtered in the comp track will be ignored. Note that 'dbSNP' has been special-cased
       * (see the --dbsnp argument).
       */
-    @Input(fullName="comp", shortName = "comp", doc="comparison VCF file", required=false)
+    @Input(fullName="comp", shortName = "comp", doc="Comparison VCF file", required=false)
     public List> comps = Collections.emptyList();
     public List> getCompRodBindings() { return comps; }
 
@@ -127,7 +156,8 @@ public class VariantAnnotator extends RodWalker implements Ann
       * '-E my_resource.AC' (-E is short for --expression, also documented on this page). In the resulting output
       * VCF, any records for which there is a record at the same position in the resource file will be annotated with
       * 'my_resource.AC=N'. Note that if there are multiple records in the resource file that overlap the given
-      * position, one is chosen randomly.
+      * position, one is chosen randomly. Check for allele concordance if using --resourceAlleleConcordance, otherwise
+      * the match is based on position only.
       */
     @Input(fullName="resource", shortName = "resource", doc="External resource VCF file", required=false)
     public List> resources = Collections.emptyList();
@@ -164,12 +194,21 @@ public class VariantAnnotator extends RodWalker implements Ann
      * 'resource_file.vcf', you tag it with '-resource:my_resource resource_file.vcf' (see the -resource argument, also
      * documented on this page) and you specify '-E my_resource.AC'. In the resulting output VCF, any records for
      * which there is a record at the same position in the resource file will be annotated with 'my_resource.AC=N'.
+     * INFO field data, ID, ALT, and FILTER fields may be used as expression values.
      * Note that if there are multiple records in the resource file that overlap the given position, one is chosen
      * randomly.
      */
     @Argument(fullName="expression", shortName="E", doc="One or more specific expressions to apply to variant calls", required=false)
     protected Set expressionsToUse = new ObjectOpenHashSet();
 
+    /**
+     * If this argument is specified, add annotations (specified by --expression) from an external resource
+     * (specified by --resource) to the input VCF (specified by --variant) only if the alleles are
+     * concordant between input and the resource VCFs. Otherwise, always add the annotations.
+     */
+    @Argument(fullName="resourceAlleleConcordance", shortName="rac", doc="Check for allele concordances when using an external resource VCF file", required=false)
+    protected Boolean expressionAlleleConcordance = false;
+
     /**
      * You can use the -XL argument in combination with this one to exclude specific annotations.Note that some
      * annotations may not be actually applied if they are not applicable to the data provided or if they are
@@ -184,20 +223,25 @@ public class VariantAnnotator extends RodWalker implements Ann
     protected Boolean USE_ALL_ANNOTATIONS = false;
 
     /**
-     * Note that the --list argument requires a fully resolved and correct command-line to work. As an alternative, you can use ListAnnotations (see Help Utilities).
+     * Note that the --list argument requires a fully resolved and correct command-line to work. As an alternative,
+     * you can use ListAnnotations (see Help Utilities).
      */
     @Argument(fullName="list", shortName="ls", doc="List the available annotations and exit", required=false)
     protected Boolean LIST = false;
 
     /**
-     * By default, the dbSNP ID is added only when the ID field in the variant VCF is empty (not already annotated).
-     * This argument allows you to override that behavior. This is used in conjuction with the -dbsnp argument.
+     * By default, a dbSNP ID is added only when the ID field in the variant record is empty (not already annotated).
+     * This argument allows you to override that behavior, and appends the new ID to the existing one. This is used
+     * in conjunction with the -dbsnp argument.
      */
-    @Argument(fullName="alwaysAppendDbsnpId", shortName="alwaysAppendDbsnpId", doc="Append the dbSNP ID even when the variant VCF already has the ID field populated", required=false)
+    @Argument(fullName="alwaysAppendDbsnpId", shortName="alwaysAppendDbsnpId", doc="Add dbSNP ID even if one is already present", required=false)
     protected Boolean ALWAYS_APPEND_DBSNP_ID = false;
     public boolean alwaysAppendDbsnpId() { return ALWAYS_APPEND_DBSNP_ID; }
 
-    @Argument(fullName="MendelViolationGenotypeQualityThreshold",shortName="mvq",required=false,doc="The genotype quality threshold in order to annotate mendelian violation ratio")
+    /**
+     * The genotype quality (GQ) threshold above which the mendelian violation ratio should be annotated.
+     */
+    @Argument(fullName="MendelViolationGenotypeQualityThreshold",shortName="mvq",required=false,doc="GQ threshold for annotating MV ratio")
     public double minGenotypeQualityP = 0.0;
 
     private VariantAnnotatorEngine engine;
@@ -221,6 +265,7 @@ public class VariantAnnotator extends RodWalker implements Ann
         else
             engine = new VariantAnnotatorEngine(annotationGroupsToUse, annotationsToUse, annotationsToExclude, this, getToolkit());
         engine.initializeExpressions(expressionsToUse);
+        engine.setExpressionAlleleConcordance(expressionAlleleConcordance);
 
         // setup the header fields
         // note that if any of the definitions conflict with our new ones, then we want to overwrite the old ones
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java
index f064bd4de..bddc020c9 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -29,18 +29,17 @@ import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import htsjdk.variant.variantcontext.*;
 import htsjdk.variant.vcf.*;
-import org.apache.commons.collections.ListUtils;
 import org.apache.log4j.Logger;
 import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
-import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
-import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
-import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
 import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.*;
 import org.broadinstitute.gatk.utils.GenomeLoc;
 import org.broadinstitute.gatk.utils.commandline.RodBinding;
+import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
+import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
 import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods;
+import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
 import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
 
 import java.util.*;
@@ -49,8 +48,11 @@ import java.util.*;
 public class VariantAnnotatorEngine {
     private final static Logger logger = Logger.getLogger(VariantAnnotatorEngine.class);
     private List requestedInfoAnnotations = Collections.emptyList();
+    private List requestedReducibleInfoAnnotations = new ArrayList<>();
+    private List requestedNonReducibleInfoAnnotations = new ArrayList<>();
     private List requestedGenotypeAnnotations = Collections.emptyList();
     private List requestedExpressions = new ArrayList<>();
+    private boolean expressionAlleleConcordance = false;
 
     private final AnnotatorCompatible walker;
     private final GenomeAnalysisEngine toolkit;
@@ -90,6 +92,7 @@ public class VariantAnnotatorEngine {
         requestedInfoAnnotations = AnnotationInterfaceManager.createAllInfoFieldAnnotations();
         requestedGenotypeAnnotations = AnnotationInterfaceManager.createAllGenotypeAnnotations();
         excludeAnnotations(annotationsToExclude);
+        setReducibleAnnotations();
         initializeDBs(toolkit);
     }
 
@@ -98,6 +101,7 @@ public class VariantAnnotatorEngine {
         this.walker = walker;
         this.toolkit = toolkit;
         initializeAnnotations(annotationGroupsToUse, annotationsToUse, annotationsToExclude);
+        setReducibleAnnotations();
         initializeDBs(toolkit);
     }
 
@@ -115,8 +119,15 @@ public class VariantAnnotatorEngine {
             requestedExpressions.add(new VAExpression(expression, walker.getResourceRodBindings()));
     }
 
+    // set whether enforing allele concordance for expression
+    public void setExpressionAlleleConcordance(Boolean expressionAlleleConcordance){
+        this.expressionAlleleConcordance = expressionAlleleConcordance;
+    }
+
     protected List getRequestedExpressions() { return requestedExpressions; }
 
+    public List getRequestedReducibleInfoAnnotations() { return Collections.unmodifiableList(requestedReducibleInfoAnnotations); }
+
     private void initializeAnnotations(List annotationGroupsToUse, List annotationsToUse, List annotationsToExclude) {
         AnnotationInterfaceManager.validateAnnotations(annotationGroupsToUse, annotationsToUse);
         requestedInfoAnnotations = AnnotationInterfaceManager.createInfoFieldAnnotations(annotationGroupsToUse, annotationsToUse);
@@ -197,53 +208,157 @@ public class VariantAnnotatorEngine {
                                           final Map stratifiedContexts,
                                           final VariantContext vc,
                                           final Map perReadAlleleLikelihoodMap) {
-        final Map infoAnnotations = new LinkedHashMap<>(vc.getAttributes());
+        // annotate genotypes
+        final VariantContextBuilder builder = new VariantContextBuilder(vc).genotypes(annotateGenotypes(tracker, ref, stratifiedContexts, vc, perReadAlleleLikelihoodMap));
+        VariantContext newGenotypeAnnotatedVC = builder.make();
 
         // annotate expressions where available
-        annotateExpressions(tracker, ref.getLocus(), vc, infoAnnotations);
+        final Map infoAnnotations = new LinkedHashMap<>(newGenotypeAnnotatedVC.getAttributes());
+        annotateExpressions(tracker, ref.getLocus(), newGenotypeAnnotatedVC, infoAnnotations);
 
         // go through all the requested info annotationTypes
         for ( final InfoFieldAnnotation annotationType : requestedInfoAnnotations ) {
-            final Map annotationsFromCurrentType = annotationType.annotate(tracker, walker, ref, stratifiedContexts, vc, perReadAlleleLikelihoodMap);
+            final Map annotationsFromCurrentType = annotationType.annotate(tracker, walker, ref, stratifiedContexts, newGenotypeAnnotatedVC, perReadAlleleLikelihoodMap);
             if ( annotationsFromCurrentType != null )
                 infoAnnotations.putAll(annotationsFromCurrentType);
         }
 
-        // generate a new annotated VC
-        final VariantContextBuilder builder = new VariantContextBuilder(vc).attributes(infoAnnotations);
-
-        // annotate genotypes, creating another new VC in the process
-        final VariantContext annotated = builder.genotypes(annotateGenotypes(tracker, ref, stratifiedContexts, vc, perReadAlleleLikelihoodMap)).make();
+        // create a new VC in the with info and genotype annotations
+        final VariantContext annotated = builder.attributes(infoAnnotations).make();
 
         // annotate db occurrences
         return annotateDBs(tracker, annotated);
     }
 
+    /**
+     *
+     * @param referenceContext
+     * @param tracker
+     * @param readLikelihoods
+     * @param vc
+     * @param useRaw    output annotation data as raw data? (Yes in the case of gVCF mode for HaplotypeCaller)
+     * @return
+     */
     public VariantContext annotateContextForActiveRegion(final ReferenceContext referenceContext,
                                                          final RefMetaDataTracker tracker,
                                                          final ReadLikelihoods readLikelihoods,
-                                                         final VariantContext vc) {
+                                                         final VariantContext vc,
+                                                         final boolean useRaw) {
         //TODO we transform the read-likelihood into the Map^2 previous version for the sake of not changing of not changing annotation interface.
         //TODO should we change those interfaces?
 
         final Map annotationLikelihoods = readLikelihoods.toPerReadAlleleLikelihoodMap();
-        return annotateContextForActiveRegion(referenceContext, tracker, annotationLikelihoods, vc);
+        return annotateContextForActiveRegion(referenceContext, tracker, annotationLikelihoods, vc, useRaw);
     }
 
+    /**
+     *
+     * @param referenceContext
+     * @param tracker
+     * @param perReadAlleleLikelihoodMap
+     * @param vc
+     * @param useRaw    output annotation data as raw data? (Yes in the case of gVCF mode for HaplotypeCaller)
+     * @return
+     */
     public VariantContext annotateContextForActiveRegion(final ReferenceContext referenceContext,
                                                          final RefMetaDataTracker tracker,
                                                          final Map perReadAlleleLikelihoodMap,
-                                                         final VariantContext vc) {
-        final Map infoAnnotations = new LinkedHashMap<>(vc.getAttributes());
+                                                         final VariantContext vc,
+                                                         final boolean useRaw) {
+        // annotate genotypes
+        final VariantContextBuilder builder = new VariantContextBuilder(vc).genotypes(annotateGenotypes(null, null, null, vc, perReadAlleleLikelihoodMap));
+        VariantContext newGenotypeAnnotatedVC = builder.make();
 
-        // go through all the requested info annotationTypes
-        for ( final InfoFieldAnnotation annotationType : requestedInfoAnnotations ) {
+        final Map infoAnnotations = new LinkedHashMap<>(newGenotypeAnnotatedVC.getAttributes());
+
+        // go through all the requested info annotationTypes that are reducible
+        if (useRaw) {
+            for (final InfoFieldAnnotation annotationType : requestedReducibleInfoAnnotations) {
+                if (!(annotationType instanceof ActiveRegionBasedAnnotation))
+                    continue;
+
+
+                    ReducibleAnnotation currentASannotation = (ReducibleAnnotation) annotationType;
+                    final Map annotationsFromCurrentType = currentASannotation.annotateRawData(null, null, referenceContext, null, newGenotypeAnnotatedVC, perReadAlleleLikelihoodMap);
+                    if (annotationsFromCurrentType != null) {
+                        infoAnnotations.putAll(annotationsFromCurrentType);
+                    }
+            }
+        }
+        //if not in reference-confidence mode, do annotate with reducible annotations, but skip the raw data and go straight to the finalized values
+        else {
+            for (final InfoFieldAnnotation annotationType : requestedReducibleInfoAnnotations) {
+                if (!(annotationType instanceof ActiveRegionBasedAnnotation))
+                    continue;
+
+                final Map annotationsFromCurrentType = annotationType.annotate(null, null, referenceContext, null, newGenotypeAnnotatedVC, perReadAlleleLikelihoodMap);
+                if (annotationsFromCurrentType != null) {
+                    infoAnnotations.putAll(annotationsFromCurrentType);
+                }
+            }
+        }
+        //leave this in or else the median will overwrite until we do truly allele-specific
+        //// for now do both allele-specific and not
+        for ( final InfoFieldAnnotation annotationType : requestedNonReducibleInfoAnnotations ) {
             if ( !(annotationType instanceof ActiveRegionBasedAnnotation) )
                 continue;
 
-            final Map annotationsFromCurrentType = annotationType.annotate(referenceContext, perReadAlleleLikelihoodMap, vc);
+                final Map annotationsFromCurrentType = annotationType.annotate(referenceContext, perReadAlleleLikelihoodMap, newGenotypeAnnotatedVC);
+                if (annotationsFromCurrentType != null) {
+                    infoAnnotations.putAll(annotationsFromCurrentType);
+                }
+        }
+
+        // create a new VC with info and genotype annotations
+        final VariantContext annotated = builder.attributes(infoAnnotations).make();
+
+        // annotate db occurrences
+        return annotateDBs(tracker, annotated);
+    }
+
+    /**
+     * Combine (raw) data for reducible annotations (those that use raw data in gVCFs)
+     * Mutates annotationMap by removing the annotations that were combined
+     * @param allelesList   the list of merged alleles across all variants being combined
+     * @param annotationMap attributes of merged variant contexts -- is modifying by removing successfully combined annotations
+     * @return  a map containing the keys and raw values for the combined annotations
+     */
+    public Map combineAnnotations(final List allelesList, Map> annotationMap) {
+        Map combinedAnnotations = new HashMap<>();
+
+        // go through all the requested reducible info annotationTypes
+        for (final InfoFieldAnnotation annotationType : requestedReducibleInfoAnnotations) {
+                ReducibleAnnotation currentASannotation = (ReducibleAnnotation) annotationType;
+                if (annotationMap.containsKey(currentASannotation.getRawKeyName())) {
+                    final List annotationValue = annotationMap.get(currentASannotation.getRawKeyName());
+                    final Map annotationsFromCurrentType = currentASannotation.combineRawData(allelesList, annotationValue);
+                    combinedAnnotations.putAll(annotationsFromCurrentType);
+                    //remove the combined annotations so that the next method only processes the non-reducible ones
+                    annotationMap.remove(currentASannotation.getRawKeyName());
+                }
+        }
+        return combinedAnnotations;
+    }
+
+    /**
+     * Finalize reducible annotations (those that use raw data in gVCFs)
+     * @param vc    the merged VC with the final set of alleles, possibly subset to the number of maxAltAlleles for genotyping
+     * @param originalVC    the merged but non-subset VC that contains the full list of merged alleles
+     * @return  a VariantContext with the final annotation values for reducible annotations
+     */
+    public VariantContext finalizeAnnotations(VariantContext vc, VariantContext originalVC) {
+        final Map infoAnnotations = new LinkedHashMap<>(vc.getAttributes());
+
+        // go through all the requested info annotationTypes
+        for ( final InfoFieldAnnotation annotationType : requestedReducibleInfoAnnotations ) {
+
+            ReducibleAnnotation currentASannotation = (ReducibleAnnotation)annotationType;
+
+            final Map annotationsFromCurrentType = currentASannotation.finalizeRawData(vc, originalVC);
             if ( annotationsFromCurrentType != null ) {
                 infoAnnotations.putAll(annotationsFromCurrentType);
+                //clean up raw annotation data after annotations are finalized
+                infoAnnotations.remove(currentASannotation.getRawKeyName());
             }
         }
 
@@ -251,10 +366,8 @@ public class VariantAnnotatorEngine {
         final VariantContextBuilder builder = new VariantContextBuilder(vc).attributes(infoAnnotations);
 
         // annotate genotypes, creating another new VC in the process
-        final VariantContext annotated = builder.genotypes(annotateGenotypes(null, null, null, vc, perReadAlleleLikelihoodMap)).make();
-
-        // annotate db occurrences
-        return annotateDBs(tracker, annotated);
+        final VariantContext annotated = builder.make();
+        return annotated;
     }
 
     /**
@@ -298,100 +411,75 @@ public class VariantAnnotatorEngine {
                     infoAnnotations.put(expression.fullName, expressionVC.getID());
             } else if (expression.fieldName.equals("ALT")) {
                 infoAnnotations.put(expression.fullName, expressionVC.getAlternateAllele(0).getDisplayString());
+            } else if (expression.fieldName.equals("FILTER")) {
+                if ( expressionVC.isFiltered() ) {
+                    infoAnnotations.put(expression.fullName, expressionVC.getFilters().toString().replace("[", "").replace("]", "").replace(" ", ""));
+                } else {
+                    infoAnnotations.put(expression.fullName, "PASS");
+                }
             } else if ( expressionVC.hasAttribute(expression.fieldName) ) {
                 // find the info field
-                final VCFInfoHeaderLine  hInfo = hInfoMap.get(expression.fullName);
+                final VCFInfoHeaderLine hInfo = hInfoMap.get(expression.fullName);
                 if ( hInfo == null ){
                     throw new UserException("Cannot annotate expression " + expression.fullName + " at " + loc + " for variant allele(s) " + vc.getAlleles() + ", missing header info");
                 }
 
-                // can not annotate if more variant than expression alleles
-                if ( expressionVC.getNAlleles() < vc.getNAlleles() ) {
-                    logger.warn("Skipping expression " + expression.fullName + " at " + loc + ", can not match " + expressionVC.getNAlleles() + " in the expression to " +
-                            vc.getNAlleles() + " in the variant");
-                    continue;
-                }
-
                 //
                 // Add the info field annotations
                 //
-
-                final boolean isMultiAllelic = expressionVC.getNAlleles() > 2;
                 final boolean useRefAndAltAlleles = VCFHeaderLineCount.R == hInfo.getCountType();
                 final boolean useAltAlleles = VCFHeaderLineCount.A == hInfo.getCountType();
-                List usedExpressionAlleles = null;
 
-                // Multiallelic and count of A or R
-                if ( isMultiAllelic && (useAltAlleles || useRefAndAltAlleles) ){
+                // Annotation uses ref and/or alt alleles or enforce allele concordance
+                if ( (useAltAlleles || useRefAndAltAlleles) || expressionAlleleConcordance ){
 
-                    // remove brackets and spaces from expression attribute
-                    final String cleanedExpression = expressionVC.getAttribute(expression.fieldName).toString().replaceAll("[\\[\\]\\s]", "");
-
-                    // map where key = expression allele string value = expression value corresponding to the allele
-                    final Map mapAlleleToExpressionValue = new HashMap();
+                    // remove brackets and spaces from expression value
+                    final String cleanedExpressionValue = expressionVC.getAttribute(expression.fieldName).toString().replaceAll("[\\[\\]\\s]", "");
 
                     // get comma separated expression values
-                    ArrayList expressionValuesList = new ArrayList(Arrays.asList(cleanedExpression.split(",")));
+                    final ArrayList expressionValuesList = new ArrayList(Arrays.asList(cleanedExpressionValue.split(",")));
 
-                    if ( vc.isSNP() && expressionVC.isMixed() ){
-                        final VariantContextBuilder builder = new VariantContextBuilder(expressionVC);
-                        List sameLengthAlleles = new ArrayList();
+                    // get the minimum biallelics without genotypes
+                    final List minBiallelicVCs = getMinRepresentationBiallelics(vc);
+                    final List minBiallelicExprVCs = getMinRepresentationBiallelics(expressionVC);
 
-                        // get alt alleles that are the same length as the ref allele
-                        Iterator expressionValuesIterator = expressionValuesList.iterator();
-                        for ( Allele allele : expressionVC.getAlleles() ){
-                            if ( allele.isNonReference() ){
-                                if ( !expressionValuesIterator.hasNext() ){
-                                    logger.warn("Cannot annotate expression " + expression.fullName + " at " + loc + " for expression allele): " + allele);
-                                    break;
-                                }
-                                expressionValuesIterator.next();
-                                if ( allele.length() == expressionVC.getReference().length() ) {
-                                    sameLengthAlleles.add(allele);
-                                }
-                                else {
-                                    // remove unused expression values
-                                    expressionValuesIterator.remove();
-                                }
-                            } else {
-                                if ( useRefAndAltAlleles )
-                                    expressionValuesIterator.remove();
+                    // check concordance
+                    final List annotationValues = new ArrayList<>();
+                    boolean canAnnotate = false;
+                    for ( final VariantContext biallelicVC : minBiallelicVCs ) {
+                        // check that ref and alt alleles are the same
+                        List exprAlleles = biallelicVC.getAlleles();
+                        boolean isAlleleConcordant = false;
+                        int i = 0;
+                        for ( final VariantContext biallelicExprVC : minBiallelicExprVCs ){
+                            List alleles = biallelicExprVC.getAlleles();
+                            // concordant
+                            if ( alleles.equals(exprAlleles) ){
+                                // get the value for the reference if needed.
+                                if ( i == 0 && useRefAndAltAlleles )
+                                    annotationValues.add(expressionValuesList.get(i++));
+                                // use annotation expression and add to vc
+                                annotationValues.add(expressionValuesList.get(i));
+                                isAlleleConcordant = true;
+                                canAnnotate = true;
+                                break;
                             }
+                            i++;
                         }
 
-                        if (!sameLengthAlleles.isEmpty()) {
-                            sameLengthAlleles.add(0, expressionVC.getReference());
-                            VariantContext variantContext = builder.alleles(sameLengthAlleles).make();
-                            // extract the SNPs
-                            VariantContext variantContextTrimmed = GATKVariantContextUtils.trimAlleles(variantContext, true, true);
-                            usedExpressionAlleles = useRefAndAltAlleles ? variantContextTrimmed.getAlleles() : variantContextTrimmed.getAlternateAlleles();
-                        }
-                    } else {
-                        // get the alleles common to the expression and variant
-                        usedExpressionAlleles = useRefAndAltAlleles ? expressionVC.getAlleles() : expressionVC.getAlternateAlleles();
+                        // can not find allele match so set to annotation value to zero
+                        if ( !isAlleleConcordant )
+                            annotationValues.add("0");
                     }
 
-                    final List commonAlleles = ListUtils.intersection(usedExpressionAlleles, vc.getAlleles());
-
-                    // the number of expression values must be the same as the number of alleles
-                    if ( expressionValuesList.size() != usedExpressionAlleles.size() ) {
-                        logger.warn("Cannot annotate expression " + expression.fullName + " at " + loc + " for variant allele(s): " + vc.getAlleles() + ", " +
-                                expressionValuesList.size() + " expression values is not equal to " + usedExpressionAlleles.size() + " expression alleles");
+                    // no allele matches so can not annotate
+                    if ( !canAnnotate )
                         continue;
-                    }
-
-                    // map the used expression alleles to it's value
-                    for (int i = 0; i != expressionValuesList.size(); i++)
-                        mapAlleleToExpressionValue.put(usedExpressionAlleles.get(i).getBaseString(), expressionValuesList.get(i));
-
-                    // add the variants expression values to the annotation
-                    final List annotationValues = new ArrayList();
-                    for (final Allele commonAllele : commonAlleles) {
-                        annotationValues.add(mapAlleleToExpressionValue.get(commonAllele.getBaseString()));
-                    }
 
+                    // add the annotation values
                     infoAnnotations.put(expression.fullName, annotationValues);
                 } else {
+                    // use all of the expression values
                     infoAnnotations.put(expression.fullName, expressionVC.getAttribute(expression.fieldName));
                 }
             }
@@ -424,4 +512,37 @@ public class VariantAnnotatorEngine {
 
         return genotypes;
     }
+
+    /**
+     * Break the variant context into bialleles (reference and alternate alleles) and trim to a minimum representation
+     *
+     * @param vc variant context to annotate
+     * @return list of biallelics trimmed to a minimum representation
+     */
+    private List getMinRepresentationBiallelics(final VariantContext vc) {
+        final List minRepresentationBiallelicVCs = new ArrayList();
+        final boolean isMultiAllelic = vc.getNAlleles() > 2;
+        if (isMultiAllelic) {
+            final List vcList = GATKVariantContextUtils.splitVariantContextToBiallelics(vc);
+            for (final VariantContext biallelicVC : vcList) {
+                if (!biallelicVC.isSNP())
+                    minRepresentationBiallelicVCs.add(GATKVariantContextUtils.trimAlleles(biallelicVC, true, true));
+                else
+                    minRepresentationBiallelicVCs.add(biallelicVC);
+            }
+        } else {
+            minRepresentationBiallelicVCs.add(vc);
+        }
+
+        return minRepresentationBiallelicVCs;
+    }
+
+    private void setReducibleAnnotations() {
+        for(final InfoFieldAnnotation annotationType : requestedInfoAnnotations) {
+            if (annotationType instanceof ReducibleAnnotation)
+                requestedReducibleInfoAnnotations.add(annotationType);
+            else
+                requestedNonReducibleInfoAnnotations.add(annotationType);
+        }
+    }
 }
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotator.java
index e7e0b5431..8fd0abe05 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotator.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AS_StandardAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AS_StandardAnnotation.java
new file mode 100644
index 000000000..55c3e47cc
--- /dev/null
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AS_StandardAnnotation.java
@@ -0,0 +1,31 @@
+/*
+* Copyright 2012-2015 Broad Institute, Inc.
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.gatk.tools.walkers.annotator.interfaces;
+
+/**
+ * Created by gauthier on 9/28/15.
+ */
+public interface AS_StandardAnnotation extends AnnotationType {}
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java
index 8a32ae150..ee818ea34 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationHelpUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationHelpUtils.java
index d8e3c8c3c..bb488679b 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationHelpUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationHelpUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationInterfaceManager.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationInterfaceManager.java
index 37b570c87..985774f51 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationInterfaceManager.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationInterfaceManager.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -133,7 +133,7 @@ public class AnnotationInterfaceManager {
 
         // note that technically an annotation can work on both the INFO and FORMAT fields
         for ( Class c : classes )
-            annotations.add(pluginManager.createByType(c));
+            annotations.add((T)pluginManager.createByType(c));
 
         return annotations;
     }
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationType.java
index 0051c978f..40a94cf70 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationType.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationType.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotatorCompatible.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotatorCompatible.java
index f1aeedeaf..363da058e 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotatorCompatible.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotatorCompatible.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ExperimentalAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ExperimentalAnnotation.java
index 9ed24db69..87954d221 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ExperimentalAnnotation.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ExperimentalAnnotation.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/GenotypeAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/GenotypeAnnotation.java
index 41c2650ca..590c6b9c1 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/GenotypeAnnotation.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/GenotypeAnnotation.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/InfoFieldAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/InfoFieldAnnotation.java
index 32f6b90f7..cc91cda52 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/InfoFieldAnnotation.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/InfoFieldAnnotation.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ReducibleAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ReducibleAnnotation.java
new file mode 100644
index 000000000..25d2d8f41
--- /dev/null
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ReducibleAnnotation.java
@@ -0,0 +1,88 @@
+/*
+* Copyright 2012-2015 Broad Institute, Inc.
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.gatk.tools.walkers.annotator.interfaces;
+
+import htsjdk.variant.variantcontext.Allele;
+import htsjdk.variant.variantcontext.VariantContext;
+import org.broadinstitute.gatk.tools.walkers.annotator.ReducibleAnnotationData;
+import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
+import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
+import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
+
+import java.util.List;
+import java.util.Map;
+
+/**
+ * An interface for annotations that are calculated using raw data across samples, rather than the median (or median of median) of samples values
+ */
+public interface ReducibleAnnotation extends AnnotationType {
+    public abstract String getRawKeyName();
+
+    /**
+     * Generate the raw data necessary to calculate the annotation. Raw data is the final endpoint for gVCFs.
+     *
+     * @param tracker
+     * @param walker
+     * @param ref
+     * @param stratifiedContexts
+     * @param vc
+     * @param stratifiedPerReadAlleleLikelihoodMap
+     * @return
+     */
+    public abstract Map annotateRawData(final RefMetaDataTracker tracker,
+                                                        final AnnotatorCompatible walker,
+                                                        final ReferenceContext ref,
+                                                        final Map stratifiedContexts,
+                                                        final VariantContext vc,
+                                                        final Map stratifiedPerReadAlleleLikelihoodMap);
+
+    /**
+     * Combine raw data, typically during the merging of raw data contained in multiple gVCFs as in CombineGVCFs and the
+     * preliminary merge for GenotypeGVCFs
+     * @param allelesList   The merged allele list across all variants being combined/merged
+     * @param listOfRawData The raw data for all the variants being combined/merged
+     * @return
+     */
+    public abstract Map combineRawData(final List allelesList, final List  listOfRawData);
+
+
+    /**
+     * Calculate the final annotation value from the raw data
+     * @param vc -- contains the final set of alleles, possibly subset by GenotypeGVCFs
+     * @param originalVC -- used to get all the alleles for all gVCFs
+     * @return
+     */
+    public abstract Map finalizeRawData(final VariantContext vc, final VariantContext originalVC);
+
+    /**
+     *
+     * @param vc
+     * @param pralm
+     * @param rawAnnotations
+     */
+    public abstract void calculateRawData(VariantContext vc, Map pralm, ReducibleAnnotationData rawAnnotations);
+}
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/RodRequiringAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/RodRequiringAnnotation.java
index 04e545ad0..c489d66bc 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/RodRequiringAnnotation.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/RodRequiringAnnotation.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardAnnotation.java
index 247af00b2..70d7c9f25 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardAnnotation.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardAnnotation.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardSomaticAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardSomaticAnnotation.java
new file mode 100644
index 000000000..72eecaa36
--- /dev/null
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardSomaticAnnotation.java
@@ -0,0 +1,28 @@
+/*
+* Copyright 2012-2015 Broad Institute, Inc.
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.gatk.tools.walkers.annotator.interfaces;
+
+public interface StandardSomaticAnnotation extends AnnotationType {}
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardUGAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardUGAnnotation.java
index 06927f8d4..13fe48b66 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardUGAnnotation.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardUGAnnotation.java
@@ -1,6 +1,6 @@
 /*
-* Copyright (c) 2012 The Broad Institute
-*
+* Copyright 2012-2015 Broad Institute, Inc.
+* 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
 * files (the "Software"), to deal in the Software without
@@ -9,10 +9,10 @@
 * copies of the Software, and to permit persons to whom the
 * Software is furnished to do so, subject to the following
 * conditions:
-*
+* 
 * The above copyright notice and this permission notice shall be
 * included in all copies or substantial portions of the Software.
-*
+* 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
 * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
 * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java
index 0c689558e..4bb9b28aa 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/WorkInProgressAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/WorkInProgressAnnotation.java
index 9daab4345..cc9a7d7b9 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/WorkInProgressAnnotation.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/WorkInProgressAnnotation.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/BeagleOutputToVCF.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/BeagleOutputToVCF.java
deleted file mode 100644
index 2656e1ef0..000000000
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/BeagleOutputToVCF.java
+++ /dev/null
@@ -1,391 +0,0 @@
-/*
-* Copyright (c) 2012 The Broad Institute
-* 
-* Permission is hereby granted, free of charge, to any person
-* obtaining a copy of this software and associated documentation
-* files (the "Software"), to deal in the Software without
-* restriction, including without limitation the rights to use,
-* copy, modify, merge, publish, distribute, sublicense, and/or sell
-* copies of the Software, and to permit persons to whom the
-* Software is furnished to do so, subject to the following
-* conditions:
-* 
-* The above copyright notice and this permission notice shall be
-* included in all copies or substantial portions of the Software.
-* 
-* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
-* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-*/
-
-package org.broadinstitute.gatk.tools.walkers.beagle;
-
-import org.broadinstitute.gatk.utils.commandline.*;
-import org.broadinstitute.gatk.engine.CommandLineGATK;
-import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection;
-import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
-import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
-import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
-import org.broadinstitute.gatk.engine.walkers.RodWalker;
-import org.broadinstitute.gatk.utils.GenomeLoc;
-import org.broadinstitute.gatk.engine.SampleUtils;
-import org.broadinstitute.gatk.utils.codecs.beagle.BeagleFeature;
-import org.broadinstitute.gatk.utils.help.HelpConstants;
-import org.broadinstitute.gatk.engine.GATKVCFUtils;
-import htsjdk.variant.vcf.*;
-import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
-import htsjdk.variant.variantcontext.*;
-import htsjdk.variant.variantcontext.writer.VariantContextWriter;
-import org.broadinstitute.gatk.utils.variant.GATKVCFConstants;
-import org.broadinstitute.gatk.utils.variant.GATKVCFHeaderLines;
-
-import java.util.*;
-
-import static java.lang.Math.log10;
-
-
-/**
- * Takes files produced by Beagle imputation engine and creates a vcf with modified annotations.
- *
- * 
    This walker is intended to be run after Beagle has successfully executed. The full calling sequence for using Beagle along with the GATK is:      
    
- *
- * 
    1. Run ProduceBeagleInputWalker.  
    
- * 
    2. Run Beagle
    
- * 
    3. Uncompress output files
    
- * 
    4. Run BeagleOutputToVCFWalker.
    
- *
- *
- * Note that this walker requires all input files produced by Beagle.
- *
- *
- * 
    Example
    
- * 
    - *     java -Xmx4000m -jar dist/GenomeAnalysisTK.jar \
- *      -R reffile.fasta -T BeagleOutputToVCF \
- *      -V input_vcf.vcf \
- *      -beagleR2:BEAGLE /myrun.beagle_output.r2 \
- *      -beaglePhased:BEAGLE /myrun.beagle_output.phased \
- *      -beagleProbs:BEAGLE /myrun.beagle_output.gprobs \
- *      -o output_vcf.vcf
- *      
    
-
- 
     Note that Beagle produces some of these files compressed as .gz, so gunzip must be run on them before walker is run in order to decompress them 
    
-
- */
-@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARDISC, extraDocs = {CommandLineGATK.class} )
-public class BeagleOutputToVCF extends RodWalker {
-
-    @ArgumentCollection
-    protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
-
-    /**
-     * If this argument is present, the original allele frequencies and counts from this vcf are added as annotations ACH,AFH and ANH. at each record present in this vcf
-     */
-    @Input(fullName="comp", shortName = "comp", doc="Comparison VCF file", required=false)
-    public RodBinding comp;
-
-
-    /**
-     * This required argument is used to annotate each site in the vcf INFO field with R2 annotation. Will be NaN if Beagle determined there are no variant samples.
-     */
-    @Input(fullName="beagleR2", shortName = "beagleR2", doc="Beagle-produced .r2 file containing R^2 values for all markers", required=true)
-    public RodBinding beagleR2;
-
-    /**
-     * These values will populate the GL field for each sample and contain the posterior probability of each genotype given the data after phasing and imputation.
-     */
-    @Input(fullName="beagleProbs", shortName = "beagleProbs", doc="Beagle-produced .probs file containing posterior genotype probabilities", required=true)
-    public RodBinding beagleProbs;
-
-    /**
-     * By default, all genotypes will be marked in the VCF as "phased", using the "|" separator after Beagle.
-     */
-    @Input(fullName="beaglePhased", shortName = "beaglePhased", doc="Beagle-produced .phased file containing phased genotypes", required=true)
-    public RodBinding beaglePhased;
-
-    @Output(doc="VCF File to which variants should be written")
-    protected VariantContextWriter vcfWriter = null;
-
-    /**
-     * If this argument is absent, and if Beagle determines that there is no sample in a site that has a variant genotype, the site will be marked as filtered (Default behavior).
-     * If the argument is present, the site won't be marked as filtered under this condition even if there are no variant genotypes.
-     */
-    @Argument(fullName="dont_mark_monomorphic_sites_as_filtered", shortName="keep_monomorphic", doc="If provided, we won't filter sites that beagle tags as monomorphic.  Useful for imputing a sample's genotypes from a reference panel" ,required=false)
-    public boolean DONT_FILTER_MONOMORPHIC_SITES = false;
-
-    /**
-     * Value between 0 and 1. If the probability of getting a genotype correctly (based on the posterior genotype probabilities and the actual genotype) is below this threshold,
-     * a genotype will be substitute by a no-call.
-     */
-    @Argument(fullName="no" +
-            "call_threshold", shortName="ncthr", doc="Threshold of confidence at which a genotype won't be called", required=false)
-    private double noCallThreshold = 0.0;
-
-    protected static String line = null;
-
-    private final double MIN_PROB_ERROR = 0.000001;
-    private final double MAX_GENOTYPE_QUALITY = -6.0;
-
-    public void initialize() {
-
-        // setup the header fields
-
-        final Set hInfo = new HashSet<>();
-        hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit()));
-        hInfo.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.ORIGINAL_GENOTYPE_KEY));
-        hInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.BEAGLE_R2_KEY));
-        hInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.NUM_GENOTYPES_CHANGED_KEY));
-        hInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.ORIGINAL_ALT_ALLELE_INFO_KEY));
-        hInfo.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.BEAGLE_MONO_FILTER_NAME));
-
-        if ( comp.isBound() ) {
-            hInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.BEAGLE_AC_COMP_KEY));
-            hInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.BEAGLE_AF_COMP_KEY));
-            hInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.BEAGLE_AN_COMP_KEY));
-        }
-
-        Set samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variantCollection.variants.getName()));
-
-        final VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
-        vcfWriter.writeHeader(vcfHeader);
-    }
-
-    public Integer map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
-
-        if ( tracker == null )
-            return 0;
-
-        GenomeLoc loc = context.getLocation();
-        VariantContext vc_input = tracker.getFirstValue(variantCollection.variants, loc);
-
-        VariantContext vc_comp = tracker.getFirstValue(comp, loc);
-
-        if ( vc_input == null  )
-            return 0;
-
-        if (vc_input.isFiltered()) {
-            vcfWriter.add(vc_input);
-            return 1;
-        }
-
-        BeagleFeature beagleR2Feature = tracker.getFirstValue(beagleR2);
-        BeagleFeature beagleProbsFeature = tracker.getFirstValue(beagleProbs);
-        BeagleFeature beaglePhasedFeature = tracker.getFirstValue(beaglePhased);
-
-        // ignore places where we don't have a variant
-        if ( beagleR2Feature == null || beagleProbsFeature == null ||  beaglePhasedFeature == null)
-        {
-            vcfWriter.add(vc_input);
-            return 1;
-        }
-
-
-        // get reference base for current position
-        byte refByte = ref.getBase();
-
-        // make new Genotypes based on Beagle results
-        GenotypesContext genotypes = GenotypesContext.create(vc_input.getGenotypes().size());
-
-        // for each genotype, create a new object with Beagle information on it
-
-        int numGenotypesChangedByBeagle = 0;
-        Integer alleleCountH = 0, chrCountH = 0;
-        Double alleleFrequencyH = 0.0;
-        int beagleVarCounts = 0;
-
-        GenotypesContext hapmapGenotypes = null;
-
-        if (vc_comp != null) {
-            hapmapGenotypes = vc_comp.getGenotypes();
-        }
-
-        for ( final Genotype g : vc_input.getGenotypes() ) {
-            boolean genotypeIsPhased = true;
-            String sample = g.getSampleName();
-
-            // If we have  a Hapmap (comp) ROD, compute Hapmap AC, AN and AF
-            // use sample as key into genotypes structure
-            if (vc_comp != null) {
-
-                if (vc_input.getGenotypes().containsSample(sample) && hapmapGenotypes.containsSample(sample))  {
-
-                    Genotype hapmapGenotype = hapmapGenotypes.get(sample);
-                    if (hapmapGenotype.isCalled()){
-                        chrCountH += 2;
-                        if (hapmapGenotype.isHet()) {
-                            alleleCountH += 1;
-                        }    else if (hapmapGenotype.isHomVar()) {
-                            alleleCountH += 2;
-                        }
-                    }
-                }
-            }
-
-            ArrayList beagleProbabilities = beagleProbsFeature.getProbLikelihoods().get(sample);
-            ArrayList beagleGenotypePairs = beaglePhasedFeature.getGenotypes().get(sample);
-
-            // original alleles at this genotype
-            Allele originalAlleleA = g.getAllele(0);
-
-            Allele originalAlleleB = (g.getAlleles().size() == 2) ? g.getAllele(1) : g.getAllele(0); // hack to deal with no-call genotypes
-
-
-            // We have phased genotype in hp. Need to set the isRef field in the allele.
-            List alleles = new ArrayList<>();
-
-            String alleleA = beagleGenotypePairs.get(0);
-            String alleleB = beagleGenotypePairs.get(1);
-
-            if ( alleleA.equals("null") || alleleB.equals("null") ) {
-                logger.warn("Beagle produced 'null' alleles at location "+ref.getLocus().toString()+". Ignoring.");
-                return 0;
-            }
-
-            // Beagle always produces genotype strings based on the strings we input in the likelihood file.
-            String refString = vc_input.getReference().getDisplayString();
-
-            Allele bglAlleleA, bglAlleleB;
-
-            if (alleleA.matches(refString))
-                bglAlleleA = Allele.create(alleleA,true);
-            else
-                bglAlleleA = Allele.create(alleleA,false);
-
-            if (alleleB.matches(refString))
-                bglAlleleB = Allele.create(alleleB,true);
-            else
-                bglAlleleB = Allele.create(alleleB,false);
-
-
-            alleles.add(bglAlleleA);
-            alleles.add(bglAlleleB);
-
-            // Compute new GQ field = -10*log10Pr(Genotype call is wrong)
-            // Beagle gives probability that genotype is AA, AB and BB.
-            // Which, by definition, are prob of hom ref, het and hom var.
-            double probWrongGenotype, genotypeQuality;
-            Double homRefProbability = Double.valueOf(beagleProbabilities.get(0));
-            Double hetProbability = Double.valueOf(beagleProbabilities.get(1));
-            Double homVarProbability = Double.valueOf(beagleProbabilities.get(2));
-
-            if (bglAlleleA.isReference() && bglAlleleB.isReference()) // HomRef call
-                probWrongGenotype = hetProbability + homVarProbability;
-            else if ((bglAlleleB.isReference() && bglAlleleA.isNonReference()) || (bglAlleleA.isReference() && bglAlleleB.isNonReference()))
-                probWrongGenotype = homRefProbability + homVarProbability;
-            else // HomVar call
-                probWrongGenotype = hetProbability + homRefProbability;
-
-            // deal with numerical errors coming from limited formatting value on Beagle output files
-            if (probWrongGenotype > 1 - MIN_PROB_ERROR)
-                probWrongGenotype = 1 - MIN_PROB_ERROR;
-
-            if (1-probWrongGenotype < noCallThreshold) {
-                // quality is bad: don't call genotype
-                alleles.clear();
-                alleles.add(originalAlleleA);
-                alleles.add(originalAlleleB);
-                genotypeIsPhased = false;
-            }
-
-            if (probWrongGenotype < MIN_PROB_ERROR)
-                genotypeQuality = MAX_GENOTYPE_QUALITY;
-            else
-                genotypeQuality = log10(probWrongGenotype);
-
-            HashMap originalAttributes = new HashMap<>(g.getExtendedAttributes());
-
-            // get original encoding and add to keynotype attributes
-            String a1, a2, og;
-            if (originalAlleleA.isNoCall())
-                a1 = ".";
-            else if (originalAlleleA.isReference())
-                a1 = "0";
-            else
-                a1 = "1";
-
-            if (originalAlleleB.isNoCall())
-                a2 = ".";
-            else if (originalAlleleB.isReference())
-                a2 = "0";
-            else
-                a2 = "1";
-
-            og = a1+"/"+a2;
-
-            // See if Beagle switched genotypes
-            if (! originalAlleleA.equals(Allele.NO_CALL) && beagleSwitchedGenotypes(bglAlleleA,originalAlleleA,bglAlleleB,originalAlleleB)){
-                originalAttributes.put(GATKVCFConstants.ORIGINAL_GENOTYPE_KEY, og);
-                numGenotypesChangedByBeagle++;
-            }
-            else {
-                originalAttributes.put(GATKVCFConstants.ORIGINAL_GENOTYPE_KEY, ".");
-            }
-            Genotype imputedGenotype = new GenotypeBuilder(g).alleles(alleles).log10PError(genotypeQuality).attributes(originalAttributes).phased(genotypeIsPhased).make();
-            if ( imputedGenotype.isHet() || imputedGenotype.isHomVar() ) {
-                beagleVarCounts++;
-            }
-
-            genotypes.add(imputedGenotype);
-        }
-
-        final VariantContextBuilder builder = new VariantContextBuilder(vc_input).source("outputvcf").genotypes(genotypes);
-        if ( ! ( beagleVarCounts > 0 || DONT_FILTER_MONOMORPHIC_SITES ) ) {
-            builder.attribute(GATKVCFConstants.ORIGINAL_ALT_ALLELE_INFO_KEY, vc_input.getAlternateAllele(0));
-            builder.alleles(Collections.singleton(vc_input.getReference())).filter(GATKVCFConstants.BEAGLE_MONO_FILTER_NAME);
-        }
-
-        // re-compute chromosome counts
-        VariantContextUtils.calculateChromosomeCounts(builder, false);
-
-        // Get Hapmap AC and AF
-        if (vc_comp != null) {
-            builder.attribute(GATKVCFConstants.BEAGLE_AC_COMP_KEY, alleleCountH.toString() );
-            builder.attribute(GATKVCFConstants.BEAGLE_AN_COMP_KEY, chrCountH.toString() );
-            builder.attribute(GATKVCFConstants.BEAGLE_AF_COMP_KEY, String.format("%4.2f", (double)alleleCountH/chrCountH) );
-
-        }
-
-        builder.attribute(GATKVCFConstants.NUM_GENOTYPES_CHANGED_KEY, numGenotypesChangedByBeagle );
-        if( !beagleR2Feature.getR2value().equals(Double.NaN) ) {
-            builder.attribute(GATKVCFConstants.BEAGLE_R2_KEY, beagleR2Feature.getR2value().toString() );
-        }
-
-        vcfWriter.add(builder.make());
-
-        return 1;
-    }
-
-    private boolean beagleSwitchedGenotypes(Allele bglAlleleA, Allele originalAlleleA, Allele bglAlleleB, Allele originalAlleleB) {
-       return !((bglAlleleA.equals(originalAlleleA) && bglAlleleB.equals(originalAlleleB) ||
-                    (bglAlleleA.equals(originalAlleleB) && bglAlleleB.equals(originalAlleleA))));
-    }
-
-    public Integer reduceInit() {
-        return 0; // Nothing to do here
-    }
-
-    /**
-     * Increment the number of loci processed.
-     *
-     * @param value result of the map.
-     * @param sum   accumulator for the reduce.
-     * @return the new number of loci processed.
-     */
-    public Integer reduce(Integer value, Integer sum) {
-        return sum + value;
-    }
-
-    /**
-     * Tell the user the number of loci processed and close out the new variants file.
-     *
-     * @param result  the number of loci seen.
-     */
-    public void onTraversalDone(Integer result) {
-        System.out.printf("Processed %d loci.\n", result);
-    }
-}
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/ProduceBeagleInput.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/ProduceBeagleInput.java
deleted file mode 100644
index 7e08defd4..000000000
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/ProduceBeagleInput.java
+++ /dev/null
@@ -1,463 +0,0 @@
-/*
-* Copyright (c) 2012 The Broad Institute
-* 
-* Permission is hereby granted, free of charge, to any person
-* obtaining a copy of this software and associated documentation
-* files (the "Software"), to deal in the Software without
-* restriction, including without limitation the rights to use,
-* copy, modify, merge, publish, distribute, sublicense, and/or sell
-* copies of the Software, and to permit persons to whom the
-* Software is furnished to do so, subject to the following
-* conditions:
-* 
-* The above copyright notice and this permission notice shall be
-* included in all copies or substantial portions of the Software.
-* 
-* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
-* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-*/
-
-package org.broadinstitute.gatk.tools.walkers.beagle;
-
-import org.broadinstitute.gatk.utils.Utils;
-import org.broadinstitute.gatk.utils.commandline.*;
-import org.broadinstitute.gatk.engine.CommandLineGATK;
-import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection;
-import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
-import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
-import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
-import org.broadinstitute.gatk.engine.samples.Gender;
-import org.broadinstitute.gatk.engine.walkers.RodWalker;
-import org.broadinstitute.gatk.tools.walkers.variantrecalibration.VQSRCalibrationCurve;
-import org.broadinstitute.gatk.utils.GenomeLoc;
-import org.broadinstitute.gatk.utils.MathUtils;
-import org.broadinstitute.gatk.engine.SampleUtils;
-import org.broadinstitute.gatk.utils.help.HelpConstants;
-import org.broadinstitute.gatk.engine.GATKVCFUtils;
-import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
-import htsjdk.variant.vcf.VCFFilterHeaderLine;
-import htsjdk.variant.vcf.VCFHeader;
-import htsjdk.variant.vcf.VCFHeaderLine;
-import org.broadinstitute.gatk.utils.exceptions.GATKException;
-import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
-import htsjdk.variant.variantcontext.*;
-import htsjdk.variant.variantcontext.writer.VariantContextWriter;
-
-import java.io.File;
-import java.io.PrintStream;
-import java.util.*;
-
-/**
- *  Converts the input VCF into a format accepted by the Beagle imputation/analysis program.
- * 
    
- *
- * 
    Input
    
- * 
    
- * A VCF with variants to convert to Beagle format
- * 
    
- *
- * 
    Outputs
    
- * 
    
- * A single text file which can be fed to Beagle
- * 
    
- * 
    
- * Optional: A file with a list of markers
- * 
    
-  *
- * 
    Examples
    
- * 
    - *     java -Xmx2g -jar dist/GenomeAnalysisTK.jar -L 20 \
- *      -R reffile.fasta -T ProduceBeagleInput \
- *      -V path_to_input_vcf/inputvcf.vcf -o path_to_beagle_output/beagle_output
- * 
    
- *
- */
-
-@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARDISC, extraDocs = {CommandLineGATK.class} )
-public class ProduceBeagleInput extends RodWalker {
-
-    @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
-
-    @Hidden
-    @Input(fullName="validation", shortName = "validation", doc="Validation VCF file", required=false)
-    public RodBinding validation;
-
-
-    @Output(doc="File to which BEAGLE input should be written")
-    protected PrintStream  beagleWriter = null;
-
-    @Hidden
-    @Output(doc="File to which BEAGLE markers should be written", shortName="markers", fullName = "markers", required = false, defaultToStdout = false)
-    protected PrintStream  markers = null;
-    int markerCounter = 1;
-
-    @Hidden
-    @Input(doc="VQSqual calibration file", shortName = "cc", required=false)
-    protected File VQSRCalibrationFile = null;
-    protected VQSRCalibrationCurve VQSRCalibrator = null;
-
-    @Hidden
-    @Argument(doc="VQSqual key", shortName = "vqskey", required=false)
-    protected String VQSLOD_KEY = "VQSqual";
-
-    @Hidden
-     @Argument(fullName = "inserted_nocall_rate", shortName = "nc_rate", doc = "Rate (0-1) at which genotype no-calls will be randomly inserted, for testing", required = false)
-    public double insertedNoCallRate  = 0;
-    @Hidden
-     @Argument(fullName = "validation_genotype_ptrue", shortName = "valp", doc = "Flat probability to assign to validation genotypes. Will override GL field.", required = false)
-    public double validationPrior = -1.0;
-    @Hidden
-     @Argument(fullName = "validation_bootstrap", shortName = "bs", doc = "Proportion of records to be used in bootstrap set", required = false)
-    public double bootstrap = 0.0;
-    @Hidden
-     @Argument(fullName = "bootstrap_vcf",shortName = "bvcf", doc = "Output a VCF with the records used for bootstrapping filtered out", required = false)
-    VariantContextWriter bootstrapVCFOutput = null;
-
-    /**
-     * If sample gender is known, this flag should be set to true to ensure that Beagle treats male Chr X properly.
-     */
-    @Argument(fullName = "checkIsMaleOnChrX", shortName = "checkIsMaleOnChrX", doc = "Set to true when Beagle-ing chrX and want to ensure male samples don't have heterozygous calls.", required = false)
-    public boolean CHECK_IS_MALE_ON_CHR_X = false;
-
-    @Hidden
-    @Argument(fullName = "variant_genotype_ptrue", shortName = "varp", doc = "Flat probability prior to assign to variant (not validation) genotypes. Does not override GL field.", required = false)
-    public double variantPrior = 0.96;
-
-    private Set samples = null;
-    private Set BOOTSTRAP_FILTER = new HashSet( Arrays.asList("bootstrap") );
-    private int bootstrapSetSize = 0;
-    private int testSetSize = 0;
-    private CachingFormatter formatter = new CachingFormatter("%5.4f ", 100000);
-    private int certainFPs = 0;
-
-    public void initialize() {
-
-        samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variantCollection.variants.getName()));
-
-        beagleWriter.print("marker alleleA alleleB");
-        for ( String sample : samples )
-            beagleWriter.print(String.format(" %s %s %s", sample, sample, sample));
-
-        beagleWriter.println();
-
-        if ( bootstrapVCFOutput != null ) {
-            initializeVcfWriter();
-        }
-
-        if ( VQSRCalibrationFile != null ) {
-            VQSRCalibrator = VQSRCalibrationCurve.readFromFile(VQSRCalibrationFile);
-            logger.info("Read calibration curve");
-            VQSRCalibrator.printInfo(logger);
-        }
-    }
-
-    public Integer map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
-        if( tracker != null ) {
-            GenomeLoc loc = context.getLocation();
-            VariantContext variant_eval = tracker.getFirstValue(variantCollection.variants, loc);
-            VariantContext validation_eval = tracker.getFirstValue(validation, loc);
-
-            if ( goodSite(variant_eval,validation_eval) ) {
-                if ( useValidation(validation_eval, ref) ) {
-                    writeBeagleOutput(validation_eval, variant_eval, true, validationPrior);
-                    return 1;
-                } else {
-                    if ( goodSite(variant_eval) ) {
-                        writeBeagleOutput(variant_eval,validation_eval,false,variantPrior);
-                        return 1;
-                    } else { // todo -- if the variant site is bad, validation is good, but not in bootstrap set -- what do?
-                        return 0;
-                    }
-                }
-            } else {
-                return 0;
-            }
-        } else {
-            return 0;
-        }
-    }
-
-    public boolean goodSite(VariantContext a, VariantContext b) {
-        return goodSite(a) || goodSite(b);
-    }
-
-    public boolean goodSite(VariantContext v) {
-        if ( canBeOutputToBeagle(v) ) {
-            if ( VQSRCalibrator != null && VQSRCalibrator.certainFalsePositive(VQSLOD_KEY, v) ) {
-                certainFPs++;
-                return false;
-            } else {
-                return true;
-            }
-        } else {
-            return false;
-        }
-    }
-
-    public static boolean canBeOutputToBeagle(VariantContext v) {
-        return v != null && ! v.isFiltered() && v.isBiallelic() && v.hasGenotypes();
-    }
-
-    public boolean useValidation(VariantContext validation, ReferenceContext ref) {
-        if( goodSite(validation) ) {
-            // if using record keeps us below expected proportion, use it
-            logger.debug(String.format("boot: %d, test: %d, total: %d", bootstrapSetSize, testSetSize, bootstrapSetSize+testSetSize+1));
-            if ( (bootstrapSetSize+1.0)/(1.0+bootstrapSetSize+testSetSize) <= bootstrap ) {
-                if ( bootstrapVCFOutput != null ) {
-                    bootstrapVCFOutput.add(new VariantContextBuilder(validation).filters(BOOTSTRAP_FILTER).make());
-                }
-                bootstrapSetSize++;
-                return true;
-            } else {
-                if ( bootstrapVCFOutput != null ) {
-                    bootstrapVCFOutput.add(validation);
-                }
-                testSetSize++;
-                return false;
-            }
-        } else {
-            if ( validation != null && bootstrapVCFOutput != null ) {
-                bootstrapVCFOutput.add(validation);
-            }
-            return false;
-        }
-    }
-
-    private final static double[] HAPLOID_FLAT_LOG10_LIKELIHOODS = MathUtils.toLog10(new double[]{ 0.5, 0.0, 0.5 });
-    private final static double[] DIPLOID_FLAT_LOG10_LIKELIHOODS = MathUtils.toLog10(new double[]{ 0.33, 0.33, 0.33 });
-
-    public void writeBeagleOutput(VariantContext preferredVC, VariantContext otherVC, boolean isValidationSite, double prior) {
-        GenomeLoc currentLoc = GATKVariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), preferredVC);
-        StringBuffer beagleOut = new StringBuffer();
-
-        String marker = String.format("%s:%d ",currentLoc.getContig(),currentLoc.getStart());
-        beagleOut.append(marker);
-        if ( markers != null ) markers.append(marker).append("\t").append(Integer.toString(markerCounter++)).append("\t");
-        for ( Allele allele : preferredVC.getAlleles() ) {
-            String bglPrintString;
-            if (allele.isNoCall())
-                bglPrintString = "-";
-            else
-                bglPrintString = allele.getBaseString();  // get rid of * in case of reference allele
-
-            beagleOut.append(String.format("%s ", bglPrintString));
-            if ( markers != null ) markers.append(bglPrintString).append("\t");
-        }
-        if ( markers != null ) markers.append("\n");
-
-        GenotypesContext preferredGenotypes = preferredVC.getGenotypes();
-        GenotypesContext otherGenotypes = goodSite(otherVC) ? otherVC.getGenotypes() : null;
-        for ( String sample : samples ) {
-            boolean isMaleOnChrX = CHECK_IS_MALE_ON_CHR_X && getSample(sample).getGender() == Gender.MALE;
-
-            Genotype genotype;
-            boolean isValidation;
-            // use sample as key into genotypes structure
-            if ( preferredGenotypes.containsSample(sample) ) {
-                genotype = preferredGenotypes.get(sample);
-                isValidation = isValidationSite;
-            } else if ( otherGenotypes != null && otherGenotypes.containsSample(sample) ) {
-                genotype = otherGenotypes.get(sample);
-                isValidation = ! isValidationSite;
-            } else {
-                // there is magically no genotype for this sample.
-                throw new GATKException("Sample "+sample+" arose with no genotype in variant or validation VCF. This should never happen.");
-            }
-
-            /*
-             * Use likelihoods if: is validation, prior is negative; or: is not validation, has genotype key
-             */
-            double [] log10Likelihoods = null;
-            if ( (isValidation && prior < 0.0) || genotype.hasLikelihoods() ) {
-                log10Likelihoods = genotype.getLikelihoods().getAsVector();
-
-                // see if we need to randomly mask out genotype in this position.
-                if ( Utils.getRandomGenerator().nextDouble() <= insertedNoCallRate ) {
-                    // we are masking out this genotype
-                    log10Likelihoods = isMaleOnChrX ? HAPLOID_FLAT_LOG10_LIKELIHOODS : DIPLOID_FLAT_LOG10_LIKELIHOODS;
-                }
-
-                if( isMaleOnChrX ) {
-                    log10Likelihoods[1] = -255;  // todo -- warning this is dangerous for multi-allele case
-                }
-            }
-            /**
-             * otherwise, use the prior uniformly
-             */
-            else if (! isValidation && genotype.isCalled() && ! genotype.hasLikelihoods() ) {
-                // hack to deal with input VCFs with no genotype likelihoods.  Just assume the called genotype
-                // is confident.  This is useful for Hapmap and 1KG release VCFs.
-                double AA = (1.0-prior)/2.0;
-                double AB = (1.0-prior)/2.0;
-                double BB = (1.0-prior)/2.0;
-
-                if (genotype.isHomRef()) { AA = prior; }
-                else if (genotype.isHet()) { AB = prior; }
-                else if (genotype.isHomVar()) { BB = prior; }
-
-                log10Likelihoods = MathUtils.toLog10(new double[]{ AA, isMaleOnChrX ? 0.0 : AB, BB });
-            }
-            else  {
-                log10Likelihoods = isMaleOnChrX ? HAPLOID_FLAT_LOG10_LIKELIHOODS : DIPLOID_FLAT_LOG10_LIKELIHOODS;
-            }
-
-            writeSampleLikelihoods(beagleOut, preferredVC, log10Likelihoods);
-        }
-
-        beagleWriter.println(beagleOut.toString());
-    }
-
-    private void writeSampleLikelihoods( StringBuffer out, VariantContext vc, double[] log10Likelihoods ) {
-        if ( VQSRCalibrator != null ) {
-            log10Likelihoods = VQSRCalibrator.includeErrorRateInLikelihoods(VQSLOD_KEY, vc, log10Likelihoods);
-        }
-
-        double[] normalizedLikelihoods = MathUtils.normalizeFromLog10(log10Likelihoods);
-        // see if we need to randomly mask out genotype in this position.
-        for (double likeVal: normalizedLikelihoods) {
-            out.append(formatter.format(likeVal));
-//            out.append(String.format("%5.4f ",likeVal));
-        }
-    }
-
-
-    public Integer reduceInit() {
-        return 0; // Nothing to do here
-    }
-
-    public Integer reduce( Integer value, Integer sum ) {
-        return value + sum; // count up the sites
-    }
-
-    public void onTraversalDone( Integer includedSites ) {
-        logger.info("Sites included in beagle likelihoods file             : " + includedSites);
-        logger.info(String.format("Certain false positive found from recalibration curve : %d (%.2f%%)",
-                certainFPs, (100.0 * certainFPs) / (Math.max(certainFPs + includedSites, 1))));
-    }
-
-    private void initializeVcfWriter() {
-        final List inputNames = Arrays.asList(validation.getName());
-
-        // setup the header fields
-        Set hInfo = new HashSet();
-        hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), inputNames));
-        hInfo.add(new VCFFilterHeaderLine("bootstrap","This site used for genotype bootstrapping with ProduceBeagleInputWalker"));
-
-        bootstrapVCFOutput.writeHeader(new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames)));
-    }
-
-    public static class CachingFormatter {
-        private String format;
-        private LRUCache cache;
-
-        public String getFormat() {
-            return format;
-        }
-
-        public String format(double value) {
-            String f = cache.get(value);
-            if ( f == null ) {
-                f = String.format(format, value);
-                cache.put(value, f);
-//                if ( cache.usedEntries() < maxCacheSize ) {
-//                    System.out.printf("CACHE size %d%n", cache.usedEntries());
-//                } else {
-//                    System.out.printf("CACHE is full %f%n", value);
-//                }
-//            }
-//            } else {
-//                System.out.printf("CACHE hit %f%n", value);
-//            }
-            }
-
-            return f;
-        }
-
-        public CachingFormatter(String format, int maxCacheSize) {
-            this.format = format;
-            this.cache = new LRUCache(maxCacheSize);
-        }
-    }
-
-    /**
-    * An LRU cache, based on LinkedHashMap.
-    *
-    * 
    
-    * This cache has a fixed maximum number of elements (cacheSize).
-    * If the cache is full and another entry is added, the LRU (least recently used) entry is dropped.
-    *
-    * 
    
-    * This class is thread-safe. All methods of this class are synchronized.
-    *
-    * 
    
-    * Author: Christian d'Heureuse, Inventec Informatik AG, Zurich, Switzerland
    
-    * Multi-licensed: EPL / LGPL / GPL / AL / BSD.
-    */
-    public static class LRUCache {
-
-    private static final float   hashTableLoadFactor = 0.75f;
-
-    private LinkedHashMap   map;
-    private int                  cacheSize;
-
-    /**
-    * Creates a new LRU cache.
-    * @param cacheSize the maximum number of entries that will be kept in this cache.
-    */
-    public LRUCache (int cacheSize) {
-       this.cacheSize = cacheSize;
-       int hashTableCapacity = (int)Math.ceil(cacheSize / hashTableLoadFactor) + 1;
-       map = new LinkedHashMap(hashTableCapacity, hashTableLoadFactor, true) {
-          // (an anonymous inner class)
-          private static final long serialVersionUID = 1;
-          @Override protected boolean removeEldestEntry (Map.Entry eldest) {
-             return size() > LRUCache.this.cacheSize; }}; }
-
-    /**
-    * Retrieves an entry from the cache.
    
-    * The retrieved entry becomes the MRU (most recently used) entry.
-    * @param key the key whose associated value is to be returned.
-    * @return    the value associated to this key, or null if no value with this key exists in the cache.
-    */
-    public synchronized V get (K key) {
-       return map.get(key); }
-
-    /**
-    * Adds an entry to this cache.
-    * The new entry becomes the MRU (most recently used) entry.
-    * If an entry with the specified key already exists in the cache, it is replaced by the new entry.
-    * If the cache is full, the LRU (least recently used) entry is removed from the cache.
-    * @param key    the key with which the specified value is to be associated.
-    * @param value  a value to be associated with the specified key.
-    */
-    public synchronized void put (K key, V value) {
-       map.put (key, value); }
-
-    /**
-    * Clears the cache.
-    */
-    public synchronized void clear() {
-       map.clear(); }
-
-    /**
-    * Returns the number of used entries in the cache.
-    * @return the number of entries currently in the cache.
-    */
-    public synchronized int usedEntries() {
-       return map.size(); }
-
-    /**
-    * Returns a Collection that contains a copy of all cache entries.
-    * @return a Collection with a copy of the cache content.
-    */
-    public synchronized Collection> getAll() {
-       return new ArrayList>(map.entrySet()); }
-
-    } // end class LRUCache
-}
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/VariantsToBeagleUnphased.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/VariantsToBeagleUnphased.java
deleted file mode 100644
index 939a52ad0..000000000
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/beagle/VariantsToBeagleUnphased.java
+++ /dev/null
@@ -1,184 +0,0 @@
-/*
-* Copyright (c) 2012 The Broad Institute
-* 
-* Permission is hereby granted, free of charge, to any person
-* obtaining a copy of this software and associated documentation
-* files (the "Software"), to deal in the Software without
-* restriction, including without limitation the rights to use,
-* copy, modify, merge, publish, distribute, sublicense, and/or sell
-* copies of the Software, and to permit persons to whom the
-* Software is furnished to do so, subject to the following
-* conditions:
-* 
-* The above copyright notice and this permission notice shall be
-* included in all copies or substantial portions of the Software.
-* 
-* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
-* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-*/
-
-package org.broadinstitute.gatk.tools.walkers.beagle;
-
-import org.broadinstitute.gatk.utils.commandline.Argument;
-import org.broadinstitute.gatk.utils.commandline.Input;
-import org.broadinstitute.gatk.utils.commandline.Output;
-import org.broadinstitute.gatk.utils.commandline.RodBinding;
-import org.broadinstitute.gatk.engine.CommandLineGATK;
-import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
-import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
-import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
-import org.broadinstitute.gatk.engine.walkers.RodWalker;
-import org.broadinstitute.gatk.utils.GenomeLoc;
-import org.broadinstitute.gatk.engine.SampleUtils;
-import org.broadinstitute.gatk.utils.help.HelpConstants;
-import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
-import htsjdk.variant.vcf.VCFHeader;
-import htsjdk.variant.vcf.VCFHeaderLine;
-import org.broadinstitute.gatk.engine.GATKVCFUtils;
-import org.broadinstitute.gatk.utils.exceptions.UserException;
-import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
-import htsjdk.variant.variantcontext.Allele;
-import htsjdk.variant.variantcontext.Genotype;
-import htsjdk.variant.variantcontext.VariantContext;
-import htsjdk.variant.variantcontext.writer.VariantContextWriter;
-
-import java.io.PrintStream;
-import java.util.Arrays;
-import java.util.Set;
-
-/**
- * Produces an input file to Beagle imputation engine, listing unphased, hard-called genotypes for a single sample
- * in input variant file.  Will additionally hold back a fraction of the sites for evaluation, marking the
- * genotypes at that sites as missing, and writing the truth of these sites to a second VCF file
- */
-@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARDISC, extraDocs = {CommandLineGATK.class} )
-public class VariantsToBeagleUnphased extends RodWalker {
-    @Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
-    public RodBinding variants;
-
-    @Output(doc="File to which BEAGLE unphased genotypes should be written")
-    protected PrintStream  beagleWriter = null;
-
-    @Argument(fullName = "bootstrap_fraction", shortName = "bs", doc = "Proportion of records to be used in bootstrap set", required = false)
-    public double bootstrap = 0.0;
-
-    @Argument(fullName = "bootstrap_vcf",shortName = "bsvcf", doc = "Output a VCF with the records used for bootstrapping filtered out", required = false)
-    VariantContextWriter bootstrapVCFOutput = null;
-
-    @Argument(fullName = "missing", shortName = "missing", doc = "String to identify missing data in beagle output", required = false)
-    public String MISSING = "?";
-
-    private Set samples = null;
-    private int bootstrapSetSize = 0;
-    private int testSetSize = 0;
-
-    public void initialize() {
-        samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getName()));
-
-        beagleWriter.print("I marker alleleA alleleB");
-        for ( String sample : samples )
-            beagleWriter.print(String.format(" %s %s", sample, sample));
-
-        beagleWriter.println();
-
-        if ( bootstrap < 0.0 | bootstrap > 1.0 )
-            throw new UserException.BadArgumentValue("bootstrap", "Bootstrap value must be fraction between 0 and 1");
-
-        if ( bootstrapVCFOutput != null ) {
-            Set hInfo = GATKVCFUtils.getHeaderFields(getToolkit());
-            bootstrapVCFOutput.writeHeader(new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit())));
-        }
-    }
-
-    /**
-     * Iterate over each site, emitting the BEAGLE unphased genotypes file format
-     * @param tracker
-     * @param ref
-     * @param context
-     * @return
-     */
-    public Integer map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
-        if( tracker != null ) {
-            GenomeLoc loc = context.getLocation();
-            VariantContext vc = tracker.getFirstValue(variants, loc);
-
-            if ( ProduceBeagleInput.canBeOutputToBeagle(vc) ) {
-                // do we want to hold back this site?
-                boolean makeMissing = dropSite(vc);
-
-                // if we are holding it back and we are writing a bootstrap VCF, write it out
-                if ( makeMissing && bootstrapVCFOutput != null ) {
-                    bootstrapVCFOutput.add(vc);
-                }
-
-                // regardless, all sites are written to the unphased genotypes file, marked as missing if appropriate
-                writeUnphasedBeagleOutput(vc, makeMissing);
-            }
-        }
-
-        return 0;
-    }
-
-    /**
-     * Do we want to hold back this site for bootstrap?  Considers the bootstrap fraction member variable
-     *
-     * @param vc
-     * @return
-     */
-    public boolean dropSite(VariantContext vc) {
-        if ( (bootstrapSetSize+1.0)/(1.0+bootstrapSetSize+testSetSize) <= bootstrap ) {
-            bootstrapSetSize++;
-            return true;
-        } else {
-            testSetSize++;
-            return false;
-        }
-    }
-
-    public void writeUnphasedBeagleOutput(VariantContext vc, boolean makeMissing) {
-        GenomeLoc currentLoc = GATKVariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vc);
-        StringBuffer beagleOut = new StringBuffer();
-
-        String marker = String.format("%s:%d ",currentLoc.getContig(), currentLoc.getStart());
-        beagleOut.append("M ").append(marker);
-
-        // write out the alleles at this site
-        for ( Allele allele : vc.getAlleles() ) {
-            beagleOut.append(allele.isNoCall() ? "-" : allele.getBaseString()).append(" ");
-        }
-
-        // write out sample level genotypes
-        for ( String sample : samples ) {
-            Genotype genotype = vc.getGenotype(sample);
-            if ( ! makeMissing && genotype.isCalled() ) {
-                addAlleles(beagleOut, genotype);
-            } else {
-                addAlleles(beagleOut, MISSING, MISSING);
-            }
-        }
-
-        beagleWriter.println(beagleOut.toString());
-    }
-
-    private void addAlleles(StringBuffer buf, Genotype g) {
-        addAlleles(buf, g.getAllele(0).getBaseString(), g.getAllele(1).getBaseString());
-
-    }
-
-    private void addAlleles(StringBuffer buf, String a, String b) {
-        buf.append(a).append(" ").append(b);
-    }
-
-    public Integer reduceInit() { return 0; }
-    public Integer reduce( Integer value, Integer sum ) { return value + sum; }
-
-    public void onTraversalDone( Integer includedSites ) {
-        logger.info("Sites included in beagle genotypes file : " + includedSites);
-    }
-}
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLoci.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLoci.java
index cc12172a1..bf2eddccb 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLoci.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLoci.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLoci.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLoci.java
index e02a10ee6..1951a43c1 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLoci.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLoci.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CoverageUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CoverageUtils.java
index e027464d4..6f0e5507f 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CoverageUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CoverageUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverage.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverage.java
index 098e81c94..96144ce13 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverage.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverage.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageStats.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageStats.java
index c8a43567f..aa7b5ae7e 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageStats.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageStats.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DoCOutputType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DoCOutputType.java
index 6e2266d48..f91c38574 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DoCOutputType.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DoCOutputType.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/GCContentByInterval.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/GCContentByInterval.java
index 441f920f7..c4d1aef25 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/GCContentByInterval.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/GCContentByInterval.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/CoveredByNSamplesSites.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/CoveredByNSamplesSites.java
deleted file mode 100644
index 4e3e91fc8..000000000
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/CoveredByNSamplesSites.java
+++ /dev/null
@@ -1,154 +0,0 @@
-/*
-* Copyright (c) 2012 The Broad Institute
-* 
-* Permission is hereby granted, free of charge, to any person
-* obtaining a copy of this software and associated documentation
-* files (the "Software"), to deal in the Software without
-* restriction, including without limitation the rights to use,
-* copy, modify, merge, publish, distribute, sublicense, and/or sell
-* copies of the Software, and to permit persons to whom the
-* Software is furnished to do so, subject to the following
-* conditions:
-* 
-* The above copyright notice and this permission notice shall be
-* included in all copies or substantial portions of the Software.
-* 
-* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
-* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-*/
-
-package org.broadinstitute.gatk.tools.walkers.diagnostics;
-
-
-import org.broadinstitute.gatk.engine.walkers.By;
-import org.broadinstitute.gatk.engine.walkers.DataSource;
-import org.broadinstitute.gatk.engine.walkers.RodWalker;
-import org.broadinstitute.gatk.engine.walkers.TreeReducible;
-import org.broadinstitute.gatk.utils.commandline.Argument;
-import org.broadinstitute.gatk.utils.commandline.ArgumentCollection;
-import org.broadinstitute.gatk.utils.commandline.Output;
-import org.broadinstitute.gatk.engine.CommandLineGATK;
-import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection;
-import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
-import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
-import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
-import org.broadinstitute.gatk.utils.GenomeLoc;
-import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.gatk.utils.help.HelpConstants;
-import htsjdk.variant.variantcontext.Genotype;
-import htsjdk.variant.variantcontext.GenotypesContext;
-import htsjdk.variant.variantcontext.VariantContext;
-
-
-import java.io.*;
-import java.util.Collection;
-
-/**
- * Report well-covered intervals
- *
- * 
    
- * This tool evaluates whether sites are well-covered or not according to specific coverage quality parameters, and
- * outputs a list of intervals that are considered well-covered, i.e. where most samples have good coverage. This is
- * useful for masking out poorly-covered sites where we cannot expect meaningful results in downstream analyses. See
- * argument defaults for what constitutes "most" samples and "good" coverage.
- * 
    
- *
- * 
    Input
    
- * 
    
- * A variant file and optionally, minimum coverage and sample percentage values.
- * 
    
- *
- * 
    Output
    
- * 
    
- * An list of well-covered intervals.
- * 
    
- *
- * 
    Usage example
    
- * 
    - * java -jar GenomeAnalysisTK.jar \
- *   -T CoveredByNSamplesSites \
- *   -R reference.fasta \
- *   -V input.vcf \
- *   -out output.intervals \
- *   -minCov 15
- * 
    
- *
- */
-@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
-@By(DataSource.REFERENCE_ORDERED_DATA)
-public class CoveredByNSamplesSites extends RodWalker implements TreeReducible {
-
-    @Output(fullName = "OutputIntervals", shortName = "out", doc = "Name of file for output intervals")
-    PrintStream outputStream;
-
-    @ArgumentCollection
-    protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
-
-    @Argument(fullName = "minCoverage", shortName = "minCov",doc = "only samples that have coverage bigger than minCoverage will be counted",required = false)
-    int minCoverage = 10;
-
-    @Argument(fullName = "percentageOfSamples", shortName = "percentage", doc = "only sites where at least percentageOfSamples of the samples have good coverage, will be emitted", required = false)
-    double percentageOfSamples = 0.9;
-
-    @Override
-    public GenomeLoc map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        if ( tracker == null )
-            return null;
-
-        Collection VCs = tracker.getValues(variantCollection.variants, context.getLocation());
-        if ( VCs.size() == 0 )
-            return null;
-
-        boolean emitSite = false;
-        for(VariantContext vc : VCs){
-            int coveredSamples = 0;
-            final GenotypesContext genotypes = vc.getGenotypes();
-            final int numOfGenotypes = genotypes.size();
-            for(Genotype g : genotypes){
-                if(g.getDP() >= minCoverage)
-                    coveredSamples++;
-            }
-            if((double)coveredSamples/numOfGenotypes > percentageOfSamples){
-                emitSite = true;
-            }
-        }
-        if (emitSite)
-            return ref.getLocus();
-        else
-            return null;
-    }
-
-    @Override
-    public Integer reduceInit() { return 0; }
-
-    @Override
-    public Integer reduce(GenomeLoc value, Integer sum) {
-        if ( value != null ) {
-            outputStream.println(value);
-            sum++;
-        }
-        return sum;
-    }
-
-    @Override
-    public Integer treeReduce(Integer lhs, Integer rhs) {
-        return lhs + rhs;
-    }
-
-    /**
-     *
-     * @param result the number of sites that passed the filter.
-     */
-    public void onTraversalDone(Integer result) {
-        logger.info(result+" sites that have "+(percentageOfSamples*100)+"% of the samples with at least "+minCoverage+" coverage.\n");
-    }
-
-
-
-}
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycle.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycle.java
index 129fa00ad..6808d927b 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycle.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycle.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadGroupProperties.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadGroupProperties.java
index 987d1a0e1..86185b174 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadGroupProperties.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadGroupProperties.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadLengthDistribution.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadLengthDistribution.java
index cfebdd29a..1f3d6c7f9 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadLengthDistribution.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadLengthDistribution.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjects.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjects.java
similarity index 99%
rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjects.java
rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjects.java
index dc71d58ee..f12d08a5e 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjects.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjects.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/examples/GATKDocsExample.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/examples/GATKDocsExample.java
index e026b286b..d95fd2b46 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/examples/GATKDocsExample.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/examples/GATKDocsExample.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/examples/GATKPaperGenotyper.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/examples/GATKPaperGenotyper.java
index bdddc5040..54db6f30e 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/examples/GATKPaperGenotyper.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/examples/GATKPaperGenotyper.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceMaker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceMaker.java
index 8ec22e5ea..5be2e8933 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceMaker.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceMaker.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -102,12 +102,17 @@ public class FastaAlternateReferenceMaker extends FastaReferenceMaker {
     protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
 
     /**
-     * Snps from this file are used as a mask (inserting N's in the sequence) when constructing the alternate reference
-     * (regardless of whether they overlap a variant site).
+     * SNPs from this file are used as a mask (inserting N's in the sequence) when constructing the alternate reference
      */
     @Input(fullName="snpmask", shortName = "snpmask", doc="SNP mask VCF file", required=false)
     protected RodBinding snpmask;
 
+    /**
+     * Gives priority to a SNP mask over an input VCF for a site. Only has an effect if the --snpmask argument is used.
+     */
+    @Argument(fullName="snpmaskPriority", shortName = "snpmaskPriority", doc="SNP mask priority", required=false)
+    protected Boolean snpmaskPriority = false;
+
     /**
      * This option will generate an error if the specified sample does not exist in the VCF.
      * Non-diploid (or non-called) genotypes are ignored.
@@ -138,6 +143,13 @@ public class FastaAlternateReferenceMaker extends FastaReferenceMaker {
 
         final String refBase = String.valueOf((char)ref.getBase());
 
+        // If we have a mask at this site, use it
+        if ( snpmaskPriority ){
+            final Pair mask = maskSnp(tracker, context);
+            if ( mask != null )
+                return mask;
+        }
+
         // Check to see if we have a called snp
         for ( final VariantContext vc : tracker.getValues(variantCollection.variants, ref.getLocus()) ) {
             if ( vc.isFiltered() )
@@ -155,17 +167,33 @@ public class FastaAlternateReferenceMaker extends FastaReferenceMaker {
             }
         }
 
-        // if we don't have a called site, and we have a mask at this site, mask it
-        for ( final VariantContext vc : tracker.getValues(snpmask) ) {
-            if ( vc.isSNP()) {
-                return new Pair<>(context.getLocation(), "N");
-            }
+        if ( !snpmaskPriority ){
+            final Pair mask = maskSnp(tracker, context);
+            if ( mask != null )
+                return mask;
         }
 
         // if we got here then we're just ref
         return new Pair<>(context.getLocation(), refBase);
     }
 
+    /**
+     * Mask a SNP (inserting N's in the sequence)
+     *
+     * @param tracker the Reference Metadata available at a particular site in the genome
+     * @param context the locus context data
+     * @return mask at the locus or null if no SNP at that locus
+     */
+    private Pair maskSnp(final RefMetaDataTracker tracker, final AlignmentContext context){
+        for (final VariantContext vc : tracker.getValues(snpmask)) {
+            if (vc.isSNP()) {
+                return new Pair<>(context.getLocation(), "N");
+            }
+        }
+
+        return null;
+    }
+
     /**
      * Returns the IUPAC encoding for the given genotype or the reference base if not possible
      *
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaReferenceMaker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaReferenceMaker.java
index 08ab3019a..4eb8f3e23 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaReferenceMaker.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaReferenceMaker.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -55,7 +55,15 @@ import java.io.PrintStream;
  *
  * 
    Output
    
  * 
    
- * A fasta file representing the requested intervals.
+ * A fasta file representing the requested intervals. Each interval has a description line starting with a greater-than (">") symbol followed by sequence data.
+ * The description begins with the contig name followed by the beginning position on the contig.
+ * 
    + * For example, the fasta file for contig 1 and intervals 1:3-1:4 and 1:6-1:9
+ * >1 1:3
+ * AT
+ * >1 1:6
+ * GGGG
+ * 
    
  * 
    
  *
  * 
    Usage example
    
@@ -104,18 +112,20 @@ public class FastaReferenceMaker extends RefWalker, Geno
         // if there is no interval to the left, then this is the first one
         if ( sum == null ) {
             sum = value.first;
+            fasta.setName(fasta.getName() + " " + sum.toString());
             fasta.append(value.second);
         }
-        // if the intervals don't overlap, print out the leftmost one and start a new one
+        // if the intervals are not contiguous, print out the leftmost one and start a new one
         // (end of contig or new interval)
-        else if ( value.first.getStart() != sum.getStop() + 1 ) {
+        else if ( value.first.getStart() != sum.getStop() + 1 || ! value.first.getContig().equals(sum.getContig()) ) {
             fasta.flush();
             sum = value.first;
+            fasta.setName(fasta.getName() + " " + sum.toString());
             fasta.append(value.second);
         }
         // otherwise, merge them
         else {
-            sum = getToolkit().getGenomeLocParser().setStop(sum, value.first.getStop());
+            sum = sum.setStop(sum, value.first.getStop());
             fasta.append(value.second);
         }
 		return sum;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaSequence.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaSequence.java
index 013e356a7..062297beb 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaSequence.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaSequence.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaStats.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaStats.java
index 7215e2b7b..01d26c04e 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaStats.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaStats.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/ClusteredSnps.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/ClusteredSnps.java
index 97bde83b1..c0de7b9d7 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/ClusteredSnps.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/ClusteredSnps.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContext.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContext.java
index c5302b9a2..e48c8f45b 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContext.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContext.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContextWindow.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContextWindow.java
index 731b1a361..e47d54b6a 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContextWindow.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContextWindow.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltration.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltration.java
index 4c4d6f02d..3c61235e3 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltration.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltration.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCMappingQualityFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCMappingQualityFilter.java
index f82985fd0..96586c030 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCMappingQualityFilter.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCMappingQualityFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDoclet.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDoclet.java
index 831655f56..ac15e7439 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDoclet.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDoclet.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDocumentationHandler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDocumentationHandler.java
index b4e586fb3..8e3881cdb 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDocumentationHandler.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDocumentationHandler.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -228,13 +228,17 @@ public class WalkerDocumentationHandler extends GenericDocumentationHandler {
      */
     private HashMap getDownSamplingSettings(Class myClass, HashMap dsSettings) {
         //
-        // Retrieve annotation
-        if (myClass.isAnnotationPresent(Downsample.class)) {
-            final Annotation thisAnnotation = myClass.getAnnotation(Downsample.class);
-            if(thisAnnotation instanceof Downsample) {
-                final Downsample dsAnnotation = (Downsample) thisAnnotation;
-                dsSettings.put("by", dsAnnotation.by().toString());
-                dsSettings.put("to_cov", dsAnnotation.toCoverage());
+        // Check for RODWalker first
+        if (!checkForRODWalker(myClass).equals("yes")) {
+            //
+            // Retrieve annotation
+            if (myClass.isAnnotationPresent(Downsample.class)) {
+                final Annotation thisAnnotation = myClass.getAnnotation(Downsample.class);
+                if(thisAnnotation instanceof Downsample) {
+                    final Downsample dsAnnotation = (Downsample) thisAnnotation;
+                    dsSettings.put("by", dsAnnotation.by().toString());
+                    dsSettings.put("to_cov", dsAnnotation.toCoverage());
+                }
             }
         }
         return dsSettings;
@@ -320,6 +324,24 @@ public class WalkerDocumentationHandler extends GenericDocumentationHandler {
         return getWalkerType(mySuperClass);
     }
 
+    /**
+     * Utility function that checks whether an instance of class c is a subclass of RODWalker.
+     *
+     * @param myClass the class to query for the annotation
+     * @return "yes" or "no" (can't use a Boolean because of the recursion)
+     */
+    private String checkForRODWalker(Class myClass) {
+        //
+        // Look up superclasses recursively until we find either RODWalker or (Walker or Object)
+        final Class mySuperClass = myClass.getSuperclass();
+        if (mySuperClass.getSimpleName().equals("RodWalker")) {
+            return "yes";
+        } else if (mySuperClass.getSimpleName().equals("Object") || mySuperClass.getSimpleName().equals("Walker")) {
+            return "";
+        }
+        return checkForRODWalker(mySuperClass);
+    }
+
     /**
      * Utility function that finds the values of ReadFilters annotation applied to an instance of class c.
      *
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/package-info.java
index 4201ef0dc..53c155f0b 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/package-info.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/package-info.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileup.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileup.java
index b76b9ff9c..d38543c5b 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileup.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileup.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountBases.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountBases.java
index 023d103e7..e0d2a3cd4 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountBases.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountBases.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountIntervals.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountIntervals.java
index 443196cff..21f04271c 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountIntervals.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountIntervals.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountLoci.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountLoci.java
index 5a0ec3370..004906c46 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountLoci.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountLoci.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountMales.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountMales.java
index 55424f67b..a8291418f 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountMales.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountMales.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODs.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODs.java
index c81f7b9ac..78f194f9e 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODs.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODs.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODsByRef.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODsByRef.java
index c359bf1c3..8934fce68 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODsByRef.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODsByRef.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadEvents.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadEvents.java
index d5f424b6f..20d60a19f 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadEvents.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadEvents.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReads.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReads.java
index 369a5878e..17aa5bc69 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReads.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReads.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountTerminusEvent.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountTerminusEvent.java
index b569a0a6c..942e7c372 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountTerminusEvent.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountTerminusEvent.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/DocumentationTest.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/DocumentationTest.java
index 9679baac3..579f43fa3 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/DocumentationTest.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/DocumentationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ErrorThrowing.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ErrorThrowing.java
index 7def2e0e3..030c964e8 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ErrorThrowing.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ErrorThrowing.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStat.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStat.java
index 57cf4d59a..fee78877c 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStat.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStat.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/Pileup.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/Pileup.java
index db6199951..cd2c33630 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/Pileup.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/Pileup.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/PrintRODs.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/PrintRODs.java
index 9c71f0934..7873af930 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/PrintRODs.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/PrintRODs.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/QCRef.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/QCRef.java
index 0a0b9b6cd..93493544d 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/QCRef.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/QCRef.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ReadClippingStats.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ReadClippingStats.java
index a2c3f796e..1517ae73b 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ReadClippingStats.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ReadClippingStats.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/RodSystemValidation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/RodSystemValidation.java
index 4e4d131a2..1043675cc 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/RodSystemValidation.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/RodSystemValidation.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReads.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReads.java
index cafaa82c5..f8b46b62d 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReads.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReads.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReads.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReads.java
index 2f609facf..6aede1b75 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReads.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReads.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ReadAdaptorTrimmer.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ReadAdaptorTrimmer.java
deleted file mode 100644
index 0e23fac95..000000000
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ReadAdaptorTrimmer.java
+++ /dev/null
@@ -1,397 +0,0 @@
-/*
-* Copyright (c) 2012 The Broad Institute
-* 
-* Permission is hereby granted, free of charge, to any person
-* obtaining a copy of this software and associated documentation
-* files (the "Software"), to deal in the Software without
-* restriction, including without limitation the rights to use,
-* copy, modify, merge, publish, distribute, sublicense, and/or sell
-* copies of the Software, and to permit persons to whom the
-* Software is furnished to do so, subject to the following
-* conditions:
-* 
-* The above copyright notice and this permission notice shall be
-* included in all copies or substantial portions of the Software.
-* 
-* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
-* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-*/
-
-package org.broadinstitute.gatk.tools.walkers.readutils;
-
-import com.google.java.contract.Ensures;
-import com.google.java.contract.Requires;
-import htsjdk.samtools.SAMFileWriter;
-import org.apache.log4j.Logger;
-import org.broadinstitute.gatk.engine.walkers.NanoSchedulable;
-import org.broadinstitute.gatk.engine.walkers.PartitionBy;
-import org.broadinstitute.gatk.engine.walkers.PartitionType;
-import org.broadinstitute.gatk.engine.walkers.ReadWalker;
-import org.broadinstitute.gatk.utils.commandline.Advanced;
-import org.broadinstitute.gatk.utils.commandline.Argument;
-import org.broadinstitute.gatk.utils.commandline.Hidden;
-import org.broadinstitute.gatk.utils.commandline.Output;
-import org.broadinstitute.gatk.engine.CommandLineGATK;
-import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
-import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
-import org.broadinstitute.gatk.utils.BaseUtils;
-import org.broadinstitute.gatk.utils.collections.Pair;
-import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.gatk.utils.help.HelpConstants;
-import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-/**
- * Utility tool to blindly strip base adaptors
- *
- * 
    This tool is mainly intended to be applied to FASTQ/unaligned BAM pre-processing where libraries
- * have very short inserts, and hence a substantial part of the sequencing data will have adaptor sequence present. By
- * design, tool will only work for Illumina-like library constructs, where the typical library architecture is:
- * [Adaptor 1]-[Genomic Insert]-[Adaptor 2 (index/barcode)]
    
- *
- * 
    We assume that when data is paired, one read will span the forward strand and one read will span the reverse strand.
- * Hence, adaptors should be specified as both forward and reverse-complement to ensure they are removed in all cases.
- * By design, as well, "circular" constructions where a read can have an insert, then adaptor, then more genomic insert, are not supported.
- * When an adaptor is detected, all bases downstream from it (i.e. in the 3' direction) will be removed.
- * Adaptor detection is carried out by looking for overlaps between forward and reverse reads in a pair.
- * If a sufficiently high overlap is found, the insert size is computed and if insert size < read lengths adaptor bases are removed from reads.
- * 
    
- *
- * 
     Advantage over ReadClipper: No previous knowledge of adaptors or library structure is necessary.
    
- *
- * 
    Advantages over 3rd party tools like SeqPrep:
    
- * 
      
- *      
    • Can do BAM streaming instead of having to convert to fastq
      • 
- *      
    • No need to merge reads; merging reads can have some advantages, but complicates downstream processing and loses information that can be used,
- *   e.g. in variant calling
      • 
- * 
    
- *
- * 
    Input
    
- * 
    
- * The input read data in BAM format. Read data MUST be in query name ordering as produced, for example with Picard's FastqToBam
- * 
    
- *
- * 
    Output
    
- * 
    
- * A merged BAM file with unaligned reads
- * 
    
- *
- * 
- * 
    - * java -jar GenomeAnalysisTK.jar \
- *   -R reference.fasta \
- *   -T ReadAdaptorTrimmer \
- *   -I my_reads.bam \
- *   -o trimmed_Reads.bam
- * 
    
- */
-@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_DATA, extraDocs = {CommandLineGATK.class} )
-@PartitionBy(PartitionType.READ)
-public class ReadAdaptorTrimmer extends ReadWalker, SAMFileWriter> implements NanoSchedulable {
-    @Output(doc="Write output to this BAM filename instead of STDOUT", required = false)
-    SAMFileWriter out;
-
-     /**
-     * Only prints the first n reads of the file - for short testing
-     */
-     @Hidden
-    @Argument(fullName = "number", shortName = "n", doc="Print the first n reads from the file, discarding the rest", required = false)
-    int nReadsToPrint = -1;
-
-    /**
-     * Argument to control strictness of match between forward and reverse reads - by default, we require 15 matches between them to declare
-     * an overlap.
-     */
-    @Advanced
-    @Argument(fullName = "minMatches", shortName = "minMatches", doc="Minimum number of substring matches to detect pair overlaps", required = false)
-    int minMatchesForOverlap = 15;
-
-
-    /**
-     * If true, this argument will make the walker discard unpaired reads instead of erroring out.
-     */
-    @Advanced
-    @Argument(fullName = "removeUnpairedReads", shortName = "removeUnpairedReads", doc="Remove unpaired reads instead of erroring out", required = false)
-    boolean cleanUnpairedReads = false;
-
-     /**
-     * private class members
-     */
-    private GATKSAMRecord firstReadInPair;
-    private TrimStats trimStats = new TrimStats();
-
-    static class TrimStats {
-        long numReadsProcessed;
-        long numReadsWithAdaptorTrimmed;
-        long numUnpairedReadsFound;
-    }
-
-   /**
-     * The reads filter function.
-     *
-     * @param ref  the reference bases that correspond to our read, if a reference was provided
-     * @param read the read itself, as a GATKSAMRecord
-     * @return true if the read passes the filter, false if it doesn't
-     */
-    public boolean filter(ReferenceContext ref, GATKSAMRecord read) {
-         // check if we've reached the output limit
-        if ( nReadsToPrint == 0 ) {
-            return false;          // n == 0 means we've printed all we needed.
-        }
-        else if (nReadsToPrint > 0) {
-            nReadsToPrint--;       // n > 0 means there are still reads to be printed.
-        }
-        return true;
-    }
-    /**
-     * reduceInit is called once before any calls to the map function.  We use it here to setup the output
-     * bam file, if it was specified on the command line
-     *
-     * @return SAMFileWriter, set to the BAM output file if the command line option was set, null otherwise
-     */
-    public SAMFileWriter reduceInit() {
-        return out;
-    }
-
-    public List map( final ReferenceContext ref, final GATKSAMRecord readIn, final RefMetaDataTracker metaDataTracker ) {
-
-
-        final List readsToEmit = new ArrayList();
-
-
-        // cache first read in pair if flag set.
-        if (readIn.getFirstOfPairFlag()) {
-            firstReadInPair = GATKSAMRecord.emptyRead(readIn);
-            firstReadInPair.setReadString(readIn.getReadString());
-            firstReadInPair.setReadName(readIn.getReadName());
-            firstReadInPair.setBaseQualities(readIn.getBaseQualities());
-        }
-        else {
-            if (!readIn.getReadName().equals(firstReadInPair.getReadName()))  {
-                if (cleanUnpairedReads) {
-                    trimStats.numUnpairedReadsFound++;
-                    return readsToEmit;
-                }
-                else // by default require that reads be completely paired
-                    throw new IllegalStateException("Second read in pair must follow first read in pair: data not ordered?");
-            }
-
-            final int oldLength1 = firstReadInPair.getReadLength();
-            final int oldLength2 = readIn.getReadLength();
-            // try to strip any adaptor sequence in read pair
-            final Integer result = trimReads(firstReadInPair, readIn, minMatchesForOverlap, logger);
-
-            if (logger.isDebugEnabled()) {
-                if (result == null)
-                    logger.debug("No overlap found, insert size cannot be computed");
-                else
-                    logger.debug("Insert size estimate = " + result);
-
-            }
-
-
-            readsToEmit.add(firstReadInPair);
-            readsToEmit.add(readIn);
-
-            if (oldLength1 != firstReadInPair.getReadLength())
-                trimStats.numReadsWithAdaptorTrimmed++;
-            if (oldLength2 != readIn.getReadLength())
-                trimStats.numReadsWithAdaptorTrimmed++;
-
-         }
-
-
-        trimStats.numReadsProcessed++;
-        return readsToEmit;
-
-    }
-
-    /**
-     * given a read and a output location, reduce by emitting the read
-     *
-     * @param readsToEmit   the read itself
-     * @param output the output source
-     * @return the SAMFileWriter, so that the next reduce can emit to the same source
-     */
-    public SAMFileWriter reduce( final List readsToEmit, final SAMFileWriter output ) {
-        for (final GATKSAMRecord read : readsToEmit)
-             output.addAlignment(read);
-
-        return output;
-    }
-
-    @Override
-    public void onTraversalDone(SAMFileWriter output) {
-
-        logger.info("Finished Trimming:");
-        logger.info("Number of processed reads:                     "+ trimStats.numReadsProcessed);
-        logger.info("Number of reads with adaptor sequence trimmed: "+ trimStats.numReadsWithAdaptorTrimmed);
-        if (cleanUnpairedReads)
-            logger.info("Number of unpaired reads thrown out: "+ trimStats.numUnpairedReadsFound);
-    }
-
-
-    /**
-     *
-     * Workhorse routines...
-     *
-     */
-        /**
-         * Core routine that does most underlying work for walker. Takes two reads and looks for overlaps in them.
-         * An overlap is defined as a contiguous chunk of N bases that matches reverse-complement between reads.
-         * Currently, the only insert structure that it will look for overlaps is as follows:
-         * CASE 1: Insert shorter than read length:
-         * 3' XXXXXXXXXXXXXXXX 5'            (second read)
-         * 5'      YYYYYYYYYYYYYYYY 3'       (first read)
-         *         ***********
-         *
-         * In this case, if X and Y are complements at the 11 positions marked by *, routine will do the following
-         * iff minMatchesForOverlap <= 11:
-         *  a) Cleave adaptor from end of second read (leftmost dangling part in diagram above)
-         *  b) Cleave adaptor from end of first read (rightmost part in diagram).
-         *
-         * CASE 2: Insert size >= read length:
-         * 3'             XXXXXXXXXXXXXXXX 5'           (second read)
-         * 5'      YYYYYYYYYYYYYYYY 3'                  (first read)
-         *                *********                        (overlap)
-         *
-         * In this case, no trimming is done and reads are left unchanged
-         * @param first                      (I/O) First read in pair - read contents (bases/quals) can be modified if adaptor is detected
-         * @param second                     (I/O) Second read in pair - read contents (bases/quals) can be modified if adaptor is detected
-         * @param minMatchesForOverlap       Reads need to match in these # of bases to be joined
-         * @return                           Offset between second and first read.
-         *                                   If there's no detectable offset, return Null
-         */
-    @Requires({"first != null","second != null","minMatchesForOverlap>0"})
-    protected static Integer trimReads(final GATKSAMRecord first,
-                                       final GATKSAMRecord second,
-                                       final int minMatchesForOverlap,
-                                       final Logger logger) {
-
-        final Integer insertSize = estimateInsertSize(first.getReadBases(), second.getReadBases(),
-                minMatchesForOverlap, logger);
-
-        if (insertSize == null)
-            return insertSize;
-        if (insertSize < first.getReadLength()) {
-            // trim adaptor sequence from read
-            first.setReadBases(Arrays.copyOfRange(first.getReadBases(),0,insertSize));
-            first.setBaseQualities(Arrays.copyOfRange(first.getBaseQualities(),0,insertSize));
-        }
-        if (insertSize < second.getReadLength()) {
-            // trim adaptor sequence from read
-            second.setReadBases(Arrays.copyOfRange(second.getReadBases(),0,insertSize));
-            second.setBaseQualities(Arrays.copyOfRange(second.getBaseQualities(),0,insertSize));
-        }
-        return insertSize;
-    }
-
-    /**
-    * Brain-dead implementation of an aligner of two sequences, where it's assumed that there might be an overlap
-    * from the first into the second. From this, an estimate of insert size is performed and returned
-    * Assumes that reads come in reverse direction, so one of the base sequences needs to be reverse-complemented.]
-    *
-    * @param firstRead                           Bytes from first read
-    * @param secondRead                          Bytes from second read (reverse direction)
-    * @return                                  Estimated insert size based on offset between first and second read.
-    *                                          If no overlap can be detected, return null
-    */
-
-    @Requires({"firstRead != null","secondRead != null","minMatches>0","firstRead.length == secondRead.length"})
-    protected static Integer estimateInsertSize(final byte[] firstRead,
-                                                                final byte[] secondRead,
-                                                                final int minMatches,
-                                                                final Logger logger) {
-        final byte[] firstBases = firstRead;
-        final byte[] secondBases = BaseUtils.simpleReverseComplement(secondRead);
-
-        final Pair overlaps = findOverlappingSequence(firstBases, secondBases);
-        final int bestOffset = overlaps.first;
-        final int maxScore = overlaps.second;
-        if ( logger.isDebugEnabled()) {
-            String sb="", s1 = new String(firstBases), s2 = new String(secondBases);
-            for (int k=0; k < Math.abs(bestOffset); k++) sb+=" ";
-            if (maxScore >= minMatches) {
-                logger.debug(String.format("Match, Max Score = %d, best offset = %d\n",maxScore, bestOffset));
-                if (bestOffset>0)
-                    s2 = sb+s2;
-                else
-                    s1 = sb+s1;
-            }
-            else logger.debug("NoMatch:");
-            logger.debug("R1:"+s1);
-            logger.debug("R2:"+s2);
-
-
-        }
-
-        if (maxScore < minMatches)
-            return null; // no overlap detected
-
-        return bestOffset+secondRead.length;
-
-
-    }
-
-
-     /**
-     * Tries to find overlapping sequence between two reads, and computes offset between them
-      * For each possible offset, computes matching score, which is = MATCH_SCORE*Num_matches + MISMATCH_SCORE*num_mismatches
-      * (like SW with infinite gap penalties).
-     * @param first                              First read bytes
-     * @param second                             Second read bytes
-     * @return                                   Pair of integers (x,y). x = best offset between reads, y = corresponding score
-     */
-    @Requires({"first != null","second != null"})
-    @Ensures("result != null")
-    protected static Pair findOverlappingSequence(final byte[] first,
-                                                 final byte[] second) {
-        final int MATCH_SCORE = 1;
-        final int MISMATCH_SCORE = -1;
-        // try every possible offset - O(N^2) algorithm
-
-        // In case of following structure,
-        //      111111111
-        // 222222222
-        // computed offset will be negative (=-5 in this case).
-        // If however,
-        //   111111111
-        //      222222222
-        // then offset will be positive (=3 in this case)
-        int maxScore = 0, bestOffset =0;
-        for (int offset = -second.length; offset < first.length; offset++) {
-            int score = 0;
-            // compute start index for each array
-            int ind1 = (offset<0)?0:offset;
-            int ind2 = (offset<0)?-offset:0;
-            for (int k=0; k < Math.min(first.length, second.length) ; k++) {
-                if (ind1 >= first.length)
-                    break;
-                if (ind2 >= second.length )
-                    break;
-                if (first[ind1] != 'N' && second[ind2] != 'N')  {
-                    if (first[ind1] == second[ind2])
-                        score += MATCH_SCORE;
-                    else
-                        score += MISMATCH_SCORE;
-                }
-                ind1++;
-                ind2++;
-            }
-            if (score > maxScore) {
-                maxScore = score;
-                bestOffset = offset;
-            }
-        }
-        return new Pair(bestOffset,maxScore);
-    }
-
-}
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java
index b015e6dc8..029d8b88a 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounter.java
index a5622d570..1e151adb4 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounter.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -27,8 +27,6 @@ package org.broadinstitute.gatk.tools.walkers.rnaseq;
 
 import htsjdk.variant.variantcontext.VariantContext;
 import org.broadinstitute.gatk.engine.CommandLineGATK;
-import org.broadinstitute.gatk.engine.filters.DuplicateReadFilter;
-import org.broadinstitute.gatk.engine.walkers.DisabledReadFilters;
 import org.broadinstitute.gatk.engine.walkers.Downsample;
 import org.broadinstitute.gatk.engine.walkers.LocusWalker;
 import org.broadinstitute.gatk.tools.walkers.coverage.CoverageUtils;
@@ -87,8 +85,8 @@ import java.util.List;
  * 
    Note
    
  * 
      
  *     
    • Like most GATK tools, this tools filters out duplicate reads by default. However, some ASE methods
- *     recommend including duplicate reads in the analysis, so the DuplicateReads filter can be disabled using the
- *     "-drf DuplicateReads" flag in the command-line.
      • 
+ *     recommend including duplicate reads in the analysis, so the DuplicateRead filter can be disabled using the
+ *     "-drf DuplicateRead" flag in the command-line.
  * 
    
  * 
    Caveat
    
  * 
      
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEval.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEval.java
index dea80d112..1617f4f39 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEval.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEval.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -29,9 +29,12 @@ import com.google.java.contract.Requires;
 import htsjdk.samtools.reference.IndexedFastaSequenceFile;
 import htsjdk.samtools.util.IntervalTree;
 import htsjdk.samtools.SAMSequenceRecord;
+import oracle.jrockit.jfr.StringConstantPool;
 import org.apache.log4j.Logger;
 import htsjdk.tribble.Feature;
+import org.broadinstitute.gatk.engine.samples.Trio;
 import org.broadinstitute.gatk.engine.walkers.*;
+import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.*;
 import org.broadinstitute.gatk.utils.commandline.*;
 import org.broadinstitute.gatk.engine.CommandLineGATK;
 import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
@@ -39,7 +42,6 @@ import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection;
 import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
 import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
 import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
-import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantEvaluator;
 import org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.IntervalStratification;
 import org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.VariantStratifier;
 import org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.manager.StratificationManager;
@@ -105,7 +107,7 @@ import java.util.*;
  * 
  * 
      
  *
- * 
      Usage example
      
+ * 
      Usage examples
      
  * 
        * java -jar GenomeAnalysisTK.jar \
  *   -T VariantEval \
@@ -116,6 +118,18 @@ import java.util.*;
  *   [--comp comp.vcf]
  * 
      
  *
+ * Count Mendelian violations for each family in a callset with multiple families (and provided pedigree)
+ * 
      + * Java -jar GenomeAnalysisTK.jar \
+ *   -T VariantEval \
+ *   -R reference.fasta \
+ *   -o output.MVs.byFamily.table \
+ *   --eval multiFamilyCallset.vcf \
+ *   -noEV -noST \
+ *   -ST Family \
+ *   -EV MendelianViolationEvaluator
+ * 
      
+ *
  * 
      Caveat
      
  *
  * 
      Some stratifications and evaluators are incompatible with each other due to their respective memory requirements,
@@ -249,14 +263,18 @@ public class VariantEval extends RodWalker implements TreeRedu
 
     private boolean isSubsettingSamples;
     private Set sampleNamesForEvaluation = new LinkedHashSet();
+    private Set familyNamesForEvaluation = new LinkedHashSet();
     private Set sampleNamesForStratification = new LinkedHashSet();
+    private Set familyNamesForStratification = new LinkedHashSet();
 
     // important stratifications
     private boolean byFilterIsEnabled = false;
     private boolean perSampleIsEnabled = false;
+    private boolean perFamilyIsEnabled = false;
 
     // Public constants
-    private static String ALL_SAMPLE_NAME = "all";
+    final private static String ALL_SAMPLE_NAME = "all";
+    final private static String ALL_FAMILY_NAME = "all";
 
     // the number of processed bp for this walker
     long nProcessedLoci = 0;
@@ -303,12 +321,22 @@ public class VariantEval extends RodWalker implements TreeRedu
         final Set allSampleNames = SampleUtils.getSamplesFromCommandLineInput(vcfSamples);
         sampleNamesForEvaluation.addAll(new TreeSet(SampleUtils.getSamplesFromCommandLineInput(vcfSamples, SAMPLE_EXPRESSIONS)));
         isSubsettingSamples = ! sampleNamesForEvaluation.containsAll(allSampleNames);
+        familyNamesForEvaluation.addAll(getSampleDB().getFamilyIDs());
 
-        if (Arrays.asList(STRATIFICATIONS_TO_USE).contains("Sample")) {
+        //If stratifying by sample name, assign a stratification for each sample we're evaluating (based on commandline args)...
+        if (Arrays.asList(STRATIFICATIONS_TO_USE).contains("Sample") ) {
             sampleNamesForStratification.addAll(sampleNamesForEvaluation);
         }
+        //...and also a stratification for the sum over all samples
         sampleNamesForStratification.add(ALL_SAMPLE_NAME);
 
+        //If stratifying by sample name, assign a stratification for each family...
+        if ( Arrays.asList(STRATIFICATIONS_TO_USE).contains("Family") ) {
+            familyNamesForStratification.addAll(familyNamesForEvaluation);
+        }
+        //...and also a stratification for the sum over all families
+        familyNamesForStratification.add(ALL_FAMILY_NAME);
+
         // Initialize select expressions
         for (VariantContextUtils.JexlVCMatchExp jexl : VariantContextUtils.initializeMatchExps(SELECT_NAMES, SELECT_EXPS)) {
             SortableJexlVCMatchExp sjexl = new SortableJexlVCMatchExp(jexl.name, jexl.exp);
@@ -327,8 +355,17 @@ public class VariantEval extends RodWalker implements TreeRedu
                 byFilterIsEnabled = true;
             else if ( vs.getName().equals("Sample") )
                 perSampleIsEnabled = true;
+            else if ( vs.getName().equals("Family"))
+                perFamilyIsEnabled = true;
         }
 
+        if (perSampleIsEnabled && perFamilyIsEnabled)
+            throw new UserException.BadArgumentValue("ST", "Variants cannot be stratified by sample and family at the same time");
+
+        if (perFamilyIsEnabled && getSampleDB().getTrios().isEmpty())
+            throw new UserException.BadArgumentValue("ST", "Cannot stratify by family without *.ped file");
+
+
         if ( intervalsFile != null ) {
             boolean fail = true;
             for ( final VariantStratifier vs : stratificationObjects ) {
@@ -420,17 +457,24 @@ public class VariantEval extends RodWalker implements TreeRedu
 //            }
 
             //      --------- track ---------           sample  - VariantContexts -
-            HashMap, HashMap>> evalVCs = variantEvalUtils.bindVariantContexts(tracker, ref, evals, byFilterIsEnabled, true, perSampleIsEnabled, mergeEvals);
-            HashMap, HashMap>> compVCs = variantEvalUtils.bindVariantContexts(tracker, ref, comps, byFilterIsEnabled, false, false, false);
+            HashMap, HashMap>> evalVCs = variantEvalUtils.bindVariantContexts(tracker, ref, evals, byFilterIsEnabled, true, perSampleIsEnabled, perFamilyIsEnabled, mergeEvals);
+            HashMap, HashMap>> compVCs = variantEvalUtils.bindVariantContexts(tracker, ref, comps, byFilterIsEnabled, false, false, false, false);
 
             // for each eval track
             for ( final RodBinding evalRod : evals ) {
                 final Map> emptyEvalMap = Collections.emptyMap();
                 final Map> evalSet = evalVCs.containsKey(evalRod) ? evalVCs.get(evalRod) : emptyEvalMap;
 
+                Set statificationLevels;
+
                 // for each sample stratifier
-                for ( final String sampleName : sampleNamesForStratification ) {
-                    Collection evalSetBySample = evalSet.get(sampleName);
+                if (perFamilyIsEnabled)
+                    statificationLevels = familyNamesForStratification;
+                else
+                    statificationLevels = sampleNamesForStratification;
+                for ( final String stratLevelName : statificationLevels ) {
+                    Collection evalSetBySample = evalSet.get(stratLevelName);
+
                     if ( evalSetBySample == null ) {
                         evalSetBySample = new HashSet(1);
                         evalSetBySample.add(null);
@@ -452,7 +496,18 @@ public class VariantEval extends RodWalker implements TreeRedu
                             // find the comp
                             final VariantContext comp = findMatchingComp(eval, compSet);
 
-                            for ( EvaluationContext nec : getEvaluationContexts(tracker, ref, eval, evalRod.getName(), comp, compRod.getName(), sampleName) ) {
+                            Collection contextsForStratification;
+                            if (perFamilyIsEnabled)
+                                contextsForStratification = getEvaluationContexts(tracker, ref, eval, evalRod.getName(), comp, compRod.getName(), null, stratLevelName);
+                            else {
+                                String familyID;
+                                if (stratLevelName.equals("all"))
+                                    familyID = "all";
+                                else
+                                    familyID = getSampleDB().getSample(stratLevelName).getFamilyID();
+                                contextsForStratification = getEvaluationContexts(tracker, ref, eval, evalRod.getName(), comp, compRod.getName(), stratLevelName, familyID);
+                            }
+                            for ( EvaluationContext nec : contextsForStratification ) {
 
                                 // eval against the comp
                                 synchronized (nec) {
@@ -521,10 +576,11 @@ public class VariantEval extends RodWalker implements TreeRedu
                                                                   final String evalName,
                                                                   final VariantContext comp,
                                                                   final String compName,
-                                                                  final String sampleName ) {
+                                                                  final String sampleName,
+                                                                  final String familyName) {
         final List> states = new LinkedList>();
         for ( final VariantStratifier vs : stratManager.getStratifiers() ) {
-            states.add(vs.getRelevantStates(ref, tracker, comp, compName, eval, evalName, sampleName));
+            states.add(vs.getRelevantStates(ref, tracker, comp, compName, eval, evalName, sampleName, familyName));
         }
         return stratManager.values(states);
     }
@@ -609,7 +665,34 @@ public class VariantEval extends RodWalker implements TreeRedu
         for ( final EvaluationContext nec : stratManager.values() )
             for ( final VariantEvaluator ve : nec.getVariantEvaluators() )
                 ve.finalizeEvaluation();
-        
+
+        //send data to MetricsCollection
+        CompOverlap compOverlap = null;
+        IndelSummary indelSummary = null;
+        CountVariants countVariants = null;
+        MultiallelicSummary multiallelicSummary = null;
+        TiTvVariantEvaluator tiTvVariantEvaluator = null;
+        MetricsCollection metricsCollection = null;
+        for(final EvaluationContext nec: stratManager.values()) {
+            for(final VariantEvaluator ve : nec.getVariantEvaluators()) {
+                if (ve instanceof CompOverlap)
+                    compOverlap = (CompOverlap) ve;
+                else if (ve instanceof IndelSummary)
+                    indelSummary = (IndelSummary) ve;
+                else if (ve instanceof CountVariants)
+                    countVariants = (CountVariants) ve;
+                else if (ve instanceof MultiallelicSummary)
+                    multiallelicSummary = (MultiallelicSummary) ve;
+                else if (ve instanceof TiTvVariantEvaluator)
+                    tiTvVariantEvaluator = (TiTvVariantEvaluator) ve;
+                else if (ve instanceof MetricsCollection)
+                    metricsCollection = (MetricsCollection) ve;
+            }
+
+        if(metricsCollection != null)
+            metricsCollection.setData(compOverlap.concordantRate, indelSummary.n_SNPs, countVariants.nSNPs, indelSummary.n_indels, multiallelicSummary.nIndels, indelSummary.insertion_to_deletion_ratio, countVariants.insertionDeletionRatio, tiTvVariantEvaluator.tiTvRatio);
+        }
+
         VariantEvalReportWriter.writeReport(out, stratManager, stratManager.getStratifiers(), stratManager.get(0).getVariantEvaluators());
     }
 
@@ -622,6 +705,7 @@ public class VariantEval extends RodWalker implements TreeRedu
     public double getMendelianViolationQualThreshold() { return MENDELIAN_VIOLATION_QUAL_THRESHOLD; }
 
     public static String getAllSampleName() { return ALL_SAMPLE_NAME; }
+    public static String getAllFamilyName() { return ALL_FAMILY_NAME; }
 
     public List> getKnowns() { return knowns; }
 
@@ -630,6 +714,8 @@ public class VariantEval extends RodWalker implements TreeRedu
     public boolean isSubsettingToSpecificSamples() { return isSubsettingSamples; }
     public Set getSampleNamesForEvaluation() { return sampleNamesForEvaluation; }
 
+    public Set getFamilyNamesForEvaluation() { return familyNamesForEvaluation; }
+
     public int getNumberOfSamplesForEvaluation() {
         if (sampleNamesForEvaluation!= null &&  !sampleNamesForEvaluation.isEmpty())
             return sampleNamesForEvaluation.size();
@@ -640,6 +726,8 @@ public class VariantEval extends RodWalker implements TreeRedu
     }
     public Set getSampleNamesForStratification() { return sampleNamesForStratification; }
 
+    public Set getFamilyNamesForStratification() { return familyNamesForStratification; }
+
     public List> getComps() { return comps; }
 
     public Set getJexlExpressions() { return jexlExpressions; }
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalReportWriter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalReportWriter.java
index 281d8d346..aef7d8b35 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalReportWriter.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalReportWriter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CompOverlap.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CompOverlap.java
index 1732b6d8d..1e634b718 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CompOverlap.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CompOverlap.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CountVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CountVariants.java
index 3ef087e51..2ab63c51b 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CountVariants.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CountVariants.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelLengthHistogram.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelLengthHistogram.java
index b0d1bbeee..21164ce36 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelLengthHistogram.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelLengthHistogram.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelSummary.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelSummary.java
index 6d2982c1c..878d6fcbe 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelSummary.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelSummary.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MendelianViolationEvaluator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
index 7adcc05c8..29d81ce96 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -172,7 +172,7 @@ public class MendelianViolationEvaluator extends VariantEvaluator {
             HomVarHet_inheritedRef += mv.getParentsVarHetInheritedRef();
             HomVarHet_inheritedVar += mv.getParentsVarHetInheritedVar();
 
-            if(mv.getFamilyCalledCount()>0){
+            if(mv.getFamilyCalledCount()>0 || mv.getFamilyLowQualsCount()>0 || mv.getFamilyCalledCount()>0){
                 nVariants++;
                 nFamCalled += mv.getFamilyCalledCount();
                 nLowQual += mv.getFamilyLowQualsCount();
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MetricsCollection.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MetricsCollection.java
new file mode 100644
index 000000000..ea7394461
--- /dev/null
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MetricsCollection.java
@@ -0,0 +1,67 @@
+/*
+* Copyright 2012-2015 Broad Institute, Inc.
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators;
+
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis;
+import org.broadinstitute.gatk.tools.walkers.varianteval.util.DataPoint;
+
+/**
+ * Created by knoblett on 9/15/15.
+ */
+
+@Analysis(description = "Metrics Collection")
+public class MetricsCollection extends VariantEvaluator {
+
+    @DataPoint(description = "The concordance rate from CompOverlap", format = "%.2f")
+    public double concordantRate;
+    @DataPoint(description = "Number of SNPs from IndelSummary", format = "%d")
+    public int nSNPs;
+    @DataPoint(description = "Number of SNP loci from CountVariants", format = "%d")
+    public long nSNPloci;
+    @DataPoint(description = "Number of indels from IndelSummary", format = "%d")
+    public int nIndels;
+    @DataPoint(description = "Number of indel loci from MultiallelicSummary", format = "%d")
+    public int nIndelLoci;
+    @DataPoint(description = "Insertion  to deletion ratio from IndelSummary")
+    public String indelRatio;
+    @DataPoint(description = "Insertion to deletion ratio from CountVariants", format = "%.2f")
+    public double indelRatioLociBased;
+    @DataPoint(description = "The transition to transversion ratio from TiTvVariantEvaluator", format = "%.2f")
+    public double tiTvRatio;
+
+    public int getComparisonOrder() {return 2;}
+
+    public void setData(double concordantRate, int nSNPs, long nSNPloci, int nIndels, int nIndelLoci, String indelRatio, double indelRatioLociBased, double tiTvRatio){
+        this.concordantRate = concordantRate;
+        this.nSNPs = nSNPs;
+        this.nSNPloci = nSNPloci;
+        this.nIndels = nIndels;
+        this.nIndelLoci = nIndelLoci;
+        this.indelRatio = indelRatio;
+        this.indelRatioLociBased = indelRatioLociBased;
+        this.tiTvRatio = tiTvRatio;
+    }
+}
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MultiallelicSummary.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MultiallelicSummary.java
index e52923db6..a45dfbcdc 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MultiallelicSummary.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MultiallelicSummary.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/PrintMissingComp.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/PrintMissingComp.java
index 8beda5c56..f9c67e872 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/PrintMissingComp.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/PrintMissingComp.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -25,6 +25,7 @@
 
 package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators;
 
+import org.apache.commons.lang.ObjectUtils;
 import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
 import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
 import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
@@ -32,9 +33,9 @@ import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis;
 import org.broadinstitute.gatk.tools.walkers.varianteval.util.DataPoint;
 import htsjdk.variant.variantcontext.VariantContext;
 
-@Analysis(name = "PrintMissingComp", description = "the overlap between eval and comp sites")
+@Analysis(name = "PrintMissingComp", description = "count the number of comp SNP sites that are not in eval")
 public class PrintMissingComp extends VariantEvaluator {
-    @DataPoint(description = "number of eval sites outside of comp sites", format = "%d")
+    @DataPoint(description = "number of comp SNP sites outside of eval sites", format = "%d")
     public long nMissing = 0;
 
     public String getName() {
@@ -49,9 +50,8 @@ public class PrintMissingComp extends VariantEvaluator {
         final boolean compIsGood = comp != null && comp.isNotFiltered() && comp.isSNP();
         final boolean evalIsGood = eval != null && eval.isSNP();
 
-        if ( compIsGood & ! evalIsGood ) {
+        if ( compIsGood && !evalIsGood ) {
             nMissing++;
-            super.getWalker().getLogger().info("MissingFrom" + eval.toString() + " is missing from " + comp.getSource());
         }
     }
 }
\ No newline at end of file
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/StandardEval.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/StandardEval.java
index c3b75c1e6..9ee366c06 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/StandardEval.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/StandardEval.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ThetaVariantEvaluator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ThetaVariantEvaluator.java
index c972d9a91..ef91df2ee 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ThetaVariantEvaluator.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ThetaVariantEvaluator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/TiTvVariantEvaluator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/TiTvVariantEvaluator.java
index c5fa247ec..b60ed8445 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/TiTvVariantEvaluator.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/TiTvVariantEvaluator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ValidationReport.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ValidationReport.java
index 337056fb0..74b280f0c 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ValidationReport.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ValidationReport.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantEvaluator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantEvaluator.java
index a1c5b21f3..f1144a097 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantEvaluator.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantEvaluator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantSummary.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantSummary.java
index 3309b815c..a34ddeb4c 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantSummary.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantSummary.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleCount.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleCount.java
index 54cc06cfb..2ab005ae2 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleCount.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleCount.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -67,7 +67,7 @@ public class AlleleCount extends VariantStratifier {
         getVariantEvalWalker().getLogger().info("AlleleCount using " + nchrom + " chromosomes");
     }
 
-    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String familyName) {
         if (eval != null) {
             int AC = 0; // by default, the site is considered monomorphic
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleFrequency.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleFrequency.java
index b0108aa58..d52ea8f41 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleFrequency.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleFrequency.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -47,7 +47,7 @@ public class AlleleFrequency extends VariantStratifier {
         }
     }
 
-    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         if (eval != null) {
             try {
                 return Collections.singletonList((Object)String.format("%.3f", (5.0 * MathUtils.round(eval.getAttributeAsDouble("AF", 0.0) / 5.0, 3))));
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CompRod.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CompRod.java
index 72bfa4b8c..72006196b 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CompRod.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CompRod.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -45,7 +45,7 @@ public class CompRod extends VariantStratifier implements RequiredStratification
         }
     }
 
-    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         return Collections.singletonList((Object)compName);
     }
 }
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Contig.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Contig.java
index cb64651ef..0645fd53f 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Contig.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Contig.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -44,7 +44,7 @@ public class Contig extends VariantStratifier {
     }
 
     @Override
-    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         if (eval != null) {
             return Arrays.asList((Object)"all", eval.getChr());
         } else {
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CpG.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CpG.java
index 72ea18718..f4c31a5d1 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CpG.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CpG.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -53,7 +53,7 @@ public class CpG extends VariantStratifier {
     }
 
     @Override
-    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         boolean isCpG = false;
         if (ref != null && ref.getBases() != null) {
             String fwRefBases = new String(ref.getBases());
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Degeneracy.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Degeneracy.java
index 2cf50e38f..1e8368f91 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Degeneracy.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Degeneracy.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -103,7 +103,7 @@ public class Degeneracy extends VariantStratifier {
         }
     }
 
-    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         ArrayList relevantStates = new ArrayList();
 
         relevantStates.add("all");
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/DynamicStratification.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/DynamicStratification.java
index 1c428982c..429396835 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/DynamicStratification.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/DynamicStratification.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/EvalRod.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/EvalRod.java
index 1f01fc611..dddb20197 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/EvalRod.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/EvalRod.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -46,7 +46,7 @@ public class EvalRod extends VariantStratifier implements RequiredStratification
         }
     }
 
-    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         return Arrays.asList((Object)evalName);
     }
 }
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Family.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Family.java
new file mode 100644
index 000000000..e4acb9ea1
--- /dev/null
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Family.java
@@ -0,0 +1,55 @@
+/*
+* Copyright 2012-2015 Broad Institute, Inc.
+*
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+*
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+*
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.gatk.tools.walkers.varianteval.stratifications;
+
+import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
+import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
+import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantEvaluator;
+import org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantSummary;
+import htsjdk.variant.variantcontext.VariantContext;
+
+import java.util.*;
+
+/**
+ * Stratifies the eval RODs by each family in the eval ROD, as described by the pedigree.
+ *
+ * This allows the system to analyze each family separately.  This is particularly useful for the MendelianViolationEvaluator module.
+ */
+public class Family extends VariantStratifier {
+    @Override
+    public void initialize() {
+        states.addAll(getVariantEvalWalker().getFamilyNamesForStratification());
+    }
+
+    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String familyName) {
+        return Collections.singletonList((Object) familyName);
+    }
+
+    @Override
+    public Set> getIncompatibleEvaluators() {
+        return new HashSet>(Arrays.asList(VariantSummary.class));
+    }
+}
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Filter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Filter.java
index 1ee8d0294..ac9b9e497 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Filter.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Filter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -43,7 +43,7 @@ public class Filter extends VariantStratifier {
         states.add("raw");
     }
 
-    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         ArrayList relevantStates = new ArrayList();
 
         relevantStates.add("raw");
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/FunctionalClass.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/FunctionalClass.java
index abb517a01..89ffe8691 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/FunctionalClass.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/FunctionalClass.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -53,7 +53,7 @@ public class FunctionalClass extends VariantStratifier {
     }
 
 
-    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         ArrayList relevantStates = new ArrayList();
 
         relevantStates.add("all");
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IndelSize.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IndelSize.java
index 6efc332a8..48efe1ee4 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IndelSize.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IndelSize.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -48,7 +48,7 @@ public class IndelSize extends VariantStratifier {
         }
     }
 
-    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         if (eval != null && eval.isIndel() && eval.isBiallelic()) {
             try {
                 int eventLength = 0;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IntervalStratification.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IntervalStratification.java
index 5b6a3e078..57ba0e7bb 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IntervalStratification.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IntervalStratification.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -75,7 +75,7 @@ public class IntervalStratification extends VariantStratifier {
         states.addAll(Arrays.asList("all", "overlaps.intervals", "outside.intervals"));
     }
 
-    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         if (eval != null) {
             final GenomeLoc loc = getVariantEvalWalker().getToolkit().getGenomeLocParser().createGenomeLoc(eval);
             IntervalTree intervalTree = intervalTreeByContig.get(loc.getContig());
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/JexlExpression.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/JexlExpression.java
index 746e4967d..7a1106241 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/JexlExpression.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/JexlExpression.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -54,7 +54,7 @@ public class JexlExpression extends VariantStratifier implements StandardStratif
         }
     }
 
-    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         ArrayList relevantStates = new ArrayList();
         relevantStates.add("none");
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Novelty.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Novelty.java
index 349535dc8..1faf818f1 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Novelty.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Novelty.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -48,7 +48,7 @@ public class Novelty extends VariantStratifier implements StandardStratification
         knowns = getVariantEvalWalker().getKnowns();
     }
 
-    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         if (tracker != null && eval != null) {
             final Collection knownComps = tracker.getValues(knowns, ref.getLocus());
             for ( final VariantContext c : knownComps ) {
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/OneBPIndel.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/OneBPIndel.java
index 9884952fa..9430d9faa 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/OneBPIndel.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/OneBPIndel.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -47,7 +47,7 @@ public class OneBPIndel extends VariantStratifier {
     }
 
     @Override
-    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         if (eval != null && eval.isIndel()) {
             for ( int l : eval.getIndelLengths() )
                 if ( Math.abs(l) > 1 )
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/RequiredStratification.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/RequiredStratification.java
index 946c723fc..9a9313cca 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/RequiredStratification.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/RequiredStratification.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Sample.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Sample.java
index 90a6ece92..c052dcaa5 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Sample.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Sample.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -46,7 +46,7 @@ public class Sample extends VariantStratifier {
         states.addAll(getVariantEvalWalker().getSampleNamesForStratification());
     }
 
-    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         return Collections.singletonList((Object) sampleName);
     }
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/SnpEffPositionModifier.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/SnpEffPositionModifier.java
index 549738ad7..a09feae98 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/SnpEffPositionModifier.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/SnpEffPositionModifier.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -64,7 +64,8 @@ public class SnpEffPositionModifier extends VariantStratifier {
 			final String compName,
 			final VariantContext eval,
 			final String evalName,
-			final String sampleName)
+			final String sampleName,
+            final String FamilyName)
 	{
 		final List relevantStates = new ArrayList();
 		if (eval != null && eval.isVariant() && eval.hasAttribute(InfoFieldKey.EFFECT_KEY.getKeyName())) {
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/StandardStratification.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/StandardStratification.java
index 41c52c2f0..de9388a5f 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/StandardStratification.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/StandardStratification.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/TandemRepeat.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/TandemRepeat.java
index 493f4fe36..7349ccbfa 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/TandemRepeat.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/TandemRepeat.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -48,7 +48,7 @@ public class TandemRepeat extends VariantStratifier {
     }
 
     @Override
-    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         if ( eval == null || ! eval.isIndel() )
             return ALL;
         else if ( GATKVariantContextUtils.isTandemRepeat(eval, ref.getForwardBases()) ) {
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantStratifier.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantStratifier.java
index a7a0543ce..5b4e6c089 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantStratifier.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantStratifier.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -54,7 +54,7 @@ public abstract class VariantStratifier implements Comparable
 
     public abstract void initialize();
 
-    public abstract List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName);
+    public abstract List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String familyName);
 
     // -------------------------------------------------------------------------------------
     //
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantType.java
index 46a9ab97b..bc017db56 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantType.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantType.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -42,7 +42,7 @@ public class VariantType extends VariantStratifier {
             states.add(t.toString());
     }
 
-    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
+    public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName, String FamilyName) {
         return eval == null ? Collections.emptyList() : Collections.singletonList((Object)eval.getType().toString());
     }
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratNode.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratNode.java
index 0db937052..4d3dcae43 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratNode.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratNode.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratNodeIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratNodeIterator.java
index a789b70e1..305f65c94 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratNodeIterator.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratNodeIterator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratificationManager.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratificationManager.java
index 729001677..c9398a15b 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratificationManager.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratificationManager.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/Stratifier.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/Stratifier.java
index b096db93d..f206a30ab 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/Stratifier.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/Stratifier.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/Analysis.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/Analysis.java
index 67dc18701..035fabaa4 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/Analysis.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/Analysis.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/AnalysisModuleScanner.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/AnalysisModuleScanner.java
index 411394bf4..d5f70a9a5 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/AnalysisModuleScanner.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/AnalysisModuleScanner.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/DataPoint.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/DataPoint.java
index 0805cb5e7..ac02b4d09 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/DataPoint.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/DataPoint.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/EvaluationContext.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/EvaluationContext.java
index e8b7fe2ec..f18c381aa 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/EvaluationContext.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/EvaluationContext.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/Molten.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/Molten.java
index 57c4fbc06..f7a156673 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/Molten.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/Molten.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/SortableJexlVCMatchExp.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/SortableJexlVCMatchExp.java
index a759eb258..3b1c1424a 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/SortableJexlVCMatchExp.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/SortableJexlVCMatchExp.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/VariantEvalUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/VariantEvalUtils.java
index 53b143b80..15198dd53 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/VariantEvalUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/VariantEvalUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -26,6 +26,7 @@
 package org.broadinstitute.gatk.tools.walkers.varianteval.util;
 
 import org.apache.log4j.Logger;
+import org.broadinstitute.gatk.engine.samples.Sample;
 import org.broadinstitute.gatk.utils.commandline.RodBinding;
 import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
 import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
@@ -176,6 +177,11 @@ public class VariantEvalUtils {
             }
         }
 
+        //add MetricsCollection if required modules are included
+
+        if(evals.contains(classMap.get("CompOverlap")) && evals.contains(classMap.get("IndelSummary")) && evals.contains(classMap.get("TiTvVariantEvaluator")) && evals.contains(classMap.get("CountVariants")) && evals.contains(classMap.get("MultiallelicSummary")) )
+            evals.add(classMap.get("MetricsCollection"));
+
         return evals;
     }
 
@@ -250,6 +256,7 @@ public class VariantEvalUtils {
                         boolean byFilter,
                         boolean subsetBySample,
                         boolean trackPerSample,
+                        boolean trackPerFamily,
                         boolean mergeTracks) {
         if (tracker == null)
             return null;
@@ -265,9 +272,10 @@ public class VariantEvalUtils {
                 // First, filter the VariantContext to represent only the samples for evaluation
                 VariantContext vcsub = vc;
 
-                if (subsetBySample && vc.hasGenotypes())
+                if ((subsetBySample) && vc.hasGenotypes())
                     vcsub = getSubsetOfVariantContext(vc, variantEvalWalker.getSampleNamesForEvaluation());
 
+                //always add a mapping for all samples together
                 if ((byFilter || !vcsub.isFiltered())) {
                     addMapping(mapping, VariantEval.getAllSampleName(), vcsub);
                 }
@@ -282,6 +290,26 @@ public class VariantEvalUtils {
                         }
                     }
                 }
+                else if (vc.hasGenotypes() && trackPerFamily) {
+                    for (final String familyName : variantEvalWalker.getFamilyNamesForEvaluation()) {
+                        Set familyMemberNames = new HashSet<>();
+                        //if the current stratification family name is "all", then add all the families to the VC for evaluation here
+                        if (familyName.equals(VariantEval.getAllFamilyName())) {
+                            familyMemberNames = variantEvalWalker.getSampleNamesForEvaluation();
+                        }
+                        else {
+                            Set familyMembers = variantEvalWalker.getToolkit().getSampleDB().getFamily(familyName);
+                            for (final Sample s : familyMembers) {
+                                familyMemberNames.add(s.getID());
+                            }
+                        }
+                        VariantContext samplevc = getSubsetOfVariantContext(vc, familyMemberNames);
+
+                        if (byFilter || !samplevc.isFiltered()) {
+                            addMapping(mapping, familyName, samplevc);
+                        }
+                    }
+                }
             }
 
             if (mergeTracks && bindings.containsKey(firstTrack)) {
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VQSRCalibrationCurve.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VQSRCalibrationCurve.java
index 355441d5b..330a723c4 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VQSRCalibrationCurve.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VQSRCalibrationCurve.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariants.java
index b538225ef..090124882 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariants.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariants.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -57,9 +57,9 @@ import java.util.*;
  * Combine variant records from different sources
  *
  * 
      CombineVariants reads in variants records from separate ROD (Reference-Ordered Data) sources and combines them into
- * a single VCF. Any (unique) name can be used to bind your ROD and any number of sources can be input. This tool aims
- * to fulfill two main possible use cases, reflected by the two combination options (MERGE and UNION), for merging
- * records at the variant level (the first 8 fields of the VCF) or at the genotype level (the rest).
      
+ * a single VCF. Any number of sources can be input. This tool aims to fulfill two main possible use cases, reflected
+ * by the two combination options (MERGE and UNION), for merging records at the variant level (the first 8 fields of
+ * the VCF) or at the genotype level (the rest).
      
  *
  * 
        
  * 
      • MERGE: combines multiple variant records present at the same site in the different input sources into a
@@ -71,6 +71,13 @@ import java.util.*;
  * It uses the priority list (if provided) to emit a single record instance at every position represented in the input RODs.
        • 
  * 
      
  *
+ * 
      By default, the input sets will be named variants, variants2, variants3, and so on. You can override this by
+ * providing an explicit name tag for each input, using the syntax " -V:format,name". Each input tagged in this
+ * way will be labeled as such in the output (i.e., set=name rather than set=variants2). For example, you could specify
+ * a set of control samples as " -V:vcf,control my_control_samples.vcf", and the resulting VCF records would contain
+ * the annotation "set=control" in the INFO field. It is strongly recommended to provide explicit names in this way
+ * when a rod priority list is provided.
      
+ *
  * 
      CombineVariants will emit a record for every site that was present in any of your input VCF files, and will annotate
  * (in the set attribute in the INFO field) whether the record had a PASS or FILTER status in each input ROD . In effect,
  * CombineVariants always produces a union of the input VCFs.  However, any part of the Venn of the merged VCFs
@@ -136,20 +143,8 @@ import java.util.*;
 @DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
 @Reference(window=@Window(start=-50,stop=50))
 public class CombineVariants extends RodWalker implements TreeReducible {
-    /**
-     * The VCF files to merge together
-     *
-     * variants can take any number of arguments on the command line.  Each -V argument
-     * will be included in the final merged output VCF.  If no explicit name is provided,
-     * the -V arguments will be named using the default algorithm: variants, variants2, variants3, etc.
-     * The user can override this by providing an explicit name -V:name,vcf for each -V argument,
-     * and each named argument will be labeled as such in the output (i.e., set=name rather than
-     * set=variants2).  The order of arguments does not matter unless except for the naming, so
-     * if you provide an rod priority list and no explicit names than variants, variants2, etc
-     * are technically order dependent.  It is strongly recommended to provide explicit names when
-     * a rod priority list is provided.
-     */
-    @Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true)
+
+    @Input(fullName="variant", shortName = "V", doc="VCF files to merge together", required=true)
     public List> variantCollections;
     final private List> variants = new ArrayList<>();
 
@@ -167,48 +162,75 @@ public class CombineVariants extends RodWalker implements Tree
     public GATKVariantContextUtils.MultipleAllelesMergeType multipleAllelesMergeType = GATKVariantContextUtils.MultipleAllelesMergeType.BY_TYPE;
 
     /**
-     * Used when taking the union of variants that contain genotypes.  A complete priority list MUST be provided.
+     * Refers to the merging priority behavior described in the tool documentation regarding the choice of which record
+     * gets emitted when taking the union of variants that contain genotypes. The list must be passed as a
+     * comma-separated string listing the names of the variant input files. The list must be complete and include all
+     * variant inputs that are being provided to the tool. Use name tags for best results.
      */
-    @Argument(fullName="rod_priority_list", shortName="priority", doc="A comma-separated string describing the priority ordering for the genotypes as far as which record gets emitted", required=false)
+    @Argument(fullName="rod_priority_list", shortName="priority", doc="Ordered list specifying priority for merging", required=false)
     public String PRIORITY_STRING = null;
 
-    @Argument(fullName="printComplexMerges", shortName="printComplexMerges", doc="Print out interesting sites requiring complex compatibility merging", required=false)
+    @Argument(fullName="printComplexMerges", shortName="printComplexMerges", doc="Emit interesting sites requiring complex compatibility merging to file", required=false)
     public boolean printComplexMerges = false;
 
-    @Argument(fullName="filteredAreUncalled", shortName="filteredAreUncalled", doc="If true, then filtered VCFs are treated as uncalled, so that filtered set annotations don't appear in the combined VCF", required=false)
+    /**
+     * If enabled, this flag causes filtered variants (i.e. variant records where the FILTER field is populated by
+     * something other than PASS or a dot) to be omitted from the output.
+     */
+    @Argument(fullName="filteredAreUncalled", shortName="filteredAreUncalled", doc="Treat filtered variants as uncalled", required=false)
     public boolean filteredAreUncalled = false;
 
     /**
-     * Used to generate a sites-only file.
+     * If this flag is enabled, the INFO, FORMAT and sample-level (genotype) fields will not be emitted to the output file.
      */
-    @Argument(fullName="minimalVCF", shortName="minimalVCF", doc="If true, then the output VCF will contain no INFO or genotype FORMAT fields", required=false)
+    @Argument(fullName="minimalVCF", shortName="minimalVCF", doc="Emit a sites-only file", required=false)
     public boolean minimalVCF = false;
 
-    @Argument(fullName="excludeNonVariants", shortName="env", doc="Don't include loci found to be non-variant after the combining procedure", required=false)
+    /**
+     * Exclude sites that do not contain any called ALT alleles in the merged callset. The evaluation is made after the
+     * merging procedure is complete.
+     */
+    @Argument(fullName="excludeNonVariants", shortName="env", doc="Exclude sites where no variation is present after merging", required=false)
     public boolean EXCLUDE_NON_VARIANTS = false;
 
     /**
-     * Set to 'null' if you don't want the set field emitted.
+     * Key used in the INFO key=value tag emitted describing which set(s) the combined record came from
+     * (e.g. set=control). This provides the option to override the default naming, so instead of set=control you could
+     * have it be origin=control, or any other word you want that is not already an INFO field attribute. Set this to
+     * 'null' if you don't want the set attribute emitted at all.
      */
-    @Argument(fullName="setKey", shortName="setKey", doc="Key used in the INFO key=value tag emitted describing which set the combined VCF record came from", required=false)
+    @Argument(fullName="setKey", shortName="setKey", doc="Key name for the set attribute", required=false)
     public String SET_KEY = "set";
 
     /**
-     * This option allows the user to perform a simple merge (concatenation) to combine the VCFs, drastically reducing the runtime.
+     * This option allows you to perform a simple merge (concatenation) to combine the VCFs, drastically reducing
+     * runtime. Note that in many cases where you think you want to use this option, you may want to check out the
+     * CatVariants tool instead, because CatVariants provides the same functionality, but does so even more efficiently.
      */
-    @Argument(fullName="assumeIdenticalSamples", shortName="assumeIdenticalSamples", doc="If true, assume input VCFs have identical sample sets and disjoint calls", required=false)
+    @Argument(fullName="assumeIdenticalSamples", shortName="assumeIdenticalSamples", doc="Assume input VCFs have identical sample sets and disjoint calls", required=false)
     public boolean ASSUME_IDENTICAL_SAMPLES = false;
 
-    @Argument(fullName="minimumN", shortName="minN", doc="Combine variants and output site only if the variant is present in at least N input files.", required=false)
+    /**
+     * Sites that are present in fewer than this number of inputs will be ignored. This is a convenient way to build
+     * a collection of common variants and exclude rare variants.
+     */
+    @Argument(fullName="minimumN", shortName="minN", doc="Minimum number of input files the site must be observed in to be included", required=false)
     public int minimumN = 1;
 
     /**
-     * This option allows the suppression of the command line in the VCF header. This is most often usefully when combining variants for dozens or hundreds of smaller VCFs.
+     * By default, this tool writes the command line that was used in the header of the output VCF file. This flag
+     * enables you to override that behavior . This is most often useful when combining variants for dozens or
+     * hundreds of smaller VCFs iteratively, to avoid cluttering the header with a lot of command lines.
      */
-    @Argument(fullName="suppressCommandLineHeader", shortName="suppressCommandLineHeader", doc="If true, do not output the header containing the command line used", required=false)
+    @Argument(fullName="suppressCommandLineHeader", shortName="suppressCommandLineHeader", doc="Do not output the command line to the header", required=false)
     public boolean SUPPRESS_COMMAND_LINE_HEADER = false;
 
-    @Argument(fullName="mergeInfoWithMaxAC", shortName="mergeInfoWithMaxAC", doc="If true, when VCF records overlap the info field is taken from the one with the max AC instead of only taking the fields which are identical across the overlapping records.", required=false)
+    /**
+     * By default, the INFO field of the merged variant record only contains the INFO field attributes for which all
+     * original overlapping records had the same values. Discordant attributes are therefore discarded. This flag allows you to
+     * override that behavior and simply copy over the INFO field contents of whichever record had the highest AC value.
+     */
+    @Argument(fullName="mergeInfoWithMaxAC", shortName="mergeInfoWithMaxAC", doc="Use the INFO content of the record with the highest AC", required=false)
     public boolean MERGE_INFO_WITH_MAX_AC = false;
 
     private List priority = null;
@@ -224,7 +246,7 @@ public class CombineVariants extends RodWalker implements Tree
             sitesOnlyVCF = ((VariantContextWriterStub)vcfWriter).getWriterOptions().contains(Options.DO_NOT_WRITE_GENOTYPES);
             if ( sitesOnlyVCF ) logger.info("Pre-stripping genotypes for performance");
         } else
-            logger.warn("VCF output file not an instance of VCFWriterStub; cannot enable sites only output option");
+            logger.warn("VCF output file not an instance of VCFWriterStub; cannot enable sites-only output option");
 
         validateAnnotateUnionArguments();
 
@@ -233,7 +255,7 @@ public class CombineVariants extends RodWalker implements Tree
         if (genotypeMergeOption == null && !ASSUME_IDENTICAL_SAMPLES) {
             if (!sampleNamesAreUnique)
                 throw new UserException("Duplicate sample names were discovered but no genotypemergeoption was supplied. " +
-                    "To combine samples without merging specify --genotypemergeoption UNIQUIFY. Merging duplicate samples " +
+                    "To combine samples without merging, specify --genotypemergeoption UNIQUIFY. Merging duplicate samples " +
                     "without specified priority is unsupported, but can be achieved by specifying --genotypemergeoption UNSORTED.");
             else
                 genotypeMergeOption = GATKVariantContextUtils.GenotypeMergeType.UNSORTED;
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetrics.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetrics.java
index 7085b515b..5019662f4 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetrics.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetrics.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/FilterLiftedVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/FilterLiftedVariants.java
deleted file mode 100644
index d04e14ceb..000000000
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/FilterLiftedVariants.java
+++ /dev/null
@@ -1,159 +0,0 @@
-/*
-* Copyright (c) 2012 The Broad Institute
-* 
-* Permission is hereby granted, free of charge, to any person
-* obtaining a copy of this software and associated documentation
-* files (the "Software"), to deal in the Software without
-* restriction, including without limitation the rights to use,
-* copy, modify, merge, publish, distribute, sublicense, and/or sell
-* copies of the Software, and to permit persons to whom the
-* Software is furnished to do so, subject to the following
-* conditions:
-* 
-* The above copyright notice and this permission notice shall be
-* included in all copies or substantial portions of the Software.
-* 
-* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
-* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-*/
-
-package org.broadinstitute.gatk.tools.walkers.variantutils;
-
-import org.broadinstitute.gatk.engine.walkers.Reference;
-import org.broadinstitute.gatk.engine.walkers.RodWalker;
-import org.broadinstitute.gatk.engine.walkers.Window;
-import org.broadinstitute.gatk.utils.commandline.ArgumentCollection;
-import org.broadinstitute.gatk.utils.commandline.Output;
-import org.broadinstitute.gatk.engine.CommandLineGATK;
-import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection;
-import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
-import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
-import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
-import org.broadinstitute.gatk.engine.SampleUtils;
-import org.broadinstitute.gatk.utils.help.HelpConstants;
-import htsjdk.variant.vcf.VCFHeader;
-import htsjdk.variant.vcf.VCFHeaderLine;
-import org.broadinstitute.gatk.engine.GATKVCFUtils;
-import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
-import htsjdk.variant.variantcontext.writer.VariantContextWriter;
-import htsjdk.variant.variantcontext.VariantContext;
-
-import java.util.*;
-
-/**
- * Filters a lifted-over VCF file for reference bases that have been changed
- *
- * 
      "Lifting over" variants means adjusting variant calls from one reference to another. Specifically, the process
- * adjusts the position of the call to match the corresponding position on the target reference. For example, if you
- * have variants called from reads aligned to the hg19 reference, and you want to compare them to calls made based on
- * the b37 reference, you need to liftover one of the callsets to the other reference.
      
- *
- * 
      This tool is intended to be the second of two processing steps for the liftover process. The first step is to
- * run LiftoverVariants on your VCF file. The second step is to run FilterLiftedVariants on the output of
- * LiftoverVariants. This will produce valid well-behaved VCF files, where you'll see that the contig names in the
- * header have all been correctly replaced.
      
- *
- * 
      Input
      
- * 
      
- * A lifted-over variant call set to filter.
- * 
      
- *
- * 
      Output
      
- * 
      
- * The filtered call set.
- * 
      
- *
- * 
      Usage example
      
- * 
      - * java -jar GenomeAnalysisTK.jar \
- *   -T FilterLiftedVariants \
- *   -R reference.fasta \
- *   -V liftedover_input.vcf \
- *   -o filtered_output.vcf
- * 
      
- *
- */
-@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
-@Reference(window=@Window(start=0,stop=100))
-public class FilterLiftedVariants extends RodWalker {
-
-    @ArgumentCollection
-    protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
-
-    private static final int MAX_VARIANT_SIZE = 100;
-
-    @Output(doc="File to which variants should be written")
-    protected VariantContextWriter writer = null;
-
-    private long failedLocs = 0, totalLocs = 0;
-
-    public void initialize() {
-        String trackName = variantCollection.variants.getName();
-        Set samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName));
-        Map vcfHeaders = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));
-
-        final VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey(trackName) ? vcfHeaders.get(trackName).getMetaDataInSortedOrder() : Collections.emptySet(), samples);
-        writer.writeHeader(vcfHeader);
-    }
-
-    /**
-     * Determines whether records should be filtered; if not, writes them to the output
-     *
-     * @param ref   the reference context
-     * @param vc    the VariantContext to process
-     * @return true if the record is not filtered, false otherwise
-     */
-    protected boolean filterOrWrite(final byte[] ref, final VariantContext vc) {
-	if ( ref == null ) throw new IllegalArgumentException("Cannot filter based on a null reference array");
-	if ( vc == null ) throw new IllegalArgumentException("Cannot filter a null Variant Context");
-
-        totalLocs++;
-
-        boolean filter = false;
-        final byte[] recordRef = vc.getReference().getBases();
-
-        // this can happen for records that get placed at the ends of chromosomes
-        if ( recordRef.length > ref.length ) {
-            filter = true;
-        } else {
-            for (int i = 0; i < recordRef.length && i < MAX_VARIANT_SIZE; i++) {
-                if ( recordRef[i] != ref[i] ) {
-                    filter = true;
-                    break;
-                }
-            }
-        }
-
-        if ( filter )
-            failedLocs++;
-        else
-            writer.add(vc);
-
-        return !filter;
-    }
-
-    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        if ( tracker == null )
-            return 0;
-
-        final Collection VCs = tracker.getValues(variantCollection.variants, context.getLocation());
-        for ( final VariantContext vc : VCs )
-            filterOrWrite(ref.getBases(), vc);
-
-        return 0;
-    }
-
-    public Integer reduceInit() { return 0; }
-
-    public Integer reduce(Integer value, Integer sum) { return 0; }
-
-    public void onTraversalDone(Integer result) {
-        System.out.println("Filtered " + failedLocs + " records out of " + totalLocs + " total records.");
-    }
-}
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordance.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordance.java
index 5597a4c67..4ac6b9b0d 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordance.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordance.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java
index 099293cc2..0ba7e1013 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -60,11 +60,12 @@ import java.util.*;
  * Left-align indels in a variant callset
  *
  * 
      
- * LeftAlignAndTrimVariants is a tool that takes a VCF file and left-aligns the indels inside it.  The same indel can often be
- * placed at multiple positions and still represent the same haplotype.  While the standard convention with VCF is to
- * place an indel at the left-most position this doesn't always happen, so this tool can be used to left-align them.
- * Note that this tool cannot handle anything other than bi-allelic, simple indels.  Complex events are written out unchanged.
- * Optionally, the tool will also trim common bases from indels, leaving them with a minimum representation.
      
+ * LeftAlignAndTrimVariants is a tool that takes a VCF file, left-aligns the indels and trims common bases from indels,
+ * leaving them with a minimum representation. The same indel can often be placed at multiple positions and still
+ * represent the same haplotype. While the standard convention with VCF is to place an indel at the left-most position
+ * this isn't always done, so this tool can be used to left-align them. This tool optionally splits multiallelic
+ * sites into biallelics and left-aligns individual alleles. Optionally, the tool will not trim common bases from indels.
+ * 
      
  *
  * 
      Input
      
  * 
      
@@ -76,7 +77,9 @@ import java.util.*;
  * A left-aligned VCF.
  * 
      
  *
- * 
      Usage example
      
+ * 
      Usage examples
      
+ *
+ * 
      Left align and trim alleles
      
  * 
        * java -jar GenomeAnalysisTK.jar \
  *   -T LeftAlignAndTrimVariants \
@@ -85,19 +88,63 @@ import java.util.*;
  *   -o output.vcf
  * 
      
  *
+ * 
      Left align and don't trim alleles
      
+ * 
      + * java -jar GenomeAnalysisTK.jar \
+ *   -T LeftAlignAndTrimVariants \
+ *   -R reference.fasta \
+ *   --variant input.vcf \
+ *   -o output.vcf \
+ *   --dontTrimAlleles
+ * 
      
+ *
+ * 
      Left align and trim alleles, process alleles <= 208 bases
      
+ * 
      + * java -jar GenomeAnalysisTK.jar \
+ *   -T LeftAlignAndTrimVariants \
+ *   -R reference.fasta \
+ *   --variant input.vcf \
+ *   -o output.vcf \
+ *   --reference_window_stop 208
+ * 
      
+ *
+ * 
      Split multiallics into biallelics, left align and trim alleles
      
+ * 
      + * java -jar GenomeAnalysisTK.jar \
+ *   -T LeftAlignAndTrimVariants \
+ *   -R reference.fasta \
+ *   --variant input.vcf \
+ *   -o output.vcf \
+ *   --splitMultiallelics
+ * 
      
+ *
+ * 
      Split multiallelics into biallics, left align but don't trim alleles
      
+ * 
      + * java -jar GenomeAnalysisTK.jar \
+ *   -T LeftAlignAndTrimVariants \
+ *   -R reference.fasta \
+ *   --variant input.vcf \
+ *   -o output.vcf \
+ *   --splitMultiallelics \
+ *   --dontTrimAlleles
+ * 
      
+ *
  */
 @DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
 @Reference(window=@Window(start=-200,stop=200))    // WARNING: if this changes,MAX_INDEL_LENGTH needs to change as well!
 public class LeftAlignAndTrimVariants extends RodWalker {
 
+    // Log message for a reference allele that is too long
+    protected static final String REFERENCE_ALLELE_TOO_LONG_MSG = "Reference allele is too long";
+
     @ArgumentCollection
     protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
 
     /**
-     * If this argument is set, bases common to all alleles will be removed, leaving only their minimal representation.
+     * If this argument is set, bases common to all alleles will not be removed and will not leave their minimal representation.
      */
-    @Argument(fullName="trimAlleles", shortName="trim", doc="Trim alleles to remove bases common to all of them", required=false)
-    protected boolean trimAlleles = false;
+    @Argument(fullName="dontTrimAlleles", shortName="notrim", doc="Do not Trim alleles to remove bases common to all of them", required=false)
+    protected boolean dontTrimAlleles = false;
 
     /**
      * If this argument is set, split multiallelic records and left-align individual alleles.
@@ -113,6 +160,10 @@ public class LeftAlignAndTrimVariants extends RodWalker {
     private VariantContextWriter writer;
 
     private static final int MAX_INDEL_LENGTH = 200; // needs to match reference window size!
+
+    // Stop of the expanded window for which the reference context should be provided, relative to the locus.
+    private int referenceWindowStop;
+
     public void initialize() {
         String trackName = variantCollection.variants.getName();
         Set samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName));
@@ -121,7 +172,9 @@ public class LeftAlignAndTrimVariants extends RodWalker {
         Set headerLines = vcfHeaders.get(trackName).getMetaDataInSortedOrder();
         baseWriter.writeHeader(new VCFHeader(headerLines, samples));
 
-        writer = VariantContextWriterFactory.sortOnTheFly(baseWriter, 200);
+        writer = VariantContextWriterFactory.sortOnTheFly(baseWriter, MAX_INDEL_LENGTH);
+
+        referenceWindowStop = getToolkit().getArguments().reference_window_stop;
     }
 
     public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
@@ -132,32 +185,16 @@ public class LeftAlignAndTrimVariants extends RodWalker {
 
         int changedSites = 0;
         for ( final VariantContext vc : VCs ) {
-            // split first into biallelics, and optionally trim alleles to minimal representation
-            Pair result = new Pair(vc,0); // default value
+            // split first into biallelics, and optionally don't trim alleles to minimal representation
             if (splitMultiallelics) {
                 final List vcList = GATKVariantContextUtils.splitVariantContextToBiallelics(vc);
                 for (final VariantContext biallelicVC: vcList) {
-                    final VariantContext v = (trimAlleles ? GATKVariantContextUtils.trimAlleles(biallelicVC,true,true) : biallelicVC);
-                    result = alignAndWrite(v, ref);
-
-                    // strip out PLs and AD if we've subsetted the alleles
-                    if ( vcList.size() > 1 )
-                        result.first = new VariantContextBuilder(result.first).genotypes(GATKVariantContextUtils.stripPLsAndAD(result.first.getGenotypes())).make();
-
-                    writer.add(result.first);
-                    changedSites += result.second;
+                    changedSites += trimAlignWrite(biallelicVC, ref, vcList.size());
                 }
             }
             else {
-                if (trimAlleles)
-                    result = alignAndWrite(GATKVariantContextUtils.trimAlleles(vc,true,true), ref);
-                else
-                    result = alignAndWrite(vc,ref);
-                writer.add(result.first);
-                changedSites += result.second;
-
+                changedSites += trimAlignWrite(vc, ref, 1);
             }
-
         }
 
         return changedSites;
@@ -175,11 +212,48 @@ public class LeftAlignAndTrimVariants extends RodWalker {
     }
 
     /**
-     * Main routine workhorse. By definitio, it will only take biallelic vc's. Splitting into multiple alleles has to be
+     * Trim, align and write out the vc.
+     *
+     * @param vc                Input VC with variants to left align
+     * @param ref               Reference context
+     * @param numBiallelics     Number of biallelics from the original VC
+     * @return                  Number of records left-aligned (0 or 1)
+     */
+    @Requires("vc != null")
+    protected int trimAlignWrite(final VariantContext vc, final ReferenceContext ref, final int numBiallelics ){
+
+        final int refLength =  vc.getReference().length();
+
+        // ignore if the reference length is greater than the reference window stop before and after expansion
+        if ( refLength > MAX_INDEL_LENGTH && refLength > referenceWindowStop ) {
+            logger.info(String.format("%s (%d) at position %s:%d; skipping that record. Set --referenceWindowStop >= %d",
+                        REFERENCE_ALLELE_TOO_LONG_MSG, refLength, vc.getChr(), vc.getStart(), refLength));
+            return 0;
+        }
+
+        // optionally don't trim VC
+        final VariantContext v = dontTrimAlleles ? vc : GATKVariantContextUtils.trimAlleles(vc, true, true);
+
+        // align the VC
+        final Pair result = alignAndWrite(v, ref);
+
+        // strip out PLs and AD if we've subsetted the alleles
+        if ( numBiallelics > 1 )
+            result.first = new VariantContextBuilder(result.first).genotypes(GATKVariantContextUtils.stripPLsAndAD(result.first.getGenotypes())).make();
+
+        // write out new VC
+        writer.add(result.first);
+
+        // number of records left aligned
+        return result.second;
+    }
+
+    /**
+     * Main routine workhorse. By definition, it will only take biallelic vc's. Splitting into multiple alleles has to be
      * handled by calling routine.
      * @param vc                  Input VC with variants to left align
      * @param ref                 Reference context
-     * @return                    # of records left-aligned (0 or 1) and new VC.
+     * @return                    Number of records left-aligned (0 or 1) and new VC.
      */
     @Requires({"vc != null","ref != null", "vc.isBiallelic() == true","ref.getBases().length>=2*MAX_INDEL_LENGTH+1"})
     @Ensures({"result != null","result.first != null", "result.second >=0"})
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LiftoverVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LiftoverVariants.java
deleted file mode 100644
index 15981d19a..000000000
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LiftoverVariants.java
+++ /dev/null
@@ -1,209 +0,0 @@
-/*
-* Copyright (c) 2012 The Broad Institute
-* 
-* Permission is hereby granted, free of charge, to any person
-* obtaining a copy of this software and associated documentation
-* files (the "Software"), to deal in the Software without
-* restriction, including without limitation the rights to use,
-* copy, modify, merge, publish, distribute, sublicense, and/or sell
-* copies of the Software, and to permit persons to whom the
-* Software is furnished to do so, subject to the following
-* conditions:
-* 
-* The above copyright notice and this permission notice shall be
-* included in all copies or substantial portions of the Software.
-* 
-* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
-* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-*/
-
-package org.broadinstitute.gatk.tools.walkers.variantutils;
-
-import htsjdk.samtools.liftover.LiftOver;
-import htsjdk.samtools.util.Interval;
-import htsjdk.samtools.SAMFileHeader;
-import htsjdk.samtools.SAMFileReader;
-import htsjdk.variant.vcf.VCFHeader;
-import htsjdk.variant.vcf.VCFHeaderLine;
-import org.broadinstitute.gatk.utils.commandline.Argument;
-import org.broadinstitute.gatk.utils.commandline.ArgumentCollection;
-import org.broadinstitute.gatk.utils.commandline.Output;
-import org.broadinstitute.gatk.engine.CommandLineGATK;
-import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection;
-import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
-import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
-import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
-import org.broadinstitute.gatk.engine.walkers.RodWalker;
-import org.broadinstitute.gatk.engine.SampleUtils;
-import org.broadinstitute.gatk.utils.help.HelpConstants;
-import org.broadinstitute.gatk.engine.GATKVCFUtils;
-import org.broadinstitute.gatk.utils.variant.GATKVCFConstants;
-import org.broadinstitute.gatk.utils.variant.GATKVCFHeaderLines;
-import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
-import htsjdk.variant.variantcontext.writer.Options;
-import org.broadinstitute.gatk.utils.exceptions.UserException;
-import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
-import htsjdk.variant.variantcontext.VariantContext;
-import htsjdk.variant.variantcontext.VariantContextBuilder;
-import htsjdk.variant.variantcontext.writer.VariantContextWriter;
-import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory;
-
-import java.io.File;
-import java.util.*;
-
-/**
- * Lifts a VCF file over from one build to another
- *
- * 
      "Lifting over" variants means adjusting variant calls from one reference to another. Specifically, the process
- * adjusts the position of the call to match the corresponding position on the target reference. For example, if you
- * have variants called from reads aligned to the hg19 reference, and you want to compare them to calls made based on
- * the b37 reference, you need to liftover one of the callsets to the other reference.
      
- *
- * 
      LiftoverVariants is intended to be the first of two processing steps for the liftover process.
- * The second step is to run FilterLiftedVariants on the output of LiftoverVariants. This will produce valid
- * well-behaved VCF files, where you'll see that the contig names in the header have all been correctly replaced.
      
- *
- * 
      Caveat
      
- * 
      To be clear, the VCF resulting from the LiftoverVariants run is not guaranteed to be valid according to the official specification.  The file could
- * possibly be mis-sorted and the header may not be complete. That is why you need to run FilterLiftedVariants on it.
      
- *
- * 
      Input
      
- * 
      
- * A variant call set to lift over, the sequence  dictionary of the new reference build and the appropriate liftover
- * chain file.
- * 
      
- *
- * 
      Output
      
- * 
      
- * The lifted-over call set.
- * 
      
- *
- * 
      Usage example
      
- * 
      - * java -jar GenomeAnalysisTK.jar \
- *   -T LiftoverVariants \
- *   -R reference_hg19.fasta \
- *   -V input_hg19.vcf \
- *   -chain liftover_hg19_to_b37.txt \
- *   -dict reference_b37.dict \
- *   -o liftedover_output_b37.vcf
- * 
      
- *
- */
-@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
-public class LiftoverVariants extends RodWalker {
-
-    @ArgumentCollection
-    protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
-
-    @Output(doc="File to which variants should be written", required=true, defaultToStdout=false)
-    protected File file = null;
-    protected VariantContextWriter writer = null;
-
-    @Argument(fullName="chain", shortName="chain", doc="Chain file", required=true)
-    protected File CHAIN = null;
-
-    @Argument(fullName="newSequenceDictionary", shortName="dict", doc="Sequence .dict file for the new build", required=true)
-    protected File NEW_SEQ_DICT = null;
-
-    @Argument(fullName="recordOriginalLocation", shortName="recordOriginalLocation", doc="Should we record what the original location was in the INFO field?", required=false)
-    protected Boolean RECORD_ORIGINAL_LOCATION = false;
-
-    private LiftOver liftOver;
-
-    private long successfulIntervals = 0, failedIntervals = 0;
-
-    public void initialize() {
-        try {
-            liftOver = new LiftOver(CHAIN);
-        } catch (RuntimeException e) {
-            throw new UserException.BadInput("there is a problem with the chain file you are using: " + e.getMessage());
-        }
-
-        liftOver.setLiftOverMinMatch(LiftOver.DEFAULT_LIFTOVER_MINMATCH);
-
-        try {
-            final SAMFileHeader toHeader = new SAMFileReader(NEW_SEQ_DICT).getFileHeader();
-            liftOver.validateToSequences(toHeader.getSequenceDictionary());
-        } catch (RuntimeException e) {
-            throw new UserException.BadInput("the chain file you are using is not compatible with the reference you are trying to lift over to; please use the appropriate chain file for the given reference");    
-        }
-
-        String trackName = variantCollection.variants.getName();
-        Set samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName));
-        Map vcfHeaders = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));
-
-        Set metaData = new HashSet<>();
-        if ( vcfHeaders.containsKey(trackName) )
-            metaData.addAll(vcfHeaders.get(trackName).getMetaDataInSortedOrder());
-        if ( RECORD_ORIGINAL_LOCATION ) {
-            metaData.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.ORIGINAL_CONTIG_KEY));
-            metaData.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.ORIGINAL_START_KEY));
-        }
-
-
-        final VCFHeader vcfHeader = new VCFHeader(metaData, samples);
-        writer = VariantContextWriterFactory.create(file, getMasterSequenceDictionary(), EnumSet.of(Options.ALLOW_MISSING_FIELDS_IN_HEADER));
-        writer.writeHeader(vcfHeader);
-    }
-
-    private void convertAndWrite(VariantContext vc, ReferenceContext ref) {
-
-        final Interval fromInterval = new Interval(vc.getChr(), vc.getStart(), vc.getStart(), false, String.format("%s:%d", vc.getChr(), vc.getStart()));
-        final int length = vc.getEnd() - vc.getStart();
-        final Interval toInterval = liftOver.liftOver(fromInterval);
-        VariantContext originalVC = vc;
-
-        if ( toInterval != null ) {
-            // check whether the strand flips, and if so reverse complement everything
-            if ( fromInterval.isPositiveStrand() != toInterval.isPositiveStrand() && vc.isPointEvent() ) {
-                vc = GATKVariantContextUtils.reverseComplement(vc);
-            }
-
-            vc = new VariantContextBuilder(vc).loc(toInterval.getSequence(), toInterval.getStart(), toInterval.getStart() + length).make();
-
-            if ( RECORD_ORIGINAL_LOCATION ) {
-                vc = new VariantContextBuilder(vc)
-                        .attribute(GATKVCFConstants.ORIGINAL_CONTIG_KEY, fromInterval.getSequence())
-                        .attribute(GATKVCFConstants.ORIGINAL_START_KEY, fromInterval.getStart()).make();
-            }
-
-            if ( originalVC.isSNP() && originalVC.isBiallelic() && GATKVariantContextUtils.getSNPSubstitutionType(originalVC) != GATKVariantContextUtils.getSNPSubstitutionType(vc) ) {
-                logger.warn(String.format("VCF at %s / %d => %s / %d is switching substitution type %s/%s to %s/%s",
-                        originalVC.getChr(), originalVC.getStart(), vc.getChr(), vc.getStart(),
-                        originalVC.getReference(), originalVC.getAlternateAllele(0), vc.getReference(), vc.getAlternateAllele(0)));
-            }
-
-            writer.add(vc);
-            successfulIntervals++;
-        } else {
-            failedIntervals++;
-        }
-    }
-
-    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        if ( tracker == null )
-            return 0;
-
-        Collection VCs = tracker.getValues(variantCollection.variants, context.getLocation());
-        for ( VariantContext vc : VCs )
-            convertAndWrite(vc, ref);
-
-        return 0;
-    }
-
-    public Integer reduceInit() { return 0; }
-
-    public Integer reduce(Integer value, Integer sum) { return 0; }
-
-    public void onTraversalDone(Integer result) {
-        System.out.println("Converted " + successfulIntervals + " records; failed to convert " + failedIntervals + " records.");
-        writer.close();
-    }
-}
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RandomlySplitVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RandomlySplitVariants.java
index 7b08bef53..41962bbcc 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RandomlySplitVariants.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RandomlySplitVariants.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectHeaders.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectHeaders.java
index a55c2215e..e95cbf379 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectHeaders.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectHeaders.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java
index d44fbc84f..abd53f9f0 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -248,8 +248,8 @@ import java.util.*;
  *   -V input.vcf \
  *   -o output.vcf \
  *   -selectType INDEL
- *   -minIndelSize 2
- *   -maxIndelSize 5
+ *   --minIndelSize 2
+ *   --maxIndelSize 5
  * 
  *
  * 
      Exclude indels from a VCF:
      
@@ -259,7 +259,7 @@ import java.util.*;
  *   -T SelectVariants \
  *   --variant input.vcf \
  *   -o output.vcf \
- *   -selectTypeToExclude INDEL
+ *   --selectTypeToExclude INDEL
  * 
  *
  * 
      Select only multi-allelic SNPs and MNPs from a VCF (i.e. SNPs with more than one allele listed in the ALT column):
      
@@ -302,7 +302,7 @@ import java.util.*;
  *   -R ref.fasta \
  *   -T SelectVariants \
  *   --variant input.vcf \
- *   --setFilteredGenotypesToNocall
+ *   --setFilteredGtToNocall
  * 
  *
  */
@@ -574,6 +574,15 @@ public class SelectVariants extends RodWalker implements TreeR
     @Argument(fullName="ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES", required=false, doc="Allow samples other than those in the VCF to be specified on the command line. These samples will be ignored.")
     private boolean allowNonOverlappingCommandLineSamples = false;
 
+    /**
+     * If this argument is provided, the output will be compliant with the version in the header, however it will also
+     * cause the tool to run slower than without the argument. Without the argument the header will be compliant with
+     * the up-to-date version, but the output in the body may not be compliant. If an up-to-date input file is used,
+     * then the output will also be up-to-date regardless of this argument.
+     */
+    @Argument(fullName="forceValidOutput", required=false, doc="Forces output VCF to be compliant to up-to-date version")
+    private boolean forceValidOutput = false;
+
     public enum NumberAlleleRestriction {
         ALL,
         BIALLELIC,
@@ -1008,7 +1017,7 @@ public class SelectVariants extends RodWalker implements TreeR
      */
     private VariantContext subsetRecord(final VariantContext vc, final boolean preserveAlleles, final boolean removeUnusedAlternates) {
         //subContextFromSamples() always decodes the vc, which is a fairly expensive operation.  Avoid if possible
-        if ( noSamplesSpecified && !removeUnusedAlternates )
+        if ( noSamplesSpecified && !removeUnusedAlternates && !forceValidOutput )
             return vc;
 
         // strip out the alternate alleles that aren't being used
@@ -1021,7 +1030,7 @@ public class SelectVariants extends RodWalker implements TreeR
         final VariantContextBuilder builder = new VariantContextBuilder(sub);
 
         // if there are fewer alternate alleles now in the selected VC, we need to fix the PL and AD values
-        GenotypesContext newGC = GATKVariantContextUtils.updatePLsAndAD(sub, vc);
+        GenotypesContext newGC = GATKVariantContextUtils.updatePLsSACsAD(sub, vc);
 
         // since the VC has been subset (either by sample or allele), we need to strip out the MLE tags
         builder.rmAttribute(GATKVCFConstants.MLE_ALLELE_COUNT_KEY);
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java
index 82a201091..a5b710acc 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -91,6 +91,16 @@ import java.util.*;
  *   --dbsnp dbsnp.vcf
  * 
  *
+ * 
      To perform VCF format tests and all strict validations with the VCFs containing alleles <= 208 bases
      
+ * 
      + * java -jar GenomeAnalysisTK.jar \
+ *   -T ValidateVariants \
+ *   -R reference.fasta \
+ *   -V input.vcf \
+ *   --dbsnp dbsnp.vcf
+ *   --reference_window_stop 208
+ * 
      
+ *
  * 
      To perform only VCF format tests
      
  * 
        * java -jar GenomeAnalysisTK.jar \
@@ -114,6 +124,9 @@ import java.util.*;
 @Reference(window=@Window(start=0,stop=100))
 public class ValidateVariants extends RodWalker {
 
+    // Log message for a reference allele that is too long
+    protected static final String REFERENCE_ALLELE_TOO_LONG_MSG = "Reference allele is too long";
+
     @ArgumentCollection
     protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
 
@@ -181,6 +194,9 @@ public class ValidateVariants extends RodWalker {
 
     private File file = null;
 
+    // Stop of the expanded window for which the reference context should be provided, relative to the locus.
+    private int referenceWindowStop;
+
     /**
      * Contains final set of validation to apply.
      */
@@ -189,6 +205,7 @@ public class ValidateVariants extends RodWalker {
     public void initialize() {
         file = new File(variantCollection.variants.getSource());
         validationTypes = calculateValidationTypesToApply(excludeTypes);
+        referenceWindowStop = getToolkit().getArguments().reference_window_stop;
     }
 
     public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
@@ -220,8 +237,11 @@ public class ValidateVariants extends RodWalker {
         // get the true reference allele
         final Allele reportedRefAllele = vc.getReference();
         final int refLength = reportedRefAllele.length();
-        if ( refLength > 100 ) {
-            logger.info(String.format("Reference allele is too long (%d) at position %s:%d; skipping that record.", refLength, vc.getChr(), vc.getStart()));
+
+        // reference length is greater than the reference window stop before and after expansion
+        if ( refLength > 100 && refLength > referenceWindowStop ) {
+            logger.info(String.format("%s (%d) at position %s:%d; skipping that record. Set --referenceWindowStop >= %d",
+                    REFERENCE_ALLELE_TOO_LONG_MSG, refLength, vc.getChr(), vc.getStart(), refLength));
             return;
         }
 
@@ -259,7 +279,7 @@ public class ValidateVariants extends RodWalker {
      * @return never {@code null} but perhaps an empty set.
      */
     private Collection calculateValidationTypesToApply(final List excludeTypes) {
-        if (excludeTypes.size() == 0)
+        if (excludeTypes.isEmpty())
             return Collections.singleton(ValidationType.ALL);
         final Set excludeTypeSet = new LinkedHashSet<>(excludeTypes);
         if (excludeTypes.size() != excludeTypeSet.size())
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantValidationAssessor.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantValidationAssessor.java
deleted file mode 100644
index 307b78289..000000000
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantValidationAssessor.java
+++ /dev/null
@@ -1,304 +0,0 @@
-/*
-* Copyright (c) 2012 The Broad Institute
-* 
-* Permission is hereby granted, free of charge, to any person
-* obtaining a copy of this software and associated documentation
-* files (the "Software"), to deal in the Software without
-* restriction, including without limitation the rights to use,
-* copy, modify, merge, publish, distribute, sublicense, and/or sell
-* copies of the Software, and to permit persons to whom the
-* Software is furnished to do so, subject to the following
-* conditions:
-* 
-* The above copyright notice and this permission notice shall be
-* included in all copies or substantial portions of the Software.
-* 
-* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
-* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-*/
-
-package org.broadinstitute.gatk.tools.walkers.variantutils;
-
-import org.broadinstitute.gatk.engine.walkers.Reference;
-import org.broadinstitute.gatk.engine.walkers.RodWalker;
-import org.broadinstitute.gatk.engine.walkers.Window;
-import org.broadinstitute.gatk.utils.commandline.*;
-import org.broadinstitute.gatk.engine.CommandLineGATK;
-import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection;
-import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
-import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
-import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
-import org.broadinstitute.gatk.utils.QualityUtils;
-import org.broadinstitute.gatk.engine.SampleUtils;
-import org.broadinstitute.gatk.utils.help.HelpConstants;
-import org.broadinstitute.gatk.engine.GATKVCFUtils;
-import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
-import htsjdk.variant.vcf.*;
-import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
-import htsjdk.variant.variantcontext.writer.VariantContextWriter;
-import htsjdk.variant.variantcontext.Allele;
-import htsjdk.variant.variantcontext.VariantContext;
-import htsjdk.variant.variantcontext.VariantContextBuilder;
-
-import java.util.*;
-
-/**
- * Annotate a validation VCF with QC metrics
- *
- * 
      
- * This tool is intended for vetting/assessing validation data (containing genotypes).
- * The tool produces a VCF that is annotated with information pertaining to plate quality control and by
- * default is soft-filtered by high no-call rate or low Hardy-Weinberg probability.
- * If you have .ped files, please first convert them to VCF format.
      
- *
- * 
      Input
      
- * 
      
- * A validation VCF to annotate.
- * 
      
- *
- * 
      Output
      
- * 
      
- * An annotated VCF.  Additionally, a table like the following will be output:
- * 
      
- * 
      - *     Total number of samples assayed:                  185
- *     Total number of records processed:                152
- *     Number of Hardy-Weinberg violations:              34 (22%)
- *     Number of no-call violations:                     12 (7%)
- *     Number of homozygous variant violations:          0 (0%)
- *     Number of records passing all filters:            106 (69%)
- *     Number of passing records that are polymorphic:   98 (92%)
- * 
      
- *
- * 
      Usage example
      
- * 
      - * java -jar GenomeAnalysisTK.jar \
- *   -T VariantValidationAssessor \
- *   -R reference.fasta \
- *   -V input.vcf \
- *   -o output.vcf
- * 
      
- *
- */
-@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VALIDATION, extraDocs = {CommandLineGATK.class} )
-@Reference(window=@Window(start=0,stop=40))
-public class VariantValidationAssessor extends RodWalker {
-
-    @ArgumentCollection
-    protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
-
-    @Output(doc="File to which variants should be written")
-    protected VariantContextWriter vcfwriter = null;
-
-    @Argument(fullName="maxHardy", doc="Maximum phred-scaled Hardy-Weinberg violation pvalue to consider an assay valid", required=false)
-    protected double maxHardy = 20.0;
-
-    /**
-     * To disable, set to a value greater than 1.
-     */
-    @Argument(fullName="maxNoCall", doc="Maximum no-call rate (as a fraction) to consider an assay valid", required=false)
-    protected double maxNoCall = 0.05;
-
-    /**
-     * To disable, set to a value greater than 1.
-     */
-    @Argument(fullName="maxHomVar", doc="Maximum homozygous variant rate (as a fraction) to consider an assay valid", required=false)
-    protected double maxHomNonref = 1.1;
-
-    //@Argument(fullName="populationFile", shortName="populations", doc="A tab-delimited file relating individuals to populations,"+
-    //          "used for smart Hardy-Weinberg annotation",required = false)
-    //private File popFile = null;
-
-    // sample names
-    private TreeSet sampleNames = null;
-
-    // variant context records
-    private ArrayList records = new ArrayList();
-
-    // statistics
-    private int numRecords = 0;
-    private int numHWViolations = 0;
-    private int numNoCallViolations = 0;
-    private int numHomVarViolations = 0;
-    private int numTrueVariants = 0;
-
-    //private HashMap samplesToPopulation;
-
-    public void initialize() {
-        //if ( popFile != null ) {
-        //    samplesToPopulation = parsePopulationFile(popFile);
-        //}
-    }
-
-    public Integer reduceInit() {
-        return 0;
-    }
-
-    public VariantContext map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        if ( tracker == null )
-            return null;
-
-        VariantContext vc = tracker.getFirstValue(variantCollection.variants, ref.getLocus());
-        // ignore places where we don't have a variant
-        if ( vc == null )
-            return null;
-
-        if ( sampleNames == null )
-            sampleNames = new TreeSet(vc.getSampleNames());        
-
-        return addVariantInformationToCall(vc);
-    }
-
-    public Integer reduce(VariantContext call, Integer numVariants) {
-        if ( call != null ) {
-            numVariants++;
-            records.add(call);
-        }
-        return numVariants;                        
-    }
-
-    public void onTraversalDone(Integer finalReduce) {
-        final List inputNames = Arrays.asList(variantCollection.variants.getName());
-
-        // setup the header fields
-        Set hInfo = new HashSet();
-        hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), inputNames));
-
-        // set up the info and filter headers
-        hInfo.add(new VCFInfoHeaderLine("NoCallPct", 1, VCFHeaderLineType.Float, "Percent of no-calls"));
-        hInfo.add(new VCFInfoHeaderLine("HomRefPct", 1, VCFHeaderLineType.Float, "Percent of homozygous reference genotypes"));
-        hInfo.add(new VCFInfoHeaderLine("HetPct", 1, VCFHeaderLineType.Float, "Percent of heterozygous genotypes"));
-        hInfo.add(new VCFInfoHeaderLine("HomVarPct", 1, VCFHeaderLineType.Float, "Percent homozygous variant genotypes"));
-        hInfo.add(new VCFInfoHeaderLine("HW", 1, VCFHeaderLineType.Float, "Phred-scaled Hardy-Weinberg violation p-value"));
-        hInfo.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_COUNT_KEY));
-        hInfo.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_NUMBER_KEY));
-        hInfo.add(new VCFFilterHeaderLine("HardyWeinbergViolation", "The validation is in Hardy-Weinberg violation"));
-        hInfo.add(new VCFFilterHeaderLine("HighNoCallRate", "The validation no-call rate is too high"));
-        hInfo.add(new VCFFilterHeaderLine("TooManyHomVars", "The validation homozygous variant rate is too high"));
-
-        // print out (and add to headers) the validation metrics
-        System.out.println(String.format("Total number of samples assayed:\t\t\t%d", sampleNames.size()));
-        hInfo.add(new VCFHeaderLine("ValidationMetrics_SamplesAssayed", String.format("%d", sampleNames.size())));
-        System.out.println(String.format("Total number of records processed:\t\t\t%d", numRecords));
-        hInfo.add(new VCFHeaderLine("ValidationMetrics_RecordsProcessed", String.format("%d", numRecords)));
-        if ( numRecords > 0 ) {
-            System.out.println(String.format("Number of Hardy-Weinberg violations:\t\t\t%d (%d%%)", numHWViolations, 100*numHWViolations/numRecords));
-            hInfo.add(new VCFHeaderLine("ValidationMetrics_HardyWeinbergViolations", String.format("\"%d (%d%%)\"", numHWViolations, 100*numHWViolations/numRecords)));
-            System.out.println(String.format("Number of no-call violations:\t\t\t\t%d (%d%%)", numNoCallViolations, 100*numNoCallViolations/numRecords));
-            hInfo.add(new VCFHeaderLine("ValidationMetrics_NoCallViolations", String.format("\"%d (%d%%)\"", numNoCallViolations, 100*numNoCallViolations/numRecords)));
-            System.out.println(String.format("Number of homozygous variant violations:\t\t%d (%d%%)", numHomVarViolations, 100*numHomVarViolations/numRecords));
-            hInfo.add(new VCFHeaderLine("ValidationMetrics_HomVarViolations", String.format("\"%d (%d%%)\"", numHomVarViolations, 100*numHomVarViolations/numRecords)));
-            int goodRecords = numRecords - numHWViolations - numNoCallViolations - numHomVarViolations;
-            System.out.println(String.format("Number of records passing all filters:\t\t\t%d (%d%%)", goodRecords, 100*goodRecords/numRecords));
-            hInfo.add(new VCFHeaderLine("ValidationMetrics_RecordsPassingFilters", String.format("\"%d (%d%%)\"", goodRecords, 100*goodRecords/numRecords)));
-            if ( goodRecords > 0 ) {
-                System.out.println(String.format("Number of passing records that are polymorphic:\t\t%d (%d%%)", numTrueVariants, 100*numTrueVariants/goodRecords));
-                hInfo.add(new VCFHeaderLine("ValidationMetrics_PolymorphicPassingRecords", String.format("\"%d (%d%%)\"", numTrueVariants, 100*numTrueVariants/goodRecords)));
-            }
-        }
-        
-        vcfwriter.writeHeader(new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames)));
-
-        for ( VariantContext record : records )
-            vcfwriter.add(record);
-    }
-
-
-    private VariantContext addVariantInformationToCall(VariantContext vContext) {
-
-        // check possible filters
-        double hwPvalue = hardyWeinbergCalculation(vContext);
-        double hwScore = Math.abs(QualityUtils.phredScaleErrorRate(hwPvalue));
-        double noCallProp = (double)vContext.getNoCallCount() / (double)vContext.getNSamples();
-        double homRefProp = (double)vContext.getHomRefCount() / (double)vContext.getNSamples();
-        double hetProp = (double)vContext.getHetCount() / (double)vContext.getNSamples();
-        double homVarProp = (double)vContext.getHomVarCount() / (double)vContext.getNSamples();
-
-        boolean isViolation = false;
-        Set filters = new HashSet();
-        if ( noCallProp > maxNoCall ) {
-            filters.add("HighNoCallRate");
-            numNoCallViolations++;
-            isViolation = true;
-        } else if ( hwScore > maxHardy ) {
-            filters.add("HardyWeinbergViolation");
-            numHWViolations++;
-            isViolation = true;
-        } else if ( homVarProp > maxHomNonref) {
-            filters.add("TooManyHomVars");
-            numHomVarViolations++;
-            isViolation = true;
-        }
-
-        VariantContextBuilder builder = new VariantContextBuilder(vContext).filters(filters);
-        numRecords++;
-
-        // add the info fields
-        builder.attribute("NoCallPct", String.format("%.1f", 100.0 * noCallProp));
-        builder.attribute("HomRefPct", String.format("%.1f", 100.0 * homRefProp));
-        builder.attribute("HomVarPct", String.format("%.1f", 100.0 * homVarProp));
-        builder.attribute("HetPct", String.format("%.1f", 100.0 * hetProp));
-        builder.attribute("HW", String.format("%.2f", hwScore));
-        Collection altAlleles = vContext.getAlternateAlleles();
-        int altAlleleCount = altAlleles.size() == 0 ? 0 : vContext.getCalledChrCount(altAlleles.iterator().next());
-        if ( !isViolation && altAlleleCount > 0 )
-            numTrueVariants++;
-        builder.attribute(VCFConstants.ALLELE_COUNT_KEY, String.format("%d", altAlleleCount));
-        builder.attribute(VCFConstants.ALLELE_NUMBER_KEY, String.format("%d", vContext.getCalledChrCount()));
-
-        return builder.make();
-    }
-
-    private double hardyWeinbergCalculation(VariantContext vc) {
-        //if ( popFile != null ) {
-        //    throw new GATKException("We still need to implement this!");
-        //} else {
-        return GATKVariantContextUtils.computeHardyWeinbergPvalue(vc);
-        //}
-    }
-
-    // TODO -- REWRITE THIS TO WORK WITH VARIANT CONTEXT
-    /******
-
-    private String smartHardy(ReferenceContext ref, VCFRecord rec) {
-        HashMap> genotypesByPopulation = new HashMap>(10);
-        HashMap hardyWeinbergByPopulation = new HashMap(10);
-
-        for ( String population : samplesToPopulation.values() ) {
-            genotypesByPopulation.put(population,new ArrayList());
-        }
-
-        //for ( String name : sampleNames ) {
-        //    String pop = samplesToPopulation.get(name);
-        //    if ( rec.getGenotype(name) != null ) {
-        //        genotypesByPopulation.get(pop).add(rec.getGenotype(name));
-        //    }
-        //}
-
-        for ( String population : samplesToPopulation.values() ) {
-            VCFVariationCall v = new VCFVariationCall(ref.getBase(),ref.getLocus(),VCFVariationCall.VARIANT_TYPE.SNP);
-            v.setGenotypeCalls(genotypesByPopulation.get(population));
-            hardyWeinbergByPopulation.put(population,HWCalc.annotate(null,ref,null,v));
-        }
-
-        return smartHardyString(hardyWeinbergByPopulation);
-    }
-
-    private String smartHardyString(HashMap hwByPop) {
-        // for now just return the maximum:
-        int maxH = -100;
-        for ( String pop : samplesToPopulation.values() ) {
-            maxH = Integer.parseInt(hwByPop.get(pop)) > maxH ? Integer.parseInt(hwByPop.get(pop)) : maxH;
-        }
-
-        return String.format("%s",maxH);
-    }
-
-    *********/
-}
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitives.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitives.java
index 0873d5b94..a75491d67 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitives.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitives.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPed.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPed.java
index 8618d816d..10f463727 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPed.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPed.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -57,12 +57,35 @@ import java.util.*;
  *
  * 
      Inputs
      
  * 
      
- * A VCF file and a metadata file
+ * A VCF file and a metadata file.
+ * 
      
+ *
+* 
      The metaData file can take two formats, the first of which is the first 6 lines of the standard pedigree file. This
+ * is what Plink describes as a .fam file. Note that the sex encoding convention is 1=male; 2=female; other=unknown. An example .fam file is as follows (note that there is no header):
      
+ * 
      + * CEUTrio NA12878 NA12891 NA12892 2 -9
+ * CEUTrio NA12891 UNKN1 UNKN2 1 -9
+ * CEUTrio NA12892 UNKN3 UNKN4 2 -9
+ * 
      
+ * 
      where the entries are: FamilyID IndividualID DadID MomID Sex Phenotype.
      
+ * 
      An alternate format is a two-column key-value file:
      
+ * 
      + * NA12878        fid=CEUTrio;dad=NA12891;mom=NA12892;sex=2;phenotype=-9
+ * NA12891        fid=CEUTrio;sex=1;phenotype=-9
+ * NA12892        fid=CEUTrio;sex=2;phenotype=-9
+ * 
      
+ * 
      where unknown parents do not need to be specified. The columns are the individual ID and a list of key-value pairs.
      
+ *
+ * 
      
+ * Regardless of which file is specified, the tool will output a .fam file alongside the pedigree file. If the
+ * command line has "-m [name].fam", the fam file will be subset and reordered to match the sample content and ordering
+ * of the VCF. However, if a metadata file of the alternate format is passed by "-m [name].txt", the tool will
+ * construct a formatted .fam file from the data.
  * 
      
  *
  * 
      Outputs
      
  * 
      
- * A binary pedigree in PLINK format, composed of three files (.bed/.bim/.fam)
+ * A binary pedigree in PLINK format, composed of three files (.bed/.bim/.fam). See the PLINK format specification for more details.
  * 
      
  *
  * 
      Example
      
@@ -85,30 +108,7 @@ public class VariantsToBinaryPed extends RodWalker {
 
     @ArgumentCollection
     protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
-
-    /**
-     * 
      The metaData file can take two formats, the first of which is the first 6 lines of the standard pedigree file. This
-     * is what Plink describes as a .fam file. An example .fam file is as follows (note that there is no header):
      
-     * 
      -     * CEUTrio NA12878 NA12891 NA12892 2 -9
-     * CEUTrio NA12891 UNKN1 UNKN2 2 -9
-     * CEUTrio NA12892 UNKN3 UNKN4 1 -9
-     * 
      
-     * 
      where the entries are: FamilyID IndividualID DadID MomID Phenotype Sex.
      
-     * 
      An alternate format is a two-column key-value file:
      
-     * 
      -     * NA12878        fid=CEUTrio;dad=NA12891;mom=NA12892;sex=2;phenotype=-9
-     * NA12891        fid=CEUTrio;sex=2;phenotype=-9
-     * NA12892        fid=CEUTrio;sex=1;phenotype=-9
-     * 
      
-     * 
      where unknown parents do not need to be specified. The columns are the individual ID and a list of key-value pairs.
      
-     * 
      
-     * Regardless of which file is specified, the tool will output a .fam file alongside the pedigree file. If the
-     * command line has "-m [name].fam", the fam file will be subset and reordered to match the sample content and ordering
-     * of the VCF. However, if a metadata file of the alternate format is passed by "-m [name].txt", the tool will
-     * construct a formatted .fam file from the data.
-     * 
      
-     */
+    
     @Input(shortName="m",fullName = "metaData",required=true,doc="Sample metadata file")
     File metaDataFile;
 
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java
index bd228f323..a2651ef29 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCF.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCF.java
index f2386d088..051137009 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCF.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCF.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java
index 69ae7a472..9e6ad827f 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -57,6 +57,8 @@ public class CatVariantsIntegrationTest {
     private final File CatVariantsVcf2 = new File(CatVariantsDir, "CatVariantsTest2.vcf");
     private final File CatVariantsBcf1 = new File(CatVariantsDir, "CatVariantsTest1.bcf");
     private final File CatVariantsBcf2 = new File(CatVariantsDir, "CatVariantsTest2.bcf");
+    private final File CatVariantsVcf3 = new File(CatVariantsDir, "CatVariantsTest3.vcf");
+    private final File CatVariantsVcf4 = new File(CatVariantsDir, "CatVariantsTest4.vcf");
 
     private class CatVariantsTestProvider extends BaseTest.TestDataProvider {
         private final File file1;
@@ -89,25 +91,25 @@ public class CatVariantsIntegrationTest {
         final File catVariantsTempList1 = BaseTest.createTempListFile("CatVariantsTest1", CatVariantsVcf1.getAbsolutePath());
         final File catVariantsTempList2 = BaseTest.createTempListFile("CatVariantsTest2", CatVariantsVcf2.getAbsolutePath());
 
-        new CatVariantsTestProvider(CatVariantsVcf1, CatVariantsVcf2, BaseTest.createTempFile("CatVariantsTest", ".vcf"), "d0d81eb7fd3905256c4ac7c0fc480094");
-        new CatVariantsTestProvider(CatVariantsBcf1, CatVariantsBcf2, BaseTest.createTempFile("CatVariantsTest", ".bcf"), "6a57fcbbf3cae490896d13a288670d83");
+        new CatVariantsTestProvider(CatVariantsVcf1, CatVariantsVcf2, BaseTest.createTempFile("CatVariantsTest", ".vcf"), "c055705e0606f4fe89d339d416c182e1");
+        new CatVariantsTestProvider(CatVariantsBcf1, CatVariantsBcf2, BaseTest.createTempFile("CatVariantsTest", ".bcf"), "2a82e959b3b07b461d64bd5ed7298aa3");
 
         for (String extension1 : AbstractFeatureReader.BLOCK_COMPRESSED_EXTENSIONS) {
             for (String extension2 : AbstractFeatureReader.BLOCK_COMPRESSED_EXTENSIONS) {
                 final File file1 = new File(CatVariantsDir, "CatVariantsTest1.vcf" + extension1);
                 final File file2 = new File(CatVariantsDir, "CatVariantsTest2.vcf" + extension2);
-                new CatVariantsTestProvider(file1, file2, BaseTest.createTempFile("CatVariantsTest.", ".vcf"), "d0d81eb7fd3905256c4ac7c0fc480094");
-                new CatVariantsTestProvider(file1, file2, BaseTest.createTempFile("CatVariantsTest.", ".bcf"), "6a57fcbbf3cae490896d13a288670d83");
-                new CatVariantsTestProvider(file1, file2, BaseTest.createTempFile("CatVariantsTest.", ".vcf" + extension1), "33f728ac5c70ce2994f3619a27f47088");
+                new CatVariantsTestProvider(file1, file2, BaseTest.createTempFile("CatVariantsTest.", ".vcf"), "c055705e0606f4fe89d339d416c182e1");
+                new CatVariantsTestProvider(file1, file2, BaseTest.createTempFile("CatVariantsTest.", ".bcf"), "2a82e959b3b07b461d64bd5ed7298aa3");
+                new CatVariantsTestProvider(file1, file2, BaseTest.createTempFile("CatVariantsTest.", ".vcf" + extension1), "3beb2c58fb795fcdc485de9868eda576");
             }
-            new CatVariantsTestProvider(CatVariantsVcf1, CatVariantsVcf2, BaseTest.createTempFile("CatVariantsTest.", ".vcf" + extension1), "33f728ac5c70ce2994f3619a27f47088");
-            new CatVariantsTestProvider(CatVariantsBcf1, CatVariantsBcf2, BaseTest.createTempFile("CatVariantsTest.", ".vcf" + extension1), "f1a55575f59707f80b8c17e2591fbf53");
+            new CatVariantsTestProvider(CatVariantsVcf1, CatVariantsVcf2, BaseTest.createTempFile("CatVariantsTest.", ".vcf" + extension1), "3beb2c58fb795fcdc485de9868eda576");
+            new CatVariantsTestProvider(CatVariantsBcf1, CatVariantsBcf2, BaseTest.createTempFile("CatVariantsTest.", ".vcf" + extension1), "b9f31b6a00226c58181c19d421503693");
         }
 
         //Test list parsing functionality
-        new CatVariantsTestProvider(catVariantsTempList1, CatVariantsVcf2, BaseTest.createTempFile("CatVariantsTest.", ".vcf"), "d0d81eb7fd3905256c4ac7c0fc480094");
-        new CatVariantsTestProvider(CatVariantsVcf1, catVariantsTempList2, BaseTest.createTempFile("CatVariantsTest.", ".vcf"), "d0d81eb7fd3905256c4ac7c0fc480094");
-        new CatVariantsTestProvider(catVariantsTempList1, catVariantsTempList2, BaseTest.createTempFile("CatVariantsTest.", ".vcf"), "d0d81eb7fd3905256c4ac7c0fc480094");
+        new CatVariantsTestProvider(catVariantsTempList1, CatVariantsVcf2, BaseTest.createTempFile("CatVariantsTest.", ".vcf"), "c055705e0606f4fe89d339d416c182e1");
+        new CatVariantsTestProvider(CatVariantsVcf1, catVariantsTempList2, BaseTest.createTempFile("CatVariantsTest.", ".vcf"), "c055705e0606f4fe89d339d416c182e1");
+        new CatVariantsTestProvider(catVariantsTempList1, catVariantsTempList2, BaseTest.createTempFile("CatVariantsTest.", ".vcf"), "c055705e0606f4fe89d339d416c182e1");
 
         return CatVariantsTestProvider.getTests(CatVariantsTestProvider.class);
     }
@@ -126,6 +128,27 @@ public class CatVariantsIntegrationTest {
         }
     }
 
+    @DataProvider(name = "SortOrderTest")
+    public Object[][] makeSortOrderTestProvider() {
+        new CatVariantsTestProvider(CatVariantsVcf3, CatVariantsVcf4, BaseTest.createTempFile("CatVariantsSortOrderTest", ".vcf"), "fb0b4ebe98ca23862b45fcd672fbfc3e");
+
+        return CatVariantsTestProvider.getTests(CatVariantsTestProvider.class);
+    }
+
+    @Test(dataProvider = "SortOrderTest")
+    public void testSortOrder(final CatVariantsTestProvider cfg) throws IOException {
+
+        ProcessController pc = ProcessController.getThreadLocal();
+        ProcessSettings ps = new ProcessSettings(Utils.escapeExpressions(cfg.getCmdLine()));
+        pc.execAndCheck(ps);
+
+        MD5DB.MD5Match result = md5db.testFileMD5("testSortOrder", "CatVariantsTestProvider", cfg.outputFile, cfg.md5, false);
+        if(result.failed) {
+            final MD5Mismatch failure = new MD5Mismatch(result.actualMD5, result.expectedMD5, result.diffEngineOutput);
+            Assert.fail(failure.toString());
+        }
+    }
+
     @DataProvider(name = "MismatchedExtensionsTest")
     public Object[][] makeMismatchedExtensionsTestProvider() {
         return new Object[][]{
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java
index 68451ef49..f26f6a90a 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -43,13 +43,13 @@ public class BAQIntegrationTest extends WalkerTest {
     // --------------------------------------------------------------------------------------------------------------
     @Test
     public void testPrintReadsNoBAQ() {
-        WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq OFF",  1, Arrays.asList("d1f74074e718c82810512bf40dbc7f72"));
+        WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq OFF",  1, Arrays.asList("e33187ca383c7f5c75c5d547ec79e1cb"));
         executeTest(String.format("testPrintReadsNoBAQ"), spec);
     }
 
     @Test
     public void testPrintReadsRecalBAQ() {
-        WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq RECALCULATE",  1, Arrays.asList("96ec97cf92f1f660bd5244c6b44539b3"));
+        WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq RECALCULATE",  1, Arrays.asList("a25043edfbfa4f21a13cc21064b460df"));
         executeTest(String.format("testPrintReadsRecalBAQ"), spec);
     }
 }
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/CNV/SymbolicAllelesIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/CNV/SymbolicAllelesIntegrationTest.java
index 16e47cda5..4e11d0df3 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/CNV/SymbolicAllelesIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/CNV/SymbolicAllelesIntegrationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -48,7 +48,7 @@ public class SymbolicAllelesIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(b36KGReference, "symbolic_alleles_1.vcf"),
                 1,
-                Arrays.asList("5bafc5a99ea839e686e55de93f91fd5c"));
+                Arrays.asList("a1de53ac340f4ca02367c40680628251"));
         executeTest("Test symbolic alleles", spec);
     }
 
@@ -57,7 +57,7 @@ public class SymbolicAllelesIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(b36KGReference, "symbolic_alleles_2.vcf"),
                 1,
-                Arrays.asList("30f66a097987330d42e87da8bcd6be21"));
+                Arrays.asList("c8b294089832bb1a2c450b550318a471"));
         executeTest("Test symbolic alleles mixed in with non-symbolic alleles", spec);
     }
 }
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/CompressedDataListUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/CompressedDataListUnitTest.java
new file mode 100644
index 000000000..521f4c237
--- /dev/null
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/CompressedDataListUnitTest.java
@@ -0,0 +1,118 @@
+/*
+* Copyright 2012-2015 Broad Institute, Inc.
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.gatk.tools.walkers.annotator;
+
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+public class CompressedDataListUnitTest {
+
+    @Test
+    public void testAddSingly(){
+        CompressedDataList intList = new CompressedDataList<>();
+        intList.add(2);
+        intList.add(5);
+        intList.add(5);
+        intList.add(2);
+        intList.add(2);
+        intList.add(3);
+        intList.add(2);
+        intList.add(2);
+        intList.add(4);
+        intList.add(4);
+        intList.add(4);
+        intList.add(2);
+
+        Assert.assertEquals(intList.isEmpty(), false);
+        Assert.assertEquals(intList.toString(), "2,6,3,1,4,3,5,2");
+    }
+
+    @Test
+    public void testAddValueCounts(){
+        CompressedDataList intList = new CompressedDataList<>();
+        intList.add(5,2);
+        intList.add(2,6);
+        intList.add(3,1);
+        intList.add(4,3);
+
+        Assert.assertEquals(intList.isEmpty(), false);
+        Assert.assertEquals(intList.toString(), "2,6,3,1,4,3,5,2");
+    }
+
+    @Test
+    public void testAddBothWays(){
+        CompressedDataList intList = new CompressedDataList<>();
+        intList.add(2);
+        intList.add(5,2);
+        intList.add(2);
+        intList.add(2);
+        intList.add(3);
+        intList.add(2);
+        intList.add(2);
+        intList.add(4,2);
+        intList.add(2);
+        intList.add(4,1);
+
+        Assert.assertEquals(intList.toString(), "2,6,3,1,4,3,5,2");
+    }
+
+    @Test
+    public void testCombineLists(){
+        CompressedDataList intList1 = new CompressedDataList<>();
+        intList1.add(5,2);
+        intList1.add(2,6);
+        intList1.add(3,1);
+        intList1.add(4,3);
+
+        CompressedDataList intList2 = new CompressedDataList<>();
+        intList2.add(2,5);
+        intList2.add(6,2);
+        intList2.add(1,3);
+        intList2.add(3,4);
+
+        intList1.add(intList2);
+
+        Assert.assertEquals(intList1.toString(), "1,3,2,11,3,5,4,3,5,2,6,2");
+
+    }
+
+    @Test
+    public void testIterator(){
+        CompressedDataList intList1 = new CompressedDataList<>();
+        intList1.add(5,2);
+        intList1.add(2,6);
+        intList1.add(3,1);
+        intList1.add(4,3);
+
+        CompressedDataList intList2 = new CompressedDataList<>();
+        for(Integer i : intList1) {
+            intList2.add(i);
+        }
+
+        Assert.assertEquals(intList1.toString(),intList2.toString());
+    }
+
+}
\ No newline at end of file
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUtilUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUtilUnitTest.java
index ec10d7d02..15279a0ad 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUtilUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUtilUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLociIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLociIntegrationTest.java
index b59794740..3ac2a3d44 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLociIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLociIntegrationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLociWalkerIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLociWalkerIntegrationTest.java
index ccfd743ee..e24564a4b 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLociWalkerIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLociWalkerIntegrationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageB36IntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageB36IntegrationTest.java
index 447515d0e..1f5e398fe 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageB36IntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageB36IntegrationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java
index f000513d2..f25ac3a94 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjectsIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjectsIntegrationTest.java
index feefd5f60..92b3d862f 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjectsIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjectsIntegrationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationUnitTest.java
index ab972a119..4d3223f30 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationUnitTest.java
@@ -1,6 +1,6 @@
 /*
-* Copyright (c) 2012 The Broad Institute
-*
+* Copyright 2012-2015 Broad Institute, Inc.
+* 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
 * files (the "Software"), to deal in the Software without
@@ -9,10 +9,10 @@
 * copies of the Software, and to permit persons to whom the
 * Software is furnished to do so, subject to the following
 * conditions:
-*
+* 
 * The above copyright notice and this permission notice shall be
 * included in all copies or substantial portions of the Software.
-*
+* 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
 * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
 * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileupIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileupIntegrationTest.java
index eae4decad..2648ed81e 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileupIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileupIntegrationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadsUnitTest.java
index e79edfdde..889646017 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/DictionaryConsistencyIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/DictionaryConsistencyIntegrationTest.java
index 69e623e5e..f29cb80e8 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/DictionaryConsistencyIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/DictionaryConsistencyIntegrationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStatIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStatIntegrationTest.java
index 7a8868198..e86c3301f 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStatIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStatIntegrationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/PileupWalkerIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/PileupWalkerIntegrationTest.java
index 38154bd6d..a64efaf26 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/PileupWalkerIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/PileupWalkerIntegrationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReadsWalkersIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReadsWalkersIntegrationTest.java
index 29f4621f0..53acd511c 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReadsWalkersIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReadsWalkersIntegrationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -47,22 +47,22 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest {
     }
 
     final static String Q10ClipOutput = "b29c5bc1cb9006ed9306d826a11d444f";
-    @Test public void testQClip0() { testClipper("clipQSum0", "-QT 0", "117a4760b54308f81789c39b1c9de578", "12be03c817d94bab88457e5afe74256a"); }
-    @Test public void testQClip2() { testClipper("clipQSum2", "-QT 2", Q10ClipOutput, "1cfc9da4867765c1e5b5bd6326984634"); }
-    @Test public void testQClip10() { testClipper("clipQSum10", "-QT 10", "b29c5bc1cb9006ed9306d826a11d444f", "1cfc9da4867765c1e5b5bd6326984634"); }
-    @Test public void testQClip20() { testClipper("clipQSum20", "-QT 20", "6c3434dce66ae5c9eeea502f10fb9bee", "0bcfd177fe4be422898eda8e161ebd6c"); }
+    @Test public void testQClip0() { testClipper("clipQSum0", "-QT 0", "117a4760b54308f81789c39b1c9de578", "bcf0d1e13537f764f006ef6d9b401ea7"); }
+    @Test public void testQClip2() { testClipper("clipQSum2", "-QT 2", Q10ClipOutput, "27847d330b962e60650df23b6efc8c3c"); }
+    @Test public void testQClip10() { testClipper("clipQSum10", "-QT 10", "b29c5bc1cb9006ed9306d826a11d444f", "27847d330b962e60650df23b6efc8c3c"); }
+    @Test public void testQClip20() { testClipper("clipQSum20", "-QT 20", "6c3434dce66ae5c9eeea502f10fb9bee", "f89ec5439e88f5a75433150da0069034"); }
 
-    @Test public void testClipRange1() { testClipper("clipRange1", "-CT 1-5", "b5acd753226e25b1e088838c1aab9117", "aed836c97c6383dd80e39a093cc25e08"); }
-    @Test public void testClipRange2() { testClipper("clipRange2", "-CT 1-5,11-15", "be4fcad5b666a5540028b774169cbad7", "5f6e08bd44d6faf5b85cde5d4ec1a36f"); }
+    @Test public void testClipRange1() { testClipper("clipRange1", "-CT 1-5", "b5acd753226e25b1e088838c1aab9117", "987007f6e430cad4cb4a8d1cc1f45d91"); }
+    @Test public void testClipRange2() { testClipper("clipRange2", "-CT 1-5,11-15", "be4fcad5b666a5540028b774169cbad7", "ec4cf54ed50a6baf69dbf98782c19aeb"); }
 
-    @Test public void testClipSeq() { testClipper("clipSeqX", "-X CCCCC", "db199bd06561c9f2122f6ffb07941fbc", "f3cb42759428df80d06e9789f9f9f762"); }
-    @Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + privateTestDir + "seqsToClip.fasta", "d011a3152b31822475afbe0281491f8d", "44658c018378467f809b443d047d5778"); }
+    @Test public void testClipSeq() { testClipper("clipSeqX", "-X CCCCC", "db199bd06561c9f2122f6ffb07941fbc", "a9cf540e4ed2514061248a878e09a09c"); }
+    @Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + privateTestDir + "seqsToClip.fasta", "d011a3152b31822475afbe0281491f8d", "906871df304dd966682e5798d59fc86b"); }
 
-    @Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + privateTestDir + "seqsToClip.fasta -X CCCCC", "a23187bd9bfb06557f799706d98441de", "bae38f83eb9b63857f5e6e3c6e62f80c"); }
+    @Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + privateTestDir + "seqsToClip.fasta -X CCCCC", "a23187bd9bfb06557f799706d98441de", "b41995fea04034ca0427c4a71504ef83"); }
 
-    @Test public void testClipNs() { testClipper("testClipNs", "-QT 10 -CR WRITE_NS", Q10ClipOutput, "1cfc9da4867765c1e5b5bd6326984634"); }
-    @Test public void testClipQ0s() { testClipper("testClipQs", "-QT 10 -CR WRITE_Q0S", Q10ClipOutput, "3b32da2eaab7a2d4729fdb486cedbb2f"); }
-    @Test public void testClipSoft() { testClipper("testClipSoft", "-QT 10 -CR SOFTCLIP_BASES", Q10ClipOutput, "9d355b0f6d2076178e92bd7fcd8f5adb"); }
+    @Test public void testClipNs() { testClipper("testClipNs", "-QT 10 -CR WRITE_NS", Q10ClipOutput, "27847d330b962e60650df23b6efc8c3c"); }
+    @Test public void testClipQ0s() { testClipper("testClipQs", "-QT 10 -CR WRITE_Q0S", Q10ClipOutput, "195b8bdfc0186fdca742764aa9b06363"); }
+    @Test public void testClipSoft() { testClipper("testClipSoft", "-QT 10 -CR SOFTCLIP_BASES", Q10ClipOutput, "08d16051be0b3fa3453eb1e6ca48b098"); }
 
     @Test
     public void testUseOriginalQuals() {
@@ -74,7 +74,7 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest {
                         " -OQ -QT 4 -CR WRITE_Q0S" +
                         " -o %s -os %s",
                 2,
-                Arrays.asList("c83b4e2ade8654a2818fe9d405f07662", "55c01ccc2e84481b22d3632cdb06c8ba"));
+                Arrays.asList("a2819d54b2110150e38511f5a55db91d", "55c01ccc2e84481b22d3632cdb06c8ba"));
         executeTest("clipOriginalQuals", spec);
     }
 }
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java
index ee179a765..cc436e1f9 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -32,6 +32,7 @@ import org.testng.annotations.Test;
 
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 
 public class PrintReadsIntegrationTest extends WalkerTest {
@@ -58,26 +59,27 @@ public class PrintReadsIntegrationTest extends WalkerTest {
     @DataProvider(name = "PRTest")
     public Object[][] createPrintReadsTestData() {
         return new Object[][]{
-                {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, "", "5aee1c592f7b0505430df4d4452b8000")},
-                {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -compress 0", "62a542230502c9e54124ebd46242e252")},
-                {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -simplifyBAM", "a054a6618ffa8cd2d1113b005335922b")},
-                {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -n 10", "0e3d1748ad1cb523e3295cab9d09d8fc")},
+                {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, "", "0aa3505ba61e05663e629011dd54e423")},
+                {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -compress 0", "0aec10d19e0dbdfe1d0cbb3eddaf623a")},
+                {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -simplifyBAM", "c565d9cd4838a313e7bdb30530c0cf71")},
+                {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -n 10", "917440a38aba707ec0e012168590981a")},
                 // See: GATKBAMIndex.getStartOfLastLinearBin(), BAMScheduler.advance(), IntervalOverlapFilteringIterator.advance()
-                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, "", "d7f23fd77d7dc7cb50d3397f644c6d8a")},
-                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1", "c601db95b20248d012b0085347fcb6d1")},
-                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L unmapped", "2d32440e47e8d9d329902fe573ad94ce")},
-                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1 -L unmapped", "c601db95b20248d012b0085347fcb6d1")},
-                {new PRTest(b37KGReference, new String[]{"oneReadAllInsertion.bam"}, "",  "349650b6aa9e574b48a2a62627f37c7d")},
-                {new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam"}, "",  "0c1cbe67296637a85e80e7a182f828ab")},
+                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, "", "0b58c903f54e8543a8b2ce1439aa769b")},
+                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1", "5b1154cc81dba6bcfe76188e4df8d79c")},
+                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.cram"}, " -L 1:10001 -L GL000192.1:500204", "e9caf8a0e6ec947cdcbdfc48a4292eb5")},
+                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L unmapped", "cbd3d1d50c8674f79033aa8c36aa3cd1")},
+                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1 -L unmapped", "5b1154cc81dba6bcfe76188e4df8d79c")},
+                {new PRTest(b37KGReference, new String[]{"oneReadAllInsertion.bam"}, "",  "e212d1799ae797e781b17e630656a9a1")},
+                {new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam"}, "",  "0387c61303140d8899fcbfdd3e72ed80")},
                 // Tests for filtering options
                 {new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam", "NA20313.highCoverageRegion.bam"},
-                        "",  "b3ae15c8af33fd5badc1a29e089bdaac")},
+                        "",  "ad56da66be0bdab5a8992de9617ae6a5")},
                 {new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam", "NA20313.highCoverageRegion.bam"},
-                        " -readGroup SRR359098",  "8bd867b30539524daa7181efd9835a8f")},
+                        " -readGroup SRR359098",  "c3bfe28722a665e666098dbb7048a9f1")},
                 {new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam", "NA20313.highCoverageRegion.bam"},
-                        " -readGroup 20FUK.3 -sn NA12878",  "93a7bc1b2b1cd27815ed1666cbb4d0cb")},
+                        " -readGroup 20FUK.3 -sn NA12878",  "8191f8d635d00b1f4d0993b785cc46c5")},
                 {new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam", "NA20313.highCoverageRegion.bam"},
-                        " -sn na12878",  "52e99cfcf03ff46285d1ba302f8df964")},
+                        " -sn na12878",  "92a85b4223ec45e114f12a1fe6ebbaeb")},
         };
     }
 
@@ -98,7 +100,7 @@ public class PrintReadsIntegrationTest extends WalkerTest {
                         params.args +
                         " --no_pg_tag" +
                         " -o %s",
-                Arrays.asList(params.md5));
+                Collections.singletonList(params.md5));
         executeTest("testPrintReads-"+params.args, spec).getFirst();
     }
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsLargeScaleTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsLargeScaleTest.java
index 956d70f61..5d1b6c056 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsLargeScaleTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsLargeScaleTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsUnitTest.java
index bb6d5bc1a..c0aec4329 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ReadAdaptorTrimmerIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ReadAdaptorTrimmerIntegrationTest.java
deleted file mode 100644
index 65ca2e7f7..000000000
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ReadAdaptorTrimmerIntegrationTest.java
+++ /dev/null
@@ -1,60 +0,0 @@
-/*
-* Copyright (c) 2012 The Broad Institute
-* 
-* Permission is hereby granted, free of charge, to any person
-* obtaining a copy of this software and associated documentation
-* files (the "Software"), to deal in the Software without
-* restriction, including without limitation the rights to use,
-* copy, modify, merge, publish, distribute, sublicense, and/or sell
-* copies of the Software, and to permit persons to whom the
-* Software is furnished to do so, subject to the following
-* conditions:
-* 
-* The above copyright notice and this permission notice shall be
-* included in all copies or substantial portions of the Software.
-* 
-* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
-* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-*/
-
-package org.broadinstitute.gatk.tools.walkers.readutils;
-
-import org.broadinstitute.gatk.engine.walkers.WalkerTest;
-import org.testng.annotations.Test;
-
-import java.util.Arrays;
-import java.util.Collections;
-
-/**
- * Created with IntelliJ IDEA.
- * User: delangel
- * Date: 4/13/13
- * Time: 7:28 AM
- * To change this template use File | Settings | File Templates.
- */
-public class ReadAdaptorTrimmerIntegrationTest extends WalkerTest {
-    private String getBaseCommand(final String BAM) {
-        return  "-T ReadAdaptorTrimmer -R " + b37KGReference +
-                " -I " + privateTestDir + BAM +
-                " -o %s";
-    }
-
-    @Test
-    public void testBasicTrimmer() {
-        WalkerTestSpec spec = new WalkerTestSpec( getBaseCommand("shortInsertTest.bam"),  1, Arrays.asList("1d42414e12b45d44e6f396d97d0f60fe"));
-        executeTest(String.format("testBasicTrimmer"), spec);
-    }
-
-    @Test
-    public void testSkippingBadPairs() {
-        WalkerTestSpec spec = new WalkerTestSpec( getBaseCommand("shortInsertTest2.bam")+" -removeUnpairedReads",  1, Arrays.asList("5e796345502fbfc31134f7736ce68868"));
-        executeTest(String.format("testSkippingBadPairs"), spec);
-    }
-
-}
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFileIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFileIntegrationTest.java
index 1c2e6bbac..87589a50c 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFileIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFileIntegrationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -43,9 +43,9 @@ public class SplitSamFileIntegrationTest extends WalkerTest {
                         " --outputRoot " + prefix,
                 Collections.emptyList()
         );
-        addSplitOutput(spec, prefix, "NA12878", "ffb8a1e76798fa78c9ffe46abc02e92f");
-        addSplitOutput(spec, prefix, "NA12891", "42154dc36451dfe98922a579d329bbe2");
-        addSplitOutput(spec, prefix, "NA12892", "6abb5d11e615310987da22212dd9fc84");
+        addSplitOutput(spec, prefix, "NA12878", "3e28b666fb673be138eca9bd3db9520b");
+        addSplitOutput(spec, prefix, "NA12891", "af01069bc3da4252ce8417a03d11f48b");
+        addSplitOutput(spec, prefix, "NA12892", "cfa1cb6aaca03900160bd5627f4f698b");
         executeTest("testSplitSamFile", spec);
     }
 
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounterIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounterIntegrationTest.java
index 238ce93c7..d656abae7 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounterIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounterIntegrationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsUnitTest.java
index 91f1a7931..df61b7c9a 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsUnitTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFIntegrationTest.java
index bbbcbdd1b..9e893a09f 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFIntegrationTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -55,7 +55,7 @@ public class VCFIntegrationTest extends WalkerTest {
     @Test(enabled = true)
     public void testReadingAndWritingWitHNoChanges() {
 
-        String md5ofInputVCF = "d991abe6c6a7a778a60a667717903be0";
+        String md5ofInputVCF = "3dc9ac85f2c0541df9bc57b4d81f480b";
         String testVCF = privateTestDir + "vcf4.1.example.vcf";
 
         String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";
@@ -76,7 +76,7 @@ public class VCFIntegrationTest extends WalkerTest {
         String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";
 
         String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
-        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("13329ba7360a8beb3afc02569e5a20c4"));
+        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("b8b18a9a015cba1f3a44af532bf45338"));
         executeTest("Test reading and writing breakpoint VCF", spec1);
     }
 
@@ -87,7 +87,7 @@ public class VCFIntegrationTest extends WalkerTest {
         String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";
 
         String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
-        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("e0e308a25e56bde1c664139bb44ed19d"));
+        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("89daaa81f64e96cf4d9aa0abf9be0b76"));
         executeTest("Test reading VCF with lower-case bases", spec1);
     }
 
@@ -98,7 +98,7 @@ public class VCFIntegrationTest extends WalkerTest {
         String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";
 
         String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
-        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("bdab26dd7648a806dbab01f64db2bdab"));
+        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("5d91e685c760f7e869cb06596d741116"));
         executeTest("Test reading and writing 1000G Phase I SVs", spec1);
     }
 
@@ -109,7 +109,7 @@ public class VCFIntegrationTest extends WalkerTest {
         String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";
 
         String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
-        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("38697c195e7abf18d95dcc16c8e6d284"));
+        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("122340e3dc333d2b4b79c5c0c443a3fe"));
         executeTest("Test reading and writing samtools vcf", spec1);
     }
 
@@ -118,7 +118,7 @@ public class VCFIntegrationTest extends WalkerTest {
         String testVCF = privateTestDir + "ex2.vcf";
         String baseCommand = "-R " + b36KGReference + " --no_cmdline_in_header -o %s ";
         String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
-        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("e8f721ce81e4fdadba13c5291027057f"));
+        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("db565efb14b2fe5f00a11762751d2476"));
         executeTest("Test writing samtools WEx BCF example", spec1);
     }
 
@@ -127,7 +127,7 @@ public class VCFIntegrationTest extends WalkerTest {
         String testVCF = privateTestDir + "ex2.bcf";
         String baseCommand = "-R " + b36KGReference + " --no_cmdline_in_header -o %s ";
         String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
-        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("0439e2b4ccc63bb4ba7c283cd9ab1b25"));
+        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("0ca1a078d4801886ef4abac327df7104"));
         executeTest("Test reading samtools WEx BCF example", spec1);
     }
 
@@ -144,7 +144,7 @@ public class VCFIntegrationTest extends WalkerTest {
 
     @Test
     public void testPassingOnVCFWithoutHeadersWithLenientProcessing() {
-        runVCFWithoutHeaders("-U LENIENT_VCF_PROCESSING", "6de8cb7457154dd355aa55befb943f88", null, true);
+        runVCFWithoutHeaders("-U LENIENT_VCF_PROCESSING", "a8f4be8ad9820286ea13a28a675133f1", null, true);
     }
 
     private void runVCFWithoutHeaders(final String moreArgs, final String expectedMD5, final Class expectedException, final boolean disableBCF) {
@@ -360,7 +360,7 @@ public class VCFIntegrationTest extends WalkerTest {
                 " -o %s ";
         final String name = "testBlockCompressedInput: " + testSpec.toString();
 
-        final WalkerTestSpec spec = new WalkerTestSpec(commandLine, 1, Arrays.asList("3b60668bd973e43783d0406de80d2ed2"));
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine, 1, Arrays.asList("ce9c0bf31ee9452ac4a12a59d5814545"));
 
         executeTest(name, spec);
     }
diff --git a/public/gatk-utils/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java b/public/gatk-utils/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java
index c2a5e8042..be38c06cb 100644
--- a/public/gatk-utils/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java
+++ b/public/gatk-utils/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/htsjdk/samtools/GATKBin.java b/public/gatk-utils/src/main/java/htsjdk/samtools/GATKBin.java
index a4a7c7246..d9698c38d 100644
--- a/public/gatk-utils/src/main/java/htsjdk/samtools/GATKBin.java
+++ b/public/gatk-utils/src/main/java/htsjdk/samtools/GATKBin.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/htsjdk/samtools/GATKChunk.java b/public/gatk-utils/src/main/java/htsjdk/samtools/GATKChunk.java
index aed7aecde..1a10819a8 100644
--- a/public/gatk-utils/src/main/java/htsjdk/samtools/GATKChunk.java
+++ b/public/gatk-utils/src/main/java/htsjdk/samtools/GATKChunk.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java b/public/gatk-utils/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java
index 00f65e54c..f861ccbbe 100644
--- a/public/gatk-utils/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java
+++ b/public/gatk-utils/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/AutoFormattingTime.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/AutoFormattingTime.java
index 31032e3f6..e77ff641a 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/AutoFormattingTime.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/AutoFormattingTime.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BaseUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BaseUtils.java
index ecb8bbde5..f0ed568ab 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BaseUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BaseUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BitSetUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BitSetUtils.java
index a9ab00de3..20b602642 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BitSetUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BitSetUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ContigComparator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ContigComparator.java
index f3f93b411..a069415df 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ContigComparator.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ContigComparator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/DeprecatedToolChecks.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/DeprecatedToolChecks.java
index 9fcd848f2..53613ca2a 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/DeprecatedToolChecks.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/DeprecatedToolChecks.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -47,7 +47,18 @@ public class DeprecatedToolChecks {
         deprecatedGATKWalkers.put("TableRecalibration", "2.0 (use PrintReads with -BQSR instead; see documentation for usage)");
         deprecatedGATKWalkers.put("AlignmentWalker", "2.2 (no replacement)");
         deprecatedGATKWalkers.put("CountBestAlignments", "2.2 (no replacement)");
-        deprecatedGATKWalkers.put("SomaticIndelDetector", "2.0 (replaced by the standalone tool Indelocator; see Cancer Tools documentation)");
+        deprecatedGATKWalkers.put("SomaticIndelDetector", "2.0 (replaced by MuTect2; see documentation for usage)");
+        deprecatedGATKWalkers.put("BeagleOutputToVCF", "3,4 (replaced by Beagle native functions; see Beagle 4 documentation at https://faculty.washington.edu/browning/beagle/beagle.html)");
+        deprecatedGATKWalkers.put("VariantsToBeagleUnphased", "3.4 (replaced by Beagle native functions; see Beagle 4 documentation at https://faculty.washington.edu/browning/beagle/beagle.html)");
+        deprecatedGATKWalkers.put("ProduceBeagleInput", "3.4 (replaced by Beagle native functions; see Beagle 4 documentation at https://faculty.washington.edu/browning/beagle/beagle.html)");
+        deprecatedGATKWalkers.put("ReadAdaptorTrimmer","3.5 (this tool was unsound and untested -- no specific replacement, see Picard tools for alternatives)");
+        deprecatedGATKWalkers.put("BaseCoverageDistribution","3.5 (use DiagnoseTargets instead; see documentation for usage)");
+        deprecatedGATKWalkers.put("CoveredByNSamplesSites","3.5 (use DiagnoseTargets instead; see documentation for usage)");
+        deprecatedGATKWalkers.put("VariantValidationAssessor","3.5 (this tool was unsound and untested -- no replacement)");
+        deprecatedGATKWalkers.put("LiftOverVariants","3.5 (use Picard LiftoverVCF instead; see documentation for usage)");
+        deprecatedGATKWalkers.put("FilterLiftedVariants","3.5 (use Picard LiftoverVCF instead; see documentation for usage)");
+        deprecatedGATKWalkers.put("ListAnnotations","3.5 (this tool was impractical; see the online documentation instead)");
+
     }
 
     // Mapping from walker name to major version number where the walker first disappeared and optional replacement options
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLoc.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLoc.java
index 101796bc0..d41072adb 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLoc.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLoc.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -62,6 +62,7 @@ public class GenomeLoc implements Comparable, Serializable, HasGenome
     // TODO - WARNING WARNING WARNING code somehow depends on the name of the contig being null!
     public static final GenomeLoc UNMAPPED = new GenomeLoc((String)null);
     public static final GenomeLoc WHOLE_GENOME = new GenomeLoc("all");
+    public static final GenomeLoc END_OF_GENOME = new GenomeLoc("Y", 23, 59347566, 59347566);
 
     public static final boolean isUnmapped(GenomeLoc loc) {
         return loc == UNMAPPED;
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLocParser.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLocParser.java
index 55e66244c..9cac5d536 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLocParser.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLocParser.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLocSortedSet.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLocSortedSet.java
index 694c27187..6e777df29 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLocSortedSet.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLocSortedSet.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/HasGenomeLocation.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/HasGenomeLocation.java
index d080d5bc0..d0309193f 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/HasGenomeLocation.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/HasGenomeLocation.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/HeapSizeMonitor.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/HeapSizeMonitor.java
index 041bf76ba..b158794ad 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/HeapSizeMonitor.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/HeapSizeMonitor.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/IndelUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/IndelUtils.java
index 3c6b48cc3..83003d24a 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/IndelUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/IndelUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/LRUCache.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/LRUCache.java
index df2e829ab..ed985c418 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/LRUCache.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/LRUCache.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequenceDictionary.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequenceDictionary.java
index 2f9a3b028..b2c2d1a5a 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequenceDictionary.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequenceDictionary.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java
index 61261f217..a768a1c55 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MathUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MathUtils.java
index 614cb927e..fb8e8d987 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MathUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MathUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Median.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Median.java
index 40e41f28d..948332209 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Median.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Median.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MultiThreadedErrorTracker.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MultiThreadedErrorTracker.java
index edbf25dca..3dfe13c19 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MultiThreadedErrorTracker.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MultiThreadedErrorTracker.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/NGSPlatform.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/NGSPlatform.java
index 829728835..1b3af7066 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/NGSPlatform.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/NGSPlatform.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/PathUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/PathUtils.java
index ef6d5a05b..f2a8340b7 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/PathUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/PathUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/QualityUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/QualityUtils.java
index cd6cfc652..d67e5abc9 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/QualityUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/QualityUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -205,7 +205,7 @@ public class QualityUtils {
     @Ensures("result <= 0.0")
     public static double qualToErrorProbLog10(final double qual) {
         if ( qual < 0.0 ) throw new IllegalArgumentException("qual must be >= 0.0 but got " + qual);
-        return qual / -10.0;
+        return qual * -0.1;
     }
 
     // ----------------------------------------------------------------------
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutor.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutor.java
index c6c4fba02..1ee279843 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutor.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutor.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutorException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutorException.java
index 233ff73a0..53ad3aca8 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutorException.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutorException.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptLibrary.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptLibrary.java
index 390edc73e..56f80e3e2 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptLibrary.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptLibrary.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RUtils.java
index 80f73139d..982cfa371 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java
index d0eb0b9f8..71d87409f 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -25,6 +25,7 @@
 
 package org.broadinstitute.gatk.utils;
 
+import java.math.BigInteger;
 import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.samtools.SAMSequenceRecord;
 import org.apache.log4j.Logger;
@@ -79,7 +80,7 @@ public class SequenceDictionaryUtils {
         IDENTICAL,                      // the dictionaries are identical
         COMMON_SUBSET,                  // there exists a common subset of equivalent contigs
         NO_COMMON_CONTIGS,              // no overlap between dictionaries
-        UNEQUAL_COMMON_CONTIGS,         // common subset has contigs that have the same name but different lengths
+        UNEQUAL_COMMON_CONTIGS,         // common subset has contigs that have the same name but different lengths and/or MD5s
         NON_CANONICAL_HUMAN_ORDER,      // human reference detected but the order of the contigs is non-standard (lexicographic, for examine)
         OUT_OF_ORDER,                   // the two dictionaries overlap but the overlapping contigs occur in different
                                         // orders with respect to each other
@@ -92,7 +93,7 @@ public class SequenceDictionaryUtils {
      * @param validationExclusion exclusions to validation
      * @return Returns true if the engine is in tolerant mode and we'll let through dangerous but not fatal dictionary inconsistency
      */
-    private static boolean allowNonFatalIncompabilities(ValidationExclusion.TYPE validationExclusion) {
+    private static boolean allowNonFatalIncompabilities(final ValidationExclusion.TYPE validationExclusion) {
         return ( validationExclusion == ValidationExclusion.TYPE.ALLOW_SEQ_DICT_INCOMPATIBILITY ||
                         validationExclusion == ValidationExclusion.TYPE.ALL );
     }
@@ -133,15 +134,23 @@ public class SequenceDictionaryUtils {
                 throw new UserException.IncompatibleSequenceDictionaries("No overlapping contigs found", name1, dict1, name2, dict2);
 
             case UNEQUAL_COMMON_CONTIGS: {
-                List x = findDisequalCommonContigs(getCommonContigsByName(dict1, dict2), dict1, dict2);
-                SAMSequenceRecord elt1 = x.get(0);
-                SAMSequenceRecord elt2 = x.get(1);
+                final List x = findNotEqualCommonContigs(getCommonContigsByName(dict1, dict2), dict1, dict2);
+                final SAMSequenceRecord elt1 = x.get(0);
+                final SAMSequenceRecord elt2 = x.get(1);
+
+                String msg = "Found contigs with the same name but different lengths";
+                String contig1  = "  contig  " + name1 + " is named " + elt1.getSequenceName()  + " with length " + Integer.toString(elt1.getSequenceLength());
+                if ( elt1.getMd5() != null )
+                    contig1 += " and MD5 " + elt1.getMd5();
+                String contig2  = "  contig  " + name2 + " is named " + elt2.getSequenceName()  + " with length " + Integer.toString(elt2.getSequenceLength());
+                if ( elt2.getMd5() != null )
+                    contig2 += " and MD5 " + elt2.getMd5();
+                if ( elt1.getMd5() != null ||  elt2.getMd5() != null )
+                    msg += " or MD5s:";
+                msg += "\n" + contig1 + "\n" + contig2;
 
                 // todo -- replace with toString when SAMSequenceRecord has a nice toString routine
-                UserException ex = new UserException.IncompatibleSequenceDictionaries(String.format("Found contigs with the same name but different lengths:\n  contig %s = %s / %d\n  contig %s = %s / %d",
-                        name1, elt1.getSequenceName(), elt1.getSequenceLength(),
-                        name2, elt2.getSequenceName(), elt2.getSequenceLength()),
-                        name1, dict1, name2, dict2);
+                final UserException ex = new UserException.IncompatibleSequenceDictionaries(msg, name1, dict1, name2, dict2);
 
                 if ( allowNonFatalIncompabilities(validationExclusion) )
                     logger.warn(ex.getMessage());
@@ -226,7 +235,7 @@ public class SequenceDictionaryUtils {
 
         final Set commonContigs = getCommonContigsByName(dict1, dict2);
 
-        if (commonContigs.size() == 0)
+        if (commonContigs.isEmpty())
             return SequenceDictionaryCompatibility.NO_COMMON_CONTIGS;
         else if ( ! commonContigsHaveSameLengths(commonContigs, dict1, dict2) )
             return SequenceDictionaryCompatibility.UNEQUAL_COMMON_CONTIGS;
@@ -250,12 +259,12 @@ public class SequenceDictionaryUtils {
      * @param dict2
      * @return true if all of the common contigs are equivalent
      */
-    private static boolean commonContigsHaveSameLengths(Set commonContigs, SAMSequenceDictionary dict1, SAMSequenceDictionary dict2) {
-        return findDisequalCommonContigs(commonContigs, dict1, dict2) == null;
+    private static boolean commonContigsHaveSameLengths(final Set commonContigs, final SAMSequenceDictionary dict1, final SAMSequenceDictionary dict2) {
+        return findNotEqualCommonContigs(commonContigs, dict1, dict2) == null;
     }
 
     /**
-     * Returns a List(x,y) that contains two disequal sequence records among the common contigs in both dicts.  Returns
+     * Returns a List(x,y) that contains two sequence records that are not equal among the common contigs in both dicts.  Returns
      * null if all common contigs are equivalent
      *
      * @param commonContigs
@@ -263,7 +272,7 @@ public class SequenceDictionaryUtils {
      * @param dict2
      * @return
      */
-    private static List findDisequalCommonContigs(Set commonContigs, SAMSequenceDictionary dict1, SAMSequenceDictionary dict2) {
+    private static List findNotEqualCommonContigs(final Set commonContigs, final SAMSequenceDictionary dict1, final SAMSequenceDictionary dict2) {
         for ( String name : commonContigs ) {
             SAMSequenceRecord elt1 = dict1.getSequence(name);
             SAMSequenceRecord elt2 = dict2.getSequence(name);
@@ -275,32 +284,32 @@ public class SequenceDictionaryUtils {
     }
 
     /**
-     * Helper routine that returns two sequence records are equivalent, defined as having the same name and
-     * lengths, if both are non-zero
+     * Helper routine that determines if two sequence records are equivalent, defined as having the same name,
+     * lengths (if both are non-zero) and MD5 (if present)
      *
-     * @param me
-     * @param that
-     * @return
+     * @param record1  a SAMSequenceRecord
+     * @param record2  a SAMSequenceRecord
+     * @return true if the records are equivalent, false otherwise
      */
-    private static boolean sequenceRecordsAreEquivalent(final SAMSequenceRecord me, final SAMSequenceRecord that) {
-        if (me == that) return true;
-        if (that == null) return false;
+    private static boolean sequenceRecordsAreEquivalent(final SAMSequenceRecord record1, final SAMSequenceRecord record2) {
+        if ( record1 == record2 ) return true;
+        if ( record1 == null || record2 == null ) return false;
 
-        if (me.getSequenceLength() != 0 && that.getSequenceLength() != 0 && me.getSequenceLength() != that.getSequenceLength())
+        // compare length
+        if ( record1.getSequenceLength() != 0 && record2.getSequenceLength() != 0 && record1.getSequenceLength() != record2.getSequenceLength() )
             return false;
 
-            // todo -- reenable if we want to be really strict here
-//        if (me.getExtendedAttribute(SAMSequenceRecord.MD5_TAG) != null && that.getExtendedAttribute(SAMSequenceRecord.MD5_TAG) != null) {
-//            final BigInteger thisMd5 = new BigInteger((String)me.getExtendedAttribute(SAMSequenceRecord.MD5_TAG), 16);
-//            final BigInteger thatMd5 = new BigInteger((String)that.getExtendedAttribute(SAMSequenceRecord.MD5_TAG), 16);
-//            if (!thisMd5.equals(thatMd5)) {
-//                return false;
-//            }
-//        }
-//        else {
-        if (me.getSequenceName() != that.getSequenceName())
-            return false; // Compare using == since we intern() the Strings
-//        }
+        // compare name
+        if ( !record1.getSequenceName().equals(record2.getSequenceName() ))
+            return false;
+
+         // compare MD5
+         if ( record1.getMd5() != null && record2.getMd5() != null ){
+            final BigInteger firstMd5 = new BigInteger(record1.getMd5(), 16);
+            final BigInteger secondMd5 = new BigInteger(record2.getMd5(), 16);
+            if ( !firstMd5.equals(secondMd5) )
+                return false;
+       }
 
         return true;
     }
@@ -313,13 +322,13 @@ public class SequenceDictionaryUtils {
      * @param dict
      * @return
      */
-    private static boolean nonCanonicalHumanContigOrder(SAMSequenceDictionary dict) {
+    private static boolean nonCanonicalHumanContigOrder(final SAMSequenceDictionary dict) {
         if ( ! ENABLE_LEXICOGRAPHIC_REQUIREMENT_FOR_HUMAN ) // if we don't want to enable this test, just return false
             return false;
 
         SAMSequenceRecord chr1 = null, chr2 = null, chr10 = null;
 
-        for ( SAMSequenceRecord elt : dict.getSequences() ) {
+        for ( final SAMSequenceRecord elt : dict.getSequences() ) {
             if ( isHumanSeqRecord(elt, CHR1_HG18, CHR1_HG19 ) ) chr1 = elt;
             if ( isHumanSeqRecord(elt, CHR2_HG18, CHR2_HG19 ) ) chr2 = elt;
             if ( isHumanSeqRecord(elt, CHR10_HG18, CHR10_HG19 ) ) chr10 = elt;
@@ -355,7 +364,7 @@ public class SequenceDictionaryUtils {
      * @param dict2 second SAMSequenceDictionary
      * @return true if the common contigs occur in the same relative order in both dict1 and dict2, otherwise false
      */
-    private static boolean commonContigsAreInSameRelativeOrder(Set commonContigs, SAMSequenceDictionary dict1, SAMSequenceDictionary dict2) {
+    private static boolean commonContigsAreInSameRelativeOrder(final Set commonContigs, final SAMSequenceDictionary dict1, final SAMSequenceDictionary dict2) {
         List list1 = sortSequenceListByIndex(getSequencesOfName(commonContigs, dict1));
         List list2 = sortSequenceListByIndex(getSequencesOfName(commonContigs, dict2));
 
@@ -376,8 +385,8 @@ public class SequenceDictionaryUtils {
      * @param dict
      * @return
      */
-    private static List getSequencesOfName(Set commonContigs, SAMSequenceDictionary dict) {
-        List l = new ArrayList(commonContigs.size());
+    private static List getSequencesOfName(final Set commonContigs, final SAMSequenceDictionary dict) {
+        final List l = new ArrayList(commonContigs.size());
         for ( String name : commonContigs ) {
             l.add(dict.getSequence(name) );
         }
@@ -401,7 +410,7 @@ public class SequenceDictionaryUtils {
      * @param unsorted
      * @return
      */
-    private static List sortSequenceListByIndex(List unsorted) {
+    private static List sortSequenceListByIndex(final List unsorted) {
         Collections.sort(unsorted, new CompareSequenceRecordsByIndex());
         return unsorted;
     }
@@ -418,8 +427,8 @@ public class SequenceDictionaryUtils {
      */
     private static boolean commonContigsAreAtSameIndices( final Set commonContigs, final SAMSequenceDictionary dict1, final SAMSequenceDictionary dict2 ) {
         for ( String commonContig : commonContigs ) {
-            SAMSequenceRecord dict1Record = dict1.getSequence(commonContig);
-            SAMSequenceRecord dict2Record = dict2.getSequence(commonContig);
+            final SAMSequenceRecord dict1Record = dict1.getSequence(commonContig);
+            final SAMSequenceRecord dict2Record = dict2.getSequence(commonContig);
 
             // Each common contig must have the same index in both dictionaries
             if ( dict1Record.getSequenceIndex() != dict2Record.getSequenceIndex() ) {
@@ -489,13 +498,13 @@ public class SequenceDictionaryUtils {
      * @return
      */
     public static Set getCommonContigsByName(SAMSequenceDictionary dict1, SAMSequenceDictionary dict2) {
-        Set intersectingSequenceNames = getContigNames(dict1);
+        final Set intersectingSequenceNames = getContigNames(dict1);
         intersectingSequenceNames.retainAll(getContigNames(dict2));
         return intersectingSequenceNames;
     }
 
     public static Set getContigNames(SAMSequenceDictionary dict) {
-        Set contigNames = new HashSet(Utils.optimumHashSize(dict.size()));
+        final Set contigNames = new HashSet(Utils.optimumHashSize(dict.size()));
         for (SAMSequenceRecord dictionaryEntry : dict.getSequences())
             contigNames.add(dictionaryEntry.getSequenceName());
         return contigNames;
@@ -515,7 +524,7 @@ public class SequenceDictionaryUtils {
             throw new IllegalArgumentException("Sequence dictionary must be non-null");
         }
 
-        StringBuilder s = new StringBuilder("[ ");
+        final StringBuilder s = new StringBuilder("[ ");
 
         for ( SAMSequenceRecord dictionaryEntry : dict.getSequences() ) {
             s.append(dictionaryEntry.getSequenceName());
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequencerFlowClass.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequencerFlowClass.java
index 7290292e7..466f42b9b 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequencerFlowClass.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequencerFlowClass.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SimpleTimer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SimpleTimer.java
index 39d6fa67b..5101064fd 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SimpleTimer.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SimpleTimer.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/UnvalidatingGenomeLoc.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/UnvalidatingGenomeLoc.java
index 2c3d24b7f..1b7ac79da 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/UnvalidatingGenomeLoc.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/UnvalidatingGenomeLoc.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Utils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Utils.java
index 883143a14..ce54e8f11 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Utils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Utils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ValidationExclusion.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ValidationExclusion.java
index 0dfce0e99..c09ebe4cc 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ValidationExclusion.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ValidationExclusion.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -40,7 +40,7 @@ public class ValidationExclusion {
         ALLOW_UNINDEXED_BAM,        // allow bam files that do not have an index; we'll traverse them using monolithic shard
         ALLOW_UNSET_BAM_SORT_ORDER, // assume that the bam is sorted, even if the SO (sort-order) flag is not set
         NO_READ_ORDER_VERIFICATION, // do not validate that the reads are in order as we take them from the bam file
-        ALLOW_SEQ_DICT_INCOMPATIBILITY, // allow dangerous, but not fatal, sequence dictionary incompabilities
+        ALLOW_SEQ_DICT_INCOMPATIBILITY, // allow dangerous, but not fatal, sequence dictionary incompatibilities
         LENIENT_VCF_PROCESSING,         // allow non-standard values for standard VCF header lines.  Don't worry about size differences between header and values, etc.
         @EnumerationArgumentDefault // set the ALL value to the default value, so if they specify just -U, we get the ALL
         ALL                         // do not check for all of the above conditions, DEFAULT
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegion.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegion.java
index 86a89c1c9..8a4deb51d 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegion.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegion.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionReadState.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionReadState.java
index 76b4eb6ca..57fd35908 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionReadState.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionReadState.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfile.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfile.java
index 2d97f69f7..cdc7cb806 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfile.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfile.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileState.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileState.java
index 915db6189..a1df0baf6 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileState.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileState.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfile.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfile.java
index 52437a846..8458b3a96 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfile.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfile.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcid.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcid.java
index 041660944..af61415aa 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcid.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcid.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidTable.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidTable.java
index 7cd89336d..e8bd5d1ec 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidTable.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidTable.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidUtils.java
index 9213e8263..175ea369a 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/baq/BAQ.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/baq/BAQ.java
index c679ec248..91562b69e 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/baq/BAQ.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/baq/BAQ.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/JVMUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/JVMUtils.java
index d695543c4..329dfa19b 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/JVMUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/JVMUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PluginManager.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PluginManager.java
index 2aa2f76d5..7ef7a154c 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PluginManager.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PluginManager.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/ProtectedPackageSource.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/ProtectedPackageSource.java
index 7c7a776a0..7a2b53696 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/ProtectedPackageSource.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/ProtectedPackageSource.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PublicPackageSource.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PublicPackageSource.java
index 5321466d4..dd2068bbd 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PublicPackageSource.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PublicPackageSource.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingOp.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingOp.java
index f4ca70e84..ad0de1da1 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingOp.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingOp.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingRepresentation.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingRepresentation.java
index 5d86e0bf7..8d556515b 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingRepresentation.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingRepresentation.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ReadClipper.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ReadClipper.java
index c31784fa4..3710698a2 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ReadClipper.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ReadClipper.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodec.java
index a8ac99def..8eaa316c2 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodec.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodec.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -112,6 +112,8 @@ public class BeagleCodec extends AsciiFeatureCodec implements Ref
     private final static Set HEADER_IDs = new HashSet(Arrays.asList("marker", "I"));
 
     private static final String delimiterRegex = "\\s+";
+    // codec file extension
+    protected static final String FILE_EXT = "beagle";
 
     /**
      * The parser to use when resolving genome-wide locations.
@@ -212,6 +214,7 @@ public class BeagleCodec extends AsciiFeatureCodec implements Ref
 
     private static Pattern MARKER_PATTERN = Pattern.compile("(.+):([0-9]+)");
 
+    @Override
     public BeagleFeature decode(String line) {
         String[] tokens;
 
@@ -273,4 +276,12 @@ public class BeagleCodec extends AsciiFeatureCodec implements Ref
 
         return bglFeature;
     }
+
+    /**
+     * Can the file be decoded?
+     * @param path path the file to test for parsability with this codec
+     * @return true if the path has the correct file extension, false otherwise
+     */
+    @Override
+    public boolean canDecode(final String path) { return path.endsWith("." + FILE_EXT); }
 }
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleFeature.java
index 673885a1b..39908366c 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleFeature.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleFeature.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapCodec.java
index ac50853e0..8f49dd063 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapCodec.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapCodec.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -77,6 +77,8 @@ public class RawHapMapCodec extends AsciiFeatureCodec {
     private static final int minimumFeatureCount = 11;
 
     private String headerLine;
+    // codec file extension
+    protected static final String FILE_EXT = "hapmap";
 
     public RawHapMapCodec() {
         super(RawHapMapFeature.class);
@@ -110,6 +112,14 @@ public class RawHapMapCodec extends AsciiFeatureCodec {
                 headerLine);
     }
 
+    /**
+     * Can the file be decoded?
+     * @param path path the file to test for parsability with this codec
+     * @return true if the path has the correct file extension, false otherwise
+     */
+    @Override
+    public boolean canDecode(final String path) { return path.endsWith("." + FILE_EXT); }
+
     @Override
     public Object readActualHeader(final LineIterator lineIterator) {
         this.headerLine = lineIterator.next();
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapFeature.java
index e760aaa83..2dc23fc55 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapFeature.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapFeature.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java
index 379fba036..4a2d15c31 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -74,6 +74,8 @@ import java.util.ArrayList;
  */
 public class RefSeqCodec extends AsciiFeatureCodec implements ReferenceDependentFeatureCodec {
 
+    // codec file extension
+    protected static final String FILE_EXT = "refseq";
     /**
      * The parser to use when resolving genome-wide locations.
      */
@@ -163,6 +165,14 @@ public class RefSeqCodec extends AsciiFeatureCodec implements Ref
         return feature;
     }
 
+    /**
+     * Can the file be decoded?
+     * @param path path the file to test for parsability with this codec
+     * @return true if the path has the correct file extension, false otherwise
+     */
+    @Override
+    public boolean canDecode(final String path) { return path.endsWith("." + FILE_EXT); }
+
     @Override
     public Object readActualHeader(LineIterator lineIterator) {
         // No header for this format
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqFeature.java
index 0e7b80d75..62d4b05ba 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqFeature.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqFeature.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/Transcript.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/Transcript.java
index 1671c79fc..b5bca03d4 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/Transcript.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/Transcript.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodec.java
index 8c4385448..407cf8962 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodec.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodec.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -128,6 +128,9 @@ public class SAMPileupCodec extends AsciiFeatureCodec {
     private static final String baseT = "T";
     private static final String emptyStr = ""; // we will use this for "reference" allele in insertions
 
+    // codec file extension
+    protected static final String FILE_EXT = "samp";
+
     public SAMPileupCodec() {
         super(SAMPileupFeature.class);
     }
@@ -240,6 +243,14 @@ public class SAMPileupCodec extends AsciiFeatureCodec {
         return feature;
     }
 
+    /**
+     * Can the file be decoded?
+     * @param path path the file to test for parsability with this codec
+     * @return true if the path has the correct file extension, false otherwise
+     */
+    @Override
+    public boolean canDecode(final String path) { return path.endsWith("." + FILE_EXT); }
+
     @Override
     public Object readActualHeader(LineIterator lineIterator) {
         // No header for this format
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupFeature.java
index 501a7b597..1768c1328 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupFeature.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupFeature.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodec.java
index d0e69db9f..447aa4761 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodec.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodec.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -57,6 +57,8 @@ public class SAMReadCodec extends AsciiFeatureCodec {
 
     // the number of tokens we expect to parse from a read line
     private static final int expectedTokenCount = 11;
+    // codec file extension
+    protected static final String FILE_EXT = "samr";
 
     public SAMReadCodec() {
         super(SAMReadFeature.class);
@@ -67,6 +69,7 @@ public class SAMReadCodec extends AsciiFeatureCodec {
      * @param line line to decode.
      * @return A SAMReadFeature modeling that line.
      */
+    @Override
     public SAMReadFeature decode(String line) {
         // we may be asked to process a header line; ignore it
         if (line.startsWith("@")) return null;        
@@ -115,6 +118,14 @@ public class SAMReadCodec extends AsciiFeatureCodec {
                                   qualities);
     }
 
+    /**
+     * Can the file be decoded?
+     * @param path path the file to test for parsability with this codec
+     * @return true if the path has the correct file extension, false otherwise
+     */
+    @Override
+    public boolean canDecode(final String path) { return path.endsWith("." + FILE_EXT); }
+
     @Override
     public Object readActualHeader(LineIterator lineIterator) {
         // No header for this format
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadFeature.java
index 857871cfd..fda2e692b 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadFeature.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadFeature.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/BedTableCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/BedTableCodec.java
index cf6cefeb8..84c071f19 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/BedTableCodec.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/BedTableCodec.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableCodec.java
index 09af2f7a5..9908ed632 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableCodec.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableCodec.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -65,10 +65,12 @@ import java.util.Collections;
  * @since 2009
  */
 public class TableCodec extends AsciiFeatureCodec implements ReferenceDependentFeatureCodec {
-    final static protected String delimiterRegex = "\\s+";
-    final static protected String headerDelimiter = "HEADER";
-    final static protected String igvHeaderDelimiter = "track";
-    final static protected String commentDelimiter = "#";
+    protected final static String delimiterRegex = "\\s+";
+    protected final static String headerDelimiter = "HEADER";
+    protected final static String igvHeaderDelimiter = "track";
+    protected final static String commentDelimiter = "#";
+    // codec file extension
+    protected final static String FILE_EXT = "tbl";
 
     protected ArrayList header = new ArrayList();
 
@@ -100,6 +102,14 @@ public class TableCodec extends AsciiFeatureCodec implements Refer
         return new TableFeature(genomeLocParser.parseGenomeLoc(split[0]),Arrays.asList(split), header);
     }
 
+    /**
+     * Can the file be decoded?
+     * @param path path the file to test for parsability with this codec
+     * @return true if the path has the correct file extension, false otherwise
+     */
+    @Override
+    public boolean canDecode(final String path) { return path.endsWith("." + FILE_EXT); }
+
     @Override
     public Object readActualHeader(final LineIterator reader) {
         boolean isFirst = true;
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableFeature.java
index 680c13f92..7960e1fdc 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableFeature.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableFeature.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/DefaultHashMap.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/DefaultHashMap.java
index 2c543dd4a..0ae22648b 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/DefaultHashMap.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/DefaultHashMap.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayList.java
index b2b23d36d..2f8adc392 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayList.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayList.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/IndexedSet.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/IndexedSet.java
index 2bedb9296..671548e64 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/IndexedSet.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/IndexedSet.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/LoggingNestedIntegerArray.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/LoggingNestedIntegerArray.java
index 3117852f5..746bb2c32 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/LoggingNestedIntegerArray.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/LoggingNestedIntegerArray.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/NestedIntegerArray.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/NestedIntegerArray.java
index 02dd15a17..495f3dda7 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/NestedIntegerArray.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/NestedIntegerArray.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/Pair.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/Pair.java
index b09c9dfc9..11229cbeb 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/Pair.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/Pair.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/Permutation.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/Permutation.java
index 53eafe704..522847e9a 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/Permutation.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/Permutation.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/PrimitivePair.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/PrimitivePair.java
index 2b759ced7..563578f0d 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/PrimitivePair.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/PrimitivePair.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/RODMergingIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/RODMergingIterator.java
index e5c7fad4e..634fb36fb 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/RODMergingIterator.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/RODMergingIterator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Advanced.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Advanced.java
index 3995ff71c..a7a98c7c9 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Advanced.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Advanced.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Argument.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Argument.java
index 66c562934..300d04c61 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Argument.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Argument.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentCollection.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentCollection.java
index c142f06e3..30ba236ce 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentCollection.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentCollection.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinition.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinition.java
index f2e7e6ef0..f5b542446 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinition.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinition.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitionGroup.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitionGroup.java
index b6bb16ca3..d6e2cb504 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitionGroup.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitionGroup.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitions.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitions.java
index 8bc17d78d..77c747f89 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitions.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitions.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentException.java
index a55da890a..e0985983c 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentException.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentException.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentIOType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentIOType.java
index 27b816324..b51023421 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentIOType.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentIOType.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatch.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatch.java
index e372b4e02..bbabd5eea 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatch.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatch.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchFileValue.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchFileValue.java
index 3b9c8d3d8..db54fb505 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchFileValue.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchFileValue.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSite.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSite.java
index 967d4c60a..095ea9e99 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSite.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSite.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSource.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSource.java
index a7ce7bad7..229af987a 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSource.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSource.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceType.java
index 9dee5be28..d7990480c 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceType.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceType.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchStringValue.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchStringValue.java
index 9f772bc89..b663b5920 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchStringValue.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchStringValue.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchValue.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchValue.java
index f37d5382b..b6ebdcb8f 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchValue.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchValue.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatches.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatches.java
index e58d8888f..6edd75f18 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatches.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatches.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentSource.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentSource.java
index 79e07a6bd..a8c4e3feb 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentSource.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentSource.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptor.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptor.java
index 944858f55..c583fb93f 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptor.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptor.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ClassType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ClassType.java
index d57d32668..2753c8f6f 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ClassType.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ClassType.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java
index 70c06e24a..f29978ede 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -421,9 +421,9 @@ public abstract class CommandLineProgram {
             throw new ReviewedGATKException("SamException found with no message!", t);
 
         errorPrintf("------------------------------------------------------------------------------------------%n");
-        errorPrintf("A BAM ERROR has occurred (version %s): %n", getVersionNumber());
+        errorPrintf("A BAM/CRAM ERROR has occurred (version %s): %n", getVersionNumber());
         errorPrintf("%n");
-        errorPrintf("This means that there is something wrong with the BAM file(s) you provided.%n");
+        errorPrintf("This means that there is something wrong with the BAM/CRAM file(s) you provided.%n");
         errorPrintf("The error message below tells you what is the problem.%n");
         errorPrintf("%n");
         printDocumentationReference();
@@ -432,6 +432,9 @@ public abstract class CommandLineProgram {
         errorPrintf("- Make sure that your BAM file is well-formed by running Picard's validator on it%n");
         errorPrintf("(see http://picard.sourceforge.net/command-line-overview.shtml#ValidateSamFile for details)%n");
         errorPrintf("- Ensure that your BAM index is not corrupted: delete the current one and regenerate it with 'samtools index'%n");
+        errorPrintf("- Ensure that your CRAM index is not corrupted: delete the current one and regenerate it with%n");
+        errorPrintf("'java -jar cramtools-3.0.jar index --bam-style-index --input-file  --reference-fasta-file '%n");
+        errorPrintf("(see https://github.com/enasequence/cramtools/tree/v3.0 for details)%n");
         errorPrintf("%n");
         errorPrintf("MESSAGE: %s%n", t.getMessage().trim());
         errorPrintf("------------------------------------------------------------------------------------------%n");
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineUtils.java
index 70f5532a4..62139fb48 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/EnumerationArgumentDefault.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/EnumerationArgumentDefault.java
index 3bbdedb01..be7a65b2a 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/EnumerationArgumentDefault.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/EnumerationArgumentDefault.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Gather.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Gather.java
index b29166352..e8e8cde7c 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Gather.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Gather.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Gatherer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Gatherer.java
index 761611f97..158095adf 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Gatherer.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Gatherer.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Hidden.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Hidden.java
index 02325a767..f5a02021d 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Hidden.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Hidden.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Input.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Input.java
index 8ec048389..9fd49782b 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Input.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Input.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalArgumentCollection.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalArgumentCollection.java
index 717a07708..8d18177f3 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalArgumentCollection.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalArgumentCollection.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalBinding.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalBinding.java
index 815b02d6b..da7fa6ee0 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalBinding.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalBinding.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/MissingArgumentValueException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/MissingArgumentValueException.java
index f8f3895ad..f71aec78b 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/MissingArgumentValueException.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/MissingArgumentValueException.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplex.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplex.java
index d00206b90..199b71eb8 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplex.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplex.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplexer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplexer.java
index 3a6fb2f71..643eae100 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplexer.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplexer.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Output.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Output.java
index 88057a235..d7512f65a 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Output.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Output.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedArgs.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedArgs.java
index 45cc055a8..ba403a1c6 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedArgs.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedArgs.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedListArgs.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedListArgs.java
index aa9e186d0..0265c8feb 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedListArgs.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedListArgs.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngine.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngine.java
index 6244b8652..e0fc36156 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngine.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngine.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentFiles.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentFiles.java
index 0361c4cc0..7d8788210 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentFiles.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentFiles.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentProvider.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentProvider.java
index d53a36ca1..b5d5add7a 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentProvider.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentProvider.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingMethod.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingMethod.java
index a93974231..5a4c99c3f 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingMethod.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingMethod.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBinding.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBinding.java
index 2c557872c..3221d21f6 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBinding.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBinding.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollection.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollection.java
index faf456538..8f90f7d14 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollection.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollection.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Tags.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Tags.java
index 2b1c7f7ce..8ea28c881 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Tags.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Tags.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/package-info.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/package-info.java
index f572d3485..3dca4245f 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/package-info.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/package-info.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContext.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContext.java
index bbbb61778..6add93bd2 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContext.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContext.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContextUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContextUtils.java
index 82e1b0eb0..92cfc74a1 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContextUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContextUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/ReferenceContext.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/ReferenceContext.java
index ae70402de..fca56dcc0 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/ReferenceContext.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/ReferenceContext.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/BAMDiffableReader.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/BAMDiffableReader.java
index 29a08cc9e..d06176e77 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/BAMDiffableReader.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/BAMDiffableReader.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffElement.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffElement.java
index 0e0b79741..f9167ff00 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffElement.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffElement.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffEngine.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffEngine.java
index 4960e6bfa..569934585 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffEngine.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffEngine.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffNode.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffNode.java
index 651af07ba..f0e8476e6 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffNode.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffNode.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffValue.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffValue.java
index c84842dab..24f2a40f2 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffValue.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffValue.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffableReader.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffableReader.java
index 43d947329..aef5e8c53 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffableReader.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffableReader.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/Difference.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/Difference.java
index 25ebc032e..9f67fd47f 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/Difference.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/Difference.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/GATKReportDiffableReader.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/GATKReportDiffableReader.java
index 9dc5e2e5e..948fa2107 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/GATKReportDiffableReader.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/GATKReportDiffableReader.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/VCFDiffableReader.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/VCFDiffableReader.java
index a60209ad3..d5d305e20 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/VCFDiffableReader.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/VCFDiffableReader.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtils.java
index fd81e4ba7..37810ba00 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsampleType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsampleType.java
index 52ece95c1..41b59ccc5 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsampleType.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsampleType.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/Downsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/Downsampler.java
index cdaec016c..910409457 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/Downsampler.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/Downsampler.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingMethod.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingMethod.java
index 5cb32386d..569eb709c 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingMethod.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingMethod.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingReadsIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingReadsIterator.java
index d7106b76a..0435e7cd6 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingReadsIterator.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingReadsIterator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingUtils.java
index 9bfc13a13..d1a895b63 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsampler.java
index 11d28c7d6..d480f23fc 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsampler.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsampler.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsamplerFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsamplerFactory.java
index c2113c4a3..74037ea9f 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsamplerFactory.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsamplerFactory.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/LevelingDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/LevelingDownsampler.java
index 537a9f8c0..89fbea0f1 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/LevelingDownsampler.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/LevelingDownsampler.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PassThroughDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PassThroughDownsampler.java
index 313a432d3..e9161b739 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PassThroughDownsampler.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PassThroughDownsampler.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PerSampleDownsamplingReadsIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PerSampleDownsamplingReadsIterator.java
index f289960ee..fc7eb7719 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PerSampleDownsamplingReadsIterator.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PerSampleDownsamplingReadsIterator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsampler.java
index ed6b4394a..455269b6c 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsampler.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsampler.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsamplerFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsamplerFactory.java
index 7cae97be5..ea7e6b079 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsamplerFactory.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsamplerFactory.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsampler.java
index e4a6ee464..b7bf2be19 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsampler.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsampler.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsamplerFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsamplerFactory.java
index 2e6207410..50e89c2bc 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsamplerFactory.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsamplerFactory.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsampler.java
index f150636f1..8a3da8a03 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsampler.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsampler.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsamplerFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsamplerFactory.java
index cdbcf0f63..bac785a91 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsamplerFactory.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsamplerFactory.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/duplicates/DupUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/duplicates/DupUtils.java
index 3d2740769..9ce7fc4be 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/duplicates/DupUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/duplicates/DupUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/duplicates/DuplicateComp.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/duplicates/DuplicateComp.java
index 9213a3e32..7aef3730a 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/duplicates/DuplicateComp.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/duplicates/DuplicateComp.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/DynamicClassResolutionException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/DynamicClassResolutionException.java
index 1c5342068..e39fd557d 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/DynamicClassResolutionException.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/DynamicClassResolutionException.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/GATKException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/GATKException.java
index 0eb0941ec..3584b79ab 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/GATKException.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/GATKException.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/ReviewedGATKException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/ReviewedGATKException.java
index 56dfc6936..d7595d0e5 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/ReviewedGATKException.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/ReviewedGATKException.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/UserException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/UserException.java
index bfb0ca039..ceb1d0f4f 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/UserException.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/UserException.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -100,11 +100,11 @@ public class UserException extends ReviewedGATKException {
 
     public static class MalformedGenomeLoc extends UserException {
         public MalformedGenomeLoc(String message, GenomeLoc loc) {
-            super(String.format("Badly formed genome loc: %s: %s", message, loc));
+            super(String.format("Badly formed genome location: %s: %s", message, loc));
         }
 
         public MalformedGenomeLoc(String message) {
-            super(String.format("Badly formed genome loc: %s", message));
+            super(String.format("Badly formed genome location: %s", message));
         }
     }
 
@@ -129,66 +129,66 @@ public class UserException extends ReviewedGATKException {
 
     public static class UnknownTribbleType extends CommandLineException {
         public UnknownTribbleType(String type, String message) {
-            super(String.format("Unknown tribble type %s: %s", type, message));
+            super(String.format("Unknown variant input file type %s: %s", type, message));
         }
     }
 
 
     public static class BadTmpDir extends UserException {
         public BadTmpDir(String message) {
-            super(String.format("Failure working with the tmp directory %s. Override with -Djava.io.tmpdir=X on the command line to a bigger/better file system.  Exact error was %s", System.getProperties().get("java.io.tmpdir"), message));
+            super(String.format("An error occurred while working with the tmp directory %s. You can specify -Djava.io.tmpdir=X on the command line (before the -jar argument) where X is a directory path, to use a more appropriate temporary directory. The exact error was %s", System.getProperties().get("java.io.tmpdir"), message));
         }
     }
 
     public static class TooManyOpenFiles extends UserException {
         public TooManyOpenFiles() {
-            super(String.format("There was a failure because there are too many files open concurrently; your system's open file handle limit is too small.  See the unix ulimit command to adjust this limit"));
+            super(String.format("An error occurred because there were too many files open concurrently; your system's open file handle limit is probably too small.  See the unix ulimit command to adjust this limit or ask your system administrator for help."));
         }
     }
 
     public static class LocalParallelizationProblem extends UserException {
         public LocalParallelizationProblem(final File file) {
-            super(String.format("There was a failure because temporary file %s could not be found while running the GATK with more than one thread.  Possible causes for this problem include: your system's open file handle limit is too small, your output or temp directories do not have sufficient space, or just an isolated file system blip", file.getAbsolutePath()));
+            super(String.format("An error occurred because temporary file %s could not be found while running the GATK with more than one thread. Possible causes for this problem include: your system's open file handle limit is too small, your output or temp directories do not have sufficient space, or your system experienced a temporary instability. Your system administrator can help you resolve these problems.", file.getAbsolutePath()));
         }
     }
 
     public static class NotEnoughMemory extends UserException {
         public NotEnoughMemory() {
-            super(String.format("There was a failure because you did not provide enough memory to run this program.  See the -Xmx JVM argument to adjust the maximum heap size provided to Java"));
+            super(String.format("An error occurred because you did not provide enough memory to run this program. You can use the -Xmx argument (before the -jar argument) to adjust the maximum heap size provided to Java. Note that this is a JVM argument, not a GATK argument."));
         }
     }
 
     public static class ErrorWritingBamFile extends UserException {
         public ErrorWritingBamFile(String message) {
-            super(String.format("An error occurred when trying to write the BAM file.  Usually this happens when there is not enough space in the directory to which the data is being written (generally the temp directory) or when your system's open file handle limit is too small.  To tell Java to use a bigger/better file system use -Djava.io.tmpdir=X on the command line.  The exact error was %s", message));
+            super(String.format("An error occurred when trying to write the BAM file.  Usually this happens when there is not enough space in the directory to which the data is being written (generally the temp directory) or when your system's open file handle limit is too small.  Your system administrator can help you resolve these issues. If you know what temporary directory to use, you can specify it by adding -Djava.io.tmpdir=X to the command line (before the -jar argument), where X is the directory path. The exact error was %s", message));
         }
     }
 
     public static class NoSpaceOnDevice extends UserException {
         public NoSpaceOnDevice() {
-            super("There is no space left on the device, so writing failed");
+            super("Writing failed because there is no space left on the disk or hard drive. Please make some space or specify a different location for writing output files.");
         }
     }
 
     public static class CouldNotReadInputFile extends UserException {
         public CouldNotReadInputFile(String message, Exception e) {
-            super(String.format("Couldn't read file because %s caused by %s", message, getMessage(e)));
+            super(String.format("Could not read file because %s caused by %s", message, getMessage(e)));
         }
 
         public CouldNotReadInputFile(File file) {
-            super(String.format("Couldn't read file %s", file.getAbsolutePath()));
+            super(String.format("Could not read file %s", file.getAbsolutePath()));
         }
 
         public CouldNotReadInputFile(File file, String message) {
-            super(String.format("Couldn't read file %s because %s", file.getAbsolutePath(), message));
+            super(String.format("Could not read file %s because %s", file.getAbsolutePath(), message));
         }
 
         public CouldNotReadInputFile(String file, String message) {
-            super(String.format("Couldn't read file %s because %s", file, message));
+            super(String.format("Could not read file %s because %s", file, message));
         }
 
         public CouldNotReadInputFile(File file, String message, Exception e) {
-            super(String.format("Couldn't read file %s because %s with exception %s", file.getAbsolutePath(), message, getMessage(e)));
+            super(String.format("Could not read file %s because %s with exception %s", file.getAbsolutePath(), message, getMessage(e)));
         }
 
         public CouldNotReadInputFile(File file, Exception e) {
@@ -203,19 +203,19 @@ public class UserException extends ReviewedGATKException {
 
     public static class CouldNotCreateOutputFile extends UserException {
         public CouldNotCreateOutputFile(File file, String message, Exception e) {
-            super(String.format("Couldn't write file %s because %s with exception %s", file.getAbsolutePath(), message, getMessage(e)));
+            super(String.format("Could not write file %s because %s with exception %s", file.getAbsolutePath(), message, getMessage(e)));
         }
 
         public CouldNotCreateOutputFile(File file, String message) {
-            super(String.format("Couldn't write file %s because %s", file.getAbsolutePath(), message));
+            super(String.format("Could not write file %s because %s", file.getAbsolutePath(), message));
         }
 
         public CouldNotCreateOutputFile(String filename, String message, Exception e) {
-            super(String.format("Couldn't write file %s because %s with exception %s", filename, message, getMessage(e)));
+            super(String.format("Could not write file %s because %s with exception %s", filename, message, getMessage(e)));
         }
 
         public CouldNotCreateOutputFile(File file, Exception e) {
-            super(String.format("Couldn't write file %s because exception %s", file.getAbsolutePath(), getMessage(e)));
+            super(String.format("Could not write file %s because exception %s", file.getAbsolutePath(), getMessage(e)));
         }
 
         public CouldNotCreateOutputFile(String message, Exception e) {
@@ -225,20 +225,20 @@ public class UserException extends ReviewedGATKException {
 
     public static class MissortedBAM extends UserException {
         public MissortedBAM(SAMFileHeader.SortOrder order, File file, SAMFileHeader header) {
-            super(String.format("Missorted Input SAM/BAM/CRAM files: %s is must be sorted in %s order but order was: %s", file, order, header.getSortOrder()));
+            super(String.format("Missorted input SAM/BAM/CRAM files: %s must be sorted in %s order but order was: %s. Please see " + HelpConstants.forumPost("discussion/1317/collected-faqs-about-input-files-for-sequence-read-data-bam-cram") + "for more information.", file, order, header.getSortOrder()));
         }
 
         public MissortedBAM(SAMFileHeader.SortOrder order, String message) {
-            super(String.format("Missorted Input SAM/BAM/CRAM files: files are not sorted in %s order; %s", order, message));
+            super(String.format("Missorted input SAM/BAM/CRAM files: files are not sorted in %s order. Please see " + HelpConstants.forumPost("discussion/1317/collected-faqs-about-input-files-for-sequence-read-data-bam-cram") + "for more information. Error details: %s", order, message));
         }
 
         public MissortedBAM(SAMFileHeader.SortOrder order, SAMRecord read, String message) {
-            super(String.format("Missorted Input SAM/BAM/CRAM file %s: file sorted in %s order but %s is required; %s",
+            super(String.format("Missorted input SAM/BAM/CRAM file %s: file sorted in %s order but %s is required. Please see " + HelpConstants.forumPost("discussion/1317/collected-faqs-about-input-files-for-sequence-read-data-bam-cram") + "for more information. Error details: %s",
                     read.getFileSource().getReader(), read.getHeader().getSortOrder(), order, message));
         }
 
         public MissortedBAM(String message) {
-            super(String.format("Missorted Input SAM/BAM/CRAM files: %s", message));
+            super(String.format("Missorted input SAM/BAM/CRAM files. Please see " + HelpConstants.forumPost("discussion/1317/collected-faqs-about-input-files-for-sequence-read-data-bam-cram") + "for more information. Error details: %s", message));
         }
     }
 
@@ -252,7 +252,7 @@ public class UserException extends ReviewedGATKException {
         }
 
         public MalformedBAM(String source, String message) {
-            super(String.format("SAM/BAM/CRAM file %s is malformed: %s", source, message));
+            super(String.format("SAM/BAM/CRAM file %s is malformed. Please see " + HelpConstants.forumPost("discussion/1317/collected-faqs-about-input-files-for-sequence-read-data-bam-cram") + "for more information. Error details: %s", source, message));
         }
     }
 
@@ -262,7 +262,7 @@ public class UserException extends ReviewedGATKException {
         }
 
         public MisencodedBAM(String source, String message) {
-            super(String.format("SAM/BAM/CRAM file %s appears to be using the wrong encoding for quality scores: %s; please see the GATK --help documentation for options related to this error", source, message));
+            super(String.format("SAM/BAM/CRAM file %s appears to be using the wrong encoding for quality scores: %s. Please see https://www.broadinstitute.org/gatk/guide?id=6470 for more details and options related to this error.", source, message));
         }
     }
 
@@ -294,25 +294,25 @@ public class UserException extends ReviewedGATKException {
 
     public static class ReadMissingReadGroup extends MalformedBAM {
         public ReadMissingReadGroup(final SAMRecord read) {
-            super(read, String.format("Read %s is missing the read group (RG) tag, which is required by the GATK.  Please use " + HelpConstants.forumPost("discussion/59/companion-utilities-replacereadgroups to fix this problem"), read.getReadName()));
+            super(read, String.format("Read %s is missing the read group (RG) tag, which is required by the GATK. Please see " + HelpConstants.forumPost("discussion/59/companion-utilities-replacereadgroups to fix this problem"), read.getReadName()));
         }
     }
 
     public static class ReadHasUndefinedReadGroup extends MalformedBAM {
         public ReadHasUndefinedReadGroup(final SAMRecord read, final String rgID) {
-            super(read, String.format("Read %s uses a read group (%s) that is not defined in the BAM header, which is not valid.  Please use " + HelpConstants.forumPost("discussion/59/companion-utilities-replacereadgroups to fix this problem"), read.getReadName(), rgID));
+            super(read, String.format("Read %s uses a read group (%s) that is not defined in the BAM header, which is not valid.  Please see " + HelpConstants.forumPost("discussion/59/companion-utilities-replacereadgroups to fix this problem"), read.getReadName(), rgID));
         }
     }
 
     public static class VariantContextMissingRequiredField extends UserException {
         public VariantContextMissingRequiredField(String field, VariantContext vc) {
-            super(String.format("Variant at %s:%d is is missing the required field %s", vc.getChr(), vc.getStart(), field));
+            super(String.format("Variant at %s:%d is is missing the required field %s.", vc.getChr(), vc.getStart(), field));
         }
     }
 
     public static class MissortedFile extends UserException {
         public MissortedFile(File file, String message, Exception e) {
-            super(String.format("Missorted Input file: %s is must be sorted in coordinate order. %s and got error %s", file, message, getMessage(e)));
+            super(String.format("Missorted input file: %s is must be sorted in coordinate order. Please see " + HelpConstants.forumPost("discussion/1317/collected-faqs-about-input-files-for-sequence-read-data-bam-cram") + "for more information. Error details: %s and got error %s", file, message, getMessage(e)));
         }
     }
 
@@ -366,18 +366,14 @@ public class UserException extends ReviewedGATKException {
 
     public static class IncompatibleSequenceDictionaries extends UserException {
         public IncompatibleSequenceDictionaries(String message, String name1, SAMSequenceDictionary dict1, String name2, SAMSequenceDictionary dict2) {
-            super(String.format("Input files %s and %s have incompatible contigs: %s.\n  %s contigs = %s\n  %s contigs = %s",
+            super(String.format("Input files %s and %s have incompatible contigs. Please see " + HelpConstants.forumPost("discussion/63/input-files-have-incompatible-contigs") + "for more information. Error details: %s.\n  %s contigs = %s\n  %s contigs = %s",
                     name1, name2, message, name1, ReadUtils.prettyPrintSequenceRecords(dict1), name2, ReadUtils.prettyPrintSequenceRecords(dict2)));
         }
     }
 
     public static class LexicographicallySortedSequenceDictionary extends UserException {
         public LexicographicallySortedSequenceDictionary(String name, SAMSequenceDictionary dict) {
-            super(String.format("Lexicographically sorted human genome sequence detected in %s."
-                    + "\nFor safety's sake the GATK requires human contigs in karyotypic order: 1, 2, ..., 10, 11, ..., 20, 21, 22, X, Y with M either leading or trailing these contigs."
-                    + "\nThis is because all distributed GATK resources are sorted in karyotypic order, and your processing will fail when you need to use these files."
-                    + "\nYou can use the ReorderSam utility to fix this problem: " + HelpConstants.forumPost("discussion/58/companion-utilities-reordersam")
-                    + "\n  %s contigs = %s",
+            super(String.format("Lexicographically sorted human genome sequence detected in %s. Please see " + HelpConstants.forumPost("discussion/58/companion-utilities-reordersam") + "for more information. Error details: %s contigs = %s",
                     name, name, ReadUtils.prettyPrintSequenceRecords(dict)));
         }
     }
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/ArtificialFastaUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/ArtificialFastaUtils.java
index bf03ec625..cbf8c4259 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/ArtificialFastaUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/ArtificialFastaUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java
index b2f65585a..a456008a5 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -125,8 +125,9 @@ public class CachingIndexedFastaSequenceFile extends IndexedFastaSequenceFile {
      * @param fasta The file to open.
      * @param cacheSize the size of the cache to use in this CachingIndexedFastaReader, must be >= 0
      * @param preserveCase If true, we will keep the case of the underlying bases in the FASTA, otherwise everything is converted to upper case
+     * @param preserveIUPAC If true, we will keep the IUPAC bases in the FASTA, otherwise they are converted to Ns
      */
-    public CachingIndexedFastaSequenceFile(final File fasta, final long cacheSize, final boolean preserveCase, final boolean  preserveIUPAC) throws FileNotFoundException {
+    public CachingIndexedFastaSequenceFile(final File fasta, final long cacheSize, final boolean preserveCase, final boolean preserveIUPAC) throws FileNotFoundException {
         super(fasta);
         if ( cacheSize < 0 ) throw new IllegalArgumentException("cacheSize must be > 0");
         this.cacheSize = cacheSize;
@@ -172,6 +173,19 @@ public class CachingIndexedFastaSequenceFile extends IndexedFastaSequenceFile {
         this(fasta, DEFAULT_CACHE_SIZE, preserveCase, false);
     }
 
+    /**
+     * Open the given indexed fasta sequence file.  Throw an exception if the file cannot be opened.
+     *
+     * Looks for a index file for fasta on disk
+     *
+     * @param fasta The file to open.
+     * @param preserveCase If true, we will keep the case of the underlying bases in the FASTA, otherwise everything is converted to upper case
+     * @param preserveIUPAC If true, we will keep the IUPAC bases in the FASTA, otherwise they are converted to Ns
+     */
+    public CachingIndexedFastaSequenceFile(final File fasta, final boolean preserveCase, final boolean preserveIUPAC) throws FileNotFoundException {
+        this(fasta, DEFAULT_CACHE_SIZE, preserveCase, preserveIUPAC);
+    }
+
     /**
      * Create reference data source from fasta file, after performing several preliminary checks on the file.
      * This static utility was refactored from the constructor of ReferenceDataSource.
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/package-info.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/package-info.java
index ec94dac77..d0d7a6a56 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/package-info.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/package-info.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/file/FSLockWithShared.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/file/FSLockWithShared.java
index 934a022d8..813d697aa 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/file/FSLockWithShared.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/file/FSLockWithShared.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentCollection.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentCollection.java
index 67d55ffff..f3811333e 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentCollection.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentCollection.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentUtils.java
index 689fdf6f8..cbcce0b3d 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleList.java
index bf7b3ddc6..3d6c58113 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleList.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleList.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListPermutation.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListPermutation.java
index f5adb8a6e..a9423faa4 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListPermutation.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListPermutation.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListUtils.java
index 568535ade..249e270b3 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotype.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotype.java
index f836f4456..0a57040cd 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotype.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotype.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedAlleleList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedAlleleList.java
index d6530238b..8c3f04885 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedAlleleList.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedAlleleList.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedSampleList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedSampleList.java
index 7a92b4e24..95f2559aa 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedSampleList.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedSampleList.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAllele.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAllele.java
index 65c1fd058..f0a1d0be8 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAllele.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAllele.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMap.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMap.java
index 1256df558..c52278e9e 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMap.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMap.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoods.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoods.java
index e35eeb26d..a4c8ca90b 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoods.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoods.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleList.java
index 00d970824..a171edd98 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleList.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleList.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleListUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleListUtils.java
index 8abfafb11..5a6364355 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleListUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleListUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java
index 271102d64..5a2735d50 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/Haplotype.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/Haplotype.java
index 153a9a4b4..5b0ec5aae 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/Haplotype.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/Haplotype.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparator.java
index 8d1dfff73..d03f0b6bb 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparator.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparator.java
index 7818d3e8a..f294076e4 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparator.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparator.java
index 48180682b..241ac7294 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparator.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ApplicationDetails.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ApplicationDetails.java
index a0c7afbf1..56b39ebdf 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ApplicationDetails.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ApplicationDetails.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocletUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocletUtils.java
index 4b94e019d..ef154246d 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocletUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocletUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeature.java
index eed95b4a6..f00fcebaa 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeature.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeature.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureHandler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureHandler.java
index f95c12690..ce4ea5f88 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureHandler.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureHandler.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureObject.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureObject.java
index 45f0c147f..1d0186c6e 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureObject.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureObject.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ForumAPIUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ForumAPIUtils.java
index fbf65287a..4a7853b6e 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ForumAPIUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ForumAPIUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ForumDiscussion.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ForumDiscussion.java
index 7b95b500d..a1818dc0b 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ForumDiscussion.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ForumDiscussion.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocUtils.java
index 8ff7e58f3..75701d660 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocWorkUnit.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocWorkUnit.java
index 005d90038..89cdabbe1 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocWorkUnit.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocWorkUnit.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java
index afae1bb6e..015f2d306 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GSONArgument.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GSONArgument.java
index db214b945..d08115601 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GSONArgument.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GSONArgument.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GSONWorkUnit.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GSONWorkUnit.java
index c4481c0fc..e9f2d4acd 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GSONWorkUnit.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GSONWorkUnit.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GenericDocumentationHandler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GenericDocumentationHandler.java
index 09c862aa0..6dad68092 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GenericDocumentationHandler.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GenericDocumentationHandler.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java
index e84108973..707cc8f5e 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpFormatter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpFormatter.java
index a8d469302..5a55f2792 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpFormatter.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpFormatter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ResourceBundleExtractorDoclet.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ResourceBundleExtractorDoclet.java
index 3de5484aa..83af1d9f1 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ResourceBundleExtractorDoclet.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ResourceBundleExtractorDoclet.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/instrumentation/Sizeof.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/instrumentation/Sizeof.java
index a31c49857..c61d895f5 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/instrumentation/Sizeof.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/instrumentation/Sizeof.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalMergingRule.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalMergingRule.java
index 3e5eb4548..ba196a1b0 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalMergingRule.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalMergingRule.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalSetRule.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalSetRule.java
index e9d20eed3..424485adf 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalSetRule.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalSetRule.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java
index 15a11023e..e272eaca9 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/FileExtension.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/FileExtension.java
index e099a45fb..22ec9fe8c 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/FileExtension.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/FileExtension.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/HardThresholdingOutputStream.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/HardThresholdingOutputStream.java
index 1d041b66a..1a38ea089 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/HardThresholdingOutputStream.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/HardThresholdingOutputStream.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/IOUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/IOUtils.java
index 7defceac7..98e1e62dd 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/IOUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/IOUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/ReferenceBacked.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/ReferenceBacked.java
index 1cf0aea2b..bb5e80b7d 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/ReferenceBacked.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/ReferenceBacked.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/Resource.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/Resource.java
index c5a1cc4d8..9b8682a7f 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/Resource.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/Resource.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIterator.java
index b91eb2526..61d8b9140 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIterator.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIterator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIteratorAdapter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIteratorAdapter.java
index 7507e0897..82aa8660b 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIteratorAdapter.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIteratorAdapter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/PushbackIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/PushbackIterator.java
index c4b867b55..836a14929 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/PushbackIterator.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/PushbackIterator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/JNAUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/JNAUtils.java
index 0c14ffa1b..cebf5e4d6 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/JNAUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/JNAUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/LibC.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/LibC.java
index dd2d7e7b0..91baead01 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/LibC.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/LibC.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobInfo.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobInfo.java
index 1a99bfa40..ea5fd19d8 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobInfo.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobInfo.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobTemplate.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobTemplate.java
index b8add996a..1afd96cb0 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobTemplate.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobTemplate.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSession.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSession.java
index 67eaad7c9..0c0745c4f 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSession.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSession.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionFactory.java
index f4dbc98d4..d97be2b3a 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionFactory.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionFactory.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaa.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaa.java
index 3e5c4e45c..73ff9cb6e 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaa.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaa.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBat.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBat.java
index e66a40dab..299b331a7 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBat.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBat.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibLsf.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibLsf.java
index cc4721d79..9c8e563c6 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibLsf.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibLsf.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachine.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachine.java
index 733932d32..15b0e011e 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachine.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachine.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSDownsamplingInfo.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSDownsamplingInfo.java
index 01bf17d6b..efbf33dcc 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSDownsamplingInfo.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSDownsamplingInfo.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSPerformance.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSPerformance.java
index 206249559..aaa518d36 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSPerformance.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSPerformance.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIterator.java
index ecbaaf670..0d2893567 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIterator.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIterator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByState.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByState.java
index 2fe8222f4..c5bf32dd7 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByState.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByState.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManager.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManager.java
index 8e16c1771..af9953eaf 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManager.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManager.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/ReadStateManager.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/ReadStateManager.java
index 0014753f6..84912897b 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/ReadStateManager.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/ReadStateManager.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/SamplePartitioner.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/SamplePartitioner.java
index 46a88588f..9ff3998d3 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/SamplePartitioner.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/SamplePartitioner.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/EOFMarkedValue.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/EOFMarkedValue.java
index c5255e42e..b0c9d8fd6 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/EOFMarkedValue.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/EOFMarkedValue.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducer.java
index 3a67b4328..5676c75bd 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducer.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducer.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResult.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResult.java
index d6628a5bc..ab737f25c 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResult.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResult.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultsQueue.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultsQueue.java
index afeafb5e2..3d6682312 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultsQueue.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultsQueue.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSMapFunction.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSMapFunction.java
index dbd58b44a..31ad7e0aa 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSMapFunction.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSMapFunction.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSProgressFunction.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSProgressFunction.java
index 27d713ead..9b1c40626 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSProgressFunction.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSProgressFunction.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSReduceFunction.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSReduceFunction.java
index acb0a78bf..7f1027fce 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSReduceFunction.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSReduceFunction.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoScheduler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoScheduler.java
index 8b027214e..50139ddab 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoScheduler.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoScheduler.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/Reducer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/Reducer.java
index 41b612f0f..cb3263c5b 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/Reducer.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/Reducer.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/package-info.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/package-info.java
index 8a42dffda..25907ebd9 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/package-info.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/package-info.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/BatchPairHMM.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/BatchPairHMM.java
index 231156489..52b51c0cd 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/BatchPairHMM.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/BatchPairHMM.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/Log10PairHMM.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/Log10PairHMM.java
index 4d84fc5e6..4ee17c803 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/Log10PairHMM.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/Log10PairHMM.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/N2MemoryPairHMM.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/N2MemoryPairHMM.java
index 0e0ffb509..387171151 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/N2MemoryPairHMM.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/N2MemoryPairHMM.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java
index 6f7962d46..9f57779ae 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModel.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModel.java
index 1cd886581..6644c2058 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModel.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModel.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMReadyHaplotypes.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMReadyHaplotypes.java
index 8728bb5de..a6fcb2bed 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMReadyHaplotypes.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMReadyHaplotypes.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/MergingPileupElementIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/MergingPileupElementIterator.java
index d36d3551b..f078d76b0 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/MergingPileupElementIterator.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/MergingPileupElementIterator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElement.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElement.java
index 4db0927bf..c90669877 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElement.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElement.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementFilter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementFilter.java
index 7f8270984..93f39ab1e 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementFilter.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementFilter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementTracker.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementTracker.java
index 7d49fcce9..b2a7e84ce 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementTracker.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementTracker.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileup.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileup.java
index e4394f161..ad2108933 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileup.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileup.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupImpl.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupImpl.java
index 7c19b715b..5dd3c6a35 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupImpl.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupImpl.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeter.java
index f77ac0460..07d5075c8 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeter.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemon.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemon.java
index f1f48e6f4..850b9f19b 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemon.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemon.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterData.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterData.java
index 680403252..0b8e984eb 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterData.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterData.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/recalibration/EventType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/recalibration/EventType.java
index 84ab785fd..5a74f7245 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/recalibration/EventType.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/recalibration/EventType.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RODRecordListImpl.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RODRecordListImpl.java
index 79631a244..7b82ae236 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RODRecordListImpl.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RODRecordListImpl.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTracker.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTracker.java
index f4fd40f7d..680091662 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTracker.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTracker.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceDependentFeatureCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceDependentFeatureCodec.java
index d8cbbd6be..72f61b20b 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceDependentFeatureCodec.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceDependentFeatureCodec.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceOrderedDatum.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceOrderedDatum.java
index daa0a3cbe..c54f9c55f 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceOrderedDatum.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceOrderedDatum.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/SeekableRODIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/SeekableRODIterator.java
index 9eb4b34e9..0e0bfda98 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/SeekableRODIterator.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/SeekableRODIterator.java
@@ -1,28 +1,28 @@
-/*
-* Copyright (c) 2012 The Broad Institute
-* 
-* Permission is hereby granted, free of charge, to any person
-* obtaining a copy of this software and associated documentation
-* files (the "Software"), to deal in the Software without
-* restriction, including without limitation the rights to use,
-* copy, modify, merge, publish, distribute, sublicense, and/or sell
-* copies of the Software, and to permit persons to whom the
-* Software is furnished to do so, subject to the following
-* conditions:
-* 
-* The above copyright notice and this permission notice shall be
-* included in all copies or substantial portions of the Software.
-* 
-* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
-* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-*/
-
+/*
+* Copyright 2012-2015 Broad Institute, Inc.
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
 package org.broadinstitute.gatk.utils.refdata;
 
 import htsjdk.samtools.SAMSequenceDictionary;
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/VariantContextAdaptors.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/VariantContextAdaptors.java
index f21975cce..8b451780e 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/VariantContextAdaptors.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/VariantContextAdaptors.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/package-info.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/package-info.java
index bc444b784..ea24c2b5a 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/package-info.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/package-info.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManager.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManager.java
index d69a37476..a450fce8b 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManager.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManager.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/IndexDictionaryUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/IndexDictionaryUtils.java
index a0473c8a4..30bd8ec6f 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/IndexDictionaryUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/IndexDictionaryUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -102,7 +102,7 @@ public class IndexDictionaryUtils {
                                                        final SAMSequenceDictionary referenceDict,
                                                        final ValidationExclusion.TYPE validationExclusionType ) {
         // if the sequence dictionary is empty (as well as null which means it doesn't have a dictionary), skip validation
-        if (trackDict == null || trackDict.size() == 0)
+        if (trackDict == null || trackDict.isEmpty())
             logger.warn("Track " + trackName + " doesn't have a sequence dictionary built in, skipping dictionary validation");
         else {
             Set trackSequences = new TreeSet();
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrack.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrack.java
index ef8b27dcc..76f2046af 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrack.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrack.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -93,7 +93,7 @@ public class RMDTrack {
      * @param dict the sam sequence dictionary
      * @param codec the feature codec we use to decode this type
      */
-    public RMDTrack(Class type, String name, File file, AbstractFeatureReader reader, SAMSequenceDictionary dict, GenomeLocParser genomeLocParser, FeatureCodec codec) {
+    public RMDTrack(final Class type, final String name, final File file, final AbstractFeatureReader reader, final SAMSequenceDictionary dict, final GenomeLocParser genomeLocParser, final FeatureCodec codec) {
         this.type = type;
         this.name = name;
         this.file = file;
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilder.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilder.java
index 86a561ade..0b84c05a2 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilder.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilder.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -26,6 +26,9 @@
 package org.broadinstitute.gatk.utils.refdata.tracks;
 
 import htsjdk.samtools.SAMSequenceDictionary;
+import htsjdk.samtools.SAMSequenceRecord;
+import htsjdk.variant.vcf.VCFContigHeaderLine;
+import htsjdk.variant.vcf.VCFHeader;
 import org.apache.log4j.Logger;
 import htsjdk.tribble.AbstractFeatureReader;
 import htsjdk.tribble.FeatureCodec;
@@ -34,6 +37,7 @@ import htsjdk.tribble.TribbleException;
 import htsjdk.tribble.index.Index;
 import htsjdk.tribble.index.IndexFactory;
 import htsjdk.tribble.util.LittleEndianOutputStream;
+import org.broadinstitute.gatk.utils.SequenceDictionaryUtils;
 import org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptor;
 import org.broadinstitute.gatk.utils.commandline.Tags;
 import org.broadinstitute.gatk.utils.ValidationExclusion;
@@ -49,6 +53,8 @@ import org.broadinstitute.gatk.utils.instrumentation.Sizeof;
 import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
 import java.util.Map;
 
 
@@ -131,7 +137,7 @@ public class RMDTrackBuilder { // extends PluginManager {
      *
      * @return an instance of the track
      */
-    public RMDTrack createInstanceOfTrack(RMDTriplet fileDescriptor) {
+    public RMDTrack createInstanceOfTrack(final RMDTriplet fileDescriptor) {
         String name = fileDescriptor.getName();
         File inputFile = new File(fileDescriptor.getFile());
 
@@ -146,9 +152,43 @@ public class RMDTrackBuilder { // extends PluginManager {
         else
             pair = getFeatureSource(descriptor, name, inputFile, fileDescriptor.getStorageType());
         if (pair == null) throw new UserException.CouldNotReadInputFile(inputFile, "Unable to make the feature reader for input file");
+
+        validateVariantAgainstSequenceDictionary(name, descriptor.getName(), pair.first, pair.second);
+
         return new RMDTrack(descriptor.getCodecClass(), name, inputFile, pair.first, pair.second, genomeLocParser, createCodec(descriptor, name, inputFile));
     }
 
+    /**
+     * Validate the VCF dictionary against the sequence dictionary.
+     *
+     * @param name      the name of this specific track
+     * @param descriptorName  the name of the feature
+     * @param reader    the feature reader to use as the underlying data source
+     * @param dict      the sam sequence dictionary
+     */
+    private void validateVariantAgainstSequenceDictionary(final String name, final String descriptorName, final AbstractFeatureReader reader, final SAMSequenceDictionary dict ) throws UserException {
+        // only process if the variant is a VCF
+        if ( name.equals("variant") && descriptorName.equals("VCF") ){
+            if ( reader != null && dict != null && reader.getHeader() != null ){
+                final List contigs = ((VCFHeader) reader.getHeader()).getContigLines();
+                if (contigs != null) {
+                    // make the VCF dictionary from the contig header fields
+                    final List vcfContigRecords = new ArrayList();
+                    for (final VCFContigHeaderLine contig : contigs)
+                        vcfContigRecords.add(contig.getSAMSequenceRecord());
+
+                    // have VCF contig fields so can make a dictionary and compare it to the sequence dictionary
+                    if (!vcfContigRecords.isEmpty()) {
+                        final SAMSequenceDictionary vcfDictionary = new SAMSequenceDictionary(vcfContigRecords);
+                        final SAMSequenceDictionary sequenceDictionary = new SAMSequenceDictionary(dict.getSequences());
+
+                        SequenceDictionaryUtils.validateDictionaries(logger, validationExclusionType, name, vcfDictionary, "sequence", sequenceDictionary, false, null);
+                    }
+                }
+            }
+        }
+    }
+
     /**
      * Convenience method simplifying track creation.  Assume unnamed track based on a file rather than a stream.
      * @param codecClass Type of Tribble codec class to build.
@@ -228,7 +268,7 @@ public class RMDTrackBuilder { // extends PluginManager {
                 sequenceDictionary = IndexDictionaryUtils.getSequenceDictionaryFromProperties(index);
 
                 // if we don't have a dictionary in the Tribble file, and we've set a dictionary for this builder, set it in the file if they match
-                if (sequenceDictionary.size() == 0 && dict != null) {
+                if (sequenceDictionary.isEmpty() && dict != null) {
                     validateAndUpdateIndexSequenceDictionary(inputFile, index, dict);
 
                     if ( ! disableAutoIndexCreation ) {
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIterator.java
index 013a6c2ad..743ee95ae 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIterator.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIterator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIterator.java
index 73ebf3cc8..4f50460a5 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIterator.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIterator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/GATKFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/GATKFeature.java
index 428055f0b..4f947d119 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/GATKFeature.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/GATKFeature.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/LocationAwareSeekableRODIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/LocationAwareSeekableRODIterator.java
index 42fa9ffb1..0bee072c2 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/LocationAwareSeekableRODIterator.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/LocationAwareSeekableRODIterator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RMDTriplet.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RMDTriplet.java
index 3c79fc5fd..dc35f7e01 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RMDTriplet.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RMDTriplet.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RODRecordList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RODRecordList.java
index 025835275..4bba78dc9 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RODRecordList.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RODRecordList.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReport.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReport.java
index 056581351..70a7c6a33 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReport.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReport.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumn.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumn.java
index d672c1ba8..0dbeb3b8e 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumn.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumn.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumnFormat.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumnFormat.java
index 97c012a5a..6249f4f21 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumnFormat.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumnFormat.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportDataType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportDataType.java
index d522dff35..a6e640feb 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportDataType.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportDataType.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportGatherer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportGatherer.java
index 359460bd0..f7f5196b3 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportGatherer.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportGatherer.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportTable.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportTable.java
index 018d05500..e40c3f37a 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportTable.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportTable.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportVersion.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportVersion.java
index e87e107c0..cf985d5e5 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportVersion.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportVersion.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/CapturedStreamOutput.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/CapturedStreamOutput.java
index 0166e9847..ee6dfbd96 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/CapturedStreamOutput.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/CapturedStreamOutput.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/InputStreamSettings.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/InputStreamSettings.java
index 56bfabde5..2fdc5bee2 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/InputStreamSettings.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/InputStreamSettings.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/OutputStreamSettings.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/OutputStreamSettings.java
index bc9229107..25375edf1 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/OutputStreamSettings.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/OutputStreamSettings.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessController.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessController.java
index 3955817ba..682c25800 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessController.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessController.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessOutput.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessOutput.java
index 9276de76f..71d90eb31 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessOutput.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessOutput.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessSettings.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessSettings.java
index 7027b9d25..52d2f0688 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessSettings.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessSettings.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtils.java
index 7a982dda5..241ebd212 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamLocation.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamLocation.java
index 37d66f097..bd4298967 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamLocation.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamLocation.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamOutput.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamOutput.java
index 9ce039ee0..e4a8b571d 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamOutput.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamOutput.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartComparator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartComparator.java
index 7e926d5d3..8aac52dfa 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartComparator.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartComparator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartWithNoTiesComparator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartWithNoTiesComparator.java
index db3f458f8..b64bbaccf 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartWithNoTiesComparator.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartWithNoTiesComparator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentUtils.java
index 7835b2190..04e3ccbe5 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilder.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilder.java
index 8233252d7..371e0f326 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilder.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilder.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialGATKSAMFileWriter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialGATKSAMFileWriter.java
index 99fd76213..d430ab7c4 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialGATKSAMFileWriter.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialGATKSAMFileWriter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialMultiSampleReadStream.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialMultiSampleReadStream.java
index 010759ecf..3d7c3c784 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialMultiSampleReadStream.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialMultiSampleReadStream.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIterator.java
index e82355da9..99b317446 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIterator.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIterator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileReader.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileReader.java
index c0390a3a9..74b953188 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileReader.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileReader.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -26,14 +26,12 @@
 package org.broadinstitute.gatk.utils.sam;
 
 import htsjdk.samtools.*;
-import htsjdk.samtools.cram.build.CramIO;
 import org.broadinstitute.gatk.utils.GenomeLoc;
 import org.broadinstitute.gatk.utils.GenomeLocParser;
 import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.io.ByteArrayInputStream;
 import java.io.InputStream;
-import java.io.UnsupportedEncodingException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Iterator;
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMIterator.java
index e4bdfbc23..aa035233c 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMIterator.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMIterator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIterator.java
index fe7f7b0e7..e4f8b799a 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIterator.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIterator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtils.java
index bad7ef643..2d192d32d 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStream.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStream.java
index 93d27f7d5..d3eb73dca 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStream.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStream.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java
index 196fa7182..3c7b2aff8 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/CigarUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/CigarUtils.java
index 06e0653f5..3017b56f2 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/CigarUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/CigarUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMFileWriter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMFileWriter.java
index 7949dd49e..e04787f22 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMFileWriter.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMFileWriter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMReadGroupRecord.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMReadGroupRecord.java
index 6af90597d..6d85d7d0b 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMReadGroupRecord.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMReadGroupRecord.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java
index 968ae0b89..8a9f0448c 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordIterator.java
index 314facdd5..1560dce92 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordIterator.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordIterator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUnclippedStartWithNoTiesComparator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUnclippedStartWithNoTiesComparator.java
index 9d2a3912e..d57238ef6 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUnclippedStartWithNoTiesComparator.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUnclippedStartWithNoTiesComparator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java
index ce56a329f..b3d945ec0 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderBuilder.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderBuilder.java
index 19d2315f4..6b72d0c08 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderBuilder.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderBuilder.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderID.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderID.java
index 4b93c3b7e..1338f7cda 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderID.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderID.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SimplifyingSAMFileWriter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SimplifyingSAMFileWriter.java
index 421461996..c431528b1 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SimplifyingSAMFileWriter.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SimplifyingSAMFileWriter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/package-info.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/package-info.java
index ee2bcec57..c41b5bfeb 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/package-info.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/package-info.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java
index 666ca8bab..66b897054 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/Parameters.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/Parameters.java
index 46cb8bee1..f423a1ad1 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/Parameters.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/Parameters.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignment.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignment.java
index aa38c064d..b750b35ca 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignment.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignment.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentMain.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentMain.java
index 3d2ddd1aa..40e45d93c 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentMain.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentMain.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWParameterSet.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWParameterSet.java
index 7226a98f5..a5152735e 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWParameterSet.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWParameterSet.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWaterman.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWaterman.java
index c4184e16e..a913c5abe 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWaterman.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWaterman.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/ListFileUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/ListFileUtils.java
index a2d796f52..91db56bf3 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/ListFileUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/ListFileUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/TextFormattingUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/TextFormattingUtils.java
index b4409a919..044a65783 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/TextFormattingUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/TextFormattingUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/XReadLines.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/XReadLines.java
index f41015612..267ab5f0c 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/XReadLines.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/XReadLines.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactory.java
index 72820832d..97d280a64 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactory.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactory.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/NamedThreadFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/NamedThreadFactory.java
index 6c840869a..ceb238052 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/NamedThreadFactory.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/NamedThreadFactory.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadEfficiencyMonitor.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadEfficiencyMonitor.java
index cee91a435..8d9bddd17 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadEfficiencyMonitor.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadEfficiencyMonitor.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadLocalArray.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadLocalArray.java
index b8dea067b..61d4c0d4d 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadLocalArray.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadLocalArray.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitor.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitor.java
index 92618709e..9af1b366b 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitor.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitor.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/package-info.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/package-info.java
index 83093ba98..6865d11ac 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/package-info.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/package-info.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/ChromosomeCountConstants.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/ChromosomeCountConstants.java
index 72ed4e4f6..8b1aa1d44 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/ChromosomeCountConstants.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/ChromosomeCountConstants.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFConstants.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFConstants.java
index a7e9bf0de..ff04c2971 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFConstants.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFConstants.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -35,6 +35,9 @@ import htsjdk.variant.variantcontext.Allele;
 public final class GATKVCFConstants {
 
     //INFO keys
+    public static final String RAW_RMS_MAPPING_QUALITY_KEY =        "RAW_MQ";
+    public static final String AS_RMS_MAPPING_QUALITY_KEY =         "AS_MQ";
+    public static final String AS_RAW_RMS_MAPPING_QUALITY_KEY =     "AS_RAW_MQ";
     public static final String ALLELE_BALANCE_HET_KEY =             "ABHet";
     public static final String ALLELE_BALANCE_HOM_KEY =             "ABHom";
     public static final String ORIGINAL_AC_KEY =                    "AC_Orig"; //SelectVariants
@@ -45,6 +48,8 @@ public final class GATKVCFConstants {
     public static final String BEAGLE_AN_COMP_KEY =                 "ANH"; //BeagleOutputToVCF
     public static final String BASE_COUNTS_KEY =                    "BaseCounts";
     public static final String BASE_QUAL_RANK_SUM_KEY =             "BaseQRankSum";
+    public static final String AS_BASE_QUAL_RANK_SUM_KEY =          "AS_BaseQRankSum";
+    public static final String AS_RAW_BASE_QUAL_RANK_SUM_KEY =      "AS_RAW_BaseQRankSum";
     public static final String GENOTYPE_AND_VALIDATE_STATUS_KEY =   "callStatus";
     public static final String CLIPPING_RANK_SUM_KEY =              "ClippingRankSum";
     public static final String CULPRIT_KEY =                        "culprit";
@@ -55,6 +60,9 @@ public final class GATKVCFConstants {
     public static final String EVENT_DISTANCE_MAX_KEY =             "MAX_ED"; //M2
     public static final String EVENT_DISTANCE_MIN_KEY =             "MIN_ED"; //M2
     public static final String FISHER_STRAND_KEY =                  "FS";
+    public static final String AS_FISHER_STRAND_KEY =               "AS_FS";
+    public static final String FRACTION_INFORMATIVE_READS_KEY =     "FractionInformativeReads";
+    public static final String AS_SB_TABLE_KEY =                    "AS_SB_TABLE";
     public static final String GC_CONTENT_KEY =                     "GC";
     public static final String GQ_MEAN_KEY =                        "GQ_MEAN";
     public static final String GQ_STDEV_KEY =                       "GQ_STDDEV";
@@ -66,6 +74,9 @@ public final class GATKVCFConstants {
     public static final String AVG_INTERVAL_DP_KEY =                "IDP"; //DiagnoseTargets
     public static final String INTERVAL_GC_CONTENT_KEY =            "IGC";
     public static final String INBREEDING_COEFFICIENT_KEY =         "InbreedingCoeff";
+    public static final String AS_INBREEDING_COEFFICIENT_KEY =      "AS_InbreedingCoeff";
+    public static final String EXCESS_HET_KEY =                     "ExcessHet";
+    public static final String AS_HETEROZYGOSITY_KEY =              "AS_InbreedingCoeff";
     public static final String LIKELIHOOD_RANK_SUM_KEY =            "LikelihoodRankSum";
     public static final String LO_CONF_DENOVO_KEY =                 "loConfDeNovo";
     public static final String LOW_MQ_KEY =                         "LowMQ";
@@ -74,6 +85,9 @@ public final class GATKVCFConstants {
     public static final String MLE_PER_SAMPLE_ALLELE_COUNT_KEY =    "MLPSAC";
     public static final String MLE_PER_SAMPLE_ALLELE_FRACTION_KEY = "MLPSAF";
     public static final String MAP_QUAL_RANK_SUM_KEY =              "MQRankSum";
+    public static final String RAW_MAP_QUAL_RANK_SUM_KEY =          "RAW_MQRankSum";
+    public static final String AS_MAP_QUAL_RANK_SUM_KEY =           "AS_MQRankSum";
+    public static final String AS_RAW_MAP_QUAL_RANK_SUM_KEY =       "AS_RAW_MQRankSum";
     public static final String MENDEL_VIOLATION_LR_KEY =            "MVLR";
     public static final String NOCALL_CHROM_KEY =                   "NCC";
     public static final String NUMBER_OF_DISCOVERED_ALLELES_KEY =   "NDA";
@@ -90,13 +104,18 @@ public final class GATKVCFConstants {
     public static final String PANEL_OF_NORMALS_COUNT_KEY =         "PON"; //M2
     public static final String POSITIVE_LABEL_KEY =                 "POSITIVE_TRAIN_SITE";
     public static final String QUAL_BY_DEPTH_KEY =                  "QD";
+    public static final String AS_QUAL_BY_DEPTH_KEY =               "AS_QD";
+    public static final String AS_QUAL_KEY =                        "AS_QUAL";
     public static final String BEAGLE_R2_KEY =                      "R2"; //BeagleOutputToVCF
+    public static final String AS_READ_POS_RANK_SUM_KEY =           "AS_ReadPosRankSum";
+    public static final String AS_RAW_READ_POS_RANK_SUM_KEY =       "AS_RAW_ReadPosRankSum";
     public static final String READ_POS_RANK_SUM_KEY =              "ReadPosRankSum";
     public static final String REFSAMPLE_DEPTH_KEY =                "REFDEPTH";
     public static final String REPEATS_PER_ALLELE_KEY =             "RPA";
     public static final String REPEAT_UNIT_KEY =                    "RU";
     public static final String SAMPLE_LIST_KEY =                    "Samples";
     public static final String STRAND_ODDS_RATIO_KEY =              "SOR";
+    public static final String AS_STRAND_ODDS_RATIO_KEY =           "AS_SOR";
     public static final String STR_PRESENT_KEY =                    "STR";
     public static final String TRANSMISSION_DISEQUILIBRIUM_KEY =    "TDT";
     public static final String TUMOR_LOD_KEY =                      "TLOD"; //M2
@@ -111,6 +130,7 @@ public final class GATKVCFConstants {
     //FORMAT keys
     public static final String ALLELE_BALANCE_KEY =                 "AB";
     public static final String ALLELE_FRACTION_KEY =                "AF"; //M2
+    public static final String BASE_COUNTS_BY_SAMPLE_KEY =          "BCS";
     public static final String PL_FOR_ALL_SNP_ALLELES_KEY =         "APL";
     public static final String RBP_HAPLOTYPE_KEY =                  "HP"; //ReadBackedPhasing
     public static final String AVG_INTERVAL_DP_BY_SAMPLE_KEY =      "IDP"; //DiagnoseTargets
@@ -144,6 +164,7 @@ public final class GATKVCFConstants {
     public static final String PON_FILTER_NAME =                              "panel_of_normals"; //M2
     public static final String STR_CONTRACTION_FILTER_NAME =                  "str_contraction"; //M2
     public static final String TUMOR_LOD_FILTER_NAME =                        "t_lod_fstar"; //M2
+    public static final String TRIALLELIC_SITE_FILTER_NAME =                  "triallelic_site"; //M2
 
     // Symbolic alleles
     public final static String SYMBOLIC_ALLELE_DEFINITION_HEADER_TAG = "ALT";
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFHeaderLines.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFHeaderLines.java
index fff7ea5f1..f0fa0724c 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFHeaderLines.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFHeaderLines.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -27,9 +27,10 @@ package org.broadinstitute.gatk.utils.variant;
 
 import htsjdk.variant.vcf.*;
 
-import static org.broadinstitute.gatk.utils.variant.GATKVCFConstants.*;
+import java.util.HashMap;
+import java.util.Map;
 
-import java.util.*;
+import static org.broadinstitute.gatk.utils.variant.GATKVCFConstants.*;
 
 /**
  * This class contains the VCFHeaderLine definitions for the annotation keys in GATKVCFConstants.
@@ -70,8 +71,10 @@ public class GATKVCFHeaderLines {
         addFilterLine(new VCFFilterHeaderLine(GATKVCFConstants.PON_FILTER_NAME, "Seen in at least 2 samples in the panel of normals"));
         addFilterLine(new VCFFilterHeaderLine(GATKVCFConstants.TUMOR_LOD_FILTER_NAME, "Tumor does not meet likelihood threshold"));
         addFilterLine(new VCFFilterHeaderLine(GATKVCFConstants.STR_CONTRACTION_FILTER_NAME, "Site filtered due to contraction of short tandem repeat region"));
+        addFilterLine(new VCFFilterHeaderLine(GATKVCFConstants.TRIALLELIC_SITE_FILTER_NAME, "Site filtered because more than two alt alleles pass tumor LOD"));
 
         addFormatLine(new VCFFormatHeaderLine(ALLELE_BALANCE_KEY, 1, VCFHeaderLineType.Float, "Allele balance for each het genotype"));
+        addFormatLine(new VCFFormatHeaderLine(BASE_COUNTS_BY_SAMPLE_KEY, 4, VCFHeaderLineType.Integer, "Counts of each base by sample"));
         addFormatLine(new VCFFormatHeaderLine(MAPPING_QUALITY_ZERO_BY_SAMPLE_KEY, 1, VCFHeaderLineType.Integer, "Number of Mapping Quality Zero Reads per sample"));
         addFormatLine(new VCFFormatHeaderLine(MLE_PER_SAMPLE_ALLELE_COUNT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Maximum likelihood expectation (MLE) for the alternate allele count, in the same order as listed, for each individual sample"));
         addFormatLine(new VCFFormatHeaderLine(MLE_PER_SAMPLE_ALLELE_FRACTION_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Maximum likelihood expectation (MLE) for the alternate allele fraction, in the same order as listed, for each individual sample"));
@@ -82,6 +85,7 @@ public class GATKVCFHeaderLines {
         addFormatLine(new VCFFormatHeaderLine(PL_FOR_ALL_SNP_ALLELES_KEY, 10, VCFHeaderLineType.Integer, "Phred-scaled genotype likelihoods for all 4 possible bases regardless of whether there is statistical evidence for them. Ordering is always PL for AA AC CC GA GC GG TA TC TG TT."));
         addFormatLine(new VCFFormatHeaderLine(HAPLOTYPE_CALLER_PHASING_ID_KEY, 1, VCFHeaderLineType.String, "Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"));
         addFormatLine(new VCFFormatHeaderLine(HAPLOTYPE_CALLER_PHASING_GT_KEY, 1, VCFHeaderLineType.String, "Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another"));
+
         addFormatLine(new VCFFormatHeaderLine(MIN_DP_FORMAT_KEY, 1, VCFHeaderLineType.Integer, "Minimum DP observed within the GVCF block"));
         addFormatLine(new VCFFormatHeaderLine(REFERENCE_GENOTYPE_QUALITY, 1, VCFHeaderLineType.Integer, "Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)"));
         addFormatLine(new VCFFormatHeaderLine(TRANSMISSION_PROBABILITY_KEY, 1, VCFHeaderLineType.Integer, "Phred score of the genotype combination and phase given that the genotypes are correct"));
@@ -113,8 +117,12 @@ public class GATKVCFHeaderLines {
         addInfoLine(new VCFInfoHeaderLine(LOW_MQ_KEY, 3, VCFHeaderLineType.Float, "3-tuple: ,,"));
         addInfoLine(new VCFInfoHeaderLine(N_BASE_COUNT_KEY, 1, VCFHeaderLineType.Float, "Percentage of N bases in the pileup"));
         addInfoLine(new VCFInfoHeaderLine(BASE_QUAL_RANK_SUM_KEY, 1, VCFHeaderLineType.Float, "Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"));
+        addInfoLine(new VCFInfoHeaderLine(AS_BASE_QUAL_RANK_SUM_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "allele specific Z-score from Wilcoxon rank sum test of each Alt Vs. Ref base qualities"));
+        addInfoLine(new VCFInfoHeaderLine(AS_RAW_BASE_QUAL_RANK_SUM_KEY, 1, VCFHeaderLineType.String, "raw data for allele specific rank sum test of base qualities"));
         addInfoLine(new VCFInfoHeaderLine(CLIPPING_RANK_SUM_KEY, 1, VCFHeaderLineType.Float, "Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases"));
         addInfoLine(new VCFInfoHeaderLine(FISHER_STRAND_KEY, 1, VCFHeaderLineType.Float, "Phred-scaled p-value using Fisher's exact test to detect strand bias"));
+        addInfoLine(new VCFInfoHeaderLine(AS_FISHER_STRAND_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "allele specific phred-scaled p-value using Fisher's exact test to detect strand bias of each alt allele"));
+        addInfoLine(new VCFInfoHeaderLine(AS_SB_TABLE_KEY, 1, VCFHeaderLineType.String, "Allele-specific forward/reverse read counts for strand bias tests"));
         addInfoLine(new VCFInfoHeaderLine(GC_CONTENT_KEY, 1, VCFHeaderLineType.Float, "GC content around the variant (see docs for window size details)"));
         addInfoLine(new VCFInfoHeaderLine(NOCALL_CHROM_KEY, 1, VCFHeaderLineType.Integer, "Number of no-called samples"));
         addInfoLine(new VCFInfoHeaderLine(GQ_MEAN_KEY, 1, VCFHeaderLineType.Float, "Mean of all GQ values"));
@@ -123,16 +131,33 @@ public class GATKVCFHeaderLines {
         addInfoLine(new VCFInfoHeaderLine(HARDY_WEINBERG_KEY, 1, VCFHeaderLineType.Float, "Phred-scaled p-value for Hardy-Weinberg violation"));
         addInfoLine(new VCFInfoHeaderLine(HOMOPOLYMER_RUN_KEY, 1, VCFHeaderLineType.Integer, "Largest Contiguous Homopolymer Run of Variant Allele In Either Direction"));
         addInfoLine(new VCFInfoHeaderLine(INBREEDING_COEFFICIENT_KEY, 1, VCFHeaderLineType.Float, "Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"));
+        addInfoLine(new VCFInfoHeaderLine(AS_INBREEDING_COEFFICIENT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele-specific inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"));
+        addInfoLine(new VCFInfoHeaderLine(EXCESS_HET_KEY, 1, VCFHeaderLineType.Float, "Phred-scaled p-value for exact test of excess heterozygosity"));
+        addInfoLine(new VCFInfoHeaderLine(AS_HETEROZYGOSITY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "allele specific heterozygosity as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation; relate to inbreeding coefficient"));
         addInfoLine(new VCFInfoHeaderLine(LIKELIHOOD_RANK_SUM_KEY, 1, VCFHeaderLineType.Float, "Z-score from Wilcoxon rank sum test of Alt Vs. Ref haplotype likelihoods"));
         addInfoLine(new VCFInfoHeaderLine(MAP_QUAL_RANK_SUM_KEY, 1, VCFHeaderLineType.Float, "Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"));
+        addInfoLine(new VCFInfoHeaderLine(AS_MAP_QUAL_RANK_SUM_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "allele specific Z-score From Wilcoxon rank sum test of each Alt vs. Ref read mapping qualities"));
+        addInfoLine(new VCFInfoHeaderLine(RAW_RMS_MAPPING_QUALITY_KEY, 1, VCFHeaderLineType.Float, "Raw data for RMS Mapping Quality"));
+        addInfoLine(new VCFInfoHeaderLine(AS_RAW_RMS_MAPPING_QUALITY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele-specfic raw data for RMS Mapping Quality"));
+        addInfoLine(new VCFInfoHeaderLine(AS_RMS_MAPPING_QUALITY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele-specific RMS Mapping Quality"));
+        addInfoLine(new VCFInfoHeaderLine(RAW_MAP_QUAL_RANK_SUM_KEY, 1, VCFHeaderLineType.Float, "Raw data for Mapping Quality Rank Sum"));
+        addInfoLine(new VCFInfoHeaderLine(AS_RAW_MAP_QUAL_RANK_SUM_KEY, 1, VCFHeaderLineType.String, "Allele-specfic raw data for Mapping Quality Rank Sum"));
+        addInfoLine(new VCFInfoHeaderLine(AS_MAP_QUAL_RANK_SUM_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele-specific Mapping Quality Rank Sum"));
+        addInfoLine(new VCFInfoHeaderLine(FRACTION_INFORMATIVE_READS_KEY, 1, VCFHeaderLineType.Float, "The fraction of informative reads out of the total reads"));
+
         addInfoLine(new VCFInfoHeaderLine(MENDEL_VIOLATION_LR_KEY, 1, VCFHeaderLineType.Float, "Mendelian violation likelihood ratio: L[MV] - L[No MV]"));
         addInfoLine(new VCFInfoHeaderLine(HI_CONF_DENOVO_KEY, 1, VCFHeaderLineType.String, "High confidence possible de novo mutation (GQ >= 20 for all trio members)=[comma-delimited list of child samples]"));
         addInfoLine(new VCFInfoHeaderLine(LO_CONF_DENOVO_KEY, 1, VCFHeaderLineType.String, "Low confidence possible de novo mutation (GQ >= 10 for child, GQ > 0 for parents)=[comma-delimited list of child samples]"));
         addInfoLine(new VCFInfoHeaderLine(QUAL_BY_DEPTH_KEY, 1, VCFHeaderLineType.Float, "Variant Confidence/Quality by Depth"));
+        addInfoLine(new VCFInfoHeaderLine(AS_QUAL_BY_DEPTH_KEY, 1, VCFHeaderLineType.Float, "Allele-specific Variant Confidence/Quality by Depth"));
+        addInfoLine(new VCFInfoHeaderLine(AS_QUAL_KEY, 1, VCFHeaderLineType.Float, "Allele-specific Variant Qual Score"));
         addInfoLine(new VCFInfoHeaderLine(READ_POS_RANK_SUM_KEY, 1, VCFHeaderLineType.Float, "Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"));
+        addInfoLine(new VCFInfoHeaderLine(AS_READ_POS_RANK_SUM_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "allele specific Z-score from Wilcoxon rank sum test of each Alt vs. Ref read position bias"));
+        addInfoLine(new VCFInfoHeaderLine(AS_RAW_READ_POS_RANK_SUM_KEY, 1, VCFHeaderLineType.String, "allele specific raw data for rank sum test of read position bias"));
         addInfoLine(new VCFInfoHeaderLine(SAMPLE_LIST_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "List of polymorphic samples"));
         addInfoLine(new VCFInfoHeaderLine(SPANNING_DELETIONS_KEY, 1, VCFHeaderLineType.Float, "Fraction of Reads Containing Spanning Deletions"));
         addInfoLine(new VCFInfoHeaderLine(STRAND_ODDS_RATIO_KEY, 1, VCFHeaderLineType.Float, "Symmetric Odds Ratio of 2x2 contingency table to detect strand bias"));
+        addInfoLine(new VCFInfoHeaderLine(AS_STRAND_ODDS_RATIO_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele specific strand Odds Ratio of 2x|Alts| contingency table to detect allele specific strand bias"));
         addInfoLine(new VCFInfoHeaderLine(STR_PRESENT_KEY, 0, VCFHeaderLineType.Flag, "Variant is a short tandem repeat"));
         addInfoLine(new VCFInfoHeaderLine(REPEAT_UNIT_KEY, 1, VCFHeaderLineType.String, "Tandem repeat unit (bases)"));
         addInfoLine(new VCFInfoHeaderLine(REPEATS_PER_ALLELE_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "Number of times tandem repeat unit is repeated, for each allele (including reference)"));
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFIndexType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFIndexType.java
index f142da261..0ca4a341f 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFIndexType.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFIndexType.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java
index 445828f58..520582a47 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -35,6 +35,7 @@ import org.apache.commons.lang.ArrayUtils;
 import org.apache.log4j.Logger;
 import org.broadinstitute.gatk.utils.*;
 import org.broadinstitute.gatk.utils.collections.Pair;
+import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
 
 import java.io.Serializable;
 import java.util.*;
@@ -148,7 +149,7 @@ public class GATKVariantContextUtils {
     }
 
     /**
-     * Calculates the total ploidy of a variant context as the sum of all plodies across genotypes.
+     * Calculates the total ploidy of a variant context as the sum of all ploidies across genotypes.
      * @param vc the target variant context.
      * @param defaultPloidy the default ploidy to be assume when there is no ploidy information for a genotype.
      * @return never {@code null}.
@@ -410,6 +411,15 @@ public class GATKVariantContextUtils {
         return new Pair, byte[]>(lengths,repeatUnit);
     }
 
+    /**
+     *
+     * @param refBases
+     * @param altBases
+     * @param remainingRefContext
+     * @return
+     * @deprecated there is still no alternative for this method but eventually there needs to be one implemented in TandemRepeatFinder (protected for now).
+     */
+    @Deprecated
     public static Pair getNumTandemRepeatUnits(final byte[] refBases, final byte[] altBases, final byte[] remainingRefContext) {
          /* we can't exactly apply same logic as in basesAreRepeated() to compute tandem unit and number of repeated units.
            Consider case where ref =ATATAT and we have an insertion of ATAT. Natural description is (AT)3 -> (AT)2.
@@ -474,18 +484,23 @@ public class GATKVariantContextUtils {
      * @param testString             String to test
      * @oaram lookForward            Look for repetitions forward (at beginning of string) or backward (at end of string)
      * @return                       Number of repetitions (0 if testString is not a concatenation of n repeatUnit's
+     * @deprecated Move to use TandemRepeatFinder in protected (move to public if needed).
      */
+    @Deprecated
     public static int findNumberOfRepetitions(byte[] repeatUnit, byte[] testString, boolean lookForward) {
+
+        if (repeatUnit == null) throw new IllegalArgumentException("the repeat unit cannot be null");
+        if (testString == null) throw new IllegalArgumentException("the test string cannot be null");
+
         int numRepeats = 0;
         if (lookForward) {
             // look forward on the test string
             for (int start = 0; start < testString.length; start += repeatUnit.length) {
-                int end = start + repeatUnit.length;
-                byte[] unit = Arrays.copyOfRange(testString,start, end);
-                if(Arrays.equals(unit,repeatUnit))
-                    numRepeats++;
-                else
+                final int end = start + repeatUnit.length;
+                final byte[] unit = Arrays.copyOfRange(testString,start, end);
+                if (!Arrays.equals(unit,repeatUnit))
                     break;
+                numRepeats++;
             }
             return numRepeats;
         }
@@ -493,8 +508,8 @@ public class GATKVariantContextUtils {
         // look backward. For example, if repeatUnit = AT and testString = GATAT, number of repeat units is still 2
         // look forward on the test string
         for (int start = testString.length - repeatUnit.length; start >= 0; start -= repeatUnit.length) {
-            int end = start + repeatUnit.length;
-            byte[] unit = Arrays.copyOfRange(testString,start, end);
+            final int end = start + repeatUnit.length;
+            final byte[] unit = Arrays.copyOfRange(testString, start, end);
             if(Arrays.equals(unit,repeatUnit))
                 numRepeats++;
             else
@@ -584,27 +599,35 @@ public class GATKVariantContextUtils {
     public static GenotypesContext subsetDiploidAlleles(final VariantContext vc,
                                                         final List allelesToUse,
                                                         final GenotypeAssignmentMethod assignGenotypes) {
+        if ( vc == null ) throw new IllegalArgumentException("the VariantContext cannot be null");
+        if ( allelesToUse == null ) throw new IllegalArgumentException("the alleles to use cannot be null");
         if ( allelesToUse.get(0).isNonReference() ) throw new IllegalArgumentException("First allele must be the reference allele");
         if ( allelesToUse.size() == 1 ) throw new IllegalArgumentException("Cannot subset to only 1 alt allele");
 
         // optimization: if no input genotypes, just exit
         if (vc.getGenotypes().isEmpty()) return GenotypesContext.create();
 
-        // we need to determine which of the alternate alleles (and hence the likelihoods) to use and carry forward
-        final List likelihoodIndexesToUse = determineLikelihoodIndexesToUse(vc, allelesToUse);
+        // find the likelihoods indexes to use from the used alternate alleles
+        final List likelihoodIndexesToUse = determineDiploidLikelihoodIndexesToUse(vc, allelesToUse);
+
+        // find the strand allele count indexes to use from the used alternate alleles
+        final List sacIndexesToUse = determineSACIndexesToUse(vc, allelesToUse);
 
         // create the new genotypes
-        return createGenotypesWithSubsettedLikelihoods(vc.getGenotypes(), vc, allelesToUse, likelihoodIndexesToUse, assignGenotypes);
+        return createGenotypesWithSubsettedLikelihoods(vc.getGenotypes(), vc, allelesToUse, likelihoodIndexesToUse, sacIndexesToUse, assignGenotypes);
     }
 
     /**
-     * Figure out which likelihood indexes to use for a selected down set of alleles
+     * Find the likelihood indexes to use for a selected set of diploid alleles
      *
      * @param originalVC        the original VariantContext
      * @param allelesToUse      the subset of alleles to use
      * @return a list of PL indexes to use or null if none
      */
-    private static List determineLikelihoodIndexesToUse(final VariantContext originalVC, final List allelesToUse) {
+    private static List determineDiploidLikelihoodIndexesToUse(final VariantContext originalVC, final List allelesToUse) {
+
+        if ( originalVC == null) throw new IllegalArgumentException("the original VariantContext cannot be null");
+        if ( allelesToUse == null ) throw new IllegalArgumentException("the alleles to use cannot be null");
 
         // the bitset representing the allele indexes we want to keep
         final boolean[] alleleIndexesToUse = getAlleleIndexBitset(originalVC, allelesToUse);
@@ -614,21 +637,53 @@ public class GATKVariantContextUtils {
         if ( MathUtils.countOccurrences(true, alleleIndexesToUse) == alleleIndexesToUse.length )
             return null;
 
-        return getLikelihoodIndexes(originalVC, alleleIndexesToUse);
+        return getDiploidLikelihoodIndexes(originalVC, alleleIndexesToUse);
     }
 
     /**
-     * Get the actual likelihoods indexes to use given the corresponding allele indexes
+     * Find the strand allele count indexes to use for a selected set of alleles
+     *
+     * @param originalVC   the original VariantContext
+     * @param allelesToUse the subset of alleles to use
+     * @return a list of SAC indexes to use or null if none
+     */
+    public static List determineSACIndexesToUse(final VariantContext originalVC, final List allelesToUse) {
+
+        if ( originalVC == null ) throw new IllegalArgumentException("the original VC cannot be null");
+        if ( allelesToUse == null ) throw new IllegalArgumentException("the alleles to use cannot be null");
+
+        // the bitset representing the allele indexes we want to keep
+        final boolean[] alleleIndexesToUse = getAlleleIndexBitset(originalVC, allelesToUse);
+
+        // an optimization: if we are supposed to use all (or none in the case of a ref call) of the alleles,
+        // then we can keep the SACs as is; otherwise, we determine which ones to keep
+        if (MathUtils.countOccurrences(true, alleleIndexesToUse) == alleleIndexesToUse.length)
+            return null;
+
+        return getSACIndexes(alleleIndexesToUse);
+    }
+
+    /**
+     * Get the actual likelihoods indexes to use given the corresponding diploid allele indexes
      *
      * @param originalVC           the original VariantContext
      * @param alleleIndexesToUse   the bitset representing the alleles to use (@see #getAlleleIndexBitset)
      * @return a non-null List
      */
-    private static List getLikelihoodIndexes(final VariantContext originalVC, final boolean[] alleleIndexesToUse) {
+    private static List getDiploidLikelihoodIndexes(final VariantContext originalVC, final boolean[] alleleIndexesToUse) {
+
+        if (originalVC == null) throw new IllegalArgumentException("the original VC cannot be null");
+        if (alleleIndexesToUse == null) throw new IllegalArgumentException("the alleles to use cannot be null");
+
+        // All samples must be diploid
+        for ( final Genotype g : originalVC.getGenotypes() ){
+            if ( g.getPloidy() != DEFAULT_PLOIDY )
+                throw new ReviewedGATKException("All samples must be diploid");
+        }
 
         final List result = new ArrayList<>(30);
 
-        // numLikelihoods takes total # of alleles. Use default # of chromosomes (ploidy) = 2
+        // numLikelihoods takes total # of alleles.
         final int numLikelihoods = GenotypeLikelihoods.numLikelihoods(originalVC.getNAlleles(), DEFAULT_PLOIDY);
 
         for ( int PLindex = 0; PLindex < numLikelihoods; PLindex++ ) {
@@ -641,48 +696,137 @@ public class GATKVariantContextUtils {
         return result;
     }
 
+    /**
+     * Get the actual strand aleele counts indexes to use given the corresponding allele indexes
+     *
+     * @param alleleIndexesToUse    the bitset representing the alleles to use (@see #getAlleleIndexBitset)
+     * @return a non-null List
+     */
+    private static List getSACIndexes(final boolean[] alleleIndexesToUse) {
+
+        if (alleleIndexesToUse == null) throw new IllegalArgumentException("the alleles to use cannot be null");
+        if (alleleIndexesToUse.length == 0) throw new IllegalArgumentException("cannot have no alleles to use");
+
+        final List result = new ArrayList<>(2 * alleleIndexesToUse.length);
+
+        for (int SACindex = 0; SACindex < alleleIndexesToUse.length; SACindex++) {
+            if (alleleIndexesToUse[SACindex]) {
+                result.add(2 * SACindex);
+                result.add(2 * SACindex + 1);
+            }
+        }
+
+        return result;
+    }
+
     /**
      * Given an original VariantContext and a list of alleles from that VC to keep,
      * returns a bitset representing which allele indexes should be kept
      *
-     * @param originalVC      the original VC
-     * @param allelesToKeep   the list of alleles to keep
+     * @param originalVC   the original VC
+     * @param allelesToUse the list of alleles to keep
      * @return non-null bitset
      */
-    private static boolean[] getAlleleIndexBitset(final VariantContext originalVC, final List allelesToKeep) {
+    private static boolean[] getAlleleIndexBitset(final VariantContext originalVC, final List allelesToUse) {
+
+        if (originalVC == null) throw new IllegalArgumentException("the original VC cannot be null");
+        if (allelesToUse == null) throw new IllegalArgumentException("the alleles to use cannot be null");
+
         final int numOriginalAltAlleles = originalVC.getNAlleles() - 1;
         final boolean[] alleleIndexesToKeep = new boolean[numOriginalAltAlleles + 1];
 
         // the reference Allele is definitely still used
         alleleIndexesToKeep[0] = true;
-        for ( int i = 0; i < numOriginalAltAlleles; i++ ) {
-            if ( allelesToKeep.contains(originalVC.getAlternateAllele(i)) )
-                alleleIndexesToKeep[i+1] = true;
+        for (int i = 0; i < numOriginalAltAlleles; i++) {
+            if (allelesToUse.contains(originalVC.getAlternateAllele(i)))
+                alleleIndexesToKeep[i + 1] = true;
         }
 
         return alleleIndexesToKeep;
     }
 
     /**
-     * Create the new GenotypesContext with the subsetted PLs and ADs
+     * Make a new SAC array from the a subset of the genotype's original SAC
+     *
+     * @param g               the genotype
+     * @param sacIndexesToUse the indexes in the SAC to use given the allelesToUse (@see #determineSACIndexesToUse())
+     * @return subset of SACs from the original genotype, the original SACs if sacIndexesToUse is null
+     */
+    public static int[] makeNewSACs(final Genotype g, final List sacIndexesToUse) {
+
+        if (g == null) throw new IllegalArgumentException("the genotype cannot be null");
+
+        final int[] oldSACs  = getSACs(g);
+
+        if (sacIndexesToUse == null) {
+            return oldSACs;
+        } else {
+            final int[] newSACs = new int[sacIndexesToUse.size()];
+            int newIndex = 0;
+            for (final int oldIndex : sacIndexesToUse) {
+                newSACs[newIndex++] = oldSACs[oldIndex];
+            }
+            return newSACs;
+        }
+    }
+
+
+    /**
+     * Get the genotype SACs
+     *
+     * @param g the genotype
+     * @return an arrays of SACs
+     * @throws ReviewedGATKException if the type of the SACs is unexpected
+     */
+    private static int[] getSACs(final Genotype g) {
+
+        if ( g == null ) throw new IllegalArgumentException("the Genotype cannot be null");
+        if ( !g.hasExtendedAttribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY) )
+            throw new IllegalArgumentException("Genotype must have SAC");
+
+        if ( g.getExtendedAttributes().get(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY).getClass().equals(String.class) ) {
+            final String SACsString = (String) g.getExtendedAttributes().get(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY);
+            ArrayList stringSACs = Utils.split(SACsString, ",");
+            final int[] intSACs = new int[stringSACs.size()];
+            int i = 0;
+            for (String sac : stringSACs)
+                intSACs[i++] = Integer.parseInt(sac);
+
+            return intSACs;
+        }
+        else if ( g.getExtendedAttributes().get(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY).getClass().equals(int[].class) )
+            return (int[]) g.getExtendedAttributes().get(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY);
+        else
+            throw new ReviewedGATKException("Unexpected SAC type");
+    }
+
+    /**
+     * Create the new GenotypesContext with the subsetted PLs, SACs and ADs
      *
      * @param originalGs               the original GenotypesContext
-     * @param vc                       the original VariantContext
+     * @param originalVC               the original VariantContext
      * @param allelesToUse             the actual alleles to use with the new Genotypes
-     * @param likelihoodIndexesToUse   the indexes in the PL to use given the allelesToUse (@see #determineLikelihoodIndexesToUse())
+     * @param likelihoodIndexesToUse   the indexes in the PL to use given the allelesToUse (@see #determineDiploidLikelihoodIndexesToUse())
+     * @param sacIndexesToUse          the indexes in the SAC to use given the allelesToUse (@see #determineSACIndexesToUse())
      * @param assignGenotypes          assignment strategy for the (subsetted) PLs
      * @return a new non-null GenotypesContext
      */
     private static GenotypesContext createGenotypesWithSubsettedLikelihoods(final GenotypesContext originalGs,
-                                                                            final VariantContext vc,
+                                                                            final VariantContext originalVC,
                                                                             final List allelesToUse,
                                                                             final List likelihoodIndexesToUse,
+                                                                            final List sacIndexesToUse,
                                                                             final GenotypeAssignmentMethod assignGenotypes) {
+
+        if ( originalGs == null ) throw new IllegalArgumentException("the original GenotypesContext cannot be null");
+        if ( originalVC == null ) throw new IllegalArgumentException("the original VariantContext cannot be null");
+        if ( allelesToUse == null ) throw new IllegalArgumentException("the alleles to use cannot be null");
+
         // the new genotypes to create
         final GenotypesContext newGTs = GenotypesContext.create(originalGs.size());
 
         // make sure we are seeing the expected number of likelihoods per sample
-        final int expectedNumLikelihoods = GenotypeLikelihoods.numLikelihoods(vc.getNAlleles(), 2);
+        final int expectedNumLikelihoods = GenotypeLikelihoods.numLikelihoods(originalVC.getNAlleles(), 2);
 
         // the samples
         final List sampleIndices = originalGs.getSampleNamesOrderedByName();
@@ -692,7 +836,7 @@ public class GATKVariantContextUtils {
             final Genotype g = originalGs.get(sampleIndices.get(k));
             final GenotypeBuilder gb = new GenotypeBuilder(g);
 
-            // create the new likelihoods array from the alleles we are allowed to use
+            // create the new likelihoods array from the used alleles
             double[] newLikelihoods;
             if ( !g.hasLikelihoods() ) {
                 // we don't have any likelihoods, so we null out PLs and make G ./.
@@ -703,7 +847,7 @@ public class GATKVariantContextUtils {
                 if ( likelihoodIndexesToUse == null ) {
                     newLikelihoods = originalLikelihoods;
                 } else if ( originalLikelihoods.length != expectedNumLikelihoods ) {
-                    logger.debug("Wrong number of likelihoods in sample " + g.getSampleName() + " at " + vc + " got " + g.getLikelihoodsString() + " but expected " + expectedNumLikelihoods);
+                    logger.debug("Wrong number of likelihoods in sample " + g.getSampleName() + " at " + originalVC + " got " + g.getLikelihoodsString() + " but expected " + expectedNumLikelihoods);
                     newLikelihoods = null;
                 } else {
                     newLikelihoods = new double[likelihoodIndexesToUse.size()];
@@ -721,11 +865,17 @@ public class GATKVariantContextUtils {
                     gb.PL(newLikelihoods);
             }
 
+            // create the new strand allele counts array from the used alleles
+            if ( g.hasExtendedAttribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY)){
+                int[] newSACs = makeNewSACs(g, sacIndexesToUse);
+                gb.attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, newSACs);
+            }
+
             updateGenotypeAfterSubsetting(g.getAlleles(), gb, assignGenotypes, newLikelihoods, allelesToUse);
             newGTs.add(gb.make());
         }
 
-        return fixADFromSubsettedAlleles(newGTs, vc, allelesToUse);
+        return fixADFromSubsettedAlleles(newGTs, originalVC, allelesToUse);
     }
 
     private static boolean likelihoodsAreUninformative(final double[] likelihoods) {
@@ -1154,20 +1304,23 @@ public class GATKVariantContextUtils {
     }
 
     /**
-     * Updates the PLs and AD of the Genotypes in the newly selected VariantContext to reflect the fact that some alleles
+     * Updates the PLs, SACs and AD of the Genotypes in the newly selected VariantContext to reflect the fact that some alleles
      * from the original VariantContext are no longer present.
      *
      * @param selectedVC  the selected (new) VariantContext
      * @param originalVC  the original VariantContext
      * @return a new non-null GenotypesContext
      */
-    public static GenotypesContext updatePLsAndAD(final VariantContext selectedVC, final VariantContext originalVC) {
+    public static GenotypesContext updatePLsSACsAD(final VariantContext selectedVC, final VariantContext originalVC) {
+        if ( selectedVC == null ) throw new IllegalArgumentException("the selected VariantContext cannot be null");
+        if ( originalVC == null ) throw new IllegalArgumentException("the original VariantContext cannot be null");
+
         final int numNewAlleles = selectedVC.getAlleles().size();
         final int numOriginalAlleles = originalVC.getAlleles().size();
 
         // if we have more alternate alleles in the selected VC than in the original VC, then something is wrong
         if ( numNewAlleles > numOriginalAlleles )
-            throw new IllegalArgumentException("Attempting to fix PLs and AD from what appears to be a *combined* VCF and not a selected one");
+            throw new IllegalArgumentException("Attempting to fix PLs, SACs and AD from what appears to be a *combined* VCF and not a selected one");
 
         final GenotypesContext oldGs = selectedVC.getGenotypes();
 
@@ -1175,24 +1328,31 @@ public class GATKVariantContextUtils {
         if ( numNewAlleles == numOriginalAlleles )
             return oldGs;
 
-        return fixGenotypesFromSubsettedAlleles(oldGs, originalVC, selectedVC.getAlleles());
+        return fixDiploidGenotypesFromSubsettedAlleles(oldGs, originalVC, selectedVC.getAlleles());
     }
 
     /**
-     * Fix the PLs and ADs for the GenotypesContext of a VariantContext that has been subset
+     * Fix the PLs, SACs and ADs for the GenotypesContext of a VariantContext that has been subset
      *
      * @param originalGs       the original GenotypesContext
      * @param originalVC       the original VariantContext
      * @param allelesToUse     the new (sub)set of alleles to use
      * @return a new non-null GenotypesContext
      */
-    static private GenotypesContext fixGenotypesFromSubsettedAlleles(final GenotypesContext originalGs, final VariantContext originalVC, final List allelesToUse) {
+    static private GenotypesContext fixDiploidGenotypesFromSubsettedAlleles(final GenotypesContext originalGs, final VariantContext originalVC, final List allelesToUse) {
 
-        // we need to determine which of the alternate alleles (and hence the likelihoods) to use and carry forward
-        final List likelihoodIndexesToUse = determineLikelihoodIndexesToUse(originalVC, allelesToUse);
+        if ( originalGs == null ) throw new IllegalArgumentException("the selected GenotypesContext cannot be null");
+        if ( originalVC == null ) throw new IllegalArgumentException("the original VariantContext cannot be null");
+        if ( allelesToUse == null ) throw new IllegalArgumentException("the alleles to use cannot be null");
+
+        // find the likelihoods indexes to use from the used alternate alleles
+        final List likelihoodIndexesToUse = determineDiploidLikelihoodIndexesToUse(originalVC, allelesToUse);
+
+        // find the strand allele count indexes to use from the used alternate alleles
+        final List sacIndexesToUse = determineSACIndexesToUse(originalVC, allelesToUse);
 
         // create the new genotypes
-        return createGenotypesWithSubsettedLikelihoods(originalGs, originalVC, allelesToUse, likelihoodIndexesToUse, GenotypeAssignmentMethod.DO_NOT_ASSIGN_GENOTYPES);
+        return createGenotypesWithSubsettedLikelihoods(originalGs, originalVC, allelesToUse, likelihoodIndexesToUse, sacIndexesToUse, GenotypeAssignmentMethod.DO_NOT_ASSIGN_GENOTYPES);
     }
 
     /**
@@ -1203,7 +1363,10 @@ public class GATKVariantContextUtils {
      * @param allelesToUse     the new (sub)set of alleles to use
      * @return a new non-null GenotypesContext
      */
-    static private GenotypesContext fixADFromSubsettedAlleles(final GenotypesContext originalGs, final VariantContext originalVC, final List allelesToUse) {
+    public static GenotypesContext fixADFromSubsettedAlleles(final GenotypesContext originalGs, final VariantContext originalVC, final List allelesToUse) {
+        if (originalGs == null) throw new IllegalArgumentException("the original Gs cannot be null");
+        if (originalVC == null) throw new IllegalArgumentException("the original VC cannot be null");
+        if (allelesToUse == null) throw new IllegalArgumentException("the alleles to use list cannot be null");
 
         // the bitset representing the allele indexes we want to keep
         final boolean[] alleleIndexesToUse = getAlleleIndexBitset(originalVC, allelesToUse);
@@ -1305,7 +1468,9 @@ public class GATKVariantContextUtils {
                     if ( extended.equals(b) )
                         extended = b;
                 map.put(a, extended);
-            } else if ( a.isSymbolic() ) {
+            }
+            // as long as it's not a reference allele then we want to add it as is (this covers e.g. symbolic and spanning deletion alleles)
+            else if ( !a.isReference() ) {
                 map.put(a, a);
             }
         }
@@ -1314,7 +1479,7 @@ public class GATKVariantContextUtils {
     }
 
     static private boolean isUsableAlternateAllele(final Allele allele) {
-        return ! (allele.isReference() || allele.isSymbolic() );
+        return ! (allele.isReference() || allele.isSymbolic() || allele == Allele.SPAN_DEL );
     }
 
     public static List sortVariantContextsByPriority(Collection unsortedVCs, List priorityListOfVCs, GenotypeMergeType mergeOption ) {
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/HomoSapiensConstants.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/HomoSapiensConstants.java
index 0b1543bf9..a8695fe84 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/HomoSapiensConstants.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/HomoSapiensConstants.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/VCIterable.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/VCIterable.java
index 3263d9bf6..85f2ba3ec 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/VCIterable.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/VCIterable.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleHeader.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleHeader.java
index 85681c40f..4368ffd70 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleHeader.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleHeader.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleWriter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleWriter.java
index af9268bb6..c7071f1dd 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleWriter.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleWriter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java b/public/gatk-utils/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java
index aaa20c0e5..f0a1c9c17 100644
--- a/public/gatk-utils/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java
+++ b/public/gatk-utils/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java b/public/gatk-utils/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java
index 2b08fc4d4..234bbcf7e 100644
--- a/public/gatk-utils/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java
+++ b/public/gatk-utils/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/AutoFormattingTimeUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/AutoFormattingTimeUnitTest.java
index 22e9517c8..fb95d6777 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/AutoFormattingTimeUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/AutoFormattingTimeUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java
index 1669406c8..e151541aa 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -98,7 +98,7 @@ public abstract class BaseTest {
     public static final String b36KGReference = "/humgen/1kg/reference/human_b36_both.fasta";
     public static final String b37KGReference = "/humgen/1kg/reference/human_g1k_v37.fasta";
     public static final String b37KGReferenceWithDecoy = "/humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37_decoy.fasta";
-    public static final String hg19RefereneWithChrPrefixInChromosomeNames = "/humgen/gsa-hpprojects/GATK/bundle/current/hg19/ucsc.hg19.fasta";
+    public static final String hg19ReferenceWithChrPrefixInChromosomeNames = "/humgen/gsa-hpprojects/GATK/bundle/current/hg19/ucsc.hg19.fasta";
     public static final String GATKDataLocation = "/humgen/gsa-hpprojects/GATK/data/";
     public static final String validationDataLocation = GATKDataLocation + "Validation_Data/";
     public static final String evaluationDataLocation = GATKDataLocation + "Evaluation_Data/";
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseUtilsUnitTest.java
index 83dfc8cd2..92a412f93 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseUtilsUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseUtilsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BitSetUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BitSetUtilsUnitTest.java
index 5a0bc0bbf..0124a0862 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BitSetUtilsUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BitSetUtilsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/ExampleToCopyUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/ExampleToCopyUnitTest.java
index 2ec1eb8d2..6f8a6789d 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/ExampleToCopyUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/ExampleToCopyUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GATKTextReporter.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GATKTextReporter.java
index 957ccd2f9..69e66fbda 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GATKTextReporter.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GATKTextReporter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserBenchmark.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserBenchmark.java
index 7f1987981..402e3edaf 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserBenchmark.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserBenchmark.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserUnitTest.java
index c3f5bbd88..2f49bbd60 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocSortedSetUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocSortedSetUnitTest.java
index 655312056..cc6315df5 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocSortedSetUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocSortedSetUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocUnitTest.java
index ae86ca5a5..c60356942 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java
index b753bc2fa..2f88c4e04 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5Mismatch.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5Mismatch.java
index 11064d109..a85debde1 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5Mismatch.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5Mismatch.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequencingDictionaryUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequencingDictionaryUnitTest.java
index 978a9a74d..ef6ef7738 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequencingDictionaryUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequencingDictionaryUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MWUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MWUnitTest.java
index c148dc92b..fb0057898 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MWUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MWUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MathUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MathUtilsUnitTest.java
index 4e2fd31d4..283558256 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MathUtilsUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MathUtilsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MedianUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MedianUnitTest.java
index 21f3d898b..74dfdb909 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MedianUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MedianUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/NGSPlatformUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/NGSPlatformUnitTest.java
index b247f590d..998ef1d6f 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/NGSPlatformUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/NGSPlatformUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/PathUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/PathUtilsUnitTest.java
index 00cc0dc20..45bef5866 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/PathUtilsUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/PathUtilsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/QualityUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/QualityUtilsUnitTest.java
index 86b436bd9..993878bf1 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/QualityUtilsUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/QualityUtilsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RScriptExecutorUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RScriptExecutorUnitTest.java
index 7a56b99de..98f973690 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RScriptExecutorUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RScriptExecutorUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RScriptLibraryUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RScriptLibraryUnitTest.java
index b89686cbe..ac3118ecb 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RScriptLibraryUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RScriptLibraryUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RUtilsUnitTest.java
index 51ab6f79c..8e96d62f9 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RUtilsUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RUtilsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtilsUnitTest.java
index c53c01bd5..bbbcb94e7 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtilsUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtilsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SimpleTimerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SimpleTimerUnitTest.java
index 85aec815e..05203ad11 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SimpleTimerUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SimpleTimerUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/TestNGTestTransformer.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/TestNGTestTransformer.java
index e804e70d9..e4772b3af 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/TestNGTestTransformer.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/TestNGTestTransformer.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/UtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/UtilsUnitTest.java
index dc3909e65..22e534844 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/UtilsUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/UtilsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionUnitTest.java
index 41f7a76dc..8fc6420a4 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileStateUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileStateUnitTest.java
index 75e9d9a37..dfc30ae03 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileStateUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileStateUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileUnitTest.java
index b3442b331..7ee1040e7 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfileUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfileUnitTest.java
index f0666aca2..fa75e7163 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfileUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfileUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/baq/BAQUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/baq/BAQUnitTest.java
index be9621e76..1e9fd88b1 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/baq/BAQUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/baq/BAQUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/classloader/JVMUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/classloader/JVMUtilsUnitTest.java
index c232e1c12..96ec5f6b2 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/classloader/JVMUtilsUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/classloader/JVMUtilsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperTestUtils.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperTestUtils.java
index 7c1fb32f6..06b70b744 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperTestUtils.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperTestUtils.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperUnitTest.java
index 0c8dd761f..69abeb2b5 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/FilterLiftedVariantsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodecUnitTest.java
similarity index 57%
rename from public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/FilterLiftedVariantsUnitTest.java
rename to public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodecUnitTest.java
index 847c8f1c6..05632d6db 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/FilterLiftedVariantsUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodecUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -23,32 +23,20 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package org.broadinstitute.gatk.tools.walkers.variantutils;
+package org.broadinstitute.gatk.utils.codecs.beagle;
 
-import org.broadinstitute.gatk.utils.BaseTest;
-import htsjdk.variant.variantcontext.Allele;
-import htsjdk.variant.variantcontext.VariantContext;
-import htsjdk.variant.variantcontext.VariantContextBuilder;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
-import java.util.ArrayList;
-import java.util.List;
-
-
-public class FilterLiftedVariantsUnitTest extends BaseTest {
+public class BeagleCodecUnitTest {
 
     @Test
-    public void testIndelAtEndOfContig() {
-
-        final List alleles = new ArrayList<>(2);
-        alleles.add(Allele.create("AAAAA", true));
-        alleles.add(Allele.create("A", false));
-        final VariantContext vc = new VariantContextBuilder("test", "1", 10, 14, alleles).make();
-
-        final FilterLiftedVariants filter = new FilterLiftedVariants();
-
-        Assert.assertFalse(filter.filterOrWrite(new byte[]{'A'}, vc));
+    public void testCanDecode() {
+        final String EXTRA_CHAR = "1";
+        BeagleCodec codec = new BeagleCodec();
+        Assert.assertTrue(codec.canDecode("filename." + BeagleCodec.FILE_EXT));
+        Assert.assertTrue(codec.canDecode("filename" + EXTRA_CHAR + "." + BeagleCodec.FILE_EXT));
+        Assert.assertFalse(codec.canDecode("filename." + BeagleCodec.FILE_EXT + EXTRA_CHAR));
+        Assert.assertFalse(codec.canDecode("filename" + BeagleCodec.FILE_EXT));
     }
-
 }
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/hapmap/HapMapUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/hapmap/HapMapUnitTest.java
index 0ff50d726..cf6bc20a7 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/hapmap/HapMapUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/hapmap/HapMapUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -142,7 +142,7 @@ public class HapMapUnitTest extends BaseTest {
             codec.readHeader(reader);
             line = reader.next();
             RawHapMapFeature feature = (RawHapMapFeature) codec.decode(line);
-            Assert.assertEquals(feature.getSampleIDs().length,87);
+            Assert.assertEquals(feature.getSampleIDs().length, 87);
 
         } catch (IOException e) {
             Assert.fail("IOException " + e.getMessage());
@@ -151,6 +151,16 @@ public class HapMapUnitTest extends BaseTest {
         }
     }
 
+    @Test
+    public void testCanDecode() {
+        final String EXTRA_CHAR = "1";
+        RawHapMapCodec codec = new RawHapMapCodec();
+        Assert.assertTrue(codec.canDecode("filename." + RawHapMapCodec.FILE_EXT));
+        Assert.assertTrue(codec.canDecode("filename" + EXTRA_CHAR + "." + RawHapMapCodec.FILE_EXT));
+        Assert.assertFalse(codec.canDecode("filename." + RawHapMapCodec.FILE_EXT + EXTRA_CHAR));
+        Assert.assertFalse(codec.canDecode("filename" + RawHapMapCodec.FILE_EXT));
+    }
+
 
     public LineIterator getLineIterator() {
         try {
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodecUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodecUnitTest.java
new file mode 100644
index 000000000..1f1f6b99e
--- /dev/null
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodecUnitTest.java
@@ -0,0 +1,42 @@
+/*
+* Copyright 2012-2015 Broad Institute, Inc.
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.gatk.utils.codecs.refseq;
+
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+public class RefSeqCodecUnitTest {
+
+    @Test
+    public void testCanDecode() {
+        final String EXTRA_CHAR = "1";
+        RefSeqCodec codec = new RefSeqCodec();
+        Assert.assertTrue(codec.canDecode("filename." + RefSeqCodec.FILE_EXT));
+        Assert.assertTrue(codec.canDecode("filename" + EXTRA_CHAR + "." + RefSeqCodec.FILE_EXT));
+        Assert.assertFalse(codec.canDecode("filename." + RefSeqCodec.FILE_EXT + EXTRA_CHAR));
+        Assert.assertFalse(codec.canDecode("filename" + RefSeqCodec.FILE_EXT));
+    }
+}
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodecUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodecUnitTest.java
new file mode 100644
index 000000000..301d671c9
--- /dev/null
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodecUnitTest.java
@@ -0,0 +1,42 @@
+/*
+* Copyright 2012-2015 Broad Institute, Inc.
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.gatk.utils.codecs.sampileup;
+
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+public class SAMPileupCodecUnitTest {
+
+    @Test
+    public void testCanDecode() {
+        final String EXTRA_CHAR = "1";
+        SAMPileupCodec codec = new SAMPileupCodec();
+        Assert.assertTrue(codec.canDecode("filename." + SAMPileupCodec.FILE_EXT));
+        Assert.assertTrue(codec.canDecode("filename" + EXTRA_CHAR + "." + SAMPileupCodec.FILE_EXT));
+        Assert.assertFalse(codec.canDecode("filename." + SAMPileupCodec.FILE_EXT + "1"));
+        Assert.assertFalse(codec.canDecode("filename" + SAMPileupCodec.FILE_EXT));
+    }
+}
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodecUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodecUnitTest.java
new file mode 100644
index 000000000..f5c0f5ff5
--- /dev/null
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodecUnitTest.java
@@ -0,0 +1,42 @@
+/*
+* Copyright 2012-2015 Broad Institute, Inc.
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.gatk.utils.codecs.samread;
+
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+public class SAMReadCodecUnitTest {
+
+    @Test
+    public void testCanDecode() {
+        final String EXTRA_CHAR = "1";
+        SAMReadCodec codec = new SAMReadCodec();
+        Assert.assertTrue(codec.canDecode("filename." + SAMReadCodec.FILE_EXT));
+        Assert.assertTrue(codec.canDecode("filename" + EXTRA_CHAR + "." + SAMReadCodec.FILE_EXT));
+        Assert.assertFalse(codec.canDecode("filename." + SAMReadCodec.FILE_EXT + "1"));
+        Assert.assertFalse(codec.canDecode("filename" + SAMReadCodec.FILE_EXT));
+    }
+}
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/table/TableCodecUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/table/TableCodecUnitTest.java
new file mode 100644
index 000000000..33ec130b4
--- /dev/null
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/table/TableCodecUnitTest.java
@@ -0,0 +1,42 @@
+/*
+* Copyright 2012-2015 Broad Institute, Inc.
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.gatk.utils.codecs.table;
+
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+public class TableCodecUnitTest {
+
+    @Test
+    public void testCanDecode() {
+        final String EXTRA_CHAR = "1";
+        TableCodec codec = new TableCodec();
+        Assert.assertTrue(codec.canDecode("filename." + TableCodec.FILE_EXT));
+        Assert.assertTrue(codec.canDecode("filename" + EXTRA_CHAR + "." + TableCodec.FILE_EXT));
+        Assert.assertFalse(codec.canDecode("filename." + TableCodec.FILE_EXT + EXTRA_CHAR));
+        Assert.assertFalse(codec.canDecode("filename" + TableCodec.FILE_EXT));
+    }
+}
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/collections/DefaultHashMapUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/collections/DefaultHashMapUnitTest.java
index a87aebacc..78865bee0 100755
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/collections/DefaultHashMapUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/collections/DefaultHashMapUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayListUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayListUnitTest.java
index 7f9d80861..78b19d6ff 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayListUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayListUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSiteUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSiteUnitTest.java
index b1ba78416..32cec45b9 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSiteUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSiteUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceUnitTest.java
index 8837f4b5d..418bfe151 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineUnitTest.java
index d3c85b6bc..6b80ebd4b 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollectionUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollectionUnitTest.java
index a846384dc..7fdd7b835 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollectionUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollectionUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingUnitTest.java
index bffb1d2cf..efed9c195 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java
index 61d346d5a..b5bea3247 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java
index 3e877b900..ef8565dba 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -236,7 +236,7 @@ public class CachingIndexedFastaSequenceFileUnitTest extends BaseTest {
     @Test(enabled = true)
     public void testIupacChanges() throws FileNotFoundException, InterruptedException {
         final String testFasta = privateTestDir + "iupacFASTA.fasta";
-        final CachingIndexedFastaSequenceFile iupacPreserving = new CachingIndexedFastaSequenceFile(new File(testFasta), CachingIndexedFastaSequenceFile.DEFAULT_CACHE_SIZE, false, true);
+        final CachingIndexedFastaSequenceFile iupacPreserving = new CachingIndexedFastaSequenceFile(new File(testFasta), false, true);
         final CachingIndexedFastaSequenceFile makeNs = new CachingIndexedFastaSequenceFile(new File(testFasta));
 
         int preservingNs = 0;
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/file/FSLockWithSharedUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/file/FSLockWithSharedUnitTest.java
index 63d98a277..7dbf3472c 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/file/FSLockWithSharedUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/file/FSLockWithSharedUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsBenchmark.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsBenchmark.java
index f388d14ef..decb8284a 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsBenchmark.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsBenchmark.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java
index 4984d0a71..1700baf12 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/EventMapUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/EventMapUnitTest.java
index c4ff9b587..2188dbce8 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/EventMapUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/EventMapUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeUnitTest.java
index e71413d12..42801a39c 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java
index 48c6cb480..0fbb0b2a8 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/io/IOUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/io/IOUtilsUnitTest.java
index 46b2e949f..66f619007 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/io/IOUtilsUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/io/IOUtilsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/clibrary/LibCUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/clibrary/LibCUnitTest.java
index f695d899b..7d622868f 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/clibrary/LibCUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/clibrary/LibCUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionQueueTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionQueueTest.java
index e683f4be8..e2dc57b9c 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionQueueTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionQueueTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaaQueueTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaaQueueTest.java
index accc0febb..ecc0f9a8e 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaaQueueTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaaQueueTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java
index e9df412e7..29b7ad015 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachineUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachineUnitTest.java
index b8d9c3149..df20a7e27 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachineUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachineUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LIBS_position.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LIBS_position.java
index 92680a7ea..60bbe6a87 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LIBS_position.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LIBS_position.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorBenchmark.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorBenchmark.java
index 0d06c61c6..ea7165b2f 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorBenchmark.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorBenchmark.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java
index 8f5d8f7b2..e39045782 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java
index cbbdf3609..78185d817 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManagerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManagerUnitTest.java
index 4a760b5d6..2522b8c35 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManagerUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManagerUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducerUnitTest.java
index d99a07966..ff4280e36 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducerUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducerUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultUnitTest.java
index 93105cdfb..2b6243745 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerUnitTest.java
index 72636f01b..f45daa270 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/ReducerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/ReducerUnitTest.java
index 987d13f2a..03c92a02d 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/ReducerUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/ReducerUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/pileup/PileupElementUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/pileup/PileupElementUnitTest.java
index 90d235f99..5c4987401 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/pileup/PileupElementUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/pileup/PileupElementUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupUnitTest.java
index 9b3b3b8c3..70377e1c7 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemonUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemonUnitTest.java
index 9d549ea21..57ce9d956 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemonUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemonUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDataUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDataUnitTest.java
index 0c97377c3..2f11f2543 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDataUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDataUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/recalibration/EventTypeUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/recalibration/EventTypeUnitTest.java
index 7749fb2c3..e514b670f 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/recalibration/EventTypeUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/recalibration/EventTypeUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTrackerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTrackerUnitTest.java
index 62a704217..3dbfbfcd6 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTrackerUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTrackerUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManagerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManagerUnitTest.java
index b0805e161..0194d4941 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManagerUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManagerUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilderUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilderUnitTest.java
index 5019e78e7..7b25724ce 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilderUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilderUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/CheckableCloseableTribbleIterator.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/CheckableCloseableTribbleIterator.java
index cee60aace..191c68993 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/CheckableCloseableTribbleIterator.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/CheckableCloseableTribbleIterator.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java
index 768bf50df..789ef1886 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIteratorUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIteratorUnitTest.java
index ee5f17ef9..5ca887edf 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIteratorUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIteratorUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestFeatureReader.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestFeatureReader.java
index 190ec846b..7b9a0feeb 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestFeatureReader.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestFeatureReader.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestRMDTrackBuilder.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestRMDTrackBuilder.java
index 2750e271e..436c4f422 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestRMDTrackBuilder.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestRMDTrackBuilder.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/GATKReportUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/GATKReportUnitTest.java
index fa34fb71b..d67851771 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/GATKReportUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/GATKReportUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/ReportMarshallerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/ReportMarshallerUnitTest.java
index ebeb1581d..5d9478ab8 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/ReportMarshallerUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/ReportMarshallerUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/runtime/ProcessControllerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/runtime/ProcessControllerUnitTest.java
index 4fa7ef5de..eeaac020a 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/runtime/ProcessControllerUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/runtime/ProcessControllerUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtilsUnitTest.java
index 95737748d..8f60ff0a8 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtilsUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtilsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/AlignmentUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/AlignmentUtilsUnitTest.java
index d0d6eb442..6dca140ba 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/AlignmentUtilsUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/AlignmentUtilsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilderUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilderUnitTest.java
index b7042a6aa..d3a7c5c0b 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilderUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilderUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java
index fe5fba7ee..b556c0eaf 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileWriterUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileWriterUnitTest.java
index d52762402..0df8bbf6d 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileWriterUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileWriterUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIteratorUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIteratorUnitTest.java
index 32409c60b..19ef63f6e 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIteratorUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIteratorUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtilsUnitTest.java
index a4e6be203..70d25a585 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtilsUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtilsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java
index 4117f7487..5f6b36c1c 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordUnitTest.java
index e703c52fb..470671d09 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java
index 14b56718e..c6233f17d 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWatermanBenchmark.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWatermanBenchmark.java
index 44ba64c82..f6aff7ba4 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWatermanBenchmark.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWatermanBenchmark.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java
index ac301ce37..aeb1101cf 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/TextFormattingUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/TextFormattingUtilsUnitTest.java
index 54573103a..b8bf04b56 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/TextFormattingUtilsUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/TextFormattingUtilsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactoryUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactoryUnitTest.java
index 0c988131e..bbd594d27 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactoryUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactoryUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitorUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitorUnitTest.java
index a73cb26f9..ecc611f7e 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitorUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitorUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java
index 410bd848f..c64c04dc1 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
@@ -986,6 +986,7 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
         tests.add(new Object[]{Arrays.asList("ACGTT", "ACCTT"), Arrays.asList("G", "C"), 2});
         tests.add(new Object[]{Arrays.asList("ACGTT", "ACCCTT"), Arrays.asList("G", "CC"), 2});
         tests.add(new Object[]{Arrays.asList("ACGTT", "ACGCTT"), Arrays.asList("G", "GC"), 2});
+        tests.add(new Object[]{Arrays.asList("ATCGAGCCGTG", "AAGCCGTG"), Arrays.asList("ATCG", "A"), 0});
 
         return tests.toArray(new Object[][]{});
     }
@@ -1150,9 +1151,9 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
         final Genotype base = new GenotypeBuilder("NA12878").DP(10).GQ(50).make();
 
         // make sure we don't screw up the simple case
-        final Genotype aaGT = new GenotypeBuilder(base).alleles(AA).AD(new int[]{10,2}).PL(homRefPL).GQ(8).make();
-        final Genotype acGT = new GenotypeBuilder(base).alleles(AC).AD(new int[]{10,2}).PL(hetPL).GQ(8).make();
-        final Genotype ccGT = new GenotypeBuilder(base).alleles(CC).AD(new int[]{10,2}).PL(homVarPL).GQ(8).make();
+        final Genotype aaGT = new GenotypeBuilder(base).alleles(AA).AD(new int[]{10,2}).PL(homRefPL).attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{5, 10, 15, 20}).GQ(8).make();
+        final Genotype acGT = new GenotypeBuilder(base).alleles(AC).AD(new int[]{10, 2}).PL(hetPL).attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{5, 10, 15, 20}).GQ(8).make();
+        final Genotype ccGT = new GenotypeBuilder(base).alleles(CC).AD(new int[]{10, 2}).PL(homVarPL).attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{5, 10, 15, 20}).GQ(8).make();
 
         tests.add(new Object[]{new VariantContextBuilder(vcBase).genotypes(aaGT).make(), AC, Arrays.asList(new GenotypeBuilder(aaGT).make())});
         tests.add(new Object[]{new VariantContextBuilder(vcBase).genotypes(acGT).make(), AC, Arrays.asList(new GenotypeBuilder(acGT).make())});
@@ -1298,9 +1299,11 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
                 builder.DP(10);
                 builder.GQ(30);
                 builder.AD(alleles.size() == 1 ? new int[]{1} : (alleles.size() == 2 ? new int[]{1, 2} : new int[]{1, 2, 3}));
-                builder.PL(alleles.size() == 1 ? new int[]{1} : (alleles.size() == 2 ? new int[]{1,2} : new int[]{1,2,3}));
+                builder.PL(alleles.size() == 1 ? new int[]{1} : (alleles.size() == 2 ? new int[]{1, 2} : new int[]{1, 2, 3}));
+                builder.attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY,
+                        alleles.size() == 1 ? new int[]{1, 2}  : (alleles.size() == 2 ? new int[]{1, 2, 3, 4} : new int[]{1, 2, 3, 4, 5, 6}));
                 final List refs = Collections.nCopies(alleles.size(), Aref);
-                tests.put(builder.make(), builder.alleles(refs).noAD().noPL().make());
+                tests.put(builder.make(), builder.alleles(refs).noAD().noPL().attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, null).make());
             }
         }
 
@@ -1311,7 +1314,6 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
 
                 Assert.assertEquals(gc.size(), genotypes.size());
                 for ( int i = 0; i < genotypes.size(); i++ ) {
-//                    logger.warn("Testing " + genotypes.get(i) + " => " + gc.get(i) + " " + tests.get(genotypes.get(i)));
                     assertGenotypesAreEqual(gc.get(i), tests.get(genotypes.get(i)));
                 }
             }
@@ -1324,8 +1326,8 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
     //
     // --------------------------------------------------------------------------------
 
-    @DataProvider(name = "updatePLsAndADData")
-    public Object[][] makeUpdatePLsAndADData() {
+    @DataProvider(name = "updatePLsSACsAndADData")
+    public Object[][] makeUpdatePLsSACsAndADData() {
         List tests = new ArrayList<>();
 
         final Allele A = Allele.create("A", true);
@@ -1350,9 +1352,9 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
         final Genotype base = new GenotypeBuilder("NA12878").DP(10).GQ(100).make();
 
         // make sure we don't screw up the simple case where no selection happens
-        final Genotype aaGT = new GenotypeBuilder(base).alleles(AA).AD(new int[]{10,2}).PL(homRefPL).GQ(8).make();
-        final Genotype acGT = new GenotypeBuilder(base).alleles(AC).AD(new int[]{10,2}).PL(hetPL).GQ(8).make();
-        final Genotype ccGT = new GenotypeBuilder(base).alleles(CC).AD(new int[]{10,2}).PL(homVarPL).GQ(8).make();
+        final Genotype aaGT = new GenotypeBuilder(base).alleles(AA).AD(new int[]{10,2}).PL(homRefPL).attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{5, 10, 15, 20}).GQ(8).make();
+        final Genotype acGT = new GenotypeBuilder(base).alleles(AC).AD(new int[]{10, 2}).PL(hetPL).attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{5, 10, 15, 20}).GQ(8).make();
+        final Genotype ccGT = new GenotypeBuilder(base).alleles(CC).AD(new int[]{10, 2}).PL(homVarPL).attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{5, 10, 15, 20}).GQ(8).make();
 
         tests.add(new Object[]{new VariantContextBuilder(vcBase).genotypes(aaGT).make(), new VariantContextBuilder(vcBase).alleles(AC).make(), Arrays.asList(new GenotypeBuilder(aaGT).make())});
         tests.add(new Object[]{new VariantContextBuilder(vcBase).genotypes(acGT).make(), new VariantContextBuilder(vcBase).alleles(AC).make(), Arrays.asList(new GenotypeBuilder(acGT).make())});
@@ -1379,44 +1381,59 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
         final int[] hetCG3AllelesAD = new int[]{0, 12, 11}; // AA, AC, CC, AG, CG, GG
         final int[] homG3AllelesAD = new int[]{0, 1, 21};  // AA, AC, CC, AG, CG, GG
 
+        final int[] homRef3AllelesSAC = new int[]{20, 19, 0, 1, 3, 4};
+        final int[] hetRefC3AllelesSAC = new int[]{10, 9, 10, 9, 1, 1};
+        final int[] homC3AllelesSAC = new int[]{0, 0, 20, 20, 1, 1};
+        final int[] hetRefG3AllelesSAC = new int[]{10, 10, 0, 0, 11, 11};
+        final int[] hetCG3AllelesSAC = new int[]{0, 0, 12, 12, 11, 11}; // AA, AC, CC, AG, CG, GG
+        final int[] homG3AllelesSAC = new int[]{0, 0, 1, 1, 21, 21};  // AA, AC, CC, AG, CG, GG
+
         tests.add(new Object[]{
-                new VariantContextBuilder(vcBase).alleles(ACG).genotypes(new GenotypeBuilder(base).alleles(AA).AD(homRef3AllelesAD).PL(homRef3AllelesPL).make()).make(),
+                new VariantContextBuilder(vcBase).alleles(ACG).genotypes(new GenotypeBuilder(base).alleles(AA).AD(homRef3AllelesAD).PL(homRef3AllelesPL).
+                        attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, homRef3AllelesSAC).make()).make(),
+                        new VariantContextBuilder(vcBase).alleles(AC).make(),
+                Arrays.asList(new GenotypeBuilder(base).alleles(AA).PL(new double[]{0, -10, -20}).AD(new int[]{20, 0}).
+                        attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{20, 19, 0, 1}).GQ(100).make())});
+        tests.add(new Object[]{
+                new VariantContextBuilder(vcBase).alleles(ACG).genotypes(new GenotypeBuilder(base).alleles(AA).AD(hetRefC3AllelesAD).PL(hetRefC3AllelesPL).
+                        attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, hetRefC3AllelesSAC).make()).make(),
                 new VariantContextBuilder(vcBase).alleles(AC).make(),
-                Arrays.asList(new GenotypeBuilder(base).alleles(AA).PL(new double[]{0, -10, -20}).AD(new int[]{20, 0}).GQ(100).make())});
-
+                Arrays.asList(new GenotypeBuilder(base).alleles(AA).PL(new double[]{-10, 0, -20}).AD(new int[]{10, 10}).
+                        attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{10, 9, 10, 9}).GQ(100).make())});
         tests.add(new Object[]{
-                new VariantContextBuilder(vcBase).alleles(ACG).genotypes(new GenotypeBuilder(base).alleles(AA).AD(hetRefC3AllelesAD).PL(hetRefC3AllelesPL).make()).make(),
+                new VariantContextBuilder(vcBase).alleles(ACG).genotypes(new GenotypeBuilder(base).alleles(AA).AD(homC3AllelesAD).PL(homC3AllelesPL).
+                        attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, homC3AllelesSAC).make()).make(),
                 new VariantContextBuilder(vcBase).alleles(AC).make(),
-                Arrays.asList(new GenotypeBuilder(base).alleles(AA).PL(new double[]{-10, 0, -20}).AD(new int[]{10, 10}).GQ(100).make())});
-
+                Arrays.asList(new GenotypeBuilder(base).alleles(AA).PL(new double[]{-20, -10, 0}).AD(new int[]{0, 20}).
+                        attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{0, 0, 20, 20}).GQ(100).make())});
         tests.add(new Object[]{
-                new VariantContextBuilder(vcBase).alleles(ACG).genotypes(new GenotypeBuilder(base).alleles(AA).AD(homC3AllelesAD).PL(homC3AllelesPL).make()).make(),
-                new VariantContextBuilder(vcBase).alleles(AC).make(),
-                Arrays.asList(new GenotypeBuilder(base).alleles(AA).PL(new double[]{-20, -10, 0}).AD(new int[]{0, 20}).GQ(100).make())});
-        tests.add(new Object[]{
-                new VariantContextBuilder(vcBase).alleles(ACG).genotypes(new GenotypeBuilder(base).alleles(AA).AD(hetRefG3AllelesAD).PL(hetRefG3AllelesPL).make()).make(),
+                new VariantContextBuilder(vcBase).alleles(ACG).genotypes(new GenotypeBuilder(base).alleles(AA).AD(hetRefG3AllelesAD).PL(hetRefG3AllelesPL).
+                        attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, hetRefG3AllelesSAC).make()).make(),
                 new VariantContextBuilder(vcBase).alleles(AG).make(),
-                Arrays.asList(new GenotypeBuilder(base).alleles(AA).PL(new double[]{-20, 0, -50}).AD(new int[]{10, 11}).GQ(100).make())});
-
+                Arrays.asList(new GenotypeBuilder(base).alleles(AA).PL(new double[]{-20, 0, -50}).AD(new int[]{10, 11}).
+                        attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{10, 10, 11, 11}).GQ(100).make())});
         tests.add(new Object[]{
-                new VariantContextBuilder(vcBase).alleles(ACG).genotypes(new GenotypeBuilder(base).alleles(AA).AD(hetCG3AllelesAD).PL(hetCG3AllelesPL).make()).make(),
+                new VariantContextBuilder(vcBase).alleles(ACG).genotypes(new GenotypeBuilder(base).alleles(AA).AD(hetCG3AllelesAD).PL(hetCG3AllelesPL).
+                        attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, hetCG3AllelesSAC).make()).make(),
                 new VariantContextBuilder(vcBase).alleles(AG).make(),
-                Arrays.asList(new GenotypeBuilder(base).alleles(AA).PL(new double[]{0, -20, -30}).AD(new int[]{0, 11}).GQ(100).make())});
-
+                Arrays.asList(new GenotypeBuilder(base).alleles(AA).PL(new double[]{0, -20, -30}).AD(new int[]{0, 11}).
+                        attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{0, 0, 11, 11}).GQ(100).make())});
         tests.add(new Object[]{
-                new VariantContextBuilder(vcBase).alleles(ACG).genotypes(new GenotypeBuilder(base).alleles(AA).AD(homG3AllelesAD).PL(homG3AllelesPL).make()).make(),
+                new VariantContextBuilder(vcBase).alleles(ACG).genotypes(new GenotypeBuilder(base).alleles(AA).AD(homG3AllelesAD).PL(homG3AllelesPL).
+                        attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, homG3AllelesSAC).make()).make(),
                 new VariantContextBuilder(vcBase).alleles(AG).make(),
-                Arrays.asList(new GenotypeBuilder(base).alleles(AA).PL(new double[]{-20, -40, 0}).AD(new int[]{0, 21}).GQ(100).make())});
+                Arrays.asList(new GenotypeBuilder(base).alleles(AA).PL(new double[]{-20, -40, 0}).AD(new int[]{0, 21}).
+                        attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{0, 0, 21, 21}).GQ(100).make())});
 
         return tests.toArray(new Object[][]{});
     }
 
-    @Test(dataProvider = "updatePLsAndADData")
+    @Test(dataProvider = "updatePLsSACsAndADData")
     public void testUpdatePLsAndADData(final VariantContext originalVC,
                                        final VariantContext selectedVC,
                                        final List expectedGenotypes) {
         final VariantContext selectedVCwithGTs = new VariantContextBuilder(selectedVC).genotypes(originalVC.getGenotypes()).make();
-        final GenotypesContext actual = GATKVariantContextUtils.updatePLsAndAD(selectedVCwithGTs, originalVC);
+        final GenotypesContext actual = GATKVariantContextUtils.updatePLsSACsAD(selectedVCwithGTs, originalVC);
 
         Assert.assertEquals(actual.size(), expectedGenotypes.size());
         for ( final Genotype expected : expectedGenotypes ) {
@@ -1629,5 +1646,20 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
         // Throws an exception if the ref allele length <= ref allele length to extend
         Map map = GATKVariantContextUtils.createAlleleMapping(Aref, vc, alleles);
     }
+
+    @Test
+    public void testDetermineSACIndexesToUse(){
+        final VariantContext vc = makeVC("vc", Arrays.asList(Aref, T, C));
+        Assert.assertEquals(GATKVariantContextUtils.determineSACIndexesToUse(vc, Arrays.asList(Aref, C)), Arrays.asList(0, 1, 4, 5));
+        Assert.assertEquals(GATKVariantContextUtils.determineSACIndexesToUse(vc, Arrays.asList(G)), Arrays.asList(0, 1));
+    }
+
+    @Test
+    public void testMakeNewSACs(){
+        int[] expected = {10, 20}  ;
+        final Genotype g = new GenotypeBuilder().alleles(Arrays.asList(Allele.create("A", true), Allele.create("G"))).
+                attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{5, 10, 15, 20}).make();
+        Assert.assertEquals(GATKVariantContextUtils.makeNewSACs(g, Arrays.asList(1, 3)), expected);
+    }
 }
 
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/VariantContextBenchmark.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/VariantContextBenchmark.java
index 7c1b2028f..79ee95611 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/VariantContextBenchmark.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/VariantContextBenchmark.java
@@ -1,5 +1,5 @@
 /*
-* Copyright (c) 2012 The Broad Institute
+* Copyright 2012-2015 Broad Institute, Inc.
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
diff --git a/public/gatk-utils/src/test/resources/exampleBAM.bam b/public/gatk-utils/src/test/resources/exampleBAM.bam
index 319dd1a72..d1c9d8001 100644
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diff --git a/public/gatk-utils/src/test/resources/exampleBAM.bam.bai b/public/gatk-utils/src/test/resources/exampleBAM.bam.bai
index 052ac614b..33beef3d1 100644
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diff --git a/public/gatk-utils/src/test/resources/exampleBAM.simple.bai b/public/gatk-utils/src/test/resources/exampleBAM.simple.bai
index 2d8268b1d..9320babb8 100644
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diff --git a/public/gatk-utils/src/test/resources/exampleBAM.simple.bam b/public/gatk-utils/src/test/resources/exampleBAM.simple.bam
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diff --git a/public/gatk-utils/src/test/resources/exampleBAM_with_unmapped.bai b/public/gatk-utils/src/test/resources/exampleBAM_with_unmapped.bai
index d651df3fd..fd1625e40 100644
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diff --git a/public/gatk-utils/src/test/resources/exampleBAM_with_unmapped.bam b/public/gatk-utils/src/test/resources/exampleBAM_with_unmapped.bam
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diff --git a/public/gatk-utils/src/test/resources/exampleCRAM-nobai-nocrai.cram b/public/gatk-utils/src/test/resources/exampleCRAM-nobai-nocrai.cram
new file mode 100644
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new file mode 100644
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diff --git a/public/gatk-utils/src/test/resources/exampleCRAM-noindex.cram b/public/gatk-utils/src/test/resources/exampleCRAM-noindex.cram
deleted file mode 100644
index 7041737ee..000000000
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diff --git a/public/gatk-utils/src/test/resources/exampleCRAM.cram b/public/gatk-utils/src/test/resources/exampleCRAM.cram
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diff --git a/public/gatk-utils/src/test/resources/exampleCRAM.cram.crai b/public/gatk-utils/src/test/resources/exampleCRAM.cram.crai
index d10c49f45..3eee8e007 100644
Binary files a/public/gatk-utils/src/test/resources/exampleCRAM.cram.crai and b/public/gatk-utils/src/test/resources/exampleCRAM.cram.crai differ
diff --git a/public/gatk-utils/src/test/resources/exampleNORG.bam b/public/gatk-utils/src/test/resources/exampleNORG.bam
index f59219fec..7967d83c3 100644
Binary files a/public/gatk-utils/src/test/resources/exampleNORG.bam and b/public/gatk-utils/src/test/resources/exampleNORG.bam differ
diff --git a/public/gatk-utils/src/test/resources/exampleNORG.bam.bai b/public/gatk-utils/src/test/resources/exampleNORG.bam.bai
index 26cfe74e7..f4536d363 100644
Binary files a/public/gatk-utils/src/test/resources/exampleNORG.bam.bai and b/public/gatk-utils/src/test/resources/exampleNORG.bam.bai differ
diff --git a/public/perl/liftOverVCF.pl b/public/perl/liftOverVCF.pl
deleted file mode 100755
index a942145d7..000000000
--- a/public/perl/liftOverVCF.pl
+++ /dev/null
@@ -1,83 +0,0 @@
-#!/usr/bin/perl -w
-
-# Runs the liftover tool on a VCF and properly handles the output
-
-use strict;
-use Getopt::Long;
-
-my $in = undef;
-my $gatk = undef;
-my $chain = undef;
-my $newRef = undef;
-my $oldRef = undef;
-my $out = undef;
-my $tmp = "/tmp";
-my $recordOriginalLocation = 0;
-GetOptions( "vcf=s" => \$in,
-	    "gatk=s" => \$gatk,
-	    "chain=s" => \$chain,
-	    "newRef=s" => \$newRef,
-	    "oldRef=s" => \$oldRef,
-            "out=s" => \$out,
-	    "tmp=s" => \$tmp,
-	    "recordOriginalLocation" => \$recordOriginalLocation);
-
-if ( !$in || !$gatk || !$chain || !$newRef || !$oldRef || !$out ) {
-    print "Usage: liftOverVCF.pl\n\t-vcf \t\t\n\t-gatk \t\t\n\t-chain \t\t\n\t-newRef \t\n\t-oldRef \t\n\t-out \t\t\n\t-tmp \t\t\n\t-recordOriginalLocation \t\t\n";
-    print "Example: ./liftOverVCF.pl\n\t-vcf /humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/1kg_snp_validation/all_validation_batches.b36.vcf\n\t-chain b36ToHg19.broad.over.chain\n\t-out lifted.hg19.vcf\n\t-gatk /humgen/gsa-scr1/ebanks/Sting_dev\n\t-newRef /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19\n\t-oldRef /humgen/1kg/reference/human_b36_both\n";
-    exit(1);
-}
-
-# generate a random number
-my $random_number = rand();
-my $tmp_prefix = "$tmp/$random_number";
-print "Writing temporary files to prefix: $tmp_prefix\n";
-my $unsorted_vcf = "$tmp_prefix.unsorted.vcf";
-
-# lift over the file
-print "Lifting over the vcf...";
-my $cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T LiftoverVariants -R $oldRef.fasta -V:variant $in -o $unsorted_vcf -chain $chain -dict $newRef.dict -U LENIENT_VCF_PROCESSING";
-if ($recordOriginalLocation) {
-  $cmd .= " -recordOriginalLocation";
-}
-system($cmd) == 0 or quit("The liftover step failed.  Please correct the necessary errors before retrying.");
-
-# we need to sort the lifted over file now
-print "\nRe-sorting the vcf...\n";
-my $sorted_vcf = "$tmp_prefix.sorted.vcf";
-open(SORTED, ">$sorted_vcf") or die "can't open $sorted_vcf: $!";
-
-# write the header
-open(UNSORTED, "< $unsorted_vcf") or die "can't open $unsorted_vcf: $!";
-my $inHeader = 1;
-while ( $inHeader == 1 ) {
-    my $line = ;
-    if ( $line !~ m/^#/ ) {
-	$inHeader = 0;
-    } else {
-	print SORTED "$line";
-    }
-}
-close(UNSORTED);
-close(SORTED);
-
-$cmd = "grep \"^#\" -v $unsorted_vcf | sort -n -k2 -T $tmp | $gatk/public/perl/sortByRef.pl --tmp $tmp - $newRef.fasta.fai >> $sorted_vcf";
-system($cmd) == 0 or quit("The sorting step failed.  Please correct the necessary errors before retrying.");
-
-# Filter the VCF for bad records
-print "\nFixing/removing bad records...\n";
-$cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T FilterLiftedVariants -R $newRef.fasta -V:variant $sorted_vcf -o $out -U LENIENT_VCF_PROCESSING";
-system($cmd) == 0 or quit("The filtering step failed.  Please correct the necessary errors before retrying.");
-
-# clean up
-unlink $unsorted_vcf;
-unlink $sorted_vcf;
-my $sorted_index = "$sorted_vcf.idx";
-unlink $sorted_index;
-
-print "\nDone!\n";
-
-sub quit {
-    print "\n$_[0]\n";
-    exit(1);
-}
diff --git a/public/perl/sortByRef.pl b/public/perl/sortByRef.pl
deleted file mode 100755
index e17707796..000000000
--- a/public/perl/sortByRef.pl
+++ /dev/null
@@ -1,127 +0,0 @@
-#!/usr/bin/perl -w
-
-use strict;
-use Getopt::Long;
-
-sub usage {
-
-    print "\nUsage:\n";
-    print "sortByRef.pl [--k POS] [--tmp dir] INPUT REF_DICT\n\n";
-
-    print " Sorts lines of the input file INFILE according\n";
-    print " to the reference contig order specified by the\n";
-    print " reference dictionary REF_DICT (.fai file).\n";
-    print " The sort is stable. If -k option is not specified,\n";
-    print " it is assumed that the contig name is the first\n";
-    print " field in each line.\n\n";
-    print "  INPUT       input file to sort. If '-' is specified, \n";
-    print "              then reads from STDIN.\n";
-    print "  REF_DICT    .fai file, or ANY file that has contigs, in the\n";
-    print "              desired soting order, as its first column.\n";
-    print "  --k POS :   contig name is in the field POS (1-based)\n";
-    print "              of input lines.\n\n";
-    print "  --tmp DIR : temp directory [default=/tmp]\n\n";
-
-    exit(1);
-}
-
-my $pos = 1;
-my $tmp = "/tmp";
-GetOptions( "k:i" => \$pos,
-	    "tmp=s" => \$tmp);
-
-$pos--;
-
-usage() if ( scalar(@ARGV) == 0 );
-
-if ( scalar(@ARGV) != 2 ) {
-    print "Wrong number of arguments\n";
-    usage();
-}
-
-my $input_file = $ARGV[0];
-my $dict_file = $ARGV[1];
-
-
-open(DICT, "< $dict_file") or die("Can not open $dict_file: $!");
-
-my %ref_order;
-
-my $n = 0;
-while (  ) {
-    chomp;
-    my ($contig, $rest) = split '\s';
-    die("Dictionary file is probably corrupt: multiple instances of contig $contig") if ( defined $ref_order{$contig} );
-
-    $ref_order{$contig} = $n;
-    $n++;
-}
-
-close DICT;
-#we have loaded contig ordering now
-
-my $INPUT;
-if ($input_file eq "-" ) {
-    $INPUT = "STDIN";
-} else {
-    open($INPUT, "< $input_file") or die("Can not open $input_file: $!");
-}
-
-my %temp_outputs;
-
-while ( <$INPUT> ) {
-    
-    my @fields = split '\s';
-    die("Specified field position exceeds the number of fields:\n$_") 
-        if ( $pos >= scalar(@fields) );
-
-    my $contig = $fields[$pos];
-    if ( $contig =~ m/:/ ) {
-        my @loc = split(/:/, $contig);
-        # print $contig . " " . $loc[0] . "\n";
-        $contig = $loc[0]
-    }
-    chomp $contig if ( $pos == scalar(@fields) - 1 ); # if last field in line
-
-    my $order;
-    if ( defined $ref_order{$contig} ) { $order = $ref_order{$contig}; }
-    else {
-        $ref_order{$contig} = $n;
-        $order = $n; # input line has contig that was not in the dict; 
-        $n++; # this contig will go at the end of the output, 
-              # after all known contigs
-    }
-
-    my $fhandle;
-    if ( defined $temp_outputs{$order} ) { $fhandle = $temp_outputs{$order} }
-    else {
-        #print "opening $order $$ $_\n";
-        open( $fhandle, " > $tmp/sortByRef.$$.$order.tmp" ) or
-            die ( "Can not open temporary file $order: $!");
-        $temp_outputs{$order} = $fhandle;
-    }
-
-    # we got the handle to the temp file that keeps all 
-    # lines with contig $contig
-
-    print $fhandle $_; # send current line to its corresponding temp file
-}
-
-close $INPUT;
-
-foreach my $f ( values %temp_outputs ) { close $f; }
-
-# now collect back into single output stream:
-
-for ( my $i = 0 ; $i < $n ; $i++ ) {
-    # if we did not have any lines on contig $i, then there's 
-    # no temp file and nothing to do
-    next if ( ! defined $temp_outputs{$i} ) ; 
-
-    my $f; 
-    open ( $f, "< $tmp/sortByRef.$$.$i.tmp" );
-    while ( <$f> ) { print ; }
-    close $f;
-
-    unlink "$tmp/sortByRef.$$.$i.tmp";    
-}
diff --git a/public/repo/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139.jar b/public/repo/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139.jar
deleted file mode 100644
index 2cbdd380d..000000000
Binary files a/public/repo/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139.jar and /dev/null differ
diff --git a/public/repo/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139.pom b/public/repo/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139.pom
deleted file mode 100644
index 5a6fb69b9..000000000
--- a/public/repo/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139.pom
+++ /dev/null
@@ -1,9 +0,0 @@
-
-  4.0.0
-  com.google.code.cofoja
-  cofoja
-  cofoja
-  1.0-r139
-
diff --git a/public/repo/com/google/code/cofoja/cofoja/1.2-20140817/cofoja-1.2-20140817.jar b/public/repo/com/google/code/cofoja/cofoja/1.2-20140817/cofoja-1.2-20140817.jar
new file mode 100644
index 000000000..2b105c88c
Binary files /dev/null and b/public/repo/com/google/code/cofoja/cofoja/1.2-20140817/cofoja-1.2-20140817.jar differ
diff --git a/public/repo/com/google/code/cofoja/cofoja/1.2-20140817/cofoja-1.2-20140817.pom b/public/repo/com/google/code/cofoja/cofoja/1.2-20140817/cofoja-1.2-20140817.pom
new file mode 100644
index 000000000..92fbea553
--- /dev/null
+++ b/public/repo/com/google/code/cofoja/cofoja/1.2-20140817/cofoja-1.2-20140817.pom
@@ -0,0 +1,89 @@
+
+  4.0.0
+
+  com.google.java.contract
+  cofoja
+  1.2-20140817
+  Contracts for Java
+  Contracts for Java is a contract programming framework for Java.
+  http://code.google.com/p/cofoja
+
+  
+    code.google.com
+    http://code.google.com/p/cofoja/issues
+  
+
+  2010
+
+  
+    
+      GNU Lesser General Public License, version 2.1 or later
+      http://www.gnu.org/licenses/lgpl-2.1.html
+      repo
+    
+  
+
+  
+    scm:svn:http://cofoja.googlecode.com/svn/trunk/
+    scm:svn:https://cofoja.googlecode.com/svn/trunk/
+    http://code.google.com/p/cofoja/source/browse
+  
+
+  
+    UTF-8
+  
+
+    
+        
+            andreasleitner
+            Andreas Leitner
+            andreasleitner@google.com
+            Google
+            http://www.google.com
+            
+                Developer
+            
+        
+        
+            davidmorgan
+            David Morgan
+            davidmorgan@google.com
+            Google
+            http://www.google.com
+            
+                Developer
+            
+        
+        
+            lenh
+            Nhat Minh Lê
+            nhat.minh.le@huoc.org
+            
+                Developer
+            
+        
+    
+
+    
+        
+            org.ow2.asm
+            asm-all
+            5.0.4
+            compile
+        
+        
+            junit
+            junit
+            4.8.2
+            test
+        
+        
+            com.sun
+            tools
+            1.5.0
+            system
+            ${toolsjar}                                                                                 
+        
+    
+
+