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Merge branch 'master' of github.com:broadinstitute/gsa-unstable

This commit is contained in:
Menachem Fromer 2013-02-04 12:03:42 -05:00
parent c33105bead 971ded341b
commit 9b77cdec4b
448 changed files with 20530 additions and 16769 deletions
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2
.gitignore vendored
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@ -12,6 +12,7 @@
*.ipr
*.iws
*.iml
*.pyc
.DS_Store
queueScatterGather
/foo*
@ -23,3 +24,4 @@ dist/
dump/
lib/
out/
/atlassian-ide-plugin.xml

27
build.xml
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@ -873,10 +873,6 @@
<property name="executable" value="GenomeAnalysisTK" />
</target>
<target name="init.executable.gatklite" depends="init.build.publiconly, init.javaonly">
<property name="executable" value="GenomeAnalysisTKLite" />
</target>
<target name="init.executable.queueall" depends="init.build.all, init.javaandscala">
<property name="executable" value="Queue" />
</target>
@ -885,10 +881,6 @@
<property name="executable" value="Queue" />
</target>
<target name="init.executable.queuelite" depends="init.build.publiconly, init.javaandscala">
<property name="executable" value="QueueLite" />
</target>
<target name="require.executable">
<condition property="no.executable.defined">
<or>
@ -939,15 +931,10 @@
<!-- Package specific versions of the GATK/Queue. ALWAYS do an ant clean before invoking these! -->
<target name="package.gatk.full" depends="init.executable.gatkfull,package" />
<target name="package.gatk.lite" depends="init.executable.gatklite,package" />
<target name="package.queue.all" depends="init.executable.queueall,package" />
<target name="package.queue.full" depends="init.executable.queuefull,package" />
<target name="package.queue.lite" depends="init.executable.queuelite,package" />
<!-- Release a build. Don't call this target directly. Call one of the specific release targets below -->
<target name="release" depends="require.executable" description="release a build, putting each file in a location specified by the package">
<ant antfile="${package.output.dir}/${executable}.xml" target="release" />
@ -956,13 +943,8 @@
<!-- Release specific versions of the GATK/Queue. ALWAYS do an ant clean before invoking these! -->
<target name="release.gatk.full" depends="package.gatk.full,release" />
<target name="release.gatk.lite" depends="package.gatk.lite,release" />
<target name="release.queue.full" depends="package.queue.full,release" />
<target name="release.queue.lite" depends="package.queue.lite,release" />
<!-- Build a subset of picard with only those classes we need by completely abusing the packaging system -->
<!-- TODO: Reuse as much as possible of the 'stage' and 'package' targets -->
<target name="build-picard-private" depends="resolve">
@ -1006,14 +988,10 @@
<!-- Maven install specific versions of the GATK/Queue. ALWAYS do an ant clean before invoking these! -->
<target name="mvninstall.gatk.full" depends="package.gatk.full,mvninstall" />
<target name="mvninstall.gatk.lite" depends="package.gatk.lite,mvninstall" />
<target name="mvninstall.queue.all" depends="package.queue.all,mvninstall" />
<target name="mvninstall.queue.full" depends="package.queue.full,mvninstall" />
<target name="mvninstall.queue.lite" depends="package.queue.lite,mvninstall" />
<!-- ******************************************************************************** -->
<!-- Clean -->
<!-- ******************************************************************************** -->
@ -1363,13 +1341,8 @@
<!-- Order of the dependencies is significant in the *.release.tests targets -->
<target name="gatkfull.binary.release.tests" depends="init.usecontracts,package.gatk.full,init.testgatkjar,unittest,integrationtest" />
<target name="gatklite.binary.release.tests" depends="init.usecontracts,package.gatk.lite,init.testgatkjar,unittest,integrationtest" />
<target name="queuefull.binary.release.tests" depends="init.usecontracts,package.queue.full,init.testqueuejar,pipelinetest" />
<target name="queuelite.binary.release.tests" depends="init.usecontracts,package.queue.lite,init.testqueuejar,pipelinetest" />
<!-- Our four different test types: UnitTest, IntegrationTest, LargeScaleTest, PipelineTest -->
<target name="unittest" depends="test.compile,test.init" description="Run unit tests">
<condition property="ttype" value="*UnitTest" else="${single}">

1
licensing/private_license.txt
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@ -1 +0,0 @@
protected_license.txt

43
licensing/private_license.txt 100644
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@ -0,0 +1,43 @@
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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
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. OWNERSHIP OF INTELLECTUAL PROPERTY
LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
Copyright 2012 Broad Institute, Inc.
Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
4. 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.
5. 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.
6. 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.
7. MISCELLANEOUS
7.1 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.
7.2 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.
7.3 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.
7.4 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.
7.5 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.
7.6 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.
7.7 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.

14
protected/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
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@ -109,13 +109,6 @@ public class StandardCallerArgumentCollection {
@Argument(fullName = "max_alternate_alleles", shortName = "maxAltAlleles", doc = "Maximum number of alternate alleles to genotype", required = false)
public int MAX_ALTERNATE_ALLELES = 6;
/**
* Controls the model used to calculate the probability that a site is variant plus the various sample genotypes in the data at a given locus.
*/
@Advanced
@Argument(fullName = "p_nonref_model", shortName = "pnrm", doc = "Non-reference probability calculation model to employ", required = false)
public AFCalcFactory.Calculation AFmodel = AFCalcFactory.Calculation.getDefaultModel();
/**
* If this fraction is greater is than zero, the caller will aggressively attempt to remove contamination through biased down-sampling of reads.
* Basically, it will ignore the contamination fraction of reads for each alternate allele. So if the pileup contains N total bases, then we
@ -125,6 +118,13 @@ public class StandardCallerArgumentCollection {
public double CONTAMINATION_FRACTION = DEFAULT_CONTAMINATION_FRACTION;
public static final double DEFAULT_CONTAMINATION_FRACTION = 0.05;
/**
* Controls the model used to calculate the probability that a site is variant plus the various sample genotypes in the data at a given locus.
*/
@Hidden
@Argument(fullName = "p_nonref_model", shortName = "pnrm", doc = "Non-reference probability calculation model to employ", required = false)
public AFCalcFactory.Calculation AFmodel = AFCalcFactory.Calculation.getDefaultModel();
@Hidden
@Argument(fullName = "logRemovedReadsFromContaminationFiltering", shortName="contaminationLog", required=false)
public PrintStream contaminationLog = null;

318
protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java
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@ -1,318 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.downsampling;
import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.pileup.*;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.variant.variantcontext.Allele;
import java.io.PrintStream;
import java.util.*;
public class AlleleBiasedDownsamplingUtils {
/**
* Computes an allele biased version of the given pileup
*
* @param pileup the original pileup
* @param downsamplingFraction the fraction of total reads to remove per allele
* @param log logging output
* @return allele biased pileup
*/
public static ReadBackedPileup createAlleleBiasedBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log) {
// special case removal of all or no reads
if ( downsamplingFraction <= 0.0 )
return pileup;
if ( downsamplingFraction >= 1.0 )
return new ReadBackedPileupImpl(pileup.getLocation(), new ArrayList<PileupElement>());
final ArrayList<PileupElement>[] alleleStratifiedElements = new ArrayList[4];
for ( int i = 0; i < 4; i++ )
alleleStratifiedElements[i] = new ArrayList<PileupElement>();
// keep all of the reduced reads
final ArrayList<PileupElement> reducedReadPileups = new ArrayList<PileupElement>();
// start by stratifying the reads by the alleles they represent at this position
for( final PileupElement pe : pileup ) {
// we do not want to remove a reduced read
if ( pe.getRead().isReducedRead() )
reducedReadPileups.add(pe);
final int baseIndex = BaseUtils.simpleBaseToBaseIndex(pe.getBase());
if ( baseIndex != -1 )
alleleStratifiedElements[baseIndex].add(pe);
}
// Unfortunately, we need to maintain the original pileup ordering of reads or FragmentUtils will complain later.
int numReadsToRemove = (int)(pileup.getNumberOfElements() * downsamplingFraction); // floor
final TreeSet<PileupElement> elementsToKeep = new TreeSet<PileupElement>(new Comparator<PileupElement>() {
@Override
public int compare(PileupElement element1, PileupElement element2) {
final int difference = element1.getRead().getAlignmentStart() - element2.getRead().getAlignmentStart();
return difference != 0 ? difference : element1.getRead().getReadName().compareTo(element2.getRead().getReadName());
}
});
elementsToKeep.addAll(reducedReadPileups);
// make a listing of allele counts
final int[] alleleCounts = new int[4];
for ( int i = 0; i < 4; i++ )
alleleCounts[i] = alleleStratifiedElements[i].size();
// do smart down-sampling
final int[] targetAlleleCounts = runSmartDownsampling(alleleCounts, numReadsToRemove);
for ( int i = 0; i < 4; i++ ) {
final ArrayList<PileupElement> alleleList = alleleStratifiedElements[i];
// if we don't need to remove any reads, keep them all
if ( alleleList.size() <= targetAlleleCounts[i] )
elementsToKeep.addAll(alleleList);
else
elementsToKeep.addAll(downsampleElements(alleleList, alleleList.size() - targetAlleleCounts[i], log));
}
// clean up pointers so memory can be garbage collected if needed
for ( int i = 0; i < 4; i++ )
alleleStratifiedElements[i].clear();
return new ReadBackedPileupImpl(pileup.getLocation(), new ArrayList<PileupElement>(elementsToKeep));
}
private static int scoreAlleleCounts(final int[] alleleCounts) {
if ( alleleCounts.length < 2 )
return 0;
// sort the counts (in ascending order)
final int[] alleleCountsCopy = alleleCounts.clone();
Arrays.sort(alleleCountsCopy);
final int maxCount = alleleCountsCopy[alleleCounts.length - 1];
final int nextBestCount = alleleCountsCopy[alleleCounts.length - 2];
int remainderCount = 0;
for ( int i = 0; i < alleleCounts.length - 2; i++ )
remainderCount += alleleCountsCopy[i];
// try to get the best score:
// - in the het case the counts should be equal with nothing else
// - in the hom case the non-max should be zero
return Math.min(maxCount - nextBestCount + remainderCount, Math.abs(nextBestCount + remainderCount));
}
/**
* Computes an allele biased version of the given pileup
*
* @param alleleCounts the original pileup
* @param numReadsToRemove fraction of total reads to remove per allele
* @return allele biased pileup
*/
protected static int[] runSmartDownsampling(final int[] alleleCounts, final int numReadsToRemove) {
final int numAlleles = alleleCounts.length;
int maxScore = scoreAlleleCounts(alleleCounts);
int[] alleleCountsOfMax = alleleCounts;
final int numReadsToRemovePerAllele = numReadsToRemove / 2;
for ( int i = 0; i < numAlleles; i++ ) {
for ( int j = i; j < numAlleles; j++ ) {
final int[] newCounts = alleleCounts.clone();
// split these cases so we don't lose on the floor (since we divided by 2)
if ( i == j ) {
newCounts[i] = Math.max(0, newCounts[i] - numReadsToRemove);
} else {
newCounts[i] = Math.max(0, newCounts[i] - numReadsToRemovePerAllele);
newCounts[j] = Math.max(0, newCounts[j] - numReadsToRemovePerAllele);
}
final int score = scoreAlleleCounts(newCounts);
if ( score < maxScore ) {
maxScore = score;
alleleCountsOfMax = newCounts;
}
}
}
return alleleCountsOfMax;
}
/**
* Performs allele biased down-sampling on a pileup and computes the list of elements to keep
*
* @param elements original list of records
* @param numElementsToRemove the number of records to remove
* @param log logging output
* @return the list of pileup elements TO KEEP
*/
private static List<PileupElement> downsampleElements(final ArrayList<PileupElement> elements, final int numElementsToRemove, final PrintStream log) {
if ( numElementsToRemove == 0 )
return elements;
final int pileupSize = elements.size();
if ( numElementsToRemove == pileupSize ) {
logAllElements(elements, log);
return new ArrayList<PileupElement>(0);
}
final BitSet itemsToRemove = new BitSet(pileupSize);
for ( Integer selectedIndex : MathUtils.sampleIndicesWithoutReplacement(pileupSize, numElementsToRemove) ) {
itemsToRemove.set(selectedIndex);
}
ArrayList<PileupElement> elementsToKeep = new ArrayList<PileupElement>(pileupSize - numElementsToRemove);
for ( int i = 0; i < pileupSize; i++ ) {
if ( itemsToRemove.get(i) )
logRead(elements.get(i).getRead(), log);
else
elementsToKeep.add(elements.get(i));
}
return elementsToKeep;
}
/**
* Computes reads to remove based on an allele biased down-sampling
*
* @param alleleReadMap original list of records per allele
* @param downsamplingFraction the fraction of total reads to remove per allele
* @param log logging output
* @return list of reads TO REMOVE from allele biased down-sampling
*/
public static List<GATKSAMRecord> selectAlleleBiasedReads(final Map<Allele, List<GATKSAMRecord>> alleleReadMap, final double downsamplingFraction, final PrintStream log) {
int totalReads = 0;
for ( final List<GATKSAMRecord> reads : alleleReadMap.values() )
totalReads += reads.size();
int numReadsToRemove = (int)(totalReads * downsamplingFraction);
// make a listing of allele counts
final List<Allele> alleles = new ArrayList<Allele>(alleleReadMap.keySet());
alleles.remove(Allele.NO_CALL); // ignore the no-call bin
final int numAlleles = alleles.size();
final int[] alleleCounts = new int[numAlleles];
for ( int i = 0; i < numAlleles; i++ )
alleleCounts[i] = alleleReadMap.get(alleles.get(i)).size();
// do smart down-sampling
final int[] targetAlleleCounts = runSmartDownsampling(alleleCounts, numReadsToRemove);
final List<GATKSAMRecord> readsToRemove = new ArrayList<GATKSAMRecord>(numReadsToRemove);
for ( int i = 0; i < numAlleles; i++ ) {
final List<GATKSAMRecord> alleleBin = alleleReadMap.get(alleles.get(i));
if ( alleleBin.size() > targetAlleleCounts[i] ) {
readsToRemove.addAll(downsampleReads(alleleBin, alleleBin.size() - targetAlleleCounts[i], log));
}
}
return readsToRemove;
}
/**
* Performs allele biased down-sampling on a pileup and computes the list of elements to remove
*
* @param reads original list of records
* @param numElementsToRemove the number of records to remove
* @param log logging output
* @return the list of pileup elements TO REMOVE
*/
private static List<GATKSAMRecord> downsampleReads(final List<GATKSAMRecord> reads, final int numElementsToRemove, final PrintStream log) {
final ArrayList<GATKSAMRecord> readsToRemove = new ArrayList<GATKSAMRecord>(numElementsToRemove);
if ( numElementsToRemove == 0 )
return readsToRemove;
final int pileupSize = reads.size();
if ( numElementsToRemove == pileupSize ) {
logAllReads(reads, log);
return reads;
}
final BitSet itemsToRemove = new BitSet(pileupSize);
for ( Integer selectedIndex : MathUtils.sampleIndicesWithoutReplacement(pileupSize, numElementsToRemove) ) {
itemsToRemove.set(selectedIndex);
}
for ( int i = 0; i < pileupSize; i++ ) {
if ( itemsToRemove.get(i) ) {
final GATKSAMRecord read = reads.get(i);
readsToRemove.add(read);
logRead(read, log);
}
}
return readsToRemove;
}
private static void logAllElements(final List<PileupElement> elements, final PrintStream log) {
if ( log != null ) {
for ( final PileupElement p : elements )
logRead(p.getRead(), log);
}
}
private static void logAllReads(final List<GATKSAMRecord> reads, final PrintStream log) {
if ( log != null ) {
for ( final GATKSAMRecord read : reads )
logRead(read, log);
}
}
private static void logRead(final SAMRecord read, final PrintStream log) {
if ( log != null ) {
final SAMReadGroupRecord readGroup = read.getReadGroup();
log.println(String.format("%s\t%s\t%s\t%s", read.getReadName(), readGroup.getSample(), readGroup.getLibrary(), readGroup.getPlatformUnit()));
}
}
}

176
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@ -1,176 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypesContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* The allele balance (fraction of ref bases over ref + alt bases) across all bialleleic het-called samples
*/
public class AlleleBalance extends InfoFieldAnnotation {
char[] BASES = {'A','C','G','T'};
public Map<String, Object> annotate(final RefMetaDataTracker tracker,
final AnnotatorCompatible walker,
final ReferenceContext ref,
final Map<String, AlignmentContext> stratifiedContexts,
final VariantContext vc,
final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
if ( stratifiedContexts.size() == 0 )
return null;
if ( !vc.isBiallelic() )
return null;
final GenotypesContext genotypes = vc.getGenotypes();
if ( !vc.hasGenotypes() )
return null;
double ratioHom = 0.0;
double ratioHet = 0.0;
double weightHom = 0.0;
double weightHet = 0.0;
double overallNonDiploid = 0.0;
for ( Genotype genotype : genotypes ) {
// we care only about het calls
AlignmentContext context = stratifiedContexts.get(genotype.getSampleName());
if ( context == null )
continue;
final ReadBackedPileup pileup = context.getBasePileup();
if ( vc.isSNP() ) {
final String bases = new String(pileup.getBases());
if ( bases.length() == 0 )
return null;
double pTrue = 1.0 - Math.pow(10.0,genotype.getLog10PError());
if ( genotype.isHet() ) {
final char refChr = vc.getReference().toString().charAt(0);
final char altChr = vc.getAlternateAllele(0).toString().charAt(0);
final int refCount = MathUtils.countOccurrences(refChr, bases);
final int altCount = MathUtils.countOccurrences(altChr, bases);
final int otherCount = bases.length()-refCount-altCount;
// sanity check
if ( refCount + altCount == 0 )
continue;
// weight the allele balance by genotype quality so that e.g. mis-called homs don't affect the ratio too much
ratioHet += pTrue * ((double)refCount / (double)(refCount + altCount));
weightHet += pTrue;
overallNonDiploid += ( (double) otherCount )/(bases.length()*genotypes.size());
} else if ( genotype.isHom() ) {
char alleleChr;
if ( genotype.isHomRef() ) {
alleleChr = vc.getReference().toString().charAt(0);
} else {
alleleChr = vc.getAlternateAllele(0).toString().charAt(0);
}
final int alleleCount = MathUtils.countOccurrences(alleleChr,bases);
int bestOtherCount = 0;
for ( char b : BASES ) {
if ( b == alleleChr )
continue;
int count = MathUtils.countOccurrences(b,bases);
if ( count > bestOtherCount )
bestOtherCount = count;
}
final int otherCount = bases.length() - alleleCount;
ratioHom += pTrue*( (double) alleleCount)/(alleleCount+bestOtherCount);
weightHom += pTrue;
overallNonDiploid += ((double ) otherCount)/(bases.length()*genotypes.size());
}
// Allele Balance for indels was not being computed correctly (since there was no allele matching). Instead of
// prolonging the life of imperfect code, I've decided to delete it. If someone else wants to try again from
// scratch, be my guest - but make sure it's done correctly! [EB]
}
}
// make sure we had a het genotype
Map<String, Object> map = new HashMap<String, Object>();
if ( weightHet > 0.0 ) {
map.put("ABHet",ratioHet/weightHet);
}
if ( weightHom > 0.0 ) {
map.put("ABHom",ratioHom/weightHom);
}
if ( overallNonDiploid > 0.0 ) {
map.put("OND",overallNonDiploid);
}
return map;
}
public List<String> getKeyNames() { return Arrays.asList("ABHet","ABHom","OND"); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("ABHet", 1, VCFHeaderLineType.Float, "Allele Balance for hets (ref/(ref+alt))"),
new VCFInfoHeaderLine("ABHom", 1, VCFHeaderLineType.Float, "Allele Balance for homs (A/(A+O))"),
new VCFInfoHeaderLine("OND", 1, VCFHeaderLineType.Float, "Overall non-diploid ratio (alleles/(alleles+non-alleles))")); }
}

131
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
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@ -1,131 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.variant.vcf.VCFFormatHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.Collection;
import java.util.List;
/**
* The allele balance (fraction of ref bases over ref + alt bases) separately for each bialleleic het-called sample
*/
public class AlleleBalanceBySample extends GenotypeAnnotation implements ExperimentalAnnotation {
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 ( stratifiedContext == null )
return;
Double ratio = annotateSNP(stratifiedContext, vc, g);
if (ratio == null)
return;
gb.attribute(getKeyNames().get(0), Double.valueOf(String.format("%.2f", ratio.doubleValue())));
}
private Double annotateSNP(AlignmentContext stratifiedContext, VariantContext vc, Genotype g) {
double ratio = -1;
if ( !vc.isSNP() )
return null;
if ( !vc.isBiallelic() )
return null;
if ( g == null || !g.isCalled() )
return null;
if (!g.isHet())
return null;
Collection<Allele> altAlleles = vc.getAlternateAlleles();
if ( altAlleles.size() == 0 )
return null;
final String bases = new String(stratifiedContext.getBasePileup().getBases());
if ( bases.length() == 0 )
return null;
char refChr = vc.getReference().toString().charAt(0);
char altChr = vc.getAlternateAllele(0).toString().charAt(0);
int refCount = MathUtils.countOccurrences(refChr, bases);
int altCount = MathUtils.countOccurrences(altChr, bases);
// sanity check
if ( refCount + altCount == 0 )
return null;
ratio = ((double)refCount / (double)(refCount + altCount));
return ratio;
}
public List<String> getKeyNames() { return Arrays.asList("AB"); }
public List<VCFFormatHeaderLine> getDescriptions() { return Arrays.asList(new VCFFormatHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Float, "Allele balance for each het genotype")); }
}

138
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AverageAltAlleleLength.java
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@ -1,138 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypesContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* Created by IntelliJ IDEA.
* User: chartl
* Date: 1/3/13
* Time: 11:36 AM
* To change this template use File | Settings | File Templates.
*/
public class AverageAltAlleleLength extends InfoFieldAnnotation implements ActiveRegionBasedAnnotation, ExperimentalAnnotation {
public List<VCFInfoHeaderLine> getDescriptions() {
return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Float, "Average Allele Length"));
}
public List<String> getKeyNames() { return Arrays.asList("AAL"); }
public Map<String, Object> annotate(final RefMetaDataTracker tracker,
final AnnotatorCompatible walker,
final ReferenceContext ref,
final Map<String, AlignmentContext> stratifiedContexts,
final VariantContext vc,
final Map<String, PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap ) {
if ( !vc.hasLog10PError() )
return null;
final GenotypesContext genotypes = vc.getGenotypes();
if ( genotypes == null || genotypes.size() == 0 )
return null;
Map<String, Object> map = new HashMap<String, Object>();
double length = getMeanAltAlleleLength(vc);
map.put(getKeyNames().get(0),String.format("%.2f",length));
return map;
}
public static double getMeanAltAlleleLength(VariantContext vc) {
double averageLength = 1.0;
if ( ! vc.isSNP() && ! vc.isSymbolic() ) {
// adjust for the event length
int averageLengthNum = 0;
int averageLengthDenom = 0;
int refLength = vc.getReference().length();
for ( Allele a : vc.getAlternateAlleles() ) {
int numAllele = vc.getCalledChrCount(a);
int alleleSize;
if ( a.length() == refLength ) {
// SNP or MNP
byte[] a_bases = a.getBases();
byte[] ref_bases = vc.getReference().getBases();
int n_mismatch = 0;
for ( int idx = 0; idx < a_bases.length; idx++ ) {
if ( a_bases[idx] != ref_bases[idx] )
n_mismatch++;
}
alleleSize = n_mismatch;
}
else if ( a.isSymbolic() ) {
alleleSize = 1;
} else {
alleleSize = Math.abs(refLength-a.length());
}
averageLengthNum += alleleSize*numAllele;
averageLengthDenom += numAllele;
}
averageLength = ( (double) averageLengthNum )/averageLengthDenom;
}
return averageLength;
}
}

97
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
View File

@ -1,97 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* Count of A, C, G, T bases across all samples
*/
public class BaseCounts extends InfoFieldAnnotation {
public Map<String, Object> annotate(final RefMetaDataTracker tracker,
final AnnotatorCompatible walker,
final ReferenceContext ref,
final Map<String, AlignmentContext> stratifiedContexts,
final VariantContext vc,
final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
if ( stratifiedContexts.size() == 0 )
return null;
int[] counts = new int[4];
for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
for (byte base : sample.getValue().getBasePileup().getBases() ) {
int index = BaseUtils.simpleBaseToBaseIndex(base);
if ( index != -1 )
counts[index]++;
}
}
Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), counts);
return map;
}
public List<String> getKeyNames() { return Arrays.asList("BaseCounts"); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("BaseCounts", 4, VCFHeaderLineType.Integer, "Counts of each base")); }
}

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
View File

@ -99,7 +99,7 @@ public class DepthOfCoverage extends InfoFieldAnnotation implements StandardAnno
for (PerReadAlleleLikelihoodMap maps : perReadAlleleLikelihoodMap.values() ) {
for (Map.Entry<GATKSAMRecord,Map<Allele,Double>> el : maps.getLikelihoodReadMap().entrySet()) {
final GATKSAMRecord read = el.getKey();
depth += (read.isReducedRead() ? read.getReducedCount(ReadUtils.getReadCoordinateForReferenceCoordinate(read, vc.getStart(), ReadUtils.ClippingTail.RIGHT_TAIL)) : 1);
depth += (read.isReducedRead() ? read.getReducedCount(ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead(read, vc.getStart(), ReadUtils.ClippingTail.RIGHT_TAIL)) : 1);
}
}
}

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
View File

@ -144,7 +144,7 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
continue; // read is non-informative
if (!vc.getAlleles().contains(a))
continue; // sanity check - shouldn't be needed
alleleCounts.put(a, alleleCounts.get(a) + (read.isReducedRead() ? read.getReducedCount(ReadUtils.getReadCoordinateForReferenceCoordinate(read, vc.getStart(), ReadUtils.ClippingTail.RIGHT_TAIL)) : 1));
alleleCounts.put(a, alleleCounts.get(a) + (read.isReducedRead() ? read.getReducedCount(ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead(read, vc.getStart(), ReadUtils.ClippingTail.RIGHT_TAIL)) : 1));
}
final int[] counts = new int[alleleCounts.size()];
counts[0] = alleleCounts.get(vc.getReference());

59
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
View File

@ -116,8 +116,8 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
else if (table1 == null)
return annotationForOneTable(pValueForContingencyTable(table2));
else { // take the one with the best (i.e., least significant pvalue)
double pvalue1 = Math.max(pValueForContingencyTable(table1), MIN_PVALUE);
double pvalue2 = Math.max(pValueForContingencyTable(table2), MIN_PVALUE);
double pvalue1 = pValueForContingencyTable(table1);
double pvalue2 = pValueForContingencyTable(table2);
return annotationForOneTable(Math.max(pvalue1, pvalue2));
}
}
@ -129,7 +129,7 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
* @return a hash map from FS -> phred-scaled pValue
*/
private Map<String, Object> annotationForOneTable(final double pValue) {
final Object value = String.format("%.3f", QualityUtils.phredScaleErrorRate(pValue));
final Object value = String.format("%.3f", QualityUtils.phredScaleErrorRate(Math.max(pValue, MIN_PVALUE))); // prevent INFINITYs
return Collections.singletonMap(FS, value);
// Map<String, Object> map = new HashMap<String, Object>();
// map.put(FS, String.format("%.3f", QualityUtils.phredScaleErrorRate(pValue)));
@ -265,24 +265,16 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
for (PerReadAlleleLikelihoodMap maps : stratifiedPerReadAlleleLikelihoodMap.values() ) {
for (Map.Entry<GATKSAMRecord,Map<Allele,Double>> el : maps.getLikelihoodReadMap().entrySet()) {
final boolean matchesRef = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue()).equals(ref,true);
final boolean matchesAlt = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue()).equals(alt,true);
if ( !matchesRef && !matchesAlt )
continue;
boolean isFW = el.getKey().getReadNegativeStrandFlag();
int row = matchesRef ? 0 : 1;
int column = isFW ? 0 : 1;
final Allele mostLikelyAllele = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue());
final GATKSAMRecord read = el.getKey();
table[row][column] += (read.isReducedRead() ? read.getReducedCount(ReadUtils.getReadCoordinateForReferenceCoordinate(read, vc.getStart(), ReadUtils.ClippingTail.RIGHT_TAIL)) : 1);
final int representativeCount = read.isReducedRead() ? read.getReducedCount(ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead(read, vc.getStart(), ReadUtils.ClippingTail.RIGHT_TAIL)) : 1;
updateTable(table, mostLikelyAllele, read, ref, alt, representativeCount);
}
}
return table;
}
/**
Allocate and fill a 2x2 strand contingency table. In the end, it'll look something like this:
* fw rc
@ -299,31 +291,36 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
for (PileupElement p : sample.getValue().getBasePileup()) {
// ignore reduced reads because they are always on the forward strand!
// TODO -- when het compression is enabled in RR, we somehow need to allow those reads through into the Fisher test
if ( p.getRead().isReducedRead() )
continue;
if ( ! RankSumTest.isUsableBase(p, false) ) // ignore deletions
continue;
if ( p.getQual() < minQScoreToConsider || p.getMappingQual() < minQScoreToConsider )
continue;
final Allele base = Allele.create(p.getBase(), false);
final boolean isFW = !p.getRead().getReadNegativeStrandFlag();
final boolean matchesRef = ref.equals(base, true);
final boolean matchesAlt = alt.equals(base, true);
if ( matchesRef || matchesAlt ) {
int row = matchesRef ? 0 : 1;
int column = isFW ? 0 : 1;
table[row][column] += p.getRepresentativeCount();
}
updateTable(table, Allele.create(p.getBase(), false), p.getRead(), ref, alt, p.getRepresentativeCount());
}
}
return table;
}
private static void updateTable(final int[][] table, final Allele allele, final GATKSAMRecord read, final Allele ref, final Allele alt, final int representativeCount) {
// ignore reduced reads because they are always on the forward strand!
// TODO -- when het compression is enabled in RR, we somehow need to allow those reads through into the Fisher test
if ( read.isReducedRead() )
return;
final boolean matchesRef = allele.equals(ref, true);
final boolean matchesAlt = allele.equals(alt, true);
if ( matchesRef || matchesAlt ) {
final boolean isFW = !read.getReadNegativeStrandFlag();
int row = matchesRef ? 0 : 1;
int column = isFW ? 0 : 1;
table[row][column] += representativeCount;
}
}
}

6
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
View File

@ -54,7 +54,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
@ -95,9 +95,9 @@ public class GCContent extends InfoFieldAnnotation implements ExperimentalAnnota
for ( byte base : ref.getBases() ) {
int baseIndex = BaseUtils.simpleBaseToBaseIndex(base);
if ( baseIndex == BaseUtils.gIndex || baseIndex == BaseUtils.cIndex )
if ( baseIndex == BaseUtils.Base.G.ordinal() || baseIndex == BaseUtils.Base.C.ordinal() )
gc++;
else if ( baseIndex == BaseUtils.aIndex || baseIndex == BaseUtils.tIndex )
else if ( baseIndex == BaseUtils.Base.A.ordinal() || baseIndex == BaseUtils.Base.T.ordinal() )
at++;
else
; // ignore

60
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
View File

@ -55,8 +55,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.Haplotype;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
@ -236,8 +235,8 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
final byte[] haplotypeBases = new byte[contextSize];
Arrays.fill(haplotypeBases, (byte) REGEXP_WILDCARD);
final double[] baseQualities = new double[contextSize];
Arrays.fill(baseQualities, 0.0);
final byte[] baseQualities = new byte[contextSize];
Arrays.fill(baseQualities, (byte)0);
byte[] readBases = read.getReadBases();
readBases = AlignmentUtils.readToAlignmentByteArray(read.getCigar(), readBases); // Adjust the read bases based on the Cigar string
@ -267,7 +266,7 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
readQuals[baseOffset] = (byte) 0;
} // quals less than 5 are used as codes and don't have actual probabilistic meaning behind them
haplotypeBases[i] = readBases[baseOffset];
baseQualities[i] = (double) readQuals[baseOffset];
baseQualities[i] = readQuals[baseOffset];
}
return new Haplotype(haplotypeBases, baseQualities);
@ -286,10 +285,10 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
final int length = a.length;
final byte[] consensusChars = new byte[length];
final double[] consensusQuals = new double[length];
final int[] consensusQuals = new int[length];
final double[] qualsA = haplotypeA.getQuals();
final double[] qualsB = haplotypeB.getQuals();
final int[] qualsA = haplotypeA.getQuals();
final int[] qualsB = haplotypeB.getQuals();
for (int i = 0; i < length; i++) {
chA = a[i];
@ -300,7 +299,7 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
if ((chA == wc) && (chB == wc)) {
consensusChars[i] = wc;
consensusQuals[i] = 0.0;
consensusQuals[i] = 0;
} else if ((chA == wc)) {
consensusChars[i] = chB;
consensusQuals[i] = qualsB[i];
@ -433,7 +432,6 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
}
public List<String> getKeyNames() {
return Arrays.asList("HaplotypeScore");
}
@ -441,4 +439,46 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
public List<VCFInfoHeaderLine> getDescriptions() {
return Arrays.asList(new VCFInfoHeaderLine("HaplotypeScore", 1, VCFHeaderLineType.Float, "Consistency of the site with at most two segregating haplotypes"));
}
private static class Haplotype {
private final byte[] bases;
private final int[] quals;
private int qualitySum = -1;
public Haplotype( final byte[] bases, final int[] quals ) {
this.bases = bases;
this.quals = quals;
}
public Haplotype( final byte[] bases, final int qual ) {
this.bases = bases;
quals = new int[bases.length];
Arrays.fill(quals, qual);
}
public Haplotype( final byte[] bases, final byte[] quals ) {
this.bases = bases;
this.quals = new int[quals.length];
for ( int i = 0 ; i < quals.length; i++ )
this.quals[i] = (int)quals[i];
}
public double getQualitySum() {
if ( qualitySum == -1 ) {
qualitySum = 0;
for ( final int qual : quals ) {
qualitySum += qual;
}
}
return qualitySum;
}
public int[] getQuals() {
return quals.clone();
}
public byte[] getBases() {
return bases.clone();
}
}
}

100
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View File

@ -1,100 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* Triplet annotation: fraction of MAQP == 0, MAPQ < 10, and count of all mapped reads
*/
public class LowMQ extends InfoFieldAnnotation {
public Map<String, Object> annotate(final RefMetaDataTracker tracker,
final AnnotatorCompatible walker,
final ReferenceContext ref,
final Map<String, AlignmentContext> stratifiedContexts,
final VariantContext vc,
final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
if ( stratifiedContexts.size() == 0 )
return null;
double mq0 = 0;
double mq10 = 0;
double total = 0;
for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() )
{
for ( PileupElement p : sample.getValue().getBasePileup() )
{
if ( p.getMappingQual() == 0 ) { mq0 += 1; }
if ( p.getMappingQual() <= 10 ) { mq10 += 1; }
total += 1;
}
}
Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%.04f,%.04f,%.00f", mq0/total, mq10/total, total));
return map;
}
public List<String> getKeyNames() { return Arrays.asList("LowMQ"); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 3, VCFHeaderLineType.Float, "3-tuple: <fraction of reads with MQ=0>,<fraction of reads with MQ<=10>,<total number of reads>")); }
}

99
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
View File

@ -1,99 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.variant.vcf.VCFFormatHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.List;
/**
* Count for each sample of mapping quality zero reads
*/
public class MappingQualityZeroBySample extends GenotypeAnnotation {
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 ( g == null || !g.isCalled() || stratifiedContext == null )
return;
int mq0 = 0;
final ReadBackedPileup pileup = stratifiedContext.getBasePileup();
for (PileupElement p : pileup ) {
if ( p.getMappingQual() == 0 )
mq0++;
}
gb.attribute(getKeyNames().get(0), mq0);
}
public List<String> getKeyNames() { return Arrays.asList(VCFConstants.MAPPING_QUALITY_ZERO_KEY); }
public List<VCFFormatHeaderLine> getDescriptions() { return Arrays.asList(
new VCFFormatHeaderLine(getKeyNames().get(0), 1,
VCFHeaderLineType.Integer, "Number of Mapping Quality Zero Reads per sample")); }
}

106
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java
View File

@ -1,106 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* Fraction of all reads across samples that have mapping quality zero
*/
public class MappingQualityZeroFraction extends InfoFieldAnnotation implements ExperimentalAnnotation {
public Map<String, Object> annotate(final RefMetaDataTracker tracker,
final AnnotatorCompatible walker,
final ReferenceContext ref,
final Map<String, AlignmentContext> stratifiedContexts,
final VariantContext vc,
final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
if ( stratifiedContexts.size() == 0 )
return null;
int mq0 = 0;
int depth = 0;
for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
AlignmentContext context = sample.getValue();
depth += context.size();
final ReadBackedPileup pileup = context.getBasePileup();
for (PileupElement p : pileup ) {
if ( p.getMappingQual() == 0 )
mq0++;
}
}
if (depth > 0) {
double mq0f = (double)mq0 / (double )depth;
Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%1.4f", mq0f));
return map;
}
else
return null;
}
public List<String> getKeyNames() { return Arrays.asList("MQ0Fraction"); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Integer, "Fraction of Mapping Quality Zero Reads")); }
}

102
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
View File

@ -1,102 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* The number of N bases, counting only SOLiD data
*/
public class NBaseCount extends InfoFieldAnnotation {
public Map<String, Object> annotate(final RefMetaDataTracker tracker,
final AnnotatorCompatible walker,
final ReferenceContext ref,
final Map<String, AlignmentContext> stratifiedContexts,
final VariantContext vc,
final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
if( stratifiedContexts.size() == 0 )
return null;
int countNBaseSolid = 0;
int countRegularBaseSolid = 0;
for( final AlignmentContext context : stratifiedContexts.values() ) {
for( final PileupElement p : context.getBasePileup()) {
final String platform = p.getRead().getReadGroup().getPlatform();
if( platform != null && platform.toUpperCase().contains("SOLID") ) {
if( BaseUtils.isNBase( p.getBase() ) ) {
countNBaseSolid++;
} else if( BaseUtils.isRegularBase( p.getBase() ) ) {
countRegularBaseSolid++;
}
}
}
}
final Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%.4f", (double)countNBaseSolid / (double)(countNBaseSolid + countRegularBaseSolid + 1)));
return map;
}
public List<String> getKeyNames() { return Arrays.asList("PercentNBaseSolid"); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("PercentNBaseSolid", 1, VCFHeaderLineType.Float, "Percentage of N bases in the pileup (counting only SOLiD reads)")); }
}

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
View File

@ -107,7 +107,7 @@ public class ReadPosRankSumTest extends RankSumTest implements StandardAnnotatio
final int offset = ReadUtils.getReadCoordinateForReferenceCoordinate( read.getSoftStart(), read.getCigar(), refLoc, ReadUtils.ClippingTail.RIGHT_TAIL, true );
if ( offset == ReadUtils.CLIPPING_GOAL_NOT_REACHED )
continue;
int readPos = AlignmentUtils.calcAlignmentByteArrayOffset( read.getCigar(), offset, false, false, 0, 0 );
int readPos = AlignmentUtils.calcAlignmentByteArrayOffset( read.getCigar(), offset, false, 0, 0 );
final int numAlignedBases = AlignmentUtils.getNumAlignedBasesCountingSoftClips( read );
if (readPos > numAlignedBases / 2)
readPos = numAlignedBases - (readPos + 1);

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java
View File

@ -54,10 +54,10 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.variant.vcf.VCFHeaderLineCount;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;

122
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java
View File

@ -1,122 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.commandline.Hidden;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* Counts of bases from Illumina, 454, and SOLiD at this site
*/
@Hidden
public class TechnologyComposition extends InfoFieldAnnotation implements ExperimentalAnnotation {
private String nIllumina = "NumIllumina";
private String n454 ="Num454";
private String nSolid = "NumSOLiD";
private String nOther = "NumOther";
public Map<String, Object> annotate(final RefMetaDataTracker tracker,
final AnnotatorCompatible walker,
final ReferenceContext ref,
final Map<String, AlignmentContext> stratifiedContexts,
final VariantContext vc,
final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
if ( stratifiedContexts.size() == 0 )
return null;
int readsIllumina = 0;
int readsSolid = 0;
int reads454 = 0;
int readsOther = 0;
for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
AlignmentContext context = sample.getValue();
final ReadBackedPileup pileup = context.getBasePileup();
for ( PileupElement p : pileup ) {
if(ReadUtils.is454Read(p.getRead()))
reads454++;
else if (ReadUtils.isSOLiDRead(p.getRead()))
readsSolid++;
else if (ReadUtils.isIlluminaRead(p.getRead()))
readsIllumina++;
else
readsOther++;
}
}
Map<String, Object> map = new HashMap<String, Object>();
map.put(nIllumina, String.format("%d", readsIllumina));
map.put(n454, String.format("%d", reads454));
map.put(nSolid, String.format("%d", readsSolid));
map.put(nOther, String.format("%d", readsOther));
return map;
}
public List<String> getKeyNames() { return Arrays.asList(nIllumina,n454,nSolid,nOther); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(nIllumina, 1, VCFHeaderLineType.Integer, "Number of Illumina reads"),
new VCFInfoHeaderLine(n454, 1, VCFHeaderLineType.Integer, "Number of 454 reads"),
new VCFInfoHeaderLine(nSolid, 1, VCFHeaderLineType.Integer, "Number of SOLiD reads"),
new VCFInfoHeaderLine(nOther, 1, VCFHeaderLineType.Integer, "Number of Other technology reads")); }
}

63
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java
View File

@ -1,63 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.annotator.interfaces;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.List;
import java.util.Map;
// TODO -- make this an abstract class when we move away from InfoFieldAnnotation
public interface ActiveRegionBasedAnnotation extends AnnotationType {
// return annotations for the given contexts split by sample and then read likelihood
public abstract Map<String, Object> annotate(final Map<String,PerReadAlleleLikelihoodMap> stratifiedContexts, final VariantContext vc);
// return the descriptions used for the VCF INFO meta field
public abstract List<VCFInfoHeaderLine> getDescriptions();
}

148
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@ -1,148 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.annotator.interfaces;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.util.*;
public class AnnotationInterfaceManager {
private static PluginManager<InfoFieldAnnotation> infoFieldAnnotationPluginManager = new PluginManager<InfoFieldAnnotation>(InfoFieldAnnotation.class);
private static PluginManager<GenotypeAnnotation> genotypeAnnotationPluginManager = new PluginManager<GenotypeAnnotation>(GenotypeAnnotation.class);
private static PluginManager<AnnotationType> annotationTypePluginManager = new PluginManager<AnnotationType>(AnnotationType.class);
public static List<InfoFieldAnnotation> createAllInfoFieldAnnotations() {
return infoFieldAnnotationPluginManager.createAllTypes();
}
public static List<GenotypeAnnotation> createAllGenotypeAnnotations() {
return genotypeAnnotationPluginManager.createAllTypes();
}
public static void validateAnnotations(List<String> annotationGroupsToUse, List<String> annotationsToUse) {
HashMap<String, Class> classMap = new HashMap<String, Class>();
for ( Class c : infoFieldAnnotationPluginManager.getPlugins() )
classMap.put(c.getSimpleName(), c);
for ( Class c : genotypeAnnotationPluginManager.getPlugins() )
classMap.put(c.getSimpleName(), c);
for ( Class c : annotationTypePluginManager.getInterfaces() )
classMap.put(c.getSimpleName(), c);
if ( annotationGroupsToUse.size() != 1 || !"none".equals(annotationGroupsToUse.get(0)) ) {
for ( String group : annotationGroupsToUse ) {
Class interfaceClass = classMap.get(group);
if ( interfaceClass == null )
interfaceClass = classMap.get(group + "Annotation");
if ( interfaceClass == null )
throw new UserException.BadArgumentValue("group", "Class " + group + " is not found; please check that you have specified the class name correctly");
}
}
// validate the specific classes provided
for ( String annotation : annotationsToUse ) {
Class annotationClass = classMap.get(annotation);
if ( annotationClass == null )
annotationClass = classMap.get(annotation + "Annotation");
if ( annotationClass == null )
throw new UserException.BadArgumentValue("annotation", "Class " + annotation + " is not found; please check that you have specified the class name correctly");
}
}
public static List<InfoFieldAnnotation> createInfoFieldAnnotations(List<String> annotationGroupsToUse, List<String> annotationsToUse) {
return createAnnotations(infoFieldAnnotationPluginManager, annotationGroupsToUse, annotationsToUse);
}
public static List<GenotypeAnnotation> createGenotypeAnnotations(List<String> annotationGroupsToUse, List<String> annotationsToUse) {
return createAnnotations(genotypeAnnotationPluginManager, annotationGroupsToUse, annotationsToUse);
}
private static <T> List<T> createAnnotations(PluginManager<T> pluginManager, List<String> annotationGroupsToUse, List<String> annotationsToUse) {
// get the instances
List<T> annotations = new ArrayList<T>();
// get the classes from the provided groups (interfaces)
// create a map for all annotation classes which implement our top-level interfaces
HashMap<String, Class> classMap = new HashMap<String, Class>();
for ( Class c : pluginManager.getPlugins() )
classMap.put(c.getSimpleName(), c);
for ( Class c : annotationTypePluginManager.getInterfaces() )
classMap.put(c.getSimpleName(), c);
// use a TreeSet so that classes are returned deterministically (the plugin manager apparently isn't deterministic)
TreeSet<Class> classes = new TreeSet<Class>(new Comparator<Class>() {
public int compare(Class o1, Class o2) {
return o1.getSimpleName().compareTo(o2.getSimpleName());
}
});
if ( annotationGroupsToUse.size() != 1 || !"none".equals(annotationGroupsToUse.get(0)) ) {
for ( String group : annotationGroupsToUse ) {
Class interfaceClass = classMap.get(group);
if ( interfaceClass == null )
interfaceClass = classMap.get(group + "Annotation");
if ( interfaceClass != null )
classes.addAll(pluginManager.getPluginsImplementing(interfaceClass));
}
}
// get the specific classes provided
for ( String annotation : annotationsToUse ) {
Class annotationClass = classMap.get(annotation);
if ( annotationClass == null )
annotationClass = classMap.get(annotation + "Annotation");
if ( annotationClass != null )
classes.add(annotationClass);
}
// note that technically an annotation can work on both the INFO and FORMAT fields
for ( Class c : classes )
annotations.add(pluginManager.createByType(c));
return annotations;
}
}

49
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@ -1,49 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.annotator.interfaces;
public interface AnnotationType {}

62
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@ -1,62 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.annotator.interfaces;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.List;
public interface AnnotatorCompatible {
// getter methods for various used bindings
public abstract RodBinding<VariantContext> getSnpEffRodBinding();
public abstract RodBinding<VariantContext> getDbsnpRodBinding();
public abstract List<RodBinding<VariantContext>> getCompRodBindings();
public abstract List<RodBinding<VariantContext>> getResourceRodBindings();
public abstract boolean alwaysAppendDbsnpId();
}

49
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@ -1,49 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.annotator.interfaces;
public interface ExperimentalAnnotation extends AnnotationType {}

75
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@ -1,75 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.annotator.interfaces;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.variant.vcf.VCFFormatHeaderLine;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.List;
public abstract class GenotypeAnnotation extends VariantAnnotatorAnnotation {
// return annotations for the given contexts/genotype split by sample
public abstract 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);
// return the descriptions used for the VCF FORMAT meta field
public abstract List<VCFFormatHeaderLine> getDescriptions();
}

83
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
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@ -1,83 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.annotator.interfaces;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.List;
import java.util.Map;
public abstract class InfoFieldAnnotation extends VariantAnnotatorAnnotation {
// return annotations for the given contexts split by sample
public Map<String, Object> annotate(final RefMetaDataTracker tracker,
final AnnotatorCompatible walker,
final ReferenceContext ref,
final Map<String, AlignmentContext> stratifiedContexts,
final VariantContext vc) {
return annotate(tracker, walker, ref, stratifiedContexts, vc, null);
}
public Map<String, Object> annotate(Map<String, PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap, VariantContext vc) {
return annotate(null, null, null, null, vc, perReadAlleleLikelihoodMap);
}
public abstract Map<String, Object> annotate(final RefMetaDataTracker tracker,
final AnnotatorCompatible walker,
final ReferenceContext ref,
final Map<String, AlignmentContext> stratifiedContexts,
final VariantContext vc,
final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap);
// return the descriptions used for the VCF INFO meta field
public abstract List<VCFInfoHeaderLine> getDescriptions();
}

49
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java
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@ -1,49 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.annotator.interfaces;
public interface RodRequiringAnnotation extends AnnotationType {}

49
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java
View File

@ -1,49 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.annotator.interfaces;
public interface StandardAnnotation extends AnnotationType {}

63
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java
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@ -1,63 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.annotator.interfaces;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.variant.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import java.util.List;
import java.util.Set;
@DocumentedGATKFeature(enable = true, groupName = "VariantAnnotator annotations", summary = "VariantAnnotator annotations")
public abstract class VariantAnnotatorAnnotation {
// return the INFO keys
public abstract List<String> getKeyNames();
// initialization method (optional for subclasses, and therefore non-abstract)
public void initialize ( AnnotatorCompatible walker, GenomeAnalysisEngine toolkit, Set<VCFHeaderLine> headerLines ) { }
}

49
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/WorkInProgressAnnotation.java
View File

@ -1,49 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.annotator.interfaces;
public interface WorkInProgressAnnotation extends AnnotationType {}

204
protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java
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@ -1,204 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.beagle;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.variant.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.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 = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
public class VariantsToBeagleUnphased extends RodWalker<Integer, Integer> {
@Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
public RodBinding<VariantContext> variants;
@Output(doc="File to which BEAGLE unphased genotypes should be written",required=true)
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<String> 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<VCFHeaderLine> 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);
}
}

8
protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
View File

@ -60,7 +60,7 @@ import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.clipping.ReadClipper;
import org.broadinstitute.sting.utils.collections.Pair;
@ -280,7 +280,7 @@ public class BaseRecalibrator extends ReadWalker<Long, Long> implements NanoSche
* @param hasEvents a vector a vectors of 0 (no event) and 1 (has event)
* @return the total number of events across all hasEvent arrays
*/
private int nEvents(final int[]... hasEvents) {
protected static int nEvents(final int[]... hasEvents) {
int n = 0;
for ( final int[] hasEvent : hasEvents ) {
n += MathUtils.sum(hasEvent);
@ -302,7 +302,7 @@ public class BaseRecalibrator extends ReadWalker<Long, Long> implements NanoSche
return ReadUtils.isSOLiDRead(read) && RAC.SOLID_RECAL_MODE != RecalUtils.SOLID_RECAL_MODE.DO_NOTHING && !RecalUtils.isColorSpaceConsistent(read, offset);
}
protected boolean[] calculateKnownSites( final GATKSAMRecord read, final List<Feature> features ) {
protected static boolean[] calculateKnownSites( final GATKSAMRecord read, final List<Feature> features ) {
final int readLength = read.getReadBases().length;
final boolean[] knownSites = new boolean[readLength];
Arrays.fill(knownSites, false);
@ -464,7 +464,7 @@ public class BaseRecalibrator extends ReadWalker<Long, Long> implements NanoSche
* @return a BAQ-style non-null byte[] counting NO_BAQ_UNCERTAINTY values
* // TODO -- could be optimized avoiding this function entirely by using this inline if the calculation code above
*/
private byte[] flatBAQArray(final GATKSAMRecord read) {
protected static byte[] flatBAQArray(final GATKSAMRecord read) {
final byte[] baq = new byte[read.getReadLength()];
Arrays.fill(baq, NO_BAQ_UNCERTAINTY);
return baq;

12
protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java
View File

@ -223,6 +223,18 @@ public class RecalibrationArgumentCollection {
@Output(fullName = "recal_table_update_log", shortName = "recal_table_update_log", required = false, doc = "If provided, log all updates to the recalibration tables to the given file. For debugging/testing purposes only")
public PrintStream RECAL_TABLE_UPDATE_LOG = null;
/**
* The repeat covariate will use a context of this size to calculate it's covariate value for base insertions and deletions
*/
@Hidden
@Argument(fullName = "max_str_unit_length", shortName = "maxstr", doc = "Max size of the k-mer context to be used for repeat covariates", required = false)
public int MAX_STR_UNIT_LENGTH = 8;
@Hidden
@Argument(fullName = "max_repeat_length", shortName = "maxrep", doc = "Max number of repetitions to be used for repeat covariates", required = false)
public int MAX_REPEAT_LENGTH = 20;
public File existingRecalibrationReport = null;
public GATKReportTable generateReportTable(final String covariateNames) {

26
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompressionStash.java
View File

@ -46,7 +46,7 @@
package org.broadinstitute.sting.gatk.walkers.compression.reducereads;
import org.broadinstitute.sting.utils.GenomeLocComparator;
import org.broadinstitute.sting.utils.*;
import java.util.Collection;
import java.util.TreeSet;
@ -61,22 +61,22 @@ import java.util.TreeSet;
* Date: 10/15/12
* Time: 4:08 PM
*/
public class CompressionStash extends TreeSet<SimpleGenomeLoc> {
public class CompressionStash extends TreeSet<FinishedGenomeLoc> {
public CompressionStash() {
super(new GenomeLocComparator());
super();
}
/**
* Adds a SimpleGenomeLoc to the stash and merges it with any overlapping (and contiguous) existing loc
* Adds a UnvalidatingGenomeLoc to the stash and merges it with any overlapping (and contiguous) existing loc
* in the stash.
*
* @param insertLoc the new loc to be inserted
* @return true if the loc, or it's merged version, wasn't present in the list before.
*/
@Override
public boolean add(SimpleGenomeLoc insertLoc) {
TreeSet<SimpleGenomeLoc> removedLocs = new TreeSet<SimpleGenomeLoc>();
for (SimpleGenomeLoc existingLoc : this) {
public boolean add(final FinishedGenomeLoc insertLoc) {
TreeSet<FinishedGenomeLoc> removedLocs = new TreeSet<FinishedGenomeLoc>();
for (FinishedGenomeLoc existingLoc : this) {
if (existingLoc.isPast(insertLoc)) {
break; // if we're past the loc we're done looking for overlaps.
}
@ -87,17 +87,17 @@ public class CompressionStash extends TreeSet<SimpleGenomeLoc> {
removedLocs.add(existingLoc); // list the original loc for merging
}
}
for (SimpleGenomeLoc loc : removedLocs) {
this.remove(loc); // remove all locs that will be merged
}
this.removeAll(removedLocs); // remove all locs that will be merged
removedLocs.add(insertLoc); // add the new loc to the list of locs that will be merged
return super.add(SimpleGenomeLoc.merge(removedLocs)); // merge them all into one loc and add to the stash
return super.add(new FinishedGenomeLoc(GenomeLoc.merge(removedLocs), insertLoc.isFinished()));
}
@Override
public boolean addAll(Collection<? extends SimpleGenomeLoc> locs) {
public boolean addAll(Collection<? extends FinishedGenomeLoc> locs) {
boolean result = false;
for (SimpleGenomeLoc loc : locs) {
for (final FinishedGenomeLoc loc : locs) {
result |= this.add(loc);
}
return result;

49
protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java → protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/FinishedGenomeLoc.java
View File

@ -44,34 +44,39 @@
* 7.7 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.sting.gatk.walkers.varianteval.stratifications;
package org.broadinstitute.sting.gatk.walkers.compression.reducereads;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.ArrayList;
import java.util.List;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.UnvalidatingGenomeLoc;
/**
* Stratifies by the FILTER status (PASS, FAIL) of the eval records
* GenomeLocs are very useful objects to keep track of genomic locations and perform set operations
* with them.
*
* However, GenomeLocs are bound to strict validation through the GenomeLocParser and cannot
* be created easily for small tasks that do not require the rigors of the GenomeLocParser validation
*
* UnvalidatingGenomeLoc is a simple utility to create GenomeLocs without going through the parser. Should
* only be used outside of the engine.
*
* User: carneiro
* Date: 10/16/12
* Time: 2:07 PM
*/
public class Filter extends VariantStratifier {
@Override
public void initialize() {
states.add("called");
states.add("filtered");
states.add("raw");
public class FinishedGenomeLoc extends UnvalidatingGenomeLoc {
private boolean finished;
public FinishedGenomeLoc(final String contigName, final int contigIndex, final int start, final int stop, final boolean finished) {
super(contigName, contigIndex, start, stop);
this.finished = finished;
}
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
ArrayList<Object> relevantStates = new ArrayList<Object>();
public FinishedGenomeLoc(final GenomeLoc loc, final boolean finished) {
super(loc.getContig(), loc.getContigIndex(), loc.getStart(), loc.getStop());
this.finished = finished;
}
relevantStates.add("raw");
if (eval != null) {
relevantStates.add(eval.isFiltered() ? "filtered" : "called");
}
return relevantStates;
public boolean isFinished() {
return finished;
}
}

8
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/HeaderElement.java
View File

@ -244,7 +244,7 @@ public class HeaderElement {
*
* @return whether or not the HeaderElement is variant due to excess insertions
*/
private boolean isVariantFromMismatches(double minVariantProportion) {
protected boolean isVariantFromMismatches(double minVariantProportion) {
BaseIndex mostCommon = consensusBaseCounts.baseIndexWithMostProbabilityWithoutIndels();
double mostCommonProportion = consensusBaseCounts.baseCountProportionWithoutIndels(mostCommon);
return mostCommonProportion != 0.0 && mostCommonProportion < (1 - minVariantProportion);
@ -256,11 +256,11 @@ public class HeaderElement {
*
* @return true if we had more soft clipped bases contributing to this site than matches/mismatches.
*/
private boolean isVariantFromSoftClips() {
return nSoftClippedBases >= (consensusBaseCounts.totalCount() - nSoftClippedBases);
protected boolean isVariantFromSoftClips() {
return nSoftClippedBases > 0 && nSoftClippedBases >= (consensusBaseCounts.totalCount() - nSoftClippedBases);
}
private boolean basePassesFilters(byte baseQual, int minBaseQual, int baseMappingQuality, int minMappingQual) {
protected boolean basePassesFilters(byte baseQual, int minBaseQual, int baseMappingQuality, int minMappingQual) {
return baseQual >= minBaseQual && baseMappingQuality >= minMappingQual;
}

5
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
View File

@ -64,7 +64,6 @@ import org.broadinstitute.sting.gatk.walkers.PartitionType;
import org.broadinstitute.sting.gatk.walkers.ReadFilters;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocComparator;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.clipping.ReadClipper;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@ -267,8 +266,8 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
public void initialize() {
super.initialize();
GenomeAnalysisEngine toolkit = getToolkit();
readNameHash = new HashMap<String, Long>(); // prepare the read name hash to keep track of what reads have had their read names compressed
intervalList = new TreeSet<GenomeLoc>(new GenomeLocComparator()); // get the interval list from the engine. If no interval list was provided, the walker will work in WGS mode
readNameHash = new HashMap<String, Long>(); // prepare the read name hash to keep track of what reads have had their read names compressed
intervalList = new TreeSet<GenomeLoc>(); // get the interval list from the engine. If no interval list was provided, the walker will work in WGS mode
if (toolkit.getIntervals() != null)
intervalList.addAll(toolkit.getIntervals());

56
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
View File

@ -46,12 +46,14 @@
package org.broadinstitute.sting.gatk.walkers.compression.reducereads;
import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import net.sf.samtools.Cigar;
import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
import net.sf.samtools.SAMFileHeader;
import org.broadinstitute.sting.gatk.downsampling.ReservoirDownsampler;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.recalibration.EventType;
@ -135,6 +137,18 @@ public class SlidingWindow {
return header.isEmpty() ? -1 : header.peek().getLocation();
}
// for testing only
protected SlidingWindow(final String contig, final int contigIndex, final int startLocation) {
this.contig = contig;
this.contigIndex = contigIndex;
contextSize = 10;
nContigs = 1;
this.windowHeader = new LinkedList<HeaderElement>();
windowHeader.addFirst(new HeaderElement(startLocation));
this.readsInWindow = new TreeSet<GATKSAMRecord>();
}
public SlidingWindow(String contig, int contigIndex, int contextSize, SAMFileHeader samHeader, GATKSAMReadGroupRecord readGroupAttribute, int windowNumber, final double minAltProportionToTriggerVariant, final double minIndelProportionToTriggerVariant, int minBaseQual, int minMappingQuality, int downsampleCoverage, final ReduceReads.DownsampleStrategy downsampleStrategy, boolean hasIndelQualities, int nContigs, boolean allowPolyploidReduction) {
this.contextSize = contextSize;
@ -193,14 +207,17 @@ public class SlidingWindow {
}
/**
* returns the next complete or incomplete variant region between 'from' (inclusive) and 'to' (exclusive)
* Returns the next complete (or incomplete if closeLastRegion is true) variant region between 'from' (inclusive) and 'to' (exclusive)
* but converted to global coordinates.
*
* @param from beginning window header index of the search window (inclusive)
* @param to end window header index of the search window (exclusive)
* @param from beginning window header index of the search window (inclusive); note that this uses local coordinates
* @param to end window header index of the search window (exclusive); note that this uses local coordinates
* @param variantSite boolean array with true marking variant regions
* @return null if nothing is variant, start/stop if there is a complete variant region, start/-1 if there is an incomplete variant region.
* @param closeLastRegion if the last index is variant (so it's an incomplete region), should we close (and return as an interval) the location or ignore it?
* @return null if nothing is variant, start/stop if there is a complete variant region, start/-1 if there is an incomplete variant region. All coordinates returned are global.
*/
private SimpleGenomeLoc findNextVariantRegion(int from, int to, boolean[] variantSite, boolean forceClose) {
@Requires({"from >= 0", "from <= to", "to <= variantSite.length"})
private FinishedGenomeLoc findNextVariantRegion(int from, int to, boolean[] variantSite, boolean closeLastRegion) {
boolean foundStart = false;
final int windowHeaderStart = getStartLocation(windowHeader);
int variantRegionStartIndex = 0;
@ -210,27 +227,32 @@ public class SlidingWindow {
foundStart = true;
}
else if(!variantSite[i] && foundStart) {
return(new SimpleGenomeLoc(contig, contigIndex, windowHeaderStart + variantRegionStartIndex, windowHeaderStart + i - 1, true));
return(new FinishedGenomeLoc(contig, contigIndex, windowHeaderStart + variantRegionStartIndex, windowHeaderStart + i - 1, true));
}
}
final int refStart = windowHeaderStart + variantRegionStartIndex;
final int refStop = windowHeaderStart + to - 1;
return (foundStart && forceClose) ? new SimpleGenomeLoc(contig, contigIndex, refStart, refStop, true) : null;
return (foundStart && closeLastRegion) ? new FinishedGenomeLoc(contig, contigIndex, refStart, refStop, true) : null;
}
/**
* Creates a list with all the complete and incomplete variant regions within 'from' (inclusive) and 'to' (exclusive)
*
* @param from beginning window header index of the search window (inclusive)
* @param to end window header index of the search window (exclusive)
* @param from beginning window header index of the search window (inclusive); note that this uses local coordinates
* @param to end window header index of the search window (exclusive); note that this uses local coordinates
* @param variantSite boolean array with true marking variant regions
* @return a list with start/stops of variant regions following findNextVariantRegion description
* @return a list with start/stops of variant regions following findNextVariantRegion description in global coordinates
*/
private CompressionStash findVariantRegions(int from, int to, boolean[] variantSite, boolean forceClose) {
@Requires({"from >= 0", "from <= to", "to <= variantSite.length"})
@Ensures("result != null")
protected CompressionStash findVariantRegions(int from, int to, boolean[] variantSite, boolean closeLastRegion) {
final int windowHeaderStart = getStartLocation(windowHeader);
CompressionStash regions = new CompressionStash();
int index = from;
while(index < to) {
SimpleGenomeLoc result = findNextVariantRegion(index, to, variantSite, forceClose);
// returns results in global coordinates
FinishedGenomeLoc result = findNextVariantRegion(index, to, variantSite, closeLastRegion);
if (result == null)
break;
@ -238,7 +260,7 @@ public class SlidingWindow {
if (!result.isFinished())
break;
index = result.getStop() + 1;
index = result.getStop() - windowHeaderStart + 1; // go back to local coordinates
}
return regions;
}
@ -274,7 +296,7 @@ public class SlidingWindow {
}
private final class MarkedSites {
protected final class MarkedSites {
private boolean[] siteIsVariant = new boolean[0];
private int startLocation = 0;
@ -283,6 +305,8 @@ public class SlidingWindow {
public boolean[] getVariantSiteBitSet() { return siteIsVariant; }
protected int getStartLocation() { return startLocation; }
/**
* Updates the variant site bitset given the new startlocation and size of the region to mark.
*
@ -681,8 +705,8 @@ public class SlidingWindow {
int lastStop = -1;
int windowHeaderStart = getStartLocation(windowHeader);
for (SimpleGenomeLoc region : regions) {
if (region.isFinished() && region.getContig() == contig && region.getStart() >= windowHeaderStart && region.getStop() < windowHeaderStart + windowHeader.size()) {
for (GenomeLoc region : regions) {
if (((FinishedGenomeLoc)region).isFinished() && region.getContig() == contig && region.getStart() >= windowHeaderStart && region.getStop() < windowHeaderStart + windowHeader.size()) {
int start = region.getStart() - windowHeaderStart;
int stop = region.getStop() - windowHeaderStart;

64
protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java → protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/BaseCoverageDistribution.java
View File

@ -44,35 +44,61 @@
* 7.7 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.sting.gatk.walkers.varianteval.evaluators;
package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.report.GATKReport;
import org.broadinstitute.sting.gatk.walkers.By;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
@Analysis(name = "PrintMissingComp", description = "the overlap between eval and comp sites")
public class PrintMissingComp extends VariantEvaluator {
@DataPoint(description = "number of eval sites outside of comp sites", format = "%d")
public long nMissing = 0;
import java.io.PrintStream;
import java.util.HashMap;
import java.util.Map;
public String getName() {
return "PrintMissingComp";
/**
* User: carneiro
* Date: 1/27/13
* Time: 11:16 AM
*/
@By(DataSource.REFERENCE)
public class BaseCoverageDistribution extends LocusWalker<Integer, Map<Integer, Long>> {
@Output(required = true)
private PrintStream out;
@Override
public boolean includeReadsWithDeletionAtLoci() {
return true;
}
public int getComparisonOrder() {
return 2; // we need to see each eval track and each comp track
@Override
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
return context.getBasePileup().getReads().size(); // I want the reads instead of the base pileup because I want to count deletions.
}
public void update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
final boolean compIsGood = comp != null && comp.isNotFiltered() && comp.isSNP();
final boolean evalIsGood = eval != null && eval.isSNP();
@Override
public Map<Integer, Long> reduceInit() {
return new HashMap<Integer, Long>(10000);
}
if ( compIsGood & ! evalIsGood ) {
nMissing++;
super.getWalker().getLogger().info("MissingFrom" + eval.toString() + " is missing from " + comp.getSource());
@Override
public Map<Integer, Long> reduce(Integer value, Map<Integer, Long> sum) {
Long curr = sum.get(value);
if (curr == null)
curr = 0L;
sum.put(value, curr + 1);
return sum;
}
@Override
public void onTraversalDone(Map<Integer, Long> result) {
GATKReport report = GATKReport.newSimpleReport("BaseCoverageDistribution", "Coverage", "Count");
for (Map.Entry<Integer, Long> entry : result.entrySet()) {
report.addRow(entry.getKey(), entry.getValue());
}
report.print(out);
}
}
}

12
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java
View File

@ -52,19 +52,19 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ActiveRegionExtension;
import org.broadinstitute.sting.gatk.walkers.ActiveRegionTraversalParameters;
import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker;
import org.broadinstitute.sting.gatk.walkers.PartitionBy;
import org.broadinstitute.sting.gatk.walkers.PartitionType;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult;
import org.broadinstitute.sting.utils.activeregion.ActivityProfileState;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import java.io.PrintStream;
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
@PartitionBy(PartitionType.CONTIG)
@ActiveRegionExtension(extension = 0, maxRegion = 50000)
@ActiveRegionTraversalParameters(extension = 0, maxRegion = 50000)
public class FindCoveredIntervals extends ActiveRegionWalker<GenomeLoc, Long> {
@Output(required = true)
private PrintStream out;
@ -74,18 +74,18 @@ public class FindCoveredIntervals extends ActiveRegionWalker<GenomeLoc, Long> {
@Override
// Look to see if the region has sufficient coverage
public ActivityProfileResult isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) {
public ActivityProfileState isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) {
int depth = ThresHolder.DEFAULTS.getFilteredCoverage(context.getBasePileup());
// note the linear probability scale
return new ActivityProfileResult(ref.getLocus(), Math.min(depth / coverageThreshold, 1));
return new ActivityProfileState(ref.getLocus(), Math.min(depth / coverageThreshold, 1));
}
@Override
public GenomeLoc map(final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion, final RefMetaDataTracker tracker) {
if (activeRegion.isActive)
if (activeRegion.isActive())
return activeRegion.getLocation();
else
return null;

139
protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
View File

@ -1,139 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.diffengine;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMRecordIterator;
import net.sf.samtools.util.BlockCompressedInputStream;
import java.io.*;
import java.util.Arrays;
/**
* Created by IntelliJ IDEA.
* User: depristo
* Date: 7/4/11
* Time: 1:09 PM
*
* Class implementing diffnode reader for VCF
*/
public class BAMDiffableReader implements DiffableReader {
@Override
public String getName() { return "BAM"; }
@Override
public DiffElement readFromFile(File file, int maxElementsToRead) {
final SAMFileReader reader = new SAMFileReader(file, null); // null because we don't want it to look for the index
reader.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
DiffNode root = DiffNode.rooted(file.getName());
SAMRecordIterator iterator = reader.iterator();
int count = 0;
while ( iterator.hasNext() ) {
final SAMRecord record = iterator.next();
// name is the read name + first of pair
String name = record.getReadName().replace('.', '_');
if ( record.getReadPairedFlag() ) {
name += record.getFirstOfPairFlag() ? "_1" : "_2";
}
DiffNode readRoot = DiffNode.empty(name, root);
// add fields
readRoot.add("NAME", record.getReadName());
readRoot.add("FLAGS", record.getFlags());
readRoot.add("RNAME", record.getReferenceName());
readRoot.add("POS", record.getAlignmentStart());
readRoot.add("MAPQ", record.getMappingQuality());
readRoot.add("CIGAR", record.getCigarString());
readRoot.add("RNEXT", record.getMateReferenceName());
readRoot.add("PNEXT", record.getMateAlignmentStart());
readRoot.add("TLEN", record.getInferredInsertSize());
readRoot.add("SEQ", record.getReadString());
readRoot.add("QUAL", record.getBaseQualityString());
for ( SAMRecord.SAMTagAndValue xt : record.getAttributes() ) {
readRoot.add(xt.tag, xt.value);
}
// add record to root
if ( ! root.hasElement(name) )
// protect ourselves from malformed files
root.add(readRoot);
count += readRoot.size();
if ( count > maxElementsToRead && maxElementsToRead != -1)
break;
}
reader.close();
return root.getBinding();
}
@Override
public boolean canRead(File file) {
final byte[] BAM_MAGIC = "BAM\1".getBytes();
final byte[] buffer = new byte[BAM_MAGIC.length];
try {
InputStream fstream = new BufferedInputStream(new FileInputStream(file));
if ( !BlockCompressedInputStream.isValidFile(fstream) )
return false;
final BlockCompressedInputStream BCIS = new BlockCompressedInputStream(fstream);
BCIS.read(buffer, 0, BAM_MAGIC.length);
BCIS.close();
return Arrays.equals(buffer, BAM_MAGIC);
} catch ( IOException e ) {
return false;
} catch ( net.sf.samtools.FileTruncatedException e ) {
return false;
}
}
}

125
protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java
View File

@ -1,125 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.diffengine;
import org.broadinstitute.sting.gatk.report.GATKReport;
import org.broadinstitute.sting.gatk.report.GATKReportColumn;
import org.broadinstitute.sting.gatk.report.GATKReportTable;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
/**
* Class implementing diffnode reader for GATKReports
*/
// TODO Version check to be added at the report level
public class GATKReportDiffableReader implements DiffableReader {
@Override
public String getName() {
return "GATKReport";
}
@Override
public DiffElement readFromFile(File file, int maxElementsToRead) {
DiffNode root = DiffNode.rooted(file.getName());
try {
// one line reads the whole thing into memory
GATKReport report = new GATKReport(file);
for (GATKReportTable table : report.getTables()) {
root.add(tableToNode(table, root));
}
return root.getBinding();
} catch (Exception e) {
return null;
}
}
private DiffNode tableToNode(GATKReportTable table, DiffNode root) {
DiffNode tableRoot = DiffNode.empty(table.getTableName(), root);
tableRoot.add("Description", table.getTableDescription());
tableRoot.add("NumberOfRows", table.getNumRows());
for ( GATKReportColumn column : table.getColumnInfo() ) {
DiffNode columnRoot = DiffNode.empty(column.getColumnName(), tableRoot);
columnRoot.add("Width", column.getColumnFormat().getWidth());
// NOTE: as the values are trimmed during parsing left/right alignment is not currently preserved
columnRoot.add("Displayable", true);
for ( int i = 0; i < table.getNumRows(); i++ ) {
String name = column.getColumnName() + (i+1);
columnRoot.add(name, table.get(i, column.getColumnName()).toString());
}
tableRoot.add(columnRoot);
}
return tableRoot;
}
@Override
public boolean canRead(File file) {
try {
final String HEADER = GATKReport.GATKREPORT_HEADER_PREFIX;
final char[] buff = new char[HEADER.length()];
final FileReader FR = new FileReader(file);
FR.read(buff, 0, HEADER.length());
FR.close();
String firstLine = new String(buff);
return firstLine.startsWith(HEADER);
} catch (IOException e) {
return false;
}
}
}

166
protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
View File

@ -1,166 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.diffengine;
import org.apache.log4j.Logger;
import org.broad.tribble.AbstractFeatureReader;
import org.broad.tribble.FeatureReader;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.variant.vcf.*;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.io.*;
import java.util.Iterator;
import java.util.Map;
/**
* Created by IntelliJ IDEA.
* User: depristo
* Date: 7/4/11
* Time: 1:09 PM
*
* Class implementing diffnode reader for VCF
*/
public class VCFDiffableReader implements DiffableReader {
private static Logger logger = Logger.getLogger(VCFDiffableReader.class);
@Override
public String getName() { return "VCF"; }
@Override
public DiffElement readFromFile(File file, int maxElementsToRead) {
DiffNode root = DiffNode.rooted(file.getName());
try {
// read the version line from the file
BufferedReader br = new BufferedReader(new FileReader(file));
final String version = br.readLine();
root.add("VERSION", version);
br.close();
final VCFCodec vcfCodec = new VCFCodec();
vcfCodec.disableOnTheFlyModifications(); // must be read as state is stored in reader itself
FeatureReader<VariantContext> reader = AbstractFeatureReader.getFeatureReader(file.getAbsolutePath(), vcfCodec, false);
VCFHeader header = (VCFHeader)reader.getHeader();
for ( VCFHeaderLine headerLine : header.getMetaDataInInputOrder() ) {
String key = headerLine.getKey();
if ( headerLine instanceof VCFIDHeaderLine)
key += "_" + ((VCFIDHeaderLine) headerLine).getID();
if ( root.hasElement(key) )
logger.warn("Skipping duplicate header line: file=" + file + " line=" + headerLine.toString());
else
root.add(key, headerLine.toString());
}
int count = 0, nRecordsAtPos = 1;
String prevName = "";
Iterator<VariantContext> it = reader.iterator();
while ( it.hasNext() ) {
VariantContext vc = it.next();
String name = vc.getChr() + ":" + vc.getStart();
if ( name.equals(prevName) ) {
name += "_" + ++nRecordsAtPos;
} else {
prevName = name;
}
DiffNode vcRoot = DiffNode.empty(name, root);
// add fields
vcRoot.add("CHROM", vc.getChr());
vcRoot.add("POS", vc.getStart());
vcRoot.add("ID", vc.getID());
vcRoot.add("REF", vc.getReference());
vcRoot.add("ALT", vc.getAlternateAlleles());
vcRoot.add("QUAL", vc.hasLog10PError() ? vc.getLog10PError() * -10 : VCFConstants.MISSING_VALUE_v4);
vcRoot.add("FILTER", ! vc.filtersWereApplied() // needs null to differentiate between PASS and .
? VCFConstants.MISSING_VALUE_v4
: ( vc.getFilters().isEmpty() ? VCFConstants.PASSES_FILTERS_v4 : vc.getFilters()) );
// add info fields
for (Map.Entry<String, Object> attribute : vc.getAttributes().entrySet()) {
if ( ! attribute.getKey().startsWith("_") )
vcRoot.add(attribute.getKey(), attribute.getValue());
}
for (Genotype g : vc.getGenotypes() ) {
DiffNode gRoot = DiffNode.empty(g.getSampleName(), vcRoot);
gRoot.add("GT", g.getGenotypeString());
if ( g.hasGQ() ) gRoot.add("GQ", g.getGQ() );
if ( g.hasDP() ) gRoot.add("DP", g.getDP() );
if ( g.hasAD() ) gRoot.add("AD", Utils.join(",", g.getAD()));
if ( g.hasPL() ) gRoot.add("PL", Utils.join(",", g.getPL()));
if ( g.getFilters() != null ) gRoot.add("FT", g.getFilters());
for (Map.Entry<String, Object> attribute : g.getExtendedAttributes().entrySet()) {
if ( ! attribute.getKey().startsWith("_") )
gRoot.add(attribute.getKey(), attribute.getValue());
}
vcRoot.add(gRoot);
}
root.add(vcRoot);
count += vcRoot.size();
if ( count > maxElementsToRead && maxElementsToRead != -1)
break;
}
reader.close();
} catch ( IOException e ) {
return null;
}
return root.getBinding();
}
@Override
public boolean canRead(File file) {
return AbstractVCFCodec.canDecodeFile(file.getPath(), VCFCodec.VCF4_MAGIC_HEADER);
}
}

160
protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java
View File

@ -1,160 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.fasta;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Collections;
import java.util.List;
/**
* Generates an alternative reference sequence over the specified interval.
*
* <p>
* Given variant tracks, it replaces the reference bases at variation sites with the bases supplied by the ROD(s).
* Additionally, allows for one or more "snpmask" VCFs to set overlapping bases to 'N'.
*
* The output format can be partially controlled using the provided command-line arguments.
* Specify intervals with the usual -L argument to output only the reference bases within your intervals.
* Overlapping intervals are automatically merged; reference bases for each disjoint interval will be output as a
* separate fasta sequence (named numerically in order).
*
* Several important notes:
* 1) if there are multiple variants that start at a site, it chooses one of them randomly.
* 2) when there are overlapping indels (but with different start positions) only the first will be chosen.
* 3) this tool works only for SNPs and for simple indels (but not for things like complex substitutions).
* Reference bases for each interval will be output as a separate fasta sequence (named numerically in order).
*
* <h2>Input</h2>
* <p>
* The reference, requested intervals, and any number of variant rod files.
* </p>
*
* <h2>Output</h2>
* <p>
* A fasta file representing the requested intervals.
* </p>
*
* <h2>Examples</h2>
* <pre>
* java -Xmx2g -jar GenomeAnalysisTK.jar \
* -R ref.fasta \
* -T FastaAlternateReferenceMaker \
* -o output.fasta \
* -L input.intervals \
* --variant input.vcf \
* [--snpmask mask.vcf]
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Companion Utilities", extraDocs = {CommandLineGATK.class} )
@Reference(window=@Window(start=-1,stop=50))
@Requires(value={DataSource.REFERENCE})
public class FastaAlternateReferenceMaker extends FastaReferenceMaker {
/**
* Variants from these input files are used by this tool to construct an alternate reference.
*/
@Input(fullName = "variant", shortName = "V", doc="variants to model", required=false)
public List<RodBinding<VariantContext>> variants = Collections.emptyList();
/**
* Snps from this file are used as a mask when constructing the alternate reference.
*/
@Input(fullName="snpmask", shortName = "snpmask", doc="SNP mask VCF file", required=false)
public RodBinding<VariantContext> snpmask;
private int deletionBasesRemaining = 0;
public Pair<GenomeLoc, String> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if (deletionBasesRemaining > 0) {
deletionBasesRemaining--;
return new Pair<GenomeLoc, String>(context.getLocation(), "");
}
String refBase = String.valueOf((char)ref.getBase());
// Check to see if we have a called snp
for ( VariantContext vc : tracker.getValues(variants, ref.getLocus()) ) {
if ( vc.isFiltered() )
continue;
if ( vc.isSimpleDeletion()) {
deletionBasesRemaining = vc.getReference().length() - 1;
// delete the next n bases, not this one
return new Pair<GenomeLoc, String>(context.getLocation(), refBase);
} else if ( vc.isSimpleInsertion()) {
return new Pair<GenomeLoc, String>(context.getLocation(), vc.getAlternateAllele(0).toString());
} else if (vc.isSNP()) {
return new Pair<GenomeLoc, String>(context.getLocation(), vc.getAlternateAllele(0).toString());
}
}
// if we don't have a called site, and we have a mask at this site, mask it
for ( VariantContext vc : tracker.getValues(snpmask) ) {
if ( vc.isSNP()) {
return new Pair<GenomeLoc, String>(context.getLocation(), "N");
}
}
// if we got here then we're just ref
return new Pair<GenomeLoc, String>(context.getLocation(), refBase);
}
}

148
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@ -1,148 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.fasta;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.RefWalker;
import org.broadinstitute.sting.gatk.walkers.WalkerName;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import java.io.PrintStream;
/**
* Renders a new reference in FASTA format consisting of only those loci provided in the input data set.
*
* <p>
* The output format can be partially controlled using the provided command-line arguments.
* Specify intervals with the usual -L argument to output only the reference bases within your intervals.
* Overlapping intervals are automatically merged; reference bases for each disjoint interval will be output as a
* separate fasta sequence (named numerically in order).
*
* <h2>Input</h2>
* <p>
* The reference and requested intervals.
* </p>
*
* <h2>Output</h2>
* <p>
* A fasta file representing the requested intervals.
* </p>
*
* <h2>Examples</h2>
* <pre>
* java -Xmx2g -jar GenomeAnalysisTK.jar \
* -R ref.fasta \
* -T FastaReferenceMaker \
* -o output.fasta \
* -L input.intervals
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Companion Utilities", extraDocs = {CommandLineGATK.class} )
public class FastaReferenceMaker extends RefWalker<Pair<GenomeLoc, String>, GenomeLoc> {
@Output PrintStream out;
@Argument(fullName="lineWidth", shortName="lw", doc="Maximum length of sequence to write per line", required=false)
public int fastaLineWidth=60;
/**
* Please note that when using this argument adjacent intervals will automatically be merged.
*/
@Argument(fullName="rawOnelineSeq", shortName="raw", doc="Print sequences with no FASTA header lines, one line per interval (i.e. lineWidth = infinity)", required=false)
public boolean fastaRawSeqs=false;
protected FastaSequence fasta;
public void initialize() {
if (fastaRawSeqs) fastaLineWidth = Integer.MAX_VALUE;
fasta = new FastaSequence(out, fastaLineWidth, fastaRawSeqs);
}
public Pair<GenomeLoc, String> map(RefMetaDataTracker rodData, ReferenceContext ref, AlignmentContext context) {
return new Pair<GenomeLoc, String>(context.getLocation(), String.valueOf((char)ref.getBase()));
}
public GenomeLoc reduceInit() {
return null;
}
public GenomeLoc reduce(Pair<GenomeLoc, String> value, GenomeLoc sum) {
if ( value == null )
return sum;
// if there is no interval to the left, then this is the first one
if ( sum == null ) {
sum = value.first;
fasta.append(value.second);
}
// if the intervals don't overlap, print out the leftmost one and start a new one
// (end of contig or new interval)
else if ( value.first.getStart() != sum.getStop() + 1 ) {
fasta.flush();
sum = value.first;
fasta.append(value.second);
}
// otherwise, merge them
else {
sum = getToolkit().getGenomeLocParser().setStop(sum, value.first.getStop());
fasta.append(value.second);
}
return sum;
}
public void onTraversalDone(GenomeLoc sum) {
fasta.flush();
}
}

122
protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java
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@ -1,122 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.fasta;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.io.PrintStream;
// fasta sequence holder class
public class FastaSequence {
private PrintStream out;
private StringBuffer sb = new StringBuffer();
private long sequenceCounter = 1;
private boolean printedHeader = false;
private String name = null;
private int lineWidth = -1;
private boolean noHeader = false;
public FastaSequence(PrintStream out, int lineWidth, boolean noHeader) {
this.out = out;
this.lineWidth = lineWidth;
this.noHeader = noHeader;
}
public void setName(String name) {
if ( printedHeader ) throw new ReviewedStingException("Can not set name for FASTA record: header is already printed.");
this.name = name;
}
public String getName() {
if ( name != null ) return name;
else return getCurrentID();
}
public void append(String s) {
sb.append(s);
printFasta(false);
}
public void flush() {
printFasta(true);
printedHeader = false;
name = null;
sequenceCounter++;
}
public long getCurrentCount() {
return sequenceCounter;
}
public String getCurrentID() {
return String.valueOf(sequenceCounter);
}
private void printFasta(boolean printAll) {
if ( sb.length() == 0 || (!printAll && sb.length() < lineWidth) )
return;
if ( !printedHeader && !noHeader) {
if ( name == null ) out.println(">" + sequenceCounter);
else out.println(">" + name);
printedHeader = true;
}
int lines = sb.length() / lineWidth;
int currentStart = 0;
for (int i=0; i < lines; i++) {
out.println(sb.substring(currentStart, currentStart+lineWidth));
currentStart += lineWidth;
}
if ( printAll ) {
out.println(sb.substring(currentStart));
sb.setLength(0);
} else {
sb.delete(0, currentStart);
}
}
}

102
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@ -1,102 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.filters;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
public class ClusteredSnps {
private GenomeLocParser genomeLocParser;
private int window = 10;
private int snpThreshold = 3;
public ClusteredSnps(GenomeLocParser genomeLocParser,int snpThreshold, int window) {
this.genomeLocParser = genomeLocParser;
this.window = window;
this.snpThreshold = snpThreshold;
if ( window < 1 || snpThreshold < 1 )
throw new IllegalArgumentException("Window and threshold values need to be positive values");
}
public boolean filter(FiltrationContextWindow contextWindow) {
FiltrationContext[] variants = contextWindow.getWindow(snpThreshold-1, snpThreshold-1);
for (int i = 0; i < snpThreshold; i++) {
// ignore positions at the beginning or end of the overall interval (where there aren't enough records)
if ( variants[i] == null || variants[i+snpThreshold-1] == null )
continue;
// note: the documentation tells users we'll blow up if ref calls are present.
// if we ever get a windowed rod context that isn't a hack, we can actually allow this...
if ( !variants[i].getVariantContext().isVariant() )
throw new UserException.BadInput("The clustered SNPs filter does not work in the presence of non-variant records; see the documentation for more details");
// find the nth variant
GenomeLoc left = GATKVariantContextUtils.getLocation(genomeLocParser, variants[i].getVariantContext());
GenomeLoc right = null;
int snpsSeen = 1;
int currentIndex = i;
while ( ++currentIndex < variants.length ) {
if ( variants[currentIndex] != null && variants[currentIndex].getVariantContext() != null && variants[currentIndex].getVariantContext().isVariant() ) {
if ( ++snpsSeen == snpThreshold ) {
right = GATKVariantContextUtils.getLocation(genomeLocParser, variants[currentIndex].getVariantContext());
break;
}
}
}
if ( right != null &&
left.getContigIndex() == right.getContigIndex() &&
Math.abs(right.getStart() - left.getStart()) <= window )
return true;
}
return false;
}
}

125
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@ -1,125 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.filters;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.LinkedList;
import java.util.List;
import java.util.ListIterator;
/**
* A window of variants surrounding the current variant being investigated
*
* @author ebanks
* @version 0.1
*/
public class FiltrationContextWindow {
/**
* The variants.
*/
private LinkedList<FiltrationContext> window = new LinkedList<FiltrationContext>();
private int currentContext;
/**
* Contructor for a variant context.
* @param firstVariants the first set of variants, comprising the right half of the window
*/
public FiltrationContextWindow(List<FiltrationContext> firstVariants) {
int windowSize = (firstVariants == null ? 1 : 2 * firstVariants.size() + 1);
currentContext = (firstVariants == null ? 0 : firstVariants.size());
window.addAll(firstVariants);
while ( window.size() < windowSize )
window.addFirst(null);
}
/**
* The context currently being examined.
* @return The current context.
*/
public FiltrationContext getContext() {
return window.get(currentContext);
}
/**
* The maximum number of elements that can be requested on either end of the current context.
* @return max.
*/
public int maxWindowElements() {
return currentContext;
}
/**
* The window around the context currently being examined.
* @param elementsToLeft number of earlier contexts to return ()
* @param elementsToRight number of later contexts to return ()
* @return The current context window.
*/
public FiltrationContext[] getWindow(int elementsToLeft, int elementsToRight) {
if ( elementsToLeft > maxWindowElements() || elementsToRight > maxWindowElements() )
throw new ReviewedStingException("Too large a window requested");
if ( elementsToLeft < 0 || elementsToRight < 0 )
throw new ReviewedStingException("Window size cannot be negative");
FiltrationContext[] array = new FiltrationContext[elementsToLeft + elementsToRight + 1];
ListIterator<FiltrationContext> iter = window.listIterator(currentContext - elementsToLeft);
for (int i = 0; i < elementsToLeft + elementsToRight + 1; i++)
array[i] = iter.next();
return array;
}
/**
* Move the window along to the next context
* @param context The new rightmost context
*/
public void moveWindow(FiltrationContext context) {
window.removeFirst();
window.addLast(context);
}
}

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
View File

@ -53,6 +53,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.clipping.ReadClipper;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@ -288,7 +289,7 @@ public class ConsensusAlleleCounter {
if (vcs.isEmpty())
return Collections.emptyList(); // nothing else to do, no alleles passed minimum count criterion
final VariantContext mergedVC = VariantContextUtils.simpleMerge(vcs, null, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, VariantContextUtils.GenotypeMergeType.UNSORTED, false, false, null, false, false);
final VariantContext mergedVC = GATKVariantContextUtils.simpleMerge(vcs, null, GATKVariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, GATKVariantContextUtils.GenotypeMergeType.UNSORTED, false, false, null, false, false);
return mergedVC.getAlleles();
}
}

4
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
View File

@ -47,7 +47,7 @@
package org.broadinstitute.sting.gatk.walkers.genotyper;
import net.sf.samtools.SAMUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.exceptions.UserException;
@ -425,7 +425,7 @@ public class DiploidSNPGenotypeLikelihoods implements Cloneable {
byte qual = p.getQual();
if ( qual > SAMUtils.MAX_PHRED_SCORE )
throw new UserException.MalformedBAM(p.getRead(), String.format("the maximum allowed quality score is %d, but a quality of %d was observed in read %s. Perhaps your BAM incorrectly encodes the quality scores in Sanger format; see http://en.wikipedia.org/wiki/FASTQ_format for more details", SAMUtils.MAX_PHRED_SCORE, qual, p.getRead().getReadName()));
throw new UserException.MisencodedBAM(p.getRead(), "we encountered an extremely high quality score (" + (int)qual + ")");
if ( capBaseQualsAtMappingQual )
qual = (byte)Math.min((int)qual, p.getMappingQual());
if ( (int)qual < minBaseQual )

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java
View File

@ -49,9 +49,8 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
import net.sf.samtools.SAMUtils;
import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactACset;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pileup.PileupElement;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java
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@ -77,7 +77,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.variantcontext.*;
import java.util.*;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
View File

@ -51,7 +51,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.pileup.PileupElement;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
View File

@ -52,7 +52,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.Haplotype;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
View File

@ -51,7 +51,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.MathUtils;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
View File

@ -176,7 +176,7 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
/**
* A raw, unfiltered, highly sensitive callset in VCF format.
*/
@Gather(className = "org.broadinstitute.sting.queue.extensions.gatk.CatVariantsGatherer")
//@Gather(className = "org.broadinstitute.sting.queue.extensions.gatk.CatVariantsGatherer")
@Output(doc="File to which variants should be written",required=true)
protected VariantContextWriter writer = null;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -62,7 +62,7 @@ import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pileup.PileupElement;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java
View File

@ -70,7 +70,7 @@ public class AFCalcFactory {
* the needs of the request (i.e., considering ploidy).
*/
public enum Calculation {
/** expt. implementation -- for testing only */
/** default implementation */
EXACT_INDEPENDENT(IndependentAllelesDiploidExactAFCalc.class, 2, -1),
/** reference implementation of multi-allelic EXACT model. Extremely slow for many alternate alleles */

4
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnEdge.java
View File

@ -86,7 +86,7 @@ public class DeBruijnEdge {
multiplicity = value;
}
public boolean getIsRef() {
public boolean isRef() {
return isRef;
}
@ -94,10 +94,12 @@ public class DeBruijnEdge {
this.isRef = isRef;
}
// For use when comparing edges pulled from the same graph
public boolean equals( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph, final DeBruijnEdge edge ) {
return (graph.getEdgeSource(this).equals(graph.getEdgeSource(edge))) && (graph.getEdgeTarget(this).equals(graph.getEdgeTarget(edge)));
}
// For use when comparing edges across graphs!
public boolean equals( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph, final DeBruijnEdge edge, final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph2 ) {
return (graph.getEdgeSource(this).equals(graph2.getEdgeSource(edge))) && (graph.getEdgeTarget(this).equals(graph2.getEdgeTarget(edge)));
}

6
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnVertex.java
View File

@ -46,6 +46,9 @@
package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
import com.google.java.contract.Ensures;
import com.google.java.contract.Invariant;
import java.util.Arrays;
/**
@ -54,6 +57,7 @@ import java.util.Arrays;
* Date: Mar 23, 2011
*/
// simple node class for storing kmer sequences
@Invariant("kmer > 0")
public class DeBruijnVertex {
protected final byte[] sequence;
@ -82,10 +86,12 @@ public class DeBruijnVertex {
return new String( getSuffix() );
}
@Ensures("result != null")
public byte[] getSequence() {
return sequence.clone();
}
@Ensures("result != null")
public byte[] getSuffix() {
return Arrays.copyOfRange( sequence, kmer - 1, sequence.length );
}

48
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
View File

@ -58,7 +58,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.variantcontext.*;
import java.io.PrintStream;
@ -84,7 +84,7 @@ public class GenotypingEngine {
final List<Haplotype> haplotypes,
final List<String> samples,
final Map<String, PerReadAlleleLikelihoodMap> haplotypeReadMap,
final Map<String, ArrayList<GATKSAMRecord>> perSampleFilteredReadList,
final Map<String, List<GATKSAMRecord>> perSampleFilteredReadList,
final byte[] ref,
final GenomeLoc refLoc,
final GenomeLoc activeRegionWindow,
@ -124,12 +124,12 @@ public class GenotypingEngine {
// Walk along each position in the key set and create each event to be outputted
for( final int loc : startPosKeySet ) {
if( loc >= activeRegionWindow.getStart() && loc <= activeRegionWindow.getStop() ) { // genotyping an event inside this active region
final ArrayList<VariantContext> eventsAtThisLoc = new ArrayList<VariantContext>(); // the overlapping events to merge into a common reference view
final ArrayList<String> priorityList = new ArrayList<String>(); // used to merge overlapping events into common reference view
final List<VariantContext> eventsAtThisLoc = new ArrayList<VariantContext>(); // the overlapping events to merge into a common reference view
final List<String> priorityList = new ArrayList<String>(); // used to merge overlapping events into common reference view
if( !in_GGA_mode ) {
for( final Haplotype h : haplotypes ) {
final HashMap<Integer,VariantContext> eventMap = h.getEventMap();
final Map<Integer,VariantContext> eventMap = h.getEventMap();
final VariantContext vc = eventMap.get(loc);
if( vc != null && !containsVCWithMatchingAlleles(eventsAtThisLoc, vc) ) {
eventsAtThisLoc.add(vc);
@ -142,7 +142,7 @@ public class GenotypingEngine {
if( compVC.getStart() == loc ) {
int alleleCount = 0;
for( final Allele compAltAllele : compVC.getAlternateAlleles() ) {
ArrayList<Allele> alleleSet = new ArrayList<Allele>(2);
List<Allele> alleleSet = new ArrayList<Allele>(2);
alleleSet.add(compVC.getReference());
alleleSet.add(compAltAllele);
final String vcSourceName = "Comp" + compCount + "Allele" + alleleCount;
@ -174,13 +174,13 @@ public class GenotypingEngine {
validatePriorityList( priorityList, eventsAtThisLoc );
// Merge the event to find a common reference representation
final VariantContext mergedVC = VariantContextUtils.simpleMerge(eventsAtThisLoc, priorityList, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, VariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, null, false, false);
final VariantContext mergedVC = GATKVariantContextUtils.simpleMerge(eventsAtThisLoc, priorityList, GATKVariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, GATKVariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, null, false, false);
if( mergedVC == null ) { continue; }
if( eventsAtThisLoc.size() != mergedVC.getAlternateAlleles().size() ) {
throw new ReviewedStingException("Record size mismatch! Something went wrong in the merging of alleles.");
}
final HashMap<VariantContext, Allele> mergeMap = new HashMap<VariantContext, Allele>();
final Map<VariantContext, Allele> mergeMap = new HashMap<VariantContext, Allele>();
mergeMap.put(null, mergedVC.getReference()); // the reference event (null) --> the reference allele
for(int iii = 0; iii < mergedVC.getAlternateAlleles().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
@ -232,7 +232,7 @@ public class GenotypingEngine {
return genotypes;
}
private void validatePriorityList( final ArrayList<String> priorityList, final ArrayList<VariantContext> eventsAtThisLoc ) {
private void validatePriorityList( final List<String> priorityList, final List<VariantContext> eventsAtThisLoc ) {
for( final VariantContext vc : eventsAtThisLoc ) {
if( !priorityList.contains(vc.getSource()) ) {
throw new ReviewedStingException("Event found on haplotype that wasn't added to priority list. Something went wrong in the merging of alleles.");
@ -251,7 +251,7 @@ public class GenotypingEngine {
private static Map<String, PerReadAlleleLikelihoodMap> filterToOnlyOverlappingReads( final GenomeLocParser parser,
final Map<String, PerReadAlleleLikelihoodMap> perSampleReadMap,
final Map<String, ArrayList<GATKSAMRecord>> perSampleFilteredReadList,
final Map<String, List<GATKSAMRecord>> perSampleFilteredReadList,
final VariantContext call ) {
final Map<String, PerReadAlleleLikelihoodMap> returnMap = new HashMap<String, PerReadAlleleLikelihoodMap>();
@ -284,7 +284,7 @@ public class GenotypingEngine {
}
protected static void cleanUpSymbolicUnassembledEvents( final List<Haplotype> haplotypes ) {
final ArrayList<Haplotype> haplotypesToRemove = new ArrayList<Haplotype>();
final List<Haplotype> haplotypesToRemove = new ArrayList<Haplotype>();
for( final Haplotype h : haplotypes ) {
for( final VariantContext vc : h.getEventMap().values() ) {
if( vc.isSymbolic() ) {
@ -407,7 +407,7 @@ public class GenotypingEngine {
// remove the old event from the eventMap on every haplotype and the start pos key set, replace with merged event
for( final Haplotype h : haplotypes ) {
final HashMap<Integer, VariantContext> eventMap = h.getEventMap();
final Map<Integer, VariantContext> eventMap = h.getEventMap();
if( eventMap.containsKey(thisStart) && eventMap.containsKey(nextStart) ) {
eventMap.remove(thisStart);
eventMap.remove(nextStart);
@ -418,7 +418,7 @@ public class GenotypingEngine {
boolean containsStart = false;
boolean containsNext = false;
for( final Haplotype h : haplotypes ) {
final HashMap<Integer, VariantContext> eventMap = h.getEventMap();
final Map<Integer, VariantContext> eventMap = h.getEventMap();
if( eventMap.containsKey(thisStart) ) { containsStart = true; }
if( eventMap.containsKey(nextStart) ) { containsNext = true; }
}
@ -457,7 +457,7 @@ public class GenotypingEngine {
if( refBases.length == altBases.length ) { // insertion + deletion of same length creates an MNP --> trim common prefix bases off the beginning of the allele
while( iii < refBases.length && refBases[iii] == altBases[iii] ) { iii++; }
}
final ArrayList<Allele> mergedAlleles = new ArrayList<Allele>();
final List<Allele> mergedAlleles = new ArrayList<Allele>();
mergedAlleles.add( Allele.create( ArrayUtils.subarray(refBases, iii, refBases.length), true ) );
mergedAlleles.add( Allele.create( ArrayUtils.subarray(altBases, iii, altBases.length), false ) );
return new VariantContextBuilder("merged", thisVC.getChr(), thisVC.getStart() + iii, nextVC.getEnd(), mergedAlleles).make();
@ -492,10 +492,10 @@ public class GenotypingEngine {
eventMapper.put(new Event(vc), new ArrayList<Haplotype>());
}
final ArrayList<Haplotype> undeterminedHaplotypes = new ArrayList<Haplotype>(haplotypes.size());
final List<Haplotype> undeterminedHaplotypes = new ArrayList<Haplotype>(haplotypes.size());
for( final Haplotype h : haplotypes ) {
if( h.isArtificialHaplotype() && loc == h.getArtificialAllelePosition() ) {
final ArrayList<Allele> alleles = new ArrayList<Allele>(2);
final List<Allele> alleles = new ArrayList<Allele>(2);
alleles.add(h.getArtificialRefAllele());
alleles.add(h.getArtificialAltAllele());
final Event artificialVC = new Event( (new VariantContextBuilder()).source("artificialHaplotype")
@ -572,13 +572,13 @@ public class GenotypingEngine {
}
@Ensures({"result.size() == haplotypeAllelesForSample.size()"})
protected static List<Allele> findEventAllelesInSample( final List<Allele> eventAlleles, final List<Allele> haplotypeAlleles, final List<Allele> haplotypeAllelesForSample, final ArrayList<ArrayList<Haplotype>> alleleMapper, final ArrayList<Haplotype> haplotypes ) {
protected static List<Allele> findEventAllelesInSample( final List<Allele> eventAlleles, final List<Allele> haplotypeAlleles, final List<Allele> haplotypeAllelesForSample, final List<List<Haplotype>> alleleMapper, final List<Haplotype> haplotypes ) {
if( haplotypeAllelesForSample.contains(Allele.NO_CALL) ) { return noCall; }
final ArrayList<Allele> eventAllelesForSample = new ArrayList<Allele>();
final List<Allele> eventAllelesForSample = new ArrayList<Allele>();
for( final Allele a : haplotypeAllelesForSample ) {
final Haplotype haplotype = haplotypes.get(haplotypeAlleles.indexOf(a));
for( int iii = 0; iii < alleleMapper.size(); iii++ ) {
final ArrayList<Haplotype> mappedHaplotypes = alleleMapper.get(iii);
final List<Haplotype> mappedHaplotypes = alleleMapper.get(iii);
if( mappedHaplotypes.contains(haplotype) ) {
eventAllelesForSample.add(eventAlleles.get(iii));
break;
@ -597,8 +597,8 @@ public class GenotypingEngine {
return false;
}
protected static HashMap<Integer,VariantContext> generateVCsFromAlignment( final Haplotype haplotype, final int alignmentStartHapwrtRef, final Cigar cigar, final byte[] ref, final byte[] alignment, final GenomeLoc refLoc, final String sourceNameToAdd ) {
final HashMap<Integer,VariantContext> vcs = new HashMap<Integer,VariantContext>();
protected static Map<Integer,VariantContext> generateVCsFromAlignment( final Haplotype haplotype, final int alignmentStartHapwrtRef, final Cigar cigar, final byte[] ref, final byte[] alignment, final GenomeLoc refLoc, final String sourceNameToAdd ) {
final Map<Integer,VariantContext> vcs = new HashMap<Integer,VariantContext>();
int refPos = alignmentStartHapwrtRef;
if( refPos < 0 ) { return null; } // Protection against SW failures
@ -609,7 +609,7 @@ public class GenotypingEngine {
switch( ce.getOperator() ) {
case I:
{
final ArrayList<Allele> insertionAlleles = new ArrayList<Allele>();
final List<Allele> insertionAlleles = new ArrayList<Allele>();
final int insertionStart = refLoc.getStart() + refPos - 1;
final byte refByte = ref[refPos-1];
if( BaseUtils.isRegularBase(refByte) ) {
@ -639,7 +639,7 @@ public class GenotypingEngine {
case D:
{
final byte[] deletionBases = Arrays.copyOfRange( ref, refPos - 1, refPos + elementLength ); // add padding base
final ArrayList<Allele> deletionAlleles = new ArrayList<Allele>();
final List<Allele> deletionAlleles = new ArrayList<Allele>();
final int deletionStart = refLoc.getStart() + refPos - 1;
// BUGBUG: how often does this symbolic deletion allele case happen?
//if( haplotype != null && ( (haplotype.leftBreakPoint + alignmentStartHapwrtRef + refLoc.getStart() + elementLength - 1 >= deletionStart && haplotype.leftBreakPoint + alignmentStartHapwrtRef + refLoc.getStart() + elementLength - 1 < deletionStart + elementLength)
@ -667,7 +667,7 @@ public class GenotypingEngine {
final byte altByte = alignment[alignmentPos];
if( refByte != altByte ) { // SNP!
if( BaseUtils.isRegularBase(refByte) && BaseUtils.isRegularBase(altByte) ) {
final ArrayList<Allele> snpAlleles = new ArrayList<Allele>();
final List<Allele> snpAlleles = new ArrayList<Allele>();
snpAlleles.add( Allele.create( refByte, true ) );
snpAlleles.add( Allele.create( altByte, false ) );
vcs.put(refLoc.getStart() + refPos, new VariantContextBuilder(sourceNameToAdd, refLoc.getContig(), refLoc.getStart() + refPos, refLoc.getStart() + refPos, snpAlleles).make());

247
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
View File

@ -47,6 +47,7 @@
package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
import com.google.java.contract.Ensures;
import net.sf.samtools.*;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
@ -57,6 +58,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.downsampling.DownsampleType;
import org.broadinstitute.sting.gatk.filters.BadMateFilter;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
@ -67,8 +69,9 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
import org.broadinstitute.sting.utils.activeregion.ActiveRegionReadState;
import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult;
import org.broadinstitute.sting.utils.activeregion.ActivityProfileState;
import org.broadinstitute.sting.utils.clipping.ReadClipper;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.*;
@ -129,8 +132,8 @@ import java.util.*;
@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
@PartitionBy(PartitionType.LOCUS)
@BAQMode(ApplicationTime = ReadTransformer.ApplicationTime.FORBIDDEN)
@ActiveRegionExtension(extension=65, maxRegion=300)
//@Downsample(by= DownsampleType.BY_SAMPLE, toCoverage=5)
@ActiveRegionTraversalParameters(extension=65, maxRegion=300)
@Downsample(by= DownsampleType.BY_SAMPLE, toCoverage=20)
public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implements AnnotatorCompatible {
/**
@ -142,6 +145,17 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
@Output(fullName="graphOutput", shortName="graph", doc="File to which debug assembly graph information should be written", required = false)
protected PrintStream graphWriter = null;
/**
* 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.
*/
@Hidden
@Output(fullName="bamOutput", shortName="bam", doc="File to which assembled haplotypes should be written", required = false)
protected StingSAMFileWriter bamWriter = null;
private SAMFileHeader bamHeader = null;
private long uniqueNameCounter = 1;
private final static String readGroupId = "ArtificialHaplotype";
/**
* The PairHMM implementation to use for genotype likelihood calculations. The various implementations balance a tradeoff of accuracy and runtime.
*/
@ -167,8 +181,15 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
@Argument(fullName="minKmer", shortName="minKmer", doc="Minimum kmer length to use in the assembly graph", required = false)
protected int minKmer = 11;
@Argument(fullName="downsampleRegion", shortName="dr", doc="coverage, per-sample, to downsample each active region to", required = false)
protected int DOWNSAMPLE_PER_SAMPLE_PER_REGION = 1000;
/**
* If this flag is provided, the haplotype caller will include unmapped reads in the assembly and calling
* when these reads occur in the region being analyzed. Typically, for paired end analyses, one pair of the
* read can map, but if its pair is too divergent then it may be unmapped and placed next to its mate, taking
* the mates contig and alignment start. If this flag is provided the haplotype caller will see such reads,
* and may make use of them in assembly and calling, where possible.
*/
@Argument(fullName="includeUmappedReads", shortName="unmapped", doc="If provided, unmapped reads with chromosomal coordinates (i.e., those placed to their maps) will be included in the assembly and calling", required = false)
protected boolean includeUnmappedReads = false;
@Argument(fullName="useAllelesTrigger", shortName="allelesTrigger", doc = "If specified, use additional trigger on variants found in an external alleles file", required=false)
protected boolean USE_ALLELES_TRIGGER = false;
@ -242,6 +263,8 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
// the genotyping engine
private GenotypingEngine genotypingEngine = null;
private VariantAnnotatorEngine annotationEngine = null;
// fasta reference reader to supplement the edges of the reference sequence
private CachingIndexedFastaSequenceFile referenceReader;
@ -251,10 +274,10 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
// bases with quality less than or equal to this value are trimmed off the tails of the reads
private static final byte MIN_TAIL_QUALITY = 20;
private ArrayList<String> samplesList = new ArrayList<String>();
private List<String> samplesList = new ArrayList<String>();
private final static double LOG_ONE_HALF = -Math.log10(2.0);
private final static double LOG_ONE_THIRD = -Math.log10(3.0);
private final ArrayList<VariantContext> allelesToGenotype = new ArrayList<VariantContext>();
private final List<VariantContext> allelesToGenotype = new ArrayList<VariantContext>();
private final static Allele FAKE_REF_ALLELE = Allele.create("N", true); // used in isActive function to call into UG Engine. Should never appear anywhere in a VCF file
private final static Allele FAKE_ALT_ALLELE = Allele.create("<FAKE_ALT>", false); // used in isActive function to call into UG Engine. Should never appear anywhere in a VCF file
@ -286,7 +309,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
UG_engine_simple_genotyper = new UnifiedGenotyperEngine(getToolkit(), simpleUAC, logger, null, null, samples, GATKVariantContextUtils.DEFAULT_PLOIDY);
// initialize the output VCF header
final VariantAnnotatorEngine annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit());
annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit());
Set<VCFHeaderLine> headerInfo = new HashSet<VCFHeaderLine>();
@ -320,6 +343,9 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
assemblyEngine = new SimpleDeBruijnAssembler( DEBUG, graphWriter, minKmer );
likelihoodCalculationEngine = new LikelihoodCalculationEngine( (byte)gcpHMM, DEBUG, pairHMM );
genotypingEngine = new GenotypingEngine( DEBUG, annotationEngine, USE_FILTERED_READ_MAP_FOR_ANNOTATIONS );
if ( bamWriter != null )
setupBamWriter();
}
//---------------------------------------------------------------------------------------------------------------
@ -335,16 +361,25 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
// enable non primary and extended reads in the active region
@Override
public EnumSet<ActiveRegionReadState> desiredReadStates() {
return EnumSet.of(
ActiveRegionReadState.PRIMARY,
ActiveRegionReadState.NONPRIMARY,
ActiveRegionReadState.EXTENDED
);
if ( includeUnmappedReads ) {
throw new UserException.BadArgumentValue("includeUmappedReads", "is not yet functional");
// return EnumSet.of(
// ActiveRegionReadState.PRIMARY,
// ActiveRegionReadState.NONPRIMARY,
// ActiveRegionReadState.EXTENDED,
// ActiveRegionReadState.UNMAPPED
// );
} else
return EnumSet.of(
ActiveRegionReadState.PRIMARY,
ActiveRegionReadState.NONPRIMARY,
ActiveRegionReadState.EXTENDED
);
}
@Override
@Ensures({"result.isActiveProb >= 0.0", "result.isActiveProb <= 1.0"})
public ActivityProfileResult isActive( final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context ) {
public ActivityProfileState isActive( final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context ) {
if( UG_engine.getUAC().GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) {
for( final VariantContext vc : tracker.getValues(UG_engine.getUAC().alleles, ref.getLocus()) ) {
@ -353,15 +388,17 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
}
}
if( tracker.getValues(UG_engine.getUAC().alleles, ref.getLocus()).size() > 0 ) {
return new ActivityProfileResult(ref.getLocus(), 1.0);
return new ActivityProfileState(ref.getLocus(), 1.0);
}
}
if( USE_ALLELES_TRIGGER ) {
return new ActivityProfileResult( ref.getLocus(), tracker.getValues(UG_engine.getUAC().alleles, ref.getLocus()).size() > 0 ? 1.0 : 0.0 );
return new ActivityProfileState( ref.getLocus(), tracker.getValues(UG_engine.getUAC().alleles, ref.getLocus()).size() > 0 ? 1.0 : 0.0 );
}
if( context == null ) { return new ActivityProfileResult(ref.getLocus(), 0.0); }
if( context == null || context.getBasePileup().isEmpty() )
// if we don't have any data, just abort early
return new ActivityProfileState(ref.getLocus(), 0.0);
final List<Allele> noCall = new ArrayList<Allele>(); // used to noCall all genotypes until the exact model is applied
noCall.add(Allele.NO_CALL);
@ -392,13 +429,13 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
genotypes.add( new GenotypeBuilder(sample.getKey()).alleles(noCall).PL(genotypeLikelihoods).make() );
}
final ArrayList<Allele> alleles = new ArrayList<Allele>();
final List<Allele> alleles = new ArrayList<Allele>();
alleles.add( FAKE_REF_ALLELE );
alleles.add( FAKE_ALT_ALLELE );
final VariantCallContext vcOut = UG_engine_simple_genotyper.calculateGenotypes(new VariantContextBuilder("HCisActive!", context.getContig(), context.getLocation().getStart(), context.getLocation().getStop(), alleles).genotypes(genotypes).make(), GenotypeLikelihoodsCalculationModel.Model.INDEL);
final double isActiveProb = vcOut == null ? 0.0 : QualityUtils.qualToProb( vcOut.getPhredScaledQual() );
return new ActivityProfileResult( ref.getLocus(), isActiveProb, averageHQSoftClips.mean() > 6.0 ? ActivityProfileResult.ActivityProfileResultState.HIGH_QUALITY_SOFT_CLIPS : ActivityProfileResult.ActivityProfileResultState.NONE, averageHQSoftClips.mean() );
return new ActivityProfileState( ref.getLocus(), isActiveProb, averageHQSoftClips.mean() > 6.0 ? ActivityProfileState.Type.HIGH_QUALITY_SOFT_CLIPS : ActivityProfileState.Type.NONE, averageHQSoftClips.mean() );
}
//---------------------------------------------------------------------------------------------------------------
@ -408,12 +445,12 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
//---------------------------------------------------------------------------------------------------------------
@Override
public Integer map( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion, final RefMetaDataTracker metaDataTracker ) {
public Integer map( final ActiveRegion activeRegion, 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 1;
final ArrayList<VariantContext> activeAllelesToGenotype = new ArrayList<VariantContext>();
final List<VariantContext> activeAllelesToGenotype = new ArrayList<VariantContext>();
if( UG_engine.getUAC().GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) {
for( final VariantContext vc : allelesToGenotype ) {
@ -424,16 +461,18 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
allelesToGenotype.removeAll( activeAllelesToGenotype );
}
if( !activeRegion.isActive ) { return 0; } // Not active so nothing to do!
if( !activeRegion.isActive() ) { return 0; } // Not active so nothing to do!
if( activeRegion.size() == 0 && UG_engine.getUAC().GenotypingMode != GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) { return 0; } // No reads here so nothing to do!
if( UG_engine.getUAC().GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES && activeAllelesToGenotype.isEmpty() ) { return 0; } // No alleles found in this region so nothing to do!
finalizeActiveRegion( activeRegion ); // merge overlapping fragments, clip adapter and low qual tails
final Haplotype referenceHaplotype = new Haplotype(activeRegion.getActiveRegionReference(referenceReader)); // Create the reference haplotype which is the bases from the reference that make up the active region
referenceHaplotype.setIsReference(true);
// note this operation must be performed before we clip the reads down, as this must correspond to the full reference region
final GenomeLoc fullSpanBeforeClipping = getPaddedLoc(activeRegion);
final Haplotype referenceHaplotype = new Haplotype(activeRegion.getActiveRegionReference(referenceReader), true); // Create the reference haplotype which is the bases from the reference that make up the active region
final byte[] fullReferenceWithPadding = activeRegion.getFullReference(referenceReader, REFERENCE_PADDING);
//int PRUNE_FACTOR = Math.max(MIN_PRUNE_FACTOR, determinePruneFactorFromCoverage( activeRegion ));
final ArrayList<Haplotype> haplotypes = assemblyEngine.runLocalAssembly( activeRegion, referenceHaplotype, fullReferenceWithPadding, getPaddedLoc(activeRegion), MIN_PRUNE_FACTOR, activeAllelesToGenotype );
final List<Haplotype> haplotypes = assemblyEngine.runLocalAssembly( activeRegion, referenceHaplotype, fullReferenceWithPadding, fullSpanBeforeClipping, MIN_PRUNE_FACTOR, activeAllelesToGenotype );
if( haplotypes.size() == 1 ) { return 1; } // only the reference haplotype remains so nothing else to do!
activeRegion.hardClipToActiveRegion(); // only evaluate the parts of reads that are overlapping the active region
@ -445,10 +484,10 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
// evaluate each sample's reads against all haplotypes
final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap = likelihoodCalculationEngine.computeReadLikelihoods( haplotypes, splitReadsBySample( activeRegion.getReads() ) );
final Map<String, ArrayList<GATKSAMRecord>> perSampleFilteredReadList = splitReadsBySample( filteredReads );
final Map<String, List<GATKSAMRecord>> perSampleFilteredReadList = splitReadsBySample( filteredReads );
// subset down to only the best haplotypes to be genotyped in all samples ( in GGA mode use all discovered haplotypes )
final ArrayList<Haplotype> bestHaplotypes = ( UG_engine.getUAC().GenotypingMode != GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ?
final List<Haplotype> bestHaplotypes = ( UG_engine.getUAC().GenotypingMode != GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ?
likelihoodCalculationEngine.selectBestHaplotypes( haplotypes, stratifiedReadMap, maxNumHaplotypesInPopulation ) : haplotypes );
for( final VariantContext call : genotypingEngine.assignGenotypeLikelihoods( UG_engine,
@ -457,13 +496,34 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
stratifiedReadMap,
perSampleFilteredReadList,
fullReferenceWithPadding,
getPaddedLoc(activeRegion),
fullSpanBeforeClipping,
activeRegion.getLocation(),
getToolkit().getGenomeLocParser(),
activeAllelesToGenotype ) ) {
annotationEngine.annotateDBs(metaDataTracker, getToolkit().getGenomeLocParser().createGenomeLoc(call), call);
vcfWriter.add( call );
}
if ( bamWriter != null ) {
// write the haplotypes to the bam
for ( Haplotype haplotype : haplotypes )
writeHaplotype(haplotype, fullSpanBeforeClipping, bestHaplotypes.contains(haplotype));
// we need to remap the Alleles back to the Haplotypes; inefficient but unfortunately this is a requirement currently
final Map<Allele, Haplotype> alleleToHaplotypeMap = new HashMap<Allele, Haplotype>(haplotypes.size());
for ( final Haplotype haplotype : haplotypes )
alleleToHaplotypeMap.put(Allele.create(haplotype.getBases()), haplotype);
// next, output the interesting reads for each sample aligned against the appropriate haplotype
for ( final PerReadAlleleLikelihoodMap readAlleleLikelihoodMap : stratifiedReadMap.values() ) {
for ( Map.Entry<GATKSAMRecord, Map<Allele, Double>> entry : readAlleleLikelihoodMap.getLikelihoodReadMap().entrySet() ) {
final Allele bestAllele = PerReadAlleleLikelihoodMap.getMostLikelyAllele(entry.getValue());
if ( bestAllele != Allele.NO_CALL )
writeReadAgainstHaplotype(entry.getKey(), alleleToHaplotypeMap.get(bestAllele), fullSpanBeforeClipping.getStart());
}
}
}
if( DEBUG ) { System.out.println("----------------------------------------------------------------------------------"); }
return 1; // One active region was processed during this map call
@ -498,8 +558,8 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
private void finalizeActiveRegion( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion ) {
if( DEBUG ) { System.out.println("\nAssembling " + activeRegion.getLocation() + " with " + activeRegion.size() + " reads: (with overlap region = " + activeRegion.getExtendedLoc() + ")"); }
final ArrayList<GATKSAMRecord> finalizedReadList = new ArrayList<GATKSAMRecord>();
final FragmentCollection<GATKSAMRecord> fragmentCollection = FragmentUtils.create( ReadUtils.sortReadsByCoordinate(activeRegion.getReads()) );
final List<GATKSAMRecord> finalizedReadList = new ArrayList<GATKSAMRecord>();
final FragmentCollection<GATKSAMRecord> fragmentCollection = FragmentUtils.create( activeRegion.getReads() );
activeRegion.clearReads();
// Join overlapping paired reads to create a single longer read
@ -508,24 +568,22 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
finalizedReadList.addAll( FragmentUtils.mergeOverlappingPairedFragments(overlappingPair) );
}
Collections.shuffle(finalizedReadList, GenomeAnalysisEngine.getRandomGenerator());
// Loop through the reads hard clipping the adaptor and low quality tails
final List<GATKSAMRecord> readsToUse = new ArrayList<GATKSAMRecord>(finalizedReadList.size());
for( final GATKSAMRecord myRead : finalizedReadList ) {
final GATKSAMRecord postAdapterRead = ( myRead.getReadUnmappedFlag() ? myRead : ReadClipper.hardClipAdaptorSequence( myRead ) );
if( postAdapterRead != null && !postAdapterRead.isEmpty() && postAdapterRead.getCigar().getReadLength() > 0 ) {
final GATKSAMRecord clippedRead = ReadClipper.hardClipLowQualEnds( postAdapterRead, MIN_TAIL_QUALITY );
// protect against INTERVALS with abnormally high coverage
// BUGBUG: remove when positional downsampler is hooked up to ART/HC
if( clippedRead.getReadLength() > 0 && activeRegion.size() < samplesList.size() * DOWNSAMPLE_PER_SAMPLE_PER_REGION ) {
activeRegion.add(clippedRead);
if( activeRegion.readOverlapsRegion(clippedRead) && clippedRead.getReadLength() > 0 ) {
readsToUse.add(clippedRead);
}
}
}
activeRegion.addAll(ReadUtils.sortReadsByCoordinate(readsToUse));
}
private List<GATKSAMRecord> filterNonPassingReads( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion ) {
final ArrayList<GATKSAMRecord> readsToRemove = new ArrayList<GATKSAMRecord>();
final List<GATKSAMRecord> readsToRemove = new ArrayList<GATKSAMRecord>();
for( final GATKSAMRecord rec : activeRegion.getReads() ) {
if( rec.getReadLength() < 24 || rec.getMappingQuality() < 20 || BadMateFilter.hasBadMate(rec) || (keepRG != null && !rec.getReadGroup().getId().equals(keepRG)) ) {
readsToRemove.add(rec);
@ -536,15 +594,15 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
}
private GenomeLoc getPaddedLoc( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion ) {
final int padLeft = Math.max(activeRegion.getReferenceLoc().getStart()-REFERENCE_PADDING, 1);
final int padRight = Math.min(activeRegion.getReferenceLoc().getStop()+REFERENCE_PADDING, referenceReader.getSequenceDictionary().getSequence(activeRegion.getReferenceLoc().getContig()).getSequenceLength());
return getToolkit().getGenomeLocParser().createGenomeLoc(activeRegion.getReferenceLoc().getContig(), padLeft, padRight);
final int padLeft = Math.max(activeRegion.getReadSpanLoc().getStart()-REFERENCE_PADDING, 1);
final int padRight = Math.min(activeRegion.getReadSpanLoc().getStop()+REFERENCE_PADDING, referenceReader.getSequenceDictionary().getSequence(activeRegion.getReadSpanLoc().getContig()).getSequenceLength());
return getToolkit().getGenomeLocParser().createGenomeLoc(activeRegion.getReadSpanLoc().getContig(), padLeft, padRight);
}
private HashMap<String, ArrayList<GATKSAMRecord>> splitReadsBySample( final List<GATKSAMRecord> reads ) {
final HashMap<String, ArrayList<GATKSAMRecord>> returnMap = new HashMap<String, ArrayList<GATKSAMRecord>>();
private Map<String, List<GATKSAMRecord>> splitReadsBySample( final List<GATKSAMRecord> reads ) {
final Map<String, List<GATKSAMRecord>> returnMap = new HashMap<String, List<GATKSAMRecord>>();
for( final String sample : samplesList) {
ArrayList<GATKSAMRecord> readList = returnMap.get( sample );
List<GATKSAMRecord> readList = returnMap.get( sample );
if( readList == null ) {
readList = new ArrayList<GATKSAMRecord>();
returnMap.put(sample, readList);
@ -557,23 +615,92 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
return returnMap;
}
/*
private int determinePruneFactorFromCoverage( final ActiveRegion activeRegion ) {
final ArrayList<Integer> readLengthDistribution = new ArrayList<Integer>();
for( final GATKSAMRecord read : activeRegion.getReads() ) {
readLengthDistribution.add(read.getReadLength());
}
final double meanReadLength = MathUtils.average(readLengthDistribution);
final double meanCoveragePerSample = (double) activeRegion.getReads().size() / ((double) activeRegion.getExtendedLoc().size() / meanReadLength) / (double) samplesList.size();
int PRUNE_FACTOR = 0;
if( meanCoveragePerSample > 8.5 ) {
PRUNE_FACTOR = (int) Math.floor( Math.sqrt( meanCoveragePerSample - 5.0 ) );
} else if( meanCoveragePerSample > 3.0 ) {
PRUNE_FACTOR = 1;
private void setupBamWriter() {
// prepare the bam header
bamHeader = new SAMFileHeader();
bamHeader.setSequenceDictionary(getToolkit().getSAMFileHeader().getSequenceDictionary());
bamHeader.setSortOrder(SAMFileHeader.SortOrder.coordinate);
// include the original read groups plus a new artificial one for the haplotypes
final List<SAMReadGroupRecord> readGroups = new ArrayList<SAMReadGroupRecord>(getToolkit().getSAMFileHeader().getReadGroups());
final SAMReadGroupRecord rg = new SAMReadGroupRecord(readGroupId);
rg.setSample("HC");
rg.setSequencingCenter("BI");
readGroups.add(rg);
bamHeader.setReadGroups(readGroups);
bamWriter.setPresorted(false);
bamWriter.writeHeader(bamHeader);
}
private void writeHaplotype(final Haplotype haplotype, final GenomeLoc paddedRefLoc, final boolean isAmongBestHaplotypes) {
final GATKSAMRecord record = new GATKSAMRecord(bamHeader);
record.setReadBases(haplotype.getBases());
record.setAlignmentStart(paddedRefLoc.getStart() + haplotype.getAlignmentStartHapwrtRef());
record.setBaseQualities(Utils.dupBytes((byte) '!', haplotype.getBases().length));
record.setCigar(haplotype.getCigar());
record.setMappingQuality(isAmongBestHaplotypes ? 60 : 0);
record.setReadName("HC" + uniqueNameCounter++);
record.setReadUnmappedFlag(false);
record.setReferenceIndex(paddedRefLoc.getContigIndex());
record.setAttribute(SAMTag.RG.toString(), readGroupId);
record.setFlags(16);
bamWriter.addAlignment(record);
}
private void writeReadAgainstHaplotype(final GATKSAMRecord read, final Haplotype haplotype, final int referenceStart) {
final SWPairwiseAlignment swPairwiseAlignment = new SWPairwiseAlignment(haplotype.getBases(), read.getReadBases(), 5.0, -10.0, -22.0, -1.2);
final int readStartOnHaplotype = swPairwiseAlignment.getAlignmentStart2wrt1();
final int readStartOnReference = referenceStart + haplotype.getAlignmentStartHapwrtRef() + readStartOnHaplotype;
read.setAlignmentStart(readStartOnReference);
final Cigar cigar = generateReadCigarFromHaplotype(read, readStartOnHaplotype, haplotype.getCigar());
read.setCigar(cigar);
bamWriter.addAlignment(read);
}
private Cigar generateReadCigarFromHaplotype(final GATKSAMRecord read, final int readStartOnHaplotype, final Cigar haplotypeCigar) {
int currentReadPos = 0;
int currentHapPos = 0;
final List<CigarElement> readCigarElements = new ArrayList<CigarElement>();
for ( final CigarElement cigarElement : haplotypeCigar.getCigarElements() ) {
if ( cigarElement.getOperator() == CigarOperator.D ) {
if ( currentReadPos > 0 )
readCigarElements.add(cigarElement);
} else if ( cigarElement.getOperator() == CigarOperator.M || cigarElement.getOperator() == CigarOperator.I ) {
final int elementLength = cigarElement.getLength();
final int nextReadPos = currentReadPos + elementLength;
final int nextHapPos = currentHapPos + elementLength;
// do we want this element?
if ( currentReadPos > 0 ) {
// do we want the entire element?
if ( nextReadPos < read.getReadLength() ) {
readCigarElements.add(cigarElement);
currentReadPos = nextReadPos;
}
// otherwise, we can finish up and return the cigar
else {
readCigarElements.add(new CigarElement(read.getReadLength() - currentReadPos, cigarElement.getOperator()));
return new Cigar(readCigarElements);
}
}
// do we want part of the element to start?
else if ( currentReadPos == 0 && nextHapPos > readStartOnHaplotype ) {
currentReadPos = Math.min(nextHapPos - readStartOnHaplotype, read.getReadLength());
readCigarElements.add(new CigarElement(currentReadPos, cigarElement.getOperator()));
}
currentHapPos = nextHapPos;
}
}
if( DEBUG ) { System.out.println(String.format("Mean coverage per sample = %.1f --> prune factor = %d", meanCoveragePerSample, PRUNE_FACTOR)); }
return PRUNE_FACTOR;
return new Cigar(readCigarElements);
}
*/
}

474
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KBestPaths.java
View File

@ -46,8 +46,15 @@
package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import net.sf.samtools.Cigar;
import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
import org.apache.commons.lang.ArrayUtils;
import org.broadinstitute.sting.utils.SWPairwiseAlignment;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.jgrapht.graph.DefaultDirectedGraph;
import java.io.Serializable;
@ -55,7 +62,7 @@ import java.util.*;
/**
* Created by IntelliJ IDEA.
* User: ebanks
* User: ebanks, rpoplin
* Date: Mar 23, 2011
*/
// Class for finding the K best paths (as determined by the sum of multiplicities of the edges) in a graph.
@ -72,47 +79,85 @@ public class KBestPaths {
protected static class Path {
// the last vertex seen in the path
private DeBruijnVertex lastVertex;
private final DeBruijnVertex lastVertex;
// the list of edges comprising the path
private ArrayList<DeBruijnEdge> edges;
private final List<DeBruijnEdge> edges;
// the scores for the path
private int totalScore = 0, lowestEdge = -1;
private final int totalScore;
public Path( final DeBruijnVertex initialVertex ) {
// the graph from which this path originated
private final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph;
// used in the bubble state machine to apply Smith-Waterman to the bubble sequence
private final double SW_MATCH = 15.0;
private final double SW_MISMATCH = -15.0;
private final double SW_GAP = -25.0;
private final double SW_GAP_EXTEND = -1.2;
public Path( final DeBruijnVertex initialVertex, final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph ) {
lastVertex = initialVertex;
edges = new ArrayList<DeBruijnEdge>(0);
totalScore = 0;
this.graph = graph;
}
public Path( final Path p, final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph, final DeBruijnEdge edge ) {
lastVertex = graph.getEdgeTarget(edge);
public Path( final Path p, final DeBruijnEdge edge ) {
if( !p.graph.getEdgeSource(edge).equals(p.lastVertex) ) { throw new IllegalStateException("Edges added to path must be contiguous."); }
graph = p.graph;
lastVertex = p.graph.getEdgeTarget(edge);
edges = new ArrayList<DeBruijnEdge>(p.edges);
edges.add(edge);
totalScore = p.totalScore + edge.getMultiplicity();
lowestEdge = ( p.lowestEdge == -1 ) ? edge.getMultiplicity() : Math.min(p.lowestEdge, edge.getMultiplicity());
}
public boolean containsEdge( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph, final DeBruijnEdge edge ) {
final DeBruijnVertex targetVertex = graph.getEdgeTarget(edge);
/**
* 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 DeBruijnEdge edge ) {
for( final DeBruijnEdge e : edges ) {
if( e.equals(graph, edge) || graph.getEdgeTarget(e).equals(targetVertex) ) {
if( e.equals(graph, edge) ) {
return true;
}
}
return false;
}
public ArrayList<DeBruijnEdge> getEdges() { return edges; }
public int numInPath( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph, final DeBruijnEdge edge ) {
int numInPath = 0;
for( final DeBruijnEdge e : edges ) {
if( e.equals(graph, edge) ) {
numInPath++;
}
}
return numInPath;
}
public boolean containsRefEdge() {
for( final DeBruijnEdge e : edges ) {
if( e.isRef() ) { return true; }
}
return false;
}
public List<DeBruijnEdge> getEdges() { return edges; }
public int getScore() { return totalScore; }
public int getLowestEdge() { return lowestEdge; }
public DeBruijnVertex getLastVertexInPath() { return lastVertex; }
public byte[] getBases( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph ) {
/**
* The base sequence for this path. Pull the full sequence for the source of the path and then the suffix for all subsequent nodes
* @return non-null sequence of bases corresponding to this path
*/
@Ensures({"result != null"})
public byte[] getBases() {
if( edges.size() == 0 ) { return lastVertex.getSequence(); }
byte[] bases = graph.getEdgeSource( edges.get(0) ).getSequence();
@ -121,6 +166,157 @@ public class KBestPaths {
}
return bases;
}
/**
* Pull the added base sequence implied by visiting this node in a path
* @param graph the graph from which the vertex originated
* @param v the vertex whose sequence to grab
* @return non-null sequence of bases corresponding to this node in the graph
*/
@Ensures({"result != null"})
public byte[] getAdditionalSequence( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph, final DeBruijnVertex v ) {
return ( edges.size()==0 || graph.getEdgeSource(edges.get(0)).equals(v) ? v.getSequence() : v.getSuffix() );
}
/**
* Calculate the cigar string for this path using a bubble traversal of the assembly graph and running a Smith-Waterman alignment on each bubble
*/
@Ensures("result != null")
public Cigar calculateCigar() {
final Cigar cigar = new Cigar();
// special case for paths that start on reference but not at the reference source node
if( edges.get(0).isRef() && !isRefSource(graph, edges.get(0)) ) {
for( final CigarElement ce : calculateCigarForCompleteBubble(graph, null, null, graph.getEdgeSource(edges.get(0))).getCigarElements() ) {
cigar.add(ce);
}
}
// reset the bubble state machine
final BubbleStateMachine bsm = new BubbleStateMachine(cigar);
for( final DeBruijnEdge e : edges ) {
if( e.equals(graph, edges.get(0)) ) {
advanceBubbleStateMachine( bsm, graph, graph.getEdgeSource(e), null );
}
advanceBubbleStateMachine( bsm, graph, graph.getEdgeTarget(e), e );
}
// special case for paths that don't end on reference
if( bsm.inBubble ) {
for( final CigarElement ce : calculateCigarForCompleteBubble(graph, bsm.bubbleBytes, bsm.lastSeenReferenceNode, null).getCigarElements() ) {
bsm.cigar.add(ce);
}
} else if( edges.get(edges.size()-1).isRef() && !isRefSink(graph, edges.get(edges.size()-1)) ) { // special case for paths that end of the reference but haven't completed the entire reference circuit
for( final CigarElement ce : calculateCigarForCompleteBubble(graph, bsm.bubbleBytes, graph.getEdgeTarget(edges.get(edges.size()-1)), null).getCigarElements() ) {
bsm.cigar.add(ce);
}
}
return AlignmentUtils.consolidateCigar(bsm.cigar);
}
@Requires({"bsm != null", "graph != null", "node != null"})
private void advanceBubbleStateMachine( final BubbleStateMachine bsm, final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph, final DeBruijnVertex node, final DeBruijnEdge e ) {
if( isReferenceNode( graph, node ) ) {
if( !bsm.inBubble ) { // just add the ref bases as M's in the Cigar string, and don't do anything else
if( e !=null && !e.isRef() ) {
if( referencePathExists( graph, graph.getEdgeSource(e), node) ) {
for( final CigarElement ce : calculateCigarForCompleteBubble(graph, null, graph.getEdgeSource(e), node).getCigarElements() ) {
bsm.cigar.add(ce);
}
bsm.cigar.add( new CigarElement( getAdditionalSequence(graph, node).length, CigarOperator.M) );
} else if ( graph.getEdgeSource(e).equals(graph.getEdgeTarget(e)) ) { // alt edge at ref node points to itself
bsm.cigar.add( new CigarElement( getAdditionalSequence(graph, node).length, CigarOperator.I) );
} else {
bsm.inBubble = true;
bsm.bubbleBytes = null;
bsm.lastSeenReferenceNode = graph.getEdgeSource(e);
bsm.bubbleBytes = ArrayUtils.addAll( bsm.bubbleBytes, getAdditionalSequence(graph, node) );
}
} else {
bsm.cigar.add( new CigarElement( getAdditionalSequence(graph, node).length, CigarOperator.M) );
}
} else if( bsm.lastSeenReferenceNode != null && !referencePathExists( graph, bsm.lastSeenReferenceNode, node ) ) { // add bases to the bubble string until we get back to the reference path
bsm.bubbleBytes = ArrayUtils.addAll( bsm.bubbleBytes, getAdditionalSequence(graph, node) );
} else { // close the bubble and use a local SW to determine the Cigar string
for( final CigarElement ce : calculateCigarForCompleteBubble(graph, bsm.bubbleBytes, bsm.lastSeenReferenceNode, node).getCigarElements() ) {
bsm.cigar.add(ce);
}
bsm.inBubble = false;
bsm.bubbleBytes = null;
bsm.lastSeenReferenceNode = null;
bsm.cigar.add( new CigarElement( getAdditionalSequence(graph, node).length, CigarOperator.M) );
}
} else { // non-ref vertex
if( bsm.inBubble ) { // just keep accumulating until we get back to the reference path
bsm.bubbleBytes = ArrayUtils.addAll( bsm.bubbleBytes, getAdditionalSequence(graph, node) );
} else { // open up a bubble
bsm.inBubble = true;
bsm.bubbleBytes = null;
bsm.lastSeenReferenceNode = (e != null ? graph.getEdgeSource(e) : null );
bsm.bubbleBytes = ArrayUtils.addAll( bsm.bubbleBytes, getAdditionalSequence(graph, node) );
}
}
}
@Requires({"graph != null"})
@Ensures({"result != null", "result.getReadLength() == bubbleBytes.length"})
private Cigar calculateCigarForCompleteBubble( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph, final byte[] bubbleBytes, final DeBruijnVertex fromVertex, final DeBruijnVertex toVertex ) {
final byte[] refBytes = getReferenceBytes(this, graph, fromVertex, toVertex);
final Cigar cigar = new Cigar();
// add padding to anchor ref/alt bases in the SW matrix
byte[] padding = "XXXXXX".getBytes();
boolean goodAlignment = false;
SWPairwiseAlignment swConsensus = null;
while( !goodAlignment && padding.length < 1000 ) {
padding = ArrayUtils.addAll(padding, padding); // double the size of the padding each time
final byte[] reference = ArrayUtils.addAll( ArrayUtils.addAll(padding, refBytes), padding );
final byte[] alternate = ArrayUtils.addAll( ArrayUtils.addAll(padding, bubbleBytes), padding );
swConsensus = new SWPairwiseAlignment( reference, alternate, SW_MATCH, SW_MISMATCH, SW_GAP, SW_GAP_EXTEND );
if( swConsensus.getAlignmentStart2wrt1() == 0 && !swConsensus.getCigar().toString().contains("S") && swConsensus.getCigar().getReferenceLength() == reference.length ) {
goodAlignment = true;
}
}
if( !goodAlignment && swConsensus != null ) {
throw new ReviewedStingException("SmithWaterman offset failure: " + (refBytes == null ? "-" : new String(refBytes)) + " against " + new String(bubbleBytes) + " = " + swConsensus.getCigar());
}
if( swConsensus != null ) {
final Cigar swCigar = swConsensus.getCigar();
for( int iii = 0; iii < swCigar.numCigarElements(); iii++ ) {
// now we need to remove the padding from the cigar string
int length = swCigar.getCigarElement(iii).getLength();
if( iii == 0 ) { length -= padding.length; }
if( iii == swCigar.numCigarElements() - 1 ) { length -= padding.length; }
if( length > 0 ) {
cigar.add( new CigarElement(length, swCigar.getCigarElement(iii).getOperator()) );
}
}
if( (refBytes == null && cigar.getReferenceLength() != 0) || ( refBytes != null && cigar.getReferenceLength() != refBytes.length ) ) {
throw new ReviewedStingException("SmithWaterman cigar failure: " + (refBytes == null ? "-" : new String(refBytes)) + " against " + new String(bubbleBytes) + " = " + swConsensus.getCigar());
}
}
return cigar;
}
// class to keep track of the bubble state machine
protected static class BubbleStateMachine {
public boolean inBubble = false;
public byte[] bubbleBytes = null;
public DeBruijnVertex lastSeenReferenceNode = null;
public Cigar cigar = null;
public BubbleStateMachine( final Cigar initialCigar ) {
inBubble = false;
bubbleBytes = null;
lastSeenReferenceNode = null;
cigar = initialCigar;
}
}
}
protected static class PathComparatorTotalScore implements Comparator<Path>, Serializable {
@ -130,13 +326,6 @@ public class KBestPaths {
}
}
//protected static class PathComparatorLowestEdge implements Comparator<Path>, Serializable {
// @Override
// public int compare(final Path path1, final Path path2) {
// return path2.lowestEdge - path1.lowestEdge;
// }
//}
public static List<Path> getKBestPaths( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph, final int k ) {
if( k > MAX_PATHS_TO_HOLD/2 ) { throw new ReviewedStingException("Asked for more paths than MAX_PATHS_TO_HOLD!"); }
final ArrayList<Path> bestPaths = new ArrayList<Path>();
@ -144,7 +333,7 @@ public class KBestPaths {
// run a DFS for best paths
for( final DeBruijnVertex v : graph.vertexSet() ) {
if( graph.inDegreeOf(v) == 0 ) {
findBestPaths(graph, new Path(v), bestPaths);
findBestPaths(new Path(v, graph), bestPaths);
}
}
@ -153,14 +342,14 @@ public class KBestPaths {
return bestPaths.subList(0, Math.min(k, bestPaths.size()));
}
private static void findBestPaths( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph, final Path path, final List<Path> bestPaths ) {
findBestPaths(graph, path, bestPaths, new MyInt());
private static void findBestPaths( final Path path, final List<Path> bestPaths ) {
findBestPaths(path, bestPaths, new MyInt());
}
private static void findBestPaths( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph, final Path path, final List<Path> bestPaths, MyInt n ) {
private static void findBestPaths( final Path path, final List<Path> bestPaths, final MyInt n ) {
// did we hit the end of a path?
if ( allOutgoingEdgesHaveBeenVisited(graph, path) ) {
if ( allOutgoingEdgesHaveBeenVisited(path) ) {
if ( bestPaths.size() >= MAX_PATHS_TO_HOLD ) {
// clean out some low scoring paths
Collections.sort(bestPaths, new PathComparatorTotalScore() );
@ -172,27 +361,242 @@ public class KBestPaths {
} else {
// recursively run DFS
final ArrayList<DeBruijnEdge> edgeArrayList = new ArrayList<DeBruijnEdge>();
edgeArrayList.addAll(graph.outgoingEdgesOf(path.lastVertex));
edgeArrayList.addAll(path.graph.outgoingEdgesOf(path.lastVertex));
Collections.sort(edgeArrayList, new DeBruijnEdge.EdgeWeightComparator());
Collections.reverse(edgeArrayList);
for ( final DeBruijnEdge edge : edgeArrayList ) {
// make sure the edge is not already in the path
if ( path.containsEdge(graph, edge) )
if ( path.containsEdge(edge) )
continue;
final Path newPath = new Path(path, graph, edge);
final Path newPath = new Path(path, edge);
n.val++;
findBestPaths(graph, newPath, bestPaths, n);
findBestPaths(newPath, bestPaths, n);
}
}
}
private static boolean allOutgoingEdgesHaveBeenVisited( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph, final Path path ) {
for( final DeBruijnEdge edge : graph.outgoingEdgesOf(path.lastVertex) ) {
if( !path.containsEdge(graph, edge) ) {
private static boolean allOutgoingEdgesHaveBeenVisited( final Path path ) {
for( final DeBruijnEdge edge : path.graph.outgoingEdgesOf(path.lastVertex) ) {
if( !path.containsEdge(edge) ) {
return false;
}
}
return true;
}
/****************************************************************
* Collection of graph functions used by KBestPaths *
***************************************************************/
/**
* Test if the vertex is on a reference path in the graph. If so it is referred to as a reference node
* @param graph the graph from which the vertex originated
* @param v the vertex to test
* @return true if the vertex is on the reference path
*/
public static boolean isReferenceNode( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph, final DeBruijnVertex v ) {
for( final DeBruijnEdge e : graph.edgesOf(v) ) {
if( e.isRef() ) { return true; }
}
return false;
}
/**
* Is this edge a source edge (the source vertex of the edge is a source node in the graph)
* @param graph the graph from which the edge originated
* @param e the edge to test
* @return true if the source vertex of the edge is a source node in the graph
*/
public static boolean isSource( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph, final DeBruijnEdge e ) {
return graph.inDegreeOf(graph.getEdgeSource(e)) == 0;
}
/**
* Is this vertex a source vertex
* @param graph the graph from which the vertex originated
* @param v the vertex to test
* @return true if the vertex is a source vertex
*/
public static boolean isSource( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph, final DeBruijnVertex v ) {
return graph.inDegreeOf(v) == 0;
}
/**
* Is this edge both a reference edge and a source edge for the reference path
* @param graph the graph from which the edge originated
* @param e the edge to test
* @return true if the edge is both a reference edge and a reference path source edge
*/
public static boolean isRefSource( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph, final DeBruijnEdge e ) {
for( final DeBruijnEdge edgeToTest : graph.incomingEdgesOf(graph.getEdgeSource(e)) ) {
if( edgeToTest.isRef() ) { return false; }
}
return true;
}
/**
* Is this vertex both a reference node and a source node for the reference path
* @param graph the graph from which the vertex originated
* @param v the vertex to test
* @return true if the vertex is both a reference node and a reference path source node
*/
public static boolean isRefSource( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph, final DeBruijnVertex v ) {
for( final DeBruijnEdge edgeToTest : graph.incomingEdgesOf(v) ) {
if( edgeToTest.isRef() ) { return false; }
}
return true;
}
/**
* Is this edge both a reference edge and a sink edge for the reference path
* @param graph the graph from which the edge originated
* @param e the edge to test
* @return true if the edge is both a reference edge and a reference path sink edge
*/
public static boolean isRefSink( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph, final DeBruijnEdge e ) {
for( final DeBruijnEdge edgeToTest : graph.outgoingEdgesOf(graph.getEdgeTarget(e)) ) {
if( edgeToTest.isRef() ) { return false; }
}
return true;
}
/**
* Is this vertex both a reference node and a sink node for the reference path
* @param graph the graph from which the node originated
* @param v the node to test
* @return true if the vertex is both a reference node and a reference path sink node
*/
public static boolean isRefSink( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph, final DeBruijnVertex v ) {
for( final DeBruijnEdge edgeToTest : graph.outgoingEdgesOf(v) ) {
if( edgeToTest.isRef() ) { return false; }
}
return true;
}
public static DeBruijnEdge getReferenceSourceEdge( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph ) {
for( final DeBruijnEdge e : graph.edgeSet() ) {
if( e.isRef() && isRefSource(graph, e) ) {
return e;
}
}
throw new ReviewedStingException("All reference graphs should have a source node");
}
public static DeBruijnVertex getReferenceSourceVertex( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph ) {
for( final DeBruijnVertex v : graph.vertexSet() ) {
if( isReferenceNode(graph, v) && isRefSource(graph, v) ) {
return v;
}
}
return null;
}
public static DeBruijnEdge getReferenceSinkEdge( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph ) {
for( final DeBruijnEdge e : graph.edgeSet() ) {
if( e.isRef() && isRefSink(graph, e) ) {
return e;
}
}
throw new ReviewedStingException("All reference graphs should have a sink node");
}
public static DeBruijnVertex getReferenceSinkVertex( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph ) {
for( final DeBruijnVertex v : graph.vertexSet() ) {
if( isReferenceNode(graph, v) && isRefSink(graph, v) ) {
return v;
}
}
throw new ReviewedStingException("All reference graphs should have a sink node");
}
public static DeBruijnEdge getNextReferenceEdge( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph, final DeBruijnEdge e ) {
if( e == null ) { return null; }
for( final DeBruijnEdge edgeToTest : graph.outgoingEdgesOf(graph.getEdgeTarget(e)) ) {
if( edgeToTest.isRef() ) {
return edgeToTest;
}
}
return null;
}
public static DeBruijnVertex getNextReferenceVertex( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph, final DeBruijnVertex v ) {
if( v == null ) { return null; }
for( final DeBruijnEdge edgeToTest : graph.outgoingEdgesOf(v) ) {
if( edgeToTest.isRef() ) {
return graph.getEdgeTarget(edgeToTest);
}
}
return null;
}
public static DeBruijnEdge getPrevReferenceEdge( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph, final DeBruijnEdge e ) {
for( final DeBruijnEdge edgeToTest : graph.incomingEdgesOf(graph.getEdgeSource(e)) ) {
if( edgeToTest.isRef() ) {
return edgeToTest;
}
}
return null;
}
public static DeBruijnVertex getPrevReferenceVertex( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph, final DeBruijnVertex v ) {
for( final DeBruijnEdge edgeToTest : graph.incomingEdgesOf(v) ) {
if( isReferenceNode(graph, graph.getEdgeSource(edgeToTest)) ) {
return graph.getEdgeSource(edgeToTest);
}
}
return null;
}
public static boolean referencePathExists(final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph, final DeBruijnEdge fromEdge, final DeBruijnEdge toEdge) {
DeBruijnEdge e = fromEdge;
if( e == null ) {
return false;
}
while( !e.equals(graph, toEdge) ) {
e = getNextReferenceEdge(graph, e);
if( e == null ) {
return false;
}
}
return true;
}
public static boolean referencePathExists(final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph, final DeBruijnVertex fromVertex, final DeBruijnVertex toVertex) {
DeBruijnVertex v = fromVertex;
if( v == null ) {
return false;
}
v = getNextReferenceVertex(graph, v);
if( v == null ) {
return false;
}
while( !v.equals(toVertex) ) {
v = getNextReferenceVertex(graph, v);
if( v == null ) {
return false;
}
}
return true;
}
// fromVertex (exclusive) -> toVertex (exclusive)
public static byte[] getReferenceBytes( final Path path, final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph, final DeBruijnVertex fromVertex, final DeBruijnVertex toVertex ) {
byte[] bytes = null;
if( fromVertex != null && toVertex != null && !referencePathExists(graph, fromVertex, toVertex) ) {
throw new ReviewedStingException("Asked for a reference path which doesn't exist. " + fromVertex + " --> " + toVertex);
}
DeBruijnVertex v = fromVertex;
if( v == null ) {
v = getReferenceSourceVertex(graph);
bytes = ArrayUtils.addAll( bytes, path.getAdditionalSequence(graph, v) );
}
v = getNextReferenceVertex(graph, v);
while( (toVertex != null && !v.equals(toVertex)) || (toVertex == null && v != null) ) {
bytes = ArrayUtils.addAll( bytes, path.getAdditionalSequence(graph, v) );
// advance along the reference path
v = getNextReferenceVertex(graph, v);
}
return bytes;
}
}

87
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
View File

@ -91,11 +91,11 @@ public class LikelihoodCalculationEngine {
DEBUG = debug;
}
public Map<String, PerReadAlleleLikelihoodMap> computeReadLikelihoods( final ArrayList<Haplotype> haplotypes, final HashMap<String, ArrayList<GATKSAMRecord>> perSampleReadList ) {
public Map<String, PerReadAlleleLikelihoodMap> computeReadLikelihoods( final List<Haplotype> haplotypes, final Map<String, List<GATKSAMRecord>> perSampleReadList ) {
final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap = new HashMap<String, PerReadAlleleLikelihoodMap>();
int X_METRIC_LENGTH = 0;
for( final Map.Entry<String, ArrayList<GATKSAMRecord>> sample : perSampleReadList.entrySet() ) {
for( final Map.Entry<String, List<GATKSAMRecord>> sample : perSampleReadList.entrySet() ) {
for( final GATKSAMRecord read : sample.getValue() ) {
final int readLength = read.getReadLength();
if( readLength > X_METRIC_LENGTH ) { X_METRIC_LENGTH = readLength; }
@ -115,7 +115,7 @@ public class LikelihoodCalculationEngine {
pairHMM.initialize(X_METRIC_LENGTH, Y_METRIC_LENGTH);
// for each sample's reads
for( final Map.Entry<String, ArrayList<GATKSAMRecord>> sampleEntry : perSampleReadList.entrySet() ) {
for( final Map.Entry<String, List<GATKSAMRecord>> sampleEntry : perSampleReadList.entrySet() ) {
//if( DEBUG ) { System.out.println("Evaluating sample " + sample + " with " + perSampleReadList.get( sample ).size() + " passing reads"); }
// evaluate the likelihood of the reads given those haplotypes
stratifiedReadMap.put(sampleEntry.getKey(), computeReadLikelihoods(haplotypes, sampleEntry.getValue()));
@ -123,10 +123,15 @@ public class LikelihoodCalculationEngine {
return stratifiedReadMap;
}
private PerReadAlleleLikelihoodMap computeReadLikelihoods( final ArrayList<Haplotype> haplotypes, final ArrayList<GATKSAMRecord> reads) {
private PerReadAlleleLikelihoodMap computeReadLikelihoods( final List<Haplotype> haplotypes, final List<GATKSAMRecord> reads) {
// first, a little set up to get copies of the Haplotypes that are Alleles (more efficient than creating them each time)
final int numHaplotypes = haplotypes.size();
final Map<Haplotype, Allele> alleleVersions = new HashMap<Haplotype, Allele>(numHaplotypes);
for ( final Haplotype haplotype : haplotypes ) {
alleleVersions.put(haplotype, Allele.create(haplotype.getBases()));
}
final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = new PerReadAlleleLikelihoodMap();
final int numHaplotypes = haplotypes.size();
for( final GATKSAMRecord read : reads ) {
final byte[] overallGCP = new byte[read.getReadLength()];
Arrays.fill( overallGCP, constantGCP ); // Is there a way to derive empirical estimates for this from the data?
@ -138,20 +143,17 @@ public class LikelihoodCalculationEngine {
readQuals[kkk] = ( readQuals[kkk] > (byte) read.getMappingQuality() ? (byte) read.getMappingQuality() : readQuals[kkk] ); // cap base quality by mapping quality
//readQuals[kkk] = ( readQuals[kkk] > readInsQuals[kkk] ? readInsQuals[kkk] : readQuals[kkk] ); // cap base quality by base insertion quality, needs to be evaluated
//readQuals[kkk] = ( readQuals[kkk] > readDelQuals[kkk] ? readDelQuals[kkk] : readQuals[kkk] ); // cap base quality by base deletion quality, needs to be evaluated
// TODO -- why is Q18 hard-coded here???
readQuals[kkk] = ( readQuals[kkk] < (byte) 18 ? QualityUtils.MIN_USABLE_Q_SCORE : readQuals[kkk] );
}
for( int jjj = 0; jjj < numHaplotypes; jjj++ ) {
final Haplotype haplotype = haplotypes.get(jjj);
// TODO -- need to test against a reference/position with non-standard bases
//if ( !Allele.acceptableAlleleBases(haplotype.getBases(), false) )
// continue;
final int haplotypeStart = ( previousHaplotypeSeen == null ? 0 : computeFirstDifferingPosition(haplotype.getBases(), previousHaplotypeSeen.getBases()) );
previousHaplotypeSeen = haplotype;
perReadAlleleLikelihoodMap.add(read, Allele.create(haplotype.getBases()),
perReadAlleleLikelihoodMap.add(read, alleleVersions.get(haplotype),
pairHMM.computeReadLikelihoodGivenHaplotypeLog10(haplotype.getBases(), read.getReadBases(),
readQuals, readInsQuals, readDelQuals, overallGCP, haplotypeStart, jjj == 0));
}
@ -233,72 +235,13 @@ public class LikelihoodCalculationEngine {
return likelihoodMatrix;
}
/*
@Requires({"haplotypes.size() > 0"})
@Ensures({"result.size() <= haplotypes.size()"})
public ArrayList<Haplotype> selectBestHaplotypes( final ArrayList<Haplotype> haplotypes ) {
// BUGBUG: This function needs a lot of work. Need to use 4-gamete test or Tajima's D to decide to break up events into separate pieces for genotyping
final int numHaplotypes = haplotypes.size();
final Set<String> sampleKeySet = haplotypes.get(0).getSampleKeySet(); // BUGBUG: assume all haplotypes saw the same samples
final ArrayList<Integer> bestHaplotypesIndexList = new ArrayList<Integer>();
bestHaplotypesIndexList.add(0); // always start with the reference haplotype
final double[][][] haplotypeLikelihoodMatrix = new double[sampleKeySet.size()][numHaplotypes][numHaplotypes];
int sampleCount = 0;
for( final String sample : sampleKeySet ) {
haplotypeLikelihoodMatrix[sampleCount++] = computeDiploidHaplotypeLikelihoods( haplotypes, sample );
}
int hap1 = 0;
int hap2 = 0;
int chosenSample = 0;
//double bestElement = Double.NEGATIVE_INFINITY;
final int maxChosenHaplotypes = Math.min( 15, sampleKeySet.size() * 2 + 1 );
while( bestHaplotypesIndexList.size() < maxChosenHaplotypes ) {
double maxElement = Double.NEGATIVE_INFINITY;
for( int kkk = 0; kkk < sampleCount; kkk++ ) {
for( int iii = 0; iii < numHaplotypes; iii++ ) {
for( int jjj = 0; jjj <= iii; jjj++ ) {
if( haplotypeLikelihoodMatrix[kkk][iii][jjj] > maxElement ) {
maxElement = haplotypeLikelihoodMatrix[kkk][iii][jjj];
hap1 = iii;
hap2 = jjj;
chosenSample = kkk;
}
}
}
}
if( maxElement == Double.NEGATIVE_INFINITY ) { break; }
if( !bestHaplotypesIndexList.contains(hap1) ) { bestHaplotypesIndexList.add(hap1); }
if( !bestHaplotypesIndexList.contains(hap2) ) { bestHaplotypesIndexList.add(hap2); }
for( int iii = 0; iii < numHaplotypes; iii++ ) {
for( int jjj = 0; jjj <= iii; jjj++ ) {
haplotypeLikelihoodMatrix[chosenSample][iii][jjj] = Double.NEGATIVE_INFINITY;
}
}
}
if( DEBUG ) { System.out.println("Chose " + (bestHaplotypesIndexList.size() - 1) + " alternate haplotypes to genotype in all samples."); }
final ArrayList<Haplotype> bestHaplotypes = new ArrayList<Haplotype>();
for( final int hIndex : bestHaplotypesIndexList ) {
bestHaplotypes.add( haplotypes.get(hIndex) );
}
return bestHaplotypes;
}
*/
@Requires({"haplotypes.size() > 0"})
@Ensures({"result.size() <= haplotypes.size()"})
public ArrayList<Haplotype> selectBestHaplotypes( final ArrayList<Haplotype> haplotypes, final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap, final int maxNumHaplotypesInPopulation ) {
public List<Haplotype> selectBestHaplotypes( final List<Haplotype> haplotypes, final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap, final int maxNumHaplotypesInPopulation ) {
final int numHaplotypes = haplotypes.size();
final Set<String> sampleKeySet = stratifiedReadMap.keySet();
final ArrayList<Integer> bestHaplotypesIndexList = new ArrayList<Integer>();
final List<Integer> bestHaplotypesIndexList = new ArrayList<Integer>();
bestHaplotypesIndexList.add( findReferenceIndex(haplotypes) ); // always start with the reference haplotype
final List<Allele> haplotypesAsAlleles = new ArrayList<Allele>();
for( final Haplotype h : haplotypes ) { haplotypesAsAlleles.add(Allele.create(h.getBases())); }
@ -330,7 +273,7 @@ public class LikelihoodCalculationEngine {
if( DEBUG ) { System.out.println("Chose " + (bestHaplotypesIndexList.size() - 1) + " alternate haplotypes to genotype in all samples."); }
final ArrayList<Haplotype> bestHaplotypes = new ArrayList<Haplotype>();
final List<Haplotype> bestHaplotypes = new ArrayList<Haplotype>();
for( final int hIndex : bestHaplotypesIndexList ) {
bestHaplotypes.add( haplotypes.get(hIndex) );
}

4
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java
View File

@ -51,7 +51,7 @@ import org.broadinstitute.sting.utils.Haplotype;
import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.ArrayList;
import java.util.List;
/**
* Created by IntelliJ IDEA.
@ -67,5 +67,5 @@ public abstract class LocalAssemblyEngine {
protected LocalAssemblyEngine() {
}
public abstract ArrayList<Haplotype> runLocalAssembly(ActiveRegion activeRegion, Haplotype refHaplotype, byte[] fullReferenceWithPadding, GenomeLoc refLoc, int PRUNE_FACTOR, ArrayList<VariantContext> activeAllelesToGenotype);
public abstract List<Haplotype> runLocalAssembly(ActiveRegion activeRegion, Haplotype refHaplotype, byte[] fullReferenceWithPadding, GenomeLoc refLoc, int PRUNE_FACTOR, List<VariantContext> activeAllelesToGenotype);
}

32
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssembler.java
View File

@ -84,7 +84,7 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
private final boolean DEBUG;
private final PrintStream GRAPH_WRITER;
private final ArrayList<DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge>> graphs = new ArrayList<DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge>>();
private final List<DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge>> graphs = new ArrayList<DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge>>();
private final int MIN_KMER;
private int PRUNE_FACTOR = 2;
@ -96,7 +96,7 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
MIN_KMER = minKmer;
}
public ArrayList<Haplotype> runLocalAssembly( final ActiveRegion activeRegion, final Haplotype refHaplotype, final byte[] fullReferenceWithPadding, final GenomeLoc refLoc, final int PRUNE_FACTOR, final ArrayList<VariantContext> activeAllelesToGenotype ) {
public List<Haplotype> runLocalAssembly( final ActiveRegion activeRegion, final Haplotype refHaplotype, final byte[] fullReferenceWithPadding, final GenomeLoc refLoc, final int PRUNE_FACTOR, final List<VariantContext> activeAllelesToGenotype ) {
this.PRUNE_FACTOR = PRUNE_FACTOR;
// create the graphs
@ -152,10 +152,10 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
final DeBruijnVertex addedVertex = new DeBruijnVertex( ArrayUtils.addAll(incomingVertex.getSequence(), outgoingVertex.getSuffix()), outgoingVertex.kmer );
graph.addVertex(addedVertex);
for( final DeBruijnEdge edge : outEdges ) {
graph.addEdge(addedVertex, graph.getEdgeTarget(edge), new DeBruijnEdge(edge.getIsRef(), edge.getMultiplicity()));
graph.addEdge(addedVertex, graph.getEdgeTarget(edge), new DeBruijnEdge(edge.isRef(), edge.getMultiplicity()));
}
for( final DeBruijnEdge edge : inEdges ) {
graph.addEdge(graph.getEdgeSource(edge), addedVertex, new DeBruijnEdge(edge.getIsRef(), edge.getMultiplicity()));
graph.addEdge(graph.getEdgeSource(edge), addedVertex, new DeBruijnEdge(edge.isRef(), edge.getMultiplicity()));
}
graph.removeVertex( incomingVertex );
@ -168,16 +168,16 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
}
protected static void pruneGraph( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph, final int pruneFactor ) {
final ArrayList<DeBruijnEdge> edgesToRemove = new ArrayList<DeBruijnEdge>();
final List<DeBruijnEdge> edgesToRemove = new ArrayList<DeBruijnEdge>();
for( final DeBruijnEdge e : graph.edgeSet() ) {
if( e.getMultiplicity() <= pruneFactor && !e.getIsRef() ) { // remove non-reference edges with weight less than or equal to the pruning factor
if( e.getMultiplicity() <= pruneFactor && !e.isRef() ) { // remove non-reference edges with weight less than or equal to the pruning factor
edgesToRemove.add(e);
}
}
graph.removeAllEdges(edgesToRemove);
// Run through the graph and clean up singular orphaned nodes
final ArrayList<DeBruijnVertex> verticesToRemove = new ArrayList<DeBruijnVertex>();
final List<DeBruijnVertex> verticesToRemove = new ArrayList<DeBruijnVertex>();
for( final DeBruijnVertex v : graph.vertexSet() ) {
if( graph.inDegreeOf(v) == 0 && graph.outDegreeOf(v) == 0 ) {
verticesToRemove.add(v);
@ -187,7 +187,7 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
}
protected static void eliminateNonRefPaths( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph ) {
final ArrayList<DeBruijnVertex> verticesToRemove = new ArrayList<DeBruijnVertex>();
final List<DeBruijnVertex> verticesToRemove = new ArrayList<DeBruijnVertex>();
boolean done = false;
while( !done ) {
done = true;
@ -195,7 +195,7 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
if( graph.inDegreeOf(v) == 0 || graph.outDegreeOf(v) == 0 ) {
boolean isRefNode = false;
for( final DeBruijnEdge e : graph.edgesOf(v) ) {
if( e.getIsRef() ) {
if( e.isRef() ) {
isRefNode = true;
break;
}
@ -299,10 +299,10 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
if( edge.getMultiplicity() > PRUNE_FACTOR ) {
GRAPH_WRITER.println("\t" + graph.getEdgeSource(edge).toString() + " -> " + graph.getEdgeTarget(edge).toString() + " [" + (edge.getMultiplicity() <= PRUNE_FACTOR ? "style=dotted,color=grey" : "label=\""+ edge.getMultiplicity() +"\"") + "];");
}
if( edge.getIsRef() ) {
if( edge.isRef() ) {
GRAPH_WRITER.println("\t" + graph.getEdgeSource(edge).toString() + " -> " + graph.getEdgeTarget(edge).toString() + " [color=red];");
}
if( !edge.getIsRef() && edge.getMultiplicity() <= PRUNE_FACTOR ) { System.out.println("Graph pruning warning!"); }
if( !edge.isRef() && edge.getMultiplicity() <= PRUNE_FACTOR ) { System.out.println("Graph pruning warning!"); }
}
for( final DeBruijnVertex v : graph.vertexSet() ) {
final String label = ( graph.inDegreeOf(v) == 0 ? v.toString() : v.getSuffixString() );
@ -313,8 +313,8 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
}
@Ensures({"result.contains(refHaplotype)"})
private ArrayList<Haplotype> findBestPaths( final Haplotype refHaplotype, final byte[] fullReferenceWithPadding, final GenomeLoc refLoc, final ArrayList<VariantContext> activeAllelesToGenotype, final GenomeLoc activeRegionWindow ) {
final ArrayList<Haplotype> returnHaplotypes = new ArrayList<Haplotype>();
private List<Haplotype> findBestPaths( final Haplotype refHaplotype, final byte[] fullReferenceWithPadding, final GenomeLoc refLoc, final List<VariantContext> activeAllelesToGenotype, final GenomeLoc activeRegionWindow ) {
final List<Haplotype> returnHaplotypes = new ArrayList<Haplotype>();
// add the reference haplotype separately from all the others
final SWPairwiseAlignment swConsensus = new SWPairwiseAlignment( fullReferenceWithPadding, refHaplotype.getBases(), SW_MATCH, SW_MISMATCH, SW_GAP, SW_GAP_EXTEND );
@ -338,12 +338,12 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
for( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph : graphs ) {
for ( final KBestPaths.Path path : KBestPaths.getKBestPaths(graph, NUM_BEST_PATHS_PER_KMER_GRAPH) ) {
final Haplotype h = new Haplotype( path.getBases( graph ), path.getScore() );
final Haplotype h = new Haplotype( path.getBases() );
if( addHaplotype( h, fullReferenceWithPadding, returnHaplotypes, activeRegionStart, activeRegionStop, false ) ) {
// for GGA mode, add the desired allele into the haplotype if it isn't already present
if( !activeAllelesToGenotype.isEmpty() ) {
final HashMap<Integer,VariantContext> eventMap = GenotypingEngine.generateVCsFromAlignment( h, h.getAlignmentStartHapwrtRef(), h.getCigar(), fullReferenceWithPadding, h.getBases(), refLoc, "HCassembly" ); // BUGBUG: need to put this function in a shared place
final Map<Integer,VariantContext> eventMap = GenotypingEngine.generateVCsFromAlignment( h, h.getAlignmentStartHapwrtRef(), h.getCigar(), fullReferenceWithPadding, h.getBases(), refLoc, "HCassembly" ); // BUGBUG: need to put this function in a shared place
for( final VariantContext compVC : activeAllelesToGenotype ) { // for GGA mode, add the desired allele into the haplotype if it isn't already present
final VariantContext vcOnHaplotype = eventMap.get(compVC.getStart());
@ -378,7 +378,7 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
return returnHaplotypes;
}
private boolean addHaplotype( final Haplotype haplotype, final byte[] ref, final ArrayList<Haplotype> haplotypeList, final int activeRegionStart, final int activeRegionStop, final boolean FORCE_INCLUSION_FOR_GGA_MODE ) {
private boolean addHaplotype( final Haplotype haplotype, final byte[] ref, final List<Haplotype> haplotypeList, final int activeRegionStart, final int activeRegionStop, final boolean FORCE_INCLUSION_FOR_GGA_MODE ) {
if( haplotype == null ) { return false; }
final SWPairwiseAlignment swConsensus = new SWPairwiseAlignment( ref, haplotype.getBases(), SW_MATCH, SW_MISMATCH, SW_GAP, SW_GAP_EXTEND );

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
View File

@ -75,7 +75,7 @@ import org.broadinstitute.sting.utils.sam.NWaySAMFileWriter;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.text.TextFormattingUtils;
import org.broadinstitute.sting.utils.text.XReadLines;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.io.File;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java
View File

@ -46,7 +46,7 @@
package org.broadinstitute.sting.gatk.walkers.phasing;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import java.util.Arrays;
import java.util.LinkedList;

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
View File

@ -59,6 +59,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.*;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
@ -444,7 +445,7 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
ArrayList<String> rodNames = new ArrayList<String>();
rodNames.add(variantCollection.variants.getName());
Map<String, VCFHeader> vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames);
Set<String> vcfSamples = SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
Set<String> vcfSamples = SampleUtils.getSampleList(vcfRods, GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
//Get the trios from the families passed as ped
setTrios();

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java
View File

@ -46,7 +46,7 @@
package org.broadinstitute.sting.gatk.walkers.phasing;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;

4
protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
View File

@ -59,7 +59,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.HasGenomeLocation;
import org.broadinstitute.sting.utils.SampleUtils;
@ -323,7 +323,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
VariantContext subvc = vc.subContextFromSamples(samplesToPhase);
// logger.debug("original VC = " + vc);
// logger.debug("sub VC = " + subvc);
return VariantContextUtils.pruneVariantContext(subvc, KEYS_TO_KEEP_IN_REDUCED_VCF);
return GATKVariantContextUtils.pruneVariantContext(subvc, KEYS_TO_KEEP_IN_REDUCED_VCF);
}
private List<VariantContext> processQueue(PhasingStats phaseStats, boolean processAll) {

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
View File

@ -46,7 +46,7 @@
package org.broadinstitute.sting.gatk.walkers.phasing;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype;

6
protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java
View File

@ -58,12 +58,12 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.variant.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
import org.broadinstitute.variant.variantcontext.VariantContextUtils;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.variant.vcf.VCFUtils;
@ -327,8 +327,8 @@ public class GenotypeAndValidate extends RodWalker<GenotypeAndValidate.CountedDa
// Initialize VCF header
if (vcfWriter != null) {
Map<String, VCFHeader> header = GATKVCFUtils.getVCFHeadersFromRodPrefix(getToolkit(), alleles.getName());
samples = SampleUtils.getSampleList(header, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(header.values(), logger);
samples = SampleUtils.getSampleList(header, GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(header.values(), true);
headerLines.add(new VCFHeaderLine("source", "GenotypeAndValidate"));
vcfWriter.writeHeader(new VCFHeader(headerLines, samples));
}

4
protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java
View File

@ -54,12 +54,12 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.variant.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextUtils;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import java.io.File;
@ -227,7 +227,7 @@ public class ValidationSiteSelector extends RodWalker<Integer, Integer> {
public void initialize() {
// Get list of samples to include in the output
Map<String, VCFHeader> vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit());
TreeSet<String> vcfSamples = new TreeSet<String>(SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE));
TreeSet<String> vcfSamples = new TreeSet<String>(SampleUtils.getSampleList(vcfRods, GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE));
Collection<String> samplesFromFile = SampleUtils.getSamplesFromFiles(sampleFiles);
Collection<String> samplesFromExpressions = SampleUtils.matchSamplesExpressions(vcfSamples, sampleExpressions);

130
protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
View File

@ -1,130 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.varianteval.evaluators;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.VariantContext;
/**
* The Broad Institute
* SOFTWARE COPYRIGHT NOTICE AGREEMENT
* This software and its documentation are copyright 2009 by the
* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
* <p/>
* This software is supplied without any warranty or guaranteed support whatsoever. Neither
* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
*/
@Analysis(description = "The overlap between eval and comp sites")
public class CompOverlap extends VariantEvaluator implements StandardEval {
@DataPoint(description = "number of eval variant sites", format = "%d")
public long nEvalVariants = 0;
@DataPoint(description = "number of eval sites outside of comp sites", format = "%d")
public long novelSites = 0;
@DataPoint(description = "number of eval sites at comp sites", format = "%d")
public long nVariantsAtComp = 0;
@DataPoint(description = "percentage of eval sites at comp sites", format = "%.2f" )
public double compRate = 0.0;
@DataPoint(description = "number of concordant sites", format = "%d")
public long nConcordant = 0;
@DataPoint(description = "the concordance rate", format = "%.2f")
public double concordantRate = 0.0;
public int getComparisonOrder() {
return 2; // we need to see each eval track and each comp track
}
public long nNovelSites() { return nEvalVariants - nVariantsAtComp; }
public double compRate() { return rate(nVariantsAtComp, nEvalVariants); }
public double concordanceRate() { return rate(nConcordant, nVariantsAtComp); }
public void finalizeEvaluation() {
compRate = 100 * compRate();
concordantRate = 100 * concordanceRate();
novelSites = nNovelSites();
}
/**
* Returns true if every allele in eval is also in comp
*
* @param eval eval context
* @param comp db context
* @return true if eval and db are discordant
*/
public boolean discordantP(VariantContext eval, VariantContext comp) {
for (Allele a : eval.getAlleles()) {
if (!comp.hasAllele(a, true))
return true;
}
return false;
}
public void update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
boolean evalIsGood = eval != null && eval.isPolymorphicInSamples();
boolean compIsGood = comp != null && comp.isNotFiltered();
if (evalIsGood) nEvalVariants++; // count the number of eval events
if (compIsGood && evalIsGood) {
nVariantsAtComp++;
if (!discordantP(eval, comp)) { // count whether we're concordant or not with the comp value
nConcordant++;
}
}
}
}

238
protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
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@ -1,238 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.varianteval.evaluators;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.VariantContext;
@Analysis(description = "Counts different classes of variants in the sample")
public class CountVariants extends VariantEvaluator implements StandardEval {
// the following fields are in output order:
// basic counts on various rates found
@DataPoint(description = "Number of processed loci", format = "%d")
public long nProcessedLoci = 0;
@DataPoint(description = "Number of called loci", format = "%d")
public long nCalledLoci = 0;
@DataPoint(description = "Number of reference loci", format = "%d")
public long nRefLoci = 0;
@DataPoint(description = "Number of variant loci", format = "%d")
public long nVariantLoci = 0;
// the following two calculations get set in the finalizeEvaluation
@DataPoint(description = "Variants per loci rate", format = "%.8f")
public double variantRate = 0;
@DataPoint(description = "Number of variants per base", format = "%.8f")
public double variantRatePerBp = 0;
@DataPoint(description = "Number of snp loci", format = "%d")
public long nSNPs = 0;
@DataPoint(description = "Number of mnp loci", format = "%d")
public long nMNPs = 0;
@DataPoint(description = "Number of insertions", format = "%d")
public long nInsertions = 0;
@DataPoint(description = "Number of deletions", format = "%d")
public long nDeletions = 0;
@DataPoint(description = "Number of complex indels", format = "%d")
public long nComplex = 0;
@DataPoint(description = "Number of symbolic events", format = "%d")
public long nSymbolic = 0;
@DataPoint(description = "Number of mixed loci (loci that can't be classified as a SNP, Indel or MNP)", format = "%d")
public long nMixed = 0;
@DataPoint(description = "Number of no calls loci", format = "%d")
public long nNoCalls = 0;
@DataPoint(description = "Number of het loci", format = "%d")
public long nHets = 0;
@DataPoint(description = "Number of hom ref loci", format = "%d")
public long nHomRef = 0;
@DataPoint(description = "Number of hom var loci", format = "%d")
public long nHomVar = 0;
@DataPoint(description = "Number of singletons", format = "%d")
public long nSingletons = 0;
@DataPoint(description = "Number of derived homozygotes", format = "%d")
public long nHomDerived = 0;
// calculations that get set in the finalizeEvaluation method
@DataPoint(description = "heterozygosity per locus rate", format = "%.2e")
public double heterozygosity = 0;
@DataPoint(description = "heterozygosity per base pair", format = "%.2f")
public double heterozygosityPerBp = 0;
@DataPoint(description = "heterozygosity to homozygosity ratio", format = "%.2f")
public double hetHomRatio = 0;
@DataPoint(description = "indel rate (insertion count + deletion count)", format = "%.2e")
public double indelRate = 0;
@DataPoint(description = "indel rate per base pair", format = "%.2f")
public double indelRatePerBp = 0;
@DataPoint(description = "insertion to deletion ratio", format = "%.2f")
public double insertionDeletionRatio = 0;
private double perLocusRate(long n) {
return rate(n, nProcessedLoci);
}
private long perLocusRInverseRate(long n) {
return inverseRate(n, nProcessedLoci);
}
public int getComparisonOrder() {
return 1; // we only need to see each eval track
}
public void update1(VariantContext vc1, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
nCalledLoci++;
// Note from Eric:
// This is really not correct. What we really want here is a polymorphic vs. monomorphic count (i.e. on the Genotypes).
// So in order to maintain consistency with the previous implementation (and the intention of the original author), I've
// added in a proxy check for monomorphic status here.
// Protect against case when vc only as no-calls too - can happen if we strafity by sample and sample as a single no-call.
if ( getWalker().ignoreAC0Sites() && vc1.isMonomorphicInSamples() ) {
nRefLoci++;
} else {
switch (vc1.getType()) {
case NO_VARIATION:
// shouldn't get here
break;
case SNP:
nVariantLoci++;
nSNPs++;
if (variantWasSingleton(vc1)) nSingletons++;
break;
case MNP:
nVariantLoci++;
nMNPs++;
if (variantWasSingleton(vc1)) nSingletons++;
break;
case INDEL:
nVariantLoci++;
if (vc1.isSimpleInsertion())
nInsertions++;
else if (vc1.isSimpleDeletion())
nDeletions++;
else
nComplex++;
break;
case MIXED:
nVariantLoci++;
nMixed++;
break;
case SYMBOLIC:
nSymbolic++;
break;
default:
throw new ReviewedStingException("Unexpected VariantContext type " + vc1.getType());
}
}
// these operations are ordered to ensure that we don't get the base string of the ref unless we need it
final String aaStr = vc1.hasAttribute("ANCESTRALALLELE") ? vc1.getAttributeAsString("ANCESTRALALLELE", null).toUpperCase() : null;
final String refStr = aaStr != null ? vc1.getReference().getBaseString().toUpperCase() : null;
// ref aa alt class
// A C A der homozygote
// A C C anc homozygote
// A A A ref homozygote
// A A C
// A C A
// A C C
for (final Genotype g : vc1.getGenotypes()) {
final String altStr = vc1.getAlternateAlleles().size() > 0 ? vc1.getAlternateAllele(0).getBaseString().toUpperCase() : null;
switch (g.getType()) {
case NO_CALL:
nNoCalls++;
break;
case HOM_REF:
nHomRef++;
if ( aaStr != null && altStr != null && !refStr.equalsIgnoreCase(aaStr) ) {
nHomDerived++;
}
break;
case HET:
nHets++;
break;
case HOM_VAR:
nHomVar++;
if ( aaStr != null && altStr != null && !altStr.equalsIgnoreCase(aaStr) ) {
nHomDerived++;
}
break;
case MIXED:
break;
default:
throw new ReviewedStingException("BUG: Unexpected genotype type: " + g);
}
}
}
public void finalizeEvaluation() {
nProcessedLoci = getWalker().getnProcessedLoci();
variantRate = perLocusRate(nVariantLoci);
variantRatePerBp = perLocusRInverseRate(nVariantLoci);
heterozygosity = perLocusRate(nHets);
heterozygosityPerBp = perLocusRInverseRate(nHets);
hetHomRatio = ratio(nHets, nHomVar);
indelRate = perLocusRate(nDeletions + nInsertions + nComplex);
indelRatePerBp = perLocusRInverseRate(nDeletions + nInsertions + nComplex);
insertionDeletionRatio = ratio(nInsertions, nDeletions);
}
}

273
protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
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@ -1,273 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.varianteval.evaluators;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Molten;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypeType;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.*;
/*
* Copyright (c) 2010 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.
*/
/**
* a table of sample names to genotype concordance figures
*/
@Analysis(name = "Genotype Concordance Detailed", description = "Determine the genotype concordance between the genotypes in difference tracks, and concordance statistics")
public class GenotypeConcordance extends VariantEvaluator {
protected final static Logger logger = Logger.getLogger(GenotypeConcordance.class);
@Molten(variableFormat = "%s", valueFormat = "%s")
public final Map<Object, Object> map = new TreeMap<Object, Object>();
// concordance counts
private final long[][] truthByCalledGenotypeCounts;
/**
* Initialize this object
*/
public GenotypeConcordance() {
final int nGenotypeTypes = GenotypeType.values().length;
truthByCalledGenotypeCounts = new long[nGenotypeTypes][nGenotypeTypes];
}
@Override
public int getComparisonOrder() {
return 2;
}
@Override
public void update2(VariantContext eval, VariantContext validation, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
// sanity check that we at least have either eval or validation data
if ( (validation != null && !validation.hasGenotypes()) || eval == null && !isValidVC(validation)) {
return;
} else {
final boolean validationIsValidVC = isValidVC(validation);
// determine concordance for eval data
if (eval != null) {
for (final Genotype g : eval.getGenotypes() ) {
final String sample = g.getSampleName();
final GenotypeType called = g.getType();
final GenotypeType truth;
if (!validationIsValidVC || !validation.hasGenotype(sample)) {
truth = GenotypeType.NO_CALL;
} else {
truth = validation.getGenotype(sample).getType();
}
incrValue(truth, called);
}
}
// otherwise, mark no-calls for all samples
else {
final GenotypeType called = GenotypeType.NO_CALL;
for (final Genotype g : validation.getGenotypes()) {
final GenotypeType truth = g.getType();
incrValue(truth, called);
// print out interesting sites
/*
if ( PRINT_INTERESTING_SITES && super.getVEWalker().gcLog != null ) {
if ( (truth == GenotypeType.HOM_VAR || truth == GenotypeType.HET) && called == GenotypeType.NO_CALL ) {
super.getVEWalker().gcLog.printf("%s FN %s%n", group, validation);
}
if ( (called == GenotypeType.HOM_VAR || called == GenotypeType.HET) && truth == GenotypeType.HOM_REF ) {
super.getVEWalker().gcLog.printf("%s FP %s%n", group, validation);
}
}
*/
}
}
}
}
private static boolean isValidVC(final VariantContext vc) {
return (vc != null && !vc.isFiltered());
}
/**
* increment the specified value
* @param truth the truth type
* @param called the called type
*/
private void incrValue(final GenotypeType truth, final GenotypeType called) {
truthByCalledGenotypeCounts[truth.ordinal()][called.ordinal()]++;
}
private long count(final GenotypeType truth, final GenotypeType called) {
return truthByCalledGenotypeCounts[truth.ordinal()][called.ordinal()];
}
private long count(final EnumSet<GenotypeType> truth, final GenotypeType called) {
return count(truth, EnumSet.of(called));
}
private long count(final GenotypeType truth, final EnumSet<GenotypeType> called) {
return count(EnumSet.of(truth), called);
}
private long count(final EnumSet<GenotypeType> truth, final EnumSet<GenotypeType> called) {
long sum = 0;
for ( final GenotypeType truth1 : truth ) {
for ( final GenotypeType called1 : called ) {
sum += count(truth1, called1);
}
}
return sum;
}
private long countDiag( final EnumSet<GenotypeType> d1 ) {
long sum = 0;
for(final GenotypeType e1 : d1 ) {
sum += truthByCalledGenotypeCounts[e1.ordinal()][e1.ordinal()];
}
return sum;
}
@Override
public void finalizeEvaluation() {
final EnumSet<GenotypeType> allVariantGenotypes = EnumSet.of(GenotypeType.HOM_VAR, GenotypeType.HET);
final EnumSet<GenotypeType> allCalledGenotypes = EnumSet.of(GenotypeType.HOM_VAR, GenotypeType.HET, GenotypeType.HOM_REF);
final EnumSet<GenotypeType> allGenotypes = EnumSet.allOf(GenotypeType.class);
// exact values of the table
for ( final GenotypeType truth : GenotypeType.values() ) {
for ( final GenotypeType called : GenotypeType.values() ) {
final String field = String.format("n_true_%s_called_%s", truth, called);
final Long value = count(truth, called);
map.put(field, value.toString());
}
}
// counts of called genotypes
for ( final GenotypeType called : GenotypeType.values() ) {
final String field = String.format("total_called_%s", called);
final Long value = count(allGenotypes, called);
map.put(field, value.toString());
}
// counts of true genotypes
for ( final GenotypeType truth : GenotypeType.values() ) {
final String field = String.format("total_true_%s", truth);
final Long value = count(truth, allGenotypes);
map.put(field, value.toString());
}
for ( final GenotypeType genotype : GenotypeType.values() ) {
final String field = String.format("percent_%s_called_%s", genotype, genotype);
long numer = count(genotype, genotype);
long denom = count(EnumSet.of(genotype), allGenotypes);
map.put(field, Utils.formattedPercent(numer, denom));
}
{
// % non-ref called as non-ref
// MAD: this is known as the non-reference sensitivity (# non-ref according to comp found in eval / # non-ref in comp)
final String field = "percent_non_reference_sensitivity";
long numer = count(allVariantGenotypes, allVariantGenotypes);
long denom = count(allVariantGenotypes, allGenotypes);
map.put(field, Utils.formattedPercent(numer, denom));
}
{
// overall genotype concordance of sites called in eval track
// MAD: this is the tradition genotype concordance
final String field = "percent_overall_genotype_concordance";
long numer = countDiag(allCalledGenotypes);
long denom = count(allCalledGenotypes, allCalledGenotypes);
map.put(field, Utils.formattedPercent(numer, denom));
}
{
// overall genotype concordance of sites called non-ref in eval track
// MAD: this is the non-reference discrepancy rate
final String field = "percent_non_reference_discrepancy_rate";
long homrefConcords = count(GenotypeType.HOM_REF, GenotypeType.HOM_REF);
long allNoHomRef = count(allCalledGenotypes, allCalledGenotypes) - homrefConcords;
long numer = allNoHomRef - countDiag(allVariantGenotypes);
long denom = count(allCalledGenotypes, allCalledGenotypes) - homrefConcords;
map.put(field, Utils.formattedPercent(numer, denom));
}
}
}

144
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@ -1,144 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.varianteval.evaluators;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Molten;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.*;
/**
* Simple utility for histogramming indel lengths
*
* Based on code from chartl
*
* @author Mark DePristo
* @since 3/21/12
*/
@Analysis(description = "Indel length histogram", molten = true)
public class IndelLengthHistogram extends VariantEvaluator implements StandardEval {
private final Map<Integer, Integer> counts = new HashMap<Integer, Integer>();
private final static boolean asFrequencies = true;
int nIndels = 0;
@Molten(variableName = "Length", valueName = "Freq", variableFormat = "%d", valueFormat = "%.2f")
public TreeMap<Object, Object> results;
public final static int MAX_SIZE_FOR_HISTOGRAM = 10;
private final static boolean INCLUDE_LONG_EVENTS_AT_MAX_SIZE = false;
public IndelLengthHistogram() {
initializeCounts(MAX_SIZE_FOR_HISTOGRAM);
}
private void initializeCounts(int size) {
for ( int i = -size; i <= size; i++ ) {
if ( i != 0 ) counts.put(i, 0);
}
}
@Override
public void finalizeEvaluation() {
if ( asFrequencies ) {
results = new TreeMap<Object, Object>();
for ( final int len : counts.keySet() ) {
final double value = nIndels == 0 ? 0.0 : counts.get(len) / (1.0 * nIndels);
results.put(len, value);
}
} else {
results = new TreeMap<Object, Object>(results);
}
}
@Override
public int getComparisonOrder() {
return 1;
}
@Override
public void update1(final VariantContext eval, final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) {
if ( eval.isIndel() && ! eval.isComplexIndel() ) {
if ( ! ( getWalker().ignoreAC0Sites() && eval.isMonomorphicInSamples() )) {
// only if we are actually polymorphic in the subsetted samples should we count the allele
for ( Allele alt : eval.getAlternateAlleles() ) {
final int alleleSize = alt.length() - eval.getReference().length();
if ( alleleSize == 0 ) throw new ReviewedStingException("Allele size not expected to be zero for indel: alt = " + alt + " ref = " + eval.getReference());
updateLengthHistogram(eval.getReference(), alt);
}
}
}
}
/**
* Update the histogram with the implied length of the indel allele between ref and alt (alt.len - ref.len).
*
* If this size is outside of MAX_SIZE_FOR_HISTOGRAM, the size is capped to MAX_SIZE_FOR_HISTOGRAM,
* if INCLUDE_LONG_EVENTS_AT_MAX_SIZE is set.
*
* @param ref
* @param alt
*/
public void updateLengthHistogram(final Allele ref, final Allele alt) {
int len = alt.length() - ref.length();
if ( INCLUDE_LONG_EVENTS_AT_MAX_SIZE ) {
if ( len > MAX_SIZE_FOR_HISTOGRAM ) len = MAX_SIZE_FOR_HISTOGRAM;
if ( len < -MAX_SIZE_FOR_HISTOGRAM ) len = -MAX_SIZE_FOR_HISTOGRAM;
}
if ( Math.abs(len) > MAX_SIZE_FOR_HISTOGRAM )
return;
nIndels++;
counts.put(len, counts.get(len) + 1);
}
}

208
protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
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/*
* 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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.varianteval.evaluators;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.samples.Sample;
import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.sting.utils.MendelianViolation;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Map;
import java.util.Set;
/**
* Mendelian violation detection and counting
* <p/>
* a violation looks like:
* Suppose dad = A/B and mom = C/D
* The child can be [A or B] / [C or D].
* If the child doesn't match this, the site is a violation
* <p/>
* Some examples:
* <p/>
* mom = A/A, dad = C/C
* child can be A/C only
* <p/>
* mom = A/C, dad = C/C
* child can be A/C or C/C
* <p/>
* mom = A/C, dad = A/C
* child can be A/A, A/C, C/C
* <p/>
* The easiest way to do this calculation is to:
* <p/>
* Get alleles for mom => A/B
* Get alleles for dad => C/D
* Make allowed genotypes for child: A/C, A/D, B/C, B/D
* Check that the child is one of these.
*/
@Analysis(name = "Mendelian Violation Evaluator", description = "Mendelian Violation Evaluator")
public class MendelianViolationEvaluator extends VariantEvaluator {
@DataPoint(description = "Number of variants found with at least one family having genotypes", format = "%d")
public long nVariants;
@DataPoint(description = "Number of variants found with no family having genotypes -- these sites do not count in the nNoCall", format = "%d")
public long nSkipped;
@DataPoint(description="Number of variants x families called (no missing genotype or lowqual)", format = "%d")
public long nFamCalled;
@DataPoint(description="Number of variants x families called (no missing genotype or lowqual) that contain at least one var allele.", format = "%d")
public long nVarFamCalled;
@DataPoint(description="Number of variants x families discarded as low quality", format = "%d")
public long nLowQual;
@DataPoint(description="Number of variants x families discarded as no call", format = "%d")
public long nNoCall;
@DataPoint(description="Number of loci with mendelian violations", format = "%d")
public long nLociViolations;
@DataPoint(description = "Number of mendelian violations found", format = "%d")
public long nViolations;
@DataPoint(description="Number of mendelian violations of the type HOM_REF/HOM_REF -> HOM_VAR", format = "%d")
public long mvRefRef_Var;
@DataPoint(description="Number of mendelian violations of the type HOM_REF/HOM_REF -> HET", format = "%d")
public long mvRefRef_Het;
@DataPoint(description="Number of mendelian violations of the type HOM_REF/HET -> HOM_VAR", format = "%d")
public long mvRefHet_Var;
@DataPoint(description="Number of mendelian violations of the type HOM_REF/HOM_VAR -> HOM_VAR", format = "%d")
public long mvRefVar_Var;
@DataPoint(description="Number of mendelian violations of the type HOM_REF/HOM_VAR -> HOM_REF", format = "%d")
public long mvRefVar_Ref;
@DataPoint(description="Number of mendelian violations of the type HOM_VAR/HET -> HOM_REF", format = "%d")
public long mvVarHet_Ref;
@DataPoint(description="Number of mendelian violations of the type HOM_VAR/HOM_VAR -> HOM_REF", format = "%d")
public long mvVarVar_Ref;
@DataPoint(description="Number of mendelian violations of the type HOM_VAR/HOM_VAR -> HET", format = "%d")
public long mvVarVar_Het;
@DataPoint(description="Number of HomRef/HomRef/HomRef trios", format = "%d")
public long HomRefHomRef_HomRef;
@DataPoint(description="Number of Het/Het/Het trios", format = "%d")
public long HetHet_Het;
@DataPoint(description="Number of Het/Het/HomRef trios", format = "%d")
public long HetHet_HomRef;
@DataPoint(description="Number of Het/Het/HomVar trios", format = "%d")
public long HetHet_HomVar;
@DataPoint(description="Number of HomVar/HomVar/HomVar trios", format = "%d")
public long HomVarHomVar_HomVar;
@DataPoint(description="Number of HomRef/HomVar/Het trios", format = "%d")
public long HomRefHomVAR_Het;
@DataPoint(description="Number of ref alleles inherited from het/het parents", format = "%d")
public long HetHet_inheritedRef;
@DataPoint(description="Number of var alleles inherited from het/het parents", format = "%d")
public long HetHet_inheritedVar;
@DataPoint(description="Number of ref alleles inherited from homRef/het parents", format = "%d")
public long HomRefHet_inheritedRef;
@DataPoint(description="Number of var alleles inherited from homRef/het parents", format = "%d")
public long HomRefHet_inheritedVar;
@DataPoint(description="Number of ref alleles inherited from homVar/het parents", format = "%d")
public long HomVarHet_inheritedRef;
@DataPoint(description="Number of var alleles inherited from homVar/het parents", format = "%d")
public long HomVarHet_inheritedVar;
MendelianViolation mv;
Map<String,Set<Sample>> families;
public void initialize(VariantEval walker) {
super.initialize(walker);
mv = new MendelianViolation(walker.getMendelianViolationQualThreshold(),false);
families = walker.getSampleDB().getFamilies();
}
public String getName() {
return "mendelian_violations";
}
public int getComparisonOrder() {
return 1; // we only need to see each eval track
}
public void update1(VariantContext vc, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if (vc.isBiallelic() && vc.hasGenotypes()) { // todo -- currently limited to biallelic loci
if(mv.countViolations(families,vc)>0){
nLociViolations++;
nViolations += mv.getViolationsCount();
mvRefRef_Var += mv.getParentsRefRefChildVar();
mvRefRef_Het += mv.getParentsRefRefChildHet();
mvRefHet_Var += mv.getParentsRefHetChildVar();
mvRefVar_Var += mv.getParentsRefVarChildVar();
mvRefVar_Ref += mv.getParentsRefVarChildRef();
mvVarHet_Ref += mv.getParentsVarHetChildRef();
mvVarVar_Ref += mv.getParentsVarVarChildRef();
mvVarVar_Het += mv.getParentsVarVarChildHet();
}
HomRefHomRef_HomRef += mv.getRefRefRef();
HetHet_Het += mv.getHetHetHet();
HetHet_HomRef += mv.getHetHetHomRef();
HetHet_HomVar += mv.getHetHetHomVar();
HomVarHomVar_HomVar += mv.getVarVarVar();
HomRefHomVAR_Het += mv.getRefVarHet();
HetHet_inheritedRef += mv.getParentsHetHetInheritedRef();
HetHet_inheritedVar += mv.getParentsHetHetInheritedVar();
HomRefHet_inheritedRef += mv.getParentsRefHetInheritedRef();
HomRefHet_inheritedVar += mv.getParentsRefHetInheritedVar();
HomVarHet_inheritedRef += mv.getParentsVarHetInheritedRef();
HomVarHet_inheritedVar += mv.getParentsVarHetInheritedVar();
if(mv.getFamilyCalledCount()>0){
nVariants++;
nFamCalled += mv.getFamilyCalledCount();
nLowQual += mv.getFamilyLowQualsCount();
nNoCall += mv.getFamilyNoCallCount();
nVarFamCalled += mv.getVarFamilyCalledCount();
}
else{
nSkipped++;
}
}
}
}

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/*
* 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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.varianteval.evaluators;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextUtils;
@Analysis(description = "Evaluation summary for multi-allelic variants")
public class MultiallelicSummary extends VariantEvaluator implements StandardEval {
final protected static Logger logger = Logger.getLogger(MultiallelicSummary.class);
public enum Type {
SNP, INDEL
}
// basic counts on various rates found
@DataPoint(description = "Number of processed loci", format = "%d")
public long nProcessedLoci = 0;
@DataPoint(description = "Number of SNPs", format = "%d")
public int nSNPs = 0;
@DataPoint(description = "Number of multi-allelic SNPs", format = "%d")
public int nMultiSNPs = 0;
@DataPoint(description = "% processed sites that are multi-allelic SNPs", format = "%.5f")
public double processedMultiSnpRatio = 0;
@DataPoint(description = "% SNP sites that are multi-allelic", format = "%.3f")
public double variantMultiSnpRatio = 0;
@DataPoint(description = "Number of Indels", format = "%d")
public int nIndels = 0;
@DataPoint(description = "Number of multi-allelic Indels", format = "%d")
public int nMultiIndels = 0;
@DataPoint(description = "% processed sites that are multi-allelic Indels", format = "%.5f")
public double processedMultiIndelRatio = 0;
@DataPoint(description = "% Indel sites that are multi-allelic", format = "%.3f")
public double variantMultiIndelRatio = 0;
@DataPoint(description = "Number of Transitions", format = "%d")
public int nTi = 0;
@DataPoint(description = "Number of Transversions", format = "%d")
public int nTv = 0;
@DataPoint(description = "Overall TiTv ratio", format = "%.2f")
public double TiTvRatio = 0;
@DataPoint(description = "Multi-allelic SNPs partially known", format = "%d")
public int knownSNPsPartial = 0;
@DataPoint(description = "Multi-allelic SNPs completely known", format = "%d")
public int knownSNPsComplete = 0;
@DataPoint(description = "Multi-allelic SNP Novelty Rate")
public String SNPNoveltyRate = "NA";
//TODO -- implement me
//@DataPoint(description = "Multi-allelic Indels partially known", format = "%d")
public int knownIndelsPartial = 0;
//@DataPoint(description = "Multi-allelic Indels completely known", format = "%d")
public int knownIndelsComplete = 0;
//@DataPoint(description = "Multi-allelic Indel Novelty Rate")
public String indelNoveltyRate = "NA";
@Override public int getComparisonOrder() { return 2; }
public void update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( eval == null || (getWalker().ignoreAC0Sites() && eval.isMonomorphicInSamples()) )
return;
// update counts
switch ( eval.getType() ) {
case SNP:
nSNPs++;
if ( !eval.isBiallelic() ) {
nMultiSNPs++;
calculatePairwiseTiTv(eval);
calculateSNPPairwiseNovelty(eval, comp);
}
break;
case INDEL:
nIndels++;
if ( !eval.isBiallelic() ) {
nMultiIndels++;
calculateIndelPairwiseNovelty(eval, comp);
}
break;
default:
//throw new UserException.BadInput("Unexpected variant context type: " + eval);
break;
}
return;
}
private void calculatePairwiseTiTv(VariantContext vc) {
for ( Allele alt : vc.getAlternateAlleles() ) {
if ( VariantContextUtils.isTransition(vc.getReference(), alt) )
nTi++;
else
nTv++;
}
}
private void calculateSNPPairwiseNovelty(VariantContext eval, VariantContext comp) {
if ( comp == null )
return;
int knownAlleles = 0;
for ( Allele alt : eval.getAlternateAlleles() ) {
if ( comp.getAlternateAlleles().contains(alt) )
knownAlleles++;
}
if ( knownAlleles == eval.getAlternateAlleles().size() )
knownSNPsComplete++;
else if ( knownAlleles > 0 )
knownSNPsPartial++;
}
private void calculateIndelPairwiseNovelty(VariantContext eval, VariantContext comp) {
// TODO -- implement me
}
public void finalizeEvaluation() {
nProcessedLoci = getWalker().getnProcessedLoci();
processedMultiSnpRatio = (double)nMultiSNPs / (double)nProcessedLoci;
variantMultiSnpRatio = (double)nMultiSNPs / (double)nSNPs;
processedMultiIndelRatio = (double)nMultiIndels / (double)nProcessedLoci;
variantMultiIndelRatio = (double)nMultiIndels / (double)nIndels;
TiTvRatio = (double)nTi / (double)nTv;
SNPNoveltyRate = Utils.formattedNoveltyRate(knownSNPsPartial + knownSNPsComplete, nMultiSNPs);
indelNoveltyRate = Utils.formattedNoveltyRate(knownIndelsPartial + knownIndelsComplete, nMultiSNPs);
}
}

49
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/*
* 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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.varianteval.evaluators;
public interface StandardEval {}

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/*
* 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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.varianteval.evaluators;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.ConcurrentMap;
@Analysis(description = "Computes different estimates of theta based on variant sites and genotypes")
public class ThetaVariantEvaluator extends VariantEvaluator {
@DataPoint(description = "Average heterozygosity at variant sites; note that missing genotypes are ignored when computing this value", format = "%.8f")
public double avgHet = 0.0;
@DataPoint(description = "Average pairwise differences at aligned sequences; averaged over both number of sequeneces and number of variant sites; note that missing genotypes are ignored when computing this value", format = "%.8f")
public double avgAvgDiffs = 0.0;
@DataPoint(description = "Sum of heterozygosity over all variant sites; divide this by total target to get estimate of per base theta", format = "%.8f")
public double totalHet = 0.0;
@DataPoint(description = "Sum of pairwise diffs over all variant sites; divide this by total target to get estimate of per base theta", format = "%.8f")
public double totalAvgDiffs = 0.0;
@DataPoint(description = "Theta for entire region estimated based on number of segregating sites; divide ths by total target to get estimate of per base theta", format = "%.8f")
public double thetaRegionNumSites = 0.0;
//helper variables
double numSites = 0;
public int getComparisonOrder() {
return 1;
}
public void update1(VariantContext vc, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if (vc == null || !vc.isSNP() || (getWalker().ignoreAC0Sites() && vc.isMonomorphicInSamples())) {
return;
}
//this maps allele to a count
ConcurrentMap<String, Integer> alleleCounts = new ConcurrentHashMap<String, Integer>();
int numHetsHere = 0;
int numGenosHere = 0;
int numIndsHere = 0;
for (final Genotype genotype : vc.getGenotypes()) {
numIndsHere++;
if (!genotype.isNoCall()) {
//increment stats for heterozygosity
if (genotype.isHet()) {
numHetsHere++;
}
numGenosHere++;
//increment stats for pairwise mismatches
for (Allele allele : genotype.getAlleles()) {
if (allele.isCalled()) {
String alleleString = allele.toString();
alleleCounts.putIfAbsent(alleleString, 0);
alleleCounts.put(alleleString, alleleCounts.get(alleleString) + 1);
}
}
}
}
if (numGenosHere > 0) {
//only if have one called genotype at least
this.numSites++;
this.totalHet += numHetsHere / (double)numGenosHere;
//compute based on num sites
float harmonicFactor = 0;
for (int i = 1; i <= numIndsHere; i++) {
harmonicFactor += 1.0 / i;
}
this.thetaRegionNumSites += 1.0 / harmonicFactor;
//now compute pairwise mismatches
float numPairwise = 0;
int numDiffs = 0;
for (String allele1 : alleleCounts.keySet()) {
int allele1Count = alleleCounts.get(allele1);
for (String allele2 : alleleCounts.keySet()) {
if (allele1.compareTo(allele2) < 0) {
continue;
}
if (allele1 .compareTo(allele2) == 0) {
numPairwise += allele1Count * (allele1Count - 1) * .5;
}
else {
int allele2Count = alleleCounts.get(allele2);
numPairwise += allele1Count * allele2Count;
numDiffs += allele1Count * allele2Count;
}
}
}
if (numPairwise > 0) {
this.totalAvgDiffs += numDiffs / numPairwise;
}
}
}
@Override
public void finalizeEvaluation() {
if (this.numSites > 0) {
this.avgHet = this.totalHet / this.numSites;
this.avgAvgDiffs = this.totalAvgDiffs / this.numSites;
}
}
}

121
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@ -1,121 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.varianteval.evaluators;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextUtils;
@Analysis(description = "Ti/Tv Variant Evaluator")
public class TiTvVariantEvaluator extends VariantEvaluator implements StandardEval {
@DataPoint(description = "number of transition loci", format = "%d")
public long nTi = 0;
@DataPoint(description = "number of transversion loci", format = "%d")
public long nTv = 0;
@DataPoint(description = "the transition to transversion ratio", format = "%.2f")
public double tiTvRatio = 0.0;
@DataPoint(description = "number of comp transition sites", format = "%d")
public long nTiInComp = 0;
@DataPoint(description = "number of comp transversion sites", format = "%d")
public long nTvInComp = 0;
@DataPoint(description = "the transition to transversion ratio for comp sites", format = "%.2f")
public double TiTvRatioStandard = 0.0;
@DataPoint(description = "number of derived transition loci", format = "%d")
public long nTiDerived = 0;
@DataPoint(description = "number of derived transversion loci", format = "%d")
public long nTvDerived = 0;
@DataPoint(description = "the derived transition to transversion ratio", format = "%.2f")
public double tiTvDerivedRatio = 0.0;
public int getComparisonOrder() {
return 2; // we only need to see each eval track
}
public void updateTiTv(VariantContext vc, boolean updateStandard) {
if (vc != null && vc.isSNP() && vc.isBiallelic() && vc.isPolymorphicInSamples()) {
if (VariantContextUtils.isTransition(vc)) {
if (updateStandard) nTiInComp++;
else nTi++;
} else {
if (updateStandard) nTvInComp++;
else nTv++;
}
if (vc.hasAttribute("ANCESTRALALLELE")) {
final String aaStr = vc.getAttributeAsString("ANCESTRALALLELE", "null").toUpperCase();
if ( ! aaStr.equals(".") ) {
switch ( BaseUtils.SNPSubstitutionType(aaStr.getBytes()[0], vc.getAlternateAllele(0).getBases()[0] ) ) {
case TRANSITION: nTiDerived++; break;
case TRANSVERSION: nTvDerived++; break;
default: break;
}
}
}
}
}
@Override
public void update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if (eval != null)
updateTiTv(eval, false);
if (comp != null)
updateTiTv(comp, true);
}
@Override
public void finalizeEvaluation() {
// the ti/tv ratio needs to be set (it's not calculated per-variant).
this.tiTvRatio = rate(nTi,nTv);
this.tiTvDerivedRatio = rate(nTiDerived,nTvDerived);
this.TiTvRatioStandard = rate(nTiInComp, nTvInComp);
}
}

204
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@ -1,204 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.varianteval.evaluators;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Collection;
import java.util.Set;
/**
* The Broad Institute
* SOFTWARE COPYRIGHT NOTICE AGREEMENT
* This software and its documentation are copyright 2009 by the
* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
* <p/>
* This software is supplied without any warranty or guaranteed support whatsoever. Neither
* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
*/
@Analysis(description = "Assess site accuracy and sensitivity of callset against follow-up validation assay")
public class ValidationReport extends VariantEvaluator implements StandardEval {
// todo -- note this isn't strictly allele away. It's really focused on sites. A/T call at a validated A/G site is currently counted as a TP
@DataPoint(description = "nComp", format = "%d") public int nComp = 0;
@DataPoint(description = "TP", format = "%d") public int TP = 0;
@DataPoint(description = "FP", format = "%d") public int FP = 0;
@DataPoint(description = "FN", format = "%d") public int FN = 0;
@DataPoint(description = "TN", format = "%d") public int TN = 0;
@DataPoint(description = "Sensitivity", format = "%.2f") public double sensitivity = 0;
@DataPoint(description = "Specificity", format = "%.2f") public double specificity = 0;
@DataPoint(description = "PPV", format = "%.2f") public double PPV = 0;
@DataPoint(description = "FDR", format = "%.2f") public double FDR = 0;
@DataPoint(description = "CompMonoEvalNoCall", format = "%d") public int CompMonoEvalNoCall = 0;
@DataPoint(description = "CompMonoEvalFiltered", format = "%d") public int CompMonoEvalFiltered = 0;
@DataPoint(description = "CompMonoEvalMono", format = "%d") public int CompMonoEvalMono = 0;
@DataPoint(description = "CompMonoEvalPoly", format = "%d") public int CompMonoEvalPoly = 0;
@DataPoint(description = "CompPolyEvalNoCall", format = "%d") public int CompPolyEvalNoCall = 0;
@DataPoint(description = "CompPolyEvalFiltered", format = "%d") public int CompPolyEvalFiltered = 0;
@DataPoint(description = "CompPolyEvalMono", format = "%d") public int CompPolyEvalMono = 0;
@DataPoint(description = "CompPolyEvalPoly", format = "%d") public int CompPolyEvalPoly = 0;
@DataPoint(description = "CompFiltered", format = "%d") public int CompFiltered = 0;
@DataPoint(description = "Eval and comp have different alleles", format = "%d") public int nDifferentAlleleSites = 0;
private static final boolean TREAT_ALL_SITES_IN_EVAL_VCF_AS_CALLED = true;
private static final boolean REQUIRE_IDENTICAL_ALLELES = false;
private enum SiteStatus { NO_CALL, FILTERED, MONO, POLY }
// Counts of ValidationSiteStatus x CallSiteStatus
final int[][] counts = new int[SiteStatus.values().length][SiteStatus.values().length];
@Override public int getComparisonOrder() { return 2; }
@Override
public void finalizeEvaluation() {
for ( SiteStatus x : SiteStatus.values() )
CompFiltered += getCounts(SiteStatus.FILTERED, x);
CompMonoEvalNoCall = getCounts(SiteStatus.MONO, SiteStatus.NO_CALL);
CompMonoEvalFiltered = getCounts(SiteStatus.MONO, SiteStatus.FILTERED);
CompMonoEvalMono = getCounts(SiteStatus.MONO, SiteStatus.MONO);
CompMonoEvalPoly = getCounts(SiteStatus.MONO, SiteStatus.POLY);
CompPolyEvalNoCall = getCounts(SiteStatus.POLY, SiteStatus.NO_CALL);
CompPolyEvalFiltered = getCounts(SiteStatus.POLY, SiteStatus.FILTERED);
CompPolyEvalMono = getCounts(SiteStatus.POLY, SiteStatus.MONO);
CompPolyEvalPoly = getCounts(SiteStatus.POLY, SiteStatus.POLY);
TP = CompPolyEvalPoly;
FN = CompPolyEvalNoCall + CompPolyEvalFiltered + CompPolyEvalMono;
FP = CompMonoEvalPoly;
TN = CompMonoEvalNoCall + CompMonoEvalFiltered + CompMonoEvalMono;
for ( SiteStatus x : SiteStatus.values() )
for ( SiteStatus y : SiteStatus.values() )
nComp += getCounts(x, y);
if ( nComp != TP + FN + FP + TN + CompFiltered )
throw new ReviewedStingException("BUG: nComp != TP + FN + FP + TN + CompFiltered!");
sensitivity = (100.0 * TP) / (TP + FN);
specificity = (TN+FP > 0) ? (100.0 * TN) / (TN + FP) : 100.0;
PPV = (100.0 * TP) / (TP + FP);
FDR = (100.0 * FP) / (FP + TP);
}
private int getCounts(SiteStatus comp, SiteStatus eval) {
return counts[comp.ordinal()][eval.ordinal()];
}
@Override
public void update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( comp != null ) { // we only need to consider sites in comp
if ( REQUIRE_IDENTICAL_ALLELES && (eval != null && haveDifferentAltAlleles(eval, comp)))
nDifferentAlleleSites++;
else {
SiteStatus evalStatus = calcSiteStatus(eval);
final Set<String> evalSamples = getWalker().getSampleNamesForEvaluation();
if ( comp.hasGenotypes() && ! evalSamples.isEmpty() && comp.hasGenotypes(evalSamples) )
// if we have genotypes in both eval and comp, subset comp down just the samples in eval
comp = comp.subContextFromSamples(evalSamples, false);
SiteStatus compStatus = calcSiteStatus(comp);
counts[compStatus.ordinal()][evalStatus.ordinal()]++;
}
}
}
//
// helper routines
//
private SiteStatus calcSiteStatus(VariantContext vc) {
if ( vc == null ) return SiteStatus.NO_CALL;
if ( vc.isFiltered() ) return SiteStatus.FILTERED;
if ( vc.isMonomorphicInSamples() ) return SiteStatus.MONO;
if ( vc.hasGenotypes() ) return SiteStatus.POLY; // must be polymorphic if isMonomorphicInSamples was false and there are genotypes
if ( vc.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) ) {
int ac = 0;
if ( vc.getNAlleles() > 2 ) {
return SiteStatus.POLY;
}
else
ac = vc.getAttributeAsInt(VCFConstants.ALLELE_COUNT_KEY, 0);
return ac > 0 ? SiteStatus.POLY : SiteStatus.MONO;
} else {
return TREAT_ALL_SITES_IN_EVAL_VCF_AS_CALLED ? SiteStatus.POLY : SiteStatus.NO_CALL; // we can't figure out what to do
}
}
private boolean haveDifferentAltAlleles(VariantContext eval, VariantContext comp) {
Collection<Allele> evalAlts = eval.getAlternateAlleles();
Collection<Allele> compAlts = comp.getAlternateAlleles();
if ( evalAlts.size() != compAlts.size() ) {
return true;
} else {
// same size => every alt from eval must be in comp
for ( Allele a : evalAlts ) {
if ( ! compAlts.contains(a) ) {
// System.out.printf("Different alleles: %s:%d eval=%s comp=%s\n\t\teval=%s\n\t\tcomp=%s%n",
// eval.getChr(), eval.getStart(), eval.getAlleles(), comp.getAlleles(), eval, comp);
return true;
}
}
return false;
}
}
}

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@ -1,154 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.varianteval.evaluators;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.variant.variantcontext.VariantContext;
public abstract class VariantEvaluator implements Comparable<VariantEvaluator> {
private VariantEval walker;
private final String simpleName;
protected VariantEvaluator() {
this.simpleName = getClass().getSimpleName();
}
public void initialize(VariantEval walker) {
this.walker = walker;
}
public VariantEval getWalker() {
return walker;
}
// Should return the number of VariantContexts expected as inputs to update. Can be 1 or 2
public abstract int getComparisonOrder();
// called at all sites, regardless of eval context itself; useful for counting processed bases
// No longer available. The processed bp is kept in VEW itself for performance reasons
// public void update0(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
public void update1(VariantContext eval, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
}
public void update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
}
public void finalizeEvaluation() {}
protected double rate(long n, long d) {
return n / (1.0 * Math.max(d, 1));
}
protected long inverseRate(long n, long d) {
return n == 0 ? 0 : d / Math.max(n, 1);
}
protected double ratio(long num, long denom) {
return ((double)num) / (Math.max(denom, 1));
}
/**
* Returns true if the variant in vc was a singleton in the original input evaluation
* set, regardless of variant context subsetting that has occurred.
* @param eval the VariantContext being assessed for this previous status as a singleton
* @return true if eval was originally a singleton site
*/
protected static boolean variantWasSingleton(final VariantContext eval) {
return eval.getAttributeAsBoolean(VariantEval.IS_SINGLETON_KEY, false);
}
public final String getSimpleName() {
return simpleName;
}
@Override
public int compareTo(final VariantEvaluator variantEvaluator) {
return getSimpleName().compareTo(variantEvaluator.getSimpleName());
}
/**
* Evaluation modules that override this function to indicate that they support
* combining the results of two independent collections of eval data into
* a single meaningful result. The purpose of this interface is to
* allow us to cut up the input data into many independent stratifications, and then
* at the end of the eval run decide which stratifications to combine. This is
* important in the case of AC, where you may have thousands of distinct AC
* values that chop up the number of variants to too small a number of variants,
* and you'd like to combine the AC values into ranges containing some percent
* of the data.
*
* For example, suppose you have an eval that
* counts variants in a variable nVariants. If you want to be able to combine
* multiple evaluations of this type, overload the combine function
* with a function that sets this.nVariants += other.nVariants.
*
* Add in the appropriate fields of the VariantEvaluator T
* (of the same type as this object) to the values of this object.
*
* The values in this and other are implicitly independent, so that
* the values can be added together.
*
* @param other a VariantEvaluator of the same type of this object
*/
public void combine(final VariantEvaluator other) {
throw new ReviewedStingException(getSimpleName() + " doesn't support combining results, sorry");
}
/**
* Must be overloaded to return true for evaluation modules that support the combine operation
*
* @return
*/
public boolean supportsCombine() {
return false;
}
}

135
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@ -1,135 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.varianteval.stratifications;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantSummary;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.*;
/**
* Stratifies the eval RODs by the allele count of the alternate allele
*
* Looks first at the MLEAC value in the INFO field, and uses that value if present.
* If not present, it then looks for the AC value in the INFO field. If both are absent,
* it computes the AC from the genotypes themselves. If no AC can be computed, 0 is used.
*/
public class AlleleCount extends VariantStratifier {
int nchrom;
@Override
public void initialize() {
// we can only work with a single eval VCF, and it must have genotypes
if ( getVariantEvalWalker().getEvals().size() != 1 && !getVariantEvalWalker().mergeEvals )
throw new UserException.BadArgumentValue("AlleleCount", "AlleleCount stratification only works with a single eval vcf");
// There are ploidy x n sample chromosomes
// TODO -- generalize to handle multiple ploidy
nchrom = getVariantEvalWalker().getNumberOfSamplesForEvaluation() * getVariantEvalWalker().getSamplePloidy();
if ( nchrom < 2 )
throw new UserException.BadArgumentValue("AlleleCount", "AlleleCount stratification requires an eval vcf with at least one sample");
// create an array containing each of the allele counts
for( int ac = 0; ac <= nchrom; ac++ ) {
states.add(ac);
}
getVariantEvalWalker().getLogger().info("AlleleCount using " + nchrom + " chromosomes");
}
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
if (eval != null) {
int AC = 0; // by default, the site is considered monomorphic
try {
if ( eval.isBiallelic() ) {
if ( eval.hasAttribute(VCFConstants.MLE_ALLELE_COUNT_KEY) ) {
// the MLEAC is allowed to be larger than the AN (e.g. in the case of all PLs being 0, the GT is ./. but the exact model may arbitrarily choose an AC>1)
AC = Math.min(eval.getAttributeAsInt(VCFConstants.MLE_ALLELE_COUNT_KEY, 0), nchrom);
} else if ( eval.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) ) {
AC = eval.getAttributeAsInt(VCFConstants.ALLELE_COUNT_KEY, 0);
}
}
} catch ( ClassCastException e ) {
// protect ourselves from bad inputs
// TODO -- fully decode VC
}
if ( AC == 0 && eval.isVariant() ) {
// fall back to the direct calculation
for (Allele allele : eval.getAlternateAlleles())
AC = Math.max(AC, eval.getCalledChrCount(allele));
}
// make sure that the AC isn't invalid
if ( AC > nchrom )
throw new UserException.MalformedVCF(String.format("The AC value (%d) at position %s:%d " +
"is larger than the number of chromosomes over all samples (%d)", AC,
eval.getChr(), eval.getStart(), nchrom));
return Collections.singletonList((Object) AC);
} else {
return Collections.emptyList();
}
}
@Override
public Set<Class<? extends VariantEvaluator>> getIncompatibleEvaluators() {
return new HashSet<Class<? extends VariantEvaluator>>(Arrays.asList(VariantSummary.class));
}
@Override
public String getFormat() {
return "%d";
}
}

82
protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java
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@ -1,82 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.varianteval.stratifications;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Collections;
import java.util.List;
/**
* Stratifies the eval RODs by the allele frequency of the alternate allele
*
* Uses a constant 0.005 frequency grid, and projects the AF INFO field value. Requires
* that AF be present in every ROD, otherwise this stratification throws an exception
*/
public class AlleleFrequency extends VariantStratifier {
@Override
public void initialize() {
for( double a = 0.000; a <= 1.005; a += 0.005 ) {
states.add(String.format("%.3f", a));
}
}
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
if (eval != null) {
try {
return Collections.singletonList((Object)String.format("%.3f", (5.0 * MathUtils.round(eval.getAttributeAsDouble("AF", 0.0) / 5.0, 3))));
} catch (Exception e) {
return Collections.emptyList();
}
}
return Collections.emptyList();
}
}

75
protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java
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@ -1,75 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.varianteval.stratifications;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
/**
* Stratifies the evaluation by each contig in the reference sequence
*/
public class Contig extends VariantStratifier {
@Override
public void initialize() {
states.addAll(getVariantEvalWalker().getContigNames());
states.add("all");
}
@Override
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
if (eval != null) {
return Arrays.asList((Object)"all", eval.getChr());
} else {
return Collections.emptyList();
}
}
}

97
protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java
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@ -1,97 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.varianteval.stratifications;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.ArrayList;
import java.util.List;
/**
* CpG is a stratification module for VariantEval that divides the input data by within/not within a CpG site
*
* <p>
* It is a three-state stratification:
* <ul>
* <li>The locus is a CpG site ("CpG")
* <li>The locus is not a CpG site ("non_CpG")
* <li>The locus is either a CpG or not a CpG site ("all")
* </ul>
* A CpG site is defined as a site where the reference base at a locus is a C and the adjacent reference base in the 3' direction is a G.
*/
public class CpG extends VariantStratifier {
@Override
public void initialize() {
states.add("all");
states.add("CpG");
states.add("non_CpG");
}
@Override
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
boolean isCpG = false;
if (ref != null && ref.getBases() != null) {
String fwRefBases = new String(ref.getBases());
//String leftFlank = fwRefBases.substring((fwRefBases.length()/2) - 1, (fwRefBases.length()/2) + 1);
String rightFlank = fwRefBases.substring((fwRefBases.length()/2), (fwRefBases.length()/2) + 2);
//if (leftFlank.equalsIgnoreCase("CG") || leftFlank.equalsIgnoreCase("GC") || rightFlank.equalsIgnoreCase("CG") || rightFlank.equalsIgnoreCase("GC")) {
if (rightFlank.equalsIgnoreCase("CG")) {
isCpG = true;
}
}
ArrayList<Object> relevantStates = new ArrayList<Object>(2);
relevantStates.add("all");
relevantStates.add(isCpG ? "CpG" : "non_CpG");
return relevantStates;
}
}

179
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@ -1,179 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.varianteval.stratifications;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
/**
* Experimental stratification by the degeneracy of an amino acid, according to VCF annotation. Not safe
*/
public class Degeneracy extends VariantStratifier {
private HashMap<String, HashMap<Integer, String>> degeneracies;
@Override
public void initialize() {
states.add("1-fold");
states.add("2-fold");
states.add("3-fold");
states.add("4-fold");
states.add("6-fold");
states.add("all");
HashMap<String, String[]> aminoAcids = new HashMap<String, String[]>();
aminoAcids.put("Ile", new String[]{"ATT", "ATC", "ATA"});
aminoAcids.put("Leu", new String[]{"CTT", "CTC", "CTA", "CTG", "TTA", "TTG"});
aminoAcids.put("Val", new String[]{"GTT", "GTC", "GTA", "GTG"});
aminoAcids.put("Phe", new String[]{"TTT", "TTC"});
aminoAcids.put("Met", new String[]{"ATG"});
aminoAcids.put("Cys", new String[]{"TGT", "TGC"});
aminoAcids.put("Ala", new String[]{"GCT", "GCC", "GCA", "GCG"});
aminoAcids.put("Gly", new String[]{"GGT", "GGC", "GGA", "GGG"});
aminoAcids.put("Pro", new String[]{"CCT", "CCC", "CCA", "CCG"});
aminoAcids.put("Thr", new String[]{"ACT", "ACC", "ACA", "ACG"});
aminoAcids.put("Ser", new String[]{"TCT", "TCC", "TCA", "TCG", "AGT", "AGC"});
aminoAcids.put("Tyr", new String[]{"TAT", "TAC"});
aminoAcids.put("Trp", new String[]{"TGG"});
aminoAcids.put("Glu", new String[]{"CAA", "CAG"});
aminoAcids.put("Asn", new String[]{"AAT", "AAC"});
aminoAcids.put("His", new String[]{"CAT", "CAC"});
aminoAcids.put("Gln", new String[]{"GAA", "GAG"});
aminoAcids.put("Asp", new String[]{"GAT", "GAC"});
aminoAcids.put("Lys", new String[]{"AAA", "AAG"});
aminoAcids.put("Arg", new String[]{"CGT", "CGC", "CGA", "CGG", "AGA", "AGG"});
aminoAcids.put("Stop", new String[]{"TAA", "TAG", "TGA"});
degeneracies = new HashMap<String, HashMap<Integer, String>>();
for (String aminoAcid : aminoAcids.keySet()) {
String[] codons = aminoAcids.get(aminoAcid);
for (int pos = 0; pos < 3; pos++) {
HashSet<Character> alleles = new HashSet<Character>();
for (String codon : codons) {
alleles.add(codon.charAt(pos));
}
String degeneracy;
switch (alleles.size()) {
case 1: degeneracy = "1-fold"; break;
case 2: degeneracy = "2-fold"; break;
case 3: degeneracy = "3-fold"; break;
case 4: degeneracy = "4-fold"; break;
case 6: degeneracy = "6-fold"; break;
default: degeneracy = "1-fold"; break;
}
if (!degeneracies.containsKey(aminoAcid)) {
degeneracies.put(aminoAcid, new HashMap<Integer, String>());
}
degeneracies.get(aminoAcid).put(pos, degeneracy);
}
}
}
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
ArrayList<Object> relevantStates = new ArrayList<Object>();
relevantStates.add("all");
if (eval != null && eval.isVariant()) {
String type = null;
String aa = null;
Integer frame = null;
if (eval.hasAttribute("refseq.functionalClass")) {
aa = eval.getAttributeAsString("refseq.variantAA", null);
frame = eval.getAttributeAsInt("refseq.frame", 0);
} else if (eval.hasAttribute("refseq.functionalClass_1")) {
int annotationId = 1;
String key;
do {
key = String.format("refseq.functionalClass_%d", annotationId);
String newtype = eval.getAttributeAsString(key, null);
if ( newtype != null &&
( type == null ||
( type.equals("silent") && !newtype.equals("silent") ) ||
( type.equals("missense") && newtype.equals("nonsense") ) )
) {
type = newtype;
String aakey = String.format("refseq.variantAA_%d", annotationId);
aa = eval.getAttributeAsString(aakey, null);
if (aa != null) {
String framekey = String.format("refseq.frame_%d", annotationId);
if (eval.hasAttribute(framekey)) {
frame = eval.getAttributeAsInt(framekey, 0);
}
}
}
annotationId++;
} while (eval.hasAttribute(key));
}
if (aa != null && degeneracies.containsKey(aa) && frame != null) {
relevantStates.add(degeneracies.get(aa).get(frame));
}
}
return relevantStates;
}
}

87
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@ -1,87 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.varianteval.stratifications;
import org.broadinstitute.variant.variantcontext.VariantContext;
/**
* Tag this stratification as dynamically determining the final strat based on the input data
*
* The paradigm here is simple. We upfront create a strat with N states that reflect the finest grained
* possible division of the data. The data is processed, and statistics collected for each of the N states.
* An update call is made to the stratification for evaluation VariantContext during each map call,
* allowing the strat to collect data about the usage of each state. A final call requests that
* the stratification map down the N states into M states (typically less than N, not necessarily
* a subset of N). This is provided by returning a map from each of M state -> N states and
* the VariantEval walker will combine all of the evaluations for N into a single value for
* each M.
*
* For example, suppose I have a dynamic strat called AC, adopting 7 possible values 0,1,2,3,4,5,6. This
* strats tracks the number of eval vcs for each state, with final counts 0=1, 1=100, 2=10, 3=5, 4=3, 5=2, 6=1.
* The stratification attempts to combine the strats down to so that each state has approximately the same
* fraction of the data in each bin. Overall there is 1+100+10+5+3+2+1=124 observations and 7 bins so we really
* want ~ 18 observations in each bin. So we merge 3-6 with 5+3+2+1 = 11 and keep 2, 1, and 0 as distinct bins. We
* return a map from 0 -> 0, 1 -> 1, 2 -> 2, 3-6 -> {3,4,5,6}.
*
* TODO - some open implementation questions
* -- We should only create one stratifier overall. How do we track this? When we create the stratifiers
* perhaps we can look at them and create a tracker?
* -- How do we create a new stratifier based on the finalStratifications() given the framework? Conceptually
* this new thing is itself a stratifier, just like before, but it's states are determined at the end. We'd
* then like to call not getRelevantStates but a different function that accepts an old state and returns
* the new state. Perhaps the process should look like:
* finalizeStratification -> new Stratifier whose states are the final ones
* getNewState(old state) -> new state (one of those in getFinalStratification)
*
* @author Mark DePristo
* @since 4/9/12
*/
public interface DynamicStratification {
public void update(final VariantContext eval);
public VariantStratifier finalizeStratification();
public Object getFinalState(final Object oldState);
}

73
protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java
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@ -1,73 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.varianteval.stratifications;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.List;
/**
* Required stratification grouping output by each eval ROD
*/
public class EvalRod extends VariantStratifier implements RequiredStratification {
@Override
public void initialize() {
for ( RodBinding<VariantContext> rod : getVariantEvalWalker().getEvals() ) {
states.add(rod.getName());
if ( getVariantEvalWalker().mergeEvals )
break;
}
}
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
return Arrays.asList((Object)evalName);
}
}

131
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@ -1,131 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.varianteval.stratifications;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.SnpEff;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.ArrayList;
import java.util.List;
/**
* Stratifies by nonsense, missense, silent, and all annotations in the input ROD, from the INFO field annotation.
*/
public class FunctionalClass extends VariantStratifier {
public enum FunctionalType {
silent,
missense,
nonsense
}
@Override
public void initialize() {
states.add("all");
for ( FunctionalType type : FunctionalType.values() )
states.add(type.name());
}
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
ArrayList<Object> relevantStates = new ArrayList<Object>();
relevantStates.add("all");
if (eval != null && eval.isVariant()) {
FunctionalType type = null;
if (eval.hasAttribute("refseq.functionalClass")) {
try {
type = FunctionalType.valueOf(eval.getAttributeAsString("refseq.functionalClass", null));
} catch ( Exception e ) {} // don't error out if the type isn't supported
} else if (eval.hasAttribute("refseq.functionalClass_1")) {
int annotationId = 1;
String key;
do {
key = String.format("refseq.functionalClass_%d", annotationId);
String newtypeStr = eval.getAttributeAsString(key, null);
if ( newtypeStr != null && !newtypeStr.equalsIgnoreCase("null") ) {
try {
FunctionalType newType = FunctionalType.valueOf(newtypeStr);
if ( type == null ||
( type == FunctionalType.silent && newType != FunctionalType.silent ) ||
( type == FunctionalType.missense && newType == FunctionalType.nonsense ) ) {
type = newType;
}
} catch ( Exception e ) {} // don't error out if the type isn't supported
}
annotationId++;
} while (eval.hasAttribute(key));
} else if ( eval.hasAttribute(SnpEff.InfoFieldKey.FUNCTIONAL_CLASS_KEY.getKeyName()) ) {
try {
SnpEff.EffectFunctionalClass snpEffFunctionalClass = SnpEff.EffectFunctionalClass.valueOf(eval.getAttribute(SnpEff.InfoFieldKey.FUNCTIONAL_CLASS_KEY.getKeyName()).toString());
if ( snpEffFunctionalClass == SnpEff.EffectFunctionalClass.NONSENSE )
type = FunctionalType.nonsense;
else if ( snpEffFunctionalClass == SnpEff.EffectFunctionalClass.MISSENSE )
type = FunctionalType.missense;
else if ( snpEffFunctionalClass == SnpEff.EffectFunctionalClass.SILENT )
type = FunctionalType.silent;
}
catch ( Exception e ) {} // don't error out if the type isn't supported
}
if ( type != null ) {
relevantStates.add(type.name());
}
}
return relevantStates;
}
}

99
protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java
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@ -1,99 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.varianteval.stratifications;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Collections;
import java.util.List;
/**
* Stratifies the eval RODs by the indel size
*
* Indel sizes are stratified from sizes -100 to +100. Sizes greater than this are lumped in the +/- 100 bin
* This stratification ignores multi-allelic indels (whose size is not defined uniquely)
*/
public class IndelSize extends VariantStratifier {
static final int MAX_INDEL_SIZE = 100;
@Override
public void initialize() {
for( int a=-MAX_INDEL_SIZE; a <=MAX_INDEL_SIZE; a++ ) {
states.add(a);
}
}
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
if (eval != null && eval.isIndel() && eval.isBiallelic()) {
try {
int eventLength = 0;
if ( eval.isSimpleInsertion() ) {
eventLength = eval.getAlternateAllele(0).length();
} else if ( eval.isSimpleDeletion() ) {
eventLength = -eval.getReference().length();
}
if (eventLength > MAX_INDEL_SIZE)
eventLength = MAX_INDEL_SIZE;
else if (eventLength < -MAX_INDEL_SIZE)
eventLength = -MAX_INDEL_SIZE;
return Collections.singletonList((Object)eventLength);
} catch (Exception e) {
return Collections.emptyList();
}
}
return Collections.emptyList();
}
@Override
public String getFormat() {
return "%d";
}
}

113
protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java
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@ -1,113 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.varianteval.stratifications;
import net.sf.picard.util.IntervalTree;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.interval.IntervalUtils;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.*;
/**
* Stratifies the variants by whether they overlap an interval in the set provided on the command line.
*
* The primary use of this stratification is to provide a mechanism to divide asssessment of a call set up
* by whether a variant overlaps an interval or not. I use this to differentiate between variants occurring
* in CCDS exons vs. those in non-coding regions, in the 1000G call set, using a command line that looks like:
*
* -T VariantEval -R human_g1k_v37.fasta -eval 1000G.vcf -stratIntervals:BED ccds.bed -ST IntervalStratification
*
* Note that the overlap algorithm properly handles symbolic alleles with an INFO field END value. In order to
* safely use this module you should provide entire contigs worth of variants, and let the interval strat decide
* overlap, as opposed to using -L which will not properly work with symbolic variants.
*/
public class IntervalStratification extends VariantStratifier {
final protected static Logger logger = Logger.getLogger(IntervalStratification.class);
Map<String, IntervalTree<GenomeLoc>> intervalTreeByContig = null;
final List<Object> OVERLAPPING = Arrays.asList((Object)"all", (Object)"overlaps.intervals");
final List<Object> NOT_OVERLAPPING = Arrays.asList((Object)"all", (Object)"outside.intervals");
@Override
public void initialize() {
if ( getVariantEvalWalker().intervalsFile == null )
throw new UserException.MissingArgument("stratIntervals", "Must be provided when IntervalStratification is enabled");
final List<GenomeLoc> locs = getVariantEvalWalker().intervalsFile.getIntervals(getVariantEvalWalker().getToolkit());
if ( locs.isEmpty() )
throw new UserException.BadArgumentValue("stratIntervals", "Contains no intervals. Perhaps the file is malformed or empty?");
intervalTreeByContig = getVariantEvalWalker().createIntervalTreeByContig(getVariantEvalWalker().intervalsFile);
logger.info(String.format("Creating IntervalStratification %s containing %d intervals covering %d bp",
getVariantEvalWalker().intervalsFile.getSource(), locs.size(), IntervalUtils.intervalSize(locs)));
states.addAll(Arrays.asList("all", "overlaps.intervals", "outside.intervals"));
}
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
if (eval != null) {
final GenomeLoc loc = getVariantEvalWalker().getToolkit().getGenomeLocParser().createGenomeLoc(eval, true);
IntervalTree<GenomeLoc> intervalTree = intervalTreeByContig.get(loc.getContig());
IntervalTree.Node<GenomeLoc> node = intervalTree.minOverlapper(loc.getStart(), loc.getStop());
//logger.info(String.format("Overlap %s found %s", loc, node));
if ( node != null )
return OVERLAPPING;
else
return NOT_OVERLAPPING;
}
return Collections.emptyList();
}
}

90
protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java
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@ -1,90 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.varianteval.stratifications;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextUtils;
import java.util.List;
import java.util.ArrayList;
import java.util.Set;
/**
* Stratifies the eval RODs by user-supplied JEXL expressions
*
* See http://gatkforums.broadinstitute.org/discussion/1255/what-are-jexl-expressions-and-how-can-i-use-them-with-the-gatk for more details
*/
public class JexlExpression extends VariantStratifier implements StandardStratification {
// needs to know the jexl expressions
private Set<SortableJexlVCMatchExp> jexlExpressions;
@Override
public void initialize() {
jexlExpressions = getVariantEvalWalker().getJexlExpressions();
states.add("none");
for ( SortableJexlVCMatchExp jexlExpression : jexlExpressions ) {
states.add(jexlExpression.name);
}
}
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
ArrayList<Object> relevantStates = new ArrayList<Object>();
relevantStates.add("none");
for ( SortableJexlVCMatchExp jexlExpression : jexlExpressions ) {
if (eval != null && VariantContextUtils.match(eval, jexlExpression)) {
relevantStates.add(jexlExpression.name);
}
}
return relevantStates;
}
}

85
protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java
View File

@ -1,85 +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 7 Cambridge Center, 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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.
* 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. OWNERSHIP OF INTELLECTUAL PROPERTY
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
* Copyright 2012 Broad Institute, Inc.
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
*
* 4. 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.
*
* 5. 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.
*
* 6. 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.
*
* 7. MISCELLANEOUS
* 7.1 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.
* 7.2 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.
* 7.3 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.
* 7.4 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.
* 7.5 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.
* 7.6 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.
* 7.7 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.sting.gatk.walkers.varianteval.stratifications;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.*;
/**
* Stratifies by whether a site in in the list of known RODs (e.g., dbsnp by default)
*/
public class Novelty extends VariantStratifier implements StandardStratification {
// needs the variant contexts and known names
private List<RodBinding<VariantContext>> knowns;
private final static List<Object> KNOWN_STATES = Arrays.asList((Object)"all", (Object)"known");
private final static List<Object> NOVEL_STATES = Arrays.asList((Object)"all", (Object)"novel");
@Override
public void initialize() {
states.addAll(Arrays.asList("all", "known", "novel"));
knowns = getVariantEvalWalker().getKnowns();
}
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
if (tracker != null && eval != null) {
final Collection<VariantContext> knownComps = tracker.getValues(knowns, ref.getLocus());
for ( final VariantContext c : knownComps ) {
// loop over sites, looking for something that matches the type eval
if ( eval.getType() == c.getType() || eval.getType() == VariantContext.Type.NO_VARIATION ) {
return KNOWN_STATES;
}
}
}
return NOVEL_STATES;
}
}

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