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

This commit is contained in:
Ami Levy-Moonshine 2013-01-25 11:47:38 -05:00
parent eaf6279d48 3f95f39be3
commit fc22a5c71c
149 changed files with 2624 additions and 1321 deletions
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1
.gitignore vendored
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@ -23,3 +23,4 @@ dist/
dump/
lib/
out/
/atlassian-ide-plugin.xml

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;

10
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java
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@ -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;
@ -74,12 +74,12 @@ 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));
}

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java
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@ -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 */

15
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
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@ -56,7 +56,6 @@ import org.broadinstitute.sting.gatk.arguments.StandardCallerArgumentCollection;
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.downsampling.DownsampleType;
import org.broadinstitute.sting.gatk.filters.BadMateFilter;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
@ -71,7 +70,7 @@ 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.*;
@ -132,7 +131,7 @@ import java.util.*;
@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
@PartitionBy(PartitionType.LOCUS)
@BAQMode(ApplicationTime = ReadTransformer.ApplicationTime.FORBIDDEN)
@ActiveRegionExtension(extension=65, maxRegion=300)
@ActiveRegionTraversalParameters(extension=65, maxRegion=300)
//@Downsample(by= DownsampleType.BY_SAMPLE, toCoverage=5)
public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implements AnnotatorCompatible {
@ -382,7 +381,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
@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()) ) {
@ -391,15 +390,15 @@ 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 ) { 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);
@ -436,7 +435,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
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() );
}
//---------------------------------------------------------------------------------------------------------------

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));
}
}
}

185
protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariants.java 100644
View File

@ -0,0 +1,185 @@
/*
* 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.
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* 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.
*
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*
* 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.
*
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*
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* 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.
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* 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.variantutils;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
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.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.variantcontext.*;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.variant.vcf.*;
import java.util.*;
/**
* Regenotypes the variants from a VCF. VCF records must contain PLs or GLs.
*
* <p>
* This tool triggers re-genotyping of the samples through the Exact Allele Frequency calculation model. Note that this is truly the
* mathematically correct way to select samples from a larger set (especially when calls were generated from low coverage sequencing data);
* using the hard genotypes to select (i.e. the default mode of SelectVariants) can lead to false positives when errors are confused for
* variants in the original genotyping. This functionality used to comprise the --regenotype option in SelectVariants but we pulled it out
* into its own tool for technical purposes.
*
* <h2>Input</h2>
* <p>
* A variant set to regenotype.
* </p>
*
* <h2>Output</h2>
* <p>
* A re-genotyped VCF.
* </p>
*
* <h2>Examples</h2>
* <pre>
* java -Xmx2g -jar GenomeAnalysisTK.jar \
* -R ref.fasta \
* -T RegenotypeVariants \
* --variant input.vcf \
* -o output.vcf
* </pre>
*
*/
@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
public class RegenotypeVariants extends RodWalker<Integer, Integer> implements TreeReducible<Integer> {
@ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
@Output(doc="File to which variants should be written",required=true)
protected VariantContextWriter vcfWriter = null;
private UnifiedGenotyperEngine UG_engine = null;
public void initialize() {
final UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();
UAC.GLmodel = GenotypeLikelihoodsCalculationModel.Model.BOTH;
UAC.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES;
UAC.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
String trackName = variantCollection.variants.getName();
Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName));
UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, GATKVariantContextUtils.DEFAULT_PLOIDY);
final Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), Arrays.asList(trackName)));
hInfo.addAll(UnifiedGenotyper.getHeaderInfo(UAC, null, null));
vcfWriter.writeHeader(new VCFHeader(hInfo, samples));
}
/**
* Subset VC record if necessary and emit the modified record (provided it satisfies criteria for printing)
*
* @param tracker the ROD tracker
* @param ref reference information
* @param context alignment info
* @return 1 if the record was printed to the output file, 0 if otherwise
*/
@Override
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( tracker == null )
return 0;
Collection<VariantContext> vcs = tracker.getValues(variantCollection.variants, context.getLocation());
if ( vcs == null || vcs.size() == 0) {
return 0;
}
for (VariantContext vc : vcs) {
if ( vc.isPolymorphicInSamples() && hasPLs(vc) ) {
synchronized (UG_engine) {
final VariantContextBuilder builder = new VariantContextBuilder(UG_engine.calculateGenotypes(vc)).filters(vc.getFiltersMaybeNull());
VariantContextUtils.calculateChromosomeCounts(builder, false);
vc = builder.make();
}
}
vcfWriter.add(vc);
}
return 1;
}
private boolean hasPLs(final VariantContext vc) {
for ( Genotype g : vc.getGenotypes() ) {
if ( g.hasLikelihoods() )
return true;
}
return false;
}
@Override
public Integer reduceInit() { return 0; }
@Override
public Integer reduce(Integer value, Integer sum) { return value + sum; }
@Override
public Integer treeReduce(Integer lhs, Integer rhs) {
return lhs + rhs;
}
public void onTraversalDone(Integer result) {
logger.info(result + " records processed.");
}
}

24
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -68,12 +68,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSample() {
HCTest(CEUTRIO_BAM, "", "b8f7b741445ce6b6ea491c794ce75c17");
HCTest(CEUTRIO_BAM, "", "11290b619bc79b629cf29b8f428254ce");
}
@Test
public void testHaplotypeCallerSingleSample() {
HCTest(NA12878_BAM, "", "a2c63f6e6e51a01019bdbd23125bdb15");
HCTest(NA12878_BAM, "", "897abb2b4f98e9e460f373f9e0db5033");
}
@Test(enabled = false)
@ -84,7 +84,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSampleGGA() {
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf",
"c679ae7f04bdfda896b5c046d35e043c");
"efc2cae94069a1d6ee5fdcc7afeaa0ed");
}
private void HCTestComplexGGA(String bam, String args, String md5) {
@ -96,13 +96,13 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSampleGGAComplex() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538",
"8730a9ebaeecae913dca2fb5a0d4e946");
"01f42c311fc3ce4f07ef86f8c01facfb");
}
@Test
public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
"d590c8d6d5e58d685401b65a23846893");
"4c117c84d1abeade1dee3f7b52a4a585");
}
private void HCTestComplexVariants(String bam, String args, String md5) {
@ -113,7 +113,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSampleComplex() {
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "6c0c441b71848c2eea38ab5e2afe1120");
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "939847eb7bbafc798916acffdb1b5697");
}
private void HCTestSymbolicVariants(String bam, String args, String md5) {
@ -124,7 +124,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleSymbolic() {
HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "0761ff5cbf279be467833fa6708bf360");
HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "25806874242973f00fb6f2a320ed4d9c");
}
private void HCTestIndelQualityScores(String bam, String args, String md5) {
@ -135,7 +135,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleIndelQualityScores() {
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "29f1125df5ab27cc937a144ae08ac735");
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "c50b06d56cf3d0ef53e73a4973207949");
}
// That problem bam came from a user on the forum and it spotted a problem where the ReadClipper
@ -146,14 +146,14 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void HCTestProblematicReadsModifiedInActiveRegions() {
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3 -L 4:49139026-49139965";
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("31db0a2d9eb07f86e0a89f0d97169072"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("ae2470e294d99ff2b825281b84730c72"));
executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
}
@Test
public void HCTestStructuralIndels() {
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("add0f4f51969b7caeea99005a7ba1aa4"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("6f18ae64bf466476d780a083dcb5fc43"));
executeTest("HCTestStructuralIndels: ", spec);
}
@ -175,7 +175,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestReducedBam() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
Arrays.asList("8a400b0c46f41447fcc35a907e34f384"));
Arrays.asList("ecdb8e30ec5dd91efc179ab6732499f9"));
executeTest("HC calling on a ReducedRead BAM", spec);
}
@ -183,7 +183,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void testReducedBamWithReadsNotFullySpanningDeletion() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "reduced.readNotFullySpanningDeletion.bam -o %s -L 1:167871297", 1,
Arrays.asList("4e8121dd9dc90478f237bd6ae4d19920"));
Arrays.asList("36a90309dde1a325c274388e302ffaa5"));
executeTest("test calling on a ReducedRead BAM where the reads do not fully span a deletion", spec);
}
}

16
protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -334,16 +334,6 @@ public class VariantEvalIntegrationTest extends WalkerTest {
executeTestParallel("testSelect1", spec);
}
@Test
public void testVEGenotypeConcordance() {
String vcfFile = "GenotypeConcordanceEval.vcf";
WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -ST CpG --eval:VCF3 " + validationDataLocation + vcfFile + " --comp:VCF3 " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s",
1,
Arrays.asList("810d55b67de592f6375d9dfb282145ef"));
executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec);
}
@Test
public void testVEMendelianViolationEvaluator() {
String vcfFile = "/MendelianViolationEval.vcf";
@ -355,12 +345,6 @@ public class VariantEvalIntegrationTest extends WalkerTest {
executeTestParallel("testVEMendelianViolationEvaluator" + vcfFile, spec);
}
@Test
public void testCompVsEvalAC() {
String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance --eval:evalYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf --comp:compYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("659a15cc842f0310106fa595a26da71d"));
executeTestParallel("testCompVsEvalAC",spec);
}
private static String withSelect(String cmd, String select, String name) {
return String.format("%s -select '%s' -selectName %s", cmd, select, name);

7
protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java
View File

@ -190,7 +190,7 @@ public class ConcordanceMetricsUnitTest extends BaseTest {
}
@Test(enabled=true)
public void testMismatchingAllele() {
public void testMismatchingAlleleInAlleleSubset() {
Pair<VariantContext,VariantContext> data = getData2();
VariantContext eval = data.getFirst();
VariantContext truth = data.getSecond();
@ -709,8 +709,13 @@ public class ConcordanceMetricsUnitTest extends BaseTest {
List<Pair<VariantContext,VariantContext>> data = getData7();
int idx = 0;
int[] expecNotMatch = new int[]{0,0,0,0,0,1,1};
for ( Pair<VariantContext,VariantContext> varPair : data ) {
metrics.update(varPair.getFirst(),varPair.getSecond());
Assert.assertEquals(metrics.getOverallSiteConcordance().get(ConcordanceMetrics.SiteConcordanceType.ALLELES_DO_NOT_MATCH),expecNotMatch[idx]);
logger.info(idx);
idx++;
}
Assert.assertEquals(metrics.getOverallSiteConcordance().get(ConcordanceMetrics.SiteConcordanceType.ALLELES_DO_NOT_MATCH),1);

67
protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordanceIntegrationTest.java
View File

@ -1,27 +1,48 @@
/*
* Copyright (c) 2010.
*
* 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.
*/
* 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.variantutils;

69
protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariantsIntegrationTest.java 100644
View File

@ -0,0 +1,69 @@
/*
* 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.variantutils;
import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.testng.annotations.Test;
import java.util.Arrays;
public class RegenotypeVariantsIntegrationTest extends WalkerTest {
@Test
public void testRegenotype() {
String testFile = privateTestDir + "combine.3.NA12892.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
"-T RegenotypeVariants -R " + b36KGReference + " --variant " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("46ff472fc7ef6734ad01170028d5924a")
);
executeTest("testRegenotype--" + testFile, spec);
}
}

26
protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
View File

@ -229,19 +229,6 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
executeTest("testUsingDbsnpName--" + testFile, spec);
}
@Test
public void testRegenotype() {
String testFile = privateTestDir + "combine.3.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("46ff472fc7ef6734ad01170028d5924a")
);
executeTest("testRegenotype--" + testFile, spec);
}
@Test
public void testRemoveMLE() {
String testFile = privateTestDir + "vcfexample.withMLE.vcf";
@ -255,19 +242,6 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
executeTest("testRemoveMLE--" + testFile, spec);
}
@Test
public void testRemoveMLEAndRegenotype() {
String testFile = privateTestDir + "vcfexample.withMLE.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("46ff472fc7ef6734ad01170028d5924a")
);
executeTest("testRemoveMLEAndRegenotype--" + testFile, spec);
}
@Test
public void testMultipleRecordsAtOnePosition() {
String testFile = privateTestDir + "selectVariants.onePosition.vcf";

6
public/java/src/org/broadinstitute/sting/commandline/IntervalArgumentCollection.java
View File

@ -1,6 +1,6 @@
/*
* Copyright (c) 2012 The Broad Institute
*
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
@ -9,10 +9,10 @@
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND

8
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java
View File

@ -214,7 +214,13 @@ public abstract class LocusView extends LocusIterator implements View {
return locus.containsP(location);
}
// TODO -- remove me
/**
* {@inheritDoc}
*
* Since this class has an actual LIBS, so this function will never throw an exception
*
* @return the LocusIteratorByState used by this view to get pileups
*/
@Override
public LocusIteratorByState getLIBS() {
return loci.getLIBS();

0
protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java → public/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java
View File

46
public/java/src/org/broadinstitute/sting/gatk/iterators/GATKSAMIterator.java
View File

@ -1,27 +1,27 @@
/*
* Copyright (c) 2012 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
* Copyright (c) 2012 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.iterators;

362
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
View File

@ -25,6 +25,7 @@
package org.broadinstitute.sting.gatk.traversals;
import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
@ -32,19 +33,18 @@ import org.broadinstitute.sting.gatk.WalkerManager;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.providers.*;
import org.broadinstitute.sting.gatk.datasources.reads.Shard;
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.DataSource;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
import org.broadinstitute.sting.utils.activeregion.ActivityProfile;
import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.activeregion.*;
import org.broadinstitute.sting.utils.progressmeter.ProgressMeter;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.io.PrintStream;
import java.util.*;
/**
@ -69,15 +69,61 @@ import java.util.*;
public class TraverseActiveRegions<M, T> extends TraversalEngine<M,T,ActiveRegionWalker<M,T>,LocusShardDataProvider> {
protected final static Logger logger = Logger.getLogger(TraversalEngine.class);
protected final static boolean DEBUG = false;
protected final static boolean LOG_READ_CARRYING = false;
// set by the tranversal
private boolean walkerHasPresetRegions = false;
private int activeRegionExtension = -1;
private int maxRegionSize = -1;
private int minRegionSize = -1;
private final LinkedList<ActiveRegion> workQueue = new LinkedList<ActiveRegion>();
private LinkedList<GATKSAMRecord> myReads = new LinkedList<GATKSAMRecord>();
private GenomeLoc spanOfLastReadSeen = null;
private ActivityProfile activityProfile = null;
int maxReadsInMemory = 0;
ActiveRegionWalker walker;
/**
* Have the debugging output streams been initialized already?
*
* We have to do lazy initialization because when the initialize() function is called
* the streams aren't yet initialized in the GATK walker.
*/
private boolean streamsInitialized = false;
@Override
public void initialize(GenomeAnalysisEngine engine, Walker walker, ProgressMeter progressMeter) {
super.initialize(engine, walker, progressMeter);
this.walker = (ActiveRegionWalker)walker;
if ( this.walker.wantsExtendedReads() && ! this.walker.wantsNonPrimaryReads() ) {
throw new IllegalArgumentException("Active region walker " + this.walker + " requested extended events but not " +
"non-primary reads, an inconsistent state. Please modify the walker");
}
ActiveRegionTraversalParameters annotation = walker.getClass().getAnnotation(ActiveRegionTraversalParameters.class);
this.activeRegionExtension = this.walker.activeRegionExtension == null ? annotation.extension() : this.walker.activeRegionExtension;
this.maxRegionSize = this.walker.activeRegionMaxSize == null ? annotation.maxRegion() : this.walker.activeRegionMaxSize;
this.minRegionSize = annotation.minRegion();
final double bandPassSigma = this.walker.bandPassSigma == null ? annotation.bandPassSigma() : this.walker.bandPassSigma;
walkerHasPresetRegions = this.walker.hasPresetActiveRegions();
activityProfile = new BandPassActivityProfile(engine.getGenomeLocParser(), BandPassActivityProfile.MAX_FILTER_SIZE, bandPassSigma);
if ( walkerHasPresetRegions ) {
// we load all of the preset locations into the
for ( final GenomeLoc loc : this.walker.getPresetActiveRegions()) {
workQueue.add(new ActiveRegion(loc, null, true, engine.getGenomeLocParser(), getActiveRegionExtension()));
}
}
}
// -------------------------------------------------------------------------------------
//
// Utility functions
//
// -------------------------------------------------------------------------------------
protected int getActiveRegionExtension() {
return activeRegionExtension;
@ -87,6 +133,10 @@ public class TraverseActiveRegions<M, T> extends TraversalEngine<M,T,ActiveRegio
return maxRegionSize;
}
protected int getMinRegionSize() {
return minRegionSize;
}
@Override
public String getTraversalUnits() {
return "active regions";
@ -97,19 +147,6 @@ public class TraverseActiveRegions<M, T> extends TraversalEngine<M,T,ActiveRegio
return "TraverseActiveRegions";
}
@Override
public void initialize(GenomeAnalysisEngine engine, Walker walker, ProgressMeter progressMeter) {
super.initialize(engine, walker, progressMeter);
activeRegionExtension = walker.getClass().getAnnotation(ActiveRegionExtension.class).extension();
maxRegionSize = walker.getClass().getAnnotation(ActiveRegionExtension.class).maxRegion();
final ActiveRegionWalker arWalker = (ActiveRegionWalker)walker;
if ( arWalker.wantsExtendedReads() && ! arWalker.wantsNonPrimaryReads() ) {
throw new IllegalArgumentException("Active region walker " + arWalker + " requested extended events but not " +
"non-primary reads, an inconsistent state. Please modify the walker");
}
}
/**
* Is the loc outside of the intervals being requested for processing by the GATK?
* @param loc
@ -119,35 +156,6 @@ public class TraverseActiveRegions<M, T> extends TraversalEngine<M,T,ActiveRegio
return engine.getIntervals() != null && ! engine.getIntervals().overlaps(loc);
}
/**
* Take the individual isActive calls and integrate them into contiguous active regions and
* add these blocks of work to the work queue
* band-pass filter the list of isActive probabilities and turn into active regions
*
* @param profile
* @param activeRegions
* @return
*/
protected ActivityProfile incorporateActiveRegions(final ActivityProfile profile,
final List<ActiveRegion> activeRegions) {
if ( profile.isEmpty() )
throw new IllegalStateException("trying to incorporate an empty active profile " + profile);
final ActivityProfile bandPassFiltered = profile.bandPassFilter();
activeRegions.addAll(bandPassFiltered.createActiveRegions( getActiveRegionExtension(), getMaxRegionSize() ));
return new ActivityProfile( engine.getGenomeLocParser(), profile.hasPresetRegions() );
}
protected final ActivityProfileResult walkerActiveProb(final ActiveRegionWalker<M, T> walker,
final RefMetaDataTracker tracker, final ReferenceContext refContext,
final AlignmentContext locus, final GenomeLoc location) {
if ( walker.hasPresetActiveRegions() ) {
return new ActivityProfileResult(location, walker.presetActiveRegions.overlaps(location) ? 1.0 : 0.0);
} else {
return walker.isActive( tracker, refContext, locus );
}
}
protected ReferenceOrderedView getReferenceOrderedView(final ActiveRegionWalker<M, T> walker,
final LocusShardDataProvider dataProvider,
final LocusView locusView) {
@ -157,19 +165,12 @@ public class TraverseActiveRegions<M, T> extends TraversalEngine<M,T,ActiveRegio
return (RodLocusView)locusView;
}
/**
* Write out each active region to the walker activeRegionOutStream
*
* @param walker
*/
protected void writeActiveRegionsToStream( final ActiveRegionWalker<M, T> walker ) {
// Just want to output the active regions to a file, not actually process them
for( final ActiveRegion activeRegion : workQueue ) {
if( activeRegion.isActive ) {
walker.activeRegionOutStream.println( activeRegion.getLocation() );
}
}
}
// -------------------------------------------------------------------------------------
//
// Actual traverse function
//
// -------------------------------------------------------------------------------------
/**
* Did read appear in the last shard?
@ -189,7 +190,7 @@ public class TraverseActiveRegions<M, T> extends TraversalEngine<M,T,ActiveRegio
* @param read the read we want to test if it's already been seen in the last shard
* @return true if read would have appeared in the last shard, false otherwise
*/
protected boolean appearedInLastShard(final GenomeLoc locOfLastReadAtTraversalStart, final GATKSAMRecord read) {
private boolean appearedInLastShard(final GenomeLoc locOfLastReadAtTraversalStart, final GATKSAMRecord read) {
if ( locOfLastReadAtTraversalStart == null )
// we're in the first shard, so obviously the answer is no
return false;
@ -202,57 +203,29 @@ public class TraverseActiveRegions<M, T> extends TraversalEngine<M,T,ActiveRegio
}
// -------------------------------------------------------------------------------------
//
// Actual traverse function
//
// -------------------------------------------------------------------------------------
/**
* Is the current shard on a new contig w.r.t. the previous shard?
* @param currentShard the current shard we are processing
* @return true if the last shard was on a different contig than the current shard
*/
private boolean onNewContig(final Shard currentShard) {
return spanOfLastSeenRead() != null
&& spanOfLastSeenRead().getContigIndex() != currentShard.getLocation().getContigIndex();
}
@Override
public T traverse( final ActiveRegionWalker<M,T> walker,
final LocusShardDataProvider dataProvider,
T sum) {
logger.debug(String.format("TraverseActiveRegions.traverse: Shard is %s", dataProvider));
if ( LOG_READ_CARRYING || logger.isDebugEnabled() )
logger.info(String.format("TraverseActiveRegions.traverse: Shard is %s", dataProvider));
final LocusView locusView = new AllLocusView(dataProvider);
final LocusReferenceView referenceView = new LocusReferenceView( walker, dataProvider );
final List<ActiveRegion> activeRegions = new LinkedList<ActiveRegion>();
ActivityProfile profile = new ActivityProfile(engine.getGenomeLocParser(), walker.hasPresetActiveRegions() );
ReferenceOrderedView referenceOrderedDataView = getReferenceOrderedView(walker, dataProvider, locusView);
final ReferenceOrderedView referenceOrderedDataView = getReferenceOrderedView(walker, dataProvider, locusView);
// We keep processing while the next reference location is within the interval
final GenomeLoc locOfLastReadAtTraversalStart = spanOfLastSeenRead();
// if we've moved onto a new contig, process all of the active regions
if ( onNewContig(dataProvider.getShard()) )
sum = processActiveRegions(walker, sum, true);
GenomeLoc prevLoc = null;
while( locusView.hasNext() ) {
final AlignmentContext locus = locusView.next();
final GenomeLoc location = locus.getLocation();
// Grab all the previously unseen reads from this pileup and add them to the massive read list
// Note that this must occur before we leave because we are outside the intervals because
// reads may occur outside our intervals but overlap them in the future
// get all of the new reads that appear in the current pileup, and them to our list of reads
// provided we haven't seen them before
final Collection<GATKSAMRecord> reads = locusView.getLIBS().transferReadsFromAllPreviousPileups();
for( final GATKSAMRecord read : reads ) {
if ( appearedInLastShard(locOfLastReadAtTraversalStart, read) ) {
if ( DEBUG ) logger.warn("Skipping duplicated " + read.getReadName());
} else {
if ( ! appearedInLastShard(locOfLastReadAtTraversalStart, read) ) {
if ( DEBUG ) logger.warn("Adding read " + read.getReadName() + " at " + engine.getGenomeLocParser().createGenomeLoc(read) + " from provider " + dataProvider);
rememberLastReadLocation(read);
myReads.add(read);
@ -263,10 +236,11 @@ public class TraverseActiveRegions<M, T> extends TraversalEngine<M,T,ActiveRegio
if ( outsideEngineIntervals(location) )
continue;
if ( prevLoc != null && location.getStart() != prevLoc.getStop() + 1 ) {
// we've move across some interval boundary, restart profile
profile = incorporateActiveRegions(profile, activeRegions);
}
// we've move across some interval boundary, restart profile
final boolean flushProfile = ! activityProfile.isEmpty()
&& ( activityProfile.getContigIndex() != location.getContigIndex()
|| location.getStart() != activityProfile.getStop() + 1);
sum = processActiveRegions(walker, sum, flushProfile, false);
dataProvider.getShard().getReadMetrics().incrementNumIterations();
@ -278,38 +252,14 @@ public class TraverseActiveRegions<M, T> extends TraversalEngine<M,T,ActiveRegio
final RefMetaDataTracker tracker = referenceOrderedDataView.getReferenceOrderedDataAtLocus(locus.getLocation(), refContext);
// Call the walkers isActive function for this locus and add them to the list to be integrated later
profile.add(walkerActiveProb(walker, tracker, refContext, locus, location));
prevLoc = location;
addIsActiveResult(walker, tracker, refContext, locus);
maxReadsInMemory = Math.max(myReads.size(), maxReadsInMemory);
printProgress(locus.getLocation());
}
updateCumulativeMetrics(dataProvider.getShard());
if ( ! profile.isEmpty() )
incorporateActiveRegions(profile, activeRegions);
// add active regions to queue of regions to process
// first check if can merge active regions over shard boundaries
if( !activeRegions.isEmpty() ) {
if( !workQueue.isEmpty() ) {
final ActiveRegion last = workQueue.getLast();
final ActiveRegion first = activeRegions.get(0);
if( last.isActive == first.isActive && last.getLocation().contiguousP(first.getLocation()) && last.getLocation().size() + first.getLocation().size() <= getMaxRegionSize() ) {
workQueue.removeLast();
activeRegions.remove(first);
workQueue.add( new ActiveRegion(last.getLocation().union(first.getLocation()), first.isActive, this.engine.getGenomeLocParser(), getActiveRegionExtension()) );
}
}
workQueue.addAll( activeRegions );
}
logger.debug("Integrated " + profile.size() + " isActive calls into " + activeRegions.size() + " regions." );
// now go and process all of the active regions
sum = processActiveRegions(walker, sum, false);
return sum;
}
@ -318,7 +268,7 @@ public class TraverseActiveRegions<M, T> extends TraversalEngine<M,T,ActiveRegio
* Ugly for now but will be cleaned up when we push this functionality more into the engine
*/
public T endTraversal(final Walker<M, T> walker, T sum) {
return processActiveRegions((ActiveRegionWalker<M, T>)walker, sum, true);
return processActiveRegions((ActiveRegionWalker<M, T>)walker, sum, true, true);
}
// -------------------------------------------------------------------------------------
@ -360,8 +310,15 @@ public class TraverseActiveRegions<M, T> extends TraversalEngine<M,T,ActiveRegio
* @return true if the extended location of region is completely within the current dead zone, false otherwise
*/
protected boolean regionCompletelyWithinDeadZone(final ActiveRegion region) {
return region.getExtendedLoc().getStop() < spanOfLastSeenRead().getStart()
|| ! region.getExtendedLoc().onSameContig(spanOfLastSeenRead());
if ( spanOfLastSeenRead() == null )
return false;
final int contigCmp = region.getExtendedLoc().compareContigs(spanOfLastSeenRead());
if ( contigCmp > 0 )
throw new IllegalStateException("Active region " + region + " on a contig after last seen read " + spanOfLastSeenRead());
else {
return contigCmp < 0 || region.getExtendedLoc().getStop() < spanOfLastSeenRead().getStart();
}
}
/**
@ -385,31 +342,153 @@ public class TraverseActiveRegions<M, T> extends TraversalEngine<M,T,ActiveRegio
*/
@Requires({"read != null", "activeRegion != null"})
private boolean readCannotOccurInAnyMoreActiveRegions(final GATKSAMRecord read, final ActiveRegion activeRegion) {
return read.getAlignmentEnd() + getActiveRegionExtension() < activeRegion.getLocation().getStop();
return read.getReferenceIndex() < activeRegion.getLocation().getContigIndex() ||
( read.getReferenceIndex() == activeRegion.getLocation().getContigIndex()
&& read.getAlignmentEnd() + getActiveRegionExtension() < activeRegion.getLocation().getStop() );
}
// -------------------------------------------------------------------------------------
//
// Functions to write out activity profiles and active regions
//
// -------------------------------------------------------------------------------------
/**
* Initialize the debugging output streams (activity profile and active regions), if not done so already
*/
@Ensures("streamsInitialized == true")
private void initializeOutputStreamsIfNecessary() {
if ( ! streamsInitialized ) {
streamsInitialized = true;
if ( walker.activityProfileOutStream != null ) {
printIGVFormatHeader(walker.activityProfileOutStream, "line", "ActivityProfile");
}
if ( walker.activeRegionOutStream != null ) {
printIGVFormatHeader(walker.activeRegionOutStream, "line", "ActiveRegions");
}
}
}
/**
* Helper function to write out a IGV formatted line to out, at loc, with values
*
* http://www.broadinstitute.org/software/igv/IGV
*
* @param out a non-null PrintStream where we'll write our line
* @param graphType the type of graph to show in IGV for this track
* @param columns the column names for this IGV track
*/
@Requires({
"out != null",
"graphType != null",
"columns.length > 0"
})
private void printIGVFormatHeader(final PrintStream out, final String graphType, final String ... columns ) {
out.printf("#track graphType=%s%n", graphType);
out.printf("Chromosome\tStart\tEnd\tFeature\t%s%n", Utils.join("\t", columns));
}
/**
* Helper function to write out a IGV formatted line to out, at loc, with values
*
* http://www.broadinstitute.org/software/igv/IGV
*
* @param out a non-null PrintStream where we'll write our line
* @param loc the location of values
* @param featureName string name of this feature (see IGV format)
* @param values the floating point values to associate with loc and feature name in out
*/
@Requires({
"out != null",
"loc != null",
"values.length > 0"
})
private void printIGVFormatRow(final PrintStream out, final GenomeLoc loc, final String featureName, final double ... values) {
// note that start and stop are 0 based, but the stop is exclusive so we don't subtract 1
out.printf("%s\t%d\t%d\t%s", loc.getContig(), loc.getStart() - 1, loc.getStop(), featureName);
for ( final double value : values )
out.print(String.format("\t%.3f", value));
out.println();
}
/**
* Write out activity profile information, if requested by the walker
*
* @param states the states in the current activity profile
*/
@Requires("states != null")
private void writeActivityProfile(final List<ActivityProfileState> states) {
if ( walker.activityProfileOutStream != null ) {
initializeOutputStreamsIfNecessary();
for ( final ActivityProfileState state : states ) {
printIGVFormatRow(walker.activityProfileOutStream, state.getLoc(), "state", Math.min(state.isActiveProb, 1.0));
}
}
}
/**
* Write out each active region to the walker activeRegionOutStream
*
* @param region the region we're currently operating on
*/
@Requires("region != null")
private void writeActiveRegion(final ActiveRegion region) {
if( walker.activeRegionOutStream != null ) {
initializeOutputStreamsIfNecessary();
printIGVFormatRow(walker.activeRegionOutStream, region.getLocation().getStartLocation(),
"end-marker", 0.0);
printIGVFormatRow(walker.activeRegionOutStream, region.getLocation(),
"size=" + region.getLocation().size(), region.isActive ? 1.0 : -1.0);
}
}
// -------------------------------------------------------------------------------------
//
// Functions to process active regions that are ready for map / reduce calls
//
// -------------------------------------------------------------------------------------
private T processActiveRegions(final ActiveRegionWalker<M, T> walker, T sum, final boolean forceRegionsToBeActive) {
if( walker.activeRegionOutStream != null ) {
writeActiveRegionsToStream(walker);
return sum;
} else {
return callWalkerMapOnActiveRegions(walker, sum, forceRegionsToBeActive);
/**
* Invoke the walker isActive function, and incorporate its result into the activity profile
*
* @param walker the walker we're running
* @param tracker the ref meta data tracker to pass on to the isActive function of walker
* @param refContext the refContext to pass on to the isActive function of walker
* @param locus the AlignmentContext to pass on to the isActive function of walker
*/
private void addIsActiveResult(final ActiveRegionWalker<M, T> walker,
final RefMetaDataTracker tracker, final ReferenceContext refContext,
final AlignmentContext locus) {
// must be called, even if we won't use the result, to satisfy walker contract
final ActivityProfileState state = walker.isActive( tracker, refContext, locus );
if ( ! walkerHasPresetRegions ) {
activityProfile.add(state);
}
}
private T callWalkerMapOnActiveRegions(final ActiveRegionWalker<M, T> walker, T sum, final boolean forceRegionsToBeActive) {
/**
* Take the individual isActive calls and integrate them into contiguous active regions and
* add these blocks of work to the work queue
* band-pass filter the list of isActive probabilities and turn into active regions
*/
private T processActiveRegions(final ActiveRegionWalker<M, T> walker, T sum, final boolean flushActivityProfile, final boolean forceAllRegionsToBeActive) {
if ( ! walkerHasPresetRegions ) {
// We don't have preset regions, so we get our regions from the activity profile
final Collection<ActiveRegion> activeRegions = activityProfile.popReadyActiveRegions(getActiveRegionExtension(), getMinRegionSize(), getMaxRegionSize(), flushActivityProfile);
workQueue.addAll(activeRegions);
if ( ! activeRegions.isEmpty() && logger.isDebugEnabled() ) logger.debug("Integrated " + activityProfile.size() + " isActive calls into " + activeRegions.size() + " regions." );
}
// Since we've traversed sufficiently past this point (or this contig!) in the workQueue we can unload those regions and process them
// TODO can implement parallel traversal here
while( workQueue.peek() != null ) {
final ActiveRegion activeRegion = workQueue.peek();
if ( forceRegionsToBeActive || regionCompletelyWithinDeadZone(activeRegion) ) {
if ( forceAllRegionsToBeActive || regionCompletelyWithinDeadZone(activeRegion) ) {
if ( DEBUG ) logger.warn("Processing active region " + activeRegion + " dead zone " + spanOfLastSeenRead());
writeActivityProfile(activeRegion.getSupportingStates());
writeActiveRegion(activeRegion);
sum = processActiveRegion( workQueue.remove(), sum, walker );
} else {
break;
@ -419,7 +498,7 @@ public class TraverseActiveRegions<M, T> extends TraversalEngine<M,T,ActiveRegio
return sum;
}
protected T processActiveRegion(final ActiveRegion activeRegion, final T sum, final ActiveRegionWalker<M, T> walker) {
private T processActiveRegion(final ActiveRegion activeRegion, final T sum, final ActiveRegionWalker<M, T> walker) {
final Iterator<GATKSAMRecord> liveReads = myReads.iterator();
while ( liveReads.hasNext() ) {
boolean killed = false;
@ -445,6 +524,11 @@ public class TraverseActiveRegions<M, T> extends TraversalEngine<M,T,ActiveRegio
}
logger.debug(">> Map call with " + activeRegion.getReads().size() + " " + (activeRegion.isActive ? "active" : "inactive") + " reads @ " + activeRegion.getLocation() + " with full extent: " + activeRegion.getReferenceLoc());
if ( LOG_READ_CARRYING )
logger.info(String.format("Processing region %20s span=%3d active?=%5b with %4d reads. Overall max reads carried is %s",
activeRegion.getLocation(), activeRegion.getLocation().size(), activeRegion.isActive, activeRegion.size(), maxReadsInMemory));
final M x = walker.map(activeRegion, null);
return walker.reduce( x, sum );
}

45
public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionExtension.java
View File

@ -1,45 +0,0 @@
/*
* Copyright (c) 2012 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.walkers;
import java.lang.annotation.Documented;
import java.lang.annotation.Inherited;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;
/**
* Describes the size of the buffer region that is added to each active region when pulling in covered reads.
* User: rpoplin
* Date: 1/18/12
*/
@Documented
@Inherited
@Retention(RetentionPolicy.RUNTIME)
public @interface ActiveRegionExtension {
public int extension() default 0;
public int maxRegion() default 1500;
}

81
public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionTraversalParameters.java 100644
View File

@ -0,0 +1,81 @@
/*
* Copyright (c) 2012 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.walkers;
import org.broadinstitute.sting.utils.activeregion.BandPassActivityProfile;
import java.lang.annotation.Documented;
import java.lang.annotation.Inherited;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;
/**
* Describes the parameters that this walker requires of the active region traversal
*
* User: rpoplin
* Date: 1/18/12
*/
@Documented
@Inherited
@Retention(RetentionPolicy.RUNTIME)
public @interface ActiveRegionTraversalParameters {
/**
* How far to either side of the active region itself should we include reads?
*
* That is, if the active region is 10 bp wide, and extension is 5, ART will provide
* the walker with active regions 10 bp, with 5 bp of extension on either side, and
* all reads that cover the 20 bp of the region + extension.
*
* @return the size of the active region extension we'd like
*/
public int extension() default 0;
/**
* The minimum number of bp for an active region, when we need to chop it up into pieces because
* it's become too big. This only comes into effect when there's literally no good place to chop
* that does make the region smaller than this value.
*
* @return the min size in bp of regions
*/
public int minRegion() default 50;
/**
* The maximum size in bp of active regions wanted by this walker
*
* Active regions larger than this value are automatically cut up by ART into smaller
* regions of size <= this value.
*
* @return the max size in bp of regions
*/
public int maxRegion() default 1500;
/**
* The variance value for the Gaussian kernel of the band pass filter employed by ART
* @return the breadth of the band pass gaussian kernel we want for our traversal
*/
public double bandPassSigma() default BandPassActivityProfile.DEFAULT_SIGMA;
}

64
public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
View File

@ -28,9 +28,7 @@ package org.broadinstitute.sting.gatk.walkers;
import com.google.java.contract.Ensures;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.commandline.IntervalBinding;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.filters.*;
@ -40,7 +38,7 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
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.interval.IntervalMergingRule;
import org.broadinstitute.sting.utils.interval.IntervalSetRule;
import org.broadinstitute.sting.utils.interval.IntervalUtils;
@ -57,22 +55,48 @@ import java.util.*;
@By(DataSource.READS)
@Requires({DataSource.READS, DataSource.REFERENCE})
@PartitionBy(PartitionType.READ)
@ActiveRegionExtension(extension=50,maxRegion=1500)
@ActiveRegionTraversalParameters(extension=50,maxRegion=1500)
@ReadFilters({UnmappedReadFilter.class, NotPrimaryAlignmentFilter.class, DuplicateReadFilter.class, FailsVendorQualityCheckFilter.class, MappingQualityUnavailableFilter.class})
@RemoveProgramRecords
public abstract class ActiveRegionWalker<MapType, ReduceType> extends Walker<MapType, ReduceType> {
/**
* If provided, this walker will write out its activity profile (per bp probabilities of being active)
* to this file in the IGV formatted TAB deliminated output:
*
* http://www.broadinstitute.org/software/igv/IGV
*
* Intended to make debugging the activity profile calculations easier
*/
@Output(fullName="activityProfileOut", shortName="APO", doc="Output the raw activity profile results in IGV format", required = false)
public PrintStream activityProfileOutStream = null;
@Output(fullName="activeRegionOut", shortName="ARO", doc="Output the active region to this interval list file", required = false)
/**
* If provided, this walker will write out its active and inactive regions
* to this file in the IGV formatted TAB deliminated output:
*
* http://www.broadinstitute.org/software/igv/IGV
*
* Intended to make debugging the active region calculations easier
*/
@Output(fullName="activeRegionOut", shortName="ARO", doc="Output the active region to this IGV formatted file", required = false)
public PrintStream activeRegionOutStream = null;
@Input(fullName="activeRegionIn", shortName="AR", doc="Use this interval list file as the active regions to process", required = false)
protected List<IntervalBinding<Feature>> activeRegionBindings = null;
public GenomeLocSortedSet presetActiveRegions = null;
@Advanced
@Argument(fullName="activeRegionExtension", shortName="activeRegionExtension", doc="The active region extension; if not provided defaults to Walker annotated default", required = false)
public Integer activeRegionExtension = null;
public boolean hasPresetActiveRegions() {
return presetActiveRegions != null;
}
@Advanced
@Argument(fullName="activeRegionMaxSize", shortName="activeRegionMaxSize", doc="The active region maximum size; if not provided defaults to Walker annotated default", required = false)
public Integer activeRegionMaxSize = null;
@Advanced
@Argument(fullName="bandPassSigma", shortName="bandPassSigma", doc="The sigma of the band pass filter Gaussian kernel; if not provided defaults to Walker annotated default", required = false)
public Double bandPassSigma = null;
private GenomeLocSortedSet presetActiveRegions = null;
@Override
public void initialize() {
@ -91,6 +115,22 @@ public abstract class ActiveRegionWalker<MapType, ReduceType> extends Walker<Map
presetActiveRegions = IntervalUtils.sortAndMergeIntervals(this.getToolkit().getGenomeLocParser(), allIntervals, IntervalMergingRule.ALL);
}
/**
* Does this walker want us to use a set of preset action regions instead of dynamically using the result of isActive?
* @return true if yes, false if no
*/
public boolean hasPresetActiveRegions() {
return presetActiveRegions != null;
}
/**
* Get the set of preset active regions, or null if none were provided
* @return a set of genome locs specifying fixed active regions requested by the walker, or null if none exist
*/
public GenomeLocSortedSet getPresetActiveRegions() {
return presetActiveRegions;
}
// Do we actually want to operate on the context?
public boolean filter(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) {
return true; // We are keeping all the reads
@ -114,13 +154,13 @@ public abstract class ActiveRegionWalker<MapType, ReduceType> extends Walker<Map
// Determine probability of active status over the AlignmentContext
@Ensures({"result.isActiveProb >= 0.0", "result.isActiveProb <= 1.0"})
public abstract ActivityProfileResult isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context);
public abstract ActivityProfileState isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context);
// Map over the ActiveRegion
public abstract MapType map(final ActiveRegion activeRegion, final RefMetaDataTracker metaDataTracker);
public final GenomeLocSortedSet extendIntervals( final GenomeLocSortedSet intervals, final GenomeLocParser genomeLocParser, IndexedFastaSequenceFile reference ) {
final int activeRegionExtension = this.getClass().getAnnotation(ActiveRegionExtension.class).extension();
final int activeRegionExtension = this.getClass().getAnnotation(ActiveRegionTraversalParameters.class).extension();
final List<GenomeLoc> allIntervals = new ArrayList<GenomeLoc>();
for( final GenomeLoc interval : intervals.toList() ) {
final int start = Math.max( 1, interval.getStart() - activeRegionExtension );

0
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java → public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
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0
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java → public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
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0
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AverageAltAlleleLength.java → public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AverageAltAlleleLength.java
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0
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java → public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
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0
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java → public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
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0
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java → public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
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0
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java → public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java
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protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java → public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java
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protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java → public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java
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protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java → public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java
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protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java → public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java
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protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java → public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java
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protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java → public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java
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protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java → public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
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protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java → public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java
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protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java → public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java
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protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java → public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
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protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java → public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java
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protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java → public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
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protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java → public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
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protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java → public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java
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protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java → public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java
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protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java → public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
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protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java → public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java
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protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java → public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java
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protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNode.java → public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNode.java
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