From fd209dd30ca391ca8943d19563faae33103a9e33 Mon Sep 17 00:00:00 2001 From: Ami Levy Moonshine Date: Fri, 13 Jul 2012 14:23:50 -0400 Subject: [PATCH 001/176] changed license --- licensing/GATK1_LICENSE | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/licensing/GATK1_LICENSE b/licensing/GATK1_LICENSE index 648ec8fc34..080ea1e68d 100644 --- a/licensing/GATK1_LICENSE +++ b/licensing/GATK1_LICENSE @@ -1,4 +1,6 @@ -Copyright (c) 2012 The Broad Institute +Copyright (c) 2013 The Broad Institute + +Extra text Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation From f5df7beeb285758a8d299aa51bc62e2dbdcdde88 Mon Sep 17 00:00:00 2001 From: Ami Levy Moonshine Date: Fri, 13 Jul 2012 15:19:45 -0400 Subject: [PATCH 002/176] remove unnecessary use in the PRIORITY list remove unneeded imports --- .../sting/gatk/walkers/variantutils/CombineVariants.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java index 94fa291730..c7bc790a90 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java @@ -35,7 +35,6 @@ import org.broadinstitute.sting.gatk.walkers.Window; import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCounts; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.variantcontext.VariantContext; @@ -185,7 +184,8 @@ public void initialize() { logger.warn("VCF output file not an instance of VCFWriterStub; cannot enable sites only output option"); if ( PRIORITY_STRING == null ) { - PRIORITY_STRING = Utils.join(",", vcfRods.keySet()); + genotypeMergeOption = VariantContextUtils.GenotypeMergeType.UNSORTED; + //PRIORITY_STRING = Utils.join(",", vcfRods.keySet()); Deleted by Ami (7/10/12) logger.info("Priority string not provided, using arbitrary genotyping order: " + PRIORITY_STRING); } From f4ff89ada8034f52482d97cb43cb6714e0722e9c Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Tue, 24 Jul 2012 12:26:39 -0400 Subject: [PATCH 003/176] Don't use old CC and TR commands. Not fixing for now, just want to see whether I can get this to pass first. From a309784da5fb310ce0da26af733072ae4caf61f3 Mon Sep 17 00:00:00 2001 From: Joel Thibault Date: Fri, 6 Jul 2012 16:38:53 -0400 Subject: [PATCH 004/176] Test for processing many BAMs at once From ab98025bac0c94331e946d81929e234d92de7d92 Mon Sep 17 00:00:00 2001 From: Joel Thibault Date: Tue, 24 Jul 2012 10:44:25 -0400 Subject: [PATCH 005/176] Combine BAMs using PrintReads From 339cf4ba4f21c89bcf8a764889d3863deb9318e2 Mon Sep 17 00:00:00 2001 From: Joel Thibault Date: Tue, 24 Jul 2012 13:56:33 -0400 Subject: [PATCH 006/176] Ensure that PrintReads has enough RAM From ca6fad704d12831da2e9737078b611e00ea97d84 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 26 Jul 2012 01:50:39 -0400 Subject: [PATCH 007/176] Initial checkpoint commit of VariantContext/Allele refactoring. There were just too many problems associated with the different representation of alleles in VCF (padded) vs. VariantContext (unpadded). We are moving VC to use the VCF representation. No more reference base for indels in VC and no more trimming and padding of alleles. Even reverse trimming has been stopped (the theory being that writers of VCF now know what they are doing and often want the reverse padding if they put it there; this has been requested on GetSatisfaction). Code compiles but presumably pretty much all tests with indels with fail at this point. --- .../gatk/refdata/VariantContextAdaptors.java | 68 +-- .../annotator/DepthPerAlleleBySample.java | 57 +-- .../walkers/beagle/BeagleOutputToVCF.java | 2 - .../walkers/beagle/ProduceBeagleInput.java | 2 +- .../beagle/VariantsToBeagleUnphased.java | 2 +- .../genotyper/ConsensusAlleleCounter.java | 12 +- ...elGenotypeLikelihoodsCalculationModel.java | 2 +- .../genotyper/UnifiedGenotyperEngine.java | 14 +- .../walkers/indels/SomaticIndelDetector.java | 28 +- .../validationsiteselector/GenomeEvent.java | 8 +- .../KeepAFSpectrumFrequencySelector.java | 2 +- .../UniformSamplingFrequencySelector.java | 2 +- .../evaluators/ThetaVariantEvaluator.java | 2 +- .../variantutils/LeftAlignVariants.java | 2 +- .../variantutils/LiftoverVariants.java | 8 +- .../variantutils/ValidateVariants.java | 39 +- .../walkers/variantutils/VariantsToTable.java | 11 +- .../walkers/variantutils/VariantsToVCF.java | 14 +- .../broadinstitute/sting/utils/BaseUtils.java | 31 ++ .../sting/utils/codecs/bcf2/BCF2Codec.java | 23 - .../utils/codecs/vcf/AbstractVCFCodec.java | 31 +- .../utils/codecs/vcf/VCFAlleleClipper.java | 434 ------------------ .../sting/utils/variantcontext/Allele.java | 67 +-- .../utils/variantcontext/VariantContext.java | 94 +--- .../variantcontext/VariantContextBuilder.java | 26 +- .../variantcontext/VariantContextUtils.java | 94 +--- .../variantcontext/writer/BCF2Writer.java | 3 - .../variantcontext/writer/VCFWriter.java | 1 - .../utils/variantcontext/AlleleUnitTest.java | 10 +- .../VariantContextUnitTest.java | 1 - 30 files changed, 192 insertions(+), 898 deletions(-) delete mode 100644 public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFAlleleClipper.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java index fe069c2d97..dd1eea8a42 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java @@ -163,43 +163,45 @@ public static List getAlleleList(OldDbSNPFeature feature) { @Override public VariantContext convert(String name, Object input, ReferenceContext ref) { OldDbSNPFeature dbsnp = (OldDbSNPFeature)input; - if ( ! Allele.acceptableAlleleBases(dbsnp.getNCBIRefBase()) ) - return null; - Allele refAllele = Allele.create(dbsnp.getNCBIRefBase(), true); - if ( isSNP(dbsnp) || isIndel(dbsnp) || isMNP(dbsnp) || dbsnp.getVariantType().contains("mixed") ) { - // add the reference allele - List alleles = new ArrayList(); - alleles.add(refAllele); + int index = dbsnp.getStart() - ref.getWindow().getStart() - 1; + if ( index < 0 ) + return null; // we weren't given enough reference context to create the VariantContext - // add all of the alt alleles - boolean sawNullAllele = refAllele.isNull(); - for ( String alt : getAlternateAlleleList(dbsnp) ) { - if ( ! Allele.acceptableAlleleBases(alt) ) { - //System.out.printf("Excluding dbsnp record %s%n", dbsnp); - return null; - } - Allele altAllele = Allele.create(alt, false); - alleles.add(altAllele); - if ( altAllele.isNull() ) - sawNullAllele = true; - } + final byte refBaseForIndel = ref.getBases()[index]; - Map attributes = new HashMap(); + Allele refAllele; + if ( dbsnp.getNCBIRefBase().equals("-") ) + refAllele = Allele.create(refBaseForIndel); + else if ( ! Allele.acceptableAlleleBases(dbsnp.getNCBIRefBase()) ) + return null; + else + refAllele = Allele.create(refBaseForIndel + dbsnp.getNCBIRefBase(), true); - int index = dbsnp.getStart() - ref.getWindow().getStart() - 1; - if ( index < 0 ) - return null; // we weren't given enough reference context to create the VariantContext - Byte refBaseForIndel = new Byte(ref.getBases()[index]); - - final VariantContextBuilder builder = new VariantContextBuilder(); - builder.source(name).id(dbsnp.getRsID()); - builder.loc(dbsnp.getChr(), dbsnp.getStart() - (sawNullAllele ? 1 : 0), dbsnp.getEnd() - (refAllele.isNull() ? 1 : 0)); - builder.alleles(alleles); - builder.referenceBaseForIndel(refBaseForIndel); - return builder.make(); - } else + boolean addPaddingBase; + if ( isSNP(dbsnp) || isMNP(dbsnp) ) + addPaddingBase = false; + else if ( isIndel(dbsnp) || dbsnp.getVariantType().contains("mixed") ) + addPaddingBase = true; + else return null; // can't handle anything else + + final List alleles = new ArrayList(); + alleles.add(refAllele); + + // add all of the alt alleles + for ( String alt : getAlternateAlleleList(dbsnp) ) { + if ( ! Allele.acceptableAlleleBases(alt) ) { + return null; + } + alleles.add(Allele.create((addPaddingBase ? refBaseForIndel : "") + alt, false)); + } + + final VariantContextBuilder builder = new VariantContextBuilder(); + builder.source(name).id(dbsnp.getRsID()); + builder.loc(dbsnp.getChr(), dbsnp.getStart() - (addPaddingBase ? 1 : 0), dbsnp.getEnd() - (addPaddingBase && refAllele.length() == 1 ? 1 : 0)); + builder.alleles(alleles); + return builder.make(); } } @@ -351,7 +353,7 @@ public VariantContext convert(String name, Object input, ReferenceContext ref) { long end = hapmap.getEnd(); if ( deletionLength > 0 ) end += deletionLength; - VariantContext vc = new VariantContextBuilder(name, hapmap.getChr(), hapmap.getStart(), end, alleles).id(hapmap.getName()).genotypes(genotypes).referenceBaseForIndel(refBaseForIndel).make(); + VariantContext vc = new VariantContextBuilder(name, hapmap.getChr(), hapmap.getStart(), end, alleles).id(hapmap.getName()).genotypes(genotypes).make(); return vc; } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java index 523aa81b13..261f6433bf 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java @@ -42,10 +42,6 @@ */ public class DepthPerAlleleBySample extends GenotypeAnnotation implements StandardAnnotation { - private static final String REF_ALLELE = "REF"; - - private static final String DEL = "DEL"; // constant, for speed: no need to create a key string for deletion allele every time - public void annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g, GenotypeBuilder gb) { if ( g == null || !g.isCalled() ) return; @@ -53,10 +49,10 @@ public void annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, Ref if ( vc.isSNP() ) annotateSNP(stratifiedContext, vc, gb); else if ( vc.isIndel() ) - annotateIndel(stratifiedContext, vc, gb); + annotateIndel(stratifiedContext, ref.getBase(), vc, gb); } - private void annotateSNP(AlignmentContext stratifiedContext, VariantContext vc, GenotypeBuilder gb) { + private void annotateSNP(final AlignmentContext stratifiedContext, final VariantContext vc, final GenotypeBuilder gb) { HashMap alleleCounts = new HashMap(); for ( Allele allele : vc.getAlleles() ) @@ -77,62 +73,47 @@ private void annotateSNP(AlignmentContext stratifiedContext, VariantContext vc, gb.AD(counts); } - private void annotateIndel(AlignmentContext stratifiedContext, VariantContext vc, GenotypeBuilder gb) { + private void annotateIndel(final AlignmentContext stratifiedContext, final byte refBase, final VariantContext vc, final GenotypeBuilder gb) { ReadBackedPileup pileup = stratifiedContext.getBasePileup(); if ( pileup == null ) return; - final HashMap alleleCounts = new HashMap(); - alleleCounts.put(REF_ALLELE, 0); + final HashMap alleleCounts = new HashMap(); final Allele refAllele = vc.getReference(); - for ( Allele allele : vc.getAlternateAlleles() ) { - - if ( allele.isNoCall() ) { - continue; // this does not look so good, should we die??? - } - - alleleCounts.put(getAlleleRepresentation(allele), 0); + for ( final Allele allele : vc.getAlleles() ) { + alleleCounts.put(allele, 0); } for ( PileupElement p : pileup ) { if ( p.isBeforeInsertion() ) { - final String b = p.getEventBases(); - if ( alleleCounts.containsKey(b) ) { - alleleCounts.put(b, alleleCounts.get(b)+1); + final Allele insertion = Allele.create(refBase + p.getEventBases(), false); + if ( alleleCounts.containsKey(insertion) ) { + alleleCounts.put(insertion, alleleCounts.get(insertion)+1); } } else if ( p.isBeforeDeletionStart() ) { - if ( p.getEventLength() == refAllele.length() ) { - // this is indeed the deletion allele recorded in VC - final String b = DEL; - if ( alleleCounts.containsKey(b) ) { - alleleCounts.put(b, alleleCounts.get(b)+1); - } + if ( p.getEventLength() == refAllele.length() + 1 ) { + // this is indeed the deletion allele recorded in VC + final Allele deletion = Allele.create(refBase); + if ( alleleCounts.containsKey(deletion) ) { + alleleCounts.put(deletion, alleleCounts.get(deletion)+1); } + } } else if ( p.getRead().getAlignmentEnd() > vc.getStart() ) { - alleleCounts.put(REF_ALLELE, alleleCounts.get(REF_ALLELE)+1); + alleleCounts.put(refAllele, alleleCounts.get(refAllele)+1); } } - int[] counts = new int[alleleCounts.size()]; - counts[0] = alleleCounts.get(REF_ALLELE); + final int[] counts = new int[alleleCounts.size()]; + counts[0] = alleleCounts.get(refAllele); for (int i = 0; i < vc.getAlternateAlleles().size(); i++) - counts[i+1] = alleleCounts.get( getAlleleRepresentation(vc.getAlternateAllele(i)) ); + counts[i+1] = alleleCounts.get( vc.getAlternateAllele(i) ); gb.AD(counts); } - private String getAlleleRepresentation(Allele allele) { - if ( allele.isNull() ) { // deletion wrt the ref - return DEL; - } else { // insertion, pass actual bases - return allele.getBaseString(); - } - - } - // public String getIndelBases() public List getKeyNames() { return Arrays.asList(VCFConstants.GENOTYPE_ALLELE_DEPTHS); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java index 627d561f63..c8abbfa5ac 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java @@ -247,8 +247,6 @@ public Integer map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentC // Beagle always produces genotype strings based on the strings we input in the likelihood file. String refString = vc_input.getReference().getDisplayString(); - if (refString.length() == 0) // ref was null - refString = Allele.NULL_ALLELE_STRING; Allele bglAlleleA, bglAlleleB; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java index 14e92a066e..470a1d4770 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java @@ -236,7 +236,7 @@ public void writeBeagleOutput(VariantContext preferredVC, VariantContext otherVC if ( markers != null ) markers.append(marker).append("\t").append(Integer.toString(markerCounter++)).append("\t"); for ( Allele allele : preferredVC.getAlleles() ) { String bglPrintString; - if (allele.isNoCall() || allele.isNull()) + if (allele.isNoCall()) bglPrintString = "-"; else bglPrintString = allele.getBaseString(); // get rid of * in case of reference allele diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java index 6d83a1d2ac..f338f01241 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java @@ -146,7 +146,7 @@ public void writeUnphasedBeagleOutput(VariantContext vc, boolean makeMissing) { // write out the alleles at this site for ( Allele allele : vc.getAlleles() ) { - beagleOut.append(allele.isNoCall() || allele.isNull() ? "-" : allele.getBaseString()).append(" "); + beagleOut.append(allele.isNoCall() ? "-" : allele.getBaseString()).append(" "); } // write out sample level genotypes diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java index cef09a9131..d2071a9fbc 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java @@ -246,18 +246,19 @@ private List consensusCountsToAlleles(final ReferenceContext ref, // get ref bases of accurate deletion final int startIdxInReference = 1 + loc.getStart() - ref.getWindow().getStart(); stop = loc.getStart() + dLen; - final byte[] refBases = Arrays.copyOfRange(ref.getBases(), startIdxInReference, startIdxInReference + dLen); + final byte[] refBases = Arrays.copyOfRange(ref.getBases(), startIdxInReference - 1, startIdxInReference + dLen); // add reference padding if (Allele.acceptableAlleleBases(refBases, false)) { refAllele = Allele.create(refBases, true); - altAllele = Allele.create(Allele.NULL_ALLELE_STRING, false); + altAllele = Allele.create(ref.getBase(), false); } else continue; // don't go on with this allele if refBases are non-standard } else { // insertion case - if (Allele.acceptableAlleleBases(s, false)) { // don't allow N's in insertions - refAllele = Allele.create(Allele.NULL_ALLELE_STRING, true); - altAllele = Allele.create(s, false); + final String insertionBases = ref.getBase() + s; // add reference padding + if (Allele.acceptableAlleleBases(insertionBases, false)) { // don't allow N's in insertions + refAllele = Allele.create(ref.getBase(), true); + altAllele = Allele.create(insertionBases, false); stop = loc.getStart(); } else continue; // go on to next allele if consensus insertion has any non-standard base. @@ -267,7 +268,6 @@ private List consensusCountsToAlleles(final ReferenceContext ref, final VariantContextBuilder builder = new VariantContextBuilder().source(""); builder.loc(loc.getContig(), loc.getStart(), stop); builder.alleles(Arrays.asList(refAllele, altAllele)); - builder.referenceBaseForIndel(ref.getBase()); builder.noGenotypes(); if (doMultiAllelicCalls) { vcs.add(builder.make()); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java index 230d6c324f..7eabe7a183 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java @@ -123,7 +123,7 @@ public VariantContext getLikelihoods(final RefMetaDataTracker tracker, final int endLoc = computeEndLocation(alleleList, loc,allelesArePadded); final int eventLength = getEventLength(alleleList); - final VariantContextBuilder builder = new VariantContextBuilder("UG_call", loc.getContig(), loc.getStart(), endLoc, alleleList).referenceBaseForIndel(ref.getBase()); + final VariantContextBuilder builder = new VariantContextBuilder("UG_call", loc.getContig(), loc.getStart(), endLoc, alleleList); // create the genotypes; no-call everyone for now GenotypesContext genotypes = GenotypesContext.create(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index 32564984a9..d4c45e19d2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -37,7 +37,6 @@ import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.classloader.PluginManager; -import org.broadinstitute.sting.utils.codecs.vcf.VCFAlleleClipper; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; @@ -283,7 +282,7 @@ private VariantCallContext generateEmptyContext(RefMetaDataTracker tracker, Refe VariantContext vcInput = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, ref, rawContext.getLocation(), false, logger, UAC.alleles); if ( vcInput == null ) return null; - vc = new VariantContextBuilder("UG_call", ref.getLocus().getContig(), vcInput.getStart(), vcInput.getEnd(), vcInput.getAlleles()).referenceBaseForIndel(vcInput.getReferenceBaseForIndel()).make(); + vc = new VariantContextBuilder("UG_call", ref.getLocus().getContig(), vcInput.getStart(), vcInput.getEnd(), vcInput.getAlleles()).make(); } else { // deal with bad/non-standard reference bases if ( !Allele.acceptableAlleleBases(new byte[]{ref.getBase()}) ) @@ -408,11 +407,6 @@ else if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_M builder.log10PError(phredScaledConfidence/-10.0); if ( ! passesCallThreshold(phredScaledConfidence) ) builder.filters(filter); - if ( limitedContext ) { - builder.referenceBaseForIndel(vc.getReferenceBaseForIndel()); - } else { - builder.referenceBaseForIndel(refContext.getBase()); - } // create the genotypes final GenotypesContext genotypes = afcm.get().subsetAlleles(vc, myAlleles, true,ploidy); @@ -491,10 +485,8 @@ else if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_M builder.attributes(attributes); VariantContext vcCall = builder.make(); - // if we are subsetting alleles (either because there were too many or because some were not polymorphic) - // then we may need to trim the alleles (because the original VariantContext may have had to pad at the end). - if ( myAlleles.size() != vc.getAlleles().size() && !limitedContext ) // TODO - this function doesn't work with mixed records or records that started as mixed and then became non-mixed - vcCall = VCFAlleleClipper.reverseTrimAlleles(vcCall); + // TODO -- if we are subsetting alleles (either because there were too many or because some were not polymorphic) + // TODO -- then we may need to trim the alleles (because the original VariantContext may have had to pad at the end). if ( annotationEngine != null && !limitedContext ) { // Note: we want to use the *unfiltered* and *unBAQed* context for the annotations diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java index 21db1412b6..0c7e2ec5fd 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java @@ -1128,12 +1128,13 @@ public void printVCFLine(VariantContextWriter vcf, IndelPrecall call, boolean di List alleles = new ArrayList(2); // actual observed (distinct!) alleles at the site List homref_alleles = null; // when needed, will contain two identical copies of ref allele - needed to generate hom-ref genotype + final byte referencePaddingBase = refBases[(int)start-1]; if ( call.getVariant() == null ) { - // we will need to cteate genotype with two (hom) ref alleles (below). + // we will need to create genotype with two (hom) ref alleles (below). // we can not use 'alleles' list here, since that list is supposed to contain // only *distinct* alleles observed at the site or VCFContext will frown upon us... - alleles.add( Allele.create(refBases[(int)start-1],true) ); + alleles.add( Allele.create(referencePaddingBase,true) ); homref_alleles = new ArrayList(2); homref_alleles.add( alleles.get(0)); homref_alleles.add( alleles.get(0)); @@ -1142,7 +1143,7 @@ public void printVCFLine(VariantContextWriter vcf, IndelPrecall call, boolean di // (Genotype will tell us whether it is an actual call or not!) int event_length = call.getVariant().lengthOnRef(); if ( event_length < 0 ) event_length = 0; - fillAlleleList(alleles,call); + fillAlleleList(alleles,call,referencePaddingBase); stop += event_length; } @@ -1162,7 +1163,7 @@ public void printVCFLine(VariantContextWriter vcf, IndelPrecall call, boolean di filters.add("NoCall"); } VariantContext vc = new VariantContextBuilder("IGv2_Indel_call", refName, start, stop, alleles) - .genotypes(genotypes).filters(filters).referenceBaseForIndel(refBases[(int)start-1]).make(); + .genotypes(genotypes).filters(filters).make(); vcf.add(vc); } @@ -1172,16 +1173,16 @@ public void printVCFLine(VariantContextWriter vcf, IndelPrecall call, boolean di * @param l * @param call */ - private void fillAlleleList(List l, IndelPrecall call) { + private void fillAlleleList(List l, IndelPrecall call, byte referencePaddingBase) { int event_length = call.getVariant().lengthOnRef(); if ( event_length == 0 ) { // insertion - l.add( Allele.create(Allele.NULL_ALLELE_STRING,true) ); - l.add( Allele.create(call.getVariant().getBases(), false )); + l.add( Allele.create(referencePaddingBase,true) ); + l.add( Allele.create(referencePaddingBase + call.getVariant().getBases(), false )); } else { //deletion: - l.add( Allele.create(call.getVariant().getBases(), true )); - l.add( Allele.create(Allele.NULL_ALLELE_STRING,false) ); + l.add( Allele.create(referencePaddingBase + call.getVariant().getBases(), true )); + l.add( Allele.create(referencePaddingBase,false) ); } } @@ -1215,19 +1216,20 @@ public void printVCFLine(VariantContextWriter vcf, IndelPrecall nCall, IndelPrec // } boolean homRefT = ( tCall.getVariant() == null ); boolean homRefN = ( nCall.getVariant() == null ); + final byte referencePaddingBase = refBases[(int)start-1]; if ( tCall.getVariant() == null && nCall.getVariant() == null) { // no indel at all ; create base-representation ref/ref alleles for genotype construction - alleles.add( Allele.create(refBases[(int)start-1],true) ); + alleles.add( Allele.create(referencePaddingBase,true) ); } else { // we got indel(s) int event_length = 0; if ( tCall.getVariant() != null ) { // indel in tumor event_length = tCall.getVariant().lengthOnRef(); - fillAlleleList(alleles, tCall); + fillAlleleList(alleles, tCall, referencePaddingBase); } else { event_length = nCall.getVariant().lengthOnRef(); - fillAlleleList(alleles, nCall); + fillAlleleList(alleles, nCall, referencePaddingBase); } if ( event_length > 0 ) stop += event_length; } @@ -1259,7 +1261,7 @@ public void printVCFLine(VariantContextWriter vcf, IndelPrecall nCall, IndelPrec } VariantContext vc = new VariantContextBuilder("IGv2_Indel_call", refName, start, stop, alleles) - .genotypes(genotypes).filters(filters).attributes(attrs).referenceBaseForIndel(refBases[(int)start-1]).make(); + .genotypes(genotypes).filters(filters).attributes(attrs).make(); vcf.add(vc); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java index af6a520026..67ddc47ff8 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java @@ -26,7 +26,6 @@ import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.VariantContext; @@ -40,14 +39,11 @@ public class GenomeEvent implements Comparable { final protected GenomeLoc loc; /** A set of the alleles segregating in this context */ final protected List alleles; - final protected Byte refBase; // final protected HashMap attributes; - public GenomeEvent(GenomeLocParser parser, final String contig, final int start, final int stop, final List alleles, HashMap attributes, - byte base) { + public GenomeEvent(GenomeLocParser parser, final String contig, final int start, final int stop, final List alleles, HashMap attributes) { this.loc = parser.createGenomeLoc(contig, start, stop); this.alleles = alleles; - this.refBase = base; // this.attributes = attributes; } @@ -68,7 +64,7 @@ public int compareTo(final Object o) { public VariantContext createVariantContextFromEvent() { return new VariantContextBuilder("event", loc.getContig(), loc.getStart(), loc.getStop(), alleles) - .log10PError(0.0).referenceBaseForIndel(refBase).make(); + .log10PError(0.0).make(); } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java index 4b68eed2ea..7c1d63f028 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java @@ -115,7 +115,7 @@ public void logCurrentSiteData(VariantContext vc, boolean selectedInTargetSample // create bare-bones event and log in corresponding bin // attributes contains AC,AF,AN pulled from original vc, and we keep them here and log in output file for bookkeeping purposes - GenomeEvent event = new GenomeEvent(parser, vc.getChr(), vc.getStart(), vc.getEnd(),vc.getAlleles(), attributes, vc.getReferenceBaseForIndel()); + GenomeEvent event = new GenomeEvent(parser, vc.getChr(), vc.getStart(), vc.getEnd(),vc.getAlleles(), attributes); binnedEventArray[binIndex].add(event); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java index eda75d6475..4019c56312 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java @@ -65,7 +65,7 @@ public void logCurrentSiteData(VariantContext vc, boolean selectedInTargetSample } // create bare-bones event and log in corresponding bin // attributes contains AC,AF,AN pulled from original vc, and we keep them here and log in output file for bookkeeping purposes - GenomeEvent event = new GenomeEvent(parser, vc.getChr(), vc.getStart(), vc.getEnd(),vc.getAlleles(), attributes, vc.getReferenceBaseForIndel()); + GenomeEvent event = new GenomeEvent(parser, vc.getChr(), vc.getStart(), vc.getEnd(),vc.getAlleles(), attributes); binnedEventArray.add(event); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java index 88bf3aef99..a509294ffd 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java @@ -56,7 +56,7 @@ public void update1(VariantContext vc, RefMetaDataTracker tracker, ReferenceCont //increment stats for pairwise mismatches for (Allele allele : genotype.getAlleles()) { - if (allele.isNonNull() && allele.isCalled()) { + if (allele.isCalled()) { String alleleString = allele.toString(); alleleCounts.putIfAbsent(alleleString, 0); alleleCounts.put(alleleString, alleleCounts.get(alleleString) + 1); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java index c1755aa005..3f19e22d98 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java @@ -226,6 +226,6 @@ public static VariantContext updateAllele(VariantContext vc, Allele newAllele, B newGenotypes.add(new GenotypeBuilder(genotype).alleles(newAlleles).make()); } - return new VariantContextBuilder(vc).alleles(alleleMap.values()).genotypes(newGenotypes).referenceBaseForIndel(refBaseForIndel).make(); + return new VariantContextBuilder(vc).alleles(alleleMap.values()).genotypes(newGenotypes).make(); } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java index 60d41abd59..094897edc8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java @@ -116,7 +116,6 @@ private void convertAndWrite(VariantContext vc, ReferenceContext ref) { if ( toInterval != null ) { // check whether the strand flips, and if so reverse complement everything - // TODO -- make this work for indels (difficult because the 'previous base' context needed will be changing based on indel type/size) if ( fromInterval.isPositiveStrand() != toInterval.isPositiveStrand() && vc.isPointEvent() ) { vc = VariantContextUtils.reverseComplement(vc); } @@ -129,11 +128,10 @@ private void convertAndWrite(VariantContext vc, ReferenceContext ref) { .attribute("OriginalStart", fromInterval.getStart()).make(); } - VariantContext newVC = VCFAlleleClipper.createVariantContextWithPaddedAlleles(vc); - if ( originalVC.isSNP() && originalVC.isBiallelic() && VariantContextUtils.getSNPSubstitutionType(originalVC) != VariantContextUtils.getSNPSubstitutionType(newVC) ) { + if ( originalVC.isSNP() && originalVC.isBiallelic() && VariantContextUtils.getSNPSubstitutionType(originalVC) != VariantContextUtils.getSNPSubstitutionType(vc) ) { logger.warn(String.format("VCF at %s / %d => %s / %d is switching substitution type %s/%s to %s/%s", - originalVC.getChr(), originalVC.getStart(), newVC.getChr(), newVC.getStart(), - originalVC.getReference(), originalVC.getAlternateAllele(0), newVC.getReference(), newVC.getAlternateAllele(0))); + originalVC.getChr(), originalVC.getStart(), vc.getChr(), vc.getStart(), + originalVC.getReference(), originalVC.getAlternateAllele(0), vc.getReference(), vc.getAlternateAllele(0))); } writer.add(vc); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java index 530258fe07..995e98931c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java @@ -127,35 +127,16 @@ private void validate(VariantContext vc, RefMetaDataTracker tracker, ReferenceCo return; // get the true reference allele - Allele reportedRefAllele = vc.getReference(); - Allele observedRefAllele = null; - // insertions - if ( vc.isSimpleInsertion() ) { - observedRefAllele = Allele.create(Allele.NULL_ALLELE_STRING); + final Allele reportedRefAllele = vc.getReference(); + final int refLength = reportedRefAllele.length(); + if ( refLength > 100 ) { + logger.info(String.format("Reference allele is too long (%d) at position %s:%d; skipping that record.", refLength, vc.getChr(), vc.getStart())); + return; } - // deletions - else if ( vc.isSimpleDeletion() || vc.isMNP() ) { - // we can't validate arbitrarily long deletions - if ( reportedRefAllele.length() > 100 ) { - logger.info(String.format("Reference allele is too long (%d) at position %s:%d; skipping that record.", reportedRefAllele.length(), vc.getChr(), vc.getStart())); - return; - } - // deletions are associated with the (position of) the last (preceding) non-deleted base; - // hence to get actually deleted bases we need offset = 1 - int offset = vc.isMNP() ? 0 : 1; - byte[] refBytes = ref.getBases(); - byte[] trueRef = new byte[reportedRefAllele.length()]; - for (int i = 0; i < reportedRefAllele.length(); i++) - trueRef[i] = refBytes[i+offset]; - observedRefAllele = Allele.create(trueRef, true); - } - // SNPs, etc. but not mixed types because they are too difficult - else if ( !vc.isMixed() ) { - byte[] refByte = new byte[1]; - refByte[0] = ref.getBase(); - observedRefAllele = Allele.create(refByte, true); - } + final byte[] observedRefBases = new byte[refLength]; + System.arraycopy(ref.getBases(), 0, observedRefBases, 0, refLength); + final Allele observedRefAllele = Allele.create(observedRefBases); // get the RS IDs Set rsIDs = null; @@ -168,10 +149,10 @@ else if ( !vc.isMixed() ) { try { switch( type ) { case ALL: - vc.extraStrictValidation(observedRefAllele, ref.getBase(), rsIDs); + vc.extraStrictValidation(reportedRefAllele, observedRefAllele, rsIDs); break; case REF: - vc.validateReferenceBases(observedRefAllele, ref.getBase()); + vc.validateReferenceBases(reportedRefAllele, observedRefAllele); break; case IDS: vc.validateRSIDs(rsIDs); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java index 996ac75e70..4806b2ebc2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java @@ -378,7 +378,7 @@ public static abstract class Getter { public abstract String get(VariantContext getters.put("REF", new Getter() { public String get(VariantContext vc) { StringBuilder x = new StringBuilder(); - x.append(vc.getAlleleStringWithRefPadding(vc.getReference())); + x.append(vc.getReference()); return x.toString(); } }); @@ -390,7 +390,7 @@ public String get(VariantContext vc) { for ( int i = 0; i < n; i++ ) { if ( i != 0 ) x.append(","); - x.append(vc.getAlleleStringWithRefPadding(vc.getAlternateAllele(i))); + x.append(vc.getAlternateAllele(i)); } return x.toString(); } @@ -432,11 +432,8 @@ public String get(VariantContext vc) { private static Object splitAltAlleles(VariantContext vc) { final int numAltAlleles = vc.getAlternateAlleles().size(); if ( numAltAlleles == 1 ) - return vc.getAlleleStringWithRefPadding(vc.getAlternateAllele(0)); + return vc.getAlternateAllele(0); - final List alleles = new ArrayList(numAltAlleles); - for ( Allele allele : vc.getAlternateAlleles() ) - alleles.add(vc.getAlleleStringWithRefPadding(allele)); - return alleles; + return vc.getAlternateAlleles(); } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java index e8c6794f24..cf568a62e9 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java @@ -100,12 +100,6 @@ public class VariantsToVCF extends RodWalker { @Argument(fullName="sample", shortName="sample", doc="The sample name represented by the variant rod", required=false) protected String sampleName = null; - /** - * This argument is useful for fixing input VCFs with bad reference bases (the output will be a fixed version of the VCF). - */ - @Argument(fullName="fixRef", shortName="fixRef", doc="Fix common reference base in case there's an indel without padding", required=false) - protected boolean fixReferenceBase = false; - private Set allowedGenotypeFormatStrings = new HashSet(); private boolean wroteHeader = false; private Set samples; @@ -137,10 +131,6 @@ public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentCo builder.genotypes(g); } - if ( fixReferenceBase ) { - builder.referenceBaseForIndel(ref.getBase()); - } - writeRecord(builder.make(), tracker, ref.getLocus()); } @@ -166,8 +156,8 @@ private Collection getVariantContexts(RefMetaDataTracker tracker continue; Map alleleMap = new HashMap(2); - alleleMap.put(RawHapMapFeature.DELETION, Allele.create(Allele.NULL_ALLELE_STRING, dbsnpVC.isSimpleInsertion())); - alleleMap.put(RawHapMapFeature.INSERTION, Allele.create(((RawHapMapFeature)record).getAlleles()[1], !dbsnpVC.isSimpleInsertion())); + alleleMap.put(RawHapMapFeature.DELETION, Allele.create(ref.getBase(), dbsnpVC.isSimpleInsertion())); + alleleMap.put(RawHapMapFeature.INSERTION, Allele.create(ref.getBase() + ((RawHapMapFeature)record).getAlleles()[1], !dbsnpVC.isSimpleInsertion())); hapmap.setActualAlleles(alleleMap); // also, use the correct positioning for insertions diff --git a/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java b/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java index 393dd57358..0065f9258b 100644 --- a/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java @@ -431,6 +431,37 @@ static public String simpleComplement(String bases) { return new String(simpleComplement(bases.getBytes())); } + /** + * Returns the uppercased version of the bases + * + * @param bases the bases + * @return the upper cased version + */ + static public byte[] convertToUpperCase(final byte[] bases) { + for ( int i = 0; i < bases.length; i++ ) { + if ( (char)bases[i] >= 'a' ) + bases[i] = toUpperCaseBase(bases[i]); + } + return bases; + } + + static public byte toUpperCaseBase(final byte base) { + switch (base) { + case 'a': + return 'A'; + case 'c': + return 'C'; + case 'g': + return 'G'; + case 't': + return 'T'; + case 'n': + return 'N'; + default: + return base; + } + } + /** * Returns the index of the most common base in the basecounts array. To be used with * pileup.getBaseCounts. diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java index 0b96546105..0f9cc34e76 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java @@ -305,27 +305,6 @@ private void decodeID( final VariantContextBuilder builder ) { builder.id(id); } - /** - * Annoying routine that deals with allele clipping from the BCF2 encoding to the standard - * GATK encoding. - * - * @param position - * @param ref - * @param unclippedAlleles - * @return - */ - @Requires({"position > 0", "ref != null && ref.length() > 0", "! unclippedAlleles.isEmpty()"}) - @Ensures("result.size() == unclippedAlleles.size()") - protected List clipAllelesIfNecessary(final int position, - final String ref, - final List unclippedAlleles) { - // the last argument of 1 allows us to safely ignore the end, because we are - // ultimately going to use the end in the record itself - final VCFAlleleClipper.ClippedAlleles clipped = VCFAlleleClipper.clipAlleles(position, ref, unclippedAlleles, 1); - if ( clipped.getError() != null ) error(clipped.getError()); - return clipped.getClippedAlleles(); - } - /** * Decode the alleles from this BCF2 file and put the results in builder * @param builder @@ -353,11 +332,9 @@ private List decodeAlleles( final VariantContextBuilder builder, final i } assert ref != null; - alleles = clipAllelesIfNecessary(pos, ref, alleles); builder.alleles(alleles); assert ref.length() > 0; - builder.referenceBaseForIndel(ref.getBytes()[0]); return alleles; } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java index b3420514bf..2b5695e3a6 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java @@ -248,6 +248,7 @@ else if ( parts[2].equals(VCFConstants.EMPTY_ID_FIELD) ) builder.id(parts[2]); final String ref = getCachedString(parts[3].toUpperCase()); + builder.stop(pos + ref.length() - 1); final String alts = getCachedString(parts[4].toUpperCase()); builder.log10PError(parseQual(parts[5])); @@ -257,8 +258,8 @@ else if ( parts[2].equals(VCFConstants.EMPTY_ID_FIELD) ) builder.attributes(attrs); // get our alleles, filters, and setup an attribute map - final List rawAlleles = parseAlleles(ref, alts, lineNo); - final List alleles = updateBuilderAllelesAndStop(builder, ref, pos, rawAlleles, attrs); + final List alleles = parseAlleles(ref, alts, lineNo); + builder.alleles(alleles); // do we have genotyping data if (parts.length > NUM_STANDARD_FIELDS && includeGenotypes) { @@ -275,7 +276,6 @@ else if ( parts[2].equals(VCFConstants.EMPTY_ID_FIELD) ) VariantContext vc = null; try { - builder.referenceBaseForIndel(ref.getBytes()[0]); vc = builder.make(); } catch (Exception e) { generateException(e.getMessage()); @@ -284,31 +284,6 @@ else if ( parts[2].equals(VCFConstants.EMPTY_ID_FIELD) ) return vc; } - private final List updateBuilderAllelesAndStop(final VariantContextBuilder builder, - final String ref, - final int pos, - final List rawAlleles, - final Map attrs) { - int endForSymbolicAlleles = pos; // by default we use the pos - if ( attrs.containsKey(VCFConstants.END_KEY) ) { - // update stop with the end key if provided - try { - endForSymbolicAlleles = Integer.valueOf(attrs.get(VCFConstants.END_KEY).toString()); - } catch (Exception e) { - generateException("the END value in the INFO field is not valid"); - } - } - - // find out our current location, and clip the alleles down to their minimum length - final VCFAlleleClipper.ClippedAlleles clipped = VCFAlleleClipper.clipAlleles(pos, ref, rawAlleles, endForSymbolicAlleles); - if ( clipped.getError() != null ) - generateException(clipped.getError(), lineNo); - - builder.stop(clipped.getStop()); - builder.alleles(clipped.getClippedAlleles()); - return clipped.getClippedAlleles(); - } - /** * get the name of this codec * @return our set name diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFAlleleClipper.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFAlleleClipper.java deleted file mode 100644 index 40ba23d9d5..0000000000 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFAlleleClipper.java +++ /dev/null @@ -1,434 +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.utils.codecs.vcf; - -import com.google.java.contract.Ensures; -import com.google.java.contract.Invariant; -import com.google.java.contract.Requires; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.variantcontext.*; - -import java.util.*; - -/** - * All of the gross allele clipping and padding routines in one place - * - * Having attempted to understand / fix / document this code myself - * I can only conclude that this entire approach needs to be rethought. This - * code just doesn't work robustly with symbolic alleles, with multiple alleles, - * requires a special "reference base for indels" stored in the VariantContext - * whose correctness isn't enforced, and overall has strange special cases - * all over the place. - * - * The reason this code is so complex is due to symbolics and multi-alleleic - * variation, which frequently occur when combining variants from multiple - * VCF files. - * - * TODO rethink this class, make it clean, and make it easy to create, mix, and write out alleles - * TODO this code doesn't work with reverse clipped alleles (ATA / GTTA -> AT / GT) - * - * @author Mark DePristo - * @since 6/12 - */ -public final class VCFAlleleClipper { - private VCFAlleleClipper() { } - - /** - * Determine whether we should clip off the first base of all unclippped alleles or not - * - * Returns true if all of the alleles in unclippedAlleles share a common first base with - * ref0. Ref0 should be the first base of the reference allele UnclippedAlleles may - * contain the reference allele itself, or just the alternate alleles, it doesn't matter. - * - * The algorithm returns true if the first base should be clipped off, or false otherwise - * - * This algorithm works even in the presence of symbolic alleles, logically ignoring these - * values. It - * - * @param unclippedAlleles list of unclipped alleles to assay - * @param ref0 the first base of the reference allele - * @return true if we should clip the first base of unclippedAlleles - */ - @Requires("unclippedAlleles != null") - public static boolean shouldClipFirstBaseP(final List unclippedAlleles, - final byte ref0) { - boolean allSymbolicAlt = true; - - for ( final Allele a : unclippedAlleles ) { - if ( a.isSymbolic() ) { - continue; - } - - // already know we aren't symbolic, so we only need to decide if we have only seen a ref - if ( ! a.isReference() ) - allSymbolicAlt = false; - - if ( a.length() < 1 || (a.getBases()[0] != ref0) ) { - return false; - } - } - - // to reach here all alleles are consistent with clipping the first base matching ref0 - // but we don't clip if all ALT alleles are symbolic - return ! allSymbolicAlt; - } - - public static int computeReverseClipping(final List unclippedAlleles, - final byte[] ref, - final int forwardClipping, - final boolean allowFullClip) { - int clipping = 0; - boolean stillClipping = true; - - while ( stillClipping ) { - for ( final Allele a : unclippedAlleles ) { - if ( a.isSymbolic() ) - continue; - - // we need to ensure that we don't reverse clip out all of the bases from an allele because we then will have the wrong - // position set for the VariantContext (although it's okay to forward clip it all out, because the position will be fine). - if ( a.length() - clipping == 0 ) - return clipping - (allowFullClip ? 0 : 1); - - if ( a.length() - clipping <= forwardClipping || a.length() - forwardClipping == 0 ) { - stillClipping = false; - } - else if ( ref.length == clipping ) { - if ( allowFullClip ) - stillClipping = false; - else - return -1; - } - else if ( a.getBases()[a.length()-clipping-1] != ref[ref.length-clipping-1] ) { - stillClipping = false; - } - } - if ( stillClipping ) - clipping++; - } - - return clipping; - } - - /** - * Are the alleles describing a polymorphism substitution one base for another? - * - * @param alleles a list of alleles, must not be empty - * @return Return true if the length of any allele in alleles isn't 1 - */ - @Requires("!alleles.isEmpty()") - private static boolean isSingleNucleotideEvent(final List alleles) { - for ( final Allele a : alleles ) { - if ( a.length() != 1 ) - return false; - } - return true; - } - - /** - * clip the alleles, based on the reference, returning a ClippedAlleles object describing what happened - * - * The ClippedAlleles object contains the implied stop position of the alleles, given the provided start - * position, after clipping. It also contains the list of alleles, in the same order as the provided - * unclipped ones, that are the fully clipped version of the input alleles. If an error occurs - * during this option the getError() function returns a string describing the problem (for use in parsers). - * - * The basic operation are: - * - * single allele - * => stop == start and clipped == unclipped - * any number of single nucleotide events - * => stop == start and clipped == unclipped - * two alleles, second being symbolic - * => stop == start and clipped == unclipped - * Note in this case that the STOP should be computed by other means (from END in VCF, for example) - * Note that if there's more than two alleles and the second is a symbolic the code produces an error - * Any other case: - * The alleles are trimmed of any sequence shared at the end of the alleles. If N bases - * are common then the alleles will all be at least N bases shorter. - * The stop position returned is the start position + the length of the - * reverse trimmed only reference allele - 1. - * If the alleles all share a single common starting sequence (just one base is considered) - * then the alleles have this leading common base removed as well. - * - * TODO This code is gross and brittle and needs to be rethought from scratch - * - * @param start the unadjusted start position (pre-clipping) - * @param ref the reference string - * @param unclippedAlleles the list of unclipped alleles, including the reference allele - * @return the new reference end position of this event - */ - @Requires({"start > 0", "ref != null && ref.length() > 0", "!unclippedAlleles.isEmpty()"}) - @Ensures("result != null") - public static ClippedAlleles clipAlleles(final int start, - final String ref, - final List unclippedAlleles, - final int endForSymbolicAllele ) { - // no variation or single nucleotide events are by definition fully clipped - if ( unclippedAlleles.size() == 1 || isSingleNucleotideEvent(unclippedAlleles) ) - return new ClippedAlleles(start, unclippedAlleles, null); - - // we've got to sort out the clipping by looking at the alleles themselves - final byte firstRefBase = (byte) ref.charAt(0); - final boolean firstBaseIsClipped = shouldClipFirstBaseP(unclippedAlleles, firstRefBase); - final int forwardClipping = firstBaseIsClipped ? 1 : 0; - final int reverseClipping = computeReverseClipping(unclippedAlleles, ref.getBytes(), forwardClipping, false); - final boolean needsClipping = forwardClipping > 0 || reverseClipping > 0; - - if ( reverseClipping == -1 ) - return new ClippedAlleles("computeReverseClipping failed due to bad alleles"); - - boolean sawSymbolic = false; - List clippedAlleles; - if ( ! needsClipping ) { - // there's nothing to clip, so clippedAlleles are the original alleles - clippedAlleles = unclippedAlleles; - } else { - clippedAlleles = new ArrayList(unclippedAlleles.size()); - for ( final Allele a : unclippedAlleles ) { - if ( a.isSymbolic() ) { - sawSymbolic = true; - clippedAlleles.add(a); - } else { - final byte[] allele = Arrays.copyOfRange(a.getBases(), forwardClipping, a.getBases().length - reverseClipping); - if ( !Allele.acceptableAlleleBases(allele) ) - return new ClippedAlleles("Unparsable vcf record with bad allele [" + allele + "]"); - clippedAlleles.add(Allele.create(allele, a.isReference())); - } - } - } - - int stop = VariantContextUtils.computeEndFromAlleles(clippedAlleles, start, endForSymbolicAllele); - - // TODO - // TODO - // TODO COMPLETELY BROKEN CODE -- THE GATK CURRENTLY ENCODES THE STOP POSITION FOR CLIPPED ALLELES AS + 1 - // TODO ITS TRUE SIZE TO DIFFERENTIATE CLIPPED VS. UNCLIPPED ALLELES. NEEDS TO BE FIXED - // TODO - // TODO - if ( needsClipping && ! sawSymbolic && ! clippedAlleles.get(0).isNull() ) stop++; - // TODO - // TODO - // TODO COMPLETELY BROKEN CODE -- THE GATK CURRENTLY ENCODES THE STOP POSITION FOR CLIPPED ALLELES AS + 1 - // TODO ITS TRUE SIZE TO DIFFERENTIATE CLIPPED VS. UNCLIPPED ALLELES. NEEDS TO BE FIXED - // TODO - // TODO - - final Byte refBaseForIndel = firstBaseIsClipped ? firstRefBase : null; - return new ClippedAlleles(stop, clippedAlleles, refBaseForIndel); - } - - /** - * Returns true if the alleles in inputVC should have reference bases added for padding - * - * We need to pad a VC with a common base if the length of the reference allele is - * less than the length of the VariantContext. This happens because the position of - * e.g. an indel is always one before the actual event (as per VCF convention). - * - * @param inputVC the VC to evaluate, cannot be null - * @return true if - */ - public static boolean needsPadding(final VariantContext inputVC) { - // biallelic sites with only symbolic never need padding - if ( inputVC.isBiallelic() && inputVC.getAlternateAllele(0).isSymbolic() ) - return false; - - final int recordLength = inputVC.getEnd() - inputVC.getStart() + 1; - final int referenceLength = inputVC.getReference().length(); - - if ( referenceLength == recordLength ) - return false; - else if ( referenceLength == recordLength - 1 ) - return true; - else if ( !inputVC.hasSymbolicAlleles() ) - throw new IllegalArgumentException("Badly formed variant context at location " + String.valueOf(inputVC.getStart()) + - " in contig " + inputVC.getChr() + ". Reference length must be at most one base shorter than location size"); - else if ( inputVC.isMixed() && inputVC.hasSymbolicAlleles() ) - throw new IllegalArgumentException("GATK infrastructure limitation prevents needsPadding from working properly with VariantContexts containing a mixture of symbolic and concrete alleles at " + inputVC); - return false; - } - - public static Allele padAllele(final VariantContext vc, final Allele allele) { - assert needsPadding(vc); - - if ( allele.isSymbolic() ) - return allele; - else { - // get bases for current allele and create a new one with trimmed bases - final StringBuilder sb = new StringBuilder(); - sb.append((char)vc.getReferenceBaseForIndel().byteValue()); - sb.append(allele.getDisplayString()); - final String newBases = sb.toString(); - return Allele.create(newBases, allele.isReference()); - } - } - - public static VariantContext createVariantContextWithPaddedAlleles(VariantContext inputVC) { - final boolean padVC = needsPadding(inputVC); - - // nothing to do if we don't need to pad bases - if ( padVC ) { - if ( !inputVC.hasReferenceBaseForIndel() ) - throw new ReviewedStingException("Badly formed variant context at location " + inputVC.getChr() + ":" + inputVC.getStart() + "; no padded reference base is available."); - - final ArrayList alleles = new ArrayList(inputVC.getNAlleles()); - final Map unpaddedToPadded = inputVC.hasGenotypes() ? new HashMap(inputVC.getNAlleles()) : null; - - boolean paddedAtLeastOne = false; - for (final Allele a : inputVC.getAlleles()) { - final Allele padded = padAllele(inputVC, a); - paddedAtLeastOne = paddedAtLeastOne || padded != a; - alleles.add(padded); - if ( unpaddedToPadded != null ) unpaddedToPadded.put(a, padded); // conditional to avoid making unnecessary make - } - - if ( ! paddedAtLeastOne ) - throw new ReviewedStingException("VC was supposed to need padding but no allele was actually changed at location " + inputVC.getChr() + ":" + inputVC.getStart() + " with allele " + inputVC.getAlleles()); - - final VariantContextBuilder vcb = new VariantContextBuilder(inputVC); - vcb.alleles(alleles); - - // the position of the inputVC is one further, if it doesn't contain symbolic alleles - vcb.computeEndFromAlleles(alleles, inputVC.getStart(), inputVC.getEnd()); - - if ( inputVC.hasGenotypes() ) { - assert unpaddedToPadded != null; - - // now we can recreate new genotypes with trimmed alleles - final GenotypesContext genotypes = GenotypesContext.create(inputVC.getNSamples()); - for (final Genotype g : inputVC.getGenotypes() ) { - final List newGenotypeAlleles = new ArrayList(g.getAlleles().size()); - for (final Allele a : g.getAlleles()) { - newGenotypeAlleles.add( a.isCalled() ? unpaddedToPadded.get(a) : Allele.NO_CALL); - } - genotypes.add(new GenotypeBuilder(g).alleles(newGenotypeAlleles).make()); - } - vcb.genotypes(genotypes); - } - - return vcb.make(); - } - else - return inputVC; - - } - - public static VariantContext reverseTrimAlleles( final VariantContext inputVC ) { - // see if we need to trim common reference base from all alleles - - final int trimExtent = computeReverseClipping(inputVC.getAlleles(), inputVC.getReference().getDisplayString().getBytes(), 0, true); - if ( trimExtent <= 0 || inputVC.getAlleles().size() <= 1 ) - return inputVC; - - final List alleles = new ArrayList(); - final GenotypesContext genotypes = GenotypesContext.create(); - final Map originalToTrimmedAlleleMap = new HashMap(); - - for (final Allele a : inputVC.getAlleles()) { - if (a.isSymbolic()) { - alleles.add(a); - originalToTrimmedAlleleMap.put(a, a); - } else { - // get bases for current allele and create a new one with trimmed bases - final byte[] newBases = Arrays.copyOfRange(a.getBases(), 0, a.length()-trimExtent); - final Allele trimmedAllele = Allele.create(newBases, a.isReference()); - alleles.add(trimmedAllele); - originalToTrimmedAlleleMap.put(a, trimmedAllele); - } - } - - // now we can recreate new genotypes with trimmed alleles - for ( final Genotype genotype : inputVC.getGenotypes() ) { - final List originalAlleles = genotype.getAlleles(); - final List trimmedAlleles = new ArrayList(); - for ( final Allele a : originalAlleles ) { - if ( a.isCalled() ) - trimmedAlleles.add(originalToTrimmedAlleleMap.get(a)); - else - trimmedAlleles.add(Allele.NO_CALL); - } - genotypes.add(new GenotypeBuilder(genotype).alleles(trimmedAlleles).make()); - } - - return new VariantContextBuilder(inputVC).stop(inputVC.getStart() + alleles.get(0).length() + (inputVC.isMixed() ? -1 : 0)).alleles(alleles).genotypes(genotypes).make(); - } - - @Invariant("stop != -1 || error != null") // we're either an error or a meaningful result but not both - public static class ClippedAlleles { - private final int stop; - private final List clippedAlleles; - private final Byte refBaseForIndel; - private final String error; - - @Requires({"stop > 0", "clippedAlleles != null"}) - private ClippedAlleles(final int stop, final List clippedAlleles, final Byte refBaseForIndel) { - this.stop = stop; - this.clippedAlleles = clippedAlleles; - this.error = null; - this.refBaseForIndel = refBaseForIndel; - } - - @Requires("error != null") - private ClippedAlleles(final String error) { - this.stop = -1; - this.clippedAlleles = null; - this.refBaseForIndel = null; - this.error = error; - } - - /** - * Get an error if it occurred - * @return the error message, or null if no error occurred - */ - public String getError() { - return error; - } - - /** - * Get the stop position to use after the clipping as been applied, given the - * provided position to clipAlleles - * @return - */ - public int getStop() { - return stop; - } - - /** - * Get the clipped alleles themselves - * @return the clipped alleles in the order of the input unclipped alleles - */ - public List getClippedAlleles() { - return clippedAlleles; - } - - /** - * Returns the reference base we should use for indels, or null if none is appropriate - * @return - */ - public Byte getRefBaseForIndel() { - return refBaseForIndel; - } - } -} diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java index 2e1770581b..1947ef01e3 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java @@ -1,9 +1,9 @@ package org.broadinstitute.sting.utils.variantcontext; -import java.util.ArrayList; +import org.broadinstitute.sting.utils.BaseUtils; + import java.util.Arrays; import java.util.Collection; -import java.util.List; /** * Immutable representation of an allele @@ -77,22 +77,19 @@ public class Allele implements Comparable { private static final byte[] EMPTY_ALLELE_BASES = new byte[0]; private boolean isRef = false; - private boolean isNull = false; private boolean isNoCall = false; private boolean isSymbolic = false; private byte[] bases = null; - public final static String NULL_ALLELE_STRING = "-"; public final static String NO_CALL_STRING = "."; /** A generic static NO_CALL allele for use */ // no public way to create an allele private Allele(byte[] bases, boolean isRef) { - // standardize our representation of null allele and bases + // null alleles are no longer allowed if ( wouldBeNullAllele(bases) ) { - bases = EMPTY_ALLELE_BASES; - isNull = true; + throw new IllegalArgumentException("Null alleles are not supported"); } else if ( wouldBeNoCallAllele(bases) ) { bases = EMPTY_ALLELE_BASES; isNoCall = true; @@ -101,8 +98,8 @@ private Allele(byte[] bases, boolean isRef) { isSymbolic = true; if ( isRef ) throw new IllegalArgumentException("Cannot tag a symbolic allele as the reference allele"); } -// else -// bases = new String(bases).toUpperCase().getBytes(); // todo -- slow performance + else + bases = BaseUtils.convertToUpperCase(bases); this.isRef = isRef; this.bases = bases; @@ -126,8 +123,6 @@ private Allele(String bases, boolean isRef) { private final static Allele ALT_T = new Allele("T", false); private final static Allele REF_N = new Allele("N", true); private final static Allele ALT_N = new Allele("N", false); - private final static Allele REF_NULL = new Allele(NULL_ALLELE_STRING, true); - private final static Allele ALT_NULL = new Allele(NULL_ALLELE_STRING, false); public final static Allele NO_CALL = new Allele(NO_CALL_STRING, false); // --------------------------------------------------------------------------------------------------------- @@ -154,7 +149,6 @@ public static Allele create(byte[] bases, boolean isRef) { case '.': if ( isRef ) throw new IllegalArgumentException("Cannot tag a NoCall allele as the reference allele"); return NO_CALL; - case '-': return isRef ? REF_NULL : ALT_NULL; case 'A': case 'a' : return isRef ? REF_A : ALT_A; case 'C': case 'c' : return isRef ? REF_C : ALT_C; case 'G': case 'g' : return isRef ? REF_G : ALT_G; @@ -179,7 +173,7 @@ public static Allele create(byte base) { public static Allele extend(Allele left, byte[] right) { if (left.isSymbolic()) throw new IllegalArgumentException("Cannot extend a symbolic allele"); - byte[] bases = null; + byte[] bases; if ( left.length() == 0 ) bases = right; else { @@ -242,7 +236,10 @@ public static boolean acceptableAlleleBases(byte[] bases) { } public static boolean acceptableAlleleBases(byte[] bases, boolean allowNsAsAcceptable) { - if ( wouldBeNullAllele(bases) || wouldBeNoCallAllele(bases) || wouldBeSymbolicAllele(bases) ) + if ( wouldBeNullAllele(bases) ) + return false; + + if ( wouldBeNoCallAllele(bases) || wouldBeSymbolicAllele(bases) ) return true; for (byte base : bases ) { @@ -299,11 +296,6 @@ public static Allele create(byte[] bases) { // // --------------------------------------------------------------------------------------------------------- - //Returns true if this is the null allele - public boolean isNull() { return isNull; } - // Returns true if this is not the null allele - public boolean isNonNull() { return ! isNull(); } - // Returns true if this is the NO_CALL allele public boolean isNoCall() { return isNoCall; } // Returns true if this is not the NO_CALL allele @@ -319,7 +311,7 @@ public static Allele create(byte[] bases) { // Returns a nice string representation of this object public String toString() { - return (isNull() ? NULL_ALLELE_STRING : ( isNoCall() ? NO_CALL_STRING : getDisplayString() )) + (isReference() ? "*" : ""); + return ( isNoCall() ? NO_CALL_STRING : getDisplayString() ) + (isReference() ? "*" : ""); } /** @@ -384,27 +376,27 @@ public int hashCode() { * @return true if this and other are equal */ public boolean equals(Allele other, boolean ignoreRefState) { - return this == other || (isRef == other.isRef || ignoreRefState) && isNull == other.isNull && isNoCall == other.isNoCall && (bases == other.bases || Arrays.equals(bases, other.bases)); + return this == other || (isRef == other.isRef || ignoreRefState) && isNoCall == other.isNoCall && (bases == other.bases || Arrays.equals(bases, other.bases)); } /** * @param test bases to test against * - * @return true if this Alelle contains the same bases as test, regardless of its reference status; handles Null and NO_CALL alleles + * @return true if this Allele contains the same bases as test, regardless of its reference status; handles Null and NO_CALL alleles */ public boolean basesMatch(byte[] test) { return !isSymbolic && (bases == test || Arrays.equals(bases, test)); } /** * @param test bases to test against * - * @return true if this Alelle contains the same bases as test, regardless of its reference status; handles Null and NO_CALL alleles + * @return true if this Allele contains the same bases as test, regardless of its reference status; handles Null and NO_CALL alleles */ public boolean basesMatch(String test) { return basesMatch(test.toUpperCase().getBytes()); } /** * @param test allele to test against * - * @return true if this Alelle contains the same bases as test, regardless of its reference status; handles Null and NO_CALL alleles + * @return true if this Allele contains the same bases as test, regardless of its reference status; handles Null and NO_CALL alleles */ public boolean basesMatch(Allele test) { return basesMatch(test.getBases()); } @@ -421,10 +413,6 @@ public int length() { // // --------------------------------------------------------------------------------------------------------- - public static Allele getMatchingAllele(Collection allAlleles, String alleleBases) { - return getMatchingAllele(allAlleles, alleleBases.getBytes()); - } - public static Allele getMatchingAllele(Collection allAlleles, byte[] alleleBases) { for ( Allele a : allAlleles ) { if ( a.basesMatch(alleleBases) ) { @@ -438,26 +426,6 @@ public static Allele getMatchingAllele(Collection allAlleles, byte[] all return null; // couldn't find anything } - public static List resolveAlleles(List possibleAlleles, List alleleStrings) { - List myAlleles = new ArrayList(alleleStrings.size()); - - for ( String alleleString : alleleStrings ) { - Allele allele = getMatchingAllele(possibleAlleles, alleleString); - - if ( allele == null ) { - if ( Allele.wouldBeNoCallAllele(alleleString.getBytes()) ) { - allele = create(alleleString); - } else { - throw new IllegalArgumentException("Allele " + alleleString + " not present in the list of alleles " + possibleAlleles); - } - } - - myAlleles.add(allele); - } - - return myAlleles; - } - public int compareTo(Allele other) { if ( isReference() && other.isNonReference() ) return -1; @@ -468,9 +436,6 @@ else if ( isNonReference() && other.isReference() ) } public static boolean oneIsPrefixOfOther(Allele a1, Allele a2) { - if ( a1.isNull() || a2.isNull() ) - return true; - if ( a2.length() >= a1.length() ) return firstIsPrefixOfSecond(a1, a2); else diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java index dcdd95d007..f298f1187f 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java @@ -188,8 +188,6 @@ public class VariantContext implements Feature { // to enable tribble integratio @Deprecated // ID is no longer stored in the attributes map private final static String ID_KEY = "ID"; - private final Byte REFERENCE_BASE_FOR_INDEL; - public final static Set PASSES_FILTERS = Collections.unmodifiableSet(new LinkedHashSet()); /** The location of this VariantContext */ @@ -228,7 +226,6 @@ public class VariantContext implements Feature { // to enable tribble integratio // --------------------------------------------------------------------------------------------------------- public enum Validation { - REF_PADDING, ALLELES, GENOTYPES } @@ -250,7 +247,7 @@ protected VariantContext(VariantContext other) { this(other.getSource(), other.getID(), other.getChr(), other.getStart(), other.getEnd(), other.getAlleles(), other.getGenotypes(), other.getLog10PError(), other.getFiltersMaybeNull(), - other.getAttributes(), other.REFERENCE_BASE_FOR_INDEL, + other.getAttributes(), other.fullyDecoded, NO_VALIDATION); } @@ -266,7 +263,6 @@ protected VariantContext(VariantContext other) { * @param log10PError qual * @param filters filters: use null for unfiltered and empty set for passes filters * @param attributes attributes - * @param referenceBaseForIndel padded reference base * @param validationToPerform set of validation steps to take */ protected VariantContext(final String source, @@ -279,7 +275,6 @@ protected VariantContext(final String source, final double log10PError, final Set filters, final Map attributes, - final Byte referenceBaseForIndel, final boolean fullyDecoded, final EnumSet validationToPerform ) { if ( contig == null ) { throw new IllegalArgumentException("Contig cannot be null"); } @@ -292,7 +287,6 @@ protected VariantContext(final String source, this.ID = ID.equals(VCFConstants.EMPTY_ID_FIELD) ? VCFConstants.EMPTY_ID_FIELD : ID; this.commonInfo = new CommonInfo(source, log10PError, filters, attributes); - REFERENCE_BASE_FOR_INDEL = referenceBaseForIndel; // todo -- remove me when this check is no longer necessary if ( this.commonInfo.hasAttribute(ID_KEY) ) @@ -340,8 +334,9 @@ protected VariantContext(final String source, * in this VC is returned as the set of alleles in the subContext, even if * some of those alleles aren't in the samples * - * @param sampleNames - * @return + * @param sampleNames the sample names + * @param rederiveAllelesFromGenotypes if true, returns the alleles to just those in use by the samples + * @return new VariantContext subsetting to just the given samples */ public VariantContext subContextFromSamples(Set sampleNames, final boolean rederiveAllelesFromGenotypes ) { if ( sampleNames.containsAll(getSampleNames()) ) { @@ -501,7 +496,7 @@ public Type getType() { */ public boolean isSimpleInsertion() { // can't just call !isSimpleDeletion() because of complex indels - return getType() == Type.INDEL && getReference().isNull() && isBiallelic(); + return getType() == Type.INDEL && isBiallelic() && getReference().length() < getAlternateAllele(0).length(); } /** @@ -509,7 +504,7 @@ public boolean isSimpleInsertion() { */ public boolean isSimpleDeletion() { // can't just call !isSimpleInsertion() because of complex indels - return getType() == Type.INDEL && getAlternateAllele(0).isNull() && isBiallelic(); + return getType() == Type.INDEL && isBiallelic() && getReference().length() > getAlternateAllele(0).length(); } /** @@ -553,22 +548,6 @@ public String getID() { return ID; } - public boolean hasReferenceBaseForIndel() { - return REFERENCE_BASE_FOR_INDEL != null; - } - - // the indel base that gets stripped off for indels - public Byte getReferenceBaseForIndel() { - return REFERENCE_BASE_FOR_INDEL; - } - - public String getAlleleStringWithRefPadding(final Allele allele) { - if ( VCFAlleleClipper.needsPadding(this) ) - return VCFAlleleClipper.padAllele(this, allele).getDisplayString(); - else - return allele.getDisplayString(); - } - // --------------------------------------------------------------------------------------------------------- // @@ -808,8 +787,8 @@ public Iterable getGenotypesOrderedBy(Iterable sampleOrdering) * Returns a map from sampleName -> Genotype for the genotype associated with sampleName. Returns a map * for consistency with the multi-get function. * - * @param sampleName - * @return + * @param sampleName the sample name + * @return mapping from sample name to genotype * @throws IllegalArgumentException if sampleName isn't bound to a genotype */ public GenotypesContext getGenotypes(String sampleName) { @@ -823,7 +802,7 @@ public GenotypesContext getGenotypes(String sampleName) { * For testing convenience only * * @param sampleNames a unique list of sample names - * @return + * @return subsetting genotypes context * @throws IllegalArgumentException if sampleName isn't bound to a genotype */ protected GenotypesContext getGenotypes(Collection sampleNames) { @@ -1011,13 +990,13 @@ public int getMixedCount() { /** * Run all extra-strict validation tests on a Variant Context object * - * @param reference the true reference allele - * @param paddedRefBase the reference base used for padding indels - * @param rsIDs the true dbSNP IDs + * @param reportedReference the reported reference allele + * @param observedReference the actual reference allele + * @param rsIDs the true dbSNP IDs */ - public void extraStrictValidation(Allele reference, Byte paddedRefBase, Set rsIDs) { + public void extraStrictValidation(final Allele reportedReference, final Allele observedReference, final Set rsIDs) { // validate the reference - validateReferenceBases(reference, paddedRefBase); + validateReferenceBases(reportedReference, observedReference); // validate the RS IDs validateRSIDs(rsIDs); @@ -1032,18 +1011,9 @@ public void extraStrictValidation(Allele reference, Byte paddedRefBase, Set validationToPerform) { for (final Validation val : validationToPerform ) { switch (val) { case ALLELES: validateAlleles(); break; - case REF_PADDING: validateReferencePadding(); break; case GENOTYPES: validateGenotypes(); break; default: throw new IllegalArgumentException("Unexpected validation mode " + val); } @@ -1164,20 +1133,11 @@ private void validateStop() { } } - private void validateReferencePadding() { - if ( hasSymbolicAlleles() ) // symbolic alleles don't need padding... - return; - - boolean needsPadding = (getReference().length() == getEnd() - getStart()); // off by one because padded base was removed + private void validateAlleles() { - if ( needsPadding && !hasReferenceBaseForIndel() ) - throw new ReviewedStingException("Badly formed variant context at location " + getChr() + ":" + getStart() + "; no padded reference base was provided."); - } + boolean alreadySeenRef = false; - private void validateAlleles() { - // check alleles - boolean alreadySeenRef = false, alreadySeenNull = false; - for ( Allele allele : alleles ) { + for ( final Allele allele : alleles ) { // make sure there's only one reference allele if ( allele.isReference() ) { if ( alreadySeenRef ) throw new IllegalArgumentException("BUG: Received two reference tagged alleles in VariantContext " + alleles + " this=" + this); @@ -1187,24 +1147,14 @@ private void validateAlleles() { if ( allele.isNoCall() ) { throw new IllegalArgumentException("BUG: Cannot add a no call allele to a variant context " + alleles + " this=" + this); } - - // make sure there's only one null allele - if ( allele.isNull() ) { - if ( alreadySeenNull ) throw new IllegalArgumentException("BUG: Received two null alleles in VariantContext " + alleles + " this=" + this); - alreadySeenNull = true; - } } // make sure there's one reference allele if ( ! alreadySeenRef ) throw new IllegalArgumentException("No reference allele found in VariantContext"); -// if ( getType() == Type.INDEL ) { -// if ( getReference().length() != (getLocation().size()-1) ) { - long length = (stop - start) + 1; - if ( ! hasSymbolicAlleles() - && ((getReference().isNull() && length != 1 ) - || (getReference().isNonNull() && (length - getReference().length() > 1)))) { + final long length = (stop - start) + 1; + if ( ! hasSymbolicAlleles() && length != getReference().length() ) { throw new IllegalStateException("BUG: GenomeLoc " + contig + ":" + start + "-" + stop + " has a size == " + length + " but the variation reference allele has length " + getReference().length() + " this = " + this); } } diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java index f2375f6f9e..d8ab4bd236 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java @@ -25,9 +25,6 @@ package org.broadinstitute.sting.utils.variantcontext; import com.google.java.contract.*; -import org.broad.tribble.Feature; -import org.broad.tribble.TribbleException; -import org.broad.tribble.util.ParsingUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; @@ -74,7 +71,6 @@ public class VariantContextBuilder { private Set filters = null; private Map attributes = null; private boolean attributesCanBeModified = false; - private Byte referenceBaseForIndel = null; /** enum of what must be validated */ final private EnumSet toValidate = EnumSet.noneOf(VariantContext.Validation.class); @@ -117,7 +113,6 @@ public VariantContextBuilder(VariantContext parent) { this.genotypes = parent.genotypes; this.ID = parent.getID(); this.log10PError = parent.getLog10PError(); - this.referenceBaseForIndel = parent.getReferenceBaseForIndel(); this.source = parent.getSource(); this.start = parent.getStart(); this.stop = parent.getEnd(); @@ -132,7 +127,6 @@ public VariantContextBuilder(VariantContextBuilder parent) { this.genotypes = parent.genotypes; this.ID = parent.ID; this.log10PError = parent.log10PError; - this.referenceBaseForIndel = parent.referenceBaseForIndel; this.source = parent.source; this.start = parent.start; this.stop = parent.stop; @@ -362,21 +356,6 @@ public VariantContextBuilder log10PError(final double log10PError) { return this; } - /** - * Tells us that the resulting VariantContext should use this byte for the reference base - * Null means no refBase is available - * @param referenceBaseForIndel - */ - public VariantContextBuilder referenceBaseForIndel(final Byte referenceBaseForIndel) { - this.referenceBaseForIndel = referenceBaseForIndel; - toValidate.add(VariantContext.Validation.REF_PADDING); - return this; - } - - public VariantContextBuilder referenceBaseForIndel(final String referenceBaseForIndel) { - return referenceBaseForIndel(referenceBaseForIndel.getBytes()[0]); - } - /** * Tells us that the resulting VariantContext should have source field set to source * @param source @@ -401,7 +380,6 @@ public VariantContextBuilder loc(final String contig, final long start, final lo this.start = start; this.stop = stop; toValidate.add(VariantContext.Validation.ALLELES); - toValidate.add(VariantContext.Validation.REF_PADDING); return this; } @@ -416,7 +394,6 @@ public VariantContextBuilder loc(final GenomeLoc loc) { this.start = loc.getStart(); this.stop = loc.getStop(); toValidate.add(VariantContext.Validation.ALLELES); - toValidate.add(VariantContext.Validation.REF_PADDING); return this; } @@ -440,7 +417,6 @@ public VariantContextBuilder chr(final String contig) { public VariantContextBuilder start(final long start) { this.start = start; toValidate.add(VariantContext.Validation.ALLELES); - toValidate.add(VariantContext.Validation.REF_PADDING); return this; } @@ -517,6 +493,6 @@ public VariantContextBuilder fullyDecoded(boolean isFullyDecoded) { public VariantContext make() { return new VariantContext(source, ID, contig, start, stop, alleles, genotypes, log10PError, filters, attributes, - referenceBaseForIndel, fullyDecoded, toValidate); + fullyDecoded, toValidate); } } diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java index d7e0729800..e1a043e942 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java @@ -64,9 +64,9 @@ public class VariantContextUtils { * Ensures that VC contains all of the samples in allSamples by adding missing samples to * the resulting VC with default diploid ./. genotypes * - * @param vc - * @param allSamples - * @return + * @param vc the VariantContext + * @param allSamples all of the samples needed + * @return a new VariantContext with missing samples added */ public static VariantContext addMissingSamples(final VariantContext vc, final Set allSamples) { // TODO -- what's the fastest way to do this calculation? @@ -376,9 +376,9 @@ private final static Map subsetAttributes(final CommonInfo igc, /** * @deprecated use variant context builder version instead - * @param vc - * @param keysToPreserve - * @return + * @param vc the variant context + * @param keysToPreserve the keys to preserve + * @return a pruned version of the original variant context */ @Deprecated public static VariantContext pruneVariantContext(final VariantContext vc, Collection keysToPreserve ) { @@ -486,14 +486,13 @@ public static VariantContext simpleMerge(final GenomeLocParser genomeLocParser, if ( genotypeMergeOptions == GenotypeMergeType.REQUIRE_UNIQUE ) verifyUniqueSampleNames(unsortedVCs); - final List prepaddedVCs = sortVariantContextsByPriority(unsortedVCs, priorityListOfVCs, genotypeMergeOptions); + final List preFilteredVCs = sortVariantContextsByPriority(unsortedVCs, priorityListOfVCs, genotypeMergeOptions); // Make sure all variant contexts are padded with reference base in case of indels if necessary final List VCs = new ArrayList(); - for (final VariantContext vc : prepaddedVCs) { - // also a reasonable place to remove filtered calls, if needed + for (final VariantContext vc : preFilteredVCs) { if ( ! filteredAreUncalled || vc.isNotFiltered() ) - VCs.add(VCFAlleleClipper.createVariantContextWithPaddedAlleles(vc)); + VCs.add(vc); } if ( VCs.size() == 0 ) // everything is filtered out and we're filteredAreUncalled return null; @@ -547,9 +546,6 @@ public static VariantContext simpleMerge(final GenomeLocParser genomeLocParser, filters.addAll(vc.getFilters()); - if ( referenceBaseForIndel == null ) - referenceBaseForIndel = vc.getReferenceBaseForIndel(); - // // add attributes // @@ -661,10 +657,9 @@ else if ( variantSources.isEmpty() ) // everyone was reference builder.genotypes(genotypes); builder.log10PError(log10PError); builder.filters(filters).attributes(mergeInfoWithMaxAC ? attributesWithMaxAC : attributes); - builder.referenceBaseForIndel(referenceBaseForIndel); // Trim the padded bases of all alleles if necessary - final VariantContext merged = createVariantContextWithTrimmedAlleles(builder.make()); + final VariantContext merged = builder.make(); if ( printMessages && remapped ) System.out.printf("Remapped => %s%n", merged); return merged; } @@ -700,73 +695,6 @@ public static boolean allelesAreSubset(VariantContext vc1, VariantContext vc2) { return true; } - private static VariantContext createVariantContextWithTrimmedAlleles(VariantContext inputVC) { - // see if we need to trim common reference base from all alleles - boolean trimVC; - - // We need to trim common reference base from all alleles in all genotypes if a ref base is common to all alleles - Allele refAllele = inputVC.getReference(); - if (!inputVC.isVariant()) - trimVC = false; - else if (refAllele.isNull()) - trimVC = false; - else { - trimVC = VCFAlleleClipper.shouldClipFirstBaseP(inputVC.getAlternateAlleles(), (byte) inputVC.getReference().getDisplayString().charAt(0)); - } - - // nothing to do if we don't need to trim bases - if (trimVC) { - List alleles = new ArrayList(); - GenotypesContext genotypes = GenotypesContext.create(); - - Map originalToTrimmedAlleleMap = new HashMap(); - - for (final Allele a : inputVC.getAlleles()) { - if (a.isSymbolic()) { - alleles.add(a); - originalToTrimmedAlleleMap.put(a, a); - } else { - // get bases for current allele and create a new one with trimmed bases - byte[] newBases = Arrays.copyOfRange(a.getBases(), 1, a.length()); - Allele trimmedAllele = Allele.create(newBases, a.isReference()); - alleles.add(trimmedAllele); - originalToTrimmedAlleleMap.put(a, trimmedAllele); - } - } - - // detect case where we're trimming bases but resulting vc doesn't have any null allele. In that case, we keep original representation - // example: mixed records such as {TA*,TGA,TG} - boolean hasNullAlleles = false; - - for (final Allele a: originalToTrimmedAlleleMap.values()) { - if (a.isNull()) - hasNullAlleles = true; - } - - if (!hasNullAlleles) - return inputVC; - // now we can recreate new genotypes with trimmed alleles - for ( final Genotype genotype : inputVC.getGenotypes() ) { - - List originalAlleles = genotype.getAlleles(); - List trimmedAlleles = new ArrayList(); - for ( final Allele a : originalAlleles ) { - if ( a.isCalled() ) - trimmedAlleles.add(originalToTrimmedAlleleMap.get(a)); - else - trimmedAlleles.add(Allele.NO_CALL); - } - genotypes.add(new GenotypeBuilder(genotype).alleles(trimmedAlleles).make()); - - } - - final VariantContextBuilder builder = new VariantContextBuilder(inputVC); - return builder.alleles(alleles).genotypes(genotypes).referenceBaseForIndel(new Byte(inputVC.getReference().getBases()[0])).make(); - } - - return inputVC; - } - public static GenotypesContext stripPLs(GenotypesContext genotypes) { GenotypesContext newGs = GenotypesContext.create(genotypes.size()); @@ -979,7 +907,7 @@ public static VariantContext reverseComplement(VariantContext vc) { HashMap alleleMap = new HashMap(vc.getAlleles().size()); for ( Allele originalAllele : vc.getAlleles() ) { Allele newAllele; - if ( originalAllele.isNoCall() || originalAllele.isNull() ) + if ( originalAllele.isNoCall() ) newAllele = originalAllele; else newAllele = Allele.create(BaseUtils.simpleReverseComplement(originalAllele.getBases()), originalAllele.isReference()); diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java index df2008e8e0..b5da206adc 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java @@ -274,10 +274,7 @@ private void buildID( VariantContext vc ) throws IOException { } private void buildAlleles( VariantContext vc ) throws IOException { - final boolean needsPadding = VCFAlleleClipper.needsPadding(vc); for ( Allele allele : vc.getAlleles() ) { - if ( needsPadding ) - allele = VCFAlleleClipper.padAllele(vc, allele); final byte[] s = allele.getDisplayBases(); if ( s == null ) throw new ReviewedStingException("BUG: BCF2Writer encountered null padded allele" + allele); diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java index 4548e026ea..ea968e153a 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java @@ -162,7 +162,6 @@ public void add(VariantContext vc) { vc = new VariantContextBuilder(vc).noGenotypes().make(); try { - vc = VCFAlleleClipper.createVariantContextWithPaddedAlleles(vc); super.add(vc); Map alleleMap = buildAlleleMap(vc); diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/AlleleUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/AlleleUnitTest.java index ed9805d19e..3bf020df76 100755 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/AlleleUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/AlleleUnitTest.java @@ -37,8 +37,6 @@ // public Allele(byte[] bases, boolean isRef) { // public Allele(boolean isRef) { // public Allele(String bases, boolean isRef) { -// public boolean isNullAllele() { return length() == 0; } -// public boolean isNonNullAllele() { return ! isNullAllele(); } // public boolean isReference() { return isRef; } // public boolean isNonReference() { return ! isReference(); } // public byte[] getBases() { return bases; } @@ -72,8 +70,6 @@ public void testCreatingSNPAlleles() { Assert.assertFalse(A.isReference()); Assert.assertTrue(A.basesMatch("A")); Assert.assertEquals(A.length(), 1); - Assert.assertTrue(A.isNonNull()); - Assert.assertFalse(A.isNull()); Assert.assertTrue(ARef.isReference()); Assert.assertFalse(ARef.isNonReference()); @@ -92,8 +88,8 @@ public void testCreatingNoCallAlleles() { Assert.assertFalse(NoCall.isReference()); Assert.assertFalse(NoCall.basesMatch(".")); Assert.assertEquals(NoCall.length(), 0); - Assert.assertTrue(NoCall.isNonNull()); - Assert.assertFalse(NoCall.isNull()); + Assert.assertTrue(NoCall.isNoCall()); + Assert.assertFalse(NoCall.isCalled()); } @@ -111,8 +107,6 @@ public void testCreatingIndelAlleles() { Assert.assertFalse(del.basesMatch("-")); Assert.assertTrue(del.basesMatch("")); Assert.assertEquals(del.length(), 0); - Assert.assertFalse(del.isNonNull()); - Assert.assertTrue(del.isNull()); } diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java index 1d290118f1..11c75ed9ae 100755 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java @@ -845,7 +845,6 @@ public void runSubContextTest(SubContextTest cfg) { Assert.assertEquals(sub.getLog10PError(), vc.getLog10PError()); Assert.assertEquals(sub.getFilters(), vc.getFilters()); Assert.assertEquals(sub.getID(), vc.getID()); - Assert.assertEquals(sub.getReferenceBaseForIndel(), vc.getReferenceBaseForIndel()); Assert.assertEquals(sub.getAttributes(), vc.getAttributes()); Set expectedGenotypes = new HashSet(); From 2274c21cfdf9b4e7073c1ceba3a3fead4dad9891 Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Thu, 26 Jul 2012 13:43:00 -0400 Subject: [PATCH 008/176] Improvements to indel calling in pool caller: a) Compute per-read likelihoods in reference sample to determine wheter a read is informative or not. b) Fixed bugs in unit tests. c) Fixed padding-related bugs when computing matches/mismatches in ErrorModel, d) Added a couple of more integration tests to increase test coverage, including testing odd ploidy --- .../sting/gatk/walkers/indels/PairHMMIndelErrorModel.java | 4 +++- .../walkers/genotyper/ArtificialReadPileupTestProvider.java | 4 ++-- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java index f49e78469a..6bfe5702df 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java @@ -25,6 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.indels; +import com.google.java.contract.Ensures; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.Haplotype; import org.broadinstitute.sting.utils.MathUtils; @@ -175,7 +176,8 @@ public synchronized double[] computeDiploidReadHaplotypeLikelihoods(ReadBackedPi } - public synchronized double[][] computeGeneralReadHaplotypeLikelihoods(final ReadBackedPileup pileup, + @Ensures("result != null && result.length == pileup.getNumberOfElements()") + public synchronized double[][] computeGeneralReadHaplotypeLikelihoods(final ReadBackedPileup pileup, final LinkedHashMap haplotypeMap, final ReferenceContext ref, final int eventLength, diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java index 256f93473f..77769a5fe9 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java @@ -90,7 +90,7 @@ public List getSampleNames() { return sampleNames; } public byte getRefByte() { - return refBases.substring(offset,offset+1).getBytes()[0]; + return referenceContext.getBase(); } public ReferenceContext getReferenceContext() { return referenceContext;} @@ -107,7 +107,7 @@ public Map getAlignmentContextFromAlleles(int eventLeng ArrayList vcAlleles = new ArrayList(); Allele refAllele, altAllele; if (eventLength == 0) {// SNP case - refAllele =Allele.create(refBases.substring(offset,offset+1),true); + refAllele =Allele.create(referenceContext.getBase(),true); altAllele = Allele.create(altBases.substring(0,1), false); } else if (eventLength>0){ From 67a7402a9b024e54756de506b6fd572e2db8a8bc Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 26 Jul 2012 23:27:11 -0400 Subject: [PATCH 009/176] Allele refactoring checkpoint 2: all code finally compiles, AD and STR annotations are fixed, and most of the UG integration tests pass. --- .../annotator/DepthPerAlleleBySample.java | 4 +- .../genotyper/ConsensusAlleleCounter.java | 2 +- ...elGenotypeLikelihoodsCalculationModel.java | 36 +-- .../broadinstitute/sting/utils/Haplotype.java | 31 +-- .../sting/utils/variantcontext/Allele.java | 15 +- .../variantcontext/VariantContextUtils.java | 7 +- .../ArtificialReadPileupTestProvider.java | 16 +- .../codecs/vcf/VCFAlleleClipperUnitTest.java | 226 ------------------ .../VariantContextTestProvider.java | 12 +- .../VariantContextUnitTest.java | 45 ++-- .../VariantContextUtilsUnitTest.java | 2 +- .../writer/VCFWriterUnitTest.java | 6 +- 12 files changed, 76 insertions(+), 326 deletions(-) delete mode 100644 public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFAlleleClipperUnitTest.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java index 261f6433bf..a9edab752f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java @@ -88,13 +88,13 @@ private void annotateIndel(final AlignmentContext stratifiedContext, final byte for ( PileupElement p : pileup ) { if ( p.isBeforeInsertion() ) { - final Allele insertion = Allele.create(refBase + p.getEventBases(), false); + final Allele insertion = Allele.create((char)refBase + p.getEventBases(), false); if ( alleleCounts.containsKey(insertion) ) { alleleCounts.put(insertion, alleleCounts.get(insertion)+1); } } else if ( p.isBeforeDeletionStart() ) { - if ( p.getEventLength() == refAllele.length() + 1 ) { + if ( p.getEventLength() == refAllele.length() - 1 ) { // this is indeed the deletion allele recorded in VC final Allele deletion = Allele.create(refBase); if ( alleleCounts.containsKey(deletion) ) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java index d2071a9fbc..869e522168 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java @@ -255,7 +255,7 @@ private List consensusCountsToAlleles(final ReferenceContext ref, else continue; // don't go on with this allele if refBases are non-standard } else { // insertion case - final String insertionBases = ref.getBase() + s; // add reference padding + final String insertionBases = (char)ref.getBase() + s; // add reference padding if (Allele.acceptableAlleleBases(insertionBases, false)) { // don't allow N's in insertions refAllele = Allele.create(ref.getBase(), true); altAllele = Allele.create(insertionBases, false); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java index 7eabe7a183..bedffa6909 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java @@ -35,7 +35,6 @@ import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.Haplotype; -import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.variantcontext.*; @@ -48,8 +47,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood private boolean DEBUG = false; private boolean ignoreSNPAllelesWhenGenotypingIndels = false; private PairHMMIndelErrorModel pairModel; - private boolean allelesArePadded; - + private static ThreadLocal>> indelLikelihoodMap = new ThreadLocal>>() { protected synchronized HashMap> initialValue() { @@ -105,22 +103,18 @@ public VariantContext getLikelihoods(final RefMetaDataTracker tracker, indelLikelihoodMap.set(new HashMap>()); haplotypeMap.clear(); - Pair,Boolean> pair = getInitialAlleleList(tracker, ref, contexts, contextType, locParser, UAC, ignoreSNPAllelesWhenGenotypingIndels); - alleleList = pair.first; - allelesArePadded = pair.second; + alleleList = getInitialAlleleList(tracker, ref, contexts, contextType, locParser, UAC, ignoreSNPAllelesWhenGenotypingIndels); if (alleleList.isEmpty()) return null; } - getHaplotypeMapFromAlleles(alleleList, ref, loc, haplotypeMap); // will update haplotypeMap adding elements if (haplotypeMap == null || haplotypeMap.isEmpty()) return null; // start making the VariantContext // For all non-snp VC types, VC end location is just startLocation + length of ref allele including padding base. - - final int endLoc = computeEndLocation(alleleList, loc,allelesArePadded); + final int endLoc = loc.getStart() + alleleList.get(0).length() - 1; final int eventLength = getEventLength(alleleList); final VariantContextBuilder builder = new VariantContextBuilder("UG_call", loc.getContig(), loc.getStart(), endLoc, alleleList); @@ -160,15 +154,6 @@ public static HashMap> getIndelLike return indelLikelihoodMap.get(); } - public static int computeEndLocation(final List alleles, final GenomeLoc loc, final boolean allelesArePadded) { - Allele refAllele = alleles.get(0); - int endLoc = loc.getStart() + refAllele.length()-1; - if (allelesArePadded) - endLoc++; - - return endLoc; - } - public static void getHaplotypeMapFromAlleles(final List alleleList, final ReferenceContext ref, final GenomeLoc loc, @@ -213,16 +198,15 @@ public static int getEventLength(List alleleList) { } - public static Pair,Boolean> getInitialAlleleList(final RefMetaDataTracker tracker, + public static List getInitialAlleleList(final RefMetaDataTracker tracker, final ReferenceContext ref, final Map contexts, final AlignmentContextUtils.ReadOrientation contextType, final GenomeLocParser locParser, final UnifiedArgumentCollection UAC, final boolean ignoreSNPAllelesWhenGenotypingIndels) { - + List alleles = new ArrayList(); - boolean allelesArePadded = true; if (UAC.GenotypingMode == GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) { VariantContext vc = null; for (final VariantContext vc_input : tracker.getValues(UAC.alleles, ref.getLocus())) { @@ -235,7 +219,7 @@ public static Pair,Boolean> getInitialAlleleList(final RefMetaDataT } // ignore places where we don't have a variant if (vc == null) - return new Pair,Boolean>(alleles,false); + return alleles; if (ignoreSNPAllelesWhenGenotypingIndels) { // if there's an allele that has same length as the reference (i.e. a SNP or MNP), ignore it and don't genotype it @@ -248,15 +232,11 @@ public static Pair,Boolean> getInitialAlleleList(final RefMetaDataT } else { alleles.addAll(vc.getAlleles()); } - if ( vc.getReference().getBases().length == vc.getEnd()-vc.getStart()+1) - allelesArePadded = false; - - } else { - alleles = IndelGenotypeLikelihoodsCalculationModel.computeConsensusAlleles(ref, contexts, contextType, locParser, UAC); + alleles = computeConsensusAlleles(ref, contexts, contextType, locParser, UAC); } - return new Pair,Boolean> (alleles,allelesArePadded); + return alleles; } // Overload function in GenotypeLikelihoodsCalculationModel so that, for an indel case, we consider a deletion as part of the pileup, diff --git a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java index 829e75682f..143a053c97 100755 --- a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java +++ b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java @@ -204,8 +204,11 @@ public Haplotype insertAllele( final Allele refAllele, final Allele altAllele, i return new Haplotype(newHaplotype); } - public static LinkedHashMap makeHaplotypeListFromAlleles(List alleleList, int startPos, ReferenceContext ref, - final int haplotypeSize, final int numPrefBases) { + public static LinkedHashMap makeHaplotypeListFromAlleles(final List alleleList, + final int startPos, + final ReferenceContext ref, + final int haplotypeSize, + final int numPrefBases) { LinkedHashMap haplotypeMap = new LinkedHashMap(); @@ -216,7 +219,6 @@ public static LinkedHashMap makeHaplotypeListFromAlleles(List< refAllele = a; break; } - } if (refAllele == null) @@ -224,19 +226,12 @@ public static LinkedHashMap makeHaplotypeListFromAlleles(List< byte[] refBases = ref.getBases(); + final int startIdxInReference = 1 + startPos - numPrefBases - ref.getWindow().getStart(); + final String basesBeforeVariant = new String(Arrays.copyOfRange(refBases, startIdxInReference, startIdxInReference + numPrefBases)); - int startIdxInReference = (int)(1+startPos-numPrefBases-ref.getWindow().getStart()); - //int numPrefBases = (int)(vc.getStart()-ref.getWindow().getStart()+1); // indel vc starts one before event - - - byte[] basesBeforeVariant = Arrays.copyOfRange(refBases,startIdxInReference,startIdxInReference+numPrefBases); - int startAfter = startIdxInReference+numPrefBases+ refAllele.getBases().length; // protect against long events that overrun available reference context - if (startAfter > refBases.length) - startAfter = refBases.length; - byte[] basesAfterVariant = Arrays.copyOfRange(refBases, - startAfter, refBases.length); - + final int startAfter = Math.min(startIdxInReference + numPrefBases + refAllele.getBases().length - 1, refBases.length); + final String basesAfterVariant = new String(Arrays.copyOfRange(refBases, startAfter, refBases.length)); // Create location for all haplotypes final int startLoc = ref.getWindow().getStart() + startIdxInReference; @@ -244,16 +239,14 @@ public static LinkedHashMap makeHaplotypeListFromAlleles(List< final GenomeLoc locus = ref.getGenomeLocParser().createGenomeLoc(ref.getLocus().getContig(),startLoc,stopLoc); - for (final Allele a : alleleList) { - byte[] alleleBases = a.getBases(); + final byte[] alleleBases = a.getBases(); // use string concatenation - String haplotypeString = new String(basesBeforeVariant) + new String(alleleBases) + new String(basesAfterVariant); + String haplotypeString = basesBeforeVariant + new String(Arrays.copyOfRange(alleleBases, 1, alleleBases.length)) + basesAfterVariant; haplotypeString = haplotypeString.substring(0,haplotypeSize); - haplotypeMap.put(a,new Haplotype(haplotypeString.getBytes(), locus)); - + haplotypeMap.put(a,new Haplotype(haplotypeString.getBytes(), locus)); } return haplotypeMap; diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java index 1947ef01e3..aa63a9dac7 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java @@ -90,16 +90,23 @@ private Allele(byte[] bases, boolean isRef) { // null alleles are no longer allowed if ( wouldBeNullAllele(bases) ) { throw new IllegalArgumentException("Null alleles are not supported"); - } else if ( wouldBeNoCallAllele(bases) ) { - bases = EMPTY_ALLELE_BASES; + } + + // no-calls are represented as no bases + if ( wouldBeNoCallAllele(bases) ) { + this.bases = EMPTY_ALLELE_BASES; isNoCall = true; if ( isRef ) throw new IllegalArgumentException("Cannot tag a NoCall allele as the reference allele"); - } else if ( wouldBeSymbolicAllele(bases) ) { + return; + } + + if ( wouldBeSymbolicAllele(bases) ) { isSymbolic = true; if ( isRef ) throw new IllegalArgumentException("Cannot tag a symbolic allele as the reference allele"); } - else + else { bases = BaseUtils.convertToUpperCase(bases); + } this.isRef = isRef; this.bases = bases; diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java index e1a043e942..e9388205fd 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java @@ -1163,13 +1163,14 @@ public static Pair,byte[]> getNumTandemRepeatUnits(final VariantCo if ( ! vc.isIndel() ) // only indels are tandem repeats return null; - final Allele ref = vc.getReference(); + final Allele refAllele = vc.getReference(); + final byte[] refAlleleBases = Arrays.copyOfRange(refAllele.getBases(), 1, refAllele.length()); byte[] repeatUnit = null; final ArrayList lengths = new ArrayList(); for ( final Allele allele : vc.getAlternateAlleles() ) { - Pair result = getNumTandemRepeatUnits(ref.getBases(), allele.getBases(), refBasesStartingAtVCWithoutPad.getBytes()); + Pair result = getNumTandemRepeatUnits(refAlleleBases, Arrays.copyOfRange(allele.getBases(), 1, allele.length()), refBasesStartingAtVCWithoutPad.getBytes()); final int[] repetitionCount = result.first; // repetition count = 0 means allele is not a tandem expansion of context @@ -1184,7 +1185,7 @@ public static Pair,byte[]> getNumTandemRepeatUnits(final VariantCo repeatUnit = result.second; if (VERBOSE) { System.out.println("RefContext:"+refBasesStartingAtVCWithoutPad); - System.out.println("Ref:"+ref.toString()+" Count:" + String.valueOf(repetitionCount[0])); + System.out.println("Ref:"+refAllele.toString()+" Count:" + String.valueOf(repetitionCount[0])); System.out.println("Allele:"+allele.toString()+" Count:" + String.valueOf(repetitionCount[1])); System.out.println("RU:"+new String(repeatUnit)); } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java index 256f93473f..aa48854065 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java @@ -103,22 +103,23 @@ public Map getAlignmentContextFromAlleles(int eventLeng boolean addBaseErrors, int phredScaledBaseErrorRate) { // RefMetaDataTracker tracker = new RefMetaDataTracker(null,referenceContext); - ArrayList vcAlleles = new ArrayList(); + String refBase = refBases.substring(offset,offset+1); // referenceContext.getBase()? Allele refAllele, altAllele; - if (eventLength == 0) {// SNP case - refAllele =Allele.create(refBases.substring(offset,offset+1),true); + if (eventLength == 0) { + // SNP case + refAllele = Allele.create(refBase,true); altAllele = Allele.create(altBases.substring(0,1), false); } else if (eventLength>0){ // insertion - refAllele = Allele.create(Allele.NULL_ALLELE_STRING, true); - altAllele = Allele.create(altBases.substring(0,eventLength), false); + refAllele = Allele.create(refBase,true); + altAllele = Allele.create(refBase + altBases.substring(0,eventLength), false); } else { // deletion - refAllele =Allele.create(refBases.substring(offset,offset+Math.abs(eventLength)),true); - altAllele = Allele.create(Allele.NULL_ALLELE_STRING, false); + refAllele = Allele.create(refBases.substring(offset,offset+Math.abs(eventLength)),true); + altAllele = Allele.create(refBase, false); } int stop = loc.getStart(); vcAlleles.add(refAllele); @@ -127,7 +128,6 @@ public Map getAlignmentContextFromAlleles(int eventLeng final VariantContextBuilder builder = new VariantContextBuilder().source(""); builder.loc(loc.getContig(), loc.getStart(), stop); builder.alleles(vcAlleles); - builder.referenceBaseForIndel(referenceContext.getBase()); builder.noGenotypes(); final VariantContext vc = builder.make(); diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFAlleleClipperUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFAlleleClipperUnitTest.java deleted file mode 100644 index 8cd051e018..0000000000 --- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFAlleleClipperUnitTest.java +++ /dev/null @@ -1,226 +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.utils.codecs.vcf; - -import com.google.java.contract.Requires; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.variantcontext.*; -import org.testng.Assert; -import org.testng.SkipException; -import org.testng.annotations.DataProvider; -import org.testng.annotations.Test; - -import java.util.*; - -public class VCFAlleleClipperUnitTest extends BaseTest { - // -------------------------------------------------------------------------------- - // - // Test allele clipping - // - // -------------------------------------------------------------------------------- - - private class ClipAllelesTest extends TestDataProvider { - final int position; - final int stop; - final String ref; - List inputs; - List expected; - - @Requires("arg.length % 2 == 0") - private ClipAllelesTest(final int position, final int stop, final String ... arg) { - super(ClipAllelesTest.class); - this.position = position; - this.stop = stop; - this.ref = arg[0]; - - int n = arg.length / 2; - inputs = new ArrayList(n); - expected = new ArrayList(n); - - for ( int i = 0; i < n; i++ ) { - final boolean ref = i % n == 0; - inputs.add(Allele.create(arg[i], ref)); - } - for ( int i = n; i < arg.length; i++ ) { - final boolean ref = i % n == 0; - expected.add(Allele.create(arg[i], ref)); - } - } - - public boolean isClipped() { - for ( int i = 0; i < inputs.size(); i++ ) { - if ( inputs.get(i).length() != expected.get(i).length() ) - return true; - } - - return false; - } - - public String toString() { - return String.format("ClipAllelesTest input=%s expected=%s", inputs, expected); - } - } - @DataProvider(name = "ClipAllelesTest") - public Object[][] makeClipAllelesTest() { - // do no harm - new ClipAllelesTest(10, 10, "A", "A"); - new ClipAllelesTest(10, 10, "A", "C", "A", "C"); - new ClipAllelesTest(10, 10, "A", "C", "G", "A", "C", "G"); - - // insertions - new ClipAllelesTest(10, 10, "A", "AA", "-", "A"); - new ClipAllelesTest(10, 10, "A", "AAA", "-", "AA"); - new ClipAllelesTest(10, 10, "A", "AG", "-", "G"); - - // deletions - new ClipAllelesTest(10, 11, "AA", "A", "A", "-"); - new ClipAllelesTest(10, 12, "AAA", "A", "AA", "-"); - new ClipAllelesTest(10, 11, "AG", "A", "G", "-"); - new ClipAllelesTest(10, 12, "AGG", "A", "GG", "-"); - - // multi-allelic insertion and deletions - new ClipAllelesTest(10, 11, "AA", "A", "AAA", "A", "-", "AA"); - new ClipAllelesTest(10, 11, "AA", "A", "AAG", "A", "-", "AG"); - new ClipAllelesTest(10, 10, "A", "AA", "AAA", "-", "A", "AA"); - new ClipAllelesTest(10, 10, "A", "AA", "ACA", "-", "A", "CA"); - new ClipAllelesTest(10, 12, "ACG", "ATC", "AGG", "CG", "TC", "GG"); - new ClipAllelesTest(10, 11, "AC", "AT", "AG", "C", "T", "G"); - - // cannot be clipped - new ClipAllelesTest(10, 11, "AC", "CT", "AG", "AC", "CT", "AG"); - new ClipAllelesTest(10, 11, "AC", "CT", "GG", "AC", "CT", "GG"); - - // symbolic - new ClipAllelesTest(10, 100, "A", "", "A", ""); - new ClipAllelesTest(50, 50, "G", "G]22:60]", "G", "G]22:60]"); - new ClipAllelesTest(51, 51, "T", "]22:55]T", "T", "]22:55]T"); - new ClipAllelesTest(52, 52, "C", "C[22:51[", "C", "C[22:51["); - new ClipAllelesTest(60, 60, "A", "A]22:50]", "A", "A]22:50]"); - - // symbolic with alleles that should be clipped - new ClipAllelesTest(10, 100, "A", "", "AA", "-", "", "A"); - new ClipAllelesTest(10, 100, "AA", "", "A", "A", "", "-"); - new ClipAllelesTest(10, 100, "AA", "", "A", "AAA", "A", "", "-", "AA"); - new ClipAllelesTest(10, 100, "AG", "", "A", "AGA", "G", "", "-", "GA"); - new ClipAllelesTest(10, 100, "G", "", "A", "G", "", "A"); - - // clipping from both ends - // - // TODO -- THIS CODE IS BROKEN BECAUSE CLIPPING DOES WORK WITH ALLELES CLIPPED FROM THE END - // -// new ClipAllelesTest(10, 10, "ATA", "ATTA", "-", "T"); -// new ClipAllelesTest(10, 10, "ATAA", "ATTAA", "-", "T"); -// new ClipAllelesTest(10, 10, "ATAAG", "ATTAAG", "-", "T"); -// new ClipAllelesTest(10, 11, "GTA", "ATTA", "G", "AT"); -// new ClipAllelesTest(10, 11, "GTAA", "ATTAA", "G", "AT"); -// new ClipAllelesTest(10, 11, "GTAAG", "ATTAAG", "G", "AT"); - - // complex substitutions - new ClipAllelesTest(10, 10, "A", "GA", "A", "GA"); - - return ClipAllelesTest.getTests(ClipAllelesTest.class); - } - - @Test(dataProvider = "ClipAllelesTest") - public void testClipAllelesTest(ClipAllelesTest cfg) { - final VCFAlleleClipper.ClippedAlleles clipped = VCFAlleleClipper.clipAlleles(cfg.position, cfg.ref, cfg.inputs, cfg.stop); - Assert.assertNull(clipped.getError(), "Unexpected error occurred"); - Assert.assertEquals(clipped.getStop(), cfg.stop, "Clipped alleles stop"); - Assert.assertEquals(clipped.getClippedAlleles(), cfg.expected, "Clipped alleles"); - } - - @Test(dataProvider = "ClipAllelesTest", dependsOnMethods = "testClipAllelesTest") - public void testPaddingAllelesInVC(final ClipAllelesTest cfg) { - final VCFAlleleClipper.ClippedAlleles clipped = VCFAlleleClipper.clipAlleles(cfg.position, cfg.ref, cfg.inputs, cfg.stop); - final VariantContext vc = new VariantContextBuilder("x", "1", cfg.position, cfg.stop, clipped.getClippedAlleles()) - .referenceBaseForIndel(clipped.getRefBaseForIndel()).make(); - - if ( vc.isMixed() && vc.hasSymbolicAlleles() ) - throw new SkipException("GATK cannot handle mixed variant contexts with symbolic and concrete alleles. Remove this check when allele clipping and padding is generalized"); - - Assert.assertEquals(VCFAlleleClipper.needsPadding(vc), cfg.isClipped(), "needPadding method"); - - if ( cfg.isClipped() ) { - // TODO - // TODO note that the GATK currently uses a broken approach to the clipped alleles, so the expected stop is - // TODO actually the original stop, as the original stop is +1 its true size. - // TODO - final int expectedStop = vc.getEnd(); // + (vc.hasSymbolicAlleles() ? 0 : 1); - - final VariantContext padded = VCFAlleleClipper.createVariantContextWithPaddedAlleles(vc); - Assert.assertEquals(padded.getStart(), vc.getStart(), "padded VC start"); - Assert.assertEquals(padded.getAlleles(), cfg.inputs, "padded VC alleles == original unclipped alleles"); - Assert.assertEquals(padded.getEnd(), expectedStop, "padded VC end should be clipped VC + 1 (added a base to ref allele)"); - Assert.assertFalse(VCFAlleleClipper.needsPadding(padded), "padded VC shouldn't need padding again"); - } - } - - // -------------------------------------------------------------------------------- - // - // basic allele clipping test - // - // -------------------------------------------------------------------------------- - - private class ReverseClippingPositionTestProvider extends TestDataProvider { - final String ref; - final List alleles = new ArrayList(); - final int expectedClip; - - private ReverseClippingPositionTestProvider(final int expectedClip, final String ref, final String... alleles) { - super(ReverseClippingPositionTestProvider.class); - this.ref = ref; - for ( final String allele : alleles ) - this.alleles.add(Allele.create(allele)); - this.expectedClip = expectedClip; - } - - @Override - public String toString() { - return String.format("ref=%s allele=%s reverse clip %d", ref, alleles, expectedClip); - } - } - - @DataProvider(name = "ReverseClippingPositionTestProvider") - public Object[][] makeReverseClippingPositionTestProvider() { - // pair clipping - new ReverseClippingPositionTestProvider(0, "ATT", "CCG"); - new ReverseClippingPositionTestProvider(1, "ATT", "CCT"); - new ReverseClippingPositionTestProvider(2, "ATT", "CTT"); - new ReverseClippingPositionTestProvider(2, "ATT", "ATT"); // cannot completely clip allele - - // triplets - new ReverseClippingPositionTestProvider(0, "ATT", "CTT", "CGG"); - new ReverseClippingPositionTestProvider(1, "ATT", "CTT", "CGT"); // the T can go - new ReverseClippingPositionTestProvider(2, "ATT", "CTT", "CTT"); // both Ts can go - - return ReverseClippingPositionTestProvider.getTests(ReverseClippingPositionTestProvider.class); - } - - - @Test(dataProvider = "ReverseClippingPositionTestProvider") - public void testReverseClippingPositionTestProvider(ReverseClippingPositionTestProvider cfg) { - int result = VCFAlleleClipper.computeReverseClipping(cfg.alleles, cfg.ref.getBytes(), 0, false); - Assert.assertEquals(result, cfg.expectedClip); - } -} diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java index 1a0e8e39da..b95e589b70 100644 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java @@ -225,10 +225,10 @@ private static void makeSyntheticTests() { add(builder()); add(builder().alleles("A")); add(builder().alleles("A", "C", "T")); - add(builder().alleles("-", "C").referenceBaseForIndel("A")); - add(builder().alleles("-", "CAGT").referenceBaseForIndel("A")); - add(builder().loc("1", 10, 11).alleles("C", "-").referenceBaseForIndel("A")); - add(builder().loc("1", 10, 13).alleles("CGT", "-").referenceBaseForIndel("A")); + add(builder().alleles("A", "AC")); + add(builder().alleles("A", "ACAGT")); + add(builder().loc("1", 10, 11).alleles("AC", "A")); + add(builder().loc("1", 10, 13).alleles("ACGT", "A")); // make sure filters work add(builder().unfiltered()); @@ -302,8 +302,8 @@ private static void addGenotypesToTestData() { sites.add(builder().alleles("A").make()); sites.add(builder().alleles("A", "C", "T").make()); - sites.add(builder().alleles("-", "C").referenceBaseForIndel("A").make()); - sites.add(builder().alleles("-", "CAGT").referenceBaseForIndel("A").make()); + sites.add(builder().alleles("A", "AC").make()); + sites.add(builder().alleles("A", "ACAGT").make()); for ( VariantContext site : sites ) { addGenotypes(site); diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java index 11c75ed9ae..46153221d8 100755 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java @@ -28,27 +28,22 @@ public class VariantContextUnitTest extends BaseTest { int snpLocStart = 10; int snpLocStop = 10; - // - / ATC [ref] from 20-23 + // - / ATC [ref] from 20-22 String delLoc = "chr1"; int delLocStart = 20; - int delLocStop = 23; + int delLocStop = 22; // - [ref] / ATC from 20-20 String insLoc = "chr1"; int insLocStart = 20; int insLocStop = 20; - // - / A / T / ATC [ref] from 20-23 - String mixedLoc = "chr1"; - int mixedLocStart = 20; - int mixedLocStop = 23; - VariantContextBuilder basicBuilder, snpBuilder, insBuilder; @BeforeSuite public void before() { - del = Allele.create("-"); - delRef = Allele.create("-", true); + del = Allele.create("A"); + delRef = Allele.create("A", true); A = Allele.create("A"); C = Allele.create("C"); @@ -62,9 +57,9 @@ public void before() { @BeforeMethod public void beforeTest() { - basicBuilder = new VariantContextBuilder("test", snpLoc,snpLocStart, snpLocStop, Arrays.asList(Aref, T)).referenceBaseForIndel((byte)'A'); - snpBuilder = new VariantContextBuilder("test", snpLoc,snpLocStart, snpLocStop, Arrays.asList(Aref, T)).referenceBaseForIndel((byte)'A'); - insBuilder = new VariantContextBuilder("test", insLoc, insLocStart, insLocStop, Arrays.asList(delRef, ATC)).referenceBaseForIndel((byte)'A'); + basicBuilder = new VariantContextBuilder("test", snpLoc,snpLocStart, snpLocStop, Arrays.asList(Aref, T)); + snpBuilder = new VariantContextBuilder("test", snpLoc,snpLocStart, snpLocStop, Arrays.asList(Aref, T)); + insBuilder = new VariantContextBuilder("test", insLoc, insLocStart, insLocStop, Arrays.asList(delRef, ATC)); } @Test @@ -213,7 +208,7 @@ public void testCreatingRefVariantContext() { @Test public void testCreatingDeletionVariantContext() { List alleles = Arrays.asList(ATCref, del); - VariantContext vc = new VariantContextBuilder("test", delLoc, delLocStart, delLocStop, alleles).referenceBaseForIndel((byte)'A').make(); + VariantContext vc = new VariantContextBuilder("test", delLoc, delLocStart, delLocStop, alleles).make(); Assert.assertEquals(vc.getChr(), delLoc); Assert.assertEquals(vc.getStart(), delLocStart); @@ -240,8 +235,8 @@ public void testCreatingDeletionVariantContext() { @Test public void testMatchingAlleles() { List alleles = Arrays.asList(ATCref, del); - VariantContext vc = new VariantContextBuilder("test", delLoc, delLocStart, delLocStop, alleles).referenceBaseForIndel((byte)'A').make(); - VariantContext vc2 = new VariantContextBuilder("test2", delLoc, delLocStart+12, delLocStop+12, alleles).referenceBaseForIndel((byte)'A').make(); + VariantContext vc = new VariantContextBuilder("test", delLoc, delLocStart, delLocStop, alleles).make(); + VariantContext vc2 = new VariantContextBuilder("test2", delLoc, delLocStart+12, delLocStop+12, alleles).make(); Assert.assertTrue(vc.hasSameAllelesAs(vc2)); Assert.assertTrue(vc.hasSameAlternateAllelesAs(vc2)); @@ -470,15 +465,15 @@ public void testFilters() { @Test public void testRepeatAllele() { - Allele nullR = Allele.create(Allele.NULL_ALLELE_STRING, true); - Allele nullA = Allele.create(Allele.NULL_ALLELE_STRING, false); - Allele atc = Allele.create("ATC", false); - Allele atcatc = Allele.create("ATCATC", false); - Allele ccccR = Allele.create("CCCC", true); - Allele cc = Allele.create("CC", false); - Allele cccccc = Allele.create("CCCCCC", false); - Allele gagaR = Allele.create("GAGA", true); - Allele gagagaga = Allele.create("GAGAGAGA", false); + Allele nullR = Allele.create("A", true); + Allele nullA = Allele.create("A", false); + Allele atc = Allele.create("AATC", false); + Allele atcatc = Allele.create("AATCATC", false); + Allele ccccR = Allele.create("ACCCC", true); + Allele cc = Allele.create("ACC", false); + Allele cccccc = Allele.create("ACCCCCC", false); + Allele gagaR = Allele.create("AGAGA", true); + Allele gagagaga = Allele.create("AGAGAGAGA", false); Pair,byte[]> result; byte[] refBytes = "TATCATCATCGGA".getBytes(); @@ -678,7 +673,7 @@ public Object[][] mergeAllelesData() { @Test(dataProvider = "getAlleles") public void testMergeAlleles(GetAllelesTest cfg) { final List altAlleles = cfg.alleles.subList(1, cfg.alleles.size()); - final VariantContext vc = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, cfg.alleles).referenceBaseForIndel((byte)'A').make(); + final VariantContext vc = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, cfg.alleles).make(); Assert.assertEquals(vc.getAlleles(), cfg.alleles, "VC alleles not the same as input alleles"); Assert.assertEquals(vc.getNAlleles(), cfg.alleles.size(), "VC getNAlleles not the same as input alleles size"); diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java index b09a10d07a..8c86a54de0 100644 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java @@ -99,7 +99,7 @@ private VariantContext makeVC(String source, List alleles, Collection alleles, Collection genotypes, Set filters) { int start = 10; int stop = start; // alleles.contains(ATC) ? start + 3 : start; - return new VariantContextBuilder(source, "1", start, stop, alleles).genotypes(genotypes).filters(filters).referenceBaseForIndel(Cref.getBases()[0]).make(); + return new VariantContextBuilder(source, "1", start, stop, alleles).genotypes(genotypes).filters(filters).make(); } // -------------------------------------------------------------------------------- diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriterUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriterUnitTest.java index a7fff45596..5876efa120 100644 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriterUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriterUnitTest.java @@ -139,8 +139,8 @@ private VariantContext createVC(VCFHeader header) { Map attributes = new HashMap(); GenotypesContext genotypes = GenotypesContext.create(header.getGenotypeSamples().size()); - alleles.add(Allele.create("-",true)); - alleles.add(Allele.create("CC",false)); + alleles.add(Allele.create("A",true)); + alleles.add(Allele.create("ACC",false)); attributes.put("DP","50"); for (String name : header.getGenotypeSamples()) { @@ -148,7 +148,7 @@ private VariantContext createVC(VCFHeader header) { genotypes.add(gt); } return new VariantContextBuilder("RANDOM", loc.getContig(), loc.getStart(), loc.getStop(), alleles) - .genotypes(genotypes).attributes(attributes).referenceBaseForIndel((byte)'A').make(); + .genotypes(genotypes).attributes(attributes).make(); } From a5ff2e92365599f8b7858d887332bbe88cf7fb67 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Fri, 27 Jul 2012 00:47:15 -0400 Subject: [PATCH 010/176] Re-enable reverse trimming of alleles in UG engine when sub-selecting alleles after genotyping. UG integration tests now pass. --- .../genotyper/UnifiedGenotyperEngine.java | 6 +- .../variantcontext/VariantContextUtils.java | 80 +++++++++++++++++++ 2 files changed, 84 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index d4c45e19d2..f73ab24715 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -485,8 +485,10 @@ else if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_M builder.attributes(attributes); VariantContext vcCall = builder.make(); - // TODO -- if we are subsetting alleles (either because there were too many or because some were not polymorphic) - // TODO -- then we may need to trim the alleles (because the original VariantContext may have had to pad at the end). + // if we are subsetting alleles (either because there were too many or because some were not polymorphic) + // then we may need to trim the alleles (because the original VariantContext may have had to pad at the end). + if ( myAlleles.size() != vc.getAlleles().size() && !limitedContext ) + vcCall = VariantContextUtils.reverseTrimAlleles(vcCall); if ( annotationEngine != null && !limitedContext ) { // Note: we want to use the *unfiltered* and *unBAQed* context for the annotations diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java index e9388205fd..70d365ef86 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java @@ -1334,4 +1334,84 @@ public static int computeEndFromAlleles(final List alleles, final int st return start + Math.max(ref.length() - 1, 0); } } + + public static VariantContext reverseTrimAlleles( final VariantContext inputVC ) { + + // TODO - this function doesn't work with mixed records or records that started as mixed and then became non-mixed + + // see whether we need to trim common reference base from all alleles + + final int trimExtent = computeReverseClipping(inputVC.getAlleles(), inputVC.getReference().getDisplayString().getBytes(), 0, false); + if ( trimExtent <= 0 || inputVC.getAlleles().size() <= 1 ) + return inputVC; + + final List alleles = new ArrayList(); + final GenotypesContext genotypes = GenotypesContext.create(); + final Map originalToTrimmedAlleleMap = new HashMap(); + + for (final Allele a : inputVC.getAlleles()) { + if (a.isSymbolic()) { + alleles.add(a); + originalToTrimmedAlleleMap.put(a, a); + } else { + // get bases for current allele and create a new one with trimmed bases + final byte[] newBases = Arrays.copyOfRange(a.getBases(), 0, a.length()-trimExtent); + final Allele trimmedAllele = Allele.create(newBases, a.isReference()); + alleles.add(trimmedAllele); + originalToTrimmedAlleleMap.put(a, trimmedAllele); + } + } + + // now we can recreate new genotypes with trimmed alleles + for ( final Genotype genotype : inputVC.getGenotypes() ) { + final List originalAlleles = genotype.getAlleles(); + final List trimmedAlleles = new ArrayList(); + for ( final Allele a : originalAlleles ) { + if ( a.isCalled() ) + trimmedAlleles.add(originalToTrimmedAlleleMap.get(a)); + else + trimmedAlleles.add(Allele.NO_CALL); + } + genotypes.add(new GenotypeBuilder(genotype).alleles(trimmedAlleles).make()); + } + + return new VariantContextBuilder(inputVC).stop(inputVC.getStart() + alleles.get(0).length() - 1).alleles(alleles).genotypes(genotypes).make(); + } + + public static int computeReverseClipping(final List unclippedAlleles, + final byte[] ref, + final int forwardClipping, + final boolean allowFullClip) { + int clipping = 0; + boolean stillClipping = true; + + while ( stillClipping ) { + for ( final Allele a : unclippedAlleles ) { + if ( a.isSymbolic() ) + continue; + + // we need to ensure that we don't reverse clip out all of the bases from an allele because we then will have the wrong + // position set for the VariantContext (although it's okay to forward clip it all out, because the position will be fine). + if ( a.length() - clipping == 0 ) + return clipping - (allowFullClip ? 0 : 1); + + if ( a.length() - clipping <= forwardClipping || a.length() - forwardClipping == 0 ) { + stillClipping = false; + } + else if ( ref.length == clipping ) { + if ( allowFullClip ) + stillClipping = false; + else + return -1; + } + else if ( a.getBases()[a.length()-clipping-1] != ref[ref.length-clipping-1] ) { + stillClipping = false; + } + } + if ( stillClipping ) + clipping++; + } + + return clipping; + } } From 7da3928b9554c549a21f02dfee8b6d14d8be8e9c Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Fri, 27 Jul 2012 02:14:25 -0400 Subject: [PATCH 011/176] Several more walkers have been brought up to use the new Allele representation. --- .../fasta/FastaAlternateReference.java | 4 +-- .../gatk/walkers/indels/IndelRealigner.java | 8 +++++- .../variantutils/LeftAlignVariants.java | 27 ++++++++++--------- .../utils/codecs/vcf/AbstractVCFCodec.java | 12 ++++++++- .../utils/variantcontext/VariantContext.java | 7 +++-- ...astaAlternateReferenceIntegrationTest.java | 2 +- 6 files changed, 38 insertions(+), 22 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java index 9c9a75fc4e..92549b821b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java @@ -107,11 +107,11 @@ public Pair map(RefMetaDataTracker tracker, ReferenceContext continue; if ( vc.isSimpleDeletion()) { - deletionBasesRemaining = vc.getReference().length(); + deletionBasesRemaining = vc.getReference().length() - 1; // delete the next n bases, not this one return new Pair(context.getLocation(), refBase); } else if ( vc.isSimpleInsertion()) { - return new Pair(context.getLocation(), refBase.concat(vc.getAlternateAllele(0).toString())); + return new Pair(context.getLocation(), vc.getAlternateAllele(0).toString()); } else if (vc.isSNP()) { return new Pair(context.getLocation(), vc.getAlternateAllele(0).toString()); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index 2153525abb..5e0f15e6aa 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -872,7 +872,13 @@ private void generateAlternateConsensesFromKnownIndels(final Set altC for ( VariantContext knownIndel : knownIndelsToTry ) { if ( knownIndel == null || !knownIndel.isIndel() || knownIndel.isComplexIndel() ) continue; - byte[] indelStr = knownIndel.isSimpleInsertion() ? knownIndel.getAlternateAllele(0).getBases() : Utils.dupBytes((byte)'-', knownIndel.getReference().length()); + final byte[] indelStr; + if ( knownIndel.isSimpleInsertion() ) { + final byte[] fullAllele = knownIndel.getAlternateAllele(0).getBases(); + indelStr = Arrays.copyOfRange(fullAllele, 1, fullAllele.length); // remove ref padding + } else { + indelStr = Utils.dupBytes((byte)'-', knownIndel.getReference().length() - 1); + } int start = knownIndel.getStart() - leftmostIndex + 1; Consensus c = createAlternateConsensus(start, reference, indelStr, knownIndel); if ( c != null ) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java index e0b723659a..9fe499a036 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java @@ -139,11 +139,11 @@ private int writeLeftAlignedIndel(final VariantContext vc, final ReferenceContex final byte[] refSeq = ref.getBases(); // get the indel length - int indelLength; + final int indelLength; if ( vc.isSimpleDeletion() ) - indelLength = vc.getReference().length(); + indelLength = vc.getReference().length() - 1; else - indelLength = vc.getAlternateAllele(0).length(); + indelLength = vc.getAlternateAllele(0).length() - 1; if ( indelLength > 200 ) { writer.add(vc); @@ -151,7 +151,7 @@ private int writeLeftAlignedIndel(final VariantContext vc, final ReferenceContex } // create an indel haplotype - int originalIndex = ref.getLocus().getStart() - ref.getWindow().getStart() + 1; + final int originalIndex = ref.getLocus().getStart() - ref.getWindow().getStart() + 1; final byte[] originalIndel = makeHaplotype(vc, refSeq, originalIndex, indelLength); // create a CIGAR string to represent the event @@ -170,11 +170,12 @@ private int writeLeftAlignedIndel(final VariantContext vc, final ReferenceContex VariantContext newVC = new VariantContextBuilder(vc).start(vc.getStart()-difference).stop(vc.getEnd()-difference).make(); //System.out.println("Moving record from " + vc.getChr()+":"+vc.getStart() + " to " + vc.getChr()+":"+(vc.getStart()-difference)); - int indelIndex = originalIndex-difference; - byte[] newBases = new byte[indelLength]; - System.arraycopy((vc.isSimpleDeletion() ? refSeq : originalIndel), indelIndex, newBases, 0, indelLength); - Allele newAllele = Allele.create(newBases, vc.isSimpleDeletion()); - newVC = updateAllele(newVC, newAllele, refSeq[indelIndex-1]); + final int indelIndex = originalIndex-difference; + final byte[] newBases = new byte[indelLength + 1]; + newBases[0] = refSeq[indelIndex-1]; + System.arraycopy((vc.isSimpleDeletion() ? refSeq : originalIndel), indelIndex, newBases, 1, indelLength); + final Allele newAllele = Allele.create(newBases, vc.isSimpleDeletion()); + newVC = updateAllele(newVC, newAllele); writer.add(newVC); return 1; @@ -195,7 +196,7 @@ private static byte[] makeHaplotype(VariantContext vc, byte[] ref, int indexOfRe if ( vc.isSimpleDeletion() ) { indexOfRef += indelLength; } else { - System.arraycopy(vc.getAlternateAllele(0).getBases(), 0, hap, currentPos, indelLength); + System.arraycopy(vc.getAlternateAllele(0).getBases(), 1, hap, currentPos, indelLength); currentPos += indelLength; } @@ -205,14 +206,14 @@ private static byte[] makeHaplotype(VariantContext vc, byte[] ref, int indexOfRe return hap; } - public static VariantContext updateAllele(VariantContext vc, Allele newAllele, Byte refBaseForIndel) { + public static VariantContext updateAllele(final VariantContext vc, final Allele newAllele) { // create a mapping from original allele to new allele HashMap alleleMap = new HashMap(vc.getAlleles().size()); if ( newAllele.isReference() ) { alleleMap.put(vc.getReference(), newAllele); - alleleMap.put(vc.getAlternateAllele(0), vc.getAlternateAllele(0)); + alleleMap.put(vc.getAlternateAllele(0), Allele.create(newAllele.getBases()[0], false)); } else { - alleleMap.put(vc.getReference(), vc.getReference()); + alleleMap.put(vc.getReference(), Allele.create(newAllele.getBases()[0], true)); alleleMap.put(vc.getAlternateAllele(0), newAllele); } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java index 2b5695e3a6..996cef8a4f 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java @@ -248,7 +248,6 @@ else if ( parts[2].equals(VCFConstants.EMPTY_ID_FIELD) ) builder.id(parts[2]); final String ref = getCachedString(parts[3].toUpperCase()); - builder.stop(pos + ref.length() - 1); final String alts = getCachedString(parts[4].toUpperCase()); builder.log10PError(parseQual(parts[5])); @@ -257,6 +256,17 @@ else if ( parts[2].equals(VCFConstants.EMPTY_ID_FIELD) ) final Map attrs = parseInfo(parts[7]); builder.attributes(attrs); + if ( attrs.containsKey(VCFConstants.END_KEY) ) { + // update stop with the end key if provided + try { + builder.stop(Integer.valueOf(attrs.get(VCFConstants.END_KEY).toString())); + } catch (Exception e) { + generateException("the END value in the INFO field is not valid"); + } + } else { + builder.stop(pos + ref.length() - 1); + } + // get our alleles, filters, and setup an attribute map final List alleles = parseAlleles(ref, alts, lineNo); builder.alleles(alleles); diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java index f298f1187f..72681ae354 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java @@ -496,7 +496,7 @@ public Type getType() { */ public boolean isSimpleInsertion() { // can't just call !isSimpleDeletion() because of complex indels - return getType() == Type.INDEL && isBiallelic() && getReference().length() < getAlternateAllele(0).length(); + return getType() == Type.INDEL && isBiallelic() && getReference().length() == 1; } /** @@ -504,7 +504,7 @@ public boolean isSimpleInsertion() { */ public boolean isSimpleDeletion() { // can't just call !isSimpleInsertion() because of complex indels - return getType() == Type.INDEL && isBiallelic() && getReference().length() > getAlternateAllele(0).length(); + return getType() == Type.INDEL && isBiallelic() && getAlternateAllele(0).length() == 1; } /** @@ -1120,8 +1120,7 @@ private void validateStop() { if ( hasAttribute(VCFConstants.END_KEY) ) { final int end = getAttributeAsInt(VCFConstants.END_KEY, -1); assert end != -1; - if ( end != getEnd() && end != getEnd() + 1 ) { - // the end is allowed to 1 bigger because of the padding + if ( end != getEnd() ) { final String message = "Badly formed variant context at location " + getChr() + ":" + getStart() + "; getEnd() was " + getEnd() + " but this VariantContext contains an END key with value " + end; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java index 1c5db4262e..4611f3a405 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java @@ -26,7 +26,7 @@ public void testIntervals() { WalkerTestSpec spec2 = new WalkerTestSpec( "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -V " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 --snpmask:vcf " + b36dbSNP129 + " -L 1:10,075,000-10,075,380 -L 1:10,093,447-10,093,847 -L 1:10,271,252-10,271,452 -o %s", 1, - Arrays.asList("0567b32ebdc26604ddf2a390de4579ac")); + Arrays.asList("ef481be9962e21d09847b8a1d4a4ff65")); executeTest("testFastaAlternateReferenceIndels", spec2); WalkerTestSpec spec3 = new WalkerTestSpec( From 8c9e3f59d5e03855468b976d28dd9fc58fc3d92a Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Fri, 27 Jul 2012 11:01:39 -0400 Subject: [PATCH 012/176] ActiveRegionWalker's isActive function returns a results object now instead of just a double. --- .../gatk/iterators/LocusIteratorByState.java | 3 +- .../traversals/TraverseActiveRegions.java | 11 ++-- .../gatk/walkers/ActiveRegionWalker.java | 3 +- .../broadinstitute/sting/utils/MathUtils.java | 10 ++++ .../utils/activeregion/ActivityProfile.java | 52 +++++++++++-------- .../activeregion/ActivityProfileResult.java | 31 +++++++++++ .../activeregion/ActivityProfileUnitTest.java | 11 +++- 7 files changed, 89 insertions(+), 32 deletions(-) create mode 100644 public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfileResult.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java index 6ff9f3bd5d..7d035d208f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java +++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java @@ -279,7 +279,6 @@ public AlignmentContext next() { */ private void lazyLoadNextAlignmentContext() { while (nextAlignmentContext == null && readStates.hasNext()) { - // this call will set hasExtendedEvents to true if it picks up a read with indel right before the current position on the ref: readStates.collectPendingReads(); final GenomeLoc location = getLocation(); @@ -378,7 +377,7 @@ private void updateReadStates() { CigarOperator op = state.stepForwardOnGenome(); if (op == null) { // we discard the read only when we are past its end AND indel at the end of the read (if any) was - // already processed. Keeping the read state that retunred null upon stepForwardOnGenome() is safe + // already processed. Keeping the read state that returned null upon stepForwardOnGenome() is safe // as the next call to stepForwardOnGenome() will return null again AND will clear hadIndel() flag. it.remove(); // we've stepped off the end of the object } diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java index 1b9c12fb06..845c4eacf3 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java +++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java @@ -13,6 +13,7 @@ import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocSortedSet; import org.broadinstitute.sting.utils.activeregion.ActivityProfile; +import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; @@ -69,8 +70,7 @@ public T traverse( final ActiveRegionWalker walker, for(int iii = prevLoc.getStop() + 1; iii < location.getStart(); iii++ ) { final GenomeLoc fakeLoc = engine.getGenomeLocParser().createGenomeLoc(prevLoc.getContig(), iii, iii); if( initialIntervals == null || initialIntervals.overlaps( fakeLoc ) ) { - final double isActiveProb = ( walker.hasPresetActiveRegions() && walker.presetActiveRegions.overlaps(fakeLoc) ? 1.0 : 0.0 ); - profile.add(fakeLoc, isActiveProb); + profile.add(fakeLoc, new ActivityProfileResult( walker.hasPresetActiveRegions() && walker.presetActiveRegions.overlaps(fakeLoc) ? 1.0 : 0.0 )); } } } @@ -86,8 +86,7 @@ public T traverse( final ActiveRegionWalker walker, // Call the walkers isActive function for this locus and add them to the list to be integrated later if( initialIntervals == null || initialIntervals.overlaps( location ) ) { - final double isActiveProb = walkerActiveProb(walker, tracker, refContext, locus, location); - profile.add(location, isActiveProb); + profile.add(location, walkerActiveProb(walker, tracker, refContext, locus, location)); } // Grab all the previously unseen reads from this pileup and add them to the massive read list @@ -144,11 +143,11 @@ public T traverse( final ActiveRegionWalker walker, // // -------------------------------------------------------------------------------- - private final double walkerActiveProb(final ActiveRegionWalker walker, + private final ActivityProfileResult walkerActiveProb(final ActiveRegionWalker walker, final RefMetaDataTracker tracker, final ReferenceContext refContext, final AlignmentContext locus, final GenomeLoc location) { if ( walker.hasPresetActiveRegions() ) { - return walker.presetActiveRegions.overlaps(location) ? 1.0 : 0.0; + return new ActivityProfileResult(walker.presetActiveRegions.overlaps(location) ? 1.0 : 0.0); } else { return walker.isActive( tracker, refContext, locus ); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java index e38e166eac..b2975cbbf8 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java @@ -12,6 +12,7 @@ import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocSortedSet; +import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult; import org.broadinstitute.sting.utils.interval.IntervalMergingRule; import org.broadinstitute.sting.utils.interval.IntervalSetRule; import org.broadinstitute.sting.utils.interval.IntervalUtils; @@ -72,7 +73,7 @@ public boolean wantsNonPrimaryReads() { } // Determine probability of active status over the AlignmentContext - public abstract double isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context); + public abstract ActivityProfileResult isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context); // Map over the ActiveRegion public abstract MapType map(final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion, final RefMetaDataTracker metaDataTracker); diff --git a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java index e024253c96..1f5eaefee8 100644 --- a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java @@ -1596,7 +1596,17 @@ public static Double dotProduct(E[] v1, E[] v2) { result += v1[k].doubleValue() * v2[k].doubleValue(); return result; + } + + public static double dotProduct(double[] v1, double[] v2) { + if (v1.length != v2.length) + throw new UserException("BUG: vectors v1, v2 of different size in vectorSum()"); + double result = 0.0; + for (int k = 0; k < v1.length; k++) + result += v1[k] * v2[k]; + + return result; } public static double[] vectorLog10(double v1[]) { diff --git a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java index 4333e471e2..1c91551dba 100644 --- a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java +++ b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java @@ -31,7 +31,6 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.ArrayList; -import java.util.Arrays; import java.util.Collections; import java.util.List; @@ -46,13 +45,13 @@ public class ActivityProfile { final GenomeLocParser parser; final boolean presetRegions; GenomeLoc regionStartLoc = null; - final List isActiveList; + final List isActiveList; private GenomeLoc lastLoc = null; private static final int FILTER_SIZE = 65; - private static final Double[] GaussianKernel; + private static final double[] GaussianKernel; static { - GaussianKernel = new Double[2*FILTER_SIZE + 1]; + GaussianKernel = new double[2*FILTER_SIZE + 1]; for( int iii = 0; iii < 2*FILTER_SIZE + 1; iii++ ) { GaussianKernel[iii] = MathUtils.NormalDistribution(FILTER_SIZE, 40.0, iii); } @@ -63,22 +62,22 @@ public class ActivityProfile { // todo -- add unit tests // TODO -- own preset regions public ActivityProfile(final GenomeLocParser parser, final boolean presetRegions) { - this(parser, presetRegions, new ArrayList(), null); + this(parser, presetRegions, new ArrayList(), null); } - protected ActivityProfile(final GenomeLocParser parser, final boolean presetRegions, final List isActiveList, final GenomeLoc regionStartLoc) { + protected ActivityProfile(final GenomeLocParser parser, final boolean presetRegions, final List isActiveList, final GenomeLoc regionStartLoc) { this.parser = parser; this.presetRegions = presetRegions; this.isActiveList = isActiveList; this.regionStartLoc = regionStartLoc; } - public void add(final GenomeLoc loc, final double score) { + public void add(final GenomeLoc loc, final ActivityProfileResult result) { if ( loc.size() != 1 ) throw new ReviewedStingException("Bad add call to ActivityProfile: loc " + loc + " size != 1" ); if ( lastLoc != null && loc.getStart() != lastLoc.getStop() + 1 ) throw new ReviewedStingException("Bad add call to ActivityProfile: lastLoc added " + lastLoc + " and next is " + loc); - isActiveList.add(score); + isActiveList.add(result); if( regionStartLoc == null ) { regionStartLoc = loc; } @@ -93,22 +92,33 @@ public int size() { * @return a new ActivityProfile that's the band-pass filtered version of this profile */ public ActivityProfile bandPassFilter() { - final Double[] activeProbArray = isActiveList.toArray(new Double[isActiveList.size()]); - final Double[] filteredProbArray = new Double[activeProbArray.length]; + final double[] activeProbArray = new double[isActiveList.size()]; + int iii = 0; + for( final ActivityProfileResult result : isActiveList ) { + activeProbArray[iii++] = result.isActiveProb; + } + final double[] filteredProbArray = new double[activeProbArray.length]; if( !presetRegions ) { - for( int iii = 0; iii < activeProbArray.length; iii++ ) { - final Double[] kernel = (Double[]) ArrayUtils.subarray(GaussianKernel, Math.max(FILTER_SIZE-iii, 0), Math.min(GaussianKernel.length,FILTER_SIZE + activeProbArray.length - iii)); - final Double[] activeProbSubArray = (Double[]) ArrayUtils.subarray(activeProbArray, Math.max(0,iii - FILTER_SIZE), Math.min(activeProbArray.length,iii + FILTER_SIZE + 1)); + for( iii = 0; iii < activeProbArray.length; iii++ ) { + final double[] kernel = ArrayUtils.subarray(GaussianKernel, Math.max(FILTER_SIZE-iii, 0), Math.min(GaussianKernel.length,FILTER_SIZE + activeProbArray.length - iii)); + final double[] activeProbSubArray = ArrayUtils.subarray(activeProbArray, Math.max(0,iii - FILTER_SIZE), Math.min(activeProbArray.length,iii + FILTER_SIZE + 1)); filteredProbArray[iii] = MathUtils.dotProduct(activeProbSubArray, kernel); } } - return new ActivityProfile(parser, presetRegions, Arrays.asList(filteredProbArray), regionStartLoc); + iii = 0; + for( final double prob : filteredProbArray ) { + final ActivityProfileResult result = isActiveList.get(iii++); + result.isActiveProb = prob; + result.resultState = ActivityProfileResult.ActivityProfileResultState.NONE; + result.resultValue = null; + } + return new ActivityProfile(parser, presetRegions, isActiveList, regionStartLoc); } /** * Partition this profile into active regions - * @param activeRegionExtension - * @return + * @param activeRegionExtension the amount of margin overlap in the active region + * @return the list of active regions */ public List createActiveRegions( final int activeRegionExtension, final int maxRegionSize ) { final double ACTIVE_PROB_THRESHOLD = 0.002; // TODO: needs to be set-able by the walker author @@ -119,14 +129,14 @@ public List createActiveRegions( final int activeRegionExtension, return Collections.emptyList(); } else if( isActiveList.size() == 1 ) { // there's a single element, it's either active or inactive - boolean isActive = isActiveList.get(0) > ACTIVE_PROB_THRESHOLD; + boolean isActive = isActiveList.get(0).isActiveProb > ACTIVE_PROB_THRESHOLD; returnList.addAll(createActiveRegion(isActive, 0, 0, activeRegionExtension, maxRegionSize)); } else { // there are 2+ elements, divide these up into regions - boolean isActive = isActiveList.get(0) > ACTIVE_PROB_THRESHOLD; + boolean isActive = isActiveList.get(0).isActiveProb > ACTIVE_PROB_THRESHOLD; int curStart = 0; for(int iii = 1; iii < isActiveList.size(); iii++ ) { - final boolean thisStatus = isActiveList.get(iii) > ACTIVE_PROB_THRESHOLD; + final boolean thisStatus = isActiveList.get(iii).isActiveProb > ACTIVE_PROB_THRESHOLD; if( isActive != thisStatus ) { returnList.addAll(createActiveRegion(isActive, curStart, iii - 1, activeRegionExtension, maxRegionSize)); isActive = thisStatus; @@ -143,7 +153,7 @@ public List createActiveRegions( final int activeRegionExtension, * @param isActive should the region be active? * @param curStart offset (0-based) from the start of this region * @param curEnd offset (0-based) from the start of this region - * @param activeRegionExtension + * @param activeRegionExtension the amount of margin overlap in the active region * @return a fully initialized ActiveRegion with the above properties */ private final List createActiveRegion(final boolean isActive, final int curStart, final int curEnd, final int activeRegionExtension, final int maxRegionSize) { @@ -161,7 +171,7 @@ private final List createActiveRegion(final boolean isActive, fina final int size = curEnd - curStart + 1; for( int iii = curStart + (int)(size*0.25); iii < curEnd - (int)(size*0.25); iii++ ) { - if( isActiveList.get(iii) < minProb ) { minProb = isActiveList.get(iii); cutPoint = iii; } + if( isActiveList.get(iii).isActiveProb < minProb ) { minProb = isActiveList.get(iii).isActiveProb; cutPoint = iii; } } final List leftList = createActiveRegion(isActive, curStart, cutPoint, activeRegionExtension, maxRegionSize, new ArrayList()); final List rightList = createActiveRegion(isActive, cutPoint+1, curEnd, activeRegionExtension, maxRegionSize, new ArrayList()); diff --git a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfileResult.java b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfileResult.java new file mode 100644 index 0000000000..8dc29aa3c9 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfileResult.java @@ -0,0 +1,31 @@ +package org.broadinstitute.sting.utils.activeregion; + +/** + * Created with IntelliJ IDEA. + * User: rpoplin + * Date: 7/27/12 + */ + +public class ActivityProfileResult { + public double isActiveProb; + public ActivityProfileResultState resultState; + public Number resultValue; + + public enum ActivityProfileResultState { + NONE, + HIGH_QUALITY_SOFT_CLIPS + } + + public ActivityProfileResult( final double isActiveProb ) { + this.isActiveProb = isActiveProb; + this.resultState = ActivityProfileResultState.NONE; + this.resultValue = null; + } + + public ActivityProfileResult( final double isActiveProb, final ActivityProfileResultState resultState, final Number resultValue ) { + this.isActiveProb = isActiveProb; + this.resultState = resultState; + this.resultValue = resultValue; + } + +} diff --git a/public/java/test/org/broadinstitute/sting/utils/activeregion/ActivityProfileUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/activeregion/ActivityProfileUnitTest.java index 282f19d8a2..f7c564c741 100644 --- a/public/java/test/org/broadinstitute/sting/utils/activeregion/ActivityProfileUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/activeregion/ActivityProfileUnitTest.java @@ -123,12 +123,12 @@ public void testBasicActivityProfile(BasicActivityProfileTestProvider cfg) { for ( int i = 0; i < cfg.probs.size(); i++ ) { double p = cfg.probs.get(i); GenomeLoc loc = genomeLocParser.createGenomeLoc(cfg.regionStart.getContig(), cfg.regionStart.getStart() + i, cfg.regionStart.getStart() + i); - profile.add(loc, p); + profile.add(loc, new ActivityProfileResult(p)); } Assert.assertEquals(profile.regionStartLoc, genomeLocParser.createGenomeLoc(cfg.regionStart.getContig(), cfg.regionStart.getStart(), cfg.regionStart.getStart() )); Assert.assertEquals(profile.size(), cfg.probs.size()); - Assert.assertEquals(profile.isActiveList, cfg.probs); + assertProbsAreEqual(profile.isActiveList, cfg.probs); assertRegionsAreEqual(profile.createActiveRegions(0, 100), cfg.expectedRegions); } @@ -140,5 +140,12 @@ private void assertRegionsAreEqual(List actual, List } } + private void assertProbsAreEqual(List actual, List expected) { + Assert.assertEquals(actual.size(), expected.size()); + for ( int i = 0; i < actual.size(); i++ ) { + Assert.assertEquals(actual.get(i).isActiveProb, expected.get(i)); + } + } + // todo -- test extensions } \ No newline at end of file From 12c5c2dcc1890801e3123d15876bfcdb18ff2d89 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Fri, 27 Jul 2012 12:44:02 -0400 Subject: [PATCH 013/176] HaplotypeCaller now use an excessive number of high quality soft clips as a triggering signal in order to capture both end points of a large deletion in a single active region. --- .../utils/activeregion/ActivityProfile.java | 16 +++++++-- .../sting/utils/sam/AlignmentUtils.java | 35 +++++++++++++++++++ 2 files changed, 48 insertions(+), 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java index 1c91551dba..7e736b7bf1 100644 --- a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java +++ b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java @@ -47,13 +47,13 @@ public class ActivityProfile { GenomeLoc regionStartLoc = null; final List isActiveList; private GenomeLoc lastLoc = null; - private static final int FILTER_SIZE = 65; + private static final int FILTER_SIZE = 80; private static final double[] GaussianKernel; static { GaussianKernel = new double[2*FILTER_SIZE + 1]; for( int iii = 0; iii < 2*FILTER_SIZE + 1; iii++ ) { - GaussianKernel[iii] = MathUtils.NormalDistribution(FILTER_SIZE, 40.0, iii); + GaussianKernel[iii] = MathUtils.NormalDistribution(FILTER_SIZE, 55.0, iii); } } @@ -97,6 +97,16 @@ public ActivityProfile bandPassFilter() { for( final ActivityProfileResult result : isActiveList ) { activeProbArray[iii++] = result.isActiveProb; } + iii = 0; + for( final ActivityProfileResult result : isActiveList ) { + if( result.resultState.equals(ActivityProfileResult.ActivityProfileResultState.HIGH_QUALITY_SOFT_CLIPS) ) { // special code to deal with the problem that high quality soft clipped bases aren't added to pileups + final int numHQClips = result.resultValue.intValue(); + for( int jjj = Math.max(0, iii - numHQClips); jjj < Math.min(activeProbArray.length, iii+numHQClips); jjj++ ) { + activeProbArray[jjj] = Math.max(activeProbArray[jjj], activeProbArray[iii]); + } + } + iii++; + } final double[] filteredProbArray = new double[activeProbArray.length]; if( !presetRegions ) { for( iii = 0; iii < activeProbArray.length; iii++ ) { @@ -170,7 +180,7 @@ private final List createActiveRegion(final boolean isActive, fina int cutPoint = -1; final int size = curEnd - curStart + 1; - for( int iii = curStart + (int)(size*0.25); iii < curEnd - (int)(size*0.25); iii++ ) { + for( int iii = curStart + (int)(size*0.15); iii < curEnd - (int)(size*0.15); iii++ ) { if( isActiveList.get(iii).isActiveProb < minProb ) { minProb = isActiveList.get(iii).isActiveProb; cutPoint = iii; } } final List leftList = createActiveRegion(isActive, curStart, cutPoint, activeRegionExtension, maxRegionSize, new ArrayList()); diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java index e5e747c2d5..895de35782 100644 --- a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java @@ -30,6 +30,7 @@ import net.sf.samtools.CigarOperator; import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.walkers.bqsr.EventType; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; @@ -405,6 +406,40 @@ public static byte[] alignmentToByteArray(final Cigar cigar, final byte[] read, return alignment; } + public static int calcNumHighQualitySoftClips( final GATKSAMRecord read, final byte qualThreshold ) { + + int numHQSoftClips = 0; + int alignPos = 0; + final Cigar cigar = read.getCigar(); + final byte[] qual = read.getBaseQualities( EventType.BASE_SUBSTITUTION ); + + for( int iii = 0; iii < cigar.numCigarElements(); iii++ ) { + + final CigarElement ce = cigar.getCigarElement(iii); + final int elementLength = ce.getLength(); + + switch( ce.getOperator() ) { + case S: + for( int jjj = 0; jjj < elementLength; jjj++ ) { + if( qual[alignPos++] > qualThreshold ) { numHQSoftClips++; } + } + break; + case M: + case I: + alignPos += elementLength; + break; + case H: + case P: + case D: + case N: + break; + default: + throw new ReviewedStingException("Unsupported cigar operator: " + ce.getOperator()); + } + } + return numHQSoftClips; + } + public static int calcAlignmentByteArrayOffset(final Cigar cigar, final PileupElement pileupElement, final int alignmentStart, final int refLocus) { return calcAlignmentByteArrayOffset( cigar, pileupElement.getOffset(), pileupElement.isInsertionAtBeginningOfRead(), pileupElement.isDeletion(), alignmentStart, refLocus ); } From 48a129af529e715ce809eb620526c3c4413a80da Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Fri, 27 Jul 2012 15:48:40 -0400 Subject: [PATCH 014/176] Allele refactoring checkpoint #3: all integration tests except for PoolCaller are passing now. Fixed a couple of bugs from old code that popped up during md5 difference review. Added VariantContextUtils.requiresPaddingBase() method for tools that create alleles to use for determining whether or not to add the ref padding base. One of the HaplotypeCaller tests wasn't passing because of RankSumTest differences, so I added a TODO for Ryan to look into this. --- .../gatk/refdata/VariantContextAdaptors.java | 37 +++++++++++++------ .../validation/ValidationAmplicons.java | 22 +++++++++-- .../walkers/variantutils/VariantsToTable.java | 2 +- .../broadinstitute/sting/utils/Haplotype.java | 9 +++-- .../utils/variantcontext/VariantContext.java | 10 ++--- .../variantcontext/VariantContextUtils.java | 35 ++++++++++++++++-- .../ValidationAmpliconsIntegrationTest.java | 6 +-- .../CombineVariantsIntegrationTest.java | 8 ++-- .../utils/codecs/vcf/VCFIntegrationTest.java | 4 +- 9 files changed, 95 insertions(+), 38 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java index dd1eea8a42..1b75a2c70e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java @@ -170,31 +170,33 @@ public VariantContext convert(String name, Object input, ReferenceContext ref) { final byte refBaseForIndel = ref.getBases()[index]; - Allele refAllele; - if ( dbsnp.getNCBIRefBase().equals("-") ) - refAllele = Allele.create(refBaseForIndel); - else if ( ! Allele.acceptableAlleleBases(dbsnp.getNCBIRefBase()) ) - return null; - else - refAllele = Allele.create(refBaseForIndel + dbsnp.getNCBIRefBase(), true); - boolean addPaddingBase; if ( isSNP(dbsnp) || isMNP(dbsnp) ) addPaddingBase = false; else if ( isIndel(dbsnp) || dbsnp.getVariantType().contains("mixed") ) - addPaddingBase = true; + addPaddingBase = VariantContextUtils.requiresPaddingBase(stripNullDashes(getAlleleList(dbsnp))); else return null; // can't handle anything else + Allele refAllele; + if ( dbsnp.getNCBIRefBase().equals("-") ) + refAllele = Allele.create(refBaseForIndel, true); + else if ( ! Allele.acceptableAlleleBases(dbsnp.getNCBIRefBase()) ) + return null; + else + refAllele = Allele.create((addPaddingBase ? (char)refBaseForIndel : "") + dbsnp.getNCBIRefBase(), true); + final List alleles = new ArrayList(); alleles.add(refAllele); // add all of the alt alleles for ( String alt : getAlternateAlleleList(dbsnp) ) { - if ( ! Allele.acceptableAlleleBases(alt) ) { + if ( Allele.wouldBeNullAllele(alt.getBytes())) + alt = ""; + else if ( ! Allele.acceptableAlleleBases(alt) ) return null; - } - alleles.add(Allele.create((addPaddingBase ? refBaseForIndel : "") + alt, false)); + + alleles.add(Allele.create((addPaddingBase ? (char)refBaseForIndel : "") + alt, false)); } final VariantContextBuilder builder = new VariantContextBuilder(); @@ -203,6 +205,17 @@ else if ( isIndel(dbsnp) || dbsnp.getVariantType().contains("mixed") ) builder.alleles(alleles); return builder.make(); } + + private static List stripNullDashes(final List alleles) { + final List newAlleles = new ArrayList(alleles.size()); + for ( final String allele : alleles ) { + if ( allele.equals("-") ) + newAlleles.add(""); + else + newAlleles.add(allele); + } + return newAlleles; + } } // -------------------------------------------------------------------------------------------------------------- diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java index 9676704c2b..9d96dedefb 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java @@ -25,6 +25,7 @@ import java.io.File; import java.io.PrintStream; import java.util.ArrayList; +import java.util.Arrays; import java.util.LinkedList; import java.util.List; @@ -262,20 +263,33 @@ public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentCo sequenceInvalid = true; invReason.add("SITE_IS_FILTERED"); } + + String refString = validate.getReference().getDisplayString(); + String altString = validate.getAlternateAllele(0).getDisplayString(); + if ( validate.isIndel() ) { sequence.append(Character.toUpperCase((char)ref.getBase())); rawSequence.append(Character.toUpperCase((char)ref.getBase())); + final byte[] refAllele = validate.getReference().getBases(); + refString = new String(Arrays.copyOfRange(refAllele, 1, refAllele.length)); + if ( refString.isEmpty() ) + refString = "-"; + final byte[] altAllele = validate.getAlternateAllele(0).getBases(); + altString = new String(Arrays.copyOfRange(altAllele, 1, altAllele.length)); + if ( altString.isEmpty() ) + altString = "-"; } + sequence.append('['); - sequence.append(validate.getAlternateAllele(0).toString()); + sequence.append(altString); sequence.append('/'); - sequence.append(validate.getReference().toString()); + sequence.append(refString); sequence.append(']'); // do this to the raw sequence to -- the indeces will line up that way rawSequence.append('['); - rawSequence.append(validate.getAlternateAllele(0).getBaseString()); + rawSequence.append(altString); rawSequence.append('/'); - rawSequence.append(validate.getReference().getBaseString()); + rawSequence.append(refString); rawSequence.append(']'); allelePos = ref.getLocus(); if ( indelCounter > 0 ) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java index adf30146f6..b73a498bc2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java @@ -381,7 +381,7 @@ public static abstract class Getter { public abstract String get(VariantContext getters.put("REF", new Getter() { public String get(VariantContext vc) { StringBuilder x = new StringBuilder(); - x.append(vc.getReference()); + x.append(vc.getReference().getDisplayString()); return x.toString(); } }); diff --git a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java index 143a053c97..54442622f5 100755 --- a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java +++ b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java @@ -176,7 +176,7 @@ public Haplotype insertAllele( final Allele refAllele, final Allele altAllele, i newHaplotype[haplotypeInsertLocation+iii] = altAllele.getBases()[iii]; } } else if( refAllele.length() < altAllele.length() ) { // insertion - final int altAlleleLength = altAllele.length(); + final int altAlleleLength = altAllele.length() - 1; newHaplotype = new byte[bases.length + altAlleleLength]; for( int iii = 0; iii < bases.length; iii++ ) { newHaplotype[iii] = bases[iii]; @@ -185,15 +185,16 @@ public Haplotype insertAllele( final Allele refAllele, final Allele altAllele, i newHaplotype[iii] = newHaplotype[iii-altAlleleLength]; } for( int iii = 0; iii < altAlleleLength; iii++ ) { - newHaplotype[haplotypeInsertLocation+iii] = altAllele.getBases()[iii]; + newHaplotype[haplotypeInsertLocation+iii] = altAllele.getBases()[iii+1]; } } else { // deletion final int shift = refAllele.length() - altAllele.length(); + final int altAlleleLength = altAllele.length() - 1; newHaplotype = new byte[bases.length - shift]; - for( int iii = 0; iii < haplotypeInsertLocation + altAllele.length(); iii++ ) { + for( int iii = 0; iii < haplotypeInsertLocation + altAlleleLength; iii++ ) { newHaplotype[iii] = bases[iii]; } - for( int iii = haplotypeInsertLocation + altAllele.length(); iii < newHaplotype.length; iii++ ) { + for( int iii = haplotypeInsertLocation + altAlleleLength; iii < newHaplotype.length; iii++ ) { newHaplotype[iii] = bases[iii+shift]; } } diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java index 72681ae354..979400350e 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java @@ -1129,6 +1129,11 @@ private void validateStop() { else throw new ReviewedStingException(message); } + } else { + final long length = (stop - start) + 1; + if ( ! hasSymbolicAlleles() && length != getReference().length() ) { + throw new IllegalStateException("BUG: GenomeLoc " + contig + ":" + start + "-" + stop + " has a size == " + length + " but the variation reference allele has length " + getReference().length() + " this = " + this); + } } } @@ -1151,11 +1156,6 @@ private void validateAlleles() { // make sure there's one reference allele if ( ! alreadySeenRef ) throw new IllegalArgumentException("No reference allele found in VariantContext"); - - final long length = (stop - start) + 1; - if ( ! hasSymbolicAlleles() && length != getReference().length() ) { - throw new IllegalStateException("BUG: GenomeLoc " + contig + ":" + start + "-" + stop + " has a size == " + length + " but the variation reference allele has length " + getReference().length() + " this = " + this); - } } private void validateGenotypes() { diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java index 70d365ef86..a8f956413d 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java @@ -747,7 +747,7 @@ else if (allelesAreSubset(vc,otherVC)) { if ( !mappedVCs.containsKey(vc.getType()) ) mappedVCs.put(vc.getType(), new ArrayList()); mappedVCs.get(vc.getType()).add(vc); - } + } } return mappedVCs; @@ -809,10 +809,10 @@ static private AlleleMapper resolveIncompatibleAlleles(Allele refAllele, Variant // // refAllele: ACGTGA // myRef: ACGT - // myAlt: - + // myAlt: A // // We need to remap all of the alleles in vc to include the extra GA so that - // myRef => refAllele and myAlt => GA + // myRef => refAllele and myAlt => AGA // Allele myRef = vc.getReference(); @@ -1335,6 +1335,35 @@ public static int computeEndFromAlleles(final List alleles, final int st } } + public static boolean requiresPaddingBase(final List alleles) { + + // see whether one of the alleles would be null if trimmed through + + for ( final String allele : alleles ) { + if ( allele.isEmpty() ) + return true; + } + + int clipping = 0; + Character currentBase = null; + + while ( true ) { + for ( final String allele : alleles ) { + if ( allele.length() - clipping == 0 ) + return true; + + char myBase = allele.charAt(clipping); + if ( currentBase == null ) + currentBase = myBase; + else if ( currentBase != myBase ) + return false; + } + + clipping++; + currentBase = null; + } + } + public static VariantContext reverseTrimAlleles( final VariantContext inputVC ) { // TODO - this function doesn't work with mixed records or records that started as mixed and then became non-mixed diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java index 7a849a8193..80eda5ed9e 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java @@ -23,7 +23,7 @@ public void testWikiExample() { testArgs += " --ProbeIntervals:table "+intervalTable+" -L:table "+intervalTable+" --MaskAlleles:VCF "+maskVCF; testArgs += " --virtualPrimerSize 30"; WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1, - Arrays.asList("27f9450afa132888a8994167f0035fd7")); + Arrays.asList("240d99b58f73985fb114abe9044c0271")); executeTest("Test probes", spec); } @@ -36,7 +36,7 @@ public void testWikiExampleNoBWA() { testArgs += " --ProbeIntervals:table "+intervalTable+" -L:table "+intervalTable+" --MaskAlleles:VCF "+maskVCF; testArgs += " --virtualPrimerSize 30 --doNotUseBWA"; WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1, - Arrays.asList("f2611ff1d9cd5bedaad003251fed8bc1")); + Arrays.asList("6e7789445e29d91979a21e78d3d53295")); executeTest("Test probes", spec); } @@ -49,7 +49,7 @@ public void testWikiExampleMonoFilter() { testArgs += " --ProbeIntervals:table "+intervalTable+" -L:table "+intervalTable+" --MaskAlleles:VCF "+maskVCF; testArgs += " --virtualPrimerSize 30 --filterMonomorphic"; WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1, - Arrays.asList("77b3f30e38fedad812125bdf6cf3255f")); + Arrays.asList("18d7236208db603e143b40db06ef2aca")); executeTest("Test probes", spec); } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java index bbee99ba67..3b60fa2c2d 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java @@ -98,16 +98,16 @@ public void combinePLs(String file1, String file2, String md5) { @Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "ac58a5fde17661e2a19004ca954d9781", " -setKey null"); } @Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "67a8076e30b4bca0ea5acdc9cd26a4e0"); } // official project VCF files in tabix format - @Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "ef2d249ea4b25311966e038aac05c661"); } - @Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "cdb448aaa92ca5a9e393d875b42581b3"); } + @Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "909c6dc74eeb5ab86f8e74073eb0c1d6"); } + @Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "f0c2cb3e3a6160e1ed0ee2fd9b120f55"); } @Test public void combineWithPLs() { combinePLs("combine.3.vcf", "combine.4.vcf", "f0ce3fb83d4ad9ba402d7cb11cd000c3"); } @Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "4efdf983918db822e4ac13d911509576"); } // official project VCF files in tabix format @Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "848d4408ee953053d2307cefebc6bd6d"); } // official project VCF files in tabix format - @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "91f6087e6e2bf3df4d1c9700eaff958b"); } + @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "4159a0c0d7c15852a3a545e0bea6bbc5"); } - @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "a9be239ab5e03e7e97caef58a3841dd2"); } + @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "61d0ded244895234ac727391f29f13a8"); } @Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "0b1815c699e71e143ed129bfadaffbcb"); } diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java index e9b845d598..8f648344d2 100644 --- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java @@ -57,7 +57,7 @@ public void testReadingAndWritingSamtools() { String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s "; String test1 = baseCommand + "-T SelectVariants -V " + testVCF; - WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("0f82ac11852e7f958c1a0ce52398c2ae")); + WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("38697c195e7abf18d95dcc16c8e6d284")); executeTest("Test reading and writing samtools vcf", spec1); } @@ -66,7 +66,7 @@ public void testWritingSamtoolsWExBCFExample() { String testVCF = privateTestDir + "ex2.vcf"; String baseCommand = "-R " + b36KGReference + " --no_cmdline_in_header -o %s "; String test1 = baseCommand + "-T SelectVariants -V " + testVCF; - WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("9773d6a121cfcb18d090965bc520f120")); + WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("a04a0fc22fedb516c663e56e51fc1e27")); executeTest("Test writing samtools WEx BCF example", spec1); } From 2a8b4d84c8b974c390cf1ab006a2d3a30cd77cd1 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Fri, 27 Jul 2012 17:03:49 -0400 Subject: [PATCH 015/176] All integration tests and VC/Allele unit tests are passing --- .../sting/utils/variantcontext/Allele.java | 11 ++--- .../utils/variantcontext/AlleleUnitTest.java | 32 +------------- .../VariantContextUnitTest.java | 42 +++++++------------ 3 files changed, 20 insertions(+), 65 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java index aa63a9dac7..2c312678e6 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java @@ -180,14 +180,9 @@ public static Allele create(byte base) { public static Allele extend(Allele left, byte[] right) { if (left.isSymbolic()) throw new IllegalArgumentException("Cannot extend a symbolic allele"); - byte[] bases; - if ( left.length() == 0 ) - bases = right; - else { - bases = new byte[left.length() + right.length]; - System.arraycopy(left.getBases(), 0, bases, 0, left.length()); - System.arraycopy(right, 0, bases, left.length(), right.length); - } + byte[] bases = new byte[left.length() + right.length]; + System.arraycopy(left.getBases(), 0, bases, 0, left.length()); + System.arraycopy(right, 0, bases, left.length(), right.length); return create(bases, left.isReference()); } diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/AlleleUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/AlleleUnitTest.java index 3bf020df76..65398c373e 100755 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/AlleleUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/AlleleUnitTest.java @@ -47,13 +47,10 @@ * Basic unit test for RecalData */ public class AlleleUnitTest { - Allele ARef, del, delRef, A, T, ATIns, ATCIns, NoCall; + Allele ARef, A, T, ATIns, ATCIns, NoCall; @BeforeSuite public void before() { - del = Allele.create("-"); - delRef = Allele.create("-", true); - A = Allele.create("A"); ARef = Allele.create("A", true); T = Allele.create("T"); @@ -99,14 +96,6 @@ public void testCreatingIndelAlleles() { Assert.assertEquals(ATCIns.length(), 3); Assert.assertEquals(ATIns.getBases(), "AT".getBytes()); Assert.assertEquals(ATCIns.getBases(), "ATC".getBytes()); - - Assert.assertTrue(del.isNonReference()); - Assert.assertFalse(delRef.isNonReference()); - Assert.assertFalse(del.isReference()); - Assert.assertTrue(delRef.isReference()); - Assert.assertFalse(del.basesMatch("-")); - Assert.assertTrue(del.basesMatch("")); - Assert.assertEquals(del.length(), 0); } @@ -122,18 +111,6 @@ public void testConstructors1() { Assert.assertFalse(a1.equals(a4)); } - @Test - public void testDelConstructors() { - Allele a1 = Allele.create("-"); - Allele a2 = Allele.create("-".getBytes()); - Allele a3 = Allele.create(""); - Allele a4 = Allele.create("", true); - - Assert.assertTrue(a1.equals(a2)); - Assert.assertTrue(a1.equals(a3)); - Assert.assertFalse(a1.equals(a4)); - } - @Test public void testInsConstructors() { Allele a1 = Allele.create("AC"); @@ -150,7 +127,6 @@ public void testInsConstructors() { public void testEquals() { Assert.assertTrue(ARef.basesMatch(A)); Assert.assertFalse(ARef.equals(A)); - Assert.assertFalse(ARef.equals(del)); Assert.assertFalse(ARef.equals(ATIns)); Assert.assertFalse(ARef.equals(ATCIns)); @@ -158,11 +134,6 @@ public void testEquals() { Assert.assertFalse(T.basesMatch(A)); Assert.assertFalse(T.equals(A)); - Assert.assertTrue(del.basesMatch(del)); - Assert.assertTrue(del.basesMatch(delRef)); - Assert.assertTrue(del.equals(del)); - Assert.assertFalse(del.equals(delRef)); - Assert.assertTrue(ATIns.equals(ATIns)); Assert.assertFalse(ATIns.equals(ATCIns)); Assert.assertTrue(ATIns.basesMatch("AT")); @@ -203,7 +174,6 @@ public void testBadConstructorArgs5() { public void testExtend() { Assert.assertEquals("AT", Allele.extend(Allele.create("A"), "T".getBytes()).toString()); Assert.assertEquals("ATA", Allele.extend(Allele.create("A"), "TA".getBytes()).toString()); - Assert.assertEquals("A", Allele.extend(Allele.create("-"), "A".getBytes()).toString()); Assert.assertEquals("A", Allele.extend(Allele.NO_CALL, "A".getBytes()).toString()); Assert.assertEquals("ATCGA", Allele.extend(Allele.create("AT"), "CGA".getBytes()).toString()); Assert.assertEquals("ATCGA", Allele.extend(Allele.create("ATC"), "GA".getBytes()).toString()); diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java index 46153221d8..272166c68c 100755 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java @@ -381,13 +381,13 @@ public void testAccessingSimpleSNPGenotypes() { @Test public void testAccessingCompleteGenotypes() { - List alleles = Arrays.asList(Aref, T, del); + List alleles = Arrays.asList(Aref, T, ATC); Genotype g1 = GenotypeBuilder.create("AA", Arrays.asList(Aref, Aref)); Genotype g2 = GenotypeBuilder.create("AT", Arrays.asList(Aref, T)); Genotype g3 = GenotypeBuilder.create("TT", Arrays.asList(T, T)); - Genotype g4 = GenotypeBuilder.create("Td", Arrays.asList(T, del)); - Genotype g5 = GenotypeBuilder.create("dd", Arrays.asList(del, del)); + Genotype g4 = GenotypeBuilder.create("Td", Arrays.asList(T, ATC)); + Genotype g5 = GenotypeBuilder.create("dd", Arrays.asList(ATC, ATC)); Genotype g6 = GenotypeBuilder.create("..", Arrays.asList(Allele.NO_CALL, Allele.NO_CALL)); VariantContext vc = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, alleles) @@ -403,7 +403,7 @@ public void testAccessingCompleteGenotypes() { Assert.assertEquals(10, vc.getCalledChrCount()); Assert.assertEquals(3, vc.getCalledChrCount(Aref)); Assert.assertEquals(4, vc.getCalledChrCount(T)); - Assert.assertEquals(3, vc.getCalledChrCount(del)); + Assert.assertEquals(3, vc.getCalledChrCount(ATC)); Assert.assertEquals(2, vc.getCalledChrCount(Allele.NO_CALL)); } @@ -411,7 +411,7 @@ public void testAccessingCompleteGenotypes() { public void testAccessingRefGenotypes() { List alleles1 = Arrays.asList(Aref, T); List alleles2 = Arrays.asList(Aref); - List alleles3 = Arrays.asList(Aref, T, del); + List alleles3 = Arrays.asList(Aref, T); for ( List alleles : Arrays.asList(alleles1, alleles2, alleles3)) { Genotype g1 = GenotypeBuilder.create("AA1", Arrays.asList(Aref, Aref)); Genotype g2 = GenotypeBuilder.create("AA2", Arrays.asList(Aref, Aref)); @@ -433,7 +433,7 @@ public void testAccessingRefGenotypes() { @Test public void testFilters() { - List alleles = Arrays.asList(Aref, T, del); + List alleles = Arrays.asList(Aref, T); Genotype g1 = GenotypeBuilder.create("AA", Arrays.asList(Aref, Aref)); Genotype g2 = GenotypeBuilder.create("AT", Arrays.asList(Aref, T)); @@ -492,15 +492,15 @@ public void testRepeatAllele() { Assert.assertEquals(VariantContextUtils.findRepeatedSubstring("AATAATA".getBytes()),7); - // -*,ATC, context = ATC ATC ATC : (ATC)3 -> (ATC)4 + // A*,ATC, context = ATC ATC ATC : (ATC)3 -> (ATC)4 VariantContext vc = new VariantContextBuilder("foo", insLoc, insLocStart, insLocStop, Arrays.asList(nullR,atc)).make(); result = VariantContextUtils.getNumTandemRepeatUnits(vc,refBytes); Assert.assertEquals(result.getFirst().toArray()[0],3); Assert.assertEquals(result.getFirst().toArray()[1],4); Assert.assertEquals(result.getSecond().length,3); - // ATC*,-,ATCATC - vc = new VariantContextBuilder("foo", insLoc, insLocStart, insLocStop, Arrays.asList(ATCref,nullA,atcatc)).make(); + // ATC*,A,ATCATC + vc = new VariantContextBuilder("foo", insLoc, insLocStart, insLocStart+3, Arrays.asList(Allele.create("AATC", true),nullA,atcatc)).make(); result = VariantContextUtils.getNumTandemRepeatUnits(vc,refBytes); Assert.assertEquals(result.getFirst().toArray()[0],3); Assert.assertEquals(result.getFirst().toArray()[1],2); @@ -517,7 +517,7 @@ public void testRepeatAllele() { // CCCC*,CC,-,CCCCCC, context = CCC: (C)7 -> (C)5,(C)3,(C)9 refBytes = "TCCCCCCCAGAGAGAG".getBytes(); - vc = new VariantContextBuilder("foo", insLoc, insLocStart, insLocStop, Arrays.asList(ccccR,cc, nullA,cccccc)).make(); + vc = new VariantContextBuilder("foo", insLoc, insLocStart, insLocStart+4, Arrays.asList(ccccR,cc, nullA,cccccc)).make(); result = VariantContextUtils.getNumTandemRepeatUnits(vc,refBytes); Assert.assertEquals(result.getFirst().toArray()[0],7); Assert.assertEquals(result.getFirst().toArray()[1],5); @@ -527,7 +527,7 @@ public void testRepeatAllele() { // GAGA*,-,GAGAGAGA refBytes = "TGAGAGAGAGATTT".getBytes(); - vc = new VariantContextBuilder("foo", insLoc, insLocStart, insLocStop, Arrays.asList(gagaR, nullA,gagagaga)).make(); + vc = new VariantContextBuilder("foo", insLoc, insLocStart, insLocStart+4, Arrays.asList(gagaR, nullA,gagagaga)).make(); result = VariantContextUtils.getNumTandemRepeatUnits(vc,refBytes); Assert.assertEquals(result.getFirst().toArray()[0],5); Assert.assertEquals(result.getFirst().toArray()[1],3); @@ -559,27 +559,24 @@ public void testGetGenotypeCounts() { @Test public void testVCFfromGenotypes() { - List alleles = Arrays.asList(Aref, T, del); + List alleles = Arrays.asList(Aref, T); Genotype g1 = GenotypeBuilder.create("AA", Arrays.asList(Aref, Aref)); Genotype g2 = GenotypeBuilder.create("AT", Arrays.asList(Aref, T)); Genotype g3 = GenotypeBuilder.create("TT", Arrays.asList(T, T)); Genotype g4 = GenotypeBuilder.create("..", Arrays.asList(Allele.NO_CALL, Allele.NO_CALL)); - Genotype g5 = GenotypeBuilder.create("--", Arrays.asList(del, del)); - VariantContext vc = new VariantContextBuilder("genotypes", snpLoc, snpLocStart, snpLocStop, alleles).genotypes(g1,g2,g3,g4,g5).make(); + VariantContext vc = new VariantContextBuilder("genotypes", snpLoc, snpLocStart, snpLocStop, alleles).genotypes(g1,g2,g3,g4).make(); VariantContext vc12 = vc.subContextFromSamples(new HashSet(Arrays.asList(g1.getSampleName(), g2.getSampleName())), true); VariantContext vc1 = vc.subContextFromSamples(new HashSet(Arrays.asList(g1.getSampleName())), true); VariantContext vc23 = vc.subContextFromSamples(new HashSet(Arrays.asList(g2.getSampleName(), g3.getSampleName())), true); VariantContext vc4 = vc.subContextFromSamples(new HashSet(Arrays.asList(g4.getSampleName())), true); VariantContext vc14 = vc.subContextFromSamples(new HashSet(Arrays.asList(g1.getSampleName(), g4.getSampleName())), true); - VariantContext vc5 = vc.subContextFromSamples(new HashSet(Arrays.asList(g5.getSampleName())), true); Assert.assertTrue(vc12.isPolymorphicInSamples()); Assert.assertTrue(vc23.isPolymorphicInSamples()); Assert.assertTrue(vc1.isMonomorphicInSamples()); Assert.assertTrue(vc4.isMonomorphicInSamples()); Assert.assertTrue(vc14.isMonomorphicInSamples()); - Assert.assertTrue(vc5.isPolymorphicInSamples()); Assert.assertTrue(vc12.isSNP()); Assert.assertTrue(vc12.isVariant()); @@ -601,17 +598,11 @@ public void testVCFfromGenotypes() { Assert.assertFalse(vc14.isVariant()); Assert.assertFalse(vc14.isBiallelic()); - Assert.assertTrue(vc5.isIndel()); - Assert.assertTrue(vc5.isSimpleDeletion()); - Assert.assertTrue(vc5.isVariant()); - Assert.assertTrue(vc5.isBiallelic()); - Assert.assertEquals(3, vc12.getCalledChrCount(Aref)); Assert.assertEquals(1, vc23.getCalledChrCount(Aref)); Assert.assertEquals(2, vc1.getCalledChrCount(Aref)); Assert.assertEquals(0, vc4.getCalledChrCount(Aref)); Assert.assertEquals(2, vc14.getCalledChrCount(Aref)); - Assert.assertEquals(0, vc5.getCalledChrCount(Aref)); } public void testGetGenotypeMethods() { @@ -659,13 +650,12 @@ public String toString() { @DataProvider(name = "getAlleles") public Object[][] mergeAllelesData() { new GetAllelesTest("A*", Aref); - new GetAllelesTest("-*", delRef); new GetAllelesTest("A*/C", Aref, C); new GetAllelesTest("A*/C/T", Aref, C, T); new GetAllelesTest("A*/T/C", Aref, T, C); - new GetAllelesTest("A*/C/T/-", Aref, C, T, del); - new GetAllelesTest("A*/T/C/-", Aref, T, C, del); - new GetAllelesTest("A*/-/T/C", Aref, del, T, C); + new GetAllelesTest("A*/C/T/ATC", Aref, C, T, ATC); + new GetAllelesTest("A*/T/C/ATC", Aref, T, C, ATC); + new GetAllelesTest("A*/ATC/T/C", Aref, ATC, T, C); return GetAllelesTest.getTests(GetAllelesTest.class); } From cbb0f8c6804d3504487a3932e0fba14cff92e2f9 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Sun, 29 Jul 2012 01:07:59 -0400 Subject: [PATCH 016/176] Final checkpoint: all tests pass. Note that there were bugs in the PoolGenotypeLikelihoodsUnitTest that needed fixing and eventually led to my needing to disable one of the tests (with a note for Guillermo to look into it). Also note that while I have moved over the GATK to use the new non-null representation of Alleles, I didn't remove all of the now-superfluous code throughout to do padding checking on merges; we'll need to do this on a subsequent push. --- .../ArtificialReadPileupTestProvider.java | 133 ++++++++---------- .../IndelGenotypeLikelihoodsUnitTest.java | 6 +- .../VariantContextUtilsUnitTest.java | 32 ++--- 3 files changed, 74 insertions(+), 97 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java index a911718c19..17149220ac 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java @@ -38,9 +38,6 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; import java.util.*; @@ -103,39 +100,27 @@ public Map getAlignmentContextFromAlleles(int eventLeng boolean addBaseErrors, int phredScaledBaseErrorRate) { // RefMetaDataTracker tracker = new RefMetaDataTracker(null,referenceContext); - ArrayList vcAlleles = new ArrayList(); - String refBase = refBases.substring(offset,offset+1); // referenceContext.getBase()? - Allele refAllele, altAllele; + String refAllele, altAllele; if (eventLength == 0) { // SNP case - refAllele = Allele.create(refBase,true); - altAllele = Allele.create(altBases.substring(0,1), false); + refAllele = new String(new byte[]{referenceContext.getBase()}); + altAllele = new String(altBases.substring(0,1)); } else if (eventLength>0){ // insertion - refAllele = Allele.create(refBase,true); - altAllele = Allele.create(refBase + altBases.substring(0,eventLength), false); + refAllele = ""; + altAllele = altBases.substring(0,eventLength); } else { // deletion - refAllele = Allele.create(refBases.substring(offset,offset+Math.abs(eventLength)),true); - altAllele = Allele.create(refBase, false); + refAllele = refBases.substring(offset,offset+Math.abs(eventLength)); + altAllele = ""; } - int stop = loc.getStart(); - vcAlleles.add(refAllele); - vcAlleles.add(altAllele); - - final VariantContextBuilder builder = new VariantContextBuilder().source(""); - builder.loc(loc.getContig(), loc.getStart(), stop); - builder.alleles(vcAlleles); - builder.noGenotypes(); - - final VariantContext vc = builder.make(); Map contexts = new HashMap(); for (String sample: sampleNames) { - AlignmentContext context = new AlignmentContext(loc, generateRBPForVariant(loc,vc, altBases, numReadsPerAllele, sample, addBaseErrors, phredScaledBaseErrorRate)); + AlignmentContext context = new AlignmentContext(loc, generateRBPForVariant(loc, refAllele, altAllele, altBases, numReadsPerAllele, sample, addBaseErrors, phredScaledBaseErrorRate)); contexts.put(sample,context); } @@ -149,73 +134,71 @@ private SAMReadGroupRecord createRG(String name) { rg.setSample(name); return rg; } - private ReadBackedPileup generateRBPForVariant( GenomeLoc loc, VariantContext vc, String altBases, + + private ReadBackedPileup generateRBPForVariant( GenomeLoc loc, String refAllele, String altAllele, String altBases, int[] numReadsPerAllele, String sample, boolean addErrors, int phredScaledErrorRate) { List pileupElements = new ArrayList(); - int readStart = contigStart; int offset = (contigStop-contigStart+1)/2; - int refAlleleLength = 0; + int refAlleleLength = refAllele.length(); + + pileupElements.addAll(createPileupElements(refAllele, loc, numReadsPerAllele[0], sample, contigStart, offset, altBases, addErrors, phredScaledErrorRate, refAlleleLength, true)); + pileupElements.addAll(createPileupElements(altAllele, loc, numReadsPerAllele[1], sample, contigStart, offset, altBases, addErrors, phredScaledErrorRate, refAlleleLength, false)); + return new ReadBackedPileupImpl(loc,pileupElements); + } + + private List createPileupElements(String allele, GenomeLoc loc, int numReadsPerAllele, String sample, int readStart, int offset, String altBases, boolean addErrors, int phredScaledErrorRate, int refAlleleLength, boolean isReference) { + + int alleleLength = allele.length(); + List pileupElements = new ArrayList(); + int readCounter = 0; - int alleleCounter = 0; - for (Allele allele: vc.getAlleles()) { - if (allele.isReference()) - refAlleleLength = allele.getBases().length; - - int alleleLength = allele.getBases().length; - - for ( int d = 0; d < numReadsPerAllele[alleleCounter]; d++ ) { - byte[] readBases = trueHaplotype(allele, offset, refAlleleLength); - if (addErrors) - addBaseErrors(readBases, phredScaledErrorRate); - - byte[] readQuals = new byte[readBases.length]; - Arrays.fill(readQuals, (byte)phredScaledErrorRate); - - GATKSAMRecord read = new GATKSAMRecord(header); - read.setBaseQualities(readQuals); - read.setReadBases(readBases); - read.setReadName(artificialReadName+readCounter++); - - boolean isBeforeDeletion = false, isBeforeInsertion = false; - if (allele.isReference()) - read.setCigarString(readBases.length + "M"); - else { - isBeforeDeletion = alleleLengthrefAlleleLength; - if (isBeforeDeletion || isBeforeInsertion) - read.setCigarString(offset+"M"+ alleleLength + (isBeforeDeletion?"D":"I") + + for ( int d = 0; d < numReadsPerAllele; d++ ) { + byte[] readBases = trueHaplotype(allele, offset, refAlleleLength); + if (addErrors) + addBaseErrors(readBases, phredScaledErrorRate); + + byte[] readQuals = new byte[readBases.length]; + Arrays.fill(readQuals, (byte)phredScaledErrorRate); + + GATKSAMRecord read = new GATKSAMRecord(header); + read.setBaseQualities(readQuals); + read.setReadBases(readBases); + read.setReadName(artificialReadName+readCounter++); + + boolean isBeforeDeletion = false, isBeforeInsertion = false; + if (isReference) + read.setCigarString(readBases.length + "M"); + else { + isBeforeDeletion = alleleLengthrefAlleleLength; + if (isBeforeDeletion || isBeforeInsertion) + read.setCigarString(offset+"M"+ alleleLength + (isBeforeDeletion?"D":"I") + (readBases.length-offset)+"M"); - else // SNP case - read.setCigarString(readBases.length+"M"); - } + else // SNP case + read.setCigarString(readBases.length+"M"); + } - int eventLength = (isBeforeDeletion?refAlleleLength:(isBeforeInsertion?alleleLength:0)); - read.setReadPairedFlag(false); - read.setAlignmentStart(readStart); - read.setMappingQuality(artificialMappingQuality); - read.setReferenceName(loc.getContig()); - read.setReadNegativeStrandFlag(false); - read.setAttribute("RG", sampleRG(sample).getReadGroupId()); + int eventLength = (isBeforeDeletion?refAlleleLength:(isBeforeInsertion?alleleLength:0)); + read.setReadPairedFlag(false); + read.setAlignmentStart(readStart); + read.setMappingQuality(artificialMappingQuality); + read.setReferenceName(loc.getContig()); + read.setReadNegativeStrandFlag(false); + read.setAttribute("RG", sampleRG(sample).getReadGroupId()); - pileupElements.add(new PileupElement(read,offset,false,isBeforeDeletion, false, isBeforeInsertion,false,false,altBases.substring(0,alleleLength),eventLength)); - } - alleleCounter++; + pileupElements.add(new PileupElement(read,offset,false,isBeforeDeletion, false, isBeforeInsertion,false,false,altBases.substring(0,alleleLength),eventLength)); } - return new ReadBackedPileupImpl(loc,pileupElements); + return pileupElements; } - private byte[] trueHaplotype(Allele allele, int offset, int refAlleleLength) { + private byte[] trueHaplotype(String allele, int offset, int refAlleleLength) { // create haplotype based on a particular allele - String prefix = refBases.substring(offset); - String alleleBases = new String(allele.getBases()); + String prefix = refBases.substring(0, offset); String postfix = refBases.substring(offset+refAlleleLength,refBases.length()); - return (prefix+alleleBases+postfix).getBytes(); - - - + return (prefix+allele+postfix).getBytes(); } private void addBaseErrors(final byte[] readBases, final int phredScaledErrorRate) { diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java index c7ef51d0cb..dfd4bc5253 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java @@ -70,7 +70,7 @@ public void testBasicConsensusCounts() { List alleles = getConsensusAlleles(eventLength,true,10,0.1, altBases); Assert.assertEquals(alleles.size(),2); - Assert.assertEquals(alleles.get(1).getBaseString(), altBases.substring(0,eventLength)); + Assert.assertEquals(alleles.get(1).getBaseString().substring(1), altBases.substring(0,eventLength)); @@ -79,7 +79,7 @@ public void testBasicConsensusCounts() { eventLength = 3; alleles = getConsensusAlleles(eventLength,false,10,0.1, altBases); Assert.assertEquals(alleles.size(),2); - Assert.assertEquals(alleles.get(0).getBaseString(), refBases.substring(pileupProvider.offset,pileupProvider.offset+eventLength)); + Assert.assertEquals(alleles.get(0).getBaseString().substring(1), refBases.substring(pileupProvider.offset,pileupProvider.offset+eventLength)); // same with min Reads = 11 alleles = getConsensusAlleles(eventLength,false,11,0.1, altBases); @@ -97,7 +97,7 @@ public void testBasicConsensusCounts() { alleles = getConsensusAlleles(eventLength,true,10,0.1, altBases); Assert.assertEquals(alleles.size(),2); - Assert.assertEquals(alleles.get(1).getBaseString(), altBases.substring(0,eventLength)); + Assert.assertEquals(alleles.get(1).getBaseString().substring(1), altBases.substring(0,eventLength)); altBases = "CCTCNTGAGA"; eventLength = 5; diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java index 8c86a54de0..8ba11db023 100644 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java @@ -39,7 +39,7 @@ import java.util.*; public class VariantContextUtilsUnitTest extends BaseTest { - Allele Aref, T, C, delRef, Cref, ATC, ATCATC; + Allele Aref, T, C, Cref, ATC, ATCATC; private GenomeLocParser genomeLocParser; @BeforeSuite @@ -56,7 +56,6 @@ public void setup() { // alleles Aref = Allele.create("A", true); Cref = Allele.create("C", true); - delRef = Allele.create("-", true); T = Allele.create("T"); C = Allele.create("C"); ATC = Allele.create("ATC"); @@ -156,28 +155,23 @@ public Object[][] mergeAllelesData() { Arrays.asList(Aref, C), Arrays.asList(Aref, T, C)); // in order of appearence - // The following is actually a pathological case - there's no way on a vcf to represent a null allele that's non-variant. - // The code converts this (correctly) to a single-base non-variant vc with whatever base was there as a reference. - new MergeAllelesTest(Arrays.asList(delRef), - Arrays.asList(Cref)); - - new MergeAllelesTest(Arrays.asList(delRef), - Arrays.asList(delRef, ATC), - Arrays.asList(delRef, ATC)); + new MergeAllelesTest(Arrays.asList(Aref), + Arrays.asList(Aref, ATC), + Arrays.asList(Aref, ATC)); - new MergeAllelesTest(Arrays.asList(delRef), - Arrays.asList(delRef, ATC, ATCATC), - Arrays.asList(delRef, ATC, ATCATC)); + new MergeAllelesTest(Arrays.asList(Aref), + Arrays.asList(Aref, ATC, ATCATC), + Arrays.asList(Aref, ATC, ATCATC)); // alleles in the order we see them - new MergeAllelesTest(Arrays.asList(delRef, ATCATC), - Arrays.asList(delRef, ATC, ATCATC), - Arrays.asList(delRef, ATCATC, ATC)); + new MergeAllelesTest(Arrays.asList(Aref, ATCATC), + Arrays.asList(Aref, ATC, ATCATC), + Arrays.asList(Aref, ATCATC, ATC)); // same - new MergeAllelesTest(Arrays.asList(delRef, ATC), - Arrays.asList(delRef, ATCATC), - Arrays.asList(delRef, ATC, ATCATC)); + new MergeAllelesTest(Arrays.asList(Aref, ATC), + Arrays.asList(Aref, ATCATC), + Arrays.asList(Aref, ATC, ATCATC)); return MergeAllelesTest.getTests(MergeAllelesTest.class); } From 844cbac1fdadf96f8f30bfd26393f32bcae214a5 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Sun, 29 Jul 2012 19:22:02 -0400 Subject: [PATCH 017/176] With the new Allele representation we can finally handle complex events (because they aren't so complex anymore). One place this manifests itself is with the strict VCF validation (ValidateVariants used to skip these events but doesn't anymore) so I've added a new test with complex events to the VV integration test. --- .../ValidateVariantsIntegrationTest.java | 10 ++++++++ .../sting/utils/HaplotypeUnitTest.java | 24 +++++++++---------- .../VariantJEXLContextUnitTest.java | 5 +--- 3 files changed, 23 insertions(+), 16 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java index 3277f5060f..6a3d755d7d 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java @@ -125,4 +125,14 @@ public void testBadAllele2() { executeTest("test bad ref allele in deletion", spec); } + @Test + public void testComplexEvents() { + WalkerTestSpec spec = new WalkerTestSpec( + baseTestString("complexEvents.vcf", "ALL"), + 0, + Arrays.asList("d41d8cd98f00b204e9800998ecf8427e") + ); + + executeTest("test validating complex events", spec); + } } diff --git a/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java index ec08d97c5d..161eefa8fc 100644 --- a/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java @@ -53,11 +53,11 @@ public void testSimpleInsertionAllele() { h1CigarList.add(new CigarElement(bases.length(), CigarOperator.M)); final Cigar h1Cigar = new Cigar(h1CigarList); String h1bases = "AACTTCTGGTCAACTGGTCAACTGGTCAACTGGTCA"; - basicInsertTest("-", "ACTT", 1, h1Cigar, bases, h1bases); + basicInsertTest("A", "AACTT", 1, h1Cigar, bases, h1bases); h1bases = "ACTGGTCACTTAACTGGTCAACTGGTCAACTGGTCA"; - basicInsertTest("-", "ACTT", 7, h1Cigar, bases, h1bases); + basicInsertTest("A", "AACTT", 7, h1Cigar, bases, h1bases); h1bases = "ACTGGTCAACTGGTCAAACTTCTGGTCAACTGGTCA"; - basicInsertTest("-", "ACTT", 17, h1Cigar, bases, h1bases); + basicInsertTest("A", "AACTT", 17, h1Cigar, bases, h1bases); } @Test @@ -68,11 +68,11 @@ public void testSimpleDeletionAllele() { h1CigarList.add(new CigarElement(bases.length(), CigarOperator.M)); final Cigar h1Cigar = new Cigar(h1CigarList); String h1bases = "ATCAACTGGTCAACTGGTCAACTGGTCA"; - basicInsertTest("ACTT", "-", 1, h1Cigar, bases, h1bases); + basicInsertTest("AACTT", "A", 1, h1Cigar, bases, h1bases); h1bases = "ACTGGTCGGTCAACTGGTCAACTGGTCA"; - basicInsertTest("ACTT", "-", 7, h1Cigar, bases, h1bases); + basicInsertTest("AACTT", "A", 7, h1Cigar, bases, h1bases); h1bases = "ACTGGTCAACTGGTCAATCAACTGGTCA"; - basicInsertTest("ACTT", "-", 17, h1Cigar, bases, h1bases); + basicInsertTest("AACTT", "A", 17, h1Cigar, bases, h1bases); } @Test @@ -102,11 +102,11 @@ public void testComplexInsertionAllele() { h1CigarList.add(new CigarElement(7 + 4, CigarOperator.M)); final Cigar h1Cigar = new Cigar(h1CigarList); String h1bases = "AACTTTCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC"; - basicInsertTest("-", "ACTT", 1, h1Cigar, bases, h1bases); + basicInsertTest("A", "AACTT", 1, h1Cigar, bases, h1bases); h1bases = "ATCG" + "CCGGCCGGCC" + "ATCACTTGATCG" + "AGGGGGA" + "AGGC"; - basicInsertTest("-", "ACTT", 7, h1Cigar, bases, h1bases); + basicInsertTest("A", "AACTT", 7, h1Cigar, bases, h1bases); h1bases = "ATCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGACTTGGGGA" + "AGGC"; - basicInsertTest("-", "ACTT", 17, h1Cigar, bases, h1bases); + basicInsertTest("A", "AACTT", 17, h1Cigar, bases, h1bases); } @Test @@ -121,11 +121,11 @@ public void testComplexDeletionAllele() { h1CigarList.add(new CigarElement(7 + 4, CigarOperator.M)); final Cigar h1Cigar = new Cigar(h1CigarList); String h1bases = "A" + "CGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC"; - basicInsertTest("ACTT", "-", 1, h1Cigar, bases, h1bases); + basicInsertTest("AACTT", "A", 1, h1Cigar, bases, h1bases); h1bases = "ATCG" + "CCGGCCGGCC" + "ATCG" + "AGGGGGA" + "AGGC"; - basicInsertTest("ACTT", "-", 7, h1Cigar, bases, h1bases); + basicInsertTest("AACTT", "A", 7, h1Cigar, bases, h1bases); h1bases = "ATCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGA" + "AGGC"; - basicInsertTest("ACTT", "-", 17, h1Cigar, bases, h1bases); + basicInsertTest("AACTT", "A", 17, h1Cigar, bases, h1bases); } @Test diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContextUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContextUnitTest.java index 6f5756bdc1..8f03f1d389 100644 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContextUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContextUnitTest.java @@ -56,7 +56,7 @@ public class VariantJEXLContextUnitTest extends BaseTest { Allele A, Aref, T, Tref; - Allele del, delRef, ATC, ATCref; + Allele ATC, ATCref; // A [ref] / T at 10 GenomeLoc snpLoc; @@ -84,9 +84,6 @@ public void beforeClass() { @BeforeMethod public void before() { - del = Allele.create("-"); - delRef = Allele.create("-", true); - A = Allele.create("A"); Aref = Allele.create("A", true); T = Allele.create("T"); From 62ce4d528b2028174dcaa7fd87f2c281c8876468 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Sun, 29 Jul 2012 22:19:49 -0400 Subject: [PATCH 018/176] Adding an integration test for another feature that I snuck in during a previous commit: we now allow lower-case bases in the REF/ALT alleles of a VCF and upper-case them (this had been turned off because the previous version used Strings to do the uppercasing whereas we stick with byte operations now). --- .../sting/utils/codecs/vcf/VCFIntegrationTest.java | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java index 8f648344d2..3948ba971e 100644 --- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java @@ -39,6 +39,17 @@ public void testReadingAndWritingBreakpointAlleles() { executeTest("Test reading and writing breakpoint VCF", spec1); } + @Test(enabled = true) + public void testReadingLowerCaseBases() { + String testVCF = privateTestDir + "lowercaseBases.vcf"; + + String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s "; + + String test1 = baseCommand + "-T SelectVariants -V " + testVCF; + WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("e0e308a25e56bde1c664139bb44ed19d")); + executeTest("Test reading VCF with lower-case bases", spec1); + } + @Test(enabled = true) public void testReadingAndWriting1000GSVs() { String testVCF = privateTestDir + "1000G_SVs.chr1.vcf"; From 9b95e6f4cc4020256e5cf4963cd4a150afcaa25a Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Sun, 29 Jul 2012 22:24:56 -0400 Subject: [PATCH 019/176] Re-enabling the unit tests for reverse allele clipping --- .../VariantContextUtilsUnitTest.java | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java index 8ba11db023..95e8458c88 100644 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java @@ -655,4 +655,52 @@ public void testRepeatDetectorTest(RepeatDetectorTest cfg) { // test alleles are equal Assert.assertEquals(VariantContextUtils.isTandemRepeat(cfg.vc, cfg.ref.getBytes()), cfg.isTrueRepeat); } + + // -------------------------------------------------------------------------------- + // + // basic allele clipping test + // + // -------------------------------------------------------------------------------- + + private class ReverseClippingPositionTestProvider extends TestDataProvider { + final String ref; + final List alleles = new ArrayList(); + final int expectedClip; + + private ReverseClippingPositionTestProvider(final int expectedClip, final String ref, final String... alleles) { + super(ReverseClippingPositionTestProvider.class); + this.ref = ref; + for ( final String allele : alleles ) + this.alleles.add(Allele.create(allele)); + this.expectedClip = expectedClip; + } + + @Override + public String toString() { + return String.format("ref=%s allele=%s reverse clip %d", ref, alleles, expectedClip); + } + } + + @DataProvider(name = "ReverseClippingPositionTestProvider") + public Object[][] makeReverseClippingPositionTestProvider() { + // pair clipping + new ReverseClippingPositionTestProvider(0, "ATT", "CCG"); + new ReverseClippingPositionTestProvider(1, "ATT", "CCT"); + new ReverseClippingPositionTestProvider(2, "ATT", "CTT"); + new ReverseClippingPositionTestProvider(2, "ATT", "ATT"); // cannot completely clip allele + + // triplets + new ReverseClippingPositionTestProvider(0, "ATT", "CTT", "CGG"); + new ReverseClippingPositionTestProvider(1, "ATT", "CTT", "CGT"); // the T can go + new ReverseClippingPositionTestProvider(2, "ATT", "CTT", "CTT"); // both Ts can go + + return ReverseClippingPositionTestProvider.getTests(ReverseClippingPositionTestProvider.class); + } + + + @Test(dataProvider = "ReverseClippingPositionTestProvider") + public void testReverseClippingPositionTestProvider(ReverseClippingPositionTestProvider cfg) { + int result = VariantContextUtils.computeReverseClipping(cfg.alleles, cfg.ref.getBytes(), 0, false); + Assert.assertEquals(result, cfg.expectedClip); + } } From 8f89501eba6092fa520cce06b98a07fdc787be70 Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Mon, 30 Jul 2012 09:56:10 -0400 Subject: [PATCH 020/176] Intermediate fix for pool GL unit test: fix up artificial read pileup provider to give consistent data. b) Increase downsampling in pool integration tests with reference sample, and shorten MT tests so they don't last too long --- .../ArtificialReadPileupTestProvider.java | 56 +++++++++++-------- 1 file changed, 32 insertions(+), 24 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java index 77769a5fe9..8011ea66b6 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java @@ -62,9 +62,9 @@ public class ArtificialReadPileupTestProvider { List sampleNames = new ArrayList(); private String sampleName(int i) { return sampleNames.get(i); } private SAMReadGroupRecord sampleRG(String name) { return sample2RG.get(name); } - public final int offset = 5; + public final int locStart = 5; // 1-based public final GenomeLocParser genomeLocParser = new GenomeLocParser(header.getSequenceDictionary()); - public final GenomeLoc loc = genomeLocParser.createGenomeLoc(artificialContig,offset,offset); + public final GenomeLoc loc = genomeLocParser.createGenomeLoc(artificialContig,locStart,locStart); //1-based public final GenomeLoc window = genomeLocParser.createGenomeLoc(artificialContig,artificialRefStart,10); public final ReferenceContext referenceContext = new ReferenceContext(genomeLocParser,loc,window,this.refBases.getBytes()); @@ -103,22 +103,22 @@ public Map getAlignmentContextFromAlleles(int eventLeng boolean addBaseErrors, int phredScaledBaseErrorRate) { // RefMetaDataTracker tracker = new RefMetaDataTracker(null,referenceContext); - + String refStr = new String(new byte[]{referenceContext.getBase()}); ArrayList vcAlleles = new ArrayList(); Allele refAllele, altAllele; if (eventLength == 0) {// SNP case - refAllele =Allele.create(referenceContext.getBase(),true); + refAllele =Allele.create(refStr,true); altAllele = Allele.create(altBases.substring(0,1), false); } else if (eventLength>0){ // insertion - refAllele = Allele.create(Allele.NULL_ALLELE_STRING, true); - altAllele = Allele.create(altBases.substring(0,eventLength), false); + refAllele = Allele.create(refStr, true); + altAllele = Allele.create(refStr+altBases.substring(0,eventLength), false); } else { // deletion - refAllele =Allele.create(refBases.substring(offset,offset+Math.abs(eventLength)),true); - altAllele = Allele.create(Allele.NULL_ALLELE_STRING, false); + refAllele =Allele.create(refBases.substring(locStart-1,locStart+Math.abs(eventLength)-1),true); + altAllele = Allele.create(refBases.substring(locStart-1,locStart), false); } int stop = loc.getStart(); vcAlleles.add(refAllele); @@ -153,18 +153,15 @@ private ReadBackedPileup generateRBPForVariant( GenomeLoc loc, VariantContext vc int[] numReadsPerAllele, String sample, boolean addErrors, int phredScaledErrorRate) { List pileupElements = new ArrayList(); int readStart = contigStart; - int offset = (contigStop-contigStart+1)/2; - int refAlleleLength = 0; + + int refAlleleLength = vc.getReference().getBases().length; int readCounter = 0; int alleleCounter = 0; for (Allele allele: vc.getAlleles()) { - if (allele.isReference()) - refAlleleLength = allele.getBases().length; - int alleleLength = allele.getBases().length; for ( int d = 0; d < numReadsPerAllele[alleleCounter]; d++ ) { - byte[] readBases = trueHaplotype(allele, offset, refAlleleLength); + byte[] readBases = trueHaplotype(allele, locStart, vc.getReference()); if (addErrors) addBaseErrors(readBases, phredScaledErrorRate); @@ -176,20 +173,20 @@ private ReadBackedPileup generateRBPForVariant( GenomeLoc loc, VariantContext vc read.setReadBases(readBases); read.setReadName(artificialReadName+readCounter++); - boolean isBeforeDeletion = false, isBeforeInsertion = false; + boolean isBeforeDeletion = alleleLengthrefAlleleLength; + + int eventLength = alleleLength - refAlleleLength; if (allele.isReference()) read.setCigarString(readBases.length + "M"); else { - isBeforeDeletion = alleleLengthrefAlleleLength; if (isBeforeDeletion || isBeforeInsertion) - read.setCigarString(offset+"M"+ alleleLength + (isBeforeDeletion?"D":"I") + - (readBases.length-offset)+"M"); + read.setCigarString(locStart+"M"+ eventLength + (isBeforeDeletion?"D":"I") + + (readBases.length-locStart)+"M"); else // SNP case read.setCigarString(readBases.length+"M"); } - int eventLength = (isBeforeDeletion?refAlleleLength:(isBeforeInsertion?alleleLength:0)); read.setReadPairedFlag(false); read.setAlignmentStart(readStart); read.setMappingQuality(artificialMappingQuality); @@ -198,7 +195,7 @@ private ReadBackedPileup generateRBPForVariant( GenomeLoc loc, VariantContext vc read.setAttribute("RG", sampleRG(sample).getReadGroupId()); - pileupElements.add(new PileupElement(read,offset,false,isBeforeDeletion, false, isBeforeInsertion,false,false,altBases.substring(0,alleleLength),eventLength)); + pileupElements.add(new PileupElement(read,locStart-1,false,isBeforeDeletion, false, isBeforeInsertion,false,false,altBases.substring(0,alleleLength-1),eventLength)); } alleleCounter++; } @@ -206,11 +203,22 @@ private ReadBackedPileup generateRBPForVariant( GenomeLoc loc, VariantContext vc return new ReadBackedPileupImpl(loc,pileupElements); } - private byte[] trueHaplotype(Allele allele, int offset, int refAlleleLength) { + /** + * create haplotype based on a particular allele + * @param allele Allele of interest. ASSUMED TO INCLUDE REF BASE AT startPosition! + * @param startPosition 1-based start position of allele + * @param refAllele REF allele + * @return + */ + private byte[] trueHaplotype(Allele allele, int startPosition, Allele refAllele) { + // create haplotype based on a particular allele - String prefix = refBases.substring(offset); + // startPosition is 1-based. + // so, if startPosition == 5, we need to include positions 1 to 4 , or indeces 0 to 3 of string + String prefix = refBases.substring(0,startPosition-1); String alleleBases = new String(allele.getBases()); - String postfix = refBases.substring(offset+refAlleleLength,refBases.length()); + // where to start postfix? We have (startPosition-1) prefix bases + refAllele.length bases before postfix + String postfix = refBases.substring(startPosition -1 + refAllele.getBases().length,refBases.length()); return (prefix+alleleBases+postfix).getBytes(); From f119a10451c9047a8df588abb92e7395b88c0d29 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 30 Jul 2012 11:59:56 -0400 Subject: [PATCH 021/176] Catch yet another class of User Errors --- .../src/org/broadinstitute/sting/gatk/CommandLineGATK.java | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java index b1ad19e696..306ebdd0ec 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java +++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java @@ -131,6 +131,12 @@ private static void checkForMaskedUserErrors(final Throwable t) { // can't close tribble index when writing if ( message.indexOf("Unable to close index for") != -1 ) exitSystemWithUserError(new UserException(t.getCause().getMessage())); + + // disk is full + if ( message.indexOf("No space left on device") != -1 ) + exitSystemWithUserError(new UserException(t.getMessage())); + if ( t.getCause().getMessage().indexOf("No space left on device") != -1 ) + exitSystemWithUserError(new UserException(t.getCause().getMessage())); } /** From 42fd08b9b8fbc01fb2d412134c94bd2927fd6d6e Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Mon, 30 Jul 2012 12:09:23 -0400 Subject: [PATCH 022/176] Bug fix for the case of merging two VCs when a deletion deletes the padding base for a consecutive indel. Added unit test to cover this case. From c0ec9849f9dd4506ee408727e8f9b7bf593eea23 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Mon, 30 Jul 2012 12:12:56 -0400 Subject: [PATCH 023/176] Fixes to the likelihood based LD calculation for deciding when to combine consecutive events. From d2813847703b6f48cecccde1ab915a4f715685c1 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Mon, 30 Jul 2012 12:16:27 -0400 Subject: [PATCH 024/176] Updating FindCoveredIntervals to use the changes to the ActiveRegionWalker. --- .../walkers/diagnostics/targets/FindCoveredIntervals.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java index c964b0b4b0..0c856c6dfe 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java @@ -34,6 +34,7 @@ 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.help.DocumentedGATKFeature; import java.io.PrintStream; @@ -47,13 +48,13 @@ public class FindCoveredIntervals extends ActiveRegionWalker { @Override // Look to see if the region has sufficient coverage - public double isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) { + public ActivityProfileResult isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) { int depth = ThresHolder.DEFAULTS.getFilteredCoverage(context.getBasePileup()); // note the linear probability scale int coverageThreshold = 20; - return Math.min((double) depth / coverageThreshold, 1); + return new ActivityProfileResult(Math.min((double) depth / coverageThreshold, 1)); } From 3b3a603b0f54632e6022dc21f25f723c4180f778 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Mon, 30 Jul 2012 12:41:40 -0400 Subject: [PATCH 025/176] updating HC integration tests after these changes. From a820e18b0a37e509a90a586c61a3158d5d405930 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Mon, 30 Jul 2012 21:26:16 -0400 Subject: [PATCH 026/176] Updating example active region walker integration test. From 5ba80cadc0117d049b30fa84bfad1dfa0aa70066 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 26 Jul 2012 09:46:56 -0400 Subject: [PATCH 027/176] Maximum wait for GATK run report upload reduced to 10 seconds --- .../org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java b/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java index f190cbcfd7..a42c73212f 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java +++ b/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java @@ -86,7 +86,7 @@ public class GATKRunReport { private static File REPORT_SENTINEL = new File(REPORT_DIR.getAbsolutePath() + "/ENABLE"); // number of milliseconds before the S3 put operation is timed-out: - private static final long S3PutTimeOut = 30 * 1000; + private static final long S3PutTimeOut = 10 * 1000; /** From 53780732119d1fece8fde3635fde91a3ab6d3e2b Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 26 Jul 2012 13:56:06 -0400 Subject: [PATCH 028/176] V1 of tool to visualize the quality score information in the context covariates -- Upgraded jgrapht to latest version (0.8.3) --- ivy.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ivy.xml b/ivy.xml index b197d0714f..6dd5be7a8a 100644 --- a/ivy.xml +++ b/ivy.xml @@ -52,7 +52,7 @@ - + From 8ede3aeda3a1f08aab093c3473c16c4f08691bb3 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 26 Jul 2012 16:51:17 -0400 Subject: [PATCH 029/176] Be clearer that dcov 50 is good for 4x, should use 200 for >30x --- .../sting/gatk/walkers/genotyper/UnifiedGenotyper.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java index cd1815d82e..6b279fd954 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java @@ -82,7 +82,7 @@ * -o snps.raw.vcf \ * -stand_call_conf [50.0] \ * -stand_emit_conf 10.0 \ - * -dcov [50] \ + * -dcov [50 for 4x, 200 for >30x WGS or Whole exome] \ * [-L targets.interval_list] * * From 55ed28a23dd0ff8b4698ab523a27f5db7230468c Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 27 Jul 2012 09:39:16 -0400 Subject: [PATCH 030/176] Initial cleanup of RecalDatum for move and further refactoring -- Moved Datum, the now unnecessary superclass, into RecalDatum -- Fixed some obviously dangerous synchronization errors in RecalDatum, though these may not have caused problems because they may not have been called in parallel mode --- .../sting/gatk/walkers/bqsr/Datum.java | 109 ------------------ .../sting/gatk/walkers/bqsr/RecalDatum.java | 70 ++++++++--- 2 files changed, 53 insertions(+), 126 deletions(-) delete mode 100644 public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/Datum.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/Datum.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/Datum.java deleted file mode 100644 index d7e8e16b5f..0000000000 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/Datum.java +++ /dev/null @@ -1,109 +0,0 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; - -import org.broadinstitute.sting.utils.QualityUtils; - -/* - * 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. - */ - -/** - * Created by IntelliJ IDEA. - * User: rpoplin - * Date: Jan 6, 2010 - * - * An individual piece of recalibration data. Optimized for CountCovariates. Extras added to make TableRecalibration fast have been removed. - * Each bin counts up the number of observations and the number of reference mismatches seen for that combination of covariates. - */ - -public class Datum { - - long numObservations; // number of bases seen in total - long numMismatches; // number of bases seen that didn't match the reference - - private static final int SMOOTHING_CONSTANT = 1; // used when calculating empirical qualities to avoid division by zero - - //--------------------------------------------------------------------------------------------------------------- - // - // constructors - // - //--------------------------------------------------------------------------------------------------------------- - - public Datum() { - numObservations = 0L; - numMismatches = 0L; - } - - public Datum(long numObservations, long numMismatches) { - this.numObservations = numObservations; - this.numMismatches = numMismatches; - } - - //--------------------------------------------------------------------------------------------------------------- - // - // increment methods - // - //--------------------------------------------------------------------------------------------------------------- - - synchronized void increment(final long incObservations, final long incMismatches) { - numObservations += incObservations; - numMismatches += incMismatches; - } - - synchronized void increment(final boolean isError) { - numObservations++; - numMismatches += isError ? 1:0; - } - - //--------------------------------------------------------------------------------------------------------------- - // - // methods to derive empirical quality score - // - //--------------------------------------------------------------------------------------------------------------- - - double empiricalQualDouble() { - final double doubleMismatches = (double) (numMismatches + SMOOTHING_CONSTANT); - final double doubleObservations = (double) (numObservations + SMOOTHING_CONSTANT + SMOOTHING_CONSTANT); // smoothing is one error and one non-error observation, for example - final double empiricalQual = -10 * Math.log10(doubleMismatches / doubleObservations); - return Math.min(empiricalQual, (double) QualityUtils.MAX_RECALIBRATED_Q_SCORE); - } - - byte empiricalQualByte() { - final double doubleMismatches = (double) (numMismatches); - final double doubleObservations = (double) (numObservations); - return QualityUtils.probToQual(1.0 - doubleMismatches / doubleObservations); // This is capped at Q40 - } - - @Override - public String toString() { - return String.format("%d,%d,%d", numObservations, numMismatches, (int) empiricalQualByte()); - } - - @Override - public boolean equals(Object o) { - if (!(o instanceof Datum)) - return false; - Datum other = (Datum) o; - return numMismatches == other.numMismatches && numObservations == other.numObservations; - } -} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDatum.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDatum.java index 9b00b18768..ed4e769b12 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDatum.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDatum.java @@ -33,20 +33,40 @@ import java.util.Random; /** + * An individual piece of recalibration data. Each bin counts up the number of observations and the number + * of reference mismatches seen for that combination of covariates. + * * Created by IntelliJ IDEA. * User: rpoplin * Date: Nov 3, 2009 - * - * An individual piece of recalibration data. Each bin counts up the number of observations and the number of reference mismatches seen for that combination of covariates. */ +public class RecalDatum { + private static final double UNINITIALIZED = -1.0; -public class RecalDatum extends Datum { + /** + * estimated reported quality score based on combined data's individual q-reporteds and number of observations + */ + private double estimatedQReported; - private static final double UNINITIALIZED = -1.0; + /** + * the empirical quality for datums that have been collapsed together (by read group and reported quality, for example) + */ + private double empiricalQuality; - private double estimatedQReported; // estimated reported quality score based on combined data's individual q-reporteds and number of observations - private double empiricalQuality; // the empirical quality for datums that have been collapsed together (by read group and reported quality, for example) + /** + * number of bases seen in total + */ + long numObservations; + /** + * number of bases seen that didn't match the reference + */ + long numMismatches; + + /** + * used when calculating empirical qualities to avoid division by zero + */ + private static final int SMOOTHING_CONSTANT = 1; //--------------------------------------------------------------------------------------------------------------- // @@ -68,26 +88,24 @@ public RecalDatum(final RecalDatum copy) { this.empiricalQuality = copy.empiricalQuality; } - public void combine(final RecalDatum other) { + public synchronized void combine(final RecalDatum other) { final double sumErrors = this.calcExpectedErrors() + other.calcExpectedErrors(); increment(other.numObservations, other.numMismatches); estimatedQReported = -10 * Math.log10(sumErrors / this.numObservations); empiricalQuality = UNINITIALIZED; } - @Override - public void increment(final boolean isError) { - super.increment(isError); - empiricalQuality = UNINITIALIZED; - } - @Requires("empiricalQuality == UNINITIALIZED") @Ensures("empiricalQuality != UNINITIALIZED") - protected final void calcEmpiricalQuality() { - empiricalQuality = empiricalQualDouble(); // cache the value so we don't call log over and over again + private synchronized final void calcEmpiricalQuality() { + // cache the value so we don't call log over and over again + final double doubleMismatches = (double) (numMismatches + SMOOTHING_CONSTANT); + final double doubleObservations = (double) (numObservations + SMOOTHING_CONSTANT); + final double empiricalQual = -10 * Math.log10(doubleMismatches / doubleObservations); + empiricalQuality = Math.min(empiricalQual, (double) QualityUtils.MAX_RECALIBRATED_Q_SCORE); } - public void setEstimatedQReported(final double estimatedQReported) { + public synchronized void setEstimatedQReported(final double estimatedQReported) { this.estimatedQReported = estimatedQReported; } @@ -95,7 +113,7 @@ public final double getEstimatedQReported() { return estimatedQReported; } - public void setEmpiricalQuality(final double empiricalQuality) { + public synchronized void setEmpiricalQuality(final double empiricalQuality) { this.empiricalQuality = empiricalQuality; } @@ -145,4 +163,22 @@ public boolean equals(Object o) { return super.equals(o) && MathUtils.compareDoubles(this.empiricalQuality, other.empiricalQuality, 0.001) == 0; } + + //--------------------------------------------------------------------------------------------------------------- + // + // increment methods + // + //--------------------------------------------------------------------------------------------------------------- + + synchronized void increment(final long incObservations, final long incMismatches) { + numObservations += incObservations; + numMismatches += incMismatches; + empiricalQuality = UNINITIALIZED; + } + + synchronized void increment(final boolean isError) { + numObservations++; + numMismatches += isError ? 1:0; + empiricalQuality = UNINITIALIZED; + } } From 4b1a74083d1792d804ac67495aa88cfd3b65d151 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 27 Jul 2012 12:25:06 -0400 Subject: [PATCH 031/176] Cleanup BQSR classes -- Moved most of BQSR classes (which are used throughout the codebase) to utils.recalibration. It's better in my opinion to keep commonly used code in utils, and only specialized code in walkers. As code becomes embedded throughout GATK its should be refactored to live in utils -- Removed unncessary imports of BQSR in VQSR v3 -- Now ready to refactor QualQuantizer and unit test into a subclass of RecalDatum, refactor unit tests into RecalDatum unit tests, and generalize into hierarchical recal datum that can be used in QualQuantizer and the analysis of adaptive context covariate -- Update PluginManager to sort the plugins and interfaces. This allows us to have a deterministic order in which the plugin classes come back, which caused BQSR integration tests to temporarily change because I moved my classes around a bit. --- .../sting/gatk/walkers/bqsr/BQSRGatherer.java | 6 +- .../gatk/walkers/bqsr/BaseRecalibrator.java | 26 +- .../bqsr/RecalibrationArgumentCollection.java | 41 ++-- .../walkers/bqsr/RecalibrationEngine.java | 1 + .../bqsr/StandardRecalibrationEngine.java | 4 + .../utils/classloader/PluginManager.java | 22 ++ .../sting/utils/clipping/ClippingOp.java | 2 +- .../sting/utils/clipping/ReadClipper.java | 2 +- .../sting/utils/fragments/FragmentUtils.java | 2 +- .../recalibration/BaseRecalibration.java | 4 +- .../recalibration}/EventType.java | 2 +- .../recalibration}/QuantizationInfo.java | 20 +- .../recalibration}/ReadCovariates.java | 2 +- .../recalibration}/RecalDatum.java | 60 +++-- .../recalibration/RecalUtils.java} | 226 +++++++++--------- .../recalibration}/RecalibrationReport.java | 63 ++--- .../recalibration/RecalibrationTables.java | 4 +- .../covariates}/BinaryTagCovariate.java | 4 +- .../covariates}/ContextCovariate.java | 4 +- .../recalibration/covariates}/Covariate.java | 9 +- .../covariates}/CycleCovariate.java | 4 +- .../covariates/ExperimentalCovariate.java | 30 +++ .../covariates}/QualityScoreCovariate.java | 4 +- .../covariates}/ReadGroupCovariate.java | 4 +- .../covariates/RequiredCovariate.java | 30 +++ .../covariates/StandardCovariate.java | 30 +++ .../sting/utils/sam/GATKSAMRecord.java | 2 +- .../walkers/bqsr/BQSRGathererUnitTest.java | 13 +- .../ContextCovariateUnitTest.java | 5 +- .../CycleCovariateUnitTest.java | 4 +- .../ReadCovariatesUnitTest.java | 6 +- .../ReadGroupCovariateUnitTest.java | 4 +- .../RecalibrationReportUnitTest.java | 7 +- 33 files changed, 408 insertions(+), 239 deletions(-) rename public/java/src/org/broadinstitute/sting/{gatk/walkers/bqsr => utils/recalibration}/EventType.java (96%) rename public/java/src/org/broadinstitute/sting/{gatk/walkers/bqsr => utils/recalibration}/QuantizationInfo.java (78%) rename public/java/src/org/broadinstitute/sting/{gatk/walkers/bqsr => utils/recalibration}/ReadCovariates.java (97%) rename public/java/src/org/broadinstitute/sting/{gatk/walkers/bqsr => utils/recalibration}/RecalDatum.java (77%) rename public/java/src/org/broadinstitute/sting/{gatk/walkers/bqsr/RecalDataManager.java => utils/recalibration/RecalUtils.java} (96%) rename public/java/src/org/broadinstitute/sting/{gatk/walkers/bqsr => utils/recalibration}/RecalibrationReport.java (82%) rename public/java/src/org/broadinstitute/sting/{gatk/walkers/bqsr => utils/recalibration/covariates}/BinaryTagCovariate.java (89%) rename public/java/src/org/broadinstitute/sting/{gatk/walkers/bqsr => utils/recalibration/covariates}/ContextCovariate.java (98%) rename public/java/src/org/broadinstitute/sting/{gatk/walkers/bqsr => utils/recalibration/covariates}/Covariate.java (94%) rename public/java/src/org/broadinstitute/sting/{gatk/walkers/bqsr => utils/recalibration/covariates}/CycleCovariate.java (97%) create mode 100644 public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ExperimentalCovariate.java rename public/java/src/org/broadinstitute/sting/{gatk/walkers/bqsr => utils/recalibration/covariates}/QualityScoreCovariate.java (92%) rename public/java/src/org/broadinstitute/sting/{gatk/walkers/bqsr => utils/recalibration/covariates}/ReadGroupCovariate.java (94%) create mode 100644 public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RequiredCovariate.java create mode 100644 public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/StandardCovariate.java rename public/java/test/org/broadinstitute/sting/{gatk/walkers/bqsr => utils/recalibration}/ContextCovariateUnitTest.java (89%) rename public/java/test/org/broadinstitute/sting/{gatk/walkers/bqsr => utils/recalibration}/CycleCovariateUnitTest.java (90%) rename public/java/test/org/broadinstitute/sting/{gatk/walkers/bqsr => utils/recalibration}/ReadCovariatesUnitTest.java (92%) rename public/java/test/org/broadinstitute/sting/{gatk/walkers/bqsr => utils/recalibration}/ReadGroupCovariateUnitTest.java (88%) rename public/java/test/org/broadinstitute/sting/{gatk/walkers/bqsr => utils/recalibration}/RecalibrationReportUnitTest.java (95%) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java index 122958ac27..a6d82d5b3b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java @@ -28,6 +28,8 @@ import org.broadinstitute.sting.commandline.Gatherer; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.recalibration.RecalUtils; +import org.broadinstitute.sting.utils.recalibration.RecalibrationReport; import java.io.File; import java.io.FileNotFoundException; @@ -71,11 +73,11 @@ public void gather(List inputs, File output) { if (RAC.recalibrationReport != null && !RAC.NO_PLOTS) { final File recal_out = new File(output.getName() + ".original"); final RecalibrationReport originalReport = new RecalibrationReport(RAC.recalibrationReport); - RecalDataManager.generateRecalibrationPlot(recal_out, originalReport.getRecalibrationTables(), generalReport.getRecalibrationTables(), generalReport.getCovariates(), RAC.KEEP_INTERMEDIATE_FILES); + RecalUtils.generateRecalibrationPlot(recal_out, originalReport.getRecalibrationTables(), generalReport.getRecalibrationTables(), generalReport.getCovariates(), RAC.KEEP_INTERMEDIATE_FILES); } else if (!RAC.NO_PLOTS) { final File recal_out = new File(output.getName() + ".recal"); - RecalDataManager.generateRecalibrationPlot(recal_out, generalReport.getRecalibrationTables(), generalReport.getCovariates(), RAC.KEEP_INTERMEDIATE_FILES); + RecalUtils.generateRecalibrationPlot(recal_out, generalReport.getRecalibrationTables(), generalReport.getCovariates(), RAC.KEEP_INTERMEDIATE_FILES); } generalReport.output(outputFile); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java index b2400a49d5..e95a0e6c17 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java @@ -34,6 +34,7 @@ import org.broadinstitute.sting.gatk.filters.MappingQualityZeroFilter; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; +import org.broadinstitute.sting.utils.recalibration.covariates.Covariate; import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.classloader.GATKLiteUtils; import org.broadinstitute.sting.utils.collections.Pair; @@ -41,6 +42,9 @@ import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.sting.utils.recalibration.QuantizationInfo; +import org.broadinstitute.sting.utils.recalibration.RecalUtils; +import org.broadinstitute.sting.utils.recalibration.RecalibrationReport; import org.broadinstitute.sting.utils.recalibration.RecalibrationTables; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; @@ -109,7 +113,7 @@ public class BaseRecalibrator extends LocusWalker implements TreeRed @ArgumentCollection private final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection(); // all the command line arguments for BQSR and it's covariates - private QuantizationInfo quantizationInfo; // an object that keeps track of the information necessary for quality score quantization + private QuantizationInfo quantizationInfo; // an object that keeps track of the information necessary for quality score quantization private RecalibrationTables recalibrationTables; @@ -143,12 +147,12 @@ public void initialize() { throw new UserException.CommandLineException(NO_DBSNP_EXCEPTION); if (RAC.LIST_ONLY) { - RecalDataManager.listAvailableCovariates(logger); + RecalUtils.listAvailableCovariates(logger); System.exit(0); } RAC.recalibrationReport = getToolkit().getArguments().BQSR_RECAL_FILE; // if we have a recalibration file, record it so it goes on the report table - Pair, ArrayList> covariates = RecalDataManager.initializeCovariates(RAC); // initialize the required and optional covariates + Pair, ArrayList> covariates = RecalUtils.initializeCovariates(RAC); // initialize the required and optional covariates ArrayList requiredCovariates = covariates.getFirst(); ArrayList optionalCovariates = covariates.getSecond(); @@ -222,17 +226,17 @@ public Long map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentConte if (readNotSeen(read)) { read.setTemporaryAttribute(SEEN_ATTRIBUTE, true); - RecalDataManager.parsePlatformForRead(read, RAC); - if (RecalDataManager.isColorSpaceConsistent(RAC.SOLID_NOCALL_STRATEGY, read)) { + RecalUtils.parsePlatformForRead(read, RAC); + if (RecalUtils.isColorSpaceConsistent(RAC.SOLID_NOCALL_STRATEGY, read)) { read.setTemporaryAttribute(SKIP_RECORD_ATTRIBUTE, true); continue; } - read.setTemporaryAttribute(COVARS_ATTRIBUTE, RecalDataManager.computeCovariates(read, requestedCovariates)); + read.setTemporaryAttribute(COVARS_ATTRIBUTE, RecalUtils.computeCovariates(read, requestedCovariates)); } if (!ReadUtils.isSOLiDRead(read) || // SOLID bams have inserted the reference base into the read if the color space in inconsistent with the read base so skip it - RAC.SOLID_RECAL_MODE == RecalDataManager.SOLID_RECAL_MODE.DO_NOTHING || - RecalDataManager.isColorSpaceConsistent(read, offset)) + RAC.SOLID_RECAL_MODE == RecalUtils.SOLID_RECAL_MODE.DO_NOTHING || + RecalUtils.isColorSpaceConsistent(read, offset)) recalibrationEngine.updateDataForPileupElement(p, ref.getBase()); // This base finally passed all the checks for a good base, so add it to the big data hashmap } countedSites++; @@ -285,10 +289,10 @@ private void generatePlots() { File recalFile = getToolkit().getArguments().BQSR_RECAL_FILE; if (recalFile != null) { RecalibrationReport report = new RecalibrationReport(recalFile); - RecalDataManager.generateRecalibrationPlot(RAC.RECAL_FILE, report.getRecalibrationTables(), recalibrationTables, requestedCovariates, RAC.KEEP_INTERMEDIATE_FILES); + RecalUtils.generateRecalibrationPlot(RAC.RECAL_FILE, report.getRecalibrationTables(), recalibrationTables, requestedCovariates, RAC.KEEP_INTERMEDIATE_FILES); } else - RecalDataManager.generateRecalibrationPlot(RAC.RECAL_FILE, recalibrationTables, requestedCovariates, RAC.KEEP_INTERMEDIATE_FILES); + RecalUtils.generateRecalibrationPlot(RAC.RECAL_FILE, recalibrationTables, requestedCovariates, RAC.KEEP_INTERMEDIATE_FILES); } @@ -309,7 +313,7 @@ private void generateReport() { throw new UserException.CouldNotCreateOutputFile(RAC.RECAL_FILE, "could not be created"); } - RecalDataManager.outputRecalibrationReport(RAC, quantizationInfo, recalibrationTables, requestedCovariates, output); + RecalUtils.outputRecalibrationReport(RAC, quantizationInfo, recalibrationTables, requestedCovariates, output); } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java index 2a94426a7e..f04e4a1b38 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java @@ -29,6 +29,7 @@ import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.report.GATKReportTable; import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.recalibration.RecalUtils; import java.io.File; import java.util.Collections; @@ -100,7 +101,7 @@ public class RecalibrationArgumentCollection { * reads which have had the reference inserted because of color space inconsistencies. */ @Argument(fullName = "solid_recal_mode", shortName = "sMode", required = false, doc = "How should we recalibrate solid bases in which the reference was inserted? Options = DO_NOTHING, SET_Q_ZERO, SET_Q_ZERO_BASE_N, or REMOVE_REF_BIAS") - public RecalDataManager.SOLID_RECAL_MODE SOLID_RECAL_MODE = RecalDataManager.SOLID_RECAL_MODE.SET_Q_ZERO; + public RecalUtils.SOLID_RECAL_MODE SOLID_RECAL_MODE = RecalUtils.SOLID_RECAL_MODE.SET_Q_ZERO; /** * CountCovariates and TableRecalibration accept a --solid_nocall_strategy flag which governs how the recalibrator handles @@ -108,7 +109,7 @@ public class RecalibrationArgumentCollection { * their color space tag can not be recalibrated. */ @Argument(fullName = "solid_nocall_strategy", shortName = "solid_nocall_strategy", doc = "Defines the behavior of the recalibrator when it encounters no calls in the color space. Options = THROW_EXCEPTION, LEAVE_READ_UNRECALIBRATED, or PURGE_READ", required = false) - public RecalDataManager.SOLID_NOCALL_STRATEGY SOLID_NOCALL_STRATEGY = RecalDataManager.SOLID_NOCALL_STRATEGY.THROW_EXCEPTION; + public RecalUtils.SOLID_NOCALL_STRATEGY SOLID_NOCALL_STRATEGY = RecalUtils.SOLID_NOCALL_STRATEGY.THROW_EXCEPTION; /** * The context covariate will use a context of this size to calculate it's covariate value for base mismatches @@ -177,41 +178,41 @@ public class RecalibrationArgumentCollection { public GATKReportTable generateReportTable() { GATKReportTable argumentsTable = new GATKReportTable("Arguments", "Recalibration argument collection values used in this run", 2); argumentsTable.addColumn("Argument"); - argumentsTable.addColumn(RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME); + argumentsTable.addColumn(RecalUtils.ARGUMENT_VALUE_COLUMN_NAME); argumentsTable.addRowID("covariate", true); - argumentsTable.set("covariate", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, (COVARIATES == null) ? "null" : Utils.join(",", COVARIATES)); + argumentsTable.set("covariate", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, (COVARIATES == null) ? "null" : Utils.join(",", COVARIATES)); argumentsTable.addRowID("no_standard_covs", true); - argumentsTable.set("no_standard_covs", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, DO_NOT_USE_STANDARD_COVARIATES); + argumentsTable.set("no_standard_covs", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, DO_NOT_USE_STANDARD_COVARIATES); argumentsTable.addRowID("run_without_dbsnp", true); - argumentsTable.set("run_without_dbsnp", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, RUN_WITHOUT_DBSNP); + argumentsTable.set("run_without_dbsnp", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, RUN_WITHOUT_DBSNP); argumentsTable.addRowID("solid_recal_mode", true); - argumentsTable.set("solid_recal_mode", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, SOLID_RECAL_MODE); + argumentsTable.set("solid_recal_mode", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, SOLID_RECAL_MODE); argumentsTable.addRowID("solid_nocall_strategy", true); - argumentsTable.set("solid_nocall_strategy", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, SOLID_NOCALL_STRATEGY); + argumentsTable.set("solid_nocall_strategy", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, SOLID_NOCALL_STRATEGY); argumentsTable.addRowID("mismatches_context_size", true); - argumentsTable.set("mismatches_context_size", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, MISMATCHES_CONTEXT_SIZE); + argumentsTable.set("mismatches_context_size", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, MISMATCHES_CONTEXT_SIZE); argumentsTable.addRowID("indels_context_size", true); - argumentsTable.set("indels_context_size", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, INDELS_CONTEXT_SIZE); + argumentsTable.set("indels_context_size", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, INDELS_CONTEXT_SIZE); argumentsTable.addRowID("mismatches_default_quality", true); - argumentsTable.set("mismatches_default_quality", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, MISMATCHES_DEFAULT_QUALITY); + argumentsTable.set("mismatches_default_quality", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, MISMATCHES_DEFAULT_QUALITY); argumentsTable.addRowID("insertions_default_quality", true); - argumentsTable.set("insertions_default_quality", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, INSERTIONS_DEFAULT_QUALITY); + argumentsTable.set("insertions_default_quality", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, INSERTIONS_DEFAULT_QUALITY); argumentsTable.addRowID("low_quality_tail", true); - argumentsTable.set("low_quality_tail", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, LOW_QUAL_TAIL); + argumentsTable.set("low_quality_tail", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, LOW_QUAL_TAIL); argumentsTable.addRowID("default_platform", true); - argumentsTable.set("default_platform", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, DEFAULT_PLATFORM); + argumentsTable.set("default_platform", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, DEFAULT_PLATFORM); argumentsTable.addRowID("force_platform", true); - argumentsTable.set("force_platform", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, FORCE_PLATFORM); + argumentsTable.set("force_platform", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, FORCE_PLATFORM); argumentsTable.addRowID("quantizing_levels", true); - argumentsTable.set("quantizing_levels", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, QUANTIZING_LEVELS); + argumentsTable.set("quantizing_levels", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, QUANTIZING_LEVELS); argumentsTable.addRowID("keep_intermediate_files", true); - argumentsTable.set("keep_intermediate_files", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, KEEP_INTERMEDIATE_FILES); + argumentsTable.set("keep_intermediate_files", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, KEEP_INTERMEDIATE_FILES); argumentsTable.addRowID("no_plots", true); - argumentsTable.set("no_plots", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, NO_PLOTS); + argumentsTable.set("no_plots", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, NO_PLOTS); argumentsTable.addRowID("recalibration_report", true); - argumentsTable.set("recalibration_report", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, recalibrationReport == null ? "null" : recalibrationReport.getAbsolutePath()); + argumentsTable.set("recalibration_report", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, recalibrationReport == null ? "null" : recalibrationReport.getAbsolutePath()); argumentsTable.addRowID("binary_tag_name", true); - argumentsTable.set("binary_tag_name", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, BINARY_TAG_NAME == null ? "null" : BINARY_TAG_NAME); + argumentsTable.set("binary_tag_name", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, BINARY_TAG_NAME == null ? "null" : BINARY_TAG_NAME); return argumentsTable; } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java index aa62a18bc0..38e3069393 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java @@ -1,5 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.bqsr; +import org.broadinstitute.sting.utils.recalibration.covariates.Covariate; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.recalibration.RecalibrationTables; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java index a24506d079..08c7da7543 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java @@ -25,10 +25,14 @@ * OTHER DEALINGS IN THE SOFTWARE. */ +import org.broadinstitute.sting.utils.recalibration.covariates.Covariate; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.classloader.PublicPackageSource; import org.broadinstitute.sting.utils.collections.NestedIntegerArray; import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.sting.utils.recalibration.EventType; +import org.broadinstitute.sting.utils.recalibration.ReadCovariates; +import org.broadinstitute.sting.utils.recalibration.RecalDatum; import org.broadinstitute.sting.utils.recalibration.RecalibrationTables; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; diff --git a/public/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java b/public/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java index f24bbb6366..9a2cb68db6 100644 --- a/public/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java +++ b/public/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java @@ -168,6 +168,28 @@ public PluginManager(Class pluginType, String pluginCategory, String String pluginName = getName(pluginClass); pluginsByName.put(pluginName, pluginClass); } + + // sort the plugins so the order of elements is deterministic + sortPlugins(plugins); + sortPlugins(interfaces); + } + + /** + * Sorts, in place, the list of plugins according to getName() on each element + * + * @param unsortedPlugins + */ + private final void sortPlugins(final List> unsortedPlugins) { + Collections.sort(unsortedPlugins, new ComparePluginsByName()); + } + + private final class ComparePluginsByName implements Comparator> { + @Override + public int compare(final Class aClass, final Class aClass1) { + String pluginName1 = getName(aClass); + String pluginName2 = getName(aClass1); + return pluginName1.compareTo(pluginName2); + } } /** diff --git a/public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java b/public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java index a4383c3aed..554188bc14 100644 --- a/public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java +++ b/public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java @@ -4,7 +4,7 @@ import net.sf.samtools.Cigar; import net.sf.samtools.CigarElement; import net.sf.samtools.CigarOperator; -import org.broadinstitute.sting.gatk.walkers.bqsr.EventType; +import org.broadinstitute.sting.utils.recalibration.EventType; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; diff --git a/public/java/src/org/broadinstitute/sting/utils/clipping/ReadClipper.java b/public/java/src/org/broadinstitute/sting/utils/clipping/ReadClipper.java index ba9267222a..6392ce4ce1 100644 --- a/public/java/src/org/broadinstitute/sting/utils/clipping/ReadClipper.java +++ b/public/java/src/org/broadinstitute/sting/utils/clipping/ReadClipper.java @@ -3,7 +3,7 @@ import com.google.java.contract.Requires; import net.sf.samtools.CigarElement; import net.sf.samtools.CigarOperator; -import org.broadinstitute.sting.gatk.walkers.bqsr.EventType; +import org.broadinstitute.sting.utils.recalibration.EventType; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; diff --git a/public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java b/public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java index c6eec24f1a..8512726739 100644 --- a/public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java @@ -4,7 +4,7 @@ import net.sf.samtools.CigarElement; import net.sf.samtools.CigarOperator; import net.sf.samtools.SAMRecord; -import org.broadinstitute.sting.gatk.walkers.bqsr.EventType; +import org.broadinstitute.sting.utils.recalibration.EventType; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.pileup.PileupElement; diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java index b5f7ad0462..c09eb00633 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java @@ -27,7 +27,7 @@ import net.sf.samtools.SAMTag; import net.sf.samtools.SAMUtils; -import org.broadinstitute.sting.gatk.walkers.bqsr.*; +import org.broadinstitute.sting.utils.recalibration.covariates.Covariate; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.collections.NestedIntegerArray; @@ -103,7 +103,7 @@ public void recalibrateRead(final GATKSAMRecord read) { } } - RecalDataManager.computeCovariates(read, requestedCovariates, readCovariates); // compute all covariates for the read + RecalUtils.computeCovariates(read, requestedCovariates, readCovariates); // compute all covariates for the read for (final EventType errorModel : EventType.values()) { // recalibrate all three quality strings if (disableIndelQuals && errorModel != EventType.BASE_SUBSTITUTION) { read.setBaseQualities(null, errorModel); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/EventType.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/EventType.java similarity index 96% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/EventType.java rename to public/java/src/org/broadinstitute/sting/utils/recalibration/EventType.java index 2650f0f8d4..1c84518eb9 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/EventType.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/EventType.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/QuantizationInfo.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java similarity index 78% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/QuantizationInfo.java rename to public/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java index fb3aef949b..2b67d12a98 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/QuantizationInfo.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java @@ -1,11 +1,9 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration; import org.broadinstitute.sting.gatk.report.GATKReportTable; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.collections.NestedIntegerArray; -import org.broadinstitute.sting.utils.recalibration.QualQuantizer; -import org.broadinstitute.sting.utils.recalibration.RecalibrationTables; import java.util.Arrays; import java.util.List; @@ -41,7 +39,7 @@ public QuantizationInfo(final RecalibrationTables recalibrationTables, final int for (final RecalDatum value : qualTable.getAllValues()) { final RecalDatum datum = value; final int empiricalQual = MathUtils.fastRound(datum.getEmpiricalQuality()); // convert the empirical quality to an integer ( it is already capped by MAX_QUAL ) - qualHistogram[empiricalQual] += datum.numObservations; // add the number of observations for every key + qualHistogram[empiricalQual] += datum.getNumObservations(); // add the number of observations for every key } empiricalQualCounts = Arrays.asList(qualHistogram); // histogram with the number of observations of the empirical qualities quantizeQualityScores(quantizationLevels); @@ -70,15 +68,15 @@ public int getQuantizationLevels() { } public GATKReportTable generateReportTable() { - GATKReportTable quantizedTable = new GATKReportTable(RecalDataManager.QUANTIZED_REPORT_TABLE_TITLE, "Quality quantization map", 3); - quantizedTable.addColumn(RecalDataManager.QUALITY_SCORE_COLUMN_NAME); - quantizedTable.addColumn(RecalDataManager.QUANTIZED_COUNT_COLUMN_NAME); - quantizedTable.addColumn(RecalDataManager.QUANTIZED_VALUE_COLUMN_NAME); + GATKReportTable quantizedTable = new GATKReportTable(RecalUtils.QUANTIZED_REPORT_TABLE_TITLE, "Quality quantization map", 3); + quantizedTable.addColumn(RecalUtils.QUALITY_SCORE_COLUMN_NAME); + quantizedTable.addColumn(RecalUtils.QUANTIZED_COUNT_COLUMN_NAME); + quantizedTable.addColumn(RecalUtils.QUANTIZED_VALUE_COLUMN_NAME); for (int qual = 0; qual <= QualityUtils.MAX_QUAL_SCORE; qual++) { - quantizedTable.set(qual, RecalDataManager.QUALITY_SCORE_COLUMN_NAME, qual); - quantizedTable.set(qual, RecalDataManager.QUANTIZED_COUNT_COLUMN_NAME, empiricalQualCounts.get(qual)); - quantizedTable.set(qual, RecalDataManager.QUANTIZED_VALUE_COLUMN_NAME, quantizedQuals.get(qual)); + quantizedTable.set(qual, RecalUtils.QUALITY_SCORE_COLUMN_NAME, qual); + quantizedTable.set(qual, RecalUtils.QUANTIZED_COUNT_COLUMN_NAME, empiricalQualCounts.get(qual)); + quantizedTable.set(qual, RecalUtils.QUANTIZED_VALUE_COLUMN_NAME, quantizedQuals.get(qual)); } return quantizedTable; } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadCovariates.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java similarity index 97% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadCovariates.java rename to public/java/src/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java index 5e907237d6..c86bd4deba 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadCovariates.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration; /** * The object temporarily held by a read that describes all of it's covariates. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDatum.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java similarity index 77% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDatum.java rename to public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java index ed4e769b12..43ff543788 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDatum.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration; /* * Copyright (c) 2009 The Broad Institute @@ -56,12 +56,12 @@ public class RecalDatum { /** * number of bases seen in total */ - long numObservations; + private long numObservations; /** * number of bases seen that didn't match the reference */ - long numMismatches; + private long numMismatches; /** * used when calculating empirical qualities to avoid division by zero @@ -82,16 +82,16 @@ public RecalDatum(final long _numObservations, final long _numMismatches, final } public RecalDatum(final RecalDatum copy) { - this.numObservations = copy.numObservations; - this.numMismatches = copy.numMismatches; + this.numObservations = copy.getNumObservations(); + this.numMismatches = copy.getNumMismatches(); this.estimatedQReported = copy.estimatedQReported; this.empiricalQuality = copy.empiricalQuality; } public synchronized void combine(final RecalDatum other) { final double sumErrors = this.calcExpectedErrors() + other.calcExpectedErrors(); - increment(other.numObservations, other.numMismatches); - estimatedQReported = -10 * Math.log10(sumErrors / this.numObservations); + increment(other.getNumObservations(), other.getNumMismatches()); + estimatedQReported = -10 * Math.log10(sumErrors / getNumObservations()); empiricalQuality = UNINITIALIZED; } @@ -100,7 +100,8 @@ public synchronized void combine(final RecalDatum other) { private synchronized final void calcEmpiricalQuality() { // cache the value so we don't call log over and over again final double doubleMismatches = (double) (numMismatches + SMOOTHING_CONSTANT); - final double doubleObservations = (double) (numObservations + SMOOTHING_CONSTANT); + // smoothing is one error and one non-error observation, for example + final double doubleObservations = (double) (numObservations + SMOOTHING_CONSTANT + SMOOTHING_CONSTANT); final double empiricalQual = -10 * Math.log10(doubleMismatches / doubleObservations); empiricalQuality = Math.min(empiricalQual, (double) QualityUtils.MAX_RECALIBRATED_Q_SCORE); } @@ -125,7 +126,7 @@ public final double getEmpiricalQuality() { @Override public String toString() { - return String.format("%d,%d,%d", numObservations, numMismatches, (byte) Math.floor(getEmpiricalQuality())); + return String.format("%d,%d,%d", getNumObservations(), getNumMismatches(), (byte) Math.floor(getEmpiricalQuality())); } public String stringForCSV() { @@ -133,7 +134,7 @@ public String stringForCSV() { } private double calcExpectedErrors() { - return (double) this.numObservations * qualToErrorProb(estimatedQReported); + return (double) getNumObservations() * qualToErrorProb(estimatedQReported); } private double qualToErrorProb(final double qual) { @@ -170,15 +171,42 @@ public boolean equals(Object o) { // //--------------------------------------------------------------------------------------------------------------- - synchronized void increment(final long incObservations, final long incMismatches) { - numObservations += incObservations; - numMismatches += incMismatches; + public long getNumObservations() { + return numObservations; + } + + public synchronized void setNumObservations(final long numObservations) { + this.numObservations = numObservations; + empiricalQuality = UNINITIALIZED; + } + + public long getNumMismatches() { + return numMismatches; + } + + public synchronized void setNumMismatches(final long numMismatches) { + this.numMismatches = numMismatches; empiricalQuality = UNINITIALIZED; } - synchronized void increment(final boolean isError) { - numObservations++; - numMismatches += isError ? 1:0; + public synchronized void incrementNumObservations(final long by) { + numObservations += by; empiricalQuality = UNINITIALIZED; } + + public synchronized void incrementNumMismatches(final long by) { + numMismatches += by; + empiricalQuality = UNINITIALIZED; + } + + public synchronized void increment(final long incObservations, final long incMismatches) { + incrementNumObservations(incObservations); + incrementNumMismatches(incMismatches); + } + + public synchronized void increment(final boolean isError) { + incrementNumObservations(1); + if ( isError ) + incrementNumMismatches(1); + } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java similarity index 96% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java rename to public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java index f40a62d53c..fe6ef70180 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java @@ -23,11 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.report.GATKReport; import org.broadinstitute.sting.gatk.report.GATKReportTable; +import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.sting.utils.recalibration.covariates.*; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.R.RScriptExecutor; import org.broadinstitute.sting.utils.Utils; @@ -39,7 +41,6 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.io.Resource; -import org.broadinstitute.sting.utils.recalibration.RecalibrationTables; import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; @@ -59,7 +60,7 @@ * This class holds the parsing methods that are shared between CountCovariates and TableRecalibration. */ -public class RecalDataManager { +public class RecalUtils { public final static String ARGUMENT_REPORT_TABLE_TITLE = "Arguments"; public final static String QUANTIZED_REPORT_TABLE_TITLE = "Quantized"; public final static String READGROUP_REPORT_TABLE_TITLE = "RecalTable0"; @@ -85,13 +86,108 @@ public class RecalDataManager { private static final String SCRIPT_FILE = "BQSR.R"; - private static final Pair covariateValue = new Pair(RecalDataManager.COVARIATE_VALUE_COLUMN_NAME, "%s"); - private static final Pair covariateName = new Pair(RecalDataManager.COVARIATE_NAME_COLUMN_NAME, "%s"); - private static final Pair eventType = new Pair(RecalDataManager.EVENT_TYPE_COLUMN_NAME, "%s"); - private static final Pair empiricalQuality = new Pair(RecalDataManager.EMPIRICAL_QUALITY_COLUMN_NAME, "%.4f"); - private static final Pair estimatedQReported = new Pair(RecalDataManager.ESTIMATED_Q_REPORTED_COLUMN_NAME, "%.4f"); - private static final Pair nObservations = new Pair(RecalDataManager.NUMBER_OBSERVATIONS_COLUMN_NAME, "%d"); - private static final Pair nErrors = new Pair(RecalDataManager.NUMBER_ERRORS_COLUMN_NAME, "%d"); + private static final Pair covariateValue = new Pair(RecalUtils.COVARIATE_VALUE_COLUMN_NAME, "%s"); + private static final Pair covariateName = new Pair(RecalUtils.COVARIATE_NAME_COLUMN_NAME, "%s"); + private static final Pair eventType = new Pair(RecalUtils.EVENT_TYPE_COLUMN_NAME, "%s"); + private static final Pair empiricalQuality = new Pair(RecalUtils.EMPIRICAL_QUALITY_COLUMN_NAME, "%.4f"); + private static final Pair estimatedQReported = new Pair(RecalUtils.ESTIMATED_Q_REPORTED_COLUMN_NAME, "%.4f"); + private static final Pair nObservations = new Pair(RecalUtils.NUMBER_OBSERVATIONS_COLUMN_NAME, "%d"); + private static final Pair nErrors = new Pair(RecalUtils.NUMBER_ERRORS_COLUMN_NAME, "%d"); + + /** + * Generates two lists : required covariates and optional covariates based on the user's requests. + * + * Performs the following tasks in order: + * 1. Adds all requierd covariates in order + * 2. Check if the user asked to use the standard covariates and adds them all if that's the case + * 3. Adds all covariates requested by the user that were not already added by the two previous steps + * + * @param argumentCollection the argument collection object for the recalibration walker + * @return a pair of ordered lists : required covariates (first) and optional covariates (second) + */ + public static Pair, ArrayList> initializeCovariates(RecalibrationArgumentCollection argumentCollection) { + final List> covariateClasses = new PluginManager(Covariate.class).getPlugins(); + final List> requiredClasses = new PluginManager(RequiredCovariate.class).getPlugins(); + final List> standardClasses = new PluginManager(StandardCovariate.class).getPlugins(); + + final ArrayList requiredCovariates = addRequiredCovariatesToList(requiredClasses); // add the required covariates + ArrayList optionalCovariates = new ArrayList(); + if (!argumentCollection.DO_NOT_USE_STANDARD_COVARIATES) + optionalCovariates = addStandardCovariatesToList(standardClasses); // add the standard covariates if -standard was specified by the user + + if (argumentCollection.COVARIATES != null) { // parse the -cov arguments that were provided, skipping over the ones already specified + for (String requestedCovariateString : argumentCollection.COVARIATES) { + boolean foundClass = false; + for (Class covClass : covariateClasses) { + if (requestedCovariateString.equalsIgnoreCase(covClass.getSimpleName())) { // -cov argument matches the class name for an implementing class + foundClass = true; + if (!requiredClasses.contains(covClass) && + (argumentCollection.DO_NOT_USE_STANDARD_COVARIATES || !standardClasses.contains(covClass))) { + try { + final Covariate covariate = covClass.newInstance(); // now that we've found a matching class, try to instantiate it + optionalCovariates.add(covariate); + } catch (Exception e) { + throw new DynamicClassResolutionException(covClass, e); + } + } + } + } + + if (!foundClass) { + throw new UserException.CommandLineException("The requested covariate type (" + requestedCovariateString + ") isn't a valid covariate option. Use --list to see possible covariates."); + } + } + } + return new Pair, ArrayList>(requiredCovariates, optionalCovariates); + } + + /** + * Adds the required covariates to a covariate list + * + * Note: this method really only checks if the classes object has the expected number of required covariates, then add them by hand. + * + * @param classes list of classes to add to the covariate list + * @return the covariate list + */ + private static ArrayList addRequiredCovariatesToList(List> classes) { + ArrayList dest = new ArrayList(classes.size()); + if (classes.size() != 2) + throw new ReviewedStingException("The number of required covariates has changed, this is a hard change in the code and needs to be inspected"); + + dest.add(new ReadGroupCovariate()); // enforce the order with RG first and QS next. + dest.add(new QualityScoreCovariate()); + return dest; + } + + /** + * Adds the standard covariates to a covariate list + * + * @param classes list of classes to add to the covariate list + * @return the covariate list + */ + private static ArrayList addStandardCovariatesToList(List> classes) { + ArrayList dest = new ArrayList(classes.size()); + for (Class covClass : classes) { + try { + final Covariate covariate = (Covariate) covClass.newInstance(); + dest.add(covariate); + } catch (Exception e) { + throw new DynamicClassResolutionException(covClass, e); + } + } + return dest; + } + + public static void listAvailableCovariates(Logger logger) { + // Get a list of all available covariates + final List> covariateClasses = new PluginManager(Covariate.class).getPlugins(); + + // Print and exit if that's what was requested + logger.info("Available covariates:"); + for (Class covClass : covariateClasses) + logger.info(covClass.getSimpleName()); + logger.info(""); + } public enum SOLID_RECAL_MODE { @@ -152,64 +248,6 @@ public static SOLID_NOCALL_STRATEGY nocallStrategyFromString(String nocallStrate } } - /** - * Generates two lists : required covariates and optional covariates based on the user's requests. - * - * Performs the following tasks in order: - * 1. Adds all requierd covariates in order - * 2. Check if the user asked to use the standard covariates and adds them all if that's the case - * 3. Adds all covariates requested by the user that were not already added by the two previous steps - * - * @param argumentCollection the argument collection object for the recalibration walker - * @return a pair of ordered lists : required covariates (first) and optional covariates (second) - */ - public static Pair, ArrayList> initializeCovariates(RecalibrationArgumentCollection argumentCollection) { - final List> covariateClasses = new PluginManager(Covariate.class).getPlugins(); - final List> requiredClasses = new PluginManager(RequiredCovariate.class).getPlugins(); - final List> standardClasses = new PluginManager(StandardCovariate.class).getPlugins(); - - final ArrayList requiredCovariates = addRequiredCovariatesToList(requiredClasses); // add the required covariates - ArrayList optionalCovariates = new ArrayList(); - if (!argumentCollection.DO_NOT_USE_STANDARD_COVARIATES) - optionalCovariates = addStandardCovariatesToList(standardClasses); // add the standard covariates if -standard was specified by the user - - if (argumentCollection.COVARIATES != null) { // parse the -cov arguments that were provided, skipping over the ones already specified - for (String requestedCovariateString : argumentCollection.COVARIATES) { - boolean foundClass = false; - for (Class covClass : covariateClasses) { - if (requestedCovariateString.equalsIgnoreCase(covClass.getSimpleName())) { // -cov argument matches the class name for an implementing class - foundClass = true; - if (!requiredClasses.contains(covClass) && - (argumentCollection.DO_NOT_USE_STANDARD_COVARIATES || !standardClasses.contains(covClass))) { - try { - final Covariate covariate = covClass.newInstance(); // now that we've found a matching class, try to instantiate it - optionalCovariates.add(covariate); - } catch (Exception e) { - throw new DynamicClassResolutionException(covClass, e); - } - } - } - } - - if (!foundClass) { - throw new UserException.CommandLineException("The requested covariate type (" + requestedCovariateString + ") isn't a valid covariate option. Use --list to see possible covariates."); - } - } - } - return new Pair, ArrayList>(requiredCovariates, optionalCovariates); - } - - public static void listAvailableCovariates(Logger logger) { - // Get a list of all available covariates - final List> covariateClasses = new PluginManager(Covariate.class).getPlugins(); - - // Print and exit if that's what was requested - logger.info("Available covariates:"); - for (Class covClass : covariateClasses) - logger.info(covClass.getSimpleName()); - logger.info(""); - } - private static List generateReportTables(final RecalibrationTables recalibrationTables, final Covariate[] requestedCovariates) { List result = new LinkedList(); int reportTableIndex = 0; @@ -272,8 +310,8 @@ private static List generateReportTables(final RecalibrationTab reportTable.set(rowIndex, columnNames.get(columnIndex++).getFirst(), datum.getEmpiricalQuality()); if (tableIndex == RecalibrationTables.TableType.READ_GROUP_TABLE.index) reportTable.set(rowIndex, columnNames.get(columnIndex++).getFirst(), datum.getEstimatedQReported()); // we only add the estimated Q reported in the RG table - reportTable.set(rowIndex, columnNames.get(columnIndex++).getFirst(), datum.numObservations); - reportTable.set(rowIndex, columnNames.get(columnIndex).getFirst(), datum.numMismatches); + reportTable.set(rowIndex, columnNames.get(columnIndex++).getFirst(), datum.getNumObservations()); + reportTable.set(rowIndex, columnNames.get(columnIndex).getFirst(), datum.getNumMismatches()); rowIndex++; } @@ -320,7 +358,7 @@ private static void outputRecalibrationPlot(Pair files, boole files.getFirst().close(); final RScriptExecutor executor = new RScriptExecutor(); - executor.addScript(new Resource(SCRIPT_FILE, RecalDataManager.class)); + executor.addScript(new Resource(SCRIPT_FILE, RecalUtils.class)); executor.addArgs(csvFileName.getAbsolutePath()); executor.addArgs(plotFileName.getAbsolutePath()); executor.exec(); @@ -480,14 +518,14 @@ public static void parsePlatformForRead(final GATKSAMRecord read, final Recalibr */ public static boolean isColorSpaceConsistent(final SOLID_NOCALL_STRATEGY strategy, final GATKSAMRecord read) { if (ReadUtils.isSOLiDRead(read)) { // If this is a SOLID read then we have to check if the color space is inconsistent. This is our only sign that SOLID has inserted the reference base - if (read.getAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG) == null) { // Haven't calculated the inconsistency array yet for this read - final Object attr = read.getAttribute(RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG); + if (read.getAttribute(RecalUtils.COLOR_SPACE_INCONSISTENCY_TAG) == null) { // Haven't calculated the inconsistency array yet for this read + final Object attr = read.getAttribute(RecalUtils.COLOR_SPACE_ATTRIBUTE_TAG); if (attr != null) { byte[] colorSpace; if (attr instanceof String) colorSpace = ((String) attr).getBytes(); else - throw new UserException.MalformedBAM(read, String.format("Value encoded by %s in %s isn't a string!", RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG, read.getReadName())); + throw new UserException.MalformedBAM(read, String.format("Value encoded by %s in %s isn't a string!", RecalUtils.COLOR_SPACE_ATTRIBUTE_TAG, read.getReadName())); byte[] readBases = read.getReadBases(); // Loop over the read and calculate first the inferred bases from the color and then check if it is consistent with the read if (read.getReadNegativeStrandFlag()) @@ -501,7 +539,7 @@ public static boolean isColorSpaceConsistent(final SOLID_NOCALL_STRATEGY strateg inconsistency[i] = (byte) (thisBase == readBases[i] ? 0 : 1); prevBase = readBases[i]; } - read.setAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG, inconsistency); + read.setAttribute(RecalUtils.COLOR_SPACE_INCONSISTENCY_TAG, inconsistency); } else if (strategy == SOLID_NOCALL_STRATEGY.THROW_EXCEPTION) // if the strategy calls for an exception, throw it throw new UserException.MalformedBAM(read, "Unable to find color space information in SOLiD read. First observed at read with name = " + read.getReadName() + " Unfortunately this .bam file can not be recalibrated without color space information because of potential reference bias."); @@ -545,7 +583,7 @@ private static byte getNextBaseFromColor(GATKSAMRecord read, final byte prevBase * @return Returns true if the base was inconsistent with the color space */ public static boolean isColorSpaceConsistent(final GATKSAMRecord read, final int offset) { - final Object attr = read.getAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG); + final Object attr = read.getAttribute(RecalUtils.COLOR_SPACE_INCONSISTENCY_TAG); if (attr != null) { final byte[] inconsistency = (byte[]) attr; // NOTE: The inconsistency array is in the direction of the read, not aligned to the reference! @@ -691,40 +729,4 @@ private static byte performColorThree(byte base) { } - /** - * Adds the required covariates to a covariate list - * - * Note: this method really only checks if the classes object has the expected number of required covariates, then add them by hand. - * - * @param classes list of classes to add to the covariate list - * @return the covariate list - */ - private static ArrayList addRequiredCovariatesToList(List> classes) { - ArrayList dest = new ArrayList(classes.size()); - if (classes.size() != 2) - throw new ReviewedStingException("The number of required covariates has changed, this is a hard change in the code and needs to be inspected"); - - dest.add(new ReadGroupCovariate()); // enforce the order with RG first and QS next. - dest.add(new QualityScoreCovariate()); - return dest; - } - - /** - * Adds the standard covariates to a covariate list - * - * @param classes list of classes to add to the covariate list - * @return the covariate list - */ - private static ArrayList addStandardCovariatesToList(List> classes) { - ArrayList dest = new ArrayList(classes.size()); - for (Class covClass : classes) { - try { - final Covariate covariate = (Covariate) covClass.newInstance(); - dest.add(covariate); - } catch (Exception e) { - throw new DynamicClassResolutionException(covClass, e); - } - } - return dest; - } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReport.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java similarity index 82% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReport.java rename to public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java index e69cf4d69e..e6ab9e38bf 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReport.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java @@ -1,11 +1,12 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration; import org.broadinstitute.sting.gatk.report.GATKReport; import org.broadinstitute.sting.gatk.report.GATKReportTable; +import org.broadinstitute.sting.gatk.walkers.bqsr.*; +import org.broadinstitute.sting.utils.recalibration.covariates.Covariate; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.collections.NestedIntegerArray; import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.recalibration.RecalibrationTables; import java.io.File; import java.io.PrintStream; @@ -33,13 +34,13 @@ public class RecalibrationReport { public RecalibrationReport(final File RECAL_FILE) { final GATKReport report = new GATKReport(RECAL_FILE); - argumentTable = report.getTable(RecalDataManager.ARGUMENT_REPORT_TABLE_TITLE); + argumentTable = report.getTable(RecalUtils.ARGUMENT_REPORT_TABLE_TITLE); RAC = initializeArgumentCollectionTable(argumentTable); - GATKReportTable quantizedTable = report.getTable(RecalDataManager.QUANTIZED_REPORT_TABLE_TITLE); + GATKReportTable quantizedTable = report.getTable(RecalUtils.QUANTIZED_REPORT_TABLE_TITLE); quantizationInfo = initializeQuantizationTable(quantizedTable); - Pair, ArrayList> covariates = RecalDataManager.initializeCovariates(RAC); // initialize the required and optional covariates + Pair, ArrayList> covariates = RecalUtils.initializeCovariates(RAC); // initialize the required and optional covariates ArrayList requiredCovariates = covariates.getFirst(); ArrayList optionalCovariates = covariates.getSecond(); requestedCovariates = new Covariate[requiredCovariates.size() + optionalCovariates.size()]; @@ -57,13 +58,13 @@ public RecalibrationReport(final File RECAL_FILE) { for (Covariate cov : requestedCovariates) cov.initialize(RAC); // initialize any covariate member variables using the shared argument collection - recalibrationTables = new RecalibrationTables(requestedCovariates, countReadGroups(report.getTable(RecalDataManager.READGROUP_REPORT_TABLE_TITLE))); + recalibrationTables = new RecalibrationTables(requestedCovariates, countReadGroups(report.getTable(RecalUtils.READGROUP_REPORT_TABLE_TITLE))); - parseReadGroupTable(report.getTable(RecalDataManager.READGROUP_REPORT_TABLE_TITLE), recalibrationTables.getTable(RecalibrationTables.TableType.READ_GROUP_TABLE)); + parseReadGroupTable(report.getTable(RecalUtils.READGROUP_REPORT_TABLE_TITLE), recalibrationTables.getTable(RecalibrationTables.TableType.READ_GROUP_TABLE)); - parseQualityScoreTable(report.getTable(RecalDataManager.QUALITY_SCORE_REPORT_TABLE_TITLE), recalibrationTables.getTable(RecalibrationTables.TableType.QUALITY_SCORE_TABLE)); + parseQualityScoreTable(report.getTable(RecalUtils.QUALITY_SCORE_REPORT_TABLE_TITLE), recalibrationTables.getTable(RecalibrationTables.TableType.QUALITY_SCORE_TABLE)); - parseAllCovariatesTable(report.getTable(RecalDataManager.ALL_COVARIATES_REPORT_TABLE_TITLE), recalibrationTables); + parseAllCovariatesTable(report.getTable(RecalUtils.ALL_COVARIATES_REPORT_TABLE_TITLE), recalibrationTables); } @@ -85,7 +86,7 @@ protected RecalibrationReport(final QuantizationInfo quantizationInfo, final Rec private int countReadGroups(final GATKReportTable reportTable) { Set readGroups = new HashSet(); for ( int i = 0; i < reportTable.getNumRows(); i++ ) - readGroups.add(reportTable.get(i, RecalDataManager.READGROUP_COLUMN_NAME).toString()); + readGroups.add(reportTable.get(i, RecalUtils.READGROUP_COLUMN_NAME).toString()); return readGroups.size(); } @@ -139,17 +140,17 @@ public Covariate[] getRequestedCovariates() { \ */ private void parseAllCovariatesTable(final GATKReportTable reportTable, final RecalibrationTables recalibrationTables) { for ( int i = 0; i < reportTable.getNumRows(); i++ ) { - final Object rg = reportTable.get(i, RecalDataManager.READGROUP_COLUMN_NAME); + final Object rg = reportTable.get(i, RecalUtils.READGROUP_COLUMN_NAME); tempCOVarray[0] = requestedCovariates[0].keyFromValue(rg); - final Object qual = reportTable.get(i, RecalDataManager.QUALITY_SCORE_COLUMN_NAME); + final Object qual = reportTable.get(i, RecalUtils.QUALITY_SCORE_COLUMN_NAME); tempCOVarray[1] = requestedCovariates[1].keyFromValue(qual); - final String covName = (String)reportTable.get(i, RecalDataManager.COVARIATE_NAME_COLUMN_NAME); + final String covName = (String)reportTable.get(i, RecalUtils.COVARIATE_NAME_COLUMN_NAME); final int covIndex = optionalCovariateIndexes.get(covName); - final Object covValue = reportTable.get(i, RecalDataManager.COVARIATE_VALUE_COLUMN_NAME); + final Object covValue = reportTable.get(i, RecalUtils.COVARIATE_VALUE_COLUMN_NAME); tempCOVarray[2] = requestedCovariates[RecalibrationTables.TableType.OPTIONAL_COVARIATE_TABLES_START.index + covIndex].keyFromValue(covValue); - final EventType event = EventType.eventFrom((String)reportTable.get(i, RecalDataManager.EVENT_TYPE_COLUMN_NAME)); + final EventType event = EventType.eventFrom((String)reportTable.get(i, RecalUtils.EVENT_TYPE_COLUMN_NAME)); tempCOVarray[3] = event.index; recalibrationTables.getTable(RecalibrationTables.TableType.OPTIONAL_COVARIATE_TABLES_START.index + covIndex).put(getRecalDatum(reportTable, i, false), tempCOVarray); @@ -164,11 +165,11 @@ private void parseAllCovariatesTable(final GATKReportTable reportTable, final Re */ private void parseQualityScoreTable(final GATKReportTable reportTable, final NestedIntegerArray qualTable) { for ( int i = 0; i < reportTable.getNumRows(); i++ ) { - final Object rg = reportTable.get(i, RecalDataManager.READGROUP_COLUMN_NAME); + final Object rg = reportTable.get(i, RecalUtils.READGROUP_COLUMN_NAME); tempQUALarray[0] = requestedCovariates[0].keyFromValue(rg); - final Object qual = reportTable.get(i, RecalDataManager.QUALITY_SCORE_COLUMN_NAME); + final Object qual = reportTable.get(i, RecalUtils.QUALITY_SCORE_COLUMN_NAME); tempQUALarray[1] = requestedCovariates[1].keyFromValue(qual); - final EventType event = EventType.eventFrom((String)reportTable.get(i, RecalDataManager.EVENT_TYPE_COLUMN_NAME)); + final EventType event = EventType.eventFrom((String)reportTable.get(i, RecalUtils.EVENT_TYPE_COLUMN_NAME)); tempQUALarray[2] = event.index; qualTable.put(getRecalDatum(reportTable, i, false), tempQUALarray); @@ -183,9 +184,9 @@ private void parseQualityScoreTable(final GATKReportTable reportTable, final Nes */ private void parseReadGroupTable(final GATKReportTable reportTable, final NestedIntegerArray rgTable) { for ( int i = 0; i < reportTable.getNumRows(); i++ ) { - final Object rg = reportTable.get(i, RecalDataManager.READGROUP_COLUMN_NAME); + final Object rg = reportTable.get(i, RecalUtils.READGROUP_COLUMN_NAME); tempRGarray[0] = requestedCovariates[0].keyFromValue(rg); - final EventType event = EventType.eventFrom((String)reportTable.get(i, RecalDataManager.EVENT_TYPE_COLUMN_NAME)); + final EventType event = EventType.eventFrom((String)reportTable.get(i, RecalUtils.EVENT_TYPE_COLUMN_NAME)); tempRGarray[1] = event.index; rgTable.put(getRecalDatum(reportTable, i, true), tempRGarray); @@ -193,13 +194,13 @@ private void parseReadGroupTable(final GATKReportTable reportTable, final Nested } private RecalDatum getRecalDatum(final GATKReportTable reportTable, final int row, final boolean hasEstimatedQReportedColumn) { - final long nObservations = (Long) reportTable.get(row, RecalDataManager.NUMBER_OBSERVATIONS_COLUMN_NAME); - final long nErrors = (Long) reportTable.get(row, RecalDataManager.NUMBER_ERRORS_COLUMN_NAME); - final double empiricalQuality = (Double) reportTable.get(row, RecalDataManager.EMPIRICAL_QUALITY_COLUMN_NAME); + final long nObservations = (Long) reportTable.get(row, RecalUtils.NUMBER_OBSERVATIONS_COLUMN_NAME); + final long nErrors = (Long) reportTable.get(row, RecalUtils.NUMBER_ERRORS_COLUMN_NAME); + final double empiricalQuality = (Double) reportTable.get(row, RecalUtils.EMPIRICAL_QUALITY_COLUMN_NAME); final double estimatedQReported = hasEstimatedQReportedColumn ? // the estimatedQreported column only exists in the ReadGroup table - (Double) reportTable.get(row, RecalDataManager.ESTIMATED_Q_REPORTED_COLUMN_NAME) : // we get it if we are in the read group table - Byte.parseByte((String) reportTable.get(row, RecalDataManager.QUALITY_SCORE_COLUMN_NAME)); // or we use the reported quality if we are in any other table + (Double) reportTable.get(row, RecalUtils.ESTIMATED_Q_REPORTED_COLUMN_NAME) : // we get it if we are in the read group table + Byte.parseByte((String) reportTable.get(row, RecalUtils.QUALITY_SCORE_COLUMN_NAME)); // or we use the reported quality if we are in any other table final RecalDatum datum = new RecalDatum(nObservations, nErrors, (byte)1); datum.setEstimatedQReported(estimatedQReported); @@ -218,8 +219,8 @@ private QuantizationInfo initializeQuantizationTable(GATKReportTable table) { final Long[] counts = new Long[QualityUtils.MAX_QUAL_SCORE + 1]; for ( int i = 0; i < table.getNumRows(); i++ ) { final byte originalQual = (byte)i; - final Object quantizedObject = table.get(i, RecalDataManager.QUANTIZED_VALUE_COLUMN_NAME); - final Object countObject = table.get(i, RecalDataManager.QUANTIZED_COUNT_COLUMN_NAME); + final Object quantizedObject = table.get(i, RecalUtils.QUANTIZED_VALUE_COLUMN_NAME); + final Object countObject = table.get(i, RecalUtils.QUANTIZED_COUNT_COLUMN_NAME); final byte quantizedQual = Byte.parseByte(quantizedObject.toString()); final long quantizedCount = Long.parseLong(countObject.toString()); quals[originalQual] = quantizedQual; @@ -239,7 +240,7 @@ private RecalibrationArgumentCollection initializeArgumentCollectionTable(GATKRe for ( int i = 0; i < table.getNumRows(); i++ ) { final String argument = table.get(i, "Argument").toString(); - Object value = table.get(i, RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME); + Object value = table.get(i, RecalUtils.ARGUMENT_VALUE_COLUMN_NAME); if (value.equals("null")) value = null; // generic translation of null values that were printed out as strings | todo -- add this capability to the GATKReport @@ -250,10 +251,10 @@ else if (argument.equals("standard_covs")) RAC.DO_NOT_USE_STANDARD_COVARIATES = Boolean.parseBoolean((String) value); else if (argument.equals("solid_recal_mode")) - RAC.SOLID_RECAL_MODE = RecalDataManager.SOLID_RECAL_MODE.recalModeFromString((String) value); + RAC.SOLID_RECAL_MODE = RecalUtils.SOLID_RECAL_MODE.recalModeFromString((String) value); else if (argument.equals("solid_nocall_strategy")) - RAC.SOLID_NOCALL_STRATEGY = RecalDataManager.SOLID_NOCALL_STRATEGY.nocallStrategyFromString((String) value); + RAC.SOLID_NOCALL_STRATEGY = RecalUtils.SOLID_NOCALL_STRATEGY.nocallStrategyFromString((String) value); else if (argument.equals("mismatches_context_size")) RAC.MISMATCHES_CONTEXT_SIZE = Integer.parseInt((String) value); @@ -307,7 +308,7 @@ public void calculateQuantizedQualities() { } public void output(PrintStream output) { - RecalDataManager.outputRecalibrationReport(argumentTable, quantizationInfo, recalibrationTables, requestedCovariates, output); + RecalUtils.outputRecalibrationReport(argumentTable, quantizationInfo, recalibrationTables, requestedCovariates, output); } public RecalibrationArgumentCollection getRAC() { diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java index 0416b5eb94..f37e69c9ad 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java @@ -25,9 +25,7 @@ package org.broadinstitute.sting.utils.recalibration; -import org.broadinstitute.sting.gatk.walkers.bqsr.Covariate; -import org.broadinstitute.sting.gatk.walkers.bqsr.EventType; -import org.broadinstitute.sting.gatk.walkers.bqsr.RecalDatum; +import org.broadinstitute.sting.utils.recalibration.covariates.Covariate; import org.broadinstitute.sting.utils.collections.NestedIntegerArray; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BinaryTagCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/BinaryTagCovariate.java similarity index 89% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BinaryTagCovariate.java rename to public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/BinaryTagCovariate.java index a89586c2c8..cebdebf9dd 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BinaryTagCovariate.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/BinaryTagCovariate.java @@ -1,5 +1,7 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration.covariates; +import org.broadinstitute.sting.utils.recalibration.ReadCovariates; +import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ContextCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ContextCovariate.java rename to public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java index 5fe8809fbc..4c20284d96 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ContextCovariate.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java @@ -23,8 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration.covariates; +import org.broadinstitute.sting.utils.recalibration.ReadCovariates; +import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.clipping.ClippingRepresentation; import org.broadinstitute.sting.utils.clipping.ReadClipper; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/Covariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/Covariate.java similarity index 94% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/Covariate.java rename to public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/Covariate.java index 1ad5346fa4..c613135bbe 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/Covariate.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/Covariate.java @@ -1,5 +1,7 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration.covariates; +import org.broadinstitute.sting.utils.recalibration.ReadCovariates; +import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; /* @@ -89,8 +91,3 @@ public interface Covariate { public int maximumKeyValue(); } -interface RequiredCovariate extends Covariate {} - -interface StandardCovariate extends Covariate {} - -interface ExperimentalCovariate extends Covariate {} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/CycleCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java similarity index 97% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/CycleCovariate.java rename to public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java index f0ff8f2bdc..4f15419c75 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/CycleCovariate.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java @@ -1,5 +1,7 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration.covariates; +import org.broadinstitute.sting.utils.recalibration.ReadCovariates; +import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.NGSPlatform; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ExperimentalCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ExperimentalCovariate.java new file mode 100644 index 0000000000..72df2a4103 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ExperimentalCovariate.java @@ -0,0 +1,30 @@ +package org.broadinstitute.sting.utils.recalibration.covariates; + +/** + * [Short one sentence description of this walker] + *

+ *

+ * [Functionality of this walker] + *

+ *

+ *

Input

+ *

+ * [Input description] + *

+ *

+ *

Output

+ *

+ * [Output description] + *

+ *

+ *

Examples

+ * 
+ *    java
+ *      -jar GenomeAnalysisTK.jar
+ *      -T $WalkerName
+ *
+ * + * @author Your Name + * @since Date created + */ +public interface ExperimentalCovariate extends Covariate {} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/QualityScoreCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/QualityScoreCovariate.java similarity index 92% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/QualityScoreCovariate.java rename to public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/QualityScoreCovariate.java index dd7060ff85..3ef8ee9310 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/QualityScoreCovariate.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/QualityScoreCovariate.java @@ -1,5 +1,7 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration.covariates; +import org.broadinstitute.sting.utils.recalibration.ReadCovariates; +import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadGroupCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java similarity index 94% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadGroupCovariate.java rename to public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java index f04d27b7a6..85568dac95 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadGroupCovariate.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java @@ -1,5 +1,7 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration.covariates; +import org.broadinstitute.sting.utils.recalibration.ReadCovariates; +import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RequiredCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RequiredCovariate.java new file mode 100644 index 0000000000..50755dbcf4 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RequiredCovariate.java @@ -0,0 +1,30 @@ +package org.broadinstitute.sting.utils.recalibration.covariates; + +/** + * [Short one sentence description of this walker] + *

+ *

+ * [Functionality of this walker] + *

+ *

+ *

Input

+ *

+ * [Input description] + *

+ *

+ *

Output

+ *

+ * [Output description] + *

+ *

+ *

Examples

+ * 
+ *    java
+ *      -jar GenomeAnalysisTK.jar
+ *      -T $WalkerName
+ *
+ * + * @author Your Name + * @since Date created + */ +public interface RequiredCovariate extends Covariate {} diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/StandardCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/StandardCovariate.java new file mode 100644 index 0000000000..444954f255 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/StandardCovariate.java @@ -0,0 +1,30 @@ +package org.broadinstitute.sting.utils.recalibration.covariates; + +/** + * [Short one sentence description of this walker] + *

+ *

+ * [Functionality of this walker] + *

+ *

+ *

Input

+ *

+ * [Input description] + *

+ *

+ *

Output

+ *

+ * [Output description] + *

+ *

+ *

Examples

+ * 
+ *    java
+ *      -jar GenomeAnalysisTK.jar
+ *      -T $WalkerName
+ *
+ * + * @author Your Name + * @since Date created + */ +public interface StandardCovariate extends Covariate {} diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java index 659615cf4f..c9b3a2df86 100755 --- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.sam; import net.sf.samtools.*; -import org.broadinstitute.sting.gatk.walkers.bqsr.EventType; +import org.broadinstitute.sting.utils.recalibration.EventType; import org.broadinstitute.sting.utils.NGSPlatform; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java index 8e9f2533f5..f1ffbe80f9 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java @@ -2,6 +2,7 @@ import org.broadinstitute.sting.gatk.report.GATKReport; import org.broadinstitute.sting.gatk.report.GATKReportTable; +import org.broadinstitute.sting.utils.recalibration.RecalUtils; import org.testng.Assert; import org.testng.annotations.Test; @@ -33,15 +34,15 @@ public void testCombineSimilarFiles() { for (GATKReportTable originalTable : originalReport.getTables()) { GATKReportTable calculatedTable = calculatedReport.getTable(originalTable.getTableName()); List columnsToTest = new LinkedList(); - columnsToTest.add(RecalDataManager.NUMBER_OBSERVATIONS_COLUMN_NAME); - columnsToTest.add(RecalDataManager.NUMBER_ERRORS_COLUMN_NAME); - if (originalTable.getTableName().equals(RecalDataManager.ARGUMENT_REPORT_TABLE_TITLE)) { // these tables must be IDENTICAL - columnsToTest.add(RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME); + columnsToTest.add(RecalUtils.NUMBER_OBSERVATIONS_COLUMN_NAME); + columnsToTest.add(RecalUtils.NUMBER_ERRORS_COLUMN_NAME); + if (originalTable.getTableName().equals(RecalUtils.ARGUMENT_REPORT_TABLE_TITLE)) { // these tables must be IDENTICAL + columnsToTest.add(RecalUtils.ARGUMENT_VALUE_COLUMN_NAME); testTablesWithColumnsAndFactor(originalTable, calculatedTable, columnsToTest, 1); } - else if (originalTable.getTableName().equals(RecalDataManager.QUANTIZED_REPORT_TABLE_TITLE)) { - columnsToTest.add(RecalDataManager.QUANTIZED_COUNT_COLUMN_NAME); + else if (originalTable.getTableName().equals(RecalUtils.QUANTIZED_REPORT_TABLE_TITLE)) { + columnsToTest.add(RecalUtils.QUANTIZED_COUNT_COLUMN_NAME); testTablesWithColumnsAndFactor(originalTable, calculatedTable, columnsToTest, 2); } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ContextCovariateUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/recalibration/ContextCovariateUnitTest.java similarity index 89% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ContextCovariateUnitTest.java rename to public/java/test/org/broadinstitute/sting/utils/recalibration/ContextCovariateUnitTest.java index 553b7e237a..2556448ada 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ContextCovariateUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/recalibration/ContextCovariateUnitTest.java @@ -1,5 +1,8 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration; +import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.sting.utils.recalibration.covariates.ContextCovariate; +import org.broadinstitute.sting.utils.recalibration.covariates.Covariate; import org.broadinstitute.sting.utils.clipping.ClippingRepresentation; import org.broadinstitute.sting.utils.clipping.ReadClipper; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/CycleCovariateUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/recalibration/CycleCovariateUnitTest.java similarity index 90% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/CycleCovariateUnitTest.java rename to public/java/test/org/broadinstitute/sting/utils/recalibration/CycleCovariateUnitTest.java index 3fa1e916de..c3d93b2cbd 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/CycleCovariateUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/recalibration/CycleCovariateUnitTest.java @@ -1,5 +1,7 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration; +import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.sting.utils.recalibration.covariates.CycleCovariate; import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ReadCovariatesUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/recalibration/ReadCovariatesUnitTest.java similarity index 92% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ReadCovariatesUnitTest.java rename to public/java/test/org/broadinstitute/sting/utils/recalibration/ReadCovariatesUnitTest.java index 37994cf121..dac26cb536 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ReadCovariatesUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/recalibration/ReadCovariatesUnitTest.java @@ -1,5 +1,7 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration; +import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.sting.utils.recalibration.covariates.*; import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; @@ -41,7 +43,7 @@ public void testCovariateGeneration() { requestedCovariates[2] = coCov; requestedCovariates[3] = cyCov; - ReadCovariates rc = RecalDataManager.computeCovariates(read, requestedCovariates); + ReadCovariates rc = RecalUtils.computeCovariates(read, requestedCovariates); // check that the length is correct Assert.assertEquals(rc.getMismatchesKeySet().length, length); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ReadGroupCovariateUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/recalibration/ReadGroupCovariateUnitTest.java similarity index 88% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ReadGroupCovariateUnitTest.java rename to public/java/test/org/broadinstitute/sting/utils/recalibration/ReadGroupCovariateUnitTest.java index a835083535..78a74d2596 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ReadGroupCovariateUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/recalibration/ReadGroupCovariateUnitTest.java @@ -1,5 +1,7 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration; +import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.sting.utils.recalibration.covariates.ReadGroupCovariate; import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReportUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java similarity index 95% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReportUnitTest.java rename to public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java index e4a77c016a..387cc94d61 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReportUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java @@ -1,9 +1,10 @@ -package org.broadinstitute.sting.gatk.walkers.bqsr; +package org.broadinstitute.sting.utils.recalibration; +import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.sting.utils.recalibration.covariates.*; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.collections.NestedIntegerArray; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.recalibration.RecalibrationTables; import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; @@ -72,7 +73,7 @@ public void testOutput() { final int expectedKeys = expectedNumberOfKeys(4, length, RAC.INDELS_CONTEXT_SIZE, RAC.MISMATCHES_CONTEXT_SIZE); int nKeys = 0; // keep track of how many keys were produced - final ReadCovariates rc = RecalDataManager.computeCovariates(read, requestedCovariates); + final ReadCovariates rc = RecalUtils.computeCovariates(read, requestedCovariates); final RecalibrationTables recalibrationTables = new RecalibrationTables(requestedCovariates); final NestedIntegerArray rgTable = recalibrationTables.getTable(RecalibrationTables.TableType.READ_GROUP_TABLE); From ffaffa92d389bf867869b6a6624874122ecc0391 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 27 Jul 2012 14:34:13 -0400 Subject: [PATCH 032/176] Extensive unit tests, contacts, and documentation for RecalDatum --- .../sting/utils/QualityUtils.java | 5 + .../sting/utils/recalibration/RecalDatum.java | 102 ++++++++++++++---- .../org/broadinstitute/sting/BaseTest.java | 10 +- 3 files changed, 93 insertions(+), 24 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java b/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java index 4acc0e2c3a..1242e5b001 100755 --- a/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java @@ -69,9 +69,14 @@ static public double qualToProbLog10(byte qual) { * @return a probability (0.0 - 1.0) */ static private double qualToErrorProbRaw(int qual) { + return qualToErrorProb((double) qual); + } + + public static double qualToErrorProb(final double qual) { return Math.pow(10.0, ((double) qual)/-10.0); } + static public double qualToErrorProb(byte qual) { return qualToErrorProbCache[(int)qual & 0xff]; // Map: 127 -> 127; -128 -> 128; -1 -> 255; etc. } diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java index 43ff543788..6ee5df68b7 100755 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java @@ -26,6 +26,7 @@ */ import com.google.java.contract.Ensures; +import com.google.java.contract.Invariant; import com.google.java.contract.Requires; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; @@ -40,6 +41,17 @@ * User: rpoplin * Date: Nov 3, 2009 */ +@Invariant({ + "estimatedQReported >= 0.0", + "! Double.isNaN(estimatedQReported)", + "! Double.isInfinite(estimatedQReported)", + "empiricalQuality >= 0.0 || empiricalQuality == UNINITIALIZED", + "! Double.isNaN(empiricalQuality)", + "! Double.isInfinite(empiricalQuality)", + "numObservations >= 0", + "numMismatches >= 0", + "numMismatches <= numObservations" +}) public class RecalDatum { private static final double UNINITIALIZED = -1.0; @@ -74,13 +86,28 @@ public class RecalDatum { // //--------------------------------------------------------------------------------------------------------------- + /** + * Create a new RecalDatum with given observation and mismatch counts, and an reported quality + * + * @param _numObservations + * @param _numMismatches + * @param reportedQuality + */ public RecalDatum(final long _numObservations, final long _numMismatches, final byte reportedQuality) { + if ( numObservations < 0 ) throw new IllegalArgumentException("numObservations < 0"); + if ( numMismatches < 0 ) throw new IllegalArgumentException("numMismatches < 0"); + if ( reportedQuality < 0 ) throw new IllegalArgumentException("reportedQuality < 0"); + numObservations = _numObservations; numMismatches = _numMismatches; estimatedQReported = reportedQuality; empiricalQuality = UNINITIALIZED; } + /** + * Copy copy into this recal datum, overwriting all of this objects data + * @param copy + */ public RecalDatum(final RecalDatum copy) { this.numObservations = copy.getNumObservations(); this.numMismatches = copy.getNumMismatches(); @@ -88,6 +115,12 @@ public RecalDatum(final RecalDatum copy) { this.empiricalQuality = copy.empiricalQuality; } + /** + * Add in all of the data from other into this object, updating the reported quality from the expected + * error rate implied by the two reported qualities + * + * @param other + */ public synchronized void combine(final RecalDatum other) { final double sumErrors = this.calcExpectedErrors() + other.calcExpectedErrors(); increment(other.getNumObservations(), other.getNumMismatches()); @@ -95,26 +128,26 @@ public synchronized void combine(final RecalDatum other) { empiricalQuality = UNINITIALIZED; } - @Requires("empiricalQuality == UNINITIALIZED") - @Ensures("empiricalQuality != UNINITIALIZED") - private synchronized final void calcEmpiricalQuality() { - // cache the value so we don't call log over and over again - final double doubleMismatches = (double) (numMismatches + SMOOTHING_CONSTANT); - // smoothing is one error and one non-error observation, for example - final double doubleObservations = (double) (numObservations + SMOOTHING_CONSTANT + SMOOTHING_CONSTANT); - final double empiricalQual = -10 * Math.log10(doubleMismatches / doubleObservations); - empiricalQuality = Math.min(empiricalQual, (double) QualityUtils.MAX_RECALIBRATED_Q_SCORE); - } - public synchronized void setEstimatedQReported(final double estimatedQReported) { + if ( estimatedQReported < 0 ) throw new IllegalArgumentException("estimatedQReported < 0"); + if ( Double.isInfinite(estimatedQReported) ) throw new IllegalArgumentException("estimatedQReported is infinite"); + if ( Double.isNaN(estimatedQReported) ) throw new IllegalArgumentException("estimatedQReported is NaN"); + this.estimatedQReported = estimatedQReported; } public final double getEstimatedQReported() { return estimatedQReported; } + public final byte getEstimatedQReportedAsByte() { + return (byte)(int)(Math.round(getEstimatedQReported())); + } public synchronized void setEmpiricalQuality(final double empiricalQuality) { + if ( empiricalQuality < 0 ) throw new IllegalArgumentException("empiricalQuality < 0"); + if ( Double.isInfinite(empiricalQuality) ) throw new IllegalArgumentException("empiricalQuality is infinite"); + if ( Double.isNaN(empiricalQuality) ) throw new IllegalArgumentException("empiricalQuality is NaN"); + this.empiricalQuality = empiricalQuality; } @@ -133,14 +166,6 @@ public String stringForCSV() { return String.format("%s,%d,%.2f", toString(), (byte) Math.floor(getEstimatedQReported()), getEmpiricalQuality() - getEstimatedQReported()); } - private double calcExpectedErrors() { - return (double) getNumObservations() * qualToErrorProb(estimatedQReported); - } - - private double qualToErrorProb(final double qual) { - return Math.pow(10.0, qual / -10.0); - } - public static RecalDatum createRandomRecalDatum(int maxObservations, int maxErrors) { final Random random = new Random(); final int nObservations = random.nextInt(maxObservations); @@ -176,6 +201,7 @@ public long getNumObservations() { } public synchronized void setNumObservations(final long numObservations) { + if ( numObservations < 0 ) throw new IllegalArgumentException("numObservations < 0"); this.numObservations = numObservations; empiricalQuality = UNINITIALIZED; } @@ -184,29 +210,67 @@ public long getNumMismatches() { return numMismatches; } + @Requires({"numMismatches >= 0"}) public synchronized void setNumMismatches(final long numMismatches) { + if ( numMismatches < 0 ) throw new IllegalArgumentException("numMismatches < 0"); this.numMismatches = numMismatches; empiricalQuality = UNINITIALIZED; } + @Requires({"by >= 0"}) public synchronized void incrementNumObservations(final long by) { numObservations += by; empiricalQuality = UNINITIALIZED; } + @Requires({"by >= 0"}) public synchronized void incrementNumMismatches(final long by) { numMismatches += by; empiricalQuality = UNINITIALIZED; } + @Requires({"incObservations >= 0", "incMismatches >= 0"}) + @Ensures({"numObservations == old(numObservations) + incObservations", "numMismatches == old(numMismatches) + incMismatches"}) public synchronized void increment(final long incObservations, final long incMismatches) { incrementNumObservations(incObservations); incrementNumMismatches(incMismatches); } + @Ensures({"numObservations == old(numObservations) + 1", "numMismatches >= old(numMismatches)"}) public synchronized void increment(final boolean isError) { incrementNumObservations(1); if ( isError ) incrementNumMismatches(1); } + + // ------------------------------------------------------------------------------------- + // + // Private implementation helper functions + // + // ------------------------------------------------------------------------------------- + + /** + * Calculate and cache the empirical quality score from mismatches and observations (expensive operation) + */ + @Requires("empiricalQuality == UNINITIALIZED") + @Ensures("empiricalQuality != UNINITIALIZED") + private synchronized final void calcEmpiricalQuality() { + // cache the value so we don't call log over and over again + final double doubleMismatches = (double) (numMismatches + SMOOTHING_CONSTANT); + // smoothing is one error and one non-error observation, for example + final double doubleObservations = (double) (numObservations + SMOOTHING_CONSTANT + SMOOTHING_CONSTANT); + final double empiricalQual = -10 * Math.log10(doubleMismatches / doubleObservations); + empiricalQuality = Math.min(empiricalQual, (double) QualityUtils.MAX_RECALIBRATED_Q_SCORE); + } + + /** + * calculate the expected number of errors given the estimated Q reported and the number of observations + * in this datum. + * + * @return a positive (potentially fractional) estimate of the number of errors + */ + @Ensures("result >= 0.0") + private double calcExpectedErrors() { + return (double) getNumObservations() * QualityUtils.qualToErrorProb(estimatedQReported); + } } diff --git a/public/java/test/org/broadinstitute/sting/BaseTest.java b/public/java/test/org/broadinstitute/sting/BaseTest.java index af48918566..76e25a3c08 100755 --- a/public/java/test/org/broadinstitute/sting/BaseTest.java +++ b/public/java/test/org/broadinstitute/sting/BaseTest.java @@ -282,12 +282,12 @@ public static void log(final String message) { private static final double DEFAULT_FLOAT_TOLERANCE = 1e-1; public static final void assertEqualsDoubleSmart(final Object actual, final Double expected) { - Assert.assertTrue(actual instanceof Double); + Assert.assertTrue(actual instanceof Double, "Not a double"); assertEqualsDoubleSmart((double)(Double)actual, (double)expected); } public static final void assertEqualsDoubleSmart(final Object actual, final Double expected, final double tolerance) { - Assert.assertTrue(actual instanceof Double); + Assert.assertTrue(actual instanceof Double, "Not a double"); assertEqualsDoubleSmart((double)(Double)actual, (double)expected, tolerance); } @@ -303,13 +303,13 @@ public static final void assertEqualsSet(final Set actual, final Set e public static final void assertEqualsDoubleSmart(final double actual, final double expected, final double tolerance) { if ( Double.isNaN(expected) ) // NaN == NaN => false unfortunately - Assert.assertTrue(Double.isNaN(actual)); + Assert.assertTrue(Double.isNaN(actual), "expected is nan, actual is not"); else if ( Double.isInfinite(expected) ) // NaN == NaN => false unfortunately - Assert.assertTrue(Double.isInfinite(actual)); + Assert.assertTrue(Double.isInfinite(actual), "expected is infinite, actual is not"); else { final double delta = Math.abs(actual - expected); final double ratio = Math.abs(actual / expected - 1.0); - Assert.assertTrue(delta < tolerance || ratio < tolerance); + Assert.assertTrue(delta < tolerance || ratio < tolerance, "expected = " + expected + " actual = " + actual + " not within tolerance " + tolerance); } } } From 5118014c9fcc2f101356dd44076381db98c5ee42 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Sun, 29 Jul 2012 13:13:13 -0400 Subject: [PATCH 033/176] Improvement to RecalDatum and VisualizeContextTree -- Reorganize functions in RecalDatum so that error rate can be computed indepentently. Added unit tests. Removed equals() method, which is a buggy without it's associated implementation for hashcode -- New class RecalDatumTree based on QualIntervals that inherits from RecalDatum but includes the concept of sub data -- VisualizeContextTree now uses RecalDatumTree and can trivially compute the penalty function for merging nodes, which it displays in the graph --- .../sting/utils/recalibration/RecalDatum.java | 85 +++++++++++++------ .../utils/recalibration/RecalDatumTree.java | 76 +++++++++++++++++ 2 files changed, 133 insertions(+), 28 deletions(-) create mode 100644 public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumTree.java diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java index 6ee5df68b7..249422c17a 100755 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java @@ -136,6 +136,14 @@ public synchronized void setEstimatedQReported(final double estimatedQReported) this.estimatedQReported = estimatedQReported; } + public static RecalDatum createRandomRecalDatum(int maxObservations, int maxErrors) { + final Random random = new Random(); + final int nObservations = random.nextInt(maxObservations); + final int nErrors = random.nextInt(maxErrors); + final int qual = random.nextInt(QualityUtils.MAX_QUAL_SCORE); + return new RecalDatum(nObservations, nErrors, (byte)qual); + } + public final double getEstimatedQReported() { return estimatedQReported; } @@ -143,6 +151,29 @@ public final byte getEstimatedQReportedAsByte() { return (byte)(int)(Math.round(getEstimatedQReported())); } + //--------------------------------------------------------------------------------------------------------------- + // + // Empirical quality score -- derived from the num mismatches and observations + // + //--------------------------------------------------------------------------------------------------------------- + + /** + * Returns the error rate (in real space) of this interval, or 0 if there are no obserations + * @return the empirical error rate ~= N errors / N obs + */ + @Ensures("result >= 0.0") + public double getEmpiricalErrorRate() { + if ( numObservations == 0 ) + return 0.0; + else { + // cache the value so we don't call log over and over again + final double doubleMismatches = (double) (numMismatches + SMOOTHING_CONSTANT); + // smoothing is one error and one non-error observation, for example + final double doubleObservations = (double) (numObservations + SMOOTHING_CONSTANT + SMOOTHING_CONSTANT); + return doubleMismatches / doubleObservations; + } + } + public synchronized void setEmpiricalQuality(final double empiricalQuality) { if ( empiricalQuality < 0 ) throw new IllegalArgumentException("empiricalQuality < 0"); if ( Double.isInfinite(empiricalQuality) ) throw new IllegalArgumentException("empiricalQuality is infinite"); @@ -157,6 +188,16 @@ public final double getEmpiricalQuality() { return empiricalQuality; } + public final byte getEmpiricalQualityAsByte() { + return (byte)(Math.round(getEmpiricalQuality())); + } + + //--------------------------------------------------------------------------------------------------------------- + // + // increment methods + // + //--------------------------------------------------------------------------------------------------------------- + @Override public String toString() { return String.format("%d,%d,%d", getNumObservations(), getNumMismatches(), (byte) Math.floor(getEmpiricalQuality())); @@ -166,29 +207,21 @@ public String stringForCSV() { return String.format("%s,%d,%.2f", toString(), (byte) Math.floor(getEstimatedQReported()), getEmpiricalQuality() - getEstimatedQReported()); } - public static RecalDatum createRandomRecalDatum(int maxObservations, int maxErrors) { - final Random random = new Random(); - final int nObservations = random.nextInt(maxObservations); - final int nErrors = random.nextInt(maxErrors); - final int qual = random.nextInt(QualityUtils.MAX_QUAL_SCORE); - return new RecalDatum(nObservations, nErrors, (byte)qual); - } - - /** - * We don't compare the estimated quality reported because it may be different when read from - * report tables. - * - * @param o the other recal datum - * @return true if the two recal datums have the same number of observations, errors and empirical quality. - */ - @Override - public boolean equals(Object o) { - if (!(o instanceof RecalDatum)) - return false; - RecalDatum other = (RecalDatum) o; - return super.equals(o) && - MathUtils.compareDoubles(this.empiricalQuality, other.empiricalQuality, 0.001) == 0; - } +// /** +// * We don't compare the estimated quality reported because it may be different when read from +// * report tables. +// * +// * @param o the other recal datum +// * @return true if the two recal datums have the same number of observations, errors and empirical quality. +// */ +// @Override +// public boolean equals(Object o) { +// if (!(o instanceof RecalDatum)) +// return false; +// RecalDatum other = (RecalDatum) o; +// return super.equals(o) && +// MathUtils.compareDoubles(this.empiricalQuality, other.empiricalQuality, 0.001) == 0; +// } //--------------------------------------------------------------------------------------------------------------- // @@ -255,11 +288,7 @@ public synchronized void increment(final boolean isError) { @Requires("empiricalQuality == UNINITIALIZED") @Ensures("empiricalQuality != UNINITIALIZED") private synchronized final void calcEmpiricalQuality() { - // cache the value so we don't call log over and over again - final double doubleMismatches = (double) (numMismatches + SMOOTHING_CONSTANT); - // smoothing is one error and one non-error observation, for example - final double doubleObservations = (double) (numObservations + SMOOTHING_CONSTANT + SMOOTHING_CONSTANT); - final double empiricalQual = -10 * Math.log10(doubleMismatches / doubleObservations); + final double empiricalQual = -10 * Math.log10(getEmpiricalErrorRate()); empiricalQuality = Math.min(empiricalQual, (double) QualityUtils.MAX_RECALIBRATED_Q_SCORE); } diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumTree.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumTree.java new file mode 100644 index 0000000000..210ea53bf6 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumTree.java @@ -0,0 +1,76 @@ +package org.broadinstitute.sting.utils.recalibration; + +import com.google.java.contract.Ensures; +import com.google.java.contract.Requires; + +import java.util.Collections; +import java.util.HashSet; +import java.util.Set; + +/** + * A tree of recal datum, where each contains a set of sub datum representing sub-states of the higher level one + * + * @author Mark DePristo + * @since 07/27/12 + */ +public class RecalDatumTree extends RecalDatum { + final Set subnodes; + + protected RecalDatumTree(final long nObservations, final long nErrors, final byte reportedQual) { + this(nObservations, nErrors, reportedQual, new HashSet()); + } + + public RecalDatumTree(final long nObservations, final long nErrors, final byte reportedQual, final Set subnodes) { + super(nObservations, nErrors, reportedQual); + this.subnodes = new HashSet(subnodes); + } + + public double getPenalty() { + return calcPenalty(getEmpiricalErrorRate()); + } + + public void addSubnode(final RecalDatumTree sub) { + subnodes.add(sub); + } + + public boolean isLeaf() { + return subnodes.isEmpty(); + } + + /** + * Calculate the penalty of this interval, given the overall error rate for the interval + * + * If the globalErrorRate is e, this value is: + * + * sum_i |log10(e_i) - log10(e)| * nObservations_i + * + * each the index i applies to all leaves of the tree accessible from this interval + * (found recursively from subnodes as necessary) + * + * @param globalErrorRate overall error rate in real space against which we calculate the penalty + * @return the cost of approximating the bins in this interval with the globalErrorRate + */ + @Requires("globalErrorRate >= 0.0") + @Ensures("result >= 0.0") + private double calcPenalty(final double globalErrorRate) { + if ( globalErrorRate == 0.0 ) // there were no observations, so there's no penalty + return 0.0; + + if ( isLeaf() ) { + // this is leave node + return (Math.abs(Math.log10(getEmpiricalErrorRate()) - Math.log10(globalErrorRate))) * getNumObservations(); + // TODO -- how we can generalize this calculation? +// if ( this.qEnd <= minInterestingQual ) +// // It's free to merge up quality scores below the smallest interesting one +// return 0; +// else { +// return (Math.abs(Math.log10(getEmpiricalErrorRate()) - Math.log10(globalErrorRate))) * getNumObservations(); +// } + } else { + double sum = 0; + for ( final RecalDatumTree hrd : subnodes) + sum += hrd.calcPenalty(globalErrorRate); + return sum; + } + } +} From bdf733f06eec97801730a0e2be20738838036a3a Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Mon, 30 Jul 2012 08:31:38 -0400 Subject: [PATCH 034/176] Preliminary version of adaptive context covariate algorithm -- Works according to visual inspection of output tree --- .../utils/recalibration/RecalDatumNode.java | 213 ++++++++++++++++++ .../utils/recalibration/RecalDatumTree.java | 76 ------- 2 files changed, 213 insertions(+), 76 deletions(-) create mode 100644 public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java delete mode 100644 public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumTree.java diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java new file mode 100644 index 0000000000..62ea67d7cd --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java @@ -0,0 +1,213 @@ +package org.broadinstitute.sting.utils.recalibration; + +import com.google.java.contract.Ensures; +import com.google.java.contract.Requires; +import org.apache.log4j.Logger; +import org.broadinstitute.sting.utils.collections.Pair; + +import java.util.HashSet; +import java.util.Set; + +/** + * A tree of recal datum, where each contains a set of sub datum representing sub-states of the higher level one + * + * @author Mark DePristo + * @since 07/27/12 + */ +public class RecalDatumNode { + protected static Logger logger = Logger.getLogger(RecalDatumNode.class); + private final static double UNINITIALIZED = -1.0; + private final T recalDatum; + private double fixedPenalty = UNINITIALIZED; + private final Set> subnodes; + + public RecalDatumNode(final T recalDatum) { + this(recalDatum, new HashSet>()); + } + + @Override + public String toString() { + return recalDatum.toString(); + } + + public RecalDatumNode(final T recalDatum, final Set> subnodes) { + this(recalDatum, UNINITIALIZED, subnodes); + } + + protected RecalDatumNode(final T recalDatum, final double fixedPenalty) { + this(recalDatum, fixedPenalty, new HashSet>()); + } + + protected RecalDatumNode(final T recalDatum, final double fixedPenalty, final Set> subnodes) { + this.recalDatum = recalDatum; + this.fixedPenalty = fixedPenalty; + this.subnodes = new HashSet>(subnodes); + } + + public T getRecalDatum() { + return recalDatum; + } + + public Set> getSubnodes() { + return subnodes; + } + + public double getPenalty() { + if ( fixedPenalty != UNINITIALIZED ) + return fixedPenalty; + else + return calcPenalty(recalDatum.getEmpiricalErrorRate()); + } + + public double calcAndSetFixedPenalty(final boolean doEntireTree) { + fixedPenalty = calcPenalty(recalDatum.getEmpiricalErrorRate()); + if ( doEntireTree ) + for ( final RecalDatumNode sub : subnodes ) + sub.calcAndSetFixedPenalty(doEntireTree); + return fixedPenalty; + } + + public void addSubnode(final RecalDatumNode sub) { + subnodes.add(sub); + } + + public boolean isLeaf() { + return subnodes.isEmpty(); + } + + public int getNumBranches() { + return subnodes.size(); + } + + public double getMinNodePenalty() { + if ( isLeaf() ) + return Double.MAX_VALUE; + else { + double minPenalty = getPenalty(); + for ( final RecalDatumNode sub : subnodes ) + minPenalty = Math.min(minPenalty, sub.getMinNodePenalty()); + return minPenalty; + } + } + + public int maxDepth() { + int subMax = 0; + for ( final RecalDatumNode sub : subnodes ) + subMax = Math.max(subMax, sub.maxDepth()); + return subMax + 1; + } + + public int size() { + int size = 1; + for ( final RecalDatumNode sub : subnodes ) + size += sub.size(); + return size; + } + + /** + * Calculate the penalty of this interval, given the overall error rate for the interval + * + * If the globalErrorRate is e, this value is: + * + * sum_i |log10(e_i) - log10(e)| * nObservations_i + * + * each the index i applies to all leaves of the tree accessible from this interval + * (found recursively from subnodes as necessary) + * + * @param globalErrorRate overall error rate in real space against which we calculate the penalty + * @return the cost of approximating the bins in this interval with the globalErrorRate + */ + @Requires("globalErrorRate >= 0.0") + @Ensures("result >= 0.0") + private double calcPenalty(final double globalErrorRate) { + if ( globalErrorRate == 0.0 ) // there were no observations, so there's no penalty + return 0.0; + + if ( isLeaf() ) { + // this is leave node + return (Math.abs(Math.log10(recalDatum.getEmpiricalErrorRate()) - Math.log10(globalErrorRate))) * recalDatum.getNumObservations(); + // TODO -- how we can generalize this calculation? +// if ( this.qEnd <= minInterestingQual ) +// // It's free to merge up quality scores below the smallest interesting one +// return 0; +// else { +// return (Math.abs(Math.log10(getEmpiricalErrorRate()) - Math.log10(globalErrorRate))) * getNumObservations(); +// } + } else { + double sum = 0; + for ( final RecalDatumNode hrd : subnodes) + sum += hrd.calcPenalty(globalErrorRate); + return sum; + } + } + + public RecalDatumNode pruneToDepth(final int maxDepth) { + if ( maxDepth < 1 ) + throw new IllegalArgumentException("maxDepth < 1"); + else { + final Set> subPruned = new HashSet>(getNumBranches()); + if ( maxDepth > 1 ) + for ( final RecalDatumNode sub : subnodes ) + subPruned.add(sub.pruneToDepth(maxDepth - 1)); + return new RecalDatumNode(getRecalDatum(), fixedPenalty, subPruned); + } + } + + public RecalDatumNode pruneByPenalty(final int maxElements) { + RecalDatumNode root = this; + + while ( root.size() > maxElements ) { + // remove the lowest penalty element, and continue + root = root.removeLowestPenaltyNode(); + } + + // our size is below the target, so we are good, return + return root; + } + + /** + * Find the lowest penalty node in the tree, and return a tree without it + * + * Note this excludes the current (root) node + * + * @return + */ + private RecalDatumNode removeLowestPenaltyNode() { + final RecalDatumNode oneRemoved = removeFirstNodeWithPenalty(getMinNodePenalty()).getFirst(); + if ( oneRemoved == null ) + throw new IllegalStateException("Removed our root node, wow, didn't expect that"); + return oneRemoved; + } + + private Pair, Boolean> removeFirstNodeWithPenalty(final double penaltyToRemove) { + if ( getPenalty() == penaltyToRemove ) { + logger.info("Removing " + this + " with penalty " + penaltyToRemove); + if ( isLeaf() ) + throw new IllegalStateException("Trying to remove a leaf node from the tree! " + this + " " + penaltyToRemove); + // node is the thing we are going to remove, but without any subnodes + final RecalDatumNode node = new RecalDatumNode(getRecalDatum(), fixedPenalty); + return new Pair, Boolean>(node, true); + } else { + // did we remove something in a sub branch? + boolean removedSomething = false; + + // our sub nodes with the penalty node removed + final Set> sub = new HashSet>(getNumBranches()); + + for ( final RecalDatumNode sub1 : subnodes ) { + if ( removedSomething ) { + // already removed something, just add sub1 back to sub + sub.add(sub1); + } else { + // haven't removed anything yet, so try + final Pair, Boolean> maybeRemoved = sub1.removeFirstNodeWithPenalty(penaltyToRemove); + removedSomething = maybeRemoved.getSecond(); + sub.add(maybeRemoved.getFirst()); + } + } + + final RecalDatumNode node = new RecalDatumNode(getRecalDatum(), fixedPenalty, sub); + return new Pair, Boolean>(node, removedSomething); + } + } +} diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumTree.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumTree.java deleted file mode 100644 index 210ea53bf6..0000000000 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumTree.java +++ /dev/null @@ -1,76 +0,0 @@ -package org.broadinstitute.sting.utils.recalibration; - -import com.google.java.contract.Ensures; -import com.google.java.contract.Requires; - -import java.util.Collections; -import java.util.HashSet; -import java.util.Set; - -/** - * A tree of recal datum, where each contains a set of sub datum representing sub-states of the higher level one - * - * @author Mark DePristo - * @since 07/27/12 - */ -public class RecalDatumTree extends RecalDatum { - final Set subnodes; - - protected RecalDatumTree(final long nObservations, final long nErrors, final byte reportedQual) { - this(nObservations, nErrors, reportedQual, new HashSet()); - } - - public RecalDatumTree(final long nObservations, final long nErrors, final byte reportedQual, final Set subnodes) { - super(nObservations, nErrors, reportedQual); - this.subnodes = new HashSet(subnodes); - } - - public double getPenalty() { - return calcPenalty(getEmpiricalErrorRate()); - } - - public void addSubnode(final RecalDatumTree sub) { - subnodes.add(sub); - } - - public boolean isLeaf() { - return subnodes.isEmpty(); - } - - /** - * Calculate the penalty of this interval, given the overall error rate for the interval - * - * If the globalErrorRate is e, this value is: - * - * sum_i |log10(e_i) - log10(e)| * nObservations_i - * - * each the index i applies to all leaves of the tree accessible from this interval - * (found recursively from subnodes as necessary) - * - * @param globalErrorRate overall error rate in real space against which we calculate the penalty - * @return the cost of approximating the bins in this interval with the globalErrorRate - */ - @Requires("globalErrorRate >= 0.0") - @Ensures("result >= 0.0") - private double calcPenalty(final double globalErrorRate) { - if ( globalErrorRate == 0.0 ) // there were no observations, so there's no penalty - return 0.0; - - if ( isLeaf() ) { - // this is leave node - return (Math.abs(Math.log10(getEmpiricalErrorRate()) - Math.log10(globalErrorRate))) * getNumObservations(); - // TODO -- how we can generalize this calculation? -// if ( this.qEnd <= minInterestingQual ) -// // It's free to merge up quality scores below the smallest interesting one -// return 0; -// else { -// return (Math.abs(Math.log10(getEmpiricalErrorRate()) - Math.log10(globalErrorRate))) * getNumObservations(); -// } - } else { - double sum = 0; - for ( final RecalDatumTree hrd : subnodes) - sum += hrd.calcPenalty(globalErrorRate); - return sum; - } - } -} From 8da3ceaa26404d9b84359222efa7b4d9e596a3e1 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Mon, 30 Jul 2012 15:44:33 -0400 Subject: [PATCH 035/176] Working version of adaptive context calculations -- Uses chi2 test for independences to determine if subcontext is worth representing. Give excellent visual results -- Writes out analysis output file producing excellent results in R -- Trivial reformatting of MathUtils --- .../utils/recalibration/RecalDatumNode.java | 128 +++++++++++++++--- 1 file changed, 112 insertions(+), 16 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java index 62ea67d7cd..3af91be164 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java @@ -2,7 +2,9 @@ import com.google.java.contract.Ensures; import com.google.java.contract.Requires; +import org.apache.commons.math.stat.inference.ChiSquareTestImpl; import org.apache.log4j.Logger; +import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.collections.Pair; import java.util.HashSet; @@ -15,8 +17,9 @@ * @since 07/27/12 */ public class RecalDatumNode { + private final static boolean USE_CHI2 = true; protected static Logger logger = Logger.getLogger(RecalDatumNode.class); - private final static double UNINITIALIZED = -1.0; + private final static double UNINITIALIZED = Double.NEGATIVE_INFINITY; private final T recalDatum; private double fixedPenalty = UNINITIALIZED; private final Set> subnodes; @@ -56,11 +59,11 @@ public double getPenalty() { if ( fixedPenalty != UNINITIALIZED ) return fixedPenalty; else - return calcPenalty(recalDatum.getEmpiricalErrorRate()); + return calcPenalty(); } public double calcAndSetFixedPenalty(final boolean doEntireTree) { - fixedPenalty = calcPenalty(recalDatum.getEmpiricalErrorRate()); + fixedPenalty = calcPenalty(); if ( doEntireTree ) for ( final RecalDatumNode sub : subnodes ) sub.calcAndSetFixedPenalty(doEntireTree); @@ -79,14 +82,23 @@ public int getNumBranches() { return subnodes.size(); } - public double getMinNodePenalty() { + /** + * Total penalty is the sum of leaf node penalties + * + * This algorithm assumes that penalties have been fixed before pruning, as leaf nodes by + * definition have 0 penalty unless they represent a pruned tree with underlying -- but now + * pruned -- subtrees + * + * @return + */ + public double totalPenalty() { if ( isLeaf() ) - return Double.MAX_VALUE; + return getPenalty(); else { - double minPenalty = getPenalty(); + double sum = 0.0; for ( final RecalDatumNode sub : subnodes ) - minPenalty = Math.min(minPenalty, sub.getMinNodePenalty()); - return minPenalty; + sum += sub.totalPenalty(); + return sum; } } @@ -97,6 +109,17 @@ public int maxDepth() { return subMax + 1; } + public int minDepth() { + if ( isLeaf() ) + return 1; + else { + int subMin = Integer.MAX_VALUE; + for ( final RecalDatumNode sub : subnodes ) + subMin = Math.min(subMin, sub.minDepth()); + return subMin + 1; + } + } + public int size() { int size = 1; for ( final RecalDatumNode sub : subnodes ) @@ -104,6 +127,58 @@ public int size() { return size; } + public int numLeaves() { + if ( isLeaf() ) + return 1; + else { + int size = 0; + for ( final RecalDatumNode sub : subnodes ) + size += sub.numLeaves(); + return size; + } + } + + private double calcPenalty() { + if ( USE_CHI2 ) + return calcPenaltyChi2(); + else + return calcPenaltyLog10(getRecalDatum().getEmpiricalErrorRate()); + } + + private double calcPenaltyChi2() { + if ( isLeaf() ) + return 0.0; + else { + final long[][] counts = new long[subnodes.size()][2]; + + int i = 0; + for ( RecalDatumNode subnode : subnodes ) { + counts[i][0] = subnode.getRecalDatum().getNumMismatches(); + counts[i][1] = subnode.getRecalDatum().getNumObservations(); + i++; + } + + final double chi2 = new ChiSquareTestImpl().chiSquare(counts); + +// StringBuilder x = new StringBuilder(); +// StringBuilder y = new StringBuilder(); +// for ( int k = 0; k < counts.length; k++) { +// if ( k != 0 ) { +// x.append(", "); +// y.append(", "); +// } +// x.append(counts[k][0]); +// y.append(counts[k][1]); +// } +// logger.info("x = c(" + x.toString() + ")"); +// logger.info("y = c(" + y.toString() + ")"); +// logger.info("chi2 = " + chi2); + + return chi2; + //return Math.log10(chi2); + } + } + /** * Calculate the penalty of this interval, given the overall error rate for the interval * @@ -119,7 +194,7 @@ public int size() { */ @Requires("globalErrorRate >= 0.0") @Ensures("result >= 0.0") - private double calcPenalty(final double globalErrorRate) { + private double calcPenaltyLog10(final double globalErrorRate) { if ( globalErrorRate == 0.0 ) // there were no observations, so there's no penalty return 0.0; @@ -136,7 +211,7 @@ private double calcPenalty(final double globalErrorRate) { } else { double sum = 0; for ( final RecalDatumNode hrd : subnodes) - sum += hrd.calcPenalty(globalErrorRate); + sum += hrd.calcPenaltyLog10(globalErrorRate); return sum; } } @@ -173,17 +248,38 @@ public RecalDatumNode pruneByPenalty(final int maxElements) { * @return */ private RecalDatumNode removeLowestPenaltyNode() { - final RecalDatumNode oneRemoved = removeFirstNodeWithPenalty(getMinNodePenalty()).getFirst(); + final Pair, Double> nodeToRemove = getMinPenaltyNode(); + logger.info("Removing " + nodeToRemove.getFirst() + " with penalty " + nodeToRemove.getSecond()); + + final Pair, Boolean> result = removeNode(nodeToRemove.getFirst()); + + if ( ! result.getSecond() ) + throw new IllegalStateException("Never removed any node!"); + + final RecalDatumNode oneRemoved = result.getFirst(); if ( oneRemoved == null ) throw new IllegalStateException("Removed our root node, wow, didn't expect that"); return oneRemoved; } - private Pair, Boolean> removeFirstNodeWithPenalty(final double penaltyToRemove) { - if ( getPenalty() == penaltyToRemove ) { - logger.info("Removing " + this + " with penalty " + penaltyToRemove); + private Pair, Double> getMinPenaltyNode() { + final double myValue = isLeaf() ? Double.MAX_VALUE : getPenalty(); + Pair, Double> maxNode = new Pair, Double>(this, myValue); + + for ( final RecalDatumNode sub : subnodes ) { + final Pair, Double> subFind = sub.getMinPenaltyNode(); + if ( subFind.getSecond() < maxNode.getSecond() ) { + maxNode = subFind; + } + } + + return maxNode; + } + + private Pair, Boolean> removeNode(final RecalDatumNode nodeToRemove) { + if ( this == nodeToRemove ) { if ( isLeaf() ) - throw new IllegalStateException("Trying to remove a leaf node from the tree! " + this + " " + penaltyToRemove); + throw new IllegalStateException("Trying to remove a leaf node from the tree! " + this + " " + nodeToRemove); // node is the thing we are going to remove, but without any subnodes final RecalDatumNode node = new RecalDatumNode(getRecalDatum(), fixedPenalty); return new Pair, Boolean>(node, true); @@ -200,7 +296,7 @@ private Pair, Boolean> removeFirstNodeWithPenalty(final double sub.add(sub1); } else { // haven't removed anything yet, so try - final Pair, Boolean> maybeRemoved = sub1.removeFirstNodeWithPenalty(penaltyToRemove); + final Pair, Boolean> maybeRemoved = sub1.removeNode(nodeToRemove); removedSomething = maybeRemoved.getSecond(); sub.add(maybeRemoved.getFirst()); } From ae3575fef4cd413f0fa9a6be4ef7c2370578d386 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Mon, 30 Jul 2012 15:46:00 -0400 Subject: [PATCH 036/176] Changes order of writing BaseRecalibrator results so that if R blows up you still get a meaningful tree --- .../sting/gatk/walkers/bqsr/BaseRecalibrator.java | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java index e95a0e6c17..ddd75e232d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java @@ -275,13 +275,16 @@ public Long treeReduce(Long sum1, Long sum2) { public void onTraversalDone(Long result) { logger.info("Calculating quantized quality scores..."); quantizeQualityScores(); + + logger.info("Writing recalibration report..."); + generateReport(); + logger.info("...done!"); + if (!RAC.NO_PLOTS) { logger.info("Generating recalibration plots..."); generatePlots(); } - logger.info("Writing recalibration report..."); - generateReport(); - logger.info("...done!"); + logger.info("Processed: " + result + " sites"); } From 2773e41cff526d491c7cea7199c179c4a6d8683b Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Mon, 30 Jul 2012 15:47:36 -0400 Subject: [PATCH 037/176] Move BQSR.R to utils/recalibration in R --- .../sting/{gatk/walkers/bqsr => utils/recalibration}/BQSR.R | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename public/R/scripts/org/broadinstitute/sting/{gatk/walkers/bqsr => utils/recalibration}/BQSR.R (100%) diff --git a/public/R/scripts/org/broadinstitute/sting/gatk/walkers/bqsr/BQSR.R b/public/R/scripts/org/broadinstitute/sting/utils/recalibration/BQSR.R similarity index 100% rename from public/R/scripts/org/broadinstitute/sting/gatk/walkers/bqsr/BQSR.R rename to public/R/scripts/org/broadinstitute/sting/utils/recalibration/BQSR.R From 47c7b70fbb85a788d107096c7ed081a88d824a98 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Tue, 31 Jul 2012 08:10:51 -0400 Subject: [PATCH 038/176] Cleanup syntax errors from BQSR reorganization --- .../src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java index 895de35782..4b56ce3097 100644 --- a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java @@ -30,12 +30,12 @@ import net.sf.samtools.CigarOperator; import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.walkers.bqsr.EventType; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.sting.utils.recalibration.EventType; import java.util.ArrayList; import java.util.Arrays; From d703bf0c28dae717218f42ab5d73fb9233ef8ae6 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Tue, 31 Jul 2012 14:23:36 -0400 Subject: [PATCH 039/176] Del/Ins ratio should really be Ins/Del ratio on the summary page of the variant QC report. From 199656312bff1c31cec81bc822c7d57c29019a08 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Tue, 31 Jul 2012 14:34:42 -0400 Subject: [PATCH 040/176] Archiving VQSRv3 From fe843b0b252994bf2ce2b3d6c4c431a5f4199258 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Tue, 31 Jul 2012 15:37:22 -0400 Subject: [PATCH 041/176] Fixed AlignmentUtils bug for handling Ns in the CIGAR string. Added a UG integration test that calls a BAM with such reads (provided by a user on GetSatisfaction). --- .../sting/utils/sam/AlignmentUtils.java | 9 +++------ .../UnifiedGenotyperIntegrationTest.java | 18 ++++++++++++++++-- 2 files changed, 19 insertions(+), 8 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java index 4b56ce3097..2c388a1e0e 100644 --- a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java @@ -476,7 +476,6 @@ public static int calcAlignmentByteArrayOffset(final Cigar cigar, final int offs } break; case D: - case N: if (!isDeletion) { alignmentPos += elementLength; } else { @@ -498,6 +497,7 @@ public static int calcAlignmentByteArrayOffset(final Cigar cigar, final int offs break; case H: case P: + case N: break; default: throw new ReviewedStingException("Unsupported cigar operator: " + ce.getOperator()); @@ -516,16 +516,13 @@ public static byte[] readToAlignmentByteArray(final Cigar cigar, final byte[] re final int elementLength = ce.getLength(); switch (ce.getOperator()) { - case I: - case S: - break; case D: case N: - alignmentLength += elementLength; - break; case M: alignmentLength += elementLength; break; + case I: + case S: case H: case P: break; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index f35eb4404c..f26486a716 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -373,13 +373,13 @@ public void testSnpEffAnnotationRequestedWithoutRodBinding() { // -------------------------------------------------------------------------------------------------------------- // - // testing SnpEff + // testing MinIndelFraction // // -------------------------------------------------------------------------------------------------------------- final static String assessMinIndelFraction = baseCommandIndelsb37 + " -I " + validationDataLocation + "978604.bam -L 1:978,586-978,626 -o %s --sites_only -rf Sample -goodSM 7377 -goodSM 22-0022 -goodSM 134 -goodSM 344029-53 -goodSM 14030"; - + @Test public void testMinIndelFraction0() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -403,4 +403,18 @@ public void testMinIndelFraction100() { Arrays.asList("3f07efb768e08650a7ce333edd4f9a52")); executeTest("test minIndelFraction 1.0", spec); } + + // -------------------------------------------------------------------------------------------------------------- + // + // testing Ns in CIGAR + // + // -------------------------------------------------------------------------------------------------------------- + + @Test + public void testNsInCigar() { + WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( + baseCommand + " -I " + validationDataLocation + "testWithNs.bam", 1, + Arrays.asList("22c9fd65ce3298bd7fbf400c9c209f29")); + executeTest("test calling on reads with Ns in CIGAR", spec); + } } From 376a648a01304b2928c28cdd83d3e9227da185aa Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Tue, 31 Jul 2012 15:50:32 -0400 Subject: [PATCH 042/176] Quick fix to user error catching --- .../src/org/broadinstitute/sting/gatk/CommandLineGATK.java | 4 ++-- .../walkers/genotyper/UnifiedGenotyperIntegrationTest.java | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java index 306ebdd0ec..312d31727d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java +++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java @@ -130,12 +130,12 @@ private static void checkForMaskedUserErrors(final Throwable t) { // can't close tribble index when writing if ( message.indexOf("Unable to close index for") != -1 ) - exitSystemWithUserError(new UserException(t.getCause().getMessage())); + exitSystemWithUserError(new UserException(t.getCause() == null ? message : t.getCause().getMessage())); // disk is full if ( message.indexOf("No space left on device") != -1 ) exitSystemWithUserError(new UserException(t.getMessage())); - if ( t.getCause().getMessage().indexOf("No space left on device") != -1 ) + if ( t.getCause() != null && t.getCause().getMessage().indexOf("No space left on device") != -1 ) exitSystemWithUserError(new UserException(t.getCause().getMessage())); } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index f26486a716..d976e3e22a 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -413,7 +413,7 @@ public void testMinIndelFraction100() { @Test public void testNsInCigar() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - baseCommand + " -I " + validationDataLocation + "testWithNs.bam", 1, + "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -I " + validationDataLocation + "testWithNs.bam -o %s -L 8:141799600-141814700", 1, Arrays.asList("22c9fd65ce3298bd7fbf400c9c209f29")); executeTest("test calling on reads with Ns in CIGAR", spec); } From adb016d0338b71682ae8f91332961e2bd97339dd Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Tue, 31 Jul 2012 16:00:36 -0400 Subject: [PATCH 043/176] Fixed older GS reported bug. Actually, the problem really lies in Picard (can't set max records in RAM without it throwing an exception, reported on their JIRA) so I just masked out the problem by removing this never-used argument from this rarely-used tool. --- .../gatk/io/storage/SAMFileWriterStorage.java | 1 + .../sting/gatk/walkers/indels/LeftAlignIndels.java | 14 +------------- 2 files changed, 2 insertions(+), 13 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java index cb8786be10..300e801e62 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java @@ -62,6 +62,7 @@ public SAMFileWriterStorage( SAMFileWriterStub stub, File file ) { if (stub.getGenerateMD5()) factory.setCreateMd5File(true); // Adjust max records in RAM. + // TODO -- this doesn't actually work because of a bug in Picard; do not use until fixed if(stub.getMaxRecordsInRam() != null) factory.setMaxRecordsInRam(stub.getMaxRecordsInRam()); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java index 6047a15b43..b08def44fc 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java @@ -73,19 +73,7 @@ public class LeftAlignIndels extends ReadWalker { @Output(required=false, doc="Output bam") protected StingSAMFileWriter writer = null; - /** - * If set too low, the tool may run out of system file descriptors needed to perform sorting; if too high, the tool - * may run out of memory. We recommend that you additionally tell Java to use a temp directory with plenty of available - * space (by setting java.io.tempdir on the command-line). - */ - @Argument(fullName="maxReadsInRam", shortName="maxInRam", doc="max reads allowed to be kept in memory at a time by the output writer", required=false) - protected int MAX_RECORDS_IN_RAM = 500000; - - public void initialize() { - // set up the output writer - if ( writer != null ) - writer.setMaxRecordsInRam(MAX_RECORDS_IN_RAM); - } + public void initialize() {} private void emit(final SAMRecord read) { if ( writer != null ) From 4331554296aa4c24f079bc07452c1d9b317f8b90 Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Tue, 31 Jul 2012 16:34:20 -0400 Subject: [PATCH 044/176] Simple cleanup of pool caller code - since usage is much more general than just calling pools, AF calculation models and GL calculation models are renamed from Pool -> GeneralPloidy. Also, don't have users specify special arguments for -glm and -pnrm. Instead, when running UG with sample ploidy != 2, the correct general ploidy modules are automatically detected and loaded. -glm now reverts to old [SNP|INDEL|BOTH] usage --- .../AlleleFrequencyCalculationModel.java | 3 +-- .../GenotypeLikelihoodsCalculationModel.java | 7 +++-- .../walkers/genotyper/UnifiedGenotyper.java | 3 ++- .../genotyper/UnifiedGenotyperEngine.java | 27 ++++++++++++------- 4 files changed, 23 insertions(+), 17 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java index 432bbd6d76..08a3334863 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java @@ -46,8 +46,7 @@ public abstract class AlleleFrequencyCalculationModel implements Cloneable { public enum Model { /** The default model with the best performance in all cases */ - EXACT, - POOL + EXACT } protected int N; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java index 4253ff3ad5..6fdc926d53 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java @@ -59,10 +59,9 @@ public abstract class GenotypeLikelihoodsCalculationModel implements Cloneable { public enum Model { SNP, INDEL, - BOTH, - POOLSNP, - POOLINDEL, - POOLBOTH + GeneralPloidySNP, + GeneralPloidyINDEL, + BOTH } public enum GENOTYPING_MODE { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java index 6b279fd954..c1c1339f5d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java @@ -241,7 +241,7 @@ public void initialize() { } else { // in full mode: check for consistency in ploidy/pool calling arguments // check for correct calculation models - if (UAC.samplePloidy != VariantContextUtils.DEFAULT_PLOIDY) { +/* if (UAC.samplePloidy != VariantContextUtils.DEFAULT_PLOIDY) { // polyploidy requires POOL GL and AF calculation models to be specified right now if (UAC.GLmodel != GenotypeLikelihoodsCalculationModel.Model.POOLSNP && UAC.GLmodel != GenotypeLikelihoodsCalculationModel.Model.POOLINDEL && UAC.GLmodel != GenotypeLikelihoodsCalculationModel.Model.POOLBOTH) { @@ -252,6 +252,7 @@ public void initialize() { throw new UserException("Incorrect AF Calculation model. Only POOL model supported if sample ploidy != 2"); } + */ // get all of the unique sample names if (UAC.TREAT_ALL_READS_AS_SINGLE_POOL) { samples.clear(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index f73ab24715..f4bd196ae2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -50,6 +50,7 @@ public class UnifiedGenotyperEngine { public static final String LOW_QUAL_FILTER_NAME = "LowQual"; + private static final String GPSTRING = "GeneralPloidy"; public static final String NUMBER_OF_DISCOVERED_ALLELES_KEY = "NDA"; @@ -273,7 +274,7 @@ private VariantContext calculateLikelihoods(RefMetaDataTracker tracker, Referenc glcm.set(getGenotypeLikelihoodsCalculationObject(logger, UAC)); } - return glcm.get().get(model.name()).getLikelihoods(tracker, refContext, stratifiedContexts, type, alternateAllelesToUse, useBAQedPileup && BAQEnabledOnCMDLine, genomeLocParser); + return glcm.get().get(model.name().toUpperCase()).getLikelihoods(tracker, refContext, stratifiedContexts, type, alternateAllelesToUse, useBAQedPileup && BAQEnabledOnCMDLine, genomeLocParser); } private VariantCallContext generateEmptyContext(RefMetaDataTracker tracker, ReferenceContext ref, Map stratifiedContexts, AlignmentContext rawContext) { @@ -640,6 +641,9 @@ private List getGLModelsToUse(final R if ( UAC.GLmodel.name().toUpperCase().contains("BOTH") ) modelPrefix = UAC.GLmodel.name().toUpperCase().replaceAll("BOTH",""); + if (!UAC.GLmodel.name().contains(GPSTRING) && UAC.samplePloidy != VariantContextUtils.DEFAULT_PLOIDY) + modelPrefix = GPSTRING + modelPrefix; + // if we're genotyping given alleles and we have a requested SNP at this position, do SNP if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) { final VariantContext vcInput = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, refContext, rawContext.getLocation(), false, logger, UAC.alleles); @@ -648,17 +652,13 @@ private List getGLModelsToUse(final R if ( vcInput.isSNP() ) { // ignore SNPs if the user chose INDEL mode only - if ( UAC.GLmodel.name().toUpperCase().contains("BOTH") ) + if ( UAC.GLmodel.name().toUpperCase().contains("BOTH") || UAC.GLmodel.name().toUpperCase().contains("SNP") ) models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix+"SNP")); - else if ( UAC.GLmodel.name().toUpperCase().contains("SNP") ) - models.add(UAC.GLmodel); - } + } else if ( vcInput.isIndel() || vcInput.isMixed() ) { // ignore INDELs if the user chose SNP mode only - if ( UAC.GLmodel.name().toUpperCase().contains("BOTH") ) + if ( UAC.GLmodel.name().toUpperCase().contains("BOTH") || UAC.GLmodel.name().toUpperCase().contains("INDEL") ) models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix+"INDEL")); - else if (UAC.GLmodel.name().toUpperCase().contains("INDEL")) - models.add(UAC.GLmodel); } // No support for other types yet } @@ -668,7 +668,7 @@ else if (UAC.GLmodel.name().toUpperCase().contains("INDEL")) models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix+"INDEL")); } else { - models.add(UAC.GLmodel); + models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix+UAC.GLmodel.name().toUpperCase())); } } @@ -730,12 +730,19 @@ private static Map getGenotypeLikel } private static AlleleFrequencyCalculationModel getAlleleFrequencyCalculationObject(int N, Logger logger, PrintStream verboseWriter, UnifiedArgumentCollection UAC) { + List> afClasses = new PluginManager(AlleleFrequencyCalculationModel.class).getPlugins(); + // user-specified name + String afModelName = UAC.AFmodel.name(); + + if (!afModelName.contains(GPSTRING) && UAC.samplePloidy != VariantContextUtils.DEFAULT_PLOIDY) + afModelName = GPSTRING + afModelName; + for (int i = 0; i < afClasses.size(); i++) { Class afClass = afClasses.get(i); String key = afClass.getSimpleName().replace("AFCalculationModel","").toUpperCase(); - if (UAC.AFmodel.name().equalsIgnoreCase(key)) { + if (afModelName.equalsIgnoreCase(key)) { try { Object args[] = new Object[]{UAC,N,logger,verboseWriter}; Constructor c = afClass.getDeclaredConstructor(UnifiedArgumentCollection.class, int.class, Logger.class, PrintStream.class); From 4115e065bf5a8b0f882f0959dba22491d82fdcc9 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 1 Aug 2012 10:33:41 -0400 Subject: [PATCH 045/176] Update docs of FastaAlternateReferenceMaker as promised in older GS thread --- .../sting/gatk/walkers/fasta/FastaAlternateReference.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java index 92549b821b..28cfdd5cd7 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java @@ -47,7 +47,8 @@ *

* Given variant tracks, it replaces the reference bases at variation sites with the bases supplied by the ROD(s). * Additionally, allows for one or more "snpmask" VCFs to set overlapping bases to 'N'. - * Note that if there are multiple variants at a site, it takes the first one seen. + * Note that if there are multiple variants at a site, it chooses one of them randomly. + * Also note that this tool works only for SNPs and for simple indels (but not for things like complex substitutions). * Reference bases for each interval will be output as a separate fasta sequence (named numerically in order). * *

Input

From e5aeb9a8fa604a256baa1fb27ddd7dacd4c2cbb6 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 1 Aug 2012 10:45:04 -0400 Subject: [PATCH 046/176] Fixed bug in FastaAlternateReferenceMaker when input VCF has overlapping deletions as reported a while back on GS --- .../sting/gatk/walkers/fasta/FastaAlternateReference.java | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java index 28cfdd5cd7..8fbd37e30b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java @@ -47,8 +47,10 @@ *

* Given variant tracks, it replaces the reference bases at variation sites with the bases supplied by the ROD(s). * Additionally, allows for one or more "snpmask" VCFs to set overlapping bases to 'N'. - * Note that if there are multiple variants at a site, it chooses one of them randomly. - * Also note that this tool works only for SNPs and for simple indels (but not for things like complex substitutions). + * Several important notes: + * 1) if there are multiple variants that start at a site, it chooses one of them randomly. + * 2) when there are overlapping indels (but with different start positions) only the first will be chosen. + * 3) this tool works only for SNPs and for simple indels (but not for things like complex substitutions). * Reference bases for each interval will be output as a separate fasta sequence (named numerically in order). * *

Input

@@ -103,7 +105,7 @@ public Pair map(RefMetaDataTracker tracker, ReferenceContext String refBase = String.valueOf((char)ref.getBase()); // Check to see if we have a called snp - for ( VariantContext vc : tracker.getValues(variants) ) { + for ( VariantContext vc : tracker.getValues(variants, ref.getLocus()) ) { if ( vc.isFiltered() ) continue; From 3cd705f7064f2e59423d8412a0d8b22c41e7c8b9 Mon Sep 17 00:00:00 2001 From: Joel Thibault Date: Mon, 30 Jul 2012 10:19:57 -0400 Subject: [PATCH 047/176] Add removeProgramRecords argument * Add unit test for the removeProgramRecords --- .../sting/gatk/GenomeAnalysisEngine.java | 3 +- .../arguments/GATKArgumentCollection.java | 3 + .../gatk/datasources/reads/SAMDataSource.java | 21 +++++- .../reads/SAMDataSourceUnitTest.java | 73 +++++++++++++++++++ 4 files changed, 95 insertions(+), 5 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index 5d6fb75ed6..228f8351a3 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -813,7 +813,8 @@ private SAMDataSource createReadsDataSource(GATKArgumentCollection argCollection getWalkerBAQQualityMode(), refReader, getBaseRecalibration(), - argCollection.defaultBaseQualities); + argCollection.defaultBaseQualities, + argCollection.removeProgramRecords); } /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java index 3fd3857c5d..91a008cbc9 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java @@ -249,6 +249,9 @@ public static DownsamplingMethod getDefaultDownsamplingMethod() { @Argument(fullName = "validation_strictness", shortName = "S", doc = "How strict should we be with validation", required = false) public SAMFileReader.ValidationStringency strictnessLevel = SAMFileReader.ValidationStringency.SILENT; + @Argument(fullName = "remove_program_records", shortName = "rpr", doc = "Should we remove program records from the SAM header", required = false) + public boolean removeProgramRecords = false; + @Argument(fullName = "unsafe", shortName = "U", doc = "If set, enables unsafe operations: nothing will be checked at runtime. For expert users only who know what they are doing. We do not support usage of this argument.", required = false) public ValidationExclusion.TYPE unsafe; diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java index 0fa4234b35..7f0a0c4c0c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java @@ -89,6 +89,11 @@ public class SAMDataSource { */ private final SAMFileReader.ValidationStringency validationStringency; + /** + * Do we want to remove the program records from this data source? + */ + private final boolean removeProgramRecords; + /** * Store BAM indices for each reader present. */ @@ -200,7 +205,8 @@ public SAMDataSource( BAQ.QualityMode.DONT_MODIFY, null, // no BAQ null, // no BQSR - (byte) -1); + (byte) -1, + false); } /** @@ -233,7 +239,8 @@ public SAMDataSource( BAQ.QualityMode qmode, IndexedFastaSequenceFile refReader, BaseRecalibration bqsrApplier, - byte defaultBaseQualities) { + byte defaultBaseQualities, + boolean removeProgramRecords) { this.readMetrics = new ReadMetrics(); this.genomeLocParser = genomeLocParser; @@ -249,6 +256,7 @@ public SAMDataSource( dispatcher = null; validationStringency = strictness; + this.removeProgramRecords = removeProgramRecords; if(readBufferSize != null) ReadShard.setReadBufferSize(readBufferSize); else { @@ -748,7 +756,7 @@ protected synchronized SAMReaderID getReaderID(SAMFileReader reader) { private synchronized void createNewResource() { if(allResources.size() > maxEntries) throw new ReviewedStingException("Cannot create a new resource pool. All resources are in use."); - SAMReaders readers = new SAMReaders(readerIDs, validationStringency); + SAMReaders readers = new SAMReaders(readerIDs, validationStringency, removeProgramRecords); allResources.add(readers); availableResources.add(readers); } @@ -777,9 +785,11 @@ private class SAMReaders implements Iterable { /** * Derive a new set of readers from the Reads metadata. * @param readerIDs reads to load. + * TODO: validationStringency is not used here * @param validationStringency validation stringency. + * @param removeProgramRecords indicate whether to clear program records from the readers */ - public SAMReaders(Collection readerIDs, SAMFileReader.ValidationStringency validationStringency) { + public SAMReaders(Collection readerIDs, SAMFileReader.ValidationStringency validationStringency, boolean removeProgramRecords) { final int totalNumberOfFiles = readerIDs.size(); int readerNumber = 1; final SimpleTimer timer = new SimpleTimer().start(); @@ -790,6 +800,9 @@ public SAMReaders(Collection readerIDs, SAMFileReader.ValidationStr long lastTick = timer.currentTime(); for(final SAMReaderID readerID: readerIDs) { final ReaderInitializer init = new ReaderInitializer(readerID).call(); + if (removeProgramRecords) { + init.reader.getFileHeader().setProgramRecords(new ArrayList()); + } if (threadAllocation.getNumIOThreads() > 0) { inputStreams.put(init.readerID, init.blockInputStream); // get from initializer } diff --git a/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSourceUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSourceUnitTest.java index 1c5dab254a..f2c5463175 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSourceUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSourceUnitTest.java @@ -24,9 +24,12 @@ package org.broadinstitute.sting.gatk.datasources.reads; +import static org.testng.Assert.assertEquals; +import static org.testng.Assert.assertTrue; import static org.testng.Assert.fail; import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.samtools.SAMFileReader; +import net.sf.samtools.SAMProgramRecord; import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.commandline.Tags; @@ -36,6 +39,7 @@ import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.sting.utils.exceptions.UserException; import org.testng.annotations.AfterMethod; @@ -143,4 +147,73 @@ public void testLinearBreakIterateAll() { fail("testLinearBreakIterateAll: We Should get a UserException.CouldNotReadInputFile exception"); } } + + /** Test that we clear program records when requested */ + @Test + public void testRemoveProgramRecords() { + logger.warn("Executing testRemoveProgramRecords"); + + // setup the data + readers.add(new SAMReaderID(new File(b37GoodBAM),new Tags())); + + // use defaults + SAMDataSource data = new SAMDataSource(readers, + new ThreadAllocation(), + null, + genomeLocParser, + false, + SAMFileReader.ValidationStringency.SILENT, + null, + null, + new ValidationExclusion(), + new ArrayList(), + false); + + List defaultProgramRecords = data.getHeader().getProgramRecords(); + assertTrue(defaultProgramRecords.size() != 0, "testRemoveProgramRecords: No program records found when using default constructor"); + + boolean removeProgramRecords = false; + data = new SAMDataSource(readers, + new ThreadAllocation(), + null, + genomeLocParser, + false, + SAMFileReader.ValidationStringency.SILENT, + null, + null, + new ValidationExclusion(), + new ArrayList(), + false, + BAQ.CalculationMode.OFF, + BAQ.QualityMode.DONT_MODIFY, + null, // no BAQ + null, // no BQSR + (byte) -1, + removeProgramRecords); + + List dontRemoveProgramRecords = data.getHeader().getProgramRecords(); + assertEquals(dontRemoveProgramRecords, defaultProgramRecords, "testRemoveProgramRecords: default program records differ from removeProgramRecords = false"); + + removeProgramRecords = true; + data = new SAMDataSource(readers, + new ThreadAllocation(), + null, + genomeLocParser, + false, + SAMFileReader.ValidationStringency.SILENT, + null, + null, + new ValidationExclusion(), + new ArrayList(), + false, + BAQ.CalculationMode.OFF, + BAQ.QualityMode.DONT_MODIFY, + null, // no BAQ + null, // no BQSR + (byte) -1, + removeProgramRecords); + + List doRemoveProgramRecords = data.getHeader().getProgramRecords(); + assertTrue(doRemoveProgramRecords.isEmpty(), "testRemoveProgramRecords: program records not cleared when removeProgramRecords = true"); + } } From b268b5372c5a88520f7835e51e9fb466637b5c21 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Wed, 1 Aug 2012 11:57:16 -0400 Subject: [PATCH 048/176] Bugfix for incorrect allele counting in IndelSummary -- Previous version would count all alt alleles as present in a sample, even if only 1 were present, because of the way VariantEval subsetted VCs -- Updated code for subsetting VCs by sample to be clearer about how it handles rederiving alleles -- Update a few pieces of code to get previous correct behavior -- Updated a few MD5s as now ref calls at sites in dbSNP are counted as having a comp sites, and therefore show up in known sites when Novelty strat is on (which I think is correct) -- Walkers that used old subsetting function with true are now using clearer version that does rederive alleles by default --- .../walkers/phasing/ReadBackedPhasing.java | 2 +- .../GLBasedSampleSelector.java | 2 +- .../GTBasedSampleSelector.java | 2 +- .../gatk/walkers/varianteval/VariantEval.java | 5 ++++- .../evaluators/TiTvVariantEvaluator.java | 9 ++++++--- .../varianteval/stratifications/Novelty.java | 2 +- .../varianteval/util/VariantEvalUtils.java | 12 +++++------- .../utils/variantcontext/VariantContext.java | 18 +++++++++++++++--- .../VariantEvalIntegrationTest.java | 6 +++--- .../VariantContextBenchmark.java | 2 +- 10 files changed, 38 insertions(+), 22 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java index f16deb701e..f49e8f8c0f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java @@ -288,7 +288,7 @@ public PhasingStatsAndOutput map(RefMetaDataTracker tracker, ReferenceContext re private VariantContext reduceVCToSamples(VariantContext vc, Set samplesToPhase) { // for ( String sample : samplesToPhase ) // logger.debug(String.format(" Sample %s has genotype %s, het = %s", sample, vc.getGenotype(sample), vc.getGenotype(sample).isHet() )); - VariantContext subvc = vc.subContextFromSamples(samplesToPhase, true); + VariantContext subvc = vc.subContextFromSamples(samplesToPhase); // logger.debug("original VC = " + vc); // logger.debug("sub VC = " + subvc); return VariantContextUtils.pruneVariantContext(subvc, KEYS_TO_KEEP_IN_REDUCED_VCF); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java index e54dc63888..3e48520a78 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java @@ -43,7 +43,7 @@ public boolean selectSiteInSamples(VariantContext vc) { return true; // want to include a site in the given samples if it is *likely* to be variant (via the EXACT model) // first subset to the samples - VariantContext subContext = vc.subContextFromSamples(samples, true); + VariantContext subContext = vc.subContextFromSamples(samples); // now check to see (using EXACT model) whether this should be variant // do we want to apply a prior? maybe user-spec? diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java index 0f55524a6e..de832b1089 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java @@ -45,7 +45,7 @@ public boolean selectSiteInSamples(VariantContext vc) { if ( samples == null || samples.isEmpty() ) return true; - VariantContext subContext = vc.subContextFromSamples(samples, false); + VariantContext subContext = vc.subContextFromSamples(samples); if ( subContext.isPolymorphicInSamples() ) { return true; } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java index 0b395bc626..58cd147370 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java @@ -500,7 +500,10 @@ private enum EvalCompMatchType { NO_MATCH, STRICT, LENIENT } @Requires({"eval != null", "comp != null"}) private EvalCompMatchType doEvalAndCompMatch(final VariantContext eval, final VariantContext comp, boolean requireStrictAlleleMatch) { - // find all of the matching comps + if ( comp.getType() == VariantContext.Type.NO_VARIATION || eval.getType() == VariantContext.Type.NO_VARIATION ) + // if either of these are NO_VARIATION they are LENIENT matches + return EvalCompMatchType.LENIENT; + if ( comp.getType() != eval.getType() ) return EvalCompMatchType.NO_MATCH; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java index 6c4fcd26d8..fe24379765 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java @@ -57,9 +57,12 @@ public void updateTiTv(VariantContext vc, boolean updateStandard) { } } - public void update2(VariantContext vc1, VariantContext vc2, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - if (vc1 != null) updateTiTv(vc1, false); - if (vc2 != null) updateTiTv(vc2, true); + @Override + public void update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + if (eval != null) + updateTiTv(eval, false); + if (comp != null) + updateTiTv(comp, true); } @Override diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java index 693bdf1988..2ad08d8064 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java @@ -28,7 +28,7 @@ public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker t final Collection knownComps = tracker.getValues(knowns, ref.getLocus()); for ( final VariantContext c : knownComps ) { // loop over sites, looking for something that matches the type eval - if ( eval.getType() == c.getType() ) { + if ( eval.getType() == c.getType() || eval.getType() == VariantContext.Type.NO_VARIATION ) { return KNOWN_STATES; } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java index 3dcc1f85f1..e84b0b10e1 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java @@ -197,7 +197,9 @@ public VariantContext getSubsetOfVariantContext(VariantContext vc, String sample * @return a new VariantContext with just the requested samples */ public VariantContext getSubsetOfVariantContext(VariantContext vc, Set sampleNames) { - return ensureAnnotations(vc, vc.subContextFromSamples(sampleNames, false)); + // if we want to preserve AC0 sites as polymorphic we need to not rederive alleles + final boolean deriveAlleles = variantEvalWalker.ignoreAC0Sites(); + return ensureAnnotations(vc, vc.subContextFromSamples(sampleNames, deriveAlleles)); } public VariantContext ensureAnnotations(final VariantContext vc, final VariantContext vcsub) { @@ -262,12 +264,8 @@ public VariantContext ensureAnnotations(final VariantContext vc, final VariantCo // First, filter the VariantContext to represent only the samples for evaluation VariantContext vcsub = vc; - if (subsetBySample && vc.hasGenotypes()) { - if ( variantEvalWalker.isSubsettingToSpecificSamples() ) - vcsub = getSubsetOfVariantContext(vc, variantEvalWalker.getSampleNamesForEvaluation()); - else - vcsub = ensureAnnotations(vc, vc); - } + if (subsetBySample && vc.hasGenotypes()) + vcsub = getSubsetOfVariantContext(vc, variantEvalWalker.getSampleNamesForEvaluation()); if ((byFilter || !vcsub.isFiltered())) { addMapping(mapping, VariantEval.getAllSampleName(), vcsub); diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java index 979400350e..2211cfe5e8 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java @@ -334,12 +334,14 @@ protected VariantContext(final String source, * in this VC is returned as the set of alleles in the subContext, even if * some of those alleles aren't in the samples * + * WARNING: BE CAREFUL WITH rederiveAllelesFromGenotypes UNLESS YOU KNOW WHAT YOU ARE DOING? + * * @param sampleNames the sample names - * @param rederiveAllelesFromGenotypes if true, returns the alleles to just those in use by the samples + * @param rederiveAllelesFromGenotypes if true, returns the alleles to just those in use by the samples, true should be default * @return new VariantContext subsetting to just the given samples */ public VariantContext subContextFromSamples(Set sampleNames, final boolean rederiveAllelesFromGenotypes ) { - if ( sampleNames.containsAll(getSampleNames()) ) { + if ( sampleNames.containsAll(getSampleNames()) && ! rederiveAllelesFromGenotypes ) { return this; // fast path when you don't have any work to do } else { VariantContextBuilder builder = new VariantContextBuilder(this); @@ -355,8 +357,18 @@ public VariantContext subContextFromSamples(Set sampleNames, final boole } } + /** + * @see #subContextFromSamples(java.util.Set, boolean) with rederiveAllelesFromGenotypes = true + * + * @param sampleNames + * @return + */ + public VariantContext subContextFromSamples(final Set sampleNames) { + return subContextFromSamples(sampleNames, true); + } + public VariantContext subContextFromSample(String sampleName) { - return subContextFromSamples(Collections.singleton(sampleName), true); + return subContextFromSamples(Collections.singleton(sampleName)); } /** diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java index d9a91c4c26..94e52c2b9e 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java @@ -34,7 +34,7 @@ import java.util.List; public class VariantEvalIntegrationTest extends WalkerTest { - private static String variantEvalTestDataRoot = validationDataLocation + "VariantEval/"; + private static String variantEvalTestDataRoot = privateTestDir + "VariantEval/"; private static String fundamentalTestVCF = variantEvalTestDataRoot + "FundamentalsTest.annotated.db.subset.snps_and_indels.vcf"; private static String fundamentalTestSNPsVCF = variantEvalTestDataRoot + "FundamentalsTest.annotated.db.subset.final.vcf"; private static String fundamentalTestSNPsWithMLEVCF = variantEvalTestDataRoot + "FundamentalsTest.annotated.db.subset.final.withMLE.vcf"; @@ -122,7 +122,7 @@ public void testFundamentalsCountVariantsSNPsAndIndelsWithNovelty() { "-o %s" ), 1, - Arrays.asList("e62a3bd9914d48e2bb2fb4f5dfc5ebc0") + Arrays.asList("40abbc9be663aed8ee1158f832463ca8") ); executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNovelty", spec); } @@ -144,7 +144,7 @@ public void testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter() { "-o %s" ), 1, - Arrays.asList("087a2d9943c53e7f49663667c3305c7e") + Arrays.asList("106a0e8753e839c0a2c030eb4b165fa9") ); executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNoveltyAndFilter", spec); } diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextBenchmark.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextBenchmark.java index 7c522eadfb..0e5522e3a9 100644 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextBenchmark.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextBenchmark.java @@ -152,7 +152,7 @@ public void run(final VariantContext vc) { public void run(final VariantContext vc) { if ( samples == null ) samples = new HashSet(new ArrayList(vc.getSampleNames()).subList(0, nSamplesToTake)); - VariantContext sub = vc.subContextFromSamples(samples, true); + VariantContext sub = vc.subContextFromSamples(samples); sub.getNSamples(); } }; From a167f29e6db4ac273da6be0cb40d011a29af04aa Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Wed, 1 Aug 2012 15:44:38 -0400 Subject: [PATCH 049/176] Adding VE integration test file to private/testdata From 891ec82f8012aa2baa5a060cd4d1d43289937168 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Wed, 1 Aug 2012 17:09:22 -0400 Subject: [PATCH 050/176] Update BCF2 to put PASS as offset 0 not at the end -- Unfortunately this commit breaks backward compatibility with all existing BCF2 files... --- .../sting/utils/codecs/bcf2/BCF2Decoder.java | 2 +- .../sting/utils/codecs/bcf2/BCF2Utils.java | 10 +++------- .../utils/codecs/bcf2/BCF2EncoderDecoderUnitTest.java | 2 +- .../sting/utils/codecs/vcf/VCFIntegrationTest.java | 2 +- 4 files changed, 6 insertions(+), 10 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java index a13be21c55..2619a4dae3 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java @@ -202,7 +202,7 @@ private final Object decodeLiteralString(final int size) { return null; else { final String s = new String(bytes, 0, goodLength); - return BCF2Utils.isCollapsedString(s) ? BCF2Utils.exploreStringList(s) : s; + return BCF2Utils.isCollapsedString(s) ? BCF2Utils.explodeStringList(s) : s; } } catch ( IOException e ) { throw new ReviewedStingException("readByte failure", e); diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java index 43e933948d..1beacd0704 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java @@ -79,23 +79,19 @@ public final static ArrayList makeDictionary(final VCFHeader header) { final Set seen = new HashSet(); final ArrayList dict = new ArrayList(); - boolean sawPASS = false; + dict.add(VCFConstants.PASSES_FILTERS_v4); // special case the special PASS field + // set up the strings dictionary for ( VCFHeaderLine line : header.getMetaDataInInputOrder() ) { if ( line instanceof VCFIDHeaderLine && ! (line instanceof VCFContigHeaderLine) ) { final VCFIDHeaderLine idLine = (VCFIDHeaderLine)line; if ( ! seen.contains(idLine.getID())) { - sawPASS = sawPASS || idLine.getID().equals(VCFConstants.PASSES_FILTERS_v4); dict.add(idLine.getID()); seen.add(idLine.getID()); } } } - - if ( ! sawPASS ) - dict.add(VCFConstants.PASSES_FILTERS_v4); // special case the special PASS field - return dict; } @@ -177,7 +173,7 @@ public static final String collapseStringList(final List strings) { */ @Requires({"collapsed != null", "isCollapsedString(collapsed)"}) @Ensures("result != null") - public static final List exploreStringList(final String collapsed) { + public static final List explodeStringList(final String collapsed) { assert isCollapsedString(collapsed); final String[] exploded = collapsed.substring(1).split(","); return Arrays.asList(exploded); diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2EncoderDecoderUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2EncoderDecoderUnitTest.java index a0feef186e..7569ce90de 100644 --- a/public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2EncoderDecoderUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2EncoderDecoderUnitTest.java @@ -351,7 +351,7 @@ public Object[][] listOfStringsProvider() { public void testEncodingListOfString(List strings, String expected) throws IOException { final String collapsed = BCF2Utils.collapseStringList(strings); Assert.assertEquals(collapsed, expected); - Assert.assertEquals(BCF2Utils.exploreStringList(collapsed), strings); + Assert.assertEquals(BCF2Utils.explodeStringList(collapsed), strings); } // ----------------------------------------------------------------- diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java index 3948ba971e..86c8c968df 100644 --- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java @@ -77,7 +77,7 @@ public void testWritingSamtoolsWExBCFExample() { String testVCF = privateTestDir + "ex2.vcf"; String baseCommand = "-R " + b36KGReference + " --no_cmdline_in_header -o %s "; String test1 = baseCommand + "-T SelectVariants -V " + testVCF; - WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("a04a0fc22fedb516c663e56e51fc1e27")); + WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("e8f721ce81e4fdadba13c5291027057f")); executeTest("Test writing samtools WEx BCF example", spec1); } From dcf33e7dbd3be756ea8e7d5f22b73def892b4158 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Wed, 1 Aug 2012 17:10:35 -0400 Subject: [PATCH 051/176] Update ex2.vcf and .bcf test files to new spec From 57859fb52b0716a4d6cfe1e7ebe0fb5f8538ab5b Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 2 Aug 2012 11:33:21 -0400 Subject: [PATCH 052/176] Missing/malformed GATK report files are user errors --- .../src/org/broadinstitute/sting/gatk/report/GATKReport.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java index bec1ea5430..47bc48f816 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java +++ b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java @@ -89,9 +89,9 @@ private void loadReport(File file) { reader = new BufferedReader(new FileReader(file)); reportHeader = reader.readLine(); } catch (FileNotFoundException e) { - throw new ReviewedStingException("Could not open file : " + file); + throw new UserException.CouldNotReadInputFile(file, "it does not exist"); } catch (IOException e) { - throw new ReviewedStingException("Could not read file : " + file); + throw new UserException.CouldNotReadInputFile(file, e); } From d0c3b332ec9c1882758225467ef1e53b8b0f5325 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 2 Aug 2012 16:44:39 -0400 Subject: [PATCH 053/176] Update BCF2 to include a minor version number so we can rev (and report errors) with BCF2 -- We are no likely to fail with an error when reading old BCF files, rather than just giving bad results -- Added new class BCFVersion that consolidates all of the version management of BCF --- .../sting/utils/codecs/bcf2/BCF2Codec.java | 22 ++++- .../sting/utils/codecs/bcf2/BCF2Utils.java | 44 +++++----- .../sting/utils/codecs/bcf2/BCFVersion.java | 80 +++++++++++++++++++ .../variantcontext/writer/BCF2Writer.java | 6 +- .../utils/codecs/vcf/VCFIntegrationTest.java | 2 +- 5 files changed, 122 insertions(+), 32 deletions(-) create mode 100644 public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCFVersion.java diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java index 0f9cc34e76..0776b3aa8f 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java @@ -53,6 +53,11 @@ public final class BCF2Codec implements FeatureCodec { final protected static Logger logger = Logger.getLogger(BCF2Codec.class); private final static boolean FORBID_SYMBOLICS = false; + private final static int ALLOWED_MAJOR_VERSION = 2; + private final static int MIN_MINOR_VERSION = 1; + + private BCFVersion bcfVersion = null; + private VCFHeader header = null; /** @@ -131,8 +136,16 @@ public Class getFeatureType() { public FeatureCodecHeader readHeader( final PositionalBufferedStream inputStream ) { try { // note that this reads the magic as well, and so does double duty - if ( ! BCF2Utils.startsWithBCF2Magic(inputStream) ) - error("Input stream does not begin with BCF2 magic"); + bcfVersion = BCFVersion.readBCFVersion(inputStream); + if ( bcfVersion == null ) + error("Input stream does not contain a BCF encoded file; BCF magic header info not found"); + + if ( bcfVersion.getMajorVersion() != ALLOWED_MAJOR_VERSION ) + error("BCF2Codec can only process BCF2 files, this file has major version " + bcfVersion.getMajorVersion()); + if ( bcfVersion.getMinorVersion() < MIN_MINOR_VERSION ) + error("BCF2Codec can only process BCF2 files with minor version >= " + MIN_MINOR_VERSION + " but this file has minor version " + bcfVersion.getMinorVersion()); + + logger.info("BCF version " + bcfVersion); final int headerSizeInBytes = BCF2Utils.readInt(BCF2Type.INT32.getSizeInBytes(), inputStream); @@ -187,7 +200,8 @@ public boolean canDecode( final String path ) { FileInputStream fis = null; try { fis = new FileInputStream(path); - return BCF2Utils.startsWithBCF2Magic(fis); + final BCFVersion version = BCFVersion.readBCFVersion(fis); + return version != null && version.getMajorVersion() == ALLOWED_MAJOR_VERSION; } catch ( FileNotFoundException e ) { return false; } catch ( IOException e ) { @@ -196,7 +210,7 @@ public boolean canDecode( final String path ) { try { if ( fis != null ) fis.close(); } catch ( IOException e ) { - ; // do nothing + // do nothing } } } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java index 1beacd0704..d3f3fc102e 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java @@ -41,8 +41,6 @@ * @since 5/12 */ public final class BCF2Utils { - public static final byte[] MAGIC_HEADER_LINE = "BCF\2".getBytes(); - public static final int MAX_ALLELES_IN_GENOTYPES = 127; public static final int OVERFLOW_ELEMENT_MARKER = 15; @@ -75,7 +73,7 @@ private BCF2Utils() {} */ @Requires("header != null") @Ensures({"result != null", "new HashSet(result).size() == result.size()"}) - public final static ArrayList makeDictionary(final VCFHeader header) { + public static ArrayList makeDictionary(final VCFHeader header) { final Set seen = new HashSet(); final ArrayList dict = new ArrayList(); @@ -96,43 +94,37 @@ public final static ArrayList makeDictionary(final VCFHeader header) { } @Requires({"nElements >= 0", "type != null"}) - public final static byte encodeTypeDescriptor(final int nElements, final BCF2Type type ) { + public static byte encodeTypeDescriptor(final int nElements, final BCF2Type type ) { int encodeSize = Math.min(nElements, OVERFLOW_ELEMENT_MARKER); byte typeByte = (byte)((0x0F & encodeSize) << 4 | (type.getID() & 0x0F)); return typeByte; } @Ensures("result >= 0") - public final static int decodeSize(final byte typeDescriptor) { + public static int decodeSize(final byte typeDescriptor) { return (0xF0 & typeDescriptor) >> 4; } @Ensures("result >= 0") - public final static int decodeTypeID(final byte typeDescriptor) { + public static int decodeTypeID(final byte typeDescriptor) { return typeDescriptor & 0x0F; } @Ensures("result != null") - public final static BCF2Type decodeType(final byte typeDescriptor) { + public static BCF2Type decodeType(final byte typeDescriptor) { return ID_TO_ENUM[decodeTypeID(typeDescriptor)]; } - public final static boolean sizeIsOverflow(final byte typeDescriptor) { + public static boolean sizeIsOverflow(final byte typeDescriptor) { return decodeSize(typeDescriptor) == OVERFLOW_ELEMENT_MARKER; } @Requires("nElements >= 0") - public final static boolean willOverflow(final long nElements) { + public static boolean willOverflow(final long nElements) { return nElements > MAX_INLINE_ELEMENTS; } - public final static boolean startsWithBCF2Magic(final InputStream stream) throws IOException { - final byte[] magicBytes = new byte[BCF2Utils.MAGIC_HEADER_LINE.length]; - stream.read(magicBytes); - return Arrays.equals(magicBytes, BCF2Utils.MAGIC_HEADER_LINE); - } - - public final static byte readByte(final InputStream stream) { + public static byte readByte(final InputStream stream) { // TODO -- shouldn't be capturing error here try { return (byte)(stream.read() & 0xFF); @@ -151,7 +143,7 @@ public final static byte readByte(final InputStream stream) { */ @Requires({"strings != null", "strings.size() > 1"}) @Ensures("result != null") - public static final String collapseStringList(final List strings) { + public static String collapseStringList(final List strings) { final StringBuilder b = new StringBuilder(); for ( final String s : strings ) { if ( s != null ) { @@ -173,14 +165,14 @@ public static final String collapseStringList(final List strings) { */ @Requires({"collapsed != null", "isCollapsedString(collapsed)"}) @Ensures("result != null") - public static final List explodeStringList(final String collapsed) { + public static List explodeStringList(final String collapsed) { assert isCollapsedString(collapsed); final String[] exploded = collapsed.substring(1).split(","); return Arrays.asList(exploded); } @Requires("s != null") - public static final boolean isCollapsedString(final String s) { + public static boolean isCollapsedString(final String s) { return s.charAt(0) == ','; } @@ -222,7 +214,7 @@ public static final File shadowBCF(final File vcfFile) { } @Ensures("result.isIntegerType()") - public final static BCF2Type determineIntegerType(final int value) { + public static BCF2Type determineIntegerType(final int value) { for ( final BCF2Type potentialType : INTEGER_TYPES_BY_SIZE) { if ( potentialType.withinRange(value) ) return potentialType; @@ -232,7 +224,7 @@ public final static BCF2Type determineIntegerType(final int value) { } @Ensures("result.isIntegerType()") - public final static BCF2Type determineIntegerType(final int[] values) { + public static BCF2Type determineIntegerType(final int[] values) { // literally a copy of the code below, but there's no general way to unify lists and arrays in java BCF2Type maxType = BCF2Type.INT8; for ( final int value : values ) { @@ -258,7 +250,7 @@ public final static BCF2Type determineIntegerType(final int[] values) { */ @Requires({"t1.isIntegerType()","t2.isIntegerType()"}) @Ensures("result.isIntegerType()") - public final static BCF2Type maxIntegerType(final BCF2Type t1, final BCF2Type t2) { + public static BCF2Type maxIntegerType(final BCF2Type t1, final BCF2Type t2) { switch ( t1 ) { case INT8: return t2; case INT16: return t2 == BCF2Type.INT32 ? t2 : t1; @@ -268,7 +260,7 @@ public final static BCF2Type maxIntegerType(final BCF2Type t1, final BCF2Type t2 } @Ensures("result.isIntegerType()") - public final static BCF2Type determineIntegerType(final List values) { + public static BCF2Type determineIntegerType(final List values) { BCF2Type maxType = BCF2Type.INT8; for ( final int value : values ) { final BCF2Type type1 = determineIntegerType(value); @@ -293,7 +285,7 @@ public final static BCF2Type determineIntegerType(final List values) { * @param o * @return */ - public final static List toList(final Object o) { + public static List toList(final Object o) { if ( o == null ) return Collections.emptyList(); else if ( o instanceof List ) return (List)o; else return Collections.singletonList(o); @@ -301,7 +293,7 @@ public final static List toList(final Object o) { @Requires({"stream != null", "bytesForEachInt > 0"}) - public final static int readInt(int bytesForEachInt, final InputStream stream) { + public static int readInt(int bytesForEachInt, final InputStream stream) { switch ( bytesForEachInt ) { case 1: { return (byte)(readByte(stream)); @@ -319,7 +311,7 @@ public final static int readInt(int bytesForEachInt, final InputStream stream) { } } - public final static void encodeRawBytes(final int value, final BCF2Type type, final OutputStream encodeStream) throws IOException { + public static void encodeRawBytes(final int value, final BCF2Type type, final OutputStream encodeStream) throws IOException { switch ( type.getSizeInBytes() ) { case 1: encodeStream.write(0xFF & value); diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCFVersion.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCFVersion.java new file mode 100644 index 0000000000..742da7c0c9 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCFVersion.java @@ -0,0 +1,80 @@ +package org.broadinstitute.sting.utils.codecs.bcf2; + +import java.io.IOException; +import java.io.InputStream; +import java.io.OutputStream; +import java.util.Arrays; + +/** + * Simple holder for BCF version information + * + * User: depristo + * Date: 8/2/12 + * Time: 2:16 PM + */ +public class BCFVersion { + /** + * BCF2 begins with the MAGIC info BCF_M_m where M is the major version (currently 2) + * and m is the minor version, currently 1 + */ + public static final byte[] MAGIC_HEADER_START = "BCF".getBytes(); + + final int majorVersion; + final int minorVersion; + + public BCFVersion(int majorVersion, int minorVersion) { + this.majorVersion = majorVersion; + this.minorVersion = minorVersion; + } + + /** + * @return the major version number of this BCF file + */ + public int getMajorVersion() { + return majorVersion; + } + + /** + * @return the minor version number of this BCF file + */ + public int getMinorVersion() { + return minorVersion; + } + + /** + * Return a new BCFVersion object describing the major and minor version of the BCF file in stream + * + * Note that stream must be at the very start of the file. + * + * @param stream + * @return a BCFVersion object, or null if stream doesn't contain a BCF file + * @throws IOException + */ + public static BCFVersion readBCFVersion(final InputStream stream) throws IOException { + final byte[] magicBytes = new byte[MAGIC_HEADER_START.length]; + stream.read(magicBytes); + if ( Arrays.equals(magicBytes, MAGIC_HEADER_START) ) { + // we're a BCF file + final int majorByte = stream.read(); + final int minorByte = stream.read(); + return new BCFVersion( majorByte, minorByte ); + } else + return null; + } + + /** + * Write out the BCF magic information indicating this is a BCF file with corresponding major and minor versions + * @param out + * @throws IOException + */ + public void write(final OutputStream out) throws IOException { + out.write(MAGIC_HEADER_START); + out.write(getMajorVersion() & 0xFF); + out.write(getMinorVersion() & 0xFF); + } + + @Override + public String toString() { + return String.format("BCF%d.%d", getMajorVersion(), getMinorVersion()); + } +} diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java index b5da206adc..32377d09ef 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java @@ -31,6 +31,7 @@ import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Codec; import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Type; import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Utils; +import org.broadinstitute.sting.utils.codecs.bcf2.BCFVersion; import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; @@ -83,6 +84,9 @@ * @since 06/12 */ class BCF2Writer extends IndexingVariantContextWriter { + public static final int MAJOR_VERSION = 2; + public static final int MINOR_VERSION = 1; + /** * If true, we will write out the undecoded raw bytes for a genotypes block, if it * is found in the input VC. This can be very dangerous as the genotype encoding @@ -153,7 +157,7 @@ public void writeHeader(VCFHeader header) { writer.close(); final byte[] headerBytes = capture.toByteArray(); - outputStream.write(BCF2Utils.MAGIC_HEADER_LINE); + new BCFVersion(MAJOR_VERSION, MINOR_VERSION).write(outputStream); BCF2Utils.encodeRawBytes(headerBytes.length, BCF2Type.INT32, outputStream); outputStream.write(headerBytes); } catch (IOException e) { diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java index 86c8c968df..71fc1d4642 100644 --- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java @@ -57,7 +57,7 @@ public void testReadingAndWriting1000GSVs() { String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s "; String test1 = baseCommand + "-T SelectVariants -V " + testVCF; - WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("")); + WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("bdab26dd7648a806dbab01f64db2bdab")); executeTest("Test reading and writing 1000G Phase I SVs", spec1); } From 1d9788d1a2b5d0ea52244d621e5f82cae9d66d7d Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 2 Aug 2012 16:45:13 -0400 Subject: [PATCH 054/176] VisualizeContextTree now loops over M, I, and D states generating trees and analyzes From 3f7c83c2f746d0c411fc185856a879869b9d7a30 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 3 Aug 2012 09:42:21 -0400 Subject: [PATCH 055/176] Bugfix for new PASS position in dictionary in BCF2 --- .../org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java index d3f3fc102e..c79abe2ae3 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java @@ -77,7 +77,9 @@ public static ArrayList makeDictionary(final VCFHeader header) { final Set seen = new HashSet(); final ArrayList dict = new ArrayList(); - dict.add(VCFConstants.PASSES_FILTERS_v4); // special case the special PASS field + // special case the special PASS field which doesn't show up in the FILTER field definitions + seen.add(VCFConstants.PASSES_FILTERS_v4); + dict.add(VCFConstants.PASSES_FILTERS_v4); // set up the strings dictionary for ( VCFHeaderLine line : header.getMetaDataInInputOrder() ) { From f189a2950147707b93eff0792715d735650043f9 Mon Sep 17 00:00:00 2001 From: Joel Thibault Date: Tue, 31 Jul 2012 15:09:36 -0400 Subject: [PATCH 056/176] Choose whether to keep program records based on Walker * Add keepProgramRecords argument * Make removeProgramRecords / keepProgramRecords override default --- .../sting/gatk/GenomeAnalysisEngine.java | 11 ++++++++++- .../sting/gatk/arguments/GATKArgumentCollection.java | 5 ++++- 2 files changed, 14 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index 228f8351a3..967fd32360 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -797,6 +797,15 @@ private SAMDataSource createReadsDataSource(GATKArgumentCollection argCollection if ( getWalkerBAQApplicationTime() == BAQ.ApplicationTime.FORBIDDEN && argCollection.BAQMode != BAQ.CalculationMode.OFF) throw new UserException.BadArgumentValue("baq", "Walker cannot accept BAQ'd base qualities, and yet BAQ mode " + argCollection.BAQMode + " was requested."); + if (argCollection.removeProgramRecords && argCollection.keepProgramRecords) + throw new UserException.BadArgumentValue("rpr / kpr", "Cannot enable both options"); + + // LocusWalkers don't use program records, so remove them by default to save memory + boolean removeProgramRecords = (this.walker instanceof LocusWalker) || argCollection.removeProgramRecords; + + if (argCollection.keepProgramRecords) + removeProgramRecords = false; + return new SAMDataSource( samReaderIDs, threadAllocation, @@ -814,7 +823,7 @@ private SAMDataSource createReadsDataSource(GATKArgumentCollection argCollection refReader, getBaseRecalibration(), argCollection.defaultBaseQualities, - argCollection.removeProgramRecords); + removeProgramRecords); } /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java index 91a008cbc9..9721169522 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java @@ -249,9 +249,12 @@ public static DownsamplingMethod getDefaultDownsamplingMethod() { @Argument(fullName = "validation_strictness", shortName = "S", doc = "How strict should we be with validation", required = false) public SAMFileReader.ValidationStringency strictnessLevel = SAMFileReader.ValidationStringency.SILENT; - @Argument(fullName = "remove_program_records", shortName = "rpr", doc = "Should we remove program records from the SAM header", required = false) + @Argument(fullName = "remove_program_records", shortName = "rpr", doc = "Should we override the Walker's default and remove program records from the SAM header", required = false) public boolean removeProgramRecords = false; + @Argument(fullName = "keep_program_records", shortName = "kpr", doc = "Should we override the Walker's default and keep program records from the SAM header", required = false) + public boolean keepProgramRecords = false; + @Argument(fullName = "unsafe", shortName = "U", doc = "If set, enables unsafe operations: nothing will be checked at runtime. For expert users only who know what they are doing. We do not support usage of this argument.", required = false) public ValidationExclusion.TYPE unsafe; From 50db428223cf4f6b209093f8d63aac0e71ab97ba Mon Sep 17 00:00:00 2001 From: Joel Thibault Date: Thu, 2 Aug 2012 14:21:30 -0400 Subject: [PATCH 057/176] Add a RemoveProgramRecords annotation * Add the RemoveProgramRecords annotation to LocusWalker --- .../sting/gatk/GenomeAnalysisEngine.java | 3 +-- .../sting/gatk/walkers/LocusWalker.java | 1 + .../gatk/walkers/RemoveProgramRecords.java | 21 +++++++++++++++++++ 3 files changed, 23 insertions(+), 2 deletions(-) create mode 100644 public/java/src/org/broadinstitute/sting/gatk/walkers/RemoveProgramRecords.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index 967fd32360..56fcf0652e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -800,8 +800,7 @@ private SAMDataSource createReadsDataSource(GATKArgumentCollection argCollection if (argCollection.removeProgramRecords && argCollection.keepProgramRecords) throw new UserException.BadArgumentValue("rpr / kpr", "Cannot enable both options"); - // LocusWalkers don't use program records, so remove them by default to save memory - boolean removeProgramRecords = (this.walker instanceof LocusWalker) || argCollection.removeProgramRecords; + boolean removeProgramRecords = argCollection.removeProgramRecords || walker.getClass().isAnnotationPresent(RemoveProgramRecords.class); if (argCollection.keepProgramRecords) removeProgramRecords = false; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java index e94d01d5af..2a92d8831e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java @@ -19,6 +19,7 @@ @Requires({DataSource.READS,DataSource.REFERENCE, DataSource.REFERENCE_BASES}) @PartitionBy(PartitionType.LOCUS) @ReadFilters({UnmappedReadFilter.class,NotPrimaryAlignmentFilter.class,DuplicateReadFilter.class,FailsVendorQualityCheckFilter.class}) +@RemoveProgramRecords public abstract class LocusWalker extends Walker { // Do we actually want to operate on the context? public boolean filter(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/RemoveProgramRecords.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/RemoveProgramRecords.java new file mode 100644 index 0000000000..d9abc79258 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/RemoveProgramRecords.java @@ -0,0 +1,21 @@ +package org.broadinstitute.sting.gatk.walkers; + +/** + * Created with IntelliJ IDEA. + * User: thibault + * Date: 8/2/12 + * Time: 1:58 PM + * To change this template use File | Settings | File Templates. + */ + +import java.lang.annotation.*; + +/** + * Indicates that program records should be removed from SAM headers by default for this walker + */ +@Documented +@Inherited +@Retention(RetentionPolicy.RUNTIME) +@Target(ElementType.TYPE) +public @interface RemoveProgramRecords { +} From d94cde236f87694fa94ec0beffef2061f9b5d9c0 Mon Sep 17 00:00:00 2001 From: Joel Thibault Date: Thu, 2 Aug 2012 14:46:00 -0400 Subject: [PATCH 058/176] Add RemoveProgramRecords annotation to ActiveRegionWalker --- .../broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java | 1 + 1 file changed, 1 insertion(+) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java index b2975cbbf8..aba508b3e9 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java @@ -32,6 +32,7 @@ @PartitionBy(PartitionType.READ) @ActiveRegionExtension(extension=50,maxRegion=1500) @ReadFilters({UnmappedReadFilter.class, NotPrimaryAlignmentFilter.class, DuplicateReadFilter.class, FailsVendorQualityCheckFilter.class, MappingQualityUnavailableFilter.class}) +@RemoveProgramRecords public abstract class ActiveRegionWalker extends Walker { @Output(fullName="activeRegionOut", shortName="ARO", doc="Output the active region to this interval list file", required = false) From 38d0fc3d6ccf19fef69f684ade0ccfa4f17e91ad Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Fri, 3 Aug 2012 12:24:23 -0400 Subject: [PATCH 059/176] First pass of implementation of Reduced Reads with HaplotypeCaller. Main changes: a) Active region: scale PL's by representative count to determine whether region is active. b) Scale per-read, per-haplotype likelihoods by read representative counts. A read representative count is (temporarily) defined as the average representative count over all bases in read, TBD whether this is good enough to avoid biases in GL's. c) DeBruijn assembler inserts kmers N times in graph, where N is min representative count of read over kmer span - TBD again whether this is the best approach. d) Bug fixes in FragmentUtils: logic to merge fragments was wrong in cases where there is discrepancy of overlaps between unclipped/soft clipped bases. Didn't affect things before but RR makes prevalence of hard-clipped bases in CIGARs more prevalent so this was exposed. e) Cache read representative counts along with read likelihoods associated with a Haplotype. Code can/should be cleaned up and unified with PairHMMIndelErrorModelCode, as well as refactored to support arbitrary ploidy in HaplotypeCaller --- .../broadinstitute/sting/utils/Haplotype.java | 14 +++++++++-- .../broadinstitute/sting/utils/MathUtils.java | 7 ++++++ .../sting/utils/fragments/FragmentUtils.java | 23 +++++++++++++++++-- 3 files changed, 40 insertions(+), 4 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java index 54442622f5..eca2e454ea 100755 --- a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java +++ b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java @@ -40,6 +40,7 @@ public class Haplotype { protected final double[] quals; private GenomeLoc genomeLocation = null; private HashMap readLikelihoodsPerSample = null; + private HashMap readCountsPerSample = null; private HashMap eventMap = null; private boolean isRef = false; private Cigar cigar; @@ -83,18 +84,27 @@ public int hashCode() { return Arrays.hashCode(bases); } - public void addReadLikelihoods( final String sample, final double[] readLikelihoods ) { + public void addReadLikelihoods( final String sample, final double[] readLikelihoods, final int[] readCounts ) { if( readLikelihoodsPerSample == null ) { readLikelihoodsPerSample = new HashMap(); } readLikelihoodsPerSample.put(sample, readLikelihoods); + if( readCountsPerSample == null ) { + readCountsPerSample = new HashMap(); + } + readCountsPerSample.put(sample, readCounts); } @Ensures({"result != null"}) public double[] getReadLikelihoods( final String sample ) { return readLikelihoodsPerSample.get(sample); } - + + @Ensures({"result != null"}) + public int[] getReadCounts( final String sample ) { + return readCountsPerSample.get(sample); + } + public Set getSampleKeySet() { return readLikelihoodsPerSample.keySet(); } diff --git a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java index 1f5eaefee8..96704f0b87 100644 --- a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java @@ -210,6 +210,13 @@ public static long sum(int[] x) { return total; } + public static int sum(byte[] x) { + int total = 0; + for (byte v : x) + total += (int)v; + return total; + } + /** * Calculates the log10 cumulative sum of an array with log10 probabilities * diff --git a/public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java b/public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java index 8512726739..2f31c154c9 100644 --- a/public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java @@ -134,17 +134,36 @@ public final static List mergeOverlappingPairedFragments( List= firstRead.getUnclippedStart() && secondRead.getUnclippedEnd() >= firstRead.getUnclippedEnd()) ) { + /* + System.out.println("read 0 unclipped start:"+overlappingPair.get(0).getUnclippedStart()); + System.out.println("read 0 unclipped end:"+overlappingPair.get(0).getUnclippedEnd()); + System.out.println("read 1 unclipped start:"+overlappingPair.get(1).getUnclippedStart()); + System.out.println("read 1 unclipped end:"+overlappingPair.get(1).getUnclippedEnd()); + System.out.println("read 0 start:"+overlappingPair.get(0).getAlignmentStart()); + System.out.println("read 0 end:"+overlappingPair.get(0).getAlignmentEnd()); + System.out.println("read 1 start:"+overlappingPair.get(1).getAlignmentStart()); + System.out.println("read 1 end:"+overlappingPair.get(1).getAlignmentEnd()); + */ + if( !(secondRead.getSoftStart() <= firstRead.getSoftEnd() && secondRead.getSoftStart() >= firstRead.getSoftStart() && secondRead.getSoftEnd() >= firstRead.getSoftEnd()) ) { firstRead = overlappingPair.get(1); // swap them secondRead = overlappingPair.get(0); } - if( !(secondRead.getUnclippedStart() <= firstRead.getUnclippedEnd() && secondRead.getUnclippedStart() >= firstRead.getUnclippedStart() && secondRead.getUnclippedEnd() >= firstRead.getUnclippedEnd()) ) { + if( !(secondRead.getSoftStart() <= firstRead.getSoftEnd() && secondRead.getSoftStart() >= firstRead.getSoftStart() && secondRead.getSoftEnd() >= firstRead.getSoftEnd()) ) { return overlappingPair; // can't merge them, yet: AAAAAAAAAAA-BBBBBBBBBBB-AAAAAAAAAAAAAA, B is contained entirely inside A } if( firstRead.getCigarString().contains("I") || firstRead.getCigarString().contains("D") || secondRead.getCigarString().contains("I") || secondRead.getCigarString().contains("D") ) { return overlappingPair; // fragments contain indels so don't merge them } +/* // check for inconsistent start positions between uncliped/soft alignment starts + if (secondRead.getAlignmentStart() >= firstRead.getAlignmentStart() && secondRead.getUnclippedStart() < firstRead.getUnclippedStart()) + return overlappingPair; + if (secondRead.getAlignmentStart() <= firstRead.getAlignmentStart() && secondRead.getUnclippedStart() > firstRead.getUnclippedStart()) + return overlappingPair; + + if (secondRead.getUnclippedStart() < firstRead.getAlignmentEnd() && secondRead.getAlignmentStart() >= firstRead.getAlignmentEnd()) + return overlappingPair; + */ final Pair pair = ReadUtils.getReadCoordinateForReferenceCoordinate(firstRead, secondRead.getSoftStart()); final int firstReadStop = ( pair.getSecond() ? pair.getFirst() + 1 : pair.getFirst() ); From 3780ce074e8f4dcc4aea249bc6ec51d486008e5b Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Fri, 3 Aug 2012 13:14:37 -0400 Subject: [PATCH 060/176] Using PathComparatorTotalScore in the assembly graph traversal does a better job of capturing low frequency branches that are inside high frequnecy haplotypes. From 6b3b0025581d1c02c1641c0182fa505a7e8e92fc Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Fri, 3 Aug 2012 14:26:51 -0400 Subject: [PATCH 061/176] Fixed 2 haplotype caller unit tests: a) new interface for addReadLikelihoods() including read counts, b) disable test that test basic DeBruijn graph assembly, not ready yet From a7a5e2c7bb24faa3a03197394415486fab70e9a9 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 3 Aug 2012 16:01:27 -0400 Subject: [PATCH 062/176] Ready for full-scale evaluation adaptive BQSR contexts -- VisualizeContextTree now can write out an equivalent BQSR table determined after adaptive context merging of all RG x QUAL x CONTEXT trees -- Docs, algorithm descriptions, etc so that it makes sense what's going on -- VisualizeContextTree should really be simplified when into a single tool that just visualize the trees when / if we decide to make adaptive contexts standard part of BQSR -- Misc. cleaning, organization of the code (recalibation tests were in private but corresponding actual files were public) --- .../sting/gatk/report/GATKReportTable.java | 31 ++- .../utils/recalibration/AdaptiveContext.java | 154 +++++++++++++ .../utils/recalibration/RecalDatumNode.java | 217 ++++++++++++++---- .../AdaptiveContextUnitTest.java | 64 ++++++ .../recalibration/QualQuantizerUnitTest.java | 169 ++++++++++++++ .../recalibration/RecalDatumUnitTest.java | 154 +++++++++++++ 6 files changed, 743 insertions(+), 46 deletions(-) create mode 100644 public/java/src/org/broadinstitute/sting/utils/recalibration/AdaptiveContext.java create mode 100644 public/java/test/org/broadinstitute/sting/utils/recalibration/AdaptiveContextUnitTest.java create mode 100644 public/java/test/org/broadinstitute/sting/utils/recalibration/QualQuantizerUnitTest.java create mode 100644 public/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java index 7a272e1551..3b4bdd087d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java +++ b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java @@ -208,11 +208,23 @@ public GATKReportTable(final String tableName, final String tableDescription, fi } /** - * Verifies that a table or column name has only alphanumeric characters - no spaces or special characters allowed - * - * @param name the name of the table or column - * @return true if the name is valid, false if otherwise + * Create a new GATKReportTable with the same structure + * @param tableToCopy */ + public GATKReportTable(final GATKReportTable tableToCopy, final boolean copyData) { + this(tableToCopy.getTableName(), tableToCopy.getTableDescription(), tableToCopy.getNumColumns(), tableToCopy.sortByRowID); + for ( final GATKReportColumn column : tableToCopy.getColumnInfo() ) + addColumn(column.getColumnName(), column.getFormat()); + if ( copyData ) + throw new IllegalArgumentException("sorry, copying data in GATKReportTable isn't supported"); + } + + /** + * Verifies that a table or column name has only alphanumeric characters - no spaces or special characters allowed + * + * @param name the name of the table or column + * @return true if the name is valid, false if otherwise + */ private boolean isValidName(String name) { Pattern p = Pattern.compile(INVALID_TABLE_NAME_REGEX); Matcher m = p.matcher(name); @@ -490,6 +502,17 @@ public Object get(final Object rowID, final String columnName) { return get(rowIdToIndex.get(rowID), columnNameToIndex.get(columnName)); } + /** + * Get a value from the given position in the table + * + * @param rowIndex the row ID + * @param columnName the name of the column + * @return the value stored at the specified position in the table + */ + public Object get(final int rowIndex, final String columnName) { + return get(rowIndex, columnNameToIndex.get(columnName)); + } + /** * Get a value from the given position in the table * diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/AdaptiveContext.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/AdaptiveContext.java new file mode 100644 index 0000000000..083b8af64b --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/AdaptiveContext.java @@ -0,0 +1,154 @@ +package org.broadinstitute.sting.utils.recalibration; + +import java.util.*; + +/** + * Functions for working with AdaptiveContexts + * + * User: depristo + * Date: 8/3/12 + * Time: 12:21 PM + * To change this template use File | Settings | File Templates. + */ +public class AdaptiveContext { + private AdaptiveContext() {} + + /** + * Return a freshly allocated tree filled in completely to fillDepth with + * all combinations of {A,C,G,T}^filldepth contexts. For nodes + * in the tree, they are simply copied. When the algorithm needs to + * generate new nodes (because they are missing) the subnodes inherit the + * observation and error counts of their parent. + * + * This algorithm produces data consistent with the standard output in a BQSR recal + * file for the Context covariate + * + * @param root + * @param fillDepth + * @return + */ + public static RecalDatumNode fillToDepth(final RecalDatumNode root, final int fillDepth) { + if ( root == null ) throw new IllegalArgumentException("root is null"); + if ( fillDepth < 0 ) throw new IllegalArgumentException("fillDepth is < 0"); + + return fillToDepthRec(root, fillDepth, 0); + } + + private static RecalDatumNode fillToDepthRec(final RecalDatumNode parent, + final int fillDepth, + final int currentDepth) { + // three cases: + // We are in the tree and so just recursively build + // We have reached our depth goal, so just return the parent since we are done + // We are outside of the tree, in which case we need to pointer to our parent node so we can + // we info (N, M) and we need a running context + if ( currentDepth < fillDepth ) { + // we need to create subnodes for each base, and propogate N and M down + final RecalDatumNode newParent = new RecalDatumNode(parent.getRecalDatum()); + + for ( final String base : Arrays.asList("A", "C", "G", "T")) { + ContextDatum subContext; + Set> subContexts; + + final RecalDatumNode subNode = findSubcontext(parent.getRecalDatum().context + base, parent); + if ( subNode != null ) { + // we have a subnode corresponding to the expected one, just copy and recurse + subContext = subNode.getRecalDatum(); + subContexts = subNode.getSubnodes(); + } else { + // have to create a new one + subContext = new ContextDatum(parent.getRecalDatum().context + base, + parent.getRecalDatum().getNumObservations(), parent.getRecalDatum().getNumMismatches()); + subContexts = Collections.emptySet(); + } + + newParent.addSubnode( + fillToDepthRec(new RecalDatumNode(subContext, subContexts), + fillDepth, currentDepth + 1)); + } + return newParent; + } else { + return parent; + } + } + + /** + * Go from a flat list of contexts to the tree implied by the contexts + * + * Implicit nodes are created as needed, and their observation and error counts are the sum of the + * all of their subnodes. + * + * Note this does not guarentee the tree is complete, as some contexts (e.g., AAT) may be missing + * from the tree because they are absent from the input list of contexts. + * + * For input AAG, AAT, AC, G would produce the following tree: + * + * - x [root] + * - A + * - A + * - T + * - G + * - C + * - G + * + * sets the fixed penalties in the resulting tree as well + * + * @param flatContexts list of flat contexts + * @return + */ + public static RecalDatumNode createTreeFromFlatContexts(final List flatContexts) { + if ( flatContexts == null || flatContexts.isEmpty() ) + throw new IllegalArgumentException("flatContexts cannot be empty or null"); + + final Queue> remaining = new LinkedList>(); + final Map> contextToNodes = new HashMap>(); + RecalDatumNode root = null; + + // initialize -- start with all of the contexts + for ( final ContextDatum cd : flatContexts ) + remaining.add(new RecalDatumNode(cd)); + + while ( remaining.peek() != null ) { + final RecalDatumNode add = remaining.poll(); + final ContextDatum cd = add.getRecalDatum(); + + final String parentContext = cd.getParentContext(); + RecalDatumNode parent = contextToNodes.get(parentContext); + if ( parent == null ) { + // haven't yet found parent, so make one, and enqueue it for processing + parent = new RecalDatumNode(new ContextDatum(parentContext, 0, 0)); + contextToNodes.put(parentContext, parent); + + if ( parentContext != ContextDatum.ROOT_CONTEXT ) + remaining.add(parent); + else + root = parent; + } + + parent.getRecalDatum().incrementNumObservations(cd.getNumObservations()); + parent.getRecalDatum().incrementNumMismatches(cd.getNumMismatches()); + parent.addSubnode(add); + } + + if ( root == null ) + throw new RuntimeException("root is unexpectedly null"); + + // set the fixed penalty everywhere in the tree, so that future modifications don't change the penalties + root.calcAndSetFixedPenalty(true); + + return root; + } + + /** + * Finds immediate subnode with contextToFind, or null if none exists + * + * @param tree whose subnodes should be searched + * @return + */ + public static RecalDatumNode findSubcontext(final String contextToFind, final RecalDatumNode tree) { + for ( final RecalDatumNode sub : tree.getSubnodes() ) + if ( sub.getRecalDatum().context.equals(contextToFind) ) + return sub; + return null; + } +} diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java index 3af91be164..1409af7d0a 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java @@ -4,10 +4,12 @@ import com.google.java.contract.Requires; import org.apache.commons.math.stat.inference.ChiSquareTestImpl; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import java.util.Collection; import java.util.HashSet; +import java.util.LinkedList; import java.util.Set; /** @@ -17,13 +19,18 @@ * @since 07/27/12 */ public class RecalDatumNode { - private final static boolean USE_CHI2 = true; protected static Logger logger = Logger.getLogger(RecalDatumNode.class); + + /** + * fixedPenalty is this value if it's considered fixed + */ private final static double UNINITIALIZED = Double.NEGATIVE_INFINITY; + private final T recalDatum; private double fixedPenalty = UNINITIALIZED; private final Set> subnodes; + @Requires({"recalDatum != null"}) public RecalDatumNode(final T recalDatum) { this(recalDatum, new HashSet>()); } @@ -33,28 +40,45 @@ public String toString() { return recalDatum.toString(); } + @Requires({"recalDatum != null", "subnodes != null"}) public RecalDatumNode(final T recalDatum, final Set> subnodes) { this(recalDatum, UNINITIALIZED, subnodes); } + @Requires({"recalDatum != null"}) protected RecalDatumNode(final T recalDatum, final double fixedPenalty) { this(recalDatum, fixedPenalty, new HashSet>()); } + @Requires({"recalDatum != null", "subnodes != null"}) protected RecalDatumNode(final T recalDatum, final double fixedPenalty, final Set> subnodes) { this.recalDatum = recalDatum; this.fixedPenalty = fixedPenalty; this.subnodes = new HashSet>(subnodes); } + /** + * Get the recal data associated with this node + * @return + */ + @Ensures("result != null") public T getRecalDatum() { return recalDatum; } + /** + * The set of all subnodes of this tree. May be modified. + * @return + */ + @Ensures("result != null") public Set> getSubnodes() { return subnodes; } + /** + * Return the fixed penalty, if set, or else the the calculated penalty for this node + * @return + */ public double getPenalty() { if ( fixedPenalty != UNINITIALIZED ) return fixedPenalty; @@ -62,6 +86,17 @@ public double getPenalty() { return calcPenalty(); } + /** + * Set the fixed penalty for this node to a fresh calculation from calcPenalty + * + * This is important in the case where you want to compute the penalty from a full + * tree and then chop the tree up afterwards while considering the previous penalties. + * If you don't call this function then manipulating the tree may result in the + * penalty functions changing with changes in the tree. + * + * @param doEntireTree recurse into all subnodes? + * @return the fixed penalty for this node + */ public double calcAndSetFixedPenalty(final boolean doEntireTree) { fixedPenalty = calcPenalty(); if ( doEntireTree ) @@ -70,15 +105,41 @@ public double calcAndSetFixedPenalty(final boolean doEntireTree) { return fixedPenalty; } + /** + * Add node to the set of subnodes of this node + * @param sub + */ + @Requires("sub != null") public void addSubnode(final RecalDatumNode sub) { subnodes.add(sub); } + /** + * Is this a leaf node (i.e., has no subnodes)? + * @return + */ public boolean isLeaf() { return subnodes.isEmpty(); } - public int getNumBranches() { + /** + * Is this node immediately above only leaf nodes? + * + * @return + */ + public boolean isAboveOnlyLeaves() { + for ( final RecalDatumNode sub : subnodes ) + if ( ! sub.isLeaf() ) + return false; + return true; + } + + /** + * What's the immediate number of subnodes from this node? + * @return + */ + @Ensures("result >= 0") + public int getNumSubnodes() { return subnodes.size(); } @@ -89,6 +150,8 @@ public int getNumBranches() { * definition have 0 penalty unless they represent a pruned tree with underlying -- but now * pruned -- subtrees * + * TODO -- can we really just add together the chi2 values? + * * @return */ public double totalPenalty() { @@ -102,6 +165,10 @@ public double totalPenalty() { } } + /** + * What's the longest branch from this node to any leaf? + * @return + */ public int maxDepth() { int subMax = 0; for ( final RecalDatumNode sub : subnodes ) @@ -109,6 +176,11 @@ public int maxDepth() { return subMax + 1; } + /** + * What's the shortest branch from this node to any leaf? Includes this node + * @return + */ + @Ensures("result > 0") public int minDepth() { if ( isLeaf() ) return 1; @@ -120,6 +192,11 @@ public int minDepth() { } } + /** + * Return the number of nodes, including this one, reachable from this node + * @return + */ + @Ensures("result > 0") public int size() { int size = 1; for ( final RecalDatumNode sub : subnodes ) @@ -127,6 +204,12 @@ public int size() { return size; } + /** + * Count the number of leaf nodes reachable from this node + * + * @return + */ + @Ensures("result >= 0") public int numLeaves() { if ( isLeaf() ) return 1; @@ -138,44 +221,37 @@ public int numLeaves() { } } + /** + * Calculate the chi^2 penalty among subnodes of this node. The chi^2 value + * indicates the degree of independence of the implied error rates among the + * immediate subnodes + * + * @return the chi2 penalty, or 0.0 if it cannot be calculated + */ private double calcPenalty() { - if ( USE_CHI2 ) - return calcPenaltyChi2(); - else - return calcPenaltyLog10(getRecalDatum().getEmpiricalErrorRate()); - } - - private double calcPenaltyChi2() { if ( isLeaf() ) return 0.0; + else if ( subnodes.size() == 1 ) + // only one value, so its free to merge away + return 0.0; else { final long[][] counts = new long[subnodes.size()][2]; int i = 0; - for ( RecalDatumNode subnode : subnodes ) { - counts[i][0] = subnode.getRecalDatum().getNumMismatches(); - counts[i][1] = subnode.getRecalDatum().getNumObservations(); + for ( final RecalDatumNode subnode : subnodes ) { + // use the yates correction to help avoid all zeros => NaN + counts[i][0] = subnode.getRecalDatum().getNumMismatches() + 1; + counts[i][1] = subnode.getRecalDatum().getNumObservations() + 2; i++; } final double chi2 = new ChiSquareTestImpl().chiSquare(counts); -// StringBuilder x = new StringBuilder(); -// StringBuilder y = new StringBuilder(); -// for ( int k = 0; k < counts.length; k++) { -// if ( k != 0 ) { -// x.append(", "); -// y.append(", "); -// } -// x.append(counts[k][0]); -// y.append(counts[k][1]); -// } -// logger.info("x = c(" + x.toString() + ")"); -// logger.info("y = c(" + y.toString() + ")"); -// logger.info("chi2 = " + chi2); + // make sure things are reasonable and fail early if not + if (Double.isInfinite(chi2) || Double.isNaN(chi2)) + throw new ReviewedStingException("chi2 value is " + chi2 + " at " + getRecalDatum()); return chi2; - //return Math.log10(chi2); } } @@ -216,11 +292,17 @@ private double calcPenaltyLog10(final double globalErrorRate) { } } + /** + * Return a freshly allocated tree prunes to have no more than maxDepth from the root to any leaf + * + * @param maxDepth + * @return + */ public RecalDatumNode pruneToDepth(final int maxDepth) { if ( maxDepth < 1 ) throw new IllegalArgumentException("maxDepth < 1"); else { - final Set> subPruned = new HashSet>(getNumBranches()); + final Set> subPruned = new HashSet>(getNumSubnodes()); if ( maxDepth > 1 ) for ( final RecalDatumNode sub : subnodes ) subPruned.add(sub.pruneToDepth(maxDepth - 1)); @@ -228,12 +310,21 @@ public RecalDatumNode pruneToDepth(final int maxDepth) { } } + /** + * Return a freshly allocated tree with to no more than maxElements in order of penalty + * + * Note that nodes must have fixed penalties to this algorithm will fail. + * + * @param maxElements + * @return + */ public RecalDatumNode pruneByPenalty(final int maxElements) { RecalDatumNode root = this; while ( root.size() > maxElements ) { // remove the lowest penalty element, and continue root = root.removeLowestPenaltyNode(); + logger.debug("pruneByPenalty root size is now " + root.size() + " of max " + maxElements); } // our size is below the target, so we are good, return @@ -241,15 +332,15 @@ public RecalDatumNode pruneByPenalty(final int maxElements) { } /** - * Find the lowest penalty node in the tree, and return a tree without it + * Find the lowest penalty above leaf node in the tree, and return a tree without it * * Note this excludes the current (root) node * * @return */ private RecalDatumNode removeLowestPenaltyNode() { - final Pair, Double> nodeToRemove = getMinPenaltyNode(); - logger.info("Removing " + nodeToRemove.getFirst() + " with penalty " + nodeToRemove.getSecond()); + final Pair, Double> nodeToRemove = getMinPenaltyAboveLeafNode(); + //logger.info("Removing " + nodeToRemove.getFirst() + " with penalty " + nodeToRemove.getSecond()); final Pair, Boolean> result = removeNode(nodeToRemove.getFirst()); @@ -262,20 +353,37 @@ private RecalDatumNode removeLowestPenaltyNode() { return oneRemoved; } - private Pair, Double> getMinPenaltyNode() { - final double myValue = isLeaf() ? Double.MAX_VALUE : getPenalty(); - Pair, Double> maxNode = new Pair, Double>(this, myValue); - - for ( final RecalDatumNode sub : subnodes ) { - final Pair, Double> subFind = sub.getMinPenaltyNode(); - if ( subFind.getSecond() < maxNode.getSecond() ) { - maxNode = subFind; + /** + * Finds in the tree the node with the lowest penalty whose subnodes are all leaves + * + * @return + */ + private Pair, Double> getMinPenaltyAboveLeafNode() { + if ( isLeaf() ) + // not allowed to remove leafs directly + return null; + if ( isAboveOnlyLeaves() ) + // we only consider removing nodes above all leaves + return new Pair, Double>(this, getPenalty()); + else { + // just recurse, taking the result with the min penalty of all subnodes + Pair, Double> minNode = null; + for ( final RecalDatumNode sub : subnodes ) { + final Pair, Double> subFind = sub.getMinPenaltyAboveLeafNode(); + if ( subFind != null && (minNode == null || subFind.getSecond() < minNode.getSecond()) ) { + minNode = subFind; + } } + return minNode; } - - return maxNode; } + /** + * Return a freshly allocated tree without the node nodeToRemove + * + * @param nodeToRemove + * @return + */ private Pair, Boolean> removeNode(final RecalDatumNode nodeToRemove) { if ( this == nodeToRemove ) { if ( isLeaf() ) @@ -288,7 +396,7 @@ private Pair, Boolean> removeNode(final RecalDatumNode node boolean removedSomething = false; // our sub nodes with the penalty node removed - final Set> sub = new HashSet>(getNumBranches()); + final Set> sub = new HashSet>(getNumSubnodes()); for ( final RecalDatumNode sub1 : subnodes ) { if ( removedSomething ) { @@ -306,4 +414,29 @@ private Pair, Boolean> removeNode(final RecalDatumNode node return new Pair, Boolean>(node, removedSomething); } } + + /** + * Return a collection of all of the data in the leaf nodes of this tree + * + * @return + */ + public Collection getAllLeaves() { + final LinkedList list = new LinkedList(); + getAllLeavesRec(list); + return list; + } + + /** + * Helpful recursive function for getAllLeaves() + * + * @param list the destination for the list of leaves + */ + private void getAllLeavesRec(final LinkedList list) { + if ( isLeaf() ) + list.add(getRecalDatum()); + else { + for ( final RecalDatumNode sub : subnodes ) + sub.getAllLeavesRec(list); + } + } } diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/AdaptiveContextUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/recalibration/AdaptiveContextUnitTest.java new file mode 100644 index 0000000000..c07c084b8a --- /dev/null +++ b/public/java/test/org/broadinstitute/sting/utils/recalibration/AdaptiveContextUnitTest.java @@ -0,0 +1,64 @@ +package org.broadinstitute.sting.utils.recalibration; + +import org.broadinstitute.sting.BaseTest; +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; + +/** + * User: depristo + * Date: 8/3/12 + * Time: 12:26 PM + * To change this template use File | Settings | File Templates. + */ +public class AdaptiveContextUnitTest { + // TODO + // TODO actually need unit tests when we have validated the value of this approach + // TODO particularly before we attempt to optimize the algorithm + // TODO + + // -------------------------------------------------------------------------------- + // + // Provider + // + // -------------------------------------------------------------------------------- + + private class AdaptiveContextTestProvider extends BaseTest.TestDataProvider { + final RecalDatumNode pruned; + final RecalDatumNode full; + + private AdaptiveContextTestProvider(Class c, RecalDatumNode pruned, RecalDatumNode full) { + super(AdaptiveContextTestProvider.class); + this.pruned = pruned; + this.full = full; + } + } + + private RecalDatumNode makeTree(final String context, final int N, final int M, + final RecalDatumNode ... sub) { + final ContextDatum contextDatum = new ContextDatum(context, N, M); + final RecalDatumNode node = new RecalDatumNode(contextDatum); + for ( final RecalDatumNode sub1 : sub ) { + node.addSubnode(sub1); + } + return node; + } + + @DataProvider(name = "AdaptiveContextTestProvider") + public Object[][] makeRecalDatumTestProvider() { +// final RecalDatumNode prune1 = +// makeTree("A", 10, 1, +// makeTree("AA", 11, 2), +// makeTree("AC", 12, 3), +// makeTree("AG", 13, 4), +// makeTree("AT", 14, 5)); +// +// new AdaptiveContextTestProvider(pruned, full); + + return AdaptiveContextTestProvider.getTests(AdaptiveContextTestProvider.class); + } + + @Test(dataProvider = "AdaptiveContextTestProvider") + public void testAdaptiveContextFill(AdaptiveContextTestProvider cfg) { + + } +} diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/QualQuantizerUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/recalibration/QualQuantizerUnitTest.java new file mode 100644 index 0000000000..0ff2eaf03a --- /dev/null +++ b/public/java/test/org/broadinstitute/sting/utils/recalibration/QualQuantizerUnitTest.java @@ -0,0 +1,169 @@ +/* + * 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. + */ + +// our package +package org.broadinstitute.sting.utils.recalibration; + + +// the imports for unit testing. + + +import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.sting.utils.QualityUtils; +import org.broadinstitute.sting.utils.Utils; +import org.testng.Assert; +import org.testng.annotations.BeforeSuite; +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; + + +public class QualQuantizerUnitTest extends BaseTest { + @BeforeSuite + public void before() { + + } + + // -------------------------------------------------------------------------------- + // + // merge case Provider + // + // -------------------------------------------------------------------------------- + + private class QualIntervalTestProvider extends TestDataProvider { + final QualQuantizer.QualInterval left, right; + int exError, exTotal, exQual; + double exErrorRate; + + private QualIntervalTestProvider(int leftE, int leftN, int rightE, int rightN, int exError, int exTotal) { + super(QualIntervalTestProvider.class); + + QualQuantizer qq = new QualQuantizer(0); + left = qq.new QualInterval(10, 10, leftN, leftE, 0); + right = qq.new QualInterval(11, 11, rightN, rightE, 0); + + this.exError = exError; + this.exTotal = exTotal; + this.exErrorRate = (leftE + rightE + 1) / (1.0 * (leftN + rightN + 1)); + this.exQual = QualityUtils.probToQual(1-this.exErrorRate, 0); + } + } + + @DataProvider(name = "QualIntervalTestProvider") + public Object[][] makeQualIntervalTestProvider() { + new QualIntervalTestProvider(10, 100, 10, 1000, 20, 1100); + new QualIntervalTestProvider(0, 100, 10, 900, 10, 1000); + new QualIntervalTestProvider(10, 900, 0, 100, 10, 1000); + new QualIntervalTestProvider(0, 0, 10, 100, 10, 100); + new QualIntervalTestProvider(1, 10, 9, 90, 10, 100); + new QualIntervalTestProvider(1, 10, 9, 100000, 10, 100010); + new QualIntervalTestProvider(1, 10, 9, 1000000, 10,1000010); + + return QualIntervalTestProvider.getTests(QualIntervalTestProvider.class); + } + + @Test(dataProvider = "QualIntervalTestProvider") + public void testQualInterval(QualIntervalTestProvider cfg) { + QualQuantizer.QualInterval merged = cfg.left.merge(cfg.right); + Assert.assertEquals(merged.nErrors, cfg.exError); + Assert.assertEquals(merged.nObservations, cfg.exTotal); + Assert.assertEquals(merged.getErrorRate(), cfg.exErrorRate); + Assert.assertEquals(merged.getQual(), cfg.exQual); + } + + @Test + public void testMinInterestingQual() { + for ( int q = 0; q < 15; q++ ) { + for ( int minQual = 0; minQual <= 10; minQual ++ ) { + QualQuantizer qq = new QualQuantizer(minQual); + QualQuantizer.QualInterval left = qq.new QualInterval(q, q, 100, 10, 0); + QualQuantizer.QualInterval right = qq.new QualInterval(q+1, q+1, 1000, 100, 0); + + QualQuantizer.QualInterval merged = left.merge(right); + boolean shouldBeFree = q+1 <= minQual; + if ( shouldBeFree ) + Assert.assertEquals(merged.getPenalty(), 0.0); + else + Assert.assertTrue(merged.getPenalty() > 0.0); + } + } + } + + + // -------------------------------------------------------------------------------- + // + // High-level case Provider + // + // -------------------------------------------------------------------------------- + + private class QuantizerTestProvider extends TestDataProvider { + final List nObservationsPerQual = new ArrayList(); + final int nLevels; + final List expectedMap; + + private QuantizerTestProvider(final List nObservationsPerQual, final int nLevels, final List expectedMap) { + super(QuantizerTestProvider.class); + + for ( int x : nObservationsPerQual ) + this.nObservationsPerQual.add((long)x); + this.nLevels = nLevels; + this.expectedMap = expectedMap; + } + + @Override + public String toString() { + return String.format("QQTest nLevels=%d nObs=[%s] map=[%s]", + nLevels, Utils.join(",", nObservationsPerQual), Utils.join(",", expectedMap)); + } + } + + @DataProvider(name = "QuantizerTestProvider") + public Object[][] makeQuantizerTestProvider() { + List allQ2 = Arrays.asList(0, 0, 1000, 0, 0); + + new QuantizerTestProvider(allQ2, 5, Arrays.asList(0, 1, 2, 3, 4)); + new QuantizerTestProvider(allQ2, 1, Arrays.asList(2, 2, 2, 2, 2)); + + new QuantizerTestProvider(Arrays.asList(0, 0, 1000, 0, 1000), 2, Arrays.asList(2, 2, 2, 2, 4)); + new QuantizerTestProvider(Arrays.asList(0, 0, 1000, 1, 1000), 2, Arrays.asList(2, 2, 2, 4, 4)); + new QuantizerTestProvider(Arrays.asList(0, 0, 1000, 10, 1000), 2, Arrays.asList(2, 2, 2, 2, 4)); + + return QuantizerTestProvider.getTests(QuantizerTestProvider.class); + } + + @Test(dataProvider = "QuantizerTestProvider", enabled = true) + public void testQuantizer(QuantizerTestProvider cfg) { + QualQuantizer qq = new QualQuantizer(cfg.nObservationsPerQual, cfg.nLevels, 0); + logger.warn("cfg: " + cfg); + for ( int i = 0; i < cfg.expectedMap.size(); i++) { + int expected = cfg.expectedMap.get(i); + int observed = qq.originalToQuantizedMap.get(i); + //logger.warn(String.format(" qq map: %s : %d => %d", i, expected, observed)); + Assert.assertEquals(observed, expected); + } + } +} \ No newline at end of file diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java new file mode 100644 index 0000000000..33985e0ac4 --- /dev/null +++ b/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java @@ -0,0 +1,154 @@ +/* + * 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. + */ + +// our package +package org.broadinstitute.sting.utils.recalibration; + + +// the imports for unit testing. + + +import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.sting.utils.QualityUtils; +import org.broadinstitute.sting.utils.Utils; +import org.testng.Assert; +import org.testng.annotations.BeforeSuite; +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; + + +public class RecalDatumUnitTest extends BaseTest { + + // -------------------------------------------------------------------------------- + // + // merge case Provider + // + // -------------------------------------------------------------------------------- + + private class RecalDatumTestProvider extends TestDataProvider { + int exError, exTotal, reportedQual; + + private RecalDatumTestProvider(int E, int N, int reportedQual) { + super(RecalDatumTestProvider.class); + + this.exError = E; + this.exTotal = N; + this.reportedQual = reportedQual; + } + + public double getErrorRate() { + return (exError + 1) / (1.0 * (exTotal + 2)); + } + + public double getErrorRatePhredScaled() { + return QualityUtils.phredScaleErrorRate(getErrorRate()); + } + + public int getReportedQual() { + return reportedQual; + } + + public RecalDatum makeRecalDatum() { + return new RecalDatum(exTotal, exError, (byte)getReportedQual()); + } + + @Override + public String toString() { + return String.format("exError=%d, exTotal=%d, reportedQual=%d", exError, exTotal, reportedQual); + } + } + + @DataProvider(name = "RecalDatumTestProvider") + public Object[][] makeRecalDatumTestProvider() { + for ( int E : Arrays.asList(1, 10, 100, 1000, 10000) ) + for ( int N : Arrays.asList(10, 100, 1000, 10000, 100000, 1000000) ) + for ( int reportedQual : Arrays.asList(10, 20) ) + if ( E <= N ) + new RecalDatumTestProvider(E, N, reportedQual); + return RecalDatumTestProvider.getTests(RecalDatumTestProvider.class); + } + + @Test(dataProvider = "RecalDatumTestProvider") + public void testRecalDatumBasics(RecalDatumTestProvider cfg) { + final RecalDatum datum = cfg.makeRecalDatum(); + assertBasicFeaturesOfRecalDatum(datum, cfg); + } + + private static void assertBasicFeaturesOfRecalDatum(final RecalDatum datum, final RecalDatumTestProvider cfg) { + Assert.assertEquals(datum.getNumMismatches(), cfg.exError); + Assert.assertEquals(datum.getNumObservations(), cfg.exTotal); + if ( cfg.getReportedQual() != -1 ) + Assert.assertEquals(datum.getEstimatedQReportedAsByte(), cfg.getReportedQual()); + BaseTest.assertEqualsDoubleSmart(datum.getEmpiricalQuality(), cfg.getErrorRatePhredScaled()); + BaseTest.assertEqualsDoubleSmart(datum.getEmpiricalErrorRate(), cfg.getErrorRate()); + } + + @Test(dataProvider = "RecalDatumTestProvider") + public void testRecalDatumCopyAndCombine(RecalDatumTestProvider cfg) { + final RecalDatum datum = cfg.makeRecalDatum(); + final RecalDatum copy = new RecalDatum(datum); + assertBasicFeaturesOfRecalDatum(copy, cfg); + + RecalDatumTestProvider combinedCfg = new RecalDatumTestProvider(cfg.exError * 2, cfg.exTotal * 2, cfg.reportedQual); + copy.combine(datum); + assertBasicFeaturesOfRecalDatum(copy, combinedCfg); + } + + @Test(dataProvider = "RecalDatumTestProvider") + public void testRecalDatumModification(RecalDatumTestProvider cfg) { + RecalDatum datum = cfg.makeRecalDatum(); + datum.setEmpiricalQuality(10.1); + Assert.assertEquals(datum.getEmpiricalQuality(), 10.1); + + datum.setEstimatedQReported(10.1); + Assert.assertEquals(datum.getEstimatedQReported(), 10.1); + Assert.assertEquals(datum.getEstimatedQReportedAsByte(), 10); + + datum = cfg.makeRecalDatum(); + cfg.exTotal = 100000; + datum.setNumObservations(cfg.exTotal); + assertBasicFeaturesOfRecalDatum(datum, cfg); + + datum = cfg.makeRecalDatum(); + cfg.exError = 1000; + datum.setNumMismatches(cfg.exError); + assertBasicFeaturesOfRecalDatum(datum, cfg); + + datum = cfg.makeRecalDatum(); + datum.increment(true); + cfg.exError++; + cfg.exTotal++; + assertBasicFeaturesOfRecalDatum(datum, cfg); + + datum = cfg.makeRecalDatum(); + datum.increment(10, 5); + cfg.exError += 5; + cfg.exTotal += 10; + assertBasicFeaturesOfRecalDatum(datum, cfg); + } +} \ No newline at end of file From 187f363fc7ea8d4ca6ca000cd833a4be47d4a5a3 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Sun, 5 Aug 2012 12:29:10 -0400 Subject: [PATCH 063/176] Bug fixes related to the changes in allele padding. If a haplotype started with an insertion it led to array index out of bounds. Haplotype allele insert function is now very simple because all alleles are treated the same way. HaplotypeUnitTest now uses a variant context instead of creating Allele objects directly. --- .../VariantRecalibrator.java | 2 +- .../broadinstitute/sting/utils/Haplotype.java | 51 ++++--------------- .../sting/utils/HaplotypeUnitTest.java | 39 +++++++------- 3 files changed, 33 insertions(+), 59 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java index ab2ff61769..c670ad2fdb 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java @@ -331,7 +331,7 @@ public void onTraversalDone( final ExpandingArrayList reduceSum ) // Find the filtering lodCutoff for display on the model PDFs. Red variants are those which were below the cutoff and filtered out of the final callset. double lodCutoff = 0.0; for( final Tranche tranche : tranches ) { - if( MathUtils.compareDoubles(tranche.ts, TS_FILTER_LEVEL, 0.0001)==0 ) { + if( MathUtils.compareDoubles(tranche.ts, TS_FILTER_LEVEL, 0.0001) == 0 ) { lodCutoff = tranche.minVQSLod; } } diff --git a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java index 54442622f5..188d010983 100755 --- a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java +++ b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java @@ -27,6 +27,7 @@ import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import net.sf.samtools.Cigar; +import org.apache.commons.lang.ArrayUtils; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.sam.ReadUtils; @@ -160,49 +161,17 @@ public void setCigar( final Cigar cigar ) { } @Requires({"refInsertLocation >= 0"}) - public Haplotype insertAllele( final Allele refAllele, final Allele altAllele, int refInsertLocation ) { - - if( refAllele.length() != altAllele.length() ) { refInsertLocation++; } + public Haplotype insertAllele( final Allele refAllele, final Allele altAllele, final int refInsertLocation ) { + // refInsertLocation is in ref haplotype offset coordinates NOT genomic coordinates final int haplotypeInsertLocation = ReadUtils.getReadCoordinateForReferenceCoordinate(alignmentStartHapwrtRef, cigar, refInsertLocation, ReadUtils.ClippingTail.RIGHT_TAIL, true); - if( haplotypeInsertLocation == -1 ) { // desired change falls inside deletion so don't bother creating a new haplotype - return new Haplotype(bases.clone()); - } - byte[] newHaplotype; - - try { - if( refAllele.length() == altAllele.length() ) { // SNP or MNP - newHaplotype = bases.clone(); - for( int iii = 0; iii < altAllele.length(); iii++ ) { - newHaplotype[haplotypeInsertLocation+iii] = altAllele.getBases()[iii]; - } - } else if( refAllele.length() < altAllele.length() ) { // insertion - final int altAlleleLength = altAllele.length() - 1; - newHaplotype = new byte[bases.length + altAlleleLength]; - for( int iii = 0; iii < bases.length; iii++ ) { - newHaplotype[iii] = bases[iii]; - } - for( int iii = newHaplotype.length - 1; iii > haplotypeInsertLocation + altAlleleLength - 1; iii-- ) { - newHaplotype[iii] = newHaplotype[iii-altAlleleLength]; - } - for( int iii = 0; iii < altAlleleLength; iii++ ) { - newHaplotype[haplotypeInsertLocation+iii] = altAllele.getBases()[iii+1]; - } - } else { // deletion - final int shift = refAllele.length() - altAllele.length(); - final int altAlleleLength = altAllele.length() - 1; - newHaplotype = new byte[bases.length - shift]; - for( int iii = 0; iii < haplotypeInsertLocation + altAlleleLength; iii++ ) { - newHaplotype[iii] = bases[iii]; - } - for( int iii = haplotypeInsertLocation + altAlleleLength; iii < newHaplotype.length; iii++ ) { - newHaplotype[iii] = bases[iii+shift]; - } - } - } catch (Exception e) { // event already on haplotype is too large/complex to insert another allele, most likely because of not enough reference padding - return new Haplotype(bases.clone()); + if( haplotypeInsertLocation == -1 || haplotypeInsertLocation + refAllele.length() >= bases.length ) { // desired change falls inside deletion so don't bother creating a new haplotype + return null; } - - return new Haplotype(newHaplotype); + byte[] newHaplotypeBases = new byte[]{}; + newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases, ArrayUtils.subarray(bases, 0, haplotypeInsertLocation)); // bases before the variant + newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases, altAllele.getBases()); // the alt allele of the variant + newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases, ArrayUtils.subarray(bases, haplotypeInsertLocation + refAllele.length(), bases.length)); // bases after the variant + return new Haplotype(newHaplotypeBases); } public static LinkedHashMap makeHaplotypeListFromAlleles(final List alleleList, diff --git a/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java index 161eefa8fc..ddffb6e4cb 100644 --- a/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java @@ -31,6 +31,8 @@ import net.sf.samtools.CigarOperator; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; @@ -53,11 +55,11 @@ public void testSimpleInsertionAllele() { h1CigarList.add(new CigarElement(bases.length(), CigarOperator.M)); final Cigar h1Cigar = new Cigar(h1CigarList); String h1bases = "AACTTCTGGTCAACTGGTCAACTGGTCAACTGGTCA"; - basicInsertTest("A", "AACTT", 1, h1Cigar, bases, h1bases); - h1bases = "ACTGGTCACTTAACTGGTCAACTGGTCAACTGGTCA"; + basicInsertTest("A", "AACTT", 0, h1Cigar, bases, h1bases); + h1bases = "ACTGGTCAACTTACTGGTCAACTGGTCAACTGGTCA"; basicInsertTest("A", "AACTT", 7, h1Cigar, bases, h1bases); h1bases = "ACTGGTCAACTGGTCAAACTTCTGGTCAACTGGTCA"; - basicInsertTest("A", "AACTT", 17, h1Cigar, bases, h1bases); + basicInsertTest("A", "AACTT", 16, h1Cigar, bases, h1bases); } @Test @@ -68,11 +70,11 @@ public void testSimpleDeletionAllele() { h1CigarList.add(new CigarElement(bases.length(), CigarOperator.M)); final Cigar h1Cigar = new Cigar(h1CigarList); String h1bases = "ATCAACTGGTCAACTGGTCAACTGGTCA"; - basicInsertTest("AACTT", "A", 1, h1Cigar, bases, h1bases); - h1bases = "ACTGGTCGGTCAACTGGTCAACTGGTCA"; - basicInsertTest("AACTT", "A", 7, h1Cigar, bases, h1bases); + basicInsertTest("ACTGG", "A", 0, h1Cigar, bases, h1bases); + h1bases = "ACTGGTCAGTCAACTGGTCAACTGGTCA"; + basicInsertTest("AACTG", "A", 7, h1Cigar, bases, h1bases); h1bases = "ACTGGTCAACTGGTCAATCAACTGGTCA"; - basicInsertTest("AACTT", "A", 17, h1Cigar, bases, h1bases); + basicInsertTest("ACTGG", "A", 16, h1Cigar, bases, h1bases); } @Test @@ -102,11 +104,11 @@ public void testComplexInsertionAllele() { h1CigarList.add(new CigarElement(7 + 4, CigarOperator.M)); final Cigar h1Cigar = new Cigar(h1CigarList); String h1bases = "AACTTTCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC"; - basicInsertTest("A", "AACTT", 1, h1Cigar, bases, h1bases); + basicInsertTest("A", "AACTT", 0, h1Cigar, bases, h1bases); h1bases = "ATCG" + "CCGGCCGGCC" + "ATCACTTGATCG" + "AGGGGGA" + "AGGC"; - basicInsertTest("A", "AACTT", 7, h1Cigar, bases, h1bases); + basicInsertTest("C", "CACTT", 6, h1Cigar, bases, h1bases); h1bases = "ATCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGACTTGGGGA" + "AGGC"; - basicInsertTest("A", "AACTT", 17, h1Cigar, bases, h1bases); + basicInsertTest("G", "GACTT", 16, h1Cigar, bases, h1bases); } @Test @@ -120,12 +122,12 @@ public void testComplexDeletionAllele() { h1CigarList.add(new CigarElement(3, CigarOperator.D)); h1CigarList.add(new CigarElement(7 + 4, CigarOperator.M)); final Cigar h1Cigar = new Cigar(h1CigarList); - String h1bases = "A" + "CGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC"; - basicInsertTest("AACTT", "A", 1, h1Cigar, bases, h1bases); - h1bases = "ATCG" + "CCGGCCGGCC" + "ATCG" + "AGGGGGA" + "AGGC"; - basicInsertTest("AACTT", "A", 7, h1Cigar, bases, h1bases); + String h1bases = "A" + "CCGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC"; + basicInsertTest("ATCG", "A", 0, h1Cigar, bases, h1bases); + h1bases = "ATCG" + "CCGGCCGGCC" + "ATAAAG" + "AGGGGGA" + "AGGC"; + basicInsertTest("CGATC", "AAA", 6, h1Cigar, bases, h1bases); h1bases = "ATCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGA" + "AGGC"; - basicInsertTest("AACTT", "A", 17, h1Cigar, bases, h1bases); + basicInsertTest("GGGGG", "G", 16, h1Cigar, bases, h1bases); } @Test @@ -148,13 +150,16 @@ public void testComplexSNPAllele() { } private void basicInsertTest(String ref, String alt, int loc, Cigar cigar, String hap, String newHap) { - final int INDEL_PADDING_BASE = (ref.length() == alt.length() ? 0 : 1); final Haplotype h = new Haplotype(hap.getBytes()); final Allele h1refAllele = Allele.create(ref, true); final Allele h1altAllele = Allele.create(alt, false); + final ArrayList alleles = new ArrayList(); + alleles.add(h1refAllele); + alleles.add(h1altAllele); + final VariantContext vc = new VariantContextBuilder().alleles(alleles).loc("1", loc, loc + h1refAllele.getBases().length - 1).make(); h.setAlignmentStartHapwrtRef(0); h.setCigar(cigar); - final Haplotype h1 = h.insertAllele(h1refAllele, h1altAllele, loc - INDEL_PADDING_BASE); + final Haplotype h1 = h.insertAllele(vc.getReference(), vc.getAlternateAllele(0), loc); final Haplotype h1expected = new Haplotype(newHap.getBytes()); Assert.assertEquals(h1, h1expected); } From 43ccca4d2bb8ade7ee80190ec2d855ffd792d3a7 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 6 Aug 2012 11:19:54 -0400 Subject: [PATCH 064/176] Prevent NumberFormatExceptions when parsing the VCF POS field --- .../sting/utils/codecs/vcf/AbstractVCFCodec.java | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java index 996cef8a4f..043e5e1851 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java @@ -237,7 +237,12 @@ private VariantContext parseVCFLine(final String[] parts, final boolean includeG // parse out the required fields final String chr = getCachedString(parts[0]); builder.chr(chr); - int pos = Integer.valueOf(parts[1]); + int pos = -1; + try { + pos = Integer.valueOf(parts[1]); + } catch (NumberFormatException e) { + generateException(parts[1] + " is not a valid start position in the VCF format"); + } builder.start(pos); if ( parts[2].length() == 0 ) From c4a850dfa679cb747bde82857366d04c2f5889dd Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 6 Aug 2012 11:31:18 -0400 Subject: [PATCH 065/176] Update -maxAlleles argument to -maxAltAlleles to make it more accurate. The hidden GSA production -capMaxAllelesForIndels argument also gets updated. --- .../gatk/walkers/genotyper/UnifiedArgumentCollection.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java index 020f7904d8..69f1176cce 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java @@ -114,11 +114,11 @@ public class UnifiedArgumentCollection { * that you not play around with this parameter. */ @Advanced - @Argument(fullName = "max_alternate_alleles", shortName = "maxAlleles", doc = "Maximum number of alternate alleles to genotype", required = false) + @Argument(fullName = "max_alternate_alleles", shortName = "maxAltAlleles", doc = "Maximum number of alternate alleles to genotype", required = false) public int MAX_ALTERNATE_ALLELES = 3; @Hidden - @Argument(fullName = "cap_max_alternate_alleles_for_indels", shortName = "capMaxAllelesForIndels", doc = "Cap the maximum number of alternate alleles to genotype for indel calls at 2; overrides the --max_alternate_alleles argument; GSA production use only", required = false) + @Argument(fullName = "cap_max_alternate_alleles_for_indels", shortName = "capMaxAltAllelesForIndels", doc = "Cap the maximum number of alternate alleles to genotype for indel calls at 2; overrides the --max_alternate_alleles argument; GSA production use only", required = false) public boolean CAP_MAX_ALTERNATE_ALLELES_FOR_INDELS = false; // indel-related arguments From b06799c970659d758e229659f27d9fbb57c9c4c9 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Mon, 6 Aug 2012 11:40:07 -0400 Subject: [PATCH 066/176] Merging together the computeDiploidHaplotypeLikelihoods functions in the HaplotypeCaller's LikelihoodEngine so they both benefit from the ReducedRead's RepresentativeCount From 6d0a371ead2b59652545d3a6c5aae92f087dac74 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 3 Aug 2012 17:53:46 -0400 Subject: [PATCH 067/176] Bug fixes and misc. improvements to running the adaptive context tools -- Better output file name defaults -- Fixed nasty bug where I included non-existant quals in the contexts to process because they showed up in the Cycle covariate -- Data is processed in qual order now, so it's easier to see progress -- Logger messages explaining where we are in the process -- When in UPDATE mode we still write out the information for an equivalent prune by depth for post analysis --- .../sting/utils/recalibration/RecalDatumNode.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java index 1409af7d0a..e6ec6a520a 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java @@ -324,7 +324,8 @@ public RecalDatumNode pruneByPenalty(final int maxElements) { while ( root.size() > maxElements ) { // remove the lowest penalty element, and continue root = root.removeLowestPenaltyNode(); - logger.debug("pruneByPenalty root size is now " + root.size() + " of max " + maxElements); + if ( logger.isDebugEnabled() ) + logger.debug("pruneByPenalty root size is now " + root.size() + " of max " + maxElements); } // our size is below the target, so we are good, return From 20e89221345f069eb00cfe578c3542705bc32fa3 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Sat, 4 Aug 2012 11:28:17 -0400 Subject: [PATCH 068/176] Major bugfix for adaptive contexts -- Basically I was treating the context history in the wrong direction, effectively predicting the further bases in the context based on the closer one. Totally backward. Updated the code to build the tree in the right direction. -- Added a few more useful outputs for analysis (minPenalty and maxPenalty) -- Misc. cleanup of the code -- Overall I'm not 100% certain this is even the right way to think about the problem. Clearly this is producing a reasonable output but the sum of chi2 values over the entire tree is just enormous. Perhaps a MCMC convergence / sampling criterion would be a better way to think about this problem? --- .../utils/recalibration/AdaptiveContext.java | 37 +++++++++++++++---- .../utils/recalibration/RecalDatumNode.java | 22 +++++++++++ 2 files changed, 51 insertions(+), 8 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/AdaptiveContext.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/AdaptiveContext.java index 083b8af64b..b8a2eaf052 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/AdaptiveContext.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/AdaptiveContext.java @@ -21,22 +21,42 @@ private AdaptiveContext() {} * observation and error counts of their parent. * * This algorithm produces data consistent with the standard output in a BQSR recal - * file for the Context covariate + * file for the Context covariate. + * + * Suppose you have input tree + * + * - x + * - A + * - C + * - T + * - C + * - T + * + * This will produce the following contexts with fill depth of 2 + * + * AA <- gets A info + * CA <- gets CA info + * GA <- gets A info + * TA <- get TA info + * .. for all 16 contexts * * @param root * @param fillDepth * @return */ - public static RecalDatumNode fillToDepth(final RecalDatumNode root, final int fillDepth) { + public static RecalDatumNode fillToDepth(final RecalDatumNode root, + final int fillDepth, + final boolean debugWriteN) { if ( root == null ) throw new IllegalArgumentException("root is null"); if ( fillDepth < 0 ) throw new IllegalArgumentException("fillDepth is < 0"); - return fillToDepthRec(root, fillDepth, 0); + return fillToDepthRec(root, fillDepth, 0, debugWriteN); } private static RecalDatumNode fillToDepthRec(final RecalDatumNode parent, final int fillDepth, - final int currentDepth) { + final int currentDepth, + final boolean debugWriteN) { // three cases: // We are in the tree and so just recursively build // We have reached our depth goal, so just return the parent since we are done @@ -47,24 +67,25 @@ private static RecalDatumNode fillToDepthRec(final RecalDatumNode< final RecalDatumNode newParent = new RecalDatumNode(parent.getRecalDatum()); for ( final String base : Arrays.asList("A", "C", "G", "T")) { + final String subContextBases = base + parent.getRecalDatum().context; ContextDatum subContext; Set> subContexts; - final RecalDatumNode subNode = findSubcontext(parent.getRecalDatum().context + base, parent); + final RecalDatumNode subNode = findSubcontext(subContextBases, parent); if ( subNode != null ) { // we have a subnode corresponding to the expected one, just copy and recurse subContext = subNode.getRecalDatum(); subContexts = subNode.getSubnodes(); } else { // have to create a new one - subContext = new ContextDatum(parent.getRecalDatum().context + base, + subContext = new ContextDatum(debugWriteN ? ("N" + parent.getRecalDatum().context ) : subContextBases, parent.getRecalDatum().getNumObservations(), parent.getRecalDatum().getNumMismatches()); subContexts = Collections.emptySet(); } newParent.addSubnode( fillToDepthRec(new RecalDatumNode(subContext, subContexts), - fillDepth, currentDepth + 1)); + fillDepth, currentDepth + 1, debugWriteN)); } return newParent; } else { @@ -119,7 +140,7 @@ public static RecalDatumNode createTreeFromFlatContexts(final List parent = new RecalDatumNode(new ContextDatum(parentContext, 0, 0)); contextToNodes.put(parentContext, parent); - if ( parentContext != ContextDatum.ROOT_CONTEXT ) + if ( ! parent.getRecalDatum().isRootContext() ) remaining.add(parent); else root = parent; diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java index e6ec6a520a..e792a808df 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java @@ -165,6 +165,28 @@ public double totalPenalty() { } } + /** + * The maximum penalty among all nodes + * @return + */ + public double maxPenalty() { + double max = getPenalty(); + for ( final RecalDatumNode sub : subnodes ) + max = Math.max(max, sub.maxPenalty()); + return max; + } + + /** + * The minimum penalty among all nodes + * @return + */ + public double minPenalty() { + double min = getPenalty(); + for ( final RecalDatumNode sub : subnodes ) + min = Math.min(min, sub.minPenalty()); + return min; + } + /** * What's the longest branch from this node to any leaf? * @return From 0005d351e8b1eb58b21eea50c86f5e34c888e7a0 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Mon, 6 Aug 2012 11:42:12 -0400 Subject: [PATCH 069/176] Fixing public -> private dep --- .../utils/recalibration/AdaptiveContext.java | 175 ------------------ 1 file changed, 175 deletions(-) delete mode 100644 public/java/src/org/broadinstitute/sting/utils/recalibration/AdaptiveContext.java diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/AdaptiveContext.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/AdaptiveContext.java deleted file mode 100644 index b8a2eaf052..0000000000 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/AdaptiveContext.java +++ /dev/null @@ -1,175 +0,0 @@ -package org.broadinstitute.sting.utils.recalibration; - -import java.util.*; - -/** - * Functions for working with AdaptiveContexts - * - * User: depristo - * Date: 8/3/12 - * Time: 12:21 PM - * To change this template use File | Settings | File Templates. - */ -public class AdaptiveContext { - private AdaptiveContext() {} - - /** - * Return a freshly allocated tree filled in completely to fillDepth with - * all combinations of {A,C,G,T}^filldepth contexts. For nodes - * in the tree, they are simply copied. When the algorithm needs to - * generate new nodes (because they are missing) the subnodes inherit the - * observation and error counts of their parent. - * - * This algorithm produces data consistent with the standard output in a BQSR recal - * file for the Context covariate. - * - * Suppose you have input tree - * - * - x - * - A - * - C - * - T - * - C - * - T - * - * This will produce the following contexts with fill depth of 2 - * - * AA <- gets A info - * CA <- gets CA info - * GA <- gets A info - * TA <- get TA info - * .. for all 16 contexts - * - * @param root - * @param fillDepth - * @return - */ - public static RecalDatumNode fillToDepth(final RecalDatumNode root, - final int fillDepth, - final boolean debugWriteN) { - if ( root == null ) throw new IllegalArgumentException("root is null"); - if ( fillDepth < 0 ) throw new IllegalArgumentException("fillDepth is < 0"); - - return fillToDepthRec(root, fillDepth, 0, debugWriteN); - } - - private static RecalDatumNode fillToDepthRec(final RecalDatumNode parent, - final int fillDepth, - final int currentDepth, - final boolean debugWriteN) { - // three cases: - // We are in the tree and so just recursively build - // We have reached our depth goal, so just return the parent since we are done - // We are outside of the tree, in which case we need to pointer to our parent node so we can - // we info (N, M) and we need a running context - if ( currentDepth < fillDepth ) { - // we need to create subnodes for each base, and propogate N and M down - final RecalDatumNode newParent = new RecalDatumNode(parent.getRecalDatum()); - - for ( final String base : Arrays.asList("A", "C", "G", "T")) { - final String subContextBases = base + parent.getRecalDatum().context; - ContextDatum subContext; - Set> subContexts; - - final RecalDatumNode subNode = findSubcontext(subContextBases, parent); - if ( subNode != null ) { - // we have a subnode corresponding to the expected one, just copy and recurse - subContext = subNode.getRecalDatum(); - subContexts = subNode.getSubnodes(); - } else { - // have to create a new one - subContext = new ContextDatum(debugWriteN ? ("N" + parent.getRecalDatum().context ) : subContextBases, - parent.getRecalDatum().getNumObservations(), parent.getRecalDatum().getNumMismatches()); - subContexts = Collections.emptySet(); - } - - newParent.addSubnode( - fillToDepthRec(new RecalDatumNode(subContext, subContexts), - fillDepth, currentDepth + 1, debugWriteN)); - } - return newParent; - } else { - return parent; - } - } - - /** - * Go from a flat list of contexts to the tree implied by the contexts - * - * Implicit nodes are created as needed, and their observation and error counts are the sum of the - * all of their subnodes. - * - * Note this does not guarentee the tree is complete, as some contexts (e.g., AAT) may be missing - * from the tree because they are absent from the input list of contexts. - * - * For input AAG, AAT, AC, G would produce the following tree: - * - * - x [root] - * - A - * - A - * - T - * - G - * - C - * - G - * - * sets the fixed penalties in the resulting tree as well - * - * @param flatContexts list of flat contexts - * @return - */ - public static RecalDatumNode createTreeFromFlatContexts(final List flatContexts) { - if ( flatContexts == null || flatContexts.isEmpty() ) - throw new IllegalArgumentException("flatContexts cannot be empty or null"); - - final Queue> remaining = new LinkedList>(); - final Map> contextToNodes = new HashMap>(); - RecalDatumNode root = null; - - // initialize -- start with all of the contexts - for ( final ContextDatum cd : flatContexts ) - remaining.add(new RecalDatumNode(cd)); - - while ( remaining.peek() != null ) { - final RecalDatumNode add = remaining.poll(); - final ContextDatum cd = add.getRecalDatum(); - - final String parentContext = cd.getParentContext(); - RecalDatumNode parent = contextToNodes.get(parentContext); - if ( parent == null ) { - // haven't yet found parent, so make one, and enqueue it for processing - parent = new RecalDatumNode(new ContextDatum(parentContext, 0, 0)); - contextToNodes.put(parentContext, parent); - - if ( ! parent.getRecalDatum().isRootContext() ) - remaining.add(parent); - else - root = parent; - } - - parent.getRecalDatum().incrementNumObservations(cd.getNumObservations()); - parent.getRecalDatum().incrementNumMismatches(cd.getNumMismatches()); - parent.addSubnode(add); - } - - if ( root == null ) - throw new RuntimeException("root is unexpectedly null"); - - // set the fixed penalty everywhere in the tree, so that future modifications don't change the penalties - root.calcAndSetFixedPenalty(true); - - return root; - } - - /** - * Finds immediate subnode with contextToFind, or null if none exists - * - * @param tree whose subnodes should be searched - * @return - */ - public static RecalDatumNode findSubcontext(final String contextToFind, final RecalDatumNode tree) { - for ( final RecalDatumNode sub : tree.getSubnodes() ) - if ( sub.getRecalDatum().context.equals(contextToFind) ) - return sub; - return null; - } -} From 34165362265bec46a76308d8c1f3732c648b88fd Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Mon, 6 Aug 2012 11:42:36 -0400 Subject: [PATCH 070/176] indelGOP and indelGCP are now advanced, not hidden arguments --- .../gatk/walkers/genotyper/UnifiedArgumentCollection.java | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java index 69f1176cce..a885d8a58a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java @@ -146,12 +146,12 @@ public class UnifiedArgumentCollection { @Argument(fullName = "indel_heterozygosity", shortName = "indelHeterozygosity", doc = "Heterozygosity for indel calling", required = false) public double INDEL_HETEROZYGOSITY = 1.0/8000; - @Hidden - @Argument(fullName = "indelGapContinuationPenalty", shortName = "indelGCP", doc = "Indel gap continuation penalty", required = false) + @Advanced + @Argument(fullName = "indelGapContinuationPenalty", shortName = "indelGCP", doc = "Indel gap continuation penalty, as Phred-scaled probability. I.e., 30 => 10^-30/10", required = false) public byte INDEL_GAP_CONTINUATION_PENALTY = 10; - @Hidden - @Argument(fullName = "indelGapOpenPenalty", shortName = "indelGOP", doc = "Indel gap open penalty", required = false) + @Advanced + @Argument(fullName = "indelGapOpenPenalty", shortName = "indelGOP", doc = "Indel gap open penalty, as Phred-scaled probability. I.e., 30 => 10^-30/10", required = false) public byte INDEL_GAP_OPEN_PENALTY = 45; @Hidden From 89aed3ba9d6944a056b25d6439ab82d437c2024b Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Mon, 6 Aug 2012 12:02:19 -0400 Subject: [PATCH 071/176] Updating HaplotypeCaller integration tests From 2e79b063dbac75b9f67e97ff85900c09be36f44d Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Mon, 6 Aug 2012 12:57:55 -0400 Subject: [PATCH 072/176] Deleting empty unit test for AdaptiveContexts --- .../AdaptiveContextUnitTest.java | 64 ------------------- 1 file changed, 64 deletions(-) delete mode 100644 public/java/test/org/broadinstitute/sting/utils/recalibration/AdaptiveContextUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/AdaptiveContextUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/recalibration/AdaptiveContextUnitTest.java deleted file mode 100644 index c07c084b8a..0000000000 --- a/public/java/test/org/broadinstitute/sting/utils/recalibration/AdaptiveContextUnitTest.java +++ /dev/null @@ -1,64 +0,0 @@ -package org.broadinstitute.sting.utils.recalibration; - -import org.broadinstitute.sting.BaseTest; -import org.testng.annotations.DataProvider; -import org.testng.annotations.Test; - -/** - * User: depristo - * Date: 8/3/12 - * Time: 12:26 PM - * To change this template use File | Settings | File Templates. - */ -public class AdaptiveContextUnitTest { - // TODO - // TODO actually need unit tests when we have validated the value of this approach - // TODO particularly before we attempt to optimize the algorithm - // TODO - - // -------------------------------------------------------------------------------- - // - // Provider - // - // -------------------------------------------------------------------------------- - - private class AdaptiveContextTestProvider extends BaseTest.TestDataProvider { - final RecalDatumNode pruned; - final RecalDatumNode full; - - private AdaptiveContextTestProvider(Class c, RecalDatumNode pruned, RecalDatumNode full) { - super(AdaptiveContextTestProvider.class); - this.pruned = pruned; - this.full = full; - } - } - - private RecalDatumNode makeTree(final String context, final int N, final int M, - final RecalDatumNode ... sub) { - final ContextDatum contextDatum = new ContextDatum(context, N, M); - final RecalDatumNode node = new RecalDatumNode(contextDatum); - for ( final RecalDatumNode sub1 : sub ) { - node.addSubnode(sub1); - } - return node; - } - - @DataProvider(name = "AdaptiveContextTestProvider") - public Object[][] makeRecalDatumTestProvider() { -// final RecalDatumNode prune1 = -// makeTree("A", 10, 1, -// makeTree("AA", 11, 2), -// makeTree("AC", 12, 3), -// makeTree("AG", 13, 4), -// makeTree("AT", 14, 5)); -// -// new AdaptiveContextTestProvider(pruned, full); - - return AdaptiveContextTestProvider.getTests(AdaptiveContextTestProvider.class); - } - - @Test(dataProvider = "AdaptiveContextTestProvider") - public void testAdaptiveContextFill(AdaptiveContextTestProvider cfg) { - - } -} From eaeeb89d8d18b7489434d88b123ffef404ea7e96 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 6 Aug 2012 15:06:36 -0400 Subject: [PATCH 073/176] We might completely overhaul the AssignSomaticStatus tool at some point, but for now I've just tweaked it a little so that it runs well with the TALEN data: fixed VCF header bugs and changed it so that any multi-sample VCF can be used and the user specifies which of the samples is the normal and which should be used as the tumor (only 1 T/N pair allowed now). From f7ca8a7fa2479bb469646a96fe46acd75bf25850 Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Mon, 6 Aug 2012 20:22:12 -0400 Subject: [PATCH 074/176] Fixes for running HaplotypeCaller with reduced reads: a) minor refactoring, pulled out code to compute mean representative count to ReadUtils, b) Don't use min representative count over kmer when constructing de Bruijn graph - this creates many paths with multiplicity=1 and makes us lose a lot of SNP's at edge of capture targets. Use mean instead --- .../org/broadinstitute/sting/utils/sam/ReadUtils.java | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java index 6b9ba79b4a..c16470c48c 100755 --- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java @@ -56,6 +56,15 @@ private ReadUtils() { private static int DEFAULT_ADAPTOR_SIZE = 100; public static int CLIPPING_GOAL_NOT_REACHED = -1; + public static int getMeanRepresentativeReadCount(GATKSAMRecord read) { + if (!read.isReducedRead()) + return 1; + + // compute mean representative read counts + final byte[] counts = read.getReducedReadCounts(); + return (int)Math.round((double)MathUtils.sum(counts)/counts.length); + } + /** * A marker to tell which end of the read has been clipped */ From 340ab396b7b9d567d178f7acbf362d95eda52d85 Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Mon, 6 Aug 2012 21:29:21 -0400 Subject: [PATCH 075/176] Fix UG integration test broken by new -maxAltAlleles nomenclature From b135912ce3d599992270b64a8131be34cd66f124 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 6 Aug 2012 22:48:04 -0400 Subject: [PATCH 076/176] Update -maxAlleles argument in integration tests From 45b3c56da2c2c5955cba941948e758124eabb0f0 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Tue, 7 Aug 2012 13:58:22 -0400 Subject: [PATCH 077/176] The UnifiedGenotyper now makes use of base insertion and base deletion quality scores if they exist in the reads. --- .../gatk/walkers/indels/PairHMMIndelErrorModel.java | 4 +++- .../genotyper/UnifiedGenotyperIntegrationTest.java | 13 +++++++++++++ 2 files changed, 16 insertions(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java index 6bfe5702df..65c5a2fbce 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java @@ -351,7 +351,9 @@ public synchronized double[][] computeGeneralReadHaplotypeLikelihoods(final Read previousHaplotypeSeen = haplotypeBases.clone(); readLikelihood = pairHMM.computeReadLikelihoodGivenHaplotype(haplotypeBases, readBases, readQuals, - contextLogGapOpenProbabilities, contextLogGapOpenProbabilities, contextLogGapContinuationProbabilities, + (read.hasBaseIndelQualities() ? read.getBaseInsertionQualities() : contextLogGapOpenProbabilities), + (read.hasBaseIndelQualities() ? read.getBaseDeletionQualities() : contextLogGapOpenProbabilities), + contextLogGapContinuationProbabilities, startIndexInHaplotype, matchMetricArray, XMetricArray, YMetricArray); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index d976e3e22a..7b6e1ee967 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -355,6 +355,19 @@ public void testGGAwithNoEvidenceInReads() { executeTest("test GENOTYPE_GIVEN_ALLELES with no evidence in reads", spec); } + @Test + public void testBaseIndelQualityScores() { + WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( + baseCommandIndelsb37 + + " -I " + privateTestDir + "NA12878.100kb.BQSRv2.example.bam" + + " -o %s" + + " -L 20:10,000,000-10,100,000", + 1, + Arrays.asList("b3c923ed9efa04b85fc18a9b45c8d2a6")); + + executeTest(String.format("test UG with base indel quality scores"), spec); + } + // -------------------------------------------------------------------------------------------------------------- // // testing SnpEff From 8420dffa07419d918074bf7fed247a2ea749c99d Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Tue, 7 Aug 2012 08:38:16 -0400 Subject: [PATCH 078/176] VisualizeAdaptiveTree now considers only leaf nodes when computing max/min penalty --- .../utils/recalibration/RecalDatumNode.java | 35 +++++++++++++------ 1 file changed, 25 insertions(+), 10 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java index e792a808df..a0b3f2b0af 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java @@ -169,10 +169,10 @@ public double totalPenalty() { * The maximum penalty among all nodes * @return */ - public double maxPenalty() { - double max = getPenalty(); + public double maxPenalty(final boolean leafOnly) { + double max = ! leafOnly || isLeaf() ? getPenalty() : Double.MIN_VALUE; for ( final RecalDatumNode sub : subnodes ) - max = Math.max(max, sub.maxPenalty()); + max = Math.max(max, sub.maxPenalty(leafOnly)); return max; } @@ -180,10 +180,10 @@ public double maxPenalty() { * The minimum penalty among all nodes * @return */ - public double minPenalty() { - double min = getPenalty(); + public double minPenalty(final boolean leafOnly) { + double min = ! leafOnly || isLeaf() ? getPenalty() : Double.MAX_VALUE; for ( final RecalDatumNode sub : subnodes ) - min = Math.min(min, sub.minPenalty()); + min = Math.min(min, sub.minPenalty(leafOnly)); return min; } @@ -251,7 +251,7 @@ public int numLeaves() { * @return the chi2 penalty, or 0.0 if it cannot be calculated */ private double calcPenalty() { - if ( isLeaf() ) + if ( isLeaf() || freeToMerge() ) return 0.0; else if ( subnodes.size() == 1 ) // only one value, so its free to merge away @@ -277,6 +277,22 @@ else if ( subnodes.size() == 1 ) } } + /** + * Is this node free to merge because its rounded Q score is the same as all nodes below + * @return + */ + private boolean freeToMerge() { + if ( isLeaf() ) // leaves are free to merge + return true; + else { + final byte myQual = getRecalDatum().getEmpiricalQualityAsByte(); + for ( final RecalDatumNode sub : subnodes ) + if ( sub.getRecalDatum().getEmpiricalQualityAsByte() != myQual ) + return false; + return true; + } + } + /** * Calculate the penalty of this interval, given the overall error rate for the interval * @@ -346,8 +362,6 @@ public RecalDatumNode pruneByPenalty(final int maxElements) { while ( root.size() > maxElements ) { // remove the lowest penalty element, and continue root = root.removeLowestPenaltyNode(); - if ( logger.isDebugEnabled() ) - logger.debug("pruneByPenalty root size is now " + root.size() + " of max " + maxElements); } // our size is below the target, so we are good, return @@ -363,7 +377,8 @@ public RecalDatumNode pruneByPenalty(final int maxElements) { */ private RecalDatumNode removeLowestPenaltyNode() { final Pair, Double> nodeToRemove = getMinPenaltyAboveLeafNode(); - //logger.info("Removing " + nodeToRemove.getFirst() + " with penalty " + nodeToRemove.getSecond()); + if ( logger.isDebugEnabled() ) + logger.debug("Removing " + nodeToRemove.getFirst() + " with penalty " + nodeToRemove.getSecond()); final Pair, Boolean> result = removeNode(nodeToRemove.getFirst()); From 74457b24c389560e87c6f21eae42dbd9bca9f0a9 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Tue, 7 Aug 2012 16:36:57 -0400 Subject: [PATCH 079/176] AdaptiveContexts implement pruning to a given chi2 p value -- Added bonferroni corrected p-value pruning, so you tell it how significant of a different you are willing to collapse in the tree, and it prunes the tree down to this maximum threshold -- Penalty is now a phred-scaled p-value not the raw chi2 value -- Split command line arguments in VisualizeContextTree into separate arguments for each type of pruning --- .../utils/recalibration/RecalDatumNode.java | 72 ++++++++++++++++--- 1 file changed, 61 insertions(+), 11 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java index a0b3f2b0af..55d3ca13f5 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java @@ -2,6 +2,7 @@ import com.google.java.contract.Ensures; import com.google.java.contract.Requires; +import org.apache.commons.math.MathException; import org.apache.commons.math.stat.inference.ChiSquareTestImpl; import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.collections.Pair; @@ -19,6 +20,7 @@ * @since 07/27/12 */ public class RecalDatumNode { + private final static double SMALLEST_CHI2_PVALUE = 1e-300; protected static Logger logger = Logger.getLogger(RecalDatumNode.class); /** @@ -150,8 +152,6 @@ public int getNumSubnodes() { * definition have 0 penalty unless they represent a pruned tree with underlying -- but now * pruned -- subtrees * - * TODO -- can we really just add together the chi2 values? - * * @return */ public double totalPenalty() { @@ -244,11 +244,12 @@ public int numLeaves() { } /** - * Calculate the chi^2 penalty among subnodes of this node. The chi^2 value - * indicates the degree of independence of the implied error rates among the + * Calculate the phred-scaled p-value for a chi^2 test for independent among subnodes of this node. + * + * The chi^2 value indicates the degree of independence of the implied error rates among the * immediate subnodes * - * @return the chi2 penalty, or 0.0 if it cannot be calculated + * @return the phred-scaled p-value for chi2 penalty, or 0.0 if it cannot be calculated */ private double calcPenalty() { if ( isLeaf() || freeToMerge() ) @@ -267,13 +268,18 @@ else if ( subnodes.size() == 1 ) i++; } - final double chi2 = new ChiSquareTestImpl().chiSquare(counts); + try { + final double chi2PValue = new ChiSquareTestImpl().chiSquareTest(counts); + final double penalty = -10 * Math.log10(Math.max(chi2PValue, SMALLEST_CHI2_PVALUE)); - // make sure things are reasonable and fail early if not - if (Double.isInfinite(chi2) || Double.isNaN(chi2)) - throw new ReviewedStingException("chi2 value is " + chi2 + " at " + getRecalDatum()); + // make sure things are reasonable and fail early if not + if (Double.isInfinite(penalty) || Double.isNaN(penalty)) + throw new ReviewedStingException("chi2 value is " + chi2PValue + " at " + getRecalDatum()); - return chi2; + return penalty; + } catch ( MathException e ) { + throw new ReviewedStingException("Failed in calculating chi2 value", e); + } } } @@ -368,6 +374,50 @@ public RecalDatumNode pruneByPenalty(final int maxElements) { return root; } + /** + * Return a freshly allocated tree where all mergable nodes with < maxPenalty are merged + * + * Note that nodes must have fixed penalties to this algorithm will fail. + * + * @param maxPenaltyIn the maximum penalty we are allowed to incur for a merge + * @param applyBonferroniCorrection if true, we will adjust penalty by the phred-scaled bonferroni correction + * for the size of the initial tree. That is, if there are 10 nodes in the + * tree and maxPenalty is 20 we will actually enforce 10^-2 / 10 = 10^-3 = 30 + * penalty for multiple testing + * @return + */ + public RecalDatumNode pruneToNoMoreThanPenalty(final double maxPenaltyIn, final boolean applyBonferroniCorrection) { + RecalDatumNode root = this; + + final double bonferroniCorrection = 10 * Math.log10(this.size()); + final double maxPenalty = applyBonferroniCorrection ? maxPenaltyIn + bonferroniCorrection : maxPenaltyIn; + + if ( applyBonferroniCorrection ) + logger.info(String.format("Applying Bonferroni correction for %d nodes = %.2f to initial penalty %.2f for total " + + "corrected max penalty of %.2f", this.size(), bonferroniCorrection, maxPenaltyIn, maxPenalty)); + + while ( true ) { + final Pair, Double> minPenaltyNode = root.getMinPenaltyAboveLeafNode(); + + if ( minPenaltyNode == null || minPenaltyNode.getSecond() > maxPenalty ) { + // nothing to merge, or the best candidate is above our max allowed + if ( minPenaltyNode == null ) + if ( logger.isDebugEnabled() ) logger.debug("Stopping because no candidates could be found"); + else + if ( logger.isDebugEnabled() ) logger.debug("Stopping because node " + minPenaltyNode.getFirst() + " has penalty " + minPenaltyNode.getSecond() + " > max " + maxPenalty); + break; + } else { + // remove the lowest penalty element, and continue + if ( logger.isDebugEnabled() ) logger.debug("Removing node " + minPenaltyNode.getFirst() + " with penalty " + minPenaltyNode.getSecond()); + root = root.removeLowestPenaltyNode(); + } + } + + // no more candidates exist with penalty < maxPenalty + return root; + } + + /** * Find the lowest penalty above leaf node in the tree, and return a tree without it * @@ -394,7 +444,7 @@ private RecalDatumNode removeLowestPenaltyNode() { /** * Finds in the tree the node with the lowest penalty whose subnodes are all leaves * - * @return + * @return the node and its penalty, or null if no such node exists */ private Pair, Double> getMinPenaltyAboveLeafNode() { if ( isLeaf() ) From abbbc922013b94eafa75658ba1a32aff81fe58d5 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Tue, 7 Aug 2012 17:22:27 -0400 Subject: [PATCH 080/176] Bugfixes for BCF with VQSR -- Old version converted doubles directly from strings. New version uses VariantContext getAttributeAsDouble() that looks at the values directly to determine how to convert from Object to Double (via Double.valueOf, (Double), or (Double)(Integer)). -- getAttributeAsDouble() is now smart in converting integers to doubles as needed -- Removed unnecessary logging info in BCF2Codec -- Added integration tests to ensure that VQSR works end-to-end with BCF2 using sites version of the file khalid sent to me -- Added vqsr.bcf_test.snps.unfiltered.bcf file for this integration test --- .../VariantDataManager.java | 2 +- .../sting/utils/codecs/bcf2/BCF2Codec.java | 1 - .../utils/variantcontext/CommonInfo.java | 1 + ...ntRecalibrationWalkersIntegrationTest.java | 59 +++++++++++++++++-- 4 files changed, 57 insertions(+), 6 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java index 45fdad4f88..e88505f992 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java @@ -235,7 +235,7 @@ private static double decodeAnnotation( final String annotationKey, final Varian double value; try { - value = Double.parseDouble( (String)vc.getAttribute( annotationKey ) ); + value = vc.getAttributeAsDouble( annotationKey, Double.NaN ); if( Double.isInfinite(value) ) { value = Double.NaN; } if( jitter && annotationKey.equalsIgnoreCase("HRUN") ) { // Integer valued annotations must be jittered a bit to work in this GMM value += -0.25 + 0.5 * GenomeAnalysisEngine.getRandomGenerator().nextDouble(); diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java index 0776b3aa8f..244af8517e 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java @@ -167,7 +167,6 @@ public FeatureCodecHeader readHeader( final PositionalBufferedStream inputStream // create the config offsets if ( ! header.getContigLines().isEmpty() ) { - logger.info("Found contig lines in BCF2 file, using those"); contigNames.clear(); for ( final VCFContigHeaderLine contig : header.getContigLines()) { if ( contig.getID() == null || contig.getID().equals("") ) diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/CommonInfo.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/CommonInfo.java index fb0d7140da..127f916778 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/CommonInfo.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/CommonInfo.java @@ -216,6 +216,7 @@ public double getAttributeAsDouble(String key, double defaultValue) { Object x = getAttribute(key); if ( x == null ) return defaultValue; if ( x instanceof Double ) return (Double)x; + if ( x instanceof Integer ) return (Integer)x; return Double.valueOf((String)x); // throws an exception if this isn't a string } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java index 74d071a908..d1ecbb0bf3 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java @@ -13,7 +13,7 @@ private static class VRTest { String recalMD5; String cutVCFMD5; public VRTest(String inVCF, String tranchesMD5, String recalMD5, String cutVCFMD5) { - this.inVCF = validationDataLocation + inVCF; + this.inVCF = inVCF; this.tranchesMD5 = tranchesMD5; this.recalMD5 = recalMD5; this.cutVCFMD5 = cutVCFMD5; @@ -25,7 +25,7 @@ public String toString() { } } - VRTest lowPass = new VRTest("phase1.projectConsensus.chr20.raw.snps.vcf", + VRTest lowPass = new VRTest(validationDataLocation + "phase1.projectConsensus.chr20.raw.snps.vcf", "f360ce3eb2b0b887301be917a9843e2b", // tranches "287fea5ea066bf3fdd71f5ce9b58eab3", // recal file "356b9570817b9389da71fbe991d8b2f5"); // cut VCF @@ -74,14 +74,65 @@ public void testApplyRecalibration(VRTest params) { executeTest("testApplyRecalibration-"+params.inVCF, spec); } + VRTest bcfTest = new VRTest(privateTestDir + "vqsr.bcf_test.snps.unfiltered.bcf", + "a8ce3cd3dccafdf7d580bcce7d660a9a", // tranches + "1cdf8c9ee77d91d1ba7f002573108bad", // recal file + "62fda105e14b619a1c263855cf56af1d"); // cut VCF + + @DataProvider(name = "VRBCFTest") + public Object[][] createVRBCFTest() { + return new Object[][]{ {bcfTest} }; + //return new Object[][]{ {yriTrio}, {lowPass} }; // Add hg19 chr20 trio calls here + } + + @Test(dataProvider = "VRBCFTest") + public void testVariantRecalibratorWithBCF(VRTest params) { + //System.out.printf("PARAMS FOR %s is %s%n", vcf, clusterFile); + WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( + "-R " + b37KGReference + + " -resource:known=true,prior=10.0 " + GATKDataLocation + "dbsnp_132_b37.leftAligned.vcf" + + " -resource:truth=true,training=true,prior=15.0 " + comparisonDataLocation + "Validated/HapMap/3.3/sites_r27_nr.b37_fwd.vcf" + + " -resource:training=true,truth=true,prior=12.0 " + comparisonDataLocation + "Validated/Omni2.5_chip/Omni25_sites_1525_samples.b37.vcf" + + " -T VariantRecalibrator" + + " -input " + params.inVCF + + " -L 20:10,000,000-20,000,000" + + " --no_cmdline_in_header" + + " -an AC " + // integer value + " -an QD -an ReadPosRankSum -an FS -an InbreedingCoeff " + // floats value + " -mG 2 "+ + " -recalFile %s" + + " -tranchesFile %s", + 2, + Arrays.asList("bcf", "txt"), + Arrays.asList(params.recalMD5, params.tranchesMD5)); + executeTest("testVariantRecalibrator-"+params.inVCF, spec).getFirst(); + } + + @Test(dataProvider = "VRBCFTest", dependsOnMethods="testVariantRecalibratorWithBCF") + public void testApplyRecalibrationWithBCF(VRTest params) { + WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( + "-R " + b37KGReference + + " -T ApplyRecalibration" + + " -L 20:10,000,000-20,000,000" + + " --no_cmdline_in_header" + + " -input " + params.inVCF + + " -U LENIENT_VCF_PROCESSING -o %s" + + " -tranchesFile " + getMd5DB().getMD5FilePath(params.tranchesMD5, null) + + " -recalFile " + getMd5DB().getMD5FilePath(params.recalMD5, null), + Arrays.asList(params.cutVCFMD5)); + spec.disableShadowBCF(); + executeTest("testApplyRecalibration-"+params.inVCF, spec); + } + + VRTest indelUnfiltered = new VRTest( - "combined.phase1.chr20.raw.indels.unfiltered.sites.vcf", // all FILTERs as . + validationDataLocation + "combined.phase1.chr20.raw.indels.unfiltered.sites.vcf", // all FILTERs as . "b7589cd098dc153ec64c02dcff2838e4", // tranches "a04a9001f62eff43d363f4d63769f3ee", // recal file "64f576881e21323dd4078262604717a2"); // cut VCF VRTest indelFiltered = new VRTest( - "combined.phase1.chr20.raw.indels.filtered.sites.vcf", // all FILTERs as PASS + validationDataLocation + "combined.phase1.chr20.raw.indels.filtered.sites.vcf", // all FILTERs as PASS "b7589cd098dc153ec64c02dcff2838e4", // tranches "a04a9001f62eff43d363f4d63769f3ee", // recal file "af22c55d91394c56a222fd40d6d54781"); // cut VCF From 99b1b2432cdeeaa83681eb2ce6f95db446ba646e Mon Sep 17 00:00:00 2001 From: David Roazen Date: Wed, 8 Aug 2012 09:29:54 -0400 Subject: [PATCH 081/176] Update URL for phone home / GATK key documentation output by the GATK upon error --- .../sting/gatk/CommandLineExecutable.java | 4 ++-- .../gatk/arguments/GATKArgumentCollection.java | 4 ++-- .../sting/gatk/phonehome/GATKRunReport.java | 1 + .../sting/utils/exceptions/UserException.java | 14 +++++++------- 4 files changed, 12 insertions(+), 11 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java index c6bb4a27c0..0286cdc524 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java +++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java @@ -130,8 +130,8 @@ private void authorizeGATKRun() { getArgumentCollection().phoneHomeType == GATKRunReport.PhoneHomeOption.STDOUT ) { if ( getArgumentCollection().gatkKeyFile == null ) { throw new UserException("Running with the -et NO_ET or -et STDOUT option requires a GATK Key file. " + - "Please see http://www.broadinstitute.org/gsa/wiki/index.php/Phone_home " + - "for more information and instructions on how to obtain a key."); + "Please see " + GATKRunReport.PHONE_HOME_DOCS_URL + + " for more information and instructions on how to obtain a key."); } else { PublicKey gatkPublicKey = CryptUtils.loadGATKDistributedPublicKey(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java index 9721169522..1e6920b829 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java @@ -66,10 +66,10 @@ public GATKArgumentCollection() { @Argument(fullName = "read_buffer_size", shortName = "rbs", doc="Number of reads per SAM file to buffer in memory", required = false) public Integer readBufferSize = null; - @Argument(fullName = "phone_home", shortName = "et", doc="What kind of GATK run report should we generate? STANDARD is the default, can be NO_ET so nothing is posted to the run repository. Please see http://www.broadinstitute.org/gsa/wiki/index.php/Phone_home for details.", required = false) + @Argument(fullName = "phone_home", shortName = "et", doc="What kind of GATK run report should we generate? STANDARD is the default, can be NO_ET so nothing is posted to the run repository. Please see " + GATKRunReport.PHONE_HOME_DOCS_URL + " for details.", required = false) public GATKRunReport.PhoneHomeOption phoneHomeType = GATKRunReport.PhoneHomeOption.STANDARD; - @Argument(fullName = "gatk_key", shortName = "K", doc="GATK Key file. Required if running with -et NO_ET. Please see http://www.broadinstitute.org/gsa/wiki/index.php/Phone_home for details.", required = false) + @Argument(fullName = "gatk_key", shortName = "K", doc="GATK Key file. Required if running with -et NO_ET. Please see " + GATKRunReport.PHONE_HOME_DOCS_URL + " for details.", required = false) public File gatkKeyFile = null; @Argument(fullName = "read_filter", shortName = "rf", doc = "Specify filtration criteria to apply to each read individually", required = false) diff --git a/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java b/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java index a42c73212f..4cf5046a24 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java +++ b/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java @@ -88,6 +88,7 @@ public class GATKRunReport { // number of milliseconds before the S3 put operation is timed-out: private static final long S3PutTimeOut = 10 * 1000; + public static final String PHONE_HOME_DOCS_URL = "http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-how-does-it-affect-me#latest"; /** * our log diff --git a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java index 52da313626..bda03f6752 100755 --- a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java +++ b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java @@ -27,6 +27,7 @@ import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMSequenceDictionary; +import org.broadinstitute.sting.gatk.phonehome.GATKRunReport; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.sam.ReadUtils; @@ -351,8 +352,8 @@ public CouldNotCreateReferenceIndexFileBecauseOfLock(File f) { public static class UnreadableKeyException extends UserException { public UnreadableKeyException ( File f, Exception e ) { super(String.format("Key file %s cannot be read (possibly the key file is corrupt?). Error was: %s. " + - "Please see http://www.broadinstitute.org/gsa/wiki/index.php/Phone_home for help.", - f.getAbsolutePath(), getMessage(e))); + "Please see %s for help.", + f.getAbsolutePath(), getMessage(e), GATKRunReport.PHONE_HOME_DOCS_URL)); } public UnreadableKeyException ( String message, Exception e ) { @@ -361,8 +362,8 @@ public UnreadableKeyException ( String message, Exception e ) { public UnreadableKeyException ( String message ) { super(String.format("Key file cannot be read (possibly the key file is corrupt?): %s. " + - "Please see http://www.broadinstitute.org/gsa/wiki/index.php/Phone_home for help.", - message)); + "Please see %s for help.", + message, GATKRunReport.PHONE_HOME_DOCS_URL)); } } @@ -370,9 +371,8 @@ public static class KeySignatureVerificationException extends UserException { public KeySignatureVerificationException ( File f ) { super(String.format("The signature in key file %s failed cryptographic verification. " + "If this key was valid in the past, it's likely been revoked. " + - "Please see http://www.broadinstitute.org/gsa/wiki/index.php/Phone_home " + - "for help.", - f.getAbsolutePath())); + "Please see %s for help.", + f.getAbsolutePath(), GATKRunReport.PHONE_HOME_DOCS_URL)); } } } From 76458b4084b1a5fb26d874ae4fbaab993379cf2c Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 8 Aug 2012 14:29:41 -0400 Subject: [PATCH 082/176] Quick pass of FindBugs 'inefficient use of keySet iterator instead of entrySet iterator' fixes for core tools. --- .../walkers/annotator/BaseQualityRankSumTest.java | 8 ++++---- .../sting/gatk/walkers/annotator/FisherStrand.java | 12 ++++++------ .../sting/gatk/walkers/annotator/HaplotypeScore.java | 4 ++-- .../walkers/annotator/MappingQualityRankSumTest.java | 8 ++++---- .../gatk/walkers/annotator/ReadPosRankSumTest.java | 9 ++++----- .../walkers/genotyper/ConsensusAlleleCounter.java | 4 ++-- .../walkers/indels/HaplotypeIndelErrorModel.java | 5 +++-- .../gatk/walkers/phasing/PhaseByTransmission.java | 8 ++++---- .../walkers/varianteval/VariantEvalReportWriter.java | 8 ++++---- .../sting/utils/interval/IntervalUtils.java | 4 ++-- 10 files changed, 35 insertions(+), 35 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java index 0b919da18c..bd884892c0 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java @@ -65,12 +65,12 @@ protected void fillIndelQualsFromPileup(ReadBackedPileup pileup, List re // by design, first element in LinkedHashMap was ref allele double refLikelihood=0.0, altLikelihood=Double.NEGATIVE_INFINITY; - for (Allele a : el.keySet()) { + for (Map.Entry entry : el.entrySet()) { - if (a.isReference()) - refLikelihood =el.get(a); + if (entry.getKey().isReference()) + refLikelihood = entry.getValue(); else { - double like = el.get(a); + double like = entry.getValue(); if (like >= altLikelihood) altLikelihood = like; } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java index 4669cfef81..1316705991 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java @@ -291,8 +291,8 @@ private static int[][] getIndelContingencyTable(Map st int[][] table = new int[2][2]; - for ( String sample : stratifiedContexts.keySet() ) { - final AlignmentContext context = stratifiedContexts.get(sample); + for ( Map.Entry sample : stratifiedContexts.entrySet() ) { + final AlignmentContext context = sample.getValue(); if ( context == null ) continue; @@ -313,12 +313,12 @@ private static int[][] getIndelContingencyTable(Map st double refLikelihood=0.0, altLikelihood=Double.NEGATIVE_INFINITY; - for (Allele a : el.keySet()) { + for (Map.Entry entry : el.entrySet()) { - if (a.isReference()) - refLikelihood =el.get(a); + if (entry.getKey().isReference()) + refLikelihood = entry.getValue(); else { - double like = el.get(a); + double like = entry.getValue(); if (like >= altLikelihood) altLikelihood = like; } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java index 45444e05d7..ff71c4c73e 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java @@ -362,8 +362,8 @@ private Double scoreIndelsAgainstHaplotypes(final ReadBackedPileup pileup) { // Score all the reads in the pileup, even the filtered ones final double[] scores = new double[el.size()]; int i = 0; - for (Allele a : el.keySet()) { - scores[i++] = -el.get(a); + for (Map.Entry a : el.entrySet()) { + scores[i++] = -a.getValue(); if (DEBUG) { System.out.printf(" vs. haplotype %d = %f%n", i - 1, scores[i - 1]); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java index c7fb7ecbab..31067e3868 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java @@ -61,12 +61,12 @@ protected void fillIndelQualsFromPileup(ReadBackedPileup pileup, List re // by design, first element in LinkedHashMap was ref allele double refLikelihood=0.0, altLikelihood=Double.NEGATIVE_INFINITY; - for (Allele a : el.keySet()) { + for (Map.Entry a : el.entrySet()) { - if (a.isReference()) - refLikelihood =el.get(a); + if (a.getKey().isReference()) + refLikelihood = a.getValue(); else { - double like = el.get(a); + double like = a.getValue(); if (like >= altLikelihood) altLikelihood = like; } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java index 630344992d..3456041c7e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java @@ -87,11 +87,11 @@ protected void fillIndelQualsFromPileup(ReadBackedPileup pileup, List re LinkedHashMap el = indelLikelihoodMap.get(p); // retrieve likelihood information corresponding to this read double refLikelihood = 0.0, altLikelihood = Double.NEGATIVE_INFINITY; // by design, first element in LinkedHashMap was ref allele - for (Allele a : el.keySet()) { - if (a.isReference()) - refLikelihood = el.get(a); + for (Map.Entry a : el.entrySet()) { + if (a.getKey().isReference()) + refLikelihood = a.getValue(); else { - double like = el.get(a); + double like = a.getValue(); if (like >= altLikelihood) altLikelihood = like; } @@ -100,7 +100,6 @@ protected void fillIndelQualsFromPileup(ReadBackedPileup pileup, List re int readPos = getOffsetFromClippedReadStart(p.getRead(), p.getOffset()); final int numAlignedBases = getNumAlignedBases(p.getRead()); - int rp = readPos; if (readPos > numAlignedBases / 2) { readPos = numAlignedBases - (readPos + 1); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java index 869e522168..7dcc95361f 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java @@ -148,8 +148,8 @@ private Map countConsensusAlleles(ReferenceContext ref, boolean foundKey = false; // copy of hashmap into temp arrayList ArrayList> cList = new ArrayList>(); - for (String s : consensusIndelStrings.keySet()) { - cList.add(new Pair(s,consensusIndelStrings.get(s))); + for (Map.Entry s : consensusIndelStrings.entrySet()) { + cList.add(new Pair(s.getKey(), s.getValue())); } if (read.getAlignmentEnd() == loc.getStart()) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java index 26023bd2ff..3a10620aad 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java @@ -35,6 +35,7 @@ import java.util.Arrays; import java.util.HashMap; +import java.util.Map; public class HaplotypeIndelErrorModel { @@ -427,8 +428,8 @@ public double[] computeReadHaplotypeLikelihoods(ReadBackedPileup pileup, HashMap // for each read/haplotype combination, compute likelihoods, ie -10*log10(Pr(R | Hi)) // = sum_j(-10*log10(Pr(R_j | Hi) since reads are assumed to be independent int j=0; - for (Allele a: haplotypesInVC.keySet()) { - readLikelihoods[i][j]= computeReadLikelihoodGivenHaplotype(haplotypesInVC.get(a), read); + for (Map.Entry a: haplotypesInVC.entrySet()) { + readLikelihoods[i][j]= computeReadLikelihoodGivenHaplotype(a.getValue(), read); if (DEBUG) { System.out.print(read.getReadName()+" "); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java index 3cf1d485ea..bbd4bf92f3 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java @@ -426,10 +426,10 @@ private void setTrios(){ Map> families = this.getSampleDB().getFamilies(); Set family; ArrayList parents; - for(String familyID : families.keySet()){ - family = families.get(familyID); + for(Map.Entry> familyEntry : families.entrySet()){ + family = familyEntry.getValue(); if(family.size()<2 || family.size()>3){ - logger.info(String.format("Caution: Family %s has %d members; At the moment Phase By Transmission only supports trios and parent/child pairs. Family skipped.",familyID,family.size())); + logger.info(String.format("Caution: Family %s has %d members; At the moment Phase By Transmission only supports trios and parent/child pairs. Family skipped.",familyEntry.getKey(),family.size())); } else{ for(Sample familyMember : family){ @@ -438,7 +438,7 @@ private void setTrios(){ if(family.containsAll(parents)) this.trios.add(familyMember); else - logger.info(String.format("Caution: Family %s skipped as it is not a trio nor a parent/child pair; At the moment Phase By Transmission only supports trios and parent/child pairs. Family skipped.",familyID)); + logger.info(String.format("Caution: Family %s skipped as it is not a trio nor a parent/child pair; At the moment Phase By Transmission only supports trios and parent/child pairs. Family skipped.",familyEntry.getKey())); break; } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java index 2a759f2f5a..97814075ca 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java @@ -183,13 +183,13 @@ private static GATKReport initializeGATKReport(final Collection field : datamap.entrySet()) { try { - field.setAccessible(true); + field.getKey().setAccessible(true); // this is an atomic value, add a column for it - final String format = datamap.get(field).format(); - table.addColumn(field.getName(), format); + final String format = field.getValue().format(); + table.addColumn(field.getKey().getName(), format); } catch (SecurityException e) { throw new StingException("SecurityException: " + e); } diff --git a/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java b/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java index 6ee4af2888..85e9f362d8 100644 --- a/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java @@ -681,8 +681,8 @@ public static List getFlankingIntervals(final GenomeLocParser parser, LinkedHashMap> locsByContig = splitByContig(sorted); List expanded = new ArrayList(); - for (String contig: locsByContig.keySet()) { - List contigLocs = locsByContig.get(contig); + for (Map.Entry> contig: locsByContig.entrySet()) { + List contigLocs = contig.getValue(); int contigLocsSize = contigLocs.size(); GenomeLoc startLoc, stopLoc; From e3daf0912eb207ca80a3b0c4ac10914fcc6793a9 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 8 Aug 2012 14:34:16 -0400 Subject: [PATCH 083/176] Quick pass of FindBugs 'method invokes inefficient Number constructor' fixes. --- .../sting/gatk/refdata/VariantContextAdaptors.java | 1 - .../sting/gatk/walkers/indels/SomaticIndelDetector.java | 2 +- .../org/broadinstitute/sting/utils/SequenceDictionaryUtils.java | 2 +- .../broadinstitute/sting/utils/recalibration/QualQuantizer.java | 2 +- 4 files changed, 3 insertions(+), 4 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java index 1b75a2c70e..2b46414a80 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java @@ -309,7 +309,6 @@ public VariantContext convert(String name, Object input, ReferenceContext ref) { int index = hapmap.getStart() - ref.getWindow().getStart(); if ( index < 0 ) return null; // we weren't given enough reference context to create the VariantContext - Byte refBaseForIndel = new Byte(ref.getBases()[index]); HashSet alleles = new HashSet(); Allele refSNPAllele = Allele.create(ref.getBase(), true); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java index 84a65b9b22..ba16fd7092 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java @@ -1304,7 +1304,7 @@ public Integer reduce(Integer value, Integer sum) { @Override public Integer reduceInit() { - return new Integer(0); + return 0; } diff --git a/public/java/src/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java b/public/java/src/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java index d7a3906928..9e10fd670b 100755 --- a/public/java/src/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java @@ -329,7 +329,7 @@ private static List getSequencesOfName(Set commonCont */ private static class CompareSequenceRecordsByIndex implements Comparator { public int compare(SAMSequenceRecord x, SAMSequenceRecord y) { - return new Integer(x.getSequenceIndex()).compareTo(y.getSequenceIndex()); + return Integer.valueOf(x.getSequenceIndex()).compareTo(y.getSequenceIndex()); } } diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java index 62edd5fac5..a5a3104a01 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java @@ -223,7 +223,7 @@ public boolean hasFixedQual() { @Override public int compareTo(final QualInterval qualInterval) { - return new Integer(this.qStart).compareTo(qualInterval.qStart); + return Integer.valueOf(this.qStart).compareTo(qualInterval.qStart); } /** From ef6f63bb102178aec142c1eaad1fb9f1764924d3 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 8 Aug 2012 14:42:06 -0400 Subject: [PATCH 084/176] Quick pass of FindBugs 'should be static inner class' fixes. --- .../src/org/broadinstitute/sting/gatk/walkers/ClipReads.java | 2 +- .../sting/gatk/walkers/annotator/HaplotypeScore.java | 2 +- .../genotyper/SNPGenotypeLikelihoodsCalculationModel.java | 2 +- .../sting/gatk/walkers/indels/ConstrainedMateFixingManager.java | 2 +- .../sting/gatk/walkers/indels/RealignerTargetCreator.java | 2 +- .../sting/gatk/walkers/variantutils/SelectVariants.java | 2 +- .../src/org/broadinstitute/sting/utils/clipping/ClippingOp.java | 2 +- 7 files changed, 7 insertions(+), 7 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java index beafd0870b..4eaa166929 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java @@ -574,7 +574,7 @@ public String toString() { } } - public class ReadClipperWithData extends ReadClipper { + public static class ReadClipperWithData extends ReadClipper { private ClippingData data; public ReadClipperWithData(GATKSAMRecord read, List clipSeqs) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java index ff71c4c73e..c6d8883c52 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java @@ -103,7 +103,7 @@ else if (vc.isIndel() || vc.isMixed()) { return map; } - private class HaplotypeComparator implements Comparator { + private static class HaplotypeComparator implements Comparator { public int compare(Haplotype a, Haplotype b) { if (a.getQualitySum() < b.getQualitySum()) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java index c767cf783e..07d5d2f2d7 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java @@ -208,7 +208,7 @@ public ReadBackedPileup createBAQedPileup( final ReadBackedPileup pileup ) { return new ReadBackedPileupImpl( pileup.getLocation(), BAQedElements ); } - public class BAQedPileupElement extends PileupElement { + public static class BAQedPileupElement extends PileupElement { public BAQedPileupElement( final PileupElement PE ) { super(PE.getRead(), PE.getOffset(), PE.isDeletion(), PE.isBeforeDeletedBase(), PE.isAfterDeletedBase(), PE.isBeforeInsertion(), PE.isAfterInsertion(), PE.isNextToSoftClip()); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java index 3dd51fa7d7..4feba35af6 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java @@ -124,7 +124,7 @@ private SAMRecord remove(TreeSet treeSet) { return first; } - private class SAMRecordHashObject { + private static class SAMRecordHashObject { public SAMRecord record; public boolean wasModified; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java index 02e4d414de..fc6df69029 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java @@ -332,7 +332,7 @@ static private Event mergeEvents(Event left, Event right) { private enum EVENT_TYPE { POINT_EVENT, INDEL_EVENT, BOTH } - class EventPair { + static class EventPair { public Event left, right; public TreeSet intervals = new TreeSet(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index e4831eaf29..cf528de092 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -329,7 +329,7 @@ public class SelectVariants extends RodWalker implements TreeR /* Private class used to store the intermediate variants in the integer random selection process */ - private class RandomVariantStructure { + private static class RandomVariantStructure { private VariantContext vc; RandomVariantStructure(VariantContext vcP) { diff --git a/public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java b/public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java index 554188bc14..08c50b982f 100644 --- a/public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java +++ b/public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java @@ -538,7 +538,7 @@ else if (cigarElement.getOperator() == CigarOperator.DELETION) return 0; } - private class CigarShift { + private static class CigarShift { private Cigar cigar; private int shiftFromStart; private int shiftFromEnd; From 7ec50c0dc363bb0bbda53ec3231f8aacae2a10cf Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 8 Aug 2012 14:44:49 -0400 Subject: [PATCH 085/176] FindBugs found an infinite loop in the code From ff0a86cfe96989ce29ffec60d95e0748f6b7ade2 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 8 Aug 2012 14:56:27 -0400 Subject: [PATCH 086/176] Other random FindBugs fixes --- .../gatk/walkers/genotyper/UnifiedArgumentCollection.java | 1 - .../gatk/walkers/variantutils/FilterLiftedVariants.java | 8 +++----- .../broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java | 2 +- .../sting/utils/recalibration/RecalDatumNode.java | 5 +++-- 4 files changed, 7 insertions(+), 9 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java index a885d8a58a..e755a1e366 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java @@ -263,7 +263,6 @@ public UnifiedArgumentCollection clone() { uac.referenceSampleName = referenceSampleName; uac.samplePloidy = samplePloidy; uac.maxQualityScore = minQualityScore; - uac.maxQualityScore = maxQualityScore; uac.phredScaledPrior = phredScaledPrior; uac.minPower = minPower; uac.minReferenceDepth = minReferenceDepth; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java index d223adefbe..f89bcb2a70 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java @@ -34,15 +34,13 @@ import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.Arrays; -import java.util.Collection; -import java.util.Map; -import java.util.Set; +import java.util.*; /** * Filters a lifted-over VCF file for ref bases that have been changed. @@ -66,7 +64,7 @@ public void initialize() { Set samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName)); Map vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName)); - final VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey(trackName) ? vcfHeaders.get(trackName).getMetaDataInSortedOrder() : null, samples); + final VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey(trackName) ? vcfHeaders.get(trackName).getMetaDataInSortedOrder() : Collections.emptySet(), samples); writer.writeHeader(vcfHeader); } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java index 244af8517e..3b9e86c8d6 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java @@ -492,6 +492,6 @@ protected BCF2GenotypeFieldDecoders.Decoder getGenotypeFieldDecoder(final String } private final void error(final String message) throws RuntimeException { - throw new UserException.MalformedBCF2(String.format("At record %d with position %d:", recordNo, pos, message)); + throw new UserException.MalformedBCF2(String.format("%s, at record %d with position %d:", message, recordNo, pos)); } } diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java index 55d3ca13f5..102aa4433c 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java @@ -401,10 +401,11 @@ public RecalDatumNode pruneToNoMoreThanPenalty(final double maxPenaltyIn, fin if ( minPenaltyNode == null || minPenaltyNode.getSecond() > maxPenalty ) { // nothing to merge, or the best candidate is above our max allowed - if ( minPenaltyNode == null ) + if ( minPenaltyNode == null ) { if ( logger.isDebugEnabled() ) logger.debug("Stopping because no candidates could be found"); - else + } else { if ( logger.isDebugEnabled() ) logger.debug("Stopping because node " + minPenaltyNode.getFirst() + " has penalty " + minPenaltyNode.getSecond() + " > max " + maxPenalty); + } break; } else { // remove the lowest penalty element, and continue From abcf8adc3cd4fa625d48706b8d23d0f9ad0de86d Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Wed, 8 Aug 2012 15:13:20 -0400 Subject: [PATCH 087/176] Removing argument from HaplotypeCaller that was made unneccesary by recent improvements to triggering around large events --- .../sting/gatk/walkers/bqsr/BaseRecalibrator.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java index 512434e6d2..f69a02002a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java @@ -246,9 +246,9 @@ public Long map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentConte } /** - * Initialize the reduce step by creating a PrintStream from the filename specified as an argument to the walker. + * Initialize the reduce step by returning 0L * - * @return returns A PrintStream created from the -recalFile filename argument specified to the walker + * @return returns 0L */ public Long reduceInit() { return 0L; From 220834347f575ac68133377678882044a45791eb Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 8 Aug 2012 21:44:24 -0400 Subject: [PATCH 088/176] Make coverage threshold in FindCoveredIntervals a command-line argument --- .../walkers/diagnostics/targets/FindCoveredIntervals.java | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java index 0c856c6dfe..23e4d5ae05 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java @@ -24,6 +24,7 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics.targets; +import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; @@ -46,6 +47,9 @@ public class FindCoveredIntervals extends ActiveRegionWalker { @Output(required = true) private PrintStream out; + @Argument(fullName = "coverage_threshold", shortName = "cov", doc = "The minimum allowable coverage to be considered covered", required = false) + private int coverageThreshold = 20; + @Override // Look to see if the region has sufficient coverage public ActivityProfileResult isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) { @@ -53,8 +57,7 @@ public ActivityProfileResult isActive(final RefMetaDataTracker tracker, final Re int depth = ThresHolder.DEFAULTS.getFilteredCoverage(context.getBasePileup()); // note the linear probability scale - int coverageThreshold = 20; - return new ActivityProfileResult(Math.min((double) depth / coverageThreshold, 1)); + return new ActivityProfileResult(Math.min(depth / coverageThreshold, 1)); } From f4a551b02cea27adb3d9bb9e1562ce9cdaaad5d7 Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Thu, 9 Aug 2012 09:58:20 -0400 Subject: [PATCH 089/176] Rename per-sample ML allelic fractions and counts so that they don't have the same name as the per-site INFO fields, and clarify wording in VCF header --- .../sting/gatk/walkers/genotyper/UnifiedGenotyper.java | 4 ++-- .../broadinstitute/sting/utils/codecs/vcf/VCFConstants.java | 2 ++ 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java index c1c1339f5d..507806fbef 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java @@ -312,8 +312,8 @@ public static Set getHeaderInfo(final UnifiedArgumentCollection U // add the pool values for each genotype if (UAC.samplePloidy != VariantContextUtils.DEFAULT_PLOIDY) { - headerInfo.add(new VCFFormatHeaderLine(VCFConstants.MLE_ALLELE_COUNT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed, for this pool")); - headerInfo.add(new VCFFormatHeaderLine(VCFConstants.MLE_ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed, for this pool")); + headerInfo.add(new VCFFormatHeaderLine(VCFConstants.MLE_PER_SAMPLE_ALLELE_COUNT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Maximum likelihood expectation (MLE) for the alternate allele count, in the same order as listed, for each individual sample")); + headerInfo.add(new VCFFormatHeaderLine(VCFConstants.MLE_PER_SAMPLE_ALLELE_FRACTION_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Maximum likelihood expectation (MLE) for the alternate allele fraction, in the same order as listed, for each individual sample")); } if (UAC.referenceSampleName != null) { headerInfo.add(new VCFInfoHeaderLine(VCFConstants.REFSAMPLE_DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Total reference sample depth")); diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java index 8790a000df..dac58eb10f 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java @@ -36,6 +36,8 @@ public final class VCFConstants { public static final String MLE_ALLELE_COUNT_KEY = "MLEAC"; public static final String ALLELE_FREQUENCY_KEY = "AF"; public static final String MLE_ALLELE_FREQUENCY_KEY = "MLEAF"; + public static final String MLE_PER_SAMPLE_ALLELE_COUNT_KEY = "MLPSAC"; + public static final String MLE_PER_SAMPLE_ALLELE_FRACTION_KEY = "MLPSAF"; public static final String ALLELE_NUMBER_KEY = "AN"; public static final String RMS_BASE_QUALITY_KEY = "BQ"; public static final String CIGAR_KEY = "CIGAR"; From 8ee906e2ec85e6070bd93feeb679f00874529e28 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 9 Aug 2012 12:42:50 -0400 Subject: [PATCH 090/176] There's actually a subtle but important difference between foo++ and ++foo --- .../gatk/walkers/diagnostics/targets/FindCoveredIntervals.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java index 23e4d5ae05..373c8232e7 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java @@ -78,7 +78,7 @@ public Long reduceInit() { public Long reduce(final GenomeLoc value, Long reduce) { if (value != null) { out.println(value.toString()); - return reduce++; + return ++reduce; } else return reduce; } From 19cf37d4e3bb5a055f330bf42ced6b7b8898cf4b Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Thu, 9 Aug 2012 16:22:08 -0400 Subject: [PATCH 091/176] A few quick, minor findbugs fixes. --- .../sting/gatk/traversals/TraverseActiveRegions.java | 2 +- .../gatk/walkers/variantrecalibration/VariantDatum.java | 1 + public/java/src/org/broadinstitute/sting/utils/PairHMM.java | 2 +- .../org/broadinstitute/sting/utils/SWPairwiseAlignment.java | 6 +++--- .../sting/utils/activeregion/ActiveRegion.java | 4 ++-- .../sting/utils/activeregion/ActivityProfile.java | 3 --- 6 files changed, 8 insertions(+), 10 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java index 845c4eacf3..979e0f2d60 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java +++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java @@ -29,7 +29,7 @@ public class TraverseActiveRegions extends TraversalEngine workQueue = new LinkedList(); private final LinkedHashSet myReads = new LinkedHashSet(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java index 32350f0fa2..a85129d78a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java @@ -52,6 +52,7 @@ public class VariantDatum implements Comparable { public int worstAnnotation; public MultivariateGaussian assignment; // used in K-means implementation + @Override public int compareTo( final VariantDatum other ) { return Double.compare(this.lod, other.lod); } diff --git a/public/java/src/org/broadinstitute/sting/utils/PairHMM.java b/public/java/src/org/broadinstitute/sting/utils/PairHMM.java index 9fcb97a4dd..ec4cf3386a 100644 --- a/public/java/src/org/broadinstitute/sting/utils/PairHMM.java +++ b/public/java/src/org/broadinstitute/sting/utils/PairHMM.java @@ -36,7 +36,7 @@ */ public class PairHMM { - private static final int MAX_CACHED_QUAL = (int)Byte.MAX_VALUE; + private static final int MAX_CACHED_QUAL = (int)Byte.MAX_VALUE - 1; private static final byte DEFAULT_GOP = (byte) 45; private static final byte DEFAULT_GCP = (byte) 10; private static final double BANDING_TOLERANCE = 22.0; diff --git a/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java b/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java index 92d73a5ced..bc1158a4d4 100755 --- a/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java +++ b/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java @@ -713,11 +713,11 @@ static Boolean extractSingleBooleanArg(String argname, Map> System.err.println("Only one "+argname+" argument is allowed"); System.exit(1); } - if ( l.get(0).equals("true") ) return new Boolean(true); - if ( l.get(0).equals("false") ) return new Boolean(false); + if ( l.get(0).equals("true") ) return Boolean.valueOf(true); + if ( l.get(0).equals("false") ) return Boolean.valueOf(false); System.err.println("Can not parse value provided for "+argname+" argument ("+l.get(0)+"); true/false are allowed"); System.exit(1); - return null; + return Boolean.valueOf(false); // This value isn't used because it is preceded by System.exit(1) } /* ############################################## diff --git a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java index 18276f932f..8e660350ff 100644 --- a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java +++ b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java @@ -90,11 +90,11 @@ public int compareTo( final ActiveRegion other ) { public void removeAll( final ArrayList readsToRemove ) { reads.removeAll( readsToRemove ); } public boolean equalExceptReads(final ActiveRegion other) { - if ( ! activeRegionLoc.equals(other.activeRegionLoc) ) return false; + if ( activeRegionLoc.compareTo(other.activeRegionLoc) != 0 ) return false; if ( isActive != other.isActive ) return false; if ( genomeLocParser != other.genomeLocParser ) return false; if ( extension != other.extension ) return false; - if ( ! extendedLoc.equals(other.extendedLoc) ) return false; + if ( extendedLoc.compareTo(other.extendedLoc) != 0 ) return false; return true; } } \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java index 7e736b7bf1..73f3cc487d 100644 --- a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java +++ b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java @@ -46,7 +46,6 @@ public class ActivityProfile { final boolean presetRegions; GenomeLoc regionStartLoc = null; final List isActiveList; - private GenomeLoc lastLoc = null; private static final int FILTER_SIZE = 80; private static final double[] GaussianKernel; @@ -75,8 +74,6 @@ protected ActivityProfile(final GenomeLocParser parser, final boolean presetRegi public void add(final GenomeLoc loc, final ActivityProfileResult result) { if ( loc.size() != 1 ) throw new ReviewedStingException("Bad add call to ActivityProfile: loc " + loc + " size != 1" ); - if ( lastLoc != null && loc.getStart() != lastLoc.getStop() + 1 ) - throw new ReviewedStingException("Bad add call to ActivityProfile: lastLoc added " + lastLoc + " and next is " + loc); isActiveList.add(result); if( regionStartLoc == null ) { regionStartLoc = loc; From c4fda743bfee85b7438edb3de46d48a4661bd329 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Thu, 9 Aug 2012 16:30:58 -0400 Subject: [PATCH 092/176] A few quick, minor findbugs fixes. --- public/java/src/org/broadinstitute/sting/utils/PairHMM.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/PairHMM.java b/public/java/src/org/broadinstitute/sting/utils/PairHMM.java index ec4cf3386a..15f7a78695 100644 --- a/public/java/src/org/broadinstitute/sting/utils/PairHMM.java +++ b/public/java/src/org/broadinstitute/sting/utils/PairHMM.java @@ -36,7 +36,7 @@ */ public class PairHMM { - private static final int MAX_CACHED_QUAL = (int)Byte.MAX_VALUE - 1; + private static final Byte MAX_CACHED_QUAL = Byte.MAX_VALUE; private static final byte DEFAULT_GOP = (byte) 45; private static final byte DEFAULT_GCP = (byte) 10; private static final double BANDING_TOLERANCE = 22.0; From 7e5c045cee30957999a5679e0cf3d4cbcbae01a8 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 9 Aug 2012 09:00:44 -0400 Subject: [PATCH 093/176] BCF2 optimizations -- All low-level reads throw IOException instead of catching it directly. This allows us to not try/catch in readByte, improving performance by 5% or so -- Optimize encodeTypeDescriptor with final variables. Avoid using Math.min instead do inline comparison -- Inlined willOverflow directly in its single use --- .../sting/utils/codecs/bcf2/BCF2Codec.java | 42 ++++++++------- .../sting/utils/codecs/bcf2/BCF2Decoder.java | 22 ++++---- .../bcf2/BCF2GenotypeFieldDecoders.java | 21 ++++---- .../codecs/bcf2/BCF2LazyGenotypesDecoder.java | 51 +++++++++++-------- .../sting/utils/codecs/bcf2/BCF2Utils.java | 21 ++------ .../variantcontext/writer/BCF2Encoder.java | 2 +- .../bcf2/BCF2EncoderDecoderUnitTest.java | 4 +- 7 files changed, 82 insertions(+), 81 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java index 3b9e86c8d6..52a8ef0d0f 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java @@ -113,18 +113,22 @@ public Feature decodeLoc( final PositionalBufferedStream inputStream ) { @Override public VariantContext decode( final PositionalBufferedStream inputStream ) { - recordNo++; - final VariantContextBuilder builder = new VariantContextBuilder(); - - final int sitesBlockSize = decoder.readBlockSize(inputStream); - final int genotypeBlockSize = decoder.readBlockSize(inputStream); - decoder.readNextBlock(sitesBlockSize, inputStream); - decodeSiteLoc(builder); - final SitesInfoForDecoding info = decodeSitesExtendedInfo(builder); - - decoder.readNextBlock(genotypeBlockSize, inputStream); - createLazyGenotypesDecoder(info, builder); - return builder.fullyDecoded(true).make(); + try { + recordNo++; + final VariantContextBuilder builder = new VariantContextBuilder(); + + final int sitesBlockSize = decoder.readBlockSize(inputStream); + final int genotypeBlockSize = decoder.readBlockSize(inputStream); + decoder.readNextBlock(sitesBlockSize, inputStream); + decodeSiteLoc(builder); + final SitesInfoForDecoding info = decodeSitesExtendedInfo(builder); + + decoder.readNextBlock(genotypeBlockSize, inputStream); + createLazyGenotypesDecoder(info, builder); + return builder.fullyDecoded(true).make(); + } catch ( IOException e ) { + throw new UserException.CouldNotReadInputFile("Failed to read BCF file", e); + } } @Override @@ -234,7 +238,7 @@ public boolean canDecode( final String path ) { * @return */ @Requires({"builder != null"}) - private final void decodeSiteLoc(final VariantContextBuilder builder) { + private final void decodeSiteLoc(final VariantContextBuilder builder) throws IOException { final int contigOffset = decoder.decodeInt(BCF2Type.INT32); final String contig = lookupContigName(contigOffset); builder.chr(contig); @@ -253,7 +257,7 @@ private final void decodeSiteLoc(final VariantContextBuilder builder) { */ @Requires({"builder != null", "decoder != null"}) @Ensures({"result != null", "result.isValid()"}) - private final SitesInfoForDecoding decodeSitesExtendedInfo(final VariantContextBuilder builder) { + private final SitesInfoForDecoding decodeSitesExtendedInfo(final VariantContextBuilder builder) throws IOException { final Object qual = decoder.decodeSingleValue(BCF2Type.FLOAT); if ( qual != null ) { builder.log10PError(((Double)qual) / -10.0); @@ -309,7 +313,7 @@ public String toString() { * Decode the id field in this BCF2 file and store it in the builder * @param builder */ - private void decodeID( final VariantContextBuilder builder ) { + private void decodeID( final VariantContextBuilder builder ) throws IOException { final String id = (String)decoder.decodeTypedValue(); if ( id == null ) @@ -326,7 +330,7 @@ private void decodeID( final VariantContextBuilder builder ) { * @return the alleles */ @Requires("nAlleles > 0") - private List decodeAlleles( final VariantContextBuilder builder, final int pos, final int nAlleles ) { + private List decodeAlleles( final VariantContextBuilder builder, final int pos, final int nAlleles ) throws IOException { // TODO -- probably need inline decoder for efficiency here (no sense in going bytes -> string -> vector -> bytes List alleles = new ArrayList(nAlleles); String ref = null; @@ -356,7 +360,7 @@ private List decodeAlleles( final VariantContextBuilder builder, final i * Decode the filter field of this BCF2 file and store the result in the builder * @param builder */ - private void decodeFilter( final VariantContextBuilder builder ) { + private void decodeFilter( final VariantContextBuilder builder ) throws IOException { final Object value = decoder.decodeTypedValue(); if ( value == null ) @@ -383,7 +387,7 @@ private void decodeFilter( final VariantContextBuilder builder ) { * @param numInfoFields */ @Requires("numInfoFields >= 0") - private void decodeInfo( final VariantContextBuilder builder, final int numInfoFields ) { + private void decodeInfo( final VariantContextBuilder builder, final int numInfoFields ) throws IOException { if ( numInfoFields == 0 ) // fast path, don't bother doing any work if there are no fields return; @@ -443,7 +447,7 @@ public LazyData(final int nGenotypeFields, final byte[] bytes) { } @Ensures("result != null") - private final String getDictionaryString() { + private final String getDictionaryString() throws IOException { return getDictionaryString((Integer) decoder.decodeTypedValue()); } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java index 2619a4dae3..73137c7940 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java @@ -129,18 +129,18 @@ public void setRecordBytes(final byte[] recordBytes) { // // ---------------------------------------------------------------------- - public final Object decodeTypedValue() { + public final Object decodeTypedValue() throws IOException { final byte typeDescriptor = readTypeDescriptor(); return decodeTypedValue(typeDescriptor); } - public final Object decodeTypedValue(final byte typeDescriptor) { + public final Object decodeTypedValue(final byte typeDescriptor) throws IOException { final int size = decodeNumberOfElements(typeDescriptor); return decodeTypedValue(typeDescriptor, size); } @Requires("size >= 0") - public final Object decodeTypedValue(final byte typeDescriptor, final int size) { + public final Object decodeTypedValue(final byte typeDescriptor, final int size) throws IOException { if ( size == 0 ) { // missing value => null in java return null; @@ -162,7 +162,7 @@ public final Object decodeTypedValue(final byte typeDescriptor, final int size) } } - public final Object decodeSingleValue(final BCF2Type type) { + public final Object decodeSingleValue(final BCF2Type type) throws IOException { // TODO -- decodeTypedValue should integrate this routine final int value = decodeInt(type); @@ -210,7 +210,7 @@ private final Object decodeLiteralString(final int size) { } @Ensures("result >= 0") - public final int decodeNumberOfElements(final byte typeDescriptor) { + public final int decodeNumberOfElements(final byte typeDescriptor) throws IOException { if ( BCF2Utils.sizeIsOverflow(typeDescriptor) ) // -1 ensures we explode immediately with a bad size if the result is missing return decodeInt(readTypeDescriptor(), -1); @@ -228,14 +228,14 @@ public final int decodeNumberOfElements(final byte typeDescriptor) { * @return */ @Requires("BCF2Utils.decodeSize(typeDescriptor) == 1") - public final int decodeInt(final byte typeDescriptor, final int missingValue) { + public final int decodeInt(final byte typeDescriptor, final int missingValue) throws IOException { final BCF2Type type = BCF2Utils.decodeType(typeDescriptor); final int i = decodeInt(type); return i == type.getMissingBytes() ? missingValue : i; } @Requires("type != null") - public final int decodeInt(final BCF2Type type) { + public final int decodeInt(final BCF2Type type) throws IOException { return BCF2Utils.readInt(type.getSizeInBytes(), recordStream); } @@ -258,7 +258,7 @@ public final int decodeInt(final BCF2Type type) { * @return see description */ @Requires({"type != null", "type.isIntegerType()", "size >= 0"}) - public final int[] decodeIntArray(final int size, final BCF2Type type, int[] maybeDest) { + public final int[] decodeIntArray(final int size, final BCF2Type type, int[] maybeDest) throws IOException { if ( size == 0 ) { return null; } else { @@ -290,7 +290,7 @@ public final int[] decodeIntArray(final int size, final BCF2Type type, int[] may } } - public final int[] decodeIntArray(final byte typeDescriptor, final int size) { + public final int[] decodeIntArray(final byte typeDescriptor, final int size) throws IOException { final BCF2Type type = BCF2Utils.decodeType(typeDescriptor); return decodeIntArray(size, type, null); } @@ -311,7 +311,7 @@ public final double rawFloatToFloat(final int rawFloat) { * @param inputStream * @return */ - public final int readBlockSize(final InputStream inputStream) { + public final int readBlockSize(final InputStream inputStream) throws IOException { return BCF2Utils.readInt(4, inputStream); } @@ -345,7 +345,7 @@ private final static void validateReadBytes(final int actuallyRead, final int ex } } - public final byte readTypeDescriptor() { + public final byte readTypeDescriptor() throws IOException { return BCF2Utils.readByte(recordStream); } } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2GenotypeFieldDecoders.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2GenotypeFieldDecoders.java index 0dadc49f9e..e4ae96262a 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2GenotypeFieldDecoders.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2GenotypeFieldDecoders.java @@ -32,6 +32,7 @@ import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder; +import java.io.IOException; import java.util.*; /** @@ -105,12 +106,12 @@ public void decode(final List siteAlleles, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, - final GenotypeBuilder[] gbs); + final GenotypeBuilder[] gbs) throws IOException; } private class GTDecoder implements Decoder { @Override - public void decode(final List siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) { + public void decode(final List siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) throws IOException { if ( ENABLE_FASTPATH_GT && siteAlleles.size() == 2 && numElements == 2 && gbs.length >= MIN_SAMPLES_FOR_FASTPATH_GENOTYPES ) fastBiallelicDiploidDecode(siteAlleles, decoder, typeDescriptor, gbs); else { @@ -135,7 +136,7 @@ public void decode(final List siteAlleles, final String field, final BCF private final void fastBiallelicDiploidDecode(final List siteAlleles, final BCF2Decoder decoder, final byte typeDescriptor, - final GenotypeBuilder[] gbs) { + final GenotypeBuilder[] gbs) throws IOException { final BCF2Type type = BCF2Utils.decodeType(typeDescriptor); final int nPossibleGenotypes = 3 * 3; @@ -177,7 +178,7 @@ private final void generalDecode(final List siteAlleles, final int ploidy, final BCF2Decoder decoder, final byte typeDescriptor, - final GenotypeBuilder[] gbs) { + final GenotypeBuilder[] gbs) throws IOException { final BCF2Type type = BCF2Utils.decodeType(typeDescriptor); // a single cache for the encoded genotypes, since we don't actually need this vector @@ -216,7 +217,7 @@ private final Allele getAlleleFromEncoded(final List siteAlleles, final private class DPDecoder implements Decoder { @Override - public void decode(final List siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) { + public void decode(final List siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) throws IOException { for ( final GenotypeBuilder gb : gbs ) { // the -1 is for missing gb.DP(decoder.decodeInt(typeDescriptor, -1)); @@ -226,7 +227,7 @@ public void decode(final List siteAlleles, final String field, final BCF private class GQDecoder implements Decoder { @Override - public void decode(final List siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) { + public void decode(final List siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) throws IOException { for ( final GenotypeBuilder gb : gbs ) { // the -1 is for missing gb.GQ(decoder.decodeInt(typeDescriptor, -1)); @@ -236,7 +237,7 @@ public void decode(final List siteAlleles, final String field, final BCF private class ADDecoder implements Decoder { @Override - public void decode(final List siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) { + public void decode(final List siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) throws IOException { for ( final GenotypeBuilder gb : gbs ) { gb.AD(decoder.decodeIntArray(typeDescriptor, numElements)); } @@ -245,7 +246,7 @@ public void decode(final List siteAlleles, final String field, final BCF private class PLDecoder implements Decoder { @Override - public void decode(final List siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) { + public void decode(final List siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) throws IOException { for ( final GenotypeBuilder gb : gbs ) { gb.PL(decoder.decodeIntArray(typeDescriptor, numElements)); } @@ -254,7 +255,7 @@ public void decode(final List siteAlleles, final String field, final BCF private class GenericDecoder implements Decoder { @Override - public void decode(final List siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) { + public void decode(final List siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) throws IOException { for ( final GenotypeBuilder gb : gbs ) { Object value = decoder.decodeTypedValue(typeDescriptor, numElements); if ( value != null ) { // don't add missing values @@ -273,7 +274,7 @@ public void decode(final List siteAlleles, final String field, final BCF private class FTDecoder implements Decoder { @Override - public void decode(final List siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) { + public void decode(final List siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) throws IOException { for ( final GenotypeBuilder gb : gbs ) { Object value = decoder.decodeTypedValue(typeDescriptor, numElements); assert value == null || value instanceof String; diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2LazyGenotypesDecoder.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2LazyGenotypesDecoder.java index 35fb2e97a3..cf34a8b48f 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2LazyGenotypesDecoder.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2LazyGenotypesDecoder.java @@ -26,9 +26,11 @@ import com.google.java.contract.Requires; import org.apache.log4j.Logger; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.variantcontext.*; +import java.io.IOException; import java.util.*; /** @@ -64,33 +66,38 @@ public LazyGenotypesContext.LazyData parse(final Object data) { if ( logger.isDebugEnabled() ) logger.debug("Decoding BCF genotypes for " + nSamples + " samples with " + nFields + " fields each"); - // load our byte[] data into the decoder - final BCF2Decoder decoder = new BCF2Decoder(((BCF2Codec.LazyData)data).bytes); + try { - for ( int i = 0; i < nSamples; i++ ) - builders[i].reset(true); + // load our byte[] data into the decoder + final BCF2Decoder decoder = new BCF2Decoder(((BCF2Codec.LazyData)data).bytes); - for ( int i = 0; i < nFields; i++ ) { - // get the field name - final int offset = (Integer) decoder.decodeTypedValue(); - final String field = codec.getDictionaryString(offset); + for ( int i = 0; i < nSamples; i++ ) + builders[i].reset(true); - // the type of each element - final byte typeDescriptor = decoder.readTypeDescriptor(); - final int numElements = decoder.decodeNumberOfElements(typeDescriptor); - final BCF2GenotypeFieldDecoders.Decoder fieldDecoder = codec.getGenotypeFieldDecoder(field); - try { - fieldDecoder.decode(siteAlleles, field, decoder, typeDescriptor, numElements, builders); - } catch ( ClassCastException e ) { - throw new UserException.MalformedBCF2("BUG: expected encoding of field " + field - + " inconsistent with the value observed in the decoded value"); + for ( int i = 0; i < nFields; i++ ) { + // get the field name + final int offset = (Integer) decoder.decodeTypedValue(); + final String field = codec.getDictionaryString(offset); + + // the type of each element + final byte typeDescriptor = decoder.readTypeDescriptor(); + final int numElements = decoder.decodeNumberOfElements(typeDescriptor); + final BCF2GenotypeFieldDecoders.Decoder fieldDecoder = codec.getGenotypeFieldDecoder(field); + try { + fieldDecoder.decode(siteAlleles, field, decoder, typeDescriptor, numElements, builders); + } catch ( ClassCastException e ) { + throw new UserException.MalformedBCF2("BUG: expected encoding of field " + field + + " inconsistent with the value observed in the decoded value"); + } } - } - final ArrayList genotypes = new ArrayList(nSamples); - for ( final GenotypeBuilder gb : builders ) - genotypes.add(gb.make()); + final ArrayList genotypes = new ArrayList(nSamples); + for ( final GenotypeBuilder gb : builders ) + genotypes.add(gb.make()); - return new LazyGenotypesContext.LazyData(genotypes, codec.getHeader().getSampleNamesInOrder(), codec.getHeader().getSampleNameToOffset()); + return new LazyGenotypesContext.LazyData(genotypes, codec.getHeader().getSampleNamesInOrder(), codec.getHeader().getSampleNameToOffset()); + } catch ( IOException e ) { + throw new ReviewedStingException("Unexpected IOException parsing already read genotypes data block", e); + } } } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java index c79abe2ae3..3454d0c3c1 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java @@ -97,9 +97,8 @@ public static ArrayList makeDictionary(final VCFHeader header) { @Requires({"nElements >= 0", "type != null"}) public static byte encodeTypeDescriptor(final int nElements, final BCF2Type type ) { - int encodeSize = Math.min(nElements, OVERFLOW_ELEMENT_MARKER); - byte typeByte = (byte)((0x0F & encodeSize) << 4 | (type.getID() & 0x0F)); - return typeByte; + final int encodeSize = nElements > MAX_INLINE_ELEMENTS ? OVERFLOW_ELEMENT_MARKER : nElements; + return (byte)((0x0F & encodeSize) << 4 | (type.getID() & 0x0F)); } @Ensures("result >= 0") @@ -121,18 +120,8 @@ public static boolean sizeIsOverflow(final byte typeDescriptor) { return decodeSize(typeDescriptor) == OVERFLOW_ELEMENT_MARKER; } - @Requires("nElements >= 0") - public static boolean willOverflow(final long nElements) { - return nElements > MAX_INLINE_ELEMENTS; - } - - public static byte readByte(final InputStream stream) { - // TODO -- shouldn't be capturing error here - try { - return (byte)(stream.read() & 0xFF); - } catch ( IOException e ) { - throw new ReviewedStingException("readByte failure", e); - } + public static byte readByte(final InputStream stream) throws IOException { + return (byte)(stream.read() & 0xFF); } /** @@ -295,7 +284,7 @@ public static List toList(final Object o) { @Requires({"stream != null", "bytesForEachInt > 0"}) - public static int readInt(int bytesForEachInt, final InputStream stream) { + public static int readInt(int bytesForEachInt, final InputStream stream) throws IOException { switch ( bytesForEachInt ) { case 1: { return (byte)(readByte(stream)); diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Encoder.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Encoder.java index 2c1d99546b..a2bbfb391c 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Encoder.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Encoder.java @@ -193,7 +193,7 @@ public final void encodeRawFloat(final double value) throws IOException { public final void encodeType(final int size, final BCF2Type type) throws IOException { final byte typeByte = BCF2Utils.encodeTypeDescriptor(size, type); encodeStream.write(typeByte); - if ( BCF2Utils.willOverflow(size) ) { + if ( size > BCF2Utils.MAX_INLINE_ELEMENTS ) { // write in the overflow size encodeTypedInt(size); } diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2EncoderDecoderUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2EncoderDecoderUnitTest.java index 7569ce90de..77050c069f 100644 --- a/public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2EncoderDecoderUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2EncoderDecoderUnitTest.java @@ -537,11 +537,11 @@ private final byte[] encodeRecord(final List toEncode) throws IO return record; } - private final void decodeRecord(final List toEncode, final byte[] record) { + private final void decodeRecord(final List toEncode, final byte[] record) throws IOException { decodeRecord(toEncode, new BCF2Decoder(record)); } - private final void decodeRecord(final List toEncode, final BCF2Decoder decoder) { + private final void decodeRecord(final List toEncode, final BCF2Decoder decoder) throws IOException { for ( final BCF2TypedValue tv : toEncode ) { Assert.assertFalse(decoder.blockIsFullyDecoded()); final Object decoded = decoder.decodeTypedValue(); From 24168bc34a3c30f6d8108233bf73ec3688f002f2 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 9 Aug 2012 11:09:09 -0400 Subject: [PATCH 094/176] BCF2 optimizations -- BCF2Type enum has an overloaded method to read the type as an int from an input stream. This gets rid of a case statement and replaces it with just minimum tiny methods that should be better optimized. As side effect of this optimization is an overall cleaner code organization --- .../sting/utils/codecs/bcf2/BCF2Codec.java | 2 +- .../sting/utils/codecs/bcf2/BCF2Decoder.java | 4 +- .../sting/utils/codecs/bcf2/BCF2Type.java | 110 ++++++++++++++++-- .../sting/utils/codecs/bcf2/BCF2Utils.java | 20 ---- 4 files changed, 103 insertions(+), 33 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java index 52a8ef0d0f..570ca7c1cb 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java @@ -151,7 +151,7 @@ public FeatureCodecHeader readHeader( final PositionalBufferedStream inputStream logger.info("BCF version " + bcfVersion); - final int headerSizeInBytes = BCF2Utils.readInt(BCF2Type.INT32.getSizeInBytes(), inputStream); + final int headerSizeInBytes = BCF2Type.INT32.read(inputStream); if ( headerSizeInBytes <= 0 || headerSizeInBytes > MAX_HEADER_SIZE) // no bigger than 8 MB error("BCF2 header has invalid length: " + headerSizeInBytes + " must be >= 0 and < "+ MAX_HEADER_SIZE); diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java index 73137c7940..8000f2e73e 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java @@ -236,7 +236,7 @@ public final int decodeInt(final byte typeDescriptor, final int missingValue) th @Requires("type != null") public final int decodeInt(final BCF2Type type) throws IOException { - return BCF2Utils.readInt(type.getSizeInBytes(), recordStream); + return type.read(recordStream); } /** @@ -312,7 +312,7 @@ public final double rawFloatToFloat(final int rawFloat) { * @return */ public final int readBlockSize(final InputStream inputStream) throws IOException { - return BCF2Utils.readInt(4, inputStream); + return BCF2Type.INT32.read(inputStream); } /** diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java index 49f375b250..cb9b0af84f 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java @@ -26,6 +26,9 @@ import com.google.java.contract.Requires; +import java.io.IOException; +import java.io.InputStream; +import java.io.OutputStream; import java.util.EnumSet; /** @@ -35,12 +38,82 @@ * @since 05/12 */ public enum BCF2Type { - MISSING(0, 0, 0x00), - INT8 (1, 1, 0xFFFFFF80, -127, 127), // todo -- confirm range - INT16(2, 2, 0xFFFF8000, -32767, 32767), - INT32(3, 4, 0x80000000, -2147483647, 2147483647), - FLOAT(5, 4, 0x7F800001), - CHAR (7, 1, 0x00000000); + // the actual values themselves + MISSING(0, 0, 0x00) { + @Override public int read(final InputStream in) throws IOException { + throw new IllegalArgumentException("Cannot read MISSING type"); + } + @Override public void write(final int value, final OutputStream out) throws IOException { + throw new IllegalArgumentException("Cannot write MISSING type"); + } + }, + + // todo -- confirm range + INT8 (1, 1, 0xFFFFFF80, -127, 127) { + @Override + public int read(final InputStream in) throws IOException { + return BCF2Utils.readByte(in); + } + + @Override + public void write(final int value, final OutputStream out) throws IOException { + //To change body of implemented methods use File | Settings | File Templates. + } + }, + + INT16(2, 2, 0xFFFF8000, -32767, 32767) { + @Override + public int read(final InputStream in) throws IOException { + final int b2 = BCF2Utils.readByte(in) & 0xFF; + final int b1 = BCF2Utils.readByte(in) & 0xFF; + return (short)((b1 << 8) | b2); + } + + @Override + public void write(final int value, final OutputStream out) throws IOException { + //To change body of implemented methods use File | Settings | File Templates. + } + }, + + INT32(3, 4, 0x80000000, -2147483647, 2147483647) { + @Override + public int read(final InputStream in) throws IOException { + final int b4 = BCF2Utils.readByte(in) & 0xFF; + final int b3 = BCF2Utils.readByte(in) & 0xFF; + final int b2 = BCF2Utils.readByte(in) & 0xFF; + final int b1 = BCF2Utils.readByte(in) & 0xFF; + return (int)(b1 << 24 | b2 << 16 | b3 << 8 | b4); + } + + @Override + public void write(final int value, final OutputStream out) throws IOException { + //To change body of implemented methods use File | Settings | File Templates. + } + }, + + FLOAT(5, 4, 0x7F800001) { + @Override + public int read(final InputStream in) throws IOException { + return INT32.read(in); + } + + @Override + public void write(final int value, final OutputStream out) throws IOException { + //To change body of implemented methods use File | Settings | File Templates. + } + }, + + CHAR (7, 1, 0x00000000) { + @Override + public int read(final InputStream in) throws IOException { + return INT8.read(in); + } + + @Override + public void write(final int value, final OutputStream out) throws IOException { + //To change body of implemented methods use File | Settings | File Templates. + } + }; private final int id; private final Object missingJavaValue; @@ -48,10 +121,6 @@ public enum BCF2Type { private final int sizeInBytes; private final long minValue, maxValue; - BCF2Type(final int id) { - this(id, -1, 0, 0, 0); - } - BCF2Type(final int id, final int sizeInBytes, final int missingBytes) { this(id, sizeInBytes, missingBytes, 0, 0); } @@ -121,4 +190,25 @@ public boolean isMissingType() { public boolean isIntegerType() { return INTEGERS.contains(this); } + + /** + * Read a value from in stream of this BCF2 type as an int [32 bit] collection of bits + * + * For intX and char values this is just the int / byte value of the underlying data represented as a 32 bit int + * For a char the result must be converted to a char by (char)(byte)(0x0F & value) + * For doubles it's necessary to convert subsequently this value to a double via Double.bitsToDouble() + * + * @param in + * @return + * @throws IOException + */ + @Requires("in != null") + public int read(final InputStream in) throws IOException { + throw new IllegalArgumentException("Not implemented"); + } + + @Requires("out != null") + public void write(final int value, final OutputStream out) throws IOException { + throw new IllegalArgumentException("Not implemented"); + } } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java index 3454d0c3c1..632977a7fb 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java @@ -282,26 +282,6 @@ public static List toList(final Object o) { else return Collections.singletonList(o); } - - @Requires({"stream != null", "bytesForEachInt > 0"}) - public static int readInt(int bytesForEachInt, final InputStream stream) throws IOException { - switch ( bytesForEachInt ) { - case 1: { - return (byte)(readByte(stream)); - } case 2: { - final int b2 = readByte(stream) & 0xFF; - final int b1 = readByte(stream) & 0xFF; - return (short)((b1 << 8) | b2); - } case 4: { - final int b4 = readByte(stream) & 0xFF; - final int b3 = readByte(stream) & 0xFF; - final int b2 = readByte(stream) & 0xFF; - final int b1 = readByte(stream) & 0xFF; - return (int)(b1 << 24 | b2 << 16 | b3 << 8 | b4); - } default: throw new ReviewedStingException("Unexpected size during decoding"); - } - } - public static void encodeRawBytes(final int value, final BCF2Type type, final OutputStream encodeStream) throws IOException { switch ( type.getSizeInBytes() ) { case 1: From 4405411190fb1213a787d45daa4b9a7bc3c53205 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 9 Aug 2012 15:34:07 -0400 Subject: [PATCH 095/176] BCF2 optimizations -- Added Write method to BCF2 types that directly converts int value to byte stream. Deleted writeRawBytes(int) -- encodeTypeDescriptor semi-inlined into encodeType so that the tests for overflow are done in just one place -- Faster implementation of determineIntegerType for int[] values --- .../sting/utils/codecs/bcf2/BCF2Decoder.java | 2 +- .../sting/utils/codecs/bcf2/BCF2Type.java | 15 ++++-- .../sting/utils/codecs/bcf2/BCF2Utils.java | 54 +++++-------------- .../variantcontext/writer/BCF2Encoder.java | 13 +++-- .../variantcontext/writer/BCF2Writer.java | 6 +-- 5 files changed, 35 insertions(+), 55 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java index 8000f2e73e..d7f59632c7 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java @@ -295,7 +295,7 @@ public final int[] decodeIntArray(final byte typeDescriptor, final int size) thr return decodeIntArray(size, type, null); } - public final double rawFloatToFloat(final int rawFloat) { + private double rawFloatToFloat(final int rawFloat) { return (double)Float.intBitsToFloat(rawFloat); } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java index cb9b0af84f..6fd698ff6d 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java @@ -57,7 +57,7 @@ public int read(final InputStream in) throws IOException { @Override public void write(final int value, final OutputStream out) throws IOException { - //To change body of implemented methods use File | Settings | File Templates. + out.write(0xFF & value); // TODO -- do we need this operation? } }, @@ -71,7 +71,9 @@ public int read(final InputStream in) throws IOException { @Override public void write(final int value, final OutputStream out) throws IOException { - //To change body of implemented methods use File | Settings | File Templates. + // TODO -- optimization -- should we put this in a local buffer? + out.write((0x00FF & value)); + out.write((0xFF00 & value) >> 8); } }, @@ -87,7 +89,10 @@ public int read(final InputStream in) throws IOException { @Override public void write(final int value, final OutputStream out) throws IOException { - //To change body of implemented methods use File | Settings | File Templates. + out.write((0x000000FF & value)); + out.write((0x0000FF00 & value) >> 8); + out.write((0x00FF0000 & value) >> 16); + out.write((0xFF000000 & value) >> 24); } }, @@ -99,7 +104,7 @@ public int read(final InputStream in) throws IOException { @Override public void write(final int value, final OutputStream out) throws IOException { - //To change body of implemented methods use File | Settings | File Templates. + INT32.write(value, out); } }, @@ -111,7 +116,7 @@ public int read(final InputStream in) throws IOException { @Override public void write(final int value, final OutputStream out) throws IOException { - //To change body of implemented methods use File | Settings | File Templates. + INT8.write(value, out); } }; diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java index 632977a7fb..e6e78d89d6 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java @@ -95,10 +95,9 @@ public static ArrayList makeDictionary(final VCFHeader header) { return dict; } - @Requires({"nElements >= 0", "type != null"}) + @Requires({"nElements >= 0", "nElements <= OVERFLOW_ELEMENT_MARKER", "type != null"}) public static byte encodeTypeDescriptor(final int nElements, final BCF2Type type ) { - final int encodeSize = nElements > MAX_INLINE_ELEMENTS ? OVERFLOW_ELEMENT_MARKER : nElements; - return (byte)((0x0F & encodeSize) << 4 | (type.getID() & 0x0F)); + return (byte)((0x0F & nElements) << 4 | (type.getID() & 0x0F)); } @Ensures("result >= 0") @@ -216,18 +215,18 @@ public static BCF2Type determineIntegerType(final int value) { @Ensures("result.isIntegerType()") public static BCF2Type determineIntegerType(final int[] values) { - // literally a copy of the code below, but there's no general way to unify lists and arrays in java - BCF2Type maxType = BCF2Type.INT8; - for ( final int value : values ) { - final BCF2Type type1 = determineIntegerType(value); - switch ( type1 ) { - case INT8: break; - case INT16: maxType = BCF2Type.INT16; break; - case INT32: return BCF2Type.INT32; // fast path for largest possible value - default: throw new ReviewedStingException("Unexpected integer type " + type1 ); - } + // find the min and max values in the array + int max = 0, min = 0; + for ( final int v : values ) { + if ( v > max ) max = v; + if ( v < min ) min = v; } - return maxType; + + final BCF2Type maxType = determineIntegerType(max); + final BCF2Type minType = determineIntegerType(min); + + // INT8 < INT16 < INT32 so this returns the larger of the two + return maxType.compareTo(minType) >= 0 ? maxType : minType; } /** @@ -281,31 +280,4 @@ public static List toList(final Object o) { else if ( o instanceof List ) return (List)o; else return Collections.singletonList(o); } - - public static void encodeRawBytes(final int value, final BCF2Type type, final OutputStream encodeStream) throws IOException { - switch ( type.getSizeInBytes() ) { - case 1: - encodeStream.write(0xFF & value); - break; - case 2: - encodeStream.write((0x00FF & value)); - encodeStream.write((0xFF00 & value) >> 8); - break; - case 4: - encodeStream.write((0x000000FF & value)); - encodeStream.write((0x0000FF00 & value) >> 8); - encodeStream.write((0x00FF0000 & value) >> 16); - encodeStream.write((0xFF000000 & value) >> 24); - break; - default: - throw new ReviewedStingException("BUG: unexpected type size " + type); - } -// general case for reference -// for ( int i = type.getSizeInBytes() - 1; i >= 0; i-- ) { -// final int shift = i * 8; -// int mask = 0xFF << shift; -// int byteValue = (mask & value) >> shift; -// encodeStream.write(byteValue); -// } - } } diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Encoder.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Encoder.java index a2bbfb391c..01dac7eb69 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Encoder.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Encoder.java @@ -191,9 +191,12 @@ public final void encodeRawFloat(final double value) throws IOException { @Requires("size >= 0") @Ensures("encodeStream.size() > old(encodeStream.size())") public final void encodeType(final int size, final BCF2Type type) throws IOException { - final byte typeByte = BCF2Utils.encodeTypeDescriptor(size, type); - encodeStream.write(typeByte); - if ( size > BCF2Utils.MAX_INLINE_ELEMENTS ) { + if ( size <= BCF2Utils.MAX_INLINE_ELEMENTS ) { + final int typeByte = BCF2Utils.encodeTypeDescriptor(size, type); + encodeStream.write(typeByte); + } else { + final int typeByte = BCF2Utils.encodeTypeDescriptor(BCF2Utils.OVERFLOW_ELEMENT_MARKER, type); + encodeStream.write(typeByte); // write in the overflow size encodeTypedInt(size); } @@ -201,12 +204,12 @@ public final void encodeType(final int size, final BCF2Type type) throws IOExcep @Ensures("encodeStream.size() > old(encodeStream.size())") public final void encodeRawInt(final int value, final BCF2Type type) throws IOException { - BCF2Utils.encodeRawBytes(value, type, encodeStream); + type.write(value, encodeStream); } @Ensures("encodeStream.size() > old(encodeStream.size())") public final void encodeRawBytes(final int value, final BCF2Type type) throws IOException { - BCF2Utils.encodeRawBytes(value, type, encodeStream); + type.write(value, encodeStream); } // -------------------------------------------------------------------------------- diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java index 32377d09ef..a080c4e624 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java @@ -158,7 +158,7 @@ public void writeHeader(VCFHeader header) { final byte[] headerBytes = capture.toByteArray(); new BCFVersion(MAJOR_VERSION, MINOR_VERSION).write(outputStream); - BCF2Utils.encodeRawBytes(headerBytes.length, BCF2Type.INT32, outputStream); + BCF2Type.INT32.write(headerBytes.length, outputStream); outputStream.write(headerBytes); } catch (IOException e) { throw new UserException.CouldNotCreateOutputFile("BCF2 stream", "Got IOException while trying to write BCF2 header", e); @@ -359,8 +359,8 @@ private final void errorUnexpectedFieldToWrite(final VariantContext vc, final St */ @Requires({"infoBlock.length > 0", "genotypesBlock.length >= 0"}) private void writeBlock(final byte[] infoBlock, final byte[] genotypesBlock) throws IOException { - BCF2Utils.encodeRawBytes(infoBlock.length, BCF2Type.INT32, outputStream); - BCF2Utils.encodeRawBytes(genotypesBlock.length, BCF2Type.INT32, outputStream); + BCF2Type.INT32.write(infoBlock.length, outputStream); + BCF2Type.INT32.write(genotypesBlock.length, outputStream); outputStream.write(infoBlock); outputStream.write(genotypesBlock); } From c3cfb7ae0df6b2051ff429f87798729f5d7eb959 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 9 Aug 2012 15:34:20 -0400 Subject: [PATCH 096/176] Updating cofoja to the latest version --- ivy.xml | 2 +- ...a-1.0-20110609.jar => cofoja-1.0-r139.jar} | Bin 377018 -> 378205 bytes ...a-1.0-20110609.xml => cofoja-1.0-r139.xml} | 2 +- 3 files changed, 2 insertions(+), 2 deletions(-) rename settings/repository/com.google.code.cofoja/{cofoja-1.0-20110609.jar => cofoja-1.0-r139.jar} (73%) rename settings/repository/com.google.code.cofoja/{cofoja-1.0-20110609.xml => cofoja-1.0-r139.xml} (57%) diff --git a/ivy.xml b/ivy.xml index 6dd5be7a8a..0761cb4111 100644 --- a/ivy.xml +++ b/ivy.xml @@ -87,7 +87,7 @@ - + diff --git a/settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.jar b/settings/repository/com.google.code.cofoja/cofoja-1.0-r139.jar similarity index 73% rename from settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.jar rename to settings/repository/com.google.code.cofoja/cofoja-1.0-r139.jar index 2197e721faa7b98dbc7ed1a4bfa88b7d7aedb8b9..2cbdd380d89da4778dc0e1e3144b9e91975a711e 100644 GIT binary patch delta 79023 zcmZ5{19W6vvvzFTnb@{%+qP|VCU(cRZQIF&6Wiv*m`sv?-tWElU+cSPtml_r1!vQ#|7DXGMQcjC3JMNNj*Y zOd}i^3ku}B@Fz(rmX2%cmdB|E7N|&r(IFmLdYpN&Gr&oQ`Q_vWc<^%GBobyxx)hhVddn=-aQo&r&NfwUZR5Kb^zj6JDbW%*)|nT 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a/settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.xml b/settings/repository/com.google.code.cofoja/cofoja-1.0-r139.xml similarity index 57% rename from settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.xml rename to settings/repository/com.google.code.cofoja/cofoja-1.0-r139.xml index 38d4e88f1a..202d3d0a3d 100644 --- a/settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.xml +++ b/settings/repository/com.google.code.cofoja/cofoja-1.0-r139.xml @@ -1,3 +1,3 @@ - + From c8b6216a0eabf2b4e4e0f4badb5a44f831cf9554 Mon Sep 17 00:00:00 2001 From: David Roazen Date: Thu, 9 Aug 2012 17:08:43 -0400 Subject: [PATCH 097/176] Update cofoja version in build.xml --- build.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.xml b/build.xml index ca5d22a5a7..135b9dac7d 100644 --- a/build.xml +++ b/build.xml @@ -92,7 +92,7 @@ - + From ebc4853558e06f27ba20e94fb8d2ab79fe5aa8e0 Mon Sep 17 00:00:00 2001 From: David Roazen Date: Thu, 9 Aug 2012 17:10:47 -0400 Subject: [PATCH 098/176] Revert unintentional license change --- licensing/GATK1_LICENSE | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/licensing/GATK1_LICENSE b/licensing/GATK1_LICENSE index 080ea1e68d..648ec8fc34 100644 --- a/licensing/GATK1_LICENSE +++ b/licensing/GATK1_LICENSE @@ -1,6 +1,4 @@ -Copyright (c) 2013 The Broad Institute - -Extra text +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 From c6e23434e76e61b2d75ebbf0b634647f064f244e Mon Sep 17 00:00:00 2001 From: Joel Thibault Date: Tue, 31 Jul 2012 10:31:17 -0400 Subject: [PATCH 099/176] Add -nt parameter From 12d8dd7d9bba4d9a29e055b82a18b49ba7adcceb Mon Sep 17 00:00:00 2001 From: Joel Thibault Date: Tue, 31 Jul 2012 11:15:54 -0400 Subject: [PATCH 100/176] Change memoryValues to List[Double] From 65bf9c40e66f38ad5b11dc01ada00373077aa9cd Mon Sep 17 00:00:00 2001 From: Joel Thibault Date: Wed, 8 Aug 2012 15:52:24 -0400 Subject: [PATCH 101/176] capMaxAllelesForIndels -> capMaxAltAllelesForIndels From 496e9386ed57909c3d257fdb9627d516b9f4bd25 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Fri, 10 Aug 2012 14:54:07 -0400 Subject: [PATCH 102/176] Adding support of X and = CIGAR operators to the GATK --- .../gatk/iterators/LocusIteratorByState.java | 2 + .../gatk/walkers/indels/IndelRealigner.java | 8 +- .../walkers/indels/SomaticIndelDetector.java | 8 +- .../broadinstitute/sting/utils/baq/BAQ.java | 2 +- .../sting/utils/sam/AlignmentUtils.java | 172 +++--------------- .../reads/TheoreticalMinimaBenchmark.java | 2 +- .../LocusIteratorByStateUnitTest.java | 40 ++++ 7 files changed, 81 insertions(+), 153 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java index 7d035d208f..1606c227de 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java +++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java @@ -195,6 +195,8 @@ public CigarOperator stepForwardOnGenome() { done = true; break; case M: + case EQ: + case X: readOffset++; genomeOffset++; done = true; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index 5e0f15e6aa..d61b9e9b6a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -1025,7 +1025,9 @@ private Consensus createAlternateConsensus(final int indexOnRef, final Cigar c, elements.add(ce); break; case M: - altIdx += elementLength; + case EQ: + case X: + altIdx += elementLength; case N: if ( reference.length < refIdx + elementLength ) ok_flag = false; @@ -1287,6 +1289,8 @@ private boolean alternateReducesEntropy(final List reads, final byt int elementLength = ce.getLength(); switch ( ce.getOperator() ) { case M: + case EQ: + case X: for (int k = 0 ; k < elementLength ; k++, refIdx++, altIdx++ ) { if ( refIdx >= reference.length ) break; @@ -1432,6 +1436,8 @@ private void getUnclippedBases() { fromIndex += elementLength; break; case M: + case EQ: + case X: case I: System.arraycopy(actualReadBases, fromIndex, readBases, toIndex, elementLength); System.arraycopy(actualBaseQuals, fromIndex, baseQuals, toIndex, elementLength); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java index ba16fd7092..b0c09f78e5 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java @@ -2057,7 +2057,9 @@ public ExpandedSAMRecord(SAMRecord r, byte [] ref, long offset, IndelListener l) break; // do not count gaps or clipped bases case I: case M: - readLength += cel.getLength(); + case EQ: + case X: + readLength += cel.getLength(); break; // advance along the gapless block in the alignment default : throw new IllegalArgumentException("Unexpected operator in cigar string: "+cel.getOperator()); @@ -2094,7 +2096,9 @@ public ExpandedSAMRecord(SAMRecord r, byte [] ref, long offset, IndelListener l) break; case M: - for ( int k = 0; k < ce.getLength(); k++, posOnRef++, posOnRead++ ) { + case EQ: + case X: + for ( int k = 0; k < ce.getLength(); k++, posOnRef++, posOnRead++ ) { if ( readBases[posOnRead] != ref[posOnRef] ) { // mismatch! mms++; mismatch_flags[posOnRef] = 1; diff --git a/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java b/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java index 1864522942..439a0d8edd 100644 --- a/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java +++ b/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java @@ -551,7 +551,7 @@ private final Pair calculateQueryRange(SAMRecord read) { switch (elt.getOperator()) { case N: return null; // cannot handle these case H : case P : case D: break; // ignore pads, hard clips, and deletions - case I : case S: case M: + case I : case S: case M: case EQ: case X: int prev = readI; readI += elt.getLength(); if ( includeClippedBases || elt.getOperator() != CigarOperator.S) { diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java index 2c388a1e0e..4f1e66ba2b 100644 --- a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java @@ -39,7 +39,6 @@ import java.util.ArrayList; import java.util.Arrays; -import java.util.BitSet; public class AlignmentUtils { @@ -71,9 +70,18 @@ public static MismatchCount getMismatchCount(SAMRecord r, byte[] refSeq, int ref if (readIdx > endOnRead) break; CigarElement ce = c.getCigarElement(i); + final int elementLength = ce.getLength(); switch (ce.getOperator()) { + case X: + mc.numMismatches += elementLength; + for (int j = 0; j < elementLength; j++) + mc.mismatchQualities += r.getBaseQualities()[readIdx+j]; + case EQ: + refIndex += elementLength; + readIdx += elementLength; + break; case M: - for (int j = 0; j < ce.getLength(); j++, refIndex++, readIdx++) { + for (int j = 0; j < elementLength; j++, refIndex++, readIdx++) { if (refIndex >= refSeq.length) continue; if (readIdx < startOnRead) continue; @@ -92,11 +100,11 @@ public static MismatchCount getMismatchCount(SAMRecord r, byte[] refSeq, int ref break; case I: case S: - readIdx += ce.getLength(); + readIdx += elementLength; break; case D: case N: - refIndex += ce.getLength(); + refIndex += elementLength; break; case H: case P: @@ -164,6 +172,8 @@ public static int mismatchesInRefWindow(PileupElement p, ReferenceContext ref, b CigarElement ce = c.getCigarElement(i); int cigarElementLength = ce.getLength(); switch (ce.getOperator()) { + case EQ: + case X: case M: for (int j = 0; j < cigarElementLength; j++, readIndex++, currentPos++) { // are we past the ref window? @@ -204,111 +214,6 @@ public static int mismatchesInRefWindow(PileupElement p, ReferenceContext ref, b return sum; } - /** - * Returns the number of mismatches in the pileup element within the given reference context. - * - * @param read the SAMRecord - * @param ref the reference context - * @param maxMismatches the maximum number of surrounding mismatches we tolerate to consider a base good - * @param windowSize window size (on each side) to test - * @return a bitset representing which bases are good - */ - public static BitSet mismatchesInRefWindow(SAMRecord read, ReferenceContext ref, int maxMismatches, int windowSize) { - // first determine the positions with mismatches - int readLength = read.getReadLength(); - BitSet mismatches = new BitSet(readLength); - - // it's possible we aren't starting at the beginning of a read, - // and we don't need to look at any of the previous context outside our window - // (although we do need future context) - int readStartPos = Math.max(read.getAlignmentStart(), ref.getLocus().getStart() - windowSize); - int currentReadPos = read.getAlignmentStart(); - - byte[] refBases = ref.getBases(); - int refIndex = readStartPos - ref.getWindow().getStart(); - if (refIndex < 0) { - throw new IllegalStateException("When calculating mismatches, we somehow don't have enough previous reference context for read " + read.getReadName() + " at position " + ref.getLocus()); - } - - byte[] readBases = read.getReadBases(); - int readIndex = 0; - - Cigar c = read.getCigar(); - - for (int i = 0; i < c.numCigarElements(); i++) { - CigarElement ce = c.getCigarElement(i); - int cigarElementLength = ce.getLength(); - switch (ce.getOperator()) { - case M: - for (int j = 0; j < cigarElementLength; j++, readIndex++) { - // skip over unwanted bases - if (currentReadPos++ < readStartPos) - continue; - - // this is possible if reads extend beyond the contig end - if (refIndex >= refBases.length) - break; - - byte refChr = refBases[refIndex]; - byte readChr = readBases[readIndex]; - if (readChr != refChr) - mismatches.set(readIndex); - - refIndex++; - } - break; - case I: - case S: - readIndex += cigarElementLength; - break; - case D: - case N: - if (currentReadPos >= readStartPos) - refIndex += cigarElementLength; - currentReadPos += cigarElementLength; - break; - case H: - case P: - break; - } - } - - // all bits are set to false by default - BitSet result = new BitSet(readLength); - - int currentPos = 0, leftPos = 0, rightPos; - int mismatchCount = 0; - - // calculate how many mismatches exist in the windows to the left/right - for (rightPos = 1; rightPos <= windowSize && rightPos < readLength; rightPos++) { - if (mismatches.get(rightPos)) - mismatchCount++; - } - if (mismatchCount <= maxMismatches) - result.set(currentPos); - - // now, traverse over the read positions - while (currentPos < readLength) { - // add a new rightmost position - if (rightPos < readLength && mismatches.get(rightPos++)) - mismatchCount++; - // re-penalize the previous position - if (mismatches.get(currentPos++)) - mismatchCount++; - // don't penalize the current position - if (mismatches.get(currentPos)) - mismatchCount--; - // subtract the leftmost position - if (leftPos < currentPos - windowSize && mismatches.get(leftPos++)) - mismatchCount--; - - if (mismatchCount <= maxMismatches) - result.set(currentPos); - } - - return result; - } - /** * Returns number of alignment blocks (continuous stretches of aligned bases) in the specified alignment. * This method follows closely the SAMRecord::getAlignmentBlocks() implemented in samtools library, but @@ -367,45 +272,6 @@ public static int getNumHardClippedBases(final SAMRecord r) { return n; } - public static byte[] alignmentToByteArray(final Cigar cigar, final byte[] read, final byte[] ref) { - - final byte[] alignment = new byte[read.length]; - int refPos = 0; - int alignPos = 0; - - for (int iii = 0; iii < cigar.numCigarElements(); iii++) { - - final CigarElement ce = cigar.getCigarElement(iii); - final int elementLength = ce.getLength(); - - switch (ce.getOperator()) { - case I: - case S: - for (int jjj = 0; jjj < elementLength; jjj++) { - alignment[alignPos++] = '+'; - } - break; - case D: - case N: - refPos += elementLength; - break; - case M: - for (int jjj = 0; jjj < elementLength; jjj++) { - alignment[alignPos] = ref[refPos]; - alignPos++; - refPos++; - } - break; - case H: - case P: - break; - default: - throw new ReviewedStingException("Unsupported cigar operator: " + ce.getOperator()); - } - } - return alignment; - } - public static int calcNumHighQualitySoftClips( final GATKSAMRecord read, final byte qualThreshold ) { int numHQSoftClips = 0; @@ -426,6 +292,8 @@ public static int calcNumHighQualitySoftClips( final GATKSAMRecord read, final b break; case M: case I: + case EQ: + case X: alignPos += elementLength; break; case H: @@ -488,6 +356,8 @@ public static int calcAlignmentByteArrayOffset(final Cigar cigar, final int offs } break; case M: + case EQ: + case X: if (pos + elementLength - 1 >= pileupOffset) { return alignmentPos + (pileupOffset - pos); } else { @@ -519,6 +389,8 @@ public static byte[] readToAlignmentByteArray(final Cigar cigar, final byte[] re case D: case N: case M: + case EQ: + case X: alignmentLength += elementLength; break; case I: @@ -565,6 +437,8 @@ public static byte[] readToAlignmentByteArray(final Cigar cigar, final byte[] re } break; case M: + case EQ: + case X: for (int jjj = 0; jjj < elementLength; jjj++) { alignment[alignPos] = read[readPos]; alignPos++; @@ -798,6 +672,8 @@ private static byte[] createIndelString(final Cigar cigar, final int indexOfInde switch (ce.getOperator()) { case M: + case EQ: + case X: readIndex += length; refIndex += length; totalRefBases += length; diff --git a/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/TheoreticalMinimaBenchmark.java b/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/TheoreticalMinimaBenchmark.java index 8e67c9efce..1abca54872 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/TheoreticalMinimaBenchmark.java +++ b/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/TheoreticalMinimaBenchmark.java @@ -94,7 +94,7 @@ public void timeIterateOverCigarString(int reps) { int elementSize = cigarElement.getLength(); while(elementSize > 0) { switch(cigarElement.getOperator()) { - case M: matchMismatches++; break; + case M: case EQ: case X: matchMismatches++; break; case I: insertions++; break; case D: deletions++; break; default: others++; break; diff --git a/public/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java index 218548b00a..dc908c323c 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java @@ -41,6 +41,46 @@ private final LocusIteratorByState makeLTBS(List reads, ReadPropertie return new LocusIteratorByState(new FakeCloseableIterator(reads.iterator()), readAttributes, genomeLocParser, LocusIteratorByState.sampleListForSAMWithoutReadGroups()); } + @Test + public void testXandEQOperators() { + final byte[] bases1 = new byte[] {'A','A','A','A','A','A','A','A','A','A'}; + final byte[] bases2 = new byte[] {'A','A','A','C','A','A','A','A','A','C'}; + + // create a test version of the Reads object + ReadProperties readAttributes = createTestReadProperties(); + + SAMRecord r1 = ArtificialSAMUtils.createArtificialRead(header,"r1",0,1,10); + r1.setReadBases(bases1); + r1.setBaseQualities(new byte[] {20,20,20,20,20,20,20,20,20,20}); + r1.setCigarString("10M"); + + SAMRecord r2 = ArtificialSAMUtils.createArtificialRead(header,"r2",0,1,10); + r2.setReadBases(bases2); + r2.setBaseQualities(new byte[] {20,20,20,20,20,20,20,20,20,20,20,20}); + r2.setCigarString("3=1X5=1X"); + + SAMRecord r3 = ArtificialSAMUtils.createArtificialRead(header,"r3",0,1,10); + r3.setReadBases(bases2); + r3.setBaseQualities(new byte[] {20,20,20,20,20,20,20,20,20,20,20,20}); + r3.setCigarString("3=1X5M1X"); + + SAMRecord r4 = ArtificialSAMUtils.createArtificialRead(header,"r4",0,1,10); + r4.setReadBases(bases2); + r4.setBaseQualities(new byte[] {20,20,20,20,20,20,20,20,20,20}); + r4.setCigarString("10M"); + + List reads = Arrays.asList(r1, r2, r3, r4); + + // create the iterator by state with the fake reads and fake records + li = makeLTBS(reads,readAttributes); + + while (li.hasNext()) { + AlignmentContext context = li.next(); + ReadBackedPileup pileup = context.getBasePileup(); + Assert.assertEquals(pileup.depthOfCoverage(), 4); + } + } + @Test public void testIndelsInRegularPileup() { final byte[] bases = new byte[] {'A','A','A','A','A','A','A','A','A','A'}; From 3a399dc26f78ebc66223bb4addf00cc62876398a Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Fri, 10 Aug 2012 14:58:29 -0400 Subject: [PATCH 103/176] When adding a unit test to LIBS for X and = CIGAR operators, I uncovered a bug with the implementation of the ReadBackedPileup.depthOfCoverage() method. --- .../sting/utils/pileup/AbstractReadBackedPileup.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java b/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java index e71cd01bec..3d986f6669 100644 --- a/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java +++ b/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java @@ -155,7 +155,7 @@ protected void calculateAbstractSize() { protected void addPileupToCumulativeStats(AbstractReadBackedPileup pileup) { size += pileup.getNumberOfElements(); - abstractSize += pileup.depthOfCoverage(); + abstractSize = pileup.depthOfCoverage() + (abstractSize == -1 ? 0 : abstractSize); nDeletions += pileup.getNumberOfDeletions(); nMQ0Reads += pileup.getNumberOfMappingQualityZeroReads(); } From a85d27ed46c8007ac2fdf69c7e3242fc92292bfd Mon Sep 17 00:00:00 2001 From: Ami Levy Moonshine Date: Fri, 10 Aug 2012 16:58:05 -0400 Subject: [PATCH 104/176] update integration tests at CombineVariantsIntegrationTest --- .../variantutils/CombineVariantsIntegrationTest.java | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java index 3b60fa2c2d..c8551657a4 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java @@ -142,10 +142,10 @@ public void combineComplexSites(String args, String md5) { cvExecuteTest("combineComplexSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec); } - @Test public void complexTestFull() { combineComplexSites("", "151a4970367dd3e73ba3e7f3c2f874f6"); } - @Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "c0625e092b878b3d3eb1703c48e216b7"); } - @Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "6978329d6a1033ac16f83b49072c679b"); } - @Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "6978329d6a1033ac16f83b49072c679b"); } + @Test public void complexTestFull() { combineComplexSites("", "9d989053826ffe5bef7c4e05ac51bcca"); } + @Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "4f38d9fd30a7ae83e2a7dec265a28772"); } + @Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "46bbbbb8fc9ae6467a4f8fe35b8d7d14"); } + @Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "46bbbbb8fc9ae6467a4f8fe35b8d7d14"); } @Test public void combineDBSNPDuplicateSites() { From d5d0137a11ff99c850a9969cdbd4b1c53286d1ab Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Sun, 12 Aug 2012 10:27:05 -0400 Subject: [PATCH 105/176] Add useful logger.info telling us the mismatch and indel context sizes --- .../utils/recalibration/covariates/ContextCovariate.java | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java index 4c20284d96..13ea0f0b37 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java @@ -25,6 +25,7 @@ package org.broadinstitute.sting.utils.recalibration.covariates; +import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.recalibration.ReadCovariates; import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; import org.broadinstitute.sting.utils.BaseUtils; @@ -43,6 +44,7 @@ */ public class ContextCovariate implements StandardCovariate { + private final static Logger logger = Logger.getLogger(ContextCovariate.class); private int mismatchesContextSize; private int indelsContextSize; @@ -63,6 +65,9 @@ public class ContextCovariate implements StandardCovariate { public void initialize(final RecalibrationArgumentCollection RAC) { mismatchesContextSize = RAC.MISMATCHES_CONTEXT_SIZE; indelsContextSize = RAC.INDELS_CONTEXT_SIZE; + + logger.info("Context sizes: base substitution model " + mismatchesContextSize + ", indel substitution model " + indelsContextSize); + if (mismatchesContextSize > MAX_DNA_CONTEXT) throw new UserException.BadArgumentValue("mismatches_context_size", String.format("context size cannot be bigger than %d, but was %d", MAX_DNA_CONTEXT, mismatchesContextSize)); if (indelsContextSize > MAX_DNA_CONTEXT) From 8a546aee90e8f7bdf70bdbe3510d01eb1c3e4243 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Sun, 12 Aug 2012 13:44:07 -0400 Subject: [PATCH 106/176] Expanded the BQSR reporting script -- Includes header page -- Table of arguments (Arguments) -- Summary of counts (RecalData0) -- Summary of counts by qual (RecalData1) -- Fixed bug in output that resulted in covariates list always being null (updated md5s accordingly) -- BQSR.R loads all relevant libaries now, include gplots, grid, and gsalib to run correctly --- .../sting/utils/recalibration/BQSR.R | 53 +++++++++++++++---- .../bqsr/RecalibrationArgumentCollection.java | 4 +- .../sting/utils/recalibration/RecalUtils.java | 23 ++++++-- 3 files changed, 65 insertions(+), 15 deletions(-) diff --git a/public/R/scripts/org/broadinstitute/sting/utils/recalibration/BQSR.R b/public/R/scripts/org/broadinstitute/sting/utils/recalibration/BQSR.R index 6c4dace1df..4fa1c97392 100644 --- a/public/R/scripts/org/broadinstitute/sting/utils/recalibration/BQSR.R +++ b/public/R/scripts/org/broadinstitute/sting/utils/recalibration/BQSR.R @@ -1,8 +1,18 @@ library("ggplot2") +library(gplots) +library("reshape") +library("grid") library("tools") #For compactPDF in R 2.13+ +library(gsalib) -args <- commandArgs(TRUE) + +if ( interactive() ) { + args <- c("NA12878.6.1.dedup.realign.recal.bqsr.grp.csv", "NA12878.6.1.dedup.realign.recal.bqsr.grp", NA) +} else { + args <- commandArgs(TRUE) +} data <- read.csv(args[1]) +gsa.report <- gsa.read.gatkreport(args[2]) data <- within(data, EventType <- factor(EventType, levels = rev(levels(EventType)))) numRG = length(unique(data$ReadGroup)) @@ -82,20 +92,45 @@ for(cov in levels(data$CovariateName)) { # for each covariate in turn p <- ggplot(d, aes(x=CovariateValue)) + xlab(paste(cov,"Covariate")) + - ylab("Number of Observations") + + ylab("No. of Observations (area normalized)") + blankTheme - d <- p + geom_histogram(aes(fill=Recalibration,weight=Observations),alpha=0.6,binwidth=1,position="identity") + scale_fill_manual(values=c("maroon1","blue")) + facet_grid(.~EventType) + - scale_y_continuous(formatter="comma") - + d <- p + geom_histogram(aes(fill=Recalibration,weight=Observations,y=..ndensity..),alpha=0.6,binwidth=1,position="identity") + d <- d + scale_fill_manual(values=c("maroon1","blue")) + d <- d + facet_grid(.~EventType) +# d <- d + scale_y_continuous(formatter="comma") } } -pdf(args[2],height=9,width=15) +if ( ! is.na(args[3]) ) + pdf(args[3],height=9,width=15) + +#frame() +textplot(gsa.report$Arguments, show.rownames=F) +title( + main="GATK BaseRecalibration report", + sub=date()) + distributeGraphRows(list(a,b,c), c(1,1,1)) distributeGraphRows(list(d,e,f), c(1,1,1)) -dev.off() +# format the overall information +rt0 <- data.frame( + ReadGroup = gsa.report$RecalTable0$ReadGroup, + EventType = gsa.report$RecalTable0$EventType, + EmpiricalQuality = sprintf("%.1f", gsa.report$RecalTable0$EmpiricalQuality), + EstimatedQReported = sprintf("%.1f", gsa.report$RecalTable0$EstimatedQReported), + Observations = sprintf("%.2e", gsa.report$RecalTable0$Observations), + Errors = sprintf("%.2e", gsa.report$RecalTable0$Errors)) +textplot(t(rt0), show.colnames=F) +title("Overall error rates by event type") + +# plot per quality score recalibration table +textplot(gsa.report$RecalTable1, show.rownames=F) +title("Rrror rates by event type and initial quality score") -if (exists('compactPDF')) { - compactPDF(args[2]) +if ( ! is.na(args[3]) ) { + dev.off() + if (exists('compactPDF')) { + compactPDF(args[2]) + } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java index f04e4a1b38..f4b00925eb 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java @@ -175,12 +175,12 @@ public class RecalibrationArgumentCollection { public File recalibrationReport = null; - public GATKReportTable generateReportTable() { + public GATKReportTable generateReportTable(final String covariateNames) { GATKReportTable argumentsTable = new GATKReportTable("Arguments", "Recalibration argument collection values used in this run", 2); argumentsTable.addColumn("Argument"); argumentsTable.addColumn(RecalUtils.ARGUMENT_VALUE_COLUMN_NAME); argumentsTable.addRowID("covariate", true); - argumentsTable.set("covariate", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, (COVARIATES == null) ? "null" : Utils.join(",", COVARIATES)); + argumentsTable.set("covariate", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, covariateNames); argumentsTable.addRowID("no_standard_covs", true); argumentsTable.set("no_standard_covs", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, DO_NOT_USE_STANDARD_COVARIATES); argumentsTable.addRowID("run_without_dbsnp", true); diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java index fe6ef70180..a605c4649d 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java @@ -326,9 +326,23 @@ private static String parseCovariateName(final Covariate covariate) { } public static void outputRecalibrationReport(final RecalibrationArgumentCollection RAC, final QuantizationInfo quantizationInfo, final RecalibrationTables recalibrationTables, final Covariate[] requestedCovariates, final PrintStream outputFile) { - outputRecalibrationReport(RAC.generateReportTable(), quantizationInfo.generateReportTable(), generateReportTables(recalibrationTables, requestedCovariates), outputFile); + outputRecalibrationReport(RAC.generateReportTable(covariateNames(requestedCovariates)), quantizationInfo.generateReportTable(), generateReportTables(recalibrationTables, requestedCovariates), outputFile); } + /** + * Return a human-readable string representing the used covariates + * + * @param requestedCovariates a vector of covariates + * @return a non-null comma-separated string + */ + public static String covariateNames(final Covariate[] requestedCovariates) { + final List names = new ArrayList(requestedCovariates.length); + for ( final Covariate cov : requestedCovariates ) + names.add(cov.getClass().getSimpleName()); + return Utils.join(",", names); + } + + public static void outputRecalibrationReport(final GATKReportTable argumentTable, final QuantizationInfo quantizationInfo, final RecalibrationTables recalibrationTables, final Covariate[] requestedCovariates, final PrintStream outputFile) { outputRecalibrationReport(argumentTable, quantizationInfo.generateReportTable(), generateReportTables(recalibrationTables, requestedCovariates), outputFile); } @@ -352,7 +366,7 @@ private static Pair initializeRecalibrationPlot(File filename return new Pair(deltaTableStream, deltaTableFileName); } - private static void outputRecalibrationPlot(Pair files, boolean keepIntermediates) { + private static void outputRecalibrationPlot(final File gatkReportFilename, Pair files, boolean keepIntermediates) { final File csvFileName = files.getSecond(); final File plotFileName = new File(csvFileName + ".pdf"); files.getFirst().close(); @@ -360,6 +374,7 @@ private static void outputRecalibrationPlot(Pair files, boole final RScriptExecutor executor = new RScriptExecutor(); executor.addScript(new Resource(SCRIPT_FILE, RecalUtils.class)); executor.addArgs(csvFileName.getAbsolutePath()); + executor.addArgs(gatkReportFilename.getAbsolutePath()); executor.addArgs(plotFileName.getAbsolutePath()); executor.exec(); @@ -372,14 +387,14 @@ private static void outputRecalibrationPlot(Pair files, boole public static void generateRecalibrationPlot(final File filename, final RecalibrationTables original, final Covariate[] requestedCovariates, final boolean keepIntermediates) { final Pair files = initializeRecalibrationPlot(filename); writeCSV(files.getFirst(), original, "ORIGINAL", requestedCovariates, true); - outputRecalibrationPlot(files, keepIntermediates); + outputRecalibrationPlot(filename, files, keepIntermediates); } public static void generateRecalibrationPlot(final File filename, final RecalibrationTables original, final RecalibrationTables recalibrated, final Covariate[] requestedCovariates, final boolean keepIntermediates) { final Pair files = initializeRecalibrationPlot(filename); writeCSV(files.getFirst(), recalibrated, "RECALIBRATED", requestedCovariates, true); writeCSV(files.getFirst(), original, "ORIGINAL", requestedCovariates, false); - outputRecalibrationPlot(files, keepIntermediates); + outputRecalibrationPlot(filename, files, keepIntermediates); } private static void writeCSV(final PrintStream deltaTableFile, final RecalibrationTables recalibrationTables, final String recalibrationMode, final Covariate[] requestedCovariates, final boolean printHeader) { From 3b7e1dbdc24e2ed4c749e37f51f1c034d7d30e2e Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Sun, 12 Aug 2012 13:45:52 -0400 Subject: [PATCH 107/176] A bit better output for ContextCovariate context size logging --- .../sting/utils/recalibration/covariates/ContextCovariate.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java index 13ea0f0b37..5709442459 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java @@ -66,7 +66,7 @@ public void initialize(final RecalibrationArgumentCollection RAC) { mismatchesContextSize = RAC.MISMATCHES_CONTEXT_SIZE; indelsContextSize = RAC.INDELS_CONTEXT_SIZE; - logger.info("Context sizes: base substitution model " + mismatchesContextSize + ", indel substitution model " + indelsContextSize); + logger.info("\t\tContext sizes: base substitution model " + mismatchesContextSize + ", indel substitution model " + indelsContextSize); if (mismatchesContextSize > MAX_DNA_CONTEXT) throw new UserException.BadArgumentValue("mismatches_context_size", String.format("context size cannot be bigger than %d, but was %d", MAX_DNA_CONTEXT, mismatchesContextSize)); From d976b7a32ae478503155117c260f83a0308b1a33 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Sun, 12 Aug 2012 13:58:14 -0400 Subject: [PATCH 108/176] Fix missing argument in unittest --- .../sting/utils/recalibration/RecalibrationReportUnitTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java index 387cc94d61..485da243f8 100644 --- a/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java @@ -98,7 +98,7 @@ public void testOutput() { } Assert.assertEquals(nKeys, expectedKeys); - final RecalibrationReport report = new RecalibrationReport(quantizationInfo, recalibrationTables, RAC.generateReportTable(), RAC); + final RecalibrationReport report = new RecalibrationReport(quantizationInfo, recalibrationTables, RAC.generateReportTable("ignore"), RAC); File output = new File("RecalibrationReportUnitTestOutuput.grp"); PrintStream out; From e600f62fc0c8f2b9b1d0a13aacf5299ceb781537 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Mon, 13 Aug 2012 10:01:33 -0400 Subject: [PATCH 109/176] Fixed spelling error in BQSR.R --- .../scripts/org/broadinstitute/sting/utils/recalibration/BQSR.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/R/scripts/org/broadinstitute/sting/utils/recalibration/BQSR.R b/public/R/scripts/org/broadinstitute/sting/utils/recalibration/BQSR.R index 4fa1c97392..8a9eecf48c 100644 --- a/public/R/scripts/org/broadinstitute/sting/utils/recalibration/BQSR.R +++ b/public/R/scripts/org/broadinstitute/sting/utils/recalibration/BQSR.R @@ -126,7 +126,7 @@ title("Overall error rates by event type") # plot per quality score recalibration table textplot(gsa.report$RecalTable1, show.rownames=F) -title("Rrror rates by event type and initial quality score") +title("Error rates by event type and initial quality score") if ( ! is.na(args[3]) ) { dev.off() From 5b65b72a6c678dbc2ae8ee5bf537a74cda3329d4 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Mon, 13 Aug 2012 14:20:26 -0400 Subject: [PATCH 110/176] Increase allowable range for BCF2 by -1 on low-end --- .../broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java index 6fd698ff6d..8a9ba87acc 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java @@ -48,8 +48,7 @@ public enum BCF2Type { } }, - // todo -- confirm range - INT8 (1, 1, 0xFFFFFF80, -127, 127) { + INT8 (1, 1, 0xFFFFFF80, -128, 127) { @Override public int read(final InputStream in) throws IOException { return BCF2Utils.readByte(in); @@ -61,7 +60,7 @@ public void write(final int value, final OutputStream out) throws IOException { } }, - INT16(2, 2, 0xFFFF8000, -32767, 32767) { + INT16(2, 2, 0xFFFF8000, -32768, 32767) { @Override public int read(final InputStream in) throws IOException { final int b2 = BCF2Utils.readByte(in) & 0xFF; @@ -77,7 +76,7 @@ public void write(final int value, final OutputStream out) throws IOException { } }, - INT32(3, 4, 0x80000000, -2147483647, 2147483647) { + INT32(3, 4, 0x80000000, -2147483648, 2147483647) { @Override public int read(final InputStream in) throws IOException { final int b4 = BCF2Utils.readByte(in) & 0xFF; From 3121725862c5ca233948f81c8e47e0d12bd98bdf Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Mon, 13 Aug 2012 15:06:28 -0400 Subject: [PATCH 111/176] Reverting changes to BCF2 ranges -- The previously expanded ones are actually the missing values in the range. The previous ranges were correct. Removed the TODO to confirm them, as they are now officially confirmed --- .../broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java index 8a9ba87acc..1162a5d1e9 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java @@ -48,7 +48,7 @@ public enum BCF2Type { } }, - INT8 (1, 1, 0xFFFFFF80, -128, 127) { + INT8 (1, 1, 0xFFFFFF80, -127, 127) { @Override public int read(final InputStream in) throws IOException { return BCF2Utils.readByte(in); @@ -60,7 +60,7 @@ public void write(final int value, final OutputStream out) throws IOException { } }, - INT16(2, 2, 0xFFFF8000, -32768, 32767) { + INT16(2, 2, 0xFFFF8000, -32767, 32767) { @Override public int read(final InputStream in) throws IOException { final int b2 = BCF2Utils.readByte(in) & 0xFF; @@ -76,7 +76,7 @@ public void write(final int value, final OutputStream out) throws IOException { } }, - INT32(3, 4, 0x80000000, -2147483648, 2147483647) { + INT32(3, 4, 0x80000000, -2147483647, 2147483647) { @Override public int read(final InputStream in) throws IOException { final int b4 = BCF2Utils.readByte(in) & 0xFF; From 959a7d18d9042e901952999d43186f140d3613a5 Mon Sep 17 00:00:00 2001 From: Khalid Shakir Date: Mon, 13 Aug 2012 15:37:35 -0400 Subject: [PATCH 112/176] Added setupRetry() to modify jobs when Queue is run with '-retry' and jobs are about to restart after an error. Implemented a mixin called "RetryMemoryLimit" which will by default double the memory. GridEngine memory request parameter can be selected on the command line via '-resMemReqParam mem_free' or '-resMemReqParam virtual_free'. Java optimizations now enabled by default: - Only 4 GC threads instead of each job using java's default O(number of cores) GC threads. Previously on a machine with N cores if you have N jobs running and java allocates N GC threads by default, then the machines are using up to N^2 threads if all jobs are in heavy GC (thanks elauzier). - Exit if GC spends more than 50% of time in GC (thanks ktibbett). - Exit if GC reclaims lest than 10% of max heap (thanks ktibbett). Added a -noGCOpt command line option to disable new java optimizations. --- .../examples/ExampleRetryMemoryLimit.scala | 22 ++++++ .../examples/ExampleUnifiedGenotyper.scala | 7 +- .../sting/queue/QSettings.scala | 9 +++ .../sting/queue/engine/FunctionEdge.scala | 19 ++--- .../sting/queue/engine/QGraph.scala | 29 +++---- .../gridengine/GridEngineJobRunner.scala | 10 +-- .../queue/function/CommandLineFunction.scala | 11 ++- .../function/JavaCommandLineFunction.scala | 52 ++++++++++++- .../sting/queue/function/QFunction.scala | 12 +++ .../queue/function/RetryMemoryLimit.scala | 78 +++++++++++++++++++ .../ExampleRetryMemoryLimitPipelineTest.scala | 44 +++++++++++ .../ExampleUnifiedGenotyperPipelineTest.scala | 47 ++++++----- 12 files changed, 279 insertions(+), 61 deletions(-) create mode 100644 public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleRetryMemoryLimit.scala create mode 100644 public/scala/src/org/broadinstitute/sting/queue/function/RetryMemoryLimit.scala create mode 100644 public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitPipelineTest.scala diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleRetryMemoryLimit.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleRetryMemoryLimit.scala new file mode 100644 index 0000000000..09a24e7822 --- /dev/null +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleRetryMemoryLimit.scala @@ -0,0 +1,22 @@ +import org.broadinstitute.sting.queue.function.RetryMemoryLimit +import org.broadinstitute.sting.queue.QScript +import org.broadinstitute.sting.queue.extensions.gatk._ + +class ExampleRetryMemoryLimit extends QScript { + @Input(doc="The reference file for the bam files.", shortName="R") + var referenceFile: File = _ + + @Input(doc="Bam file to genotype.", shortName="I") + var bamFile: File = _ + + def script() { + val ug = new UnifiedGenotyper with RetryMemoryLimit + // First run with 1m + ug.memoryLimit = .001 + // On retry run with 1g + ug.retryMemoryFunction = (d => d * 1000) + ug.reference_sequence = referenceFile + ug.input_file = Seq(bamFile) + add(ug) + } +} diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala index 8cb86db0b2..f5d750ac31 100644 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala @@ -5,7 +5,8 @@ import org.broadinstitute.sting.queue.extensions.gatk._ /** * An example building on the intro ExampleCountReads.scala. - * Runs an INCOMPLETE version of the UnifiedGenotyper with VariantEval and optional VariantFiltration. + * Runs an INCOMPLETE variant calling pipeline with just the UnifiedGenotyper, VariantEval and optional VariantFiltration. + * For a complete description of the suggested for a variant calling pipeline see the latest version of the Best Practice Variant Detection document */ class ExampleUnifiedGenotyper extends QScript { // Create an alias 'qscript' to be able to access variables @@ -43,14 +44,12 @@ class ExampleUnifiedGenotyper extends QScript { } def script() { - // Create the four function that we can run. + // Create the four functions that we may run depending on options. val genotyper = new UnifiedGenotyper with UnifiedGenotyperArguments val variantFilter = new VariantFiltration with UnifiedGenotyperArguments val evalUnfiltered = new VariantEval with UnifiedGenotyperArguments val evalFiltered = new VariantEval with UnifiedGenotyperArguments - // If you are running this on a compute farm, make sure that the Sting/shell - // folder is in your path to use mergeText.sh and splitIntervals.sh. genotyper.scatterCount = 3 genotyper.input_file :+= qscript.bamFile genotyper.out = swapExt(qscript.bamFile, "bam", "unfiltered.vcf") diff --git a/public/scala/src/org/broadinstitute/sting/queue/QSettings.scala b/public/scala/src/org/broadinstitute/sting/queue/QSettings.scala index d9fed4ce8b..1a50301f10 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/QSettings.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/QSettings.scala @@ -55,12 +55,18 @@ class QSettings { @Argument(fullName="memory_limit", shortName="memLimit", doc="Default memory limit for jobs, in gigabytes.", required=false) var memoryLimit: Option[Double] = None + @Argument(fullName="memory_limit_threshold", shortName="memLimitThresh", doc="After passing this threshold stop increasing memory limit for jobs, in gigabytes.", required=false) + var memoryLimitThreshold: Option[Double] = None + @Argument(fullName="resident_memory_limit", shortName="resMemLimit", doc="Default resident memory limit for jobs, in gigabytes.", required=false) var residentLimit: Option[Double] = None @Argument(fullName="resident_memory_request", shortName="resMemReq", doc="Default resident memory request for jobs, in gigabytes.", required=false) var residentRequest: Option[Double] = None + @Argument(fullName="resident_memory_request_parameter", shortName="resMemReqParam", doc="Parameter for resident memory requests. By default not requested.", required=false) + var residentRequestParameter: String = _ + /** The name of the parallel environment (required for SGE, for example) */ @Argument(fullName="job_parallel_env", shortName="jobParaEnv", doc="An SGE style parallel environment to use for jobs requesting more than 1 core. Equivalent to submitting jobs with -pe ARG nt for jobs with nt > 1", required=false) var parallelEnvironmentName: String = "smp_pe" // Broad default @@ -68,6 +74,9 @@ class QSettings { @Argument(fullName="dontRequestMultipleCores", shortName="multiCoreJerk", doc="If provided, Queue will not request multiple processors for jobs using multiple processors. Sometimes you eat the bear, sometimes the bear eats you.", required=false) var dontRequestMultipleCores: Boolean = false + @Argument(fullName="disableDefaultJavaGCOptimizations", shortName="noGCOpt", doc="If provided, Queue will not ensure that java GC threads are limited and that the a minimum amount of time is spent in GC.") + var disableDefaultJavaGCOptimizations = false + @Argument(fullName="run_directory", shortName="runDir", doc="Root directory to run functions from.", required=false) var runDirectory = new File(".") diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/FunctionEdge.scala b/public/scala/src/org/broadinstitute/sting/queue/engine/FunctionEdge.scala index 8225d28ab3..2d4ff60f5c 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/engine/FunctionEdge.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/engine/FunctionEdge.scala @@ -40,11 +40,6 @@ import org.apache.commons.lang.StringUtils class FunctionEdge(val function: QFunction, val inputs: QNode, val outputs: QNode) extends QEdge with Logging { var runner: JobRunner[_] =_ - /** - * The number of times this edge has been run. - */ - var retries = 0 - /** * The depth of this edge in the graph. */ @@ -87,14 +82,14 @@ class FunctionEdge(val function: QFunction, val inputs: QNode, val outputs: QNod runner.init() runner.start() } catch { - case e => + case e: Throwable => currentStatus = RunnerStatus.FAILED try { runner.cleanup() function.failOutputs.foreach(_.createNewFile()) writeStackTrace(e) } catch { - case _ => /* ignore errors in the exception handler */ + case _: Throwable => /* ignore errors in the exception handler */ } logger.error("Error: " + function.description, e) } @@ -114,7 +109,7 @@ class FunctionEdge(val function: QFunction, val inputs: QNode, val outputs: QNod runner.cleanup() function.failOutputs.foreach(_.createNewFile()) } catch { - case _ => /* ignore errors in the error handler */ + case _: Throwable => /* ignore errors in the error handler */ } logger.error("Error: " + function.description) tailError() @@ -123,19 +118,19 @@ class FunctionEdge(val function: QFunction, val inputs: QNode, val outputs: QNod runner.cleanup() function.doneOutputs.foreach(_.createNewFile()) } catch { - case _ => /* ignore errors in the done handler */ + case _: Throwable => /* ignore errors in the done handler */ } logger.info("Done: " + function.description) } } catch { - case e => + case e: Throwable => currentStatus = RunnerStatus.FAILED try { runner.cleanup() function.failOutputs.foreach(_.createNewFile()) writeStackTrace(e) } catch { - case _ => /* ignore errors in the exception handler */ + case _: Throwable => /* ignore errors in the exception handler */ } logger.error("Error retrieving status: " + function.description, e) } @@ -168,6 +163,7 @@ class FunctionEdge(val function: QFunction, val inputs: QNode, val outputs: QNod currentStatus = RunnerStatus.PENDING if (cleanOutputs) function.deleteOutputs() + function.jobErrorLines = Nil runner = null } @@ -189,6 +185,7 @@ class FunctionEdge(val function: QFunction, val inputs: QNode, val outputs: QNod val tailLines = IOUtils.tail(errorFile, maxLines) val nl = "%n".format() val summary = if (tailLines.size > maxLines) "Last %d lines".format(maxLines) else "Contents" + this.function.jobErrorLines = collection.JavaConversions.asScalaIterable(tailLines).toSeq logger.error("%s of %s:%n%s".format(summary, errorFile, StringUtils.join(tailLines, nl))) } else { logger.error("Unable to access log file: %s".format(errorFile)) diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala b/public/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala index cee2c6e56a..e3a1714ffe 100755 --- a/public/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala @@ -116,7 +116,7 @@ class QGraph extends Logging { val isReady = numMissingValues == 0 if (this.jobGraph.edgeSet.isEmpty) { - logger.warn("Nothing to run! Were any Functions added?"); + logger.warn("Nothing to run! Were any Functions added?") } else if (settings.getStatus) { logger.info("Checking pipeline status.") logStatus() @@ -320,7 +320,7 @@ class QGraph extends Logging { if (settings.startFromScratch) logger.info("Will remove outputs from previous runs.") - updateGraphStatus(false) + updateGraphStatus(cleanOutputs = false) var readyJobs = getReadyJobs while (running && readyJobs.size > 0) { @@ -361,7 +361,7 @@ class QGraph extends Logging { * Logs job statuses by traversing the graph and looking for status-related files */ private def logStatus() { - updateGraphStatus(false) + updateGraphStatus(cleanOutputs = false) doStatus(status => logger.info(status)) } @@ -388,7 +388,7 @@ class QGraph extends Logging { if (settings.startFromScratch) logger.info("Removing outputs from previous runs.") - updateGraphStatus(true) + updateGraphStatus(cleanOutputs = true) var readyJobs = TreeSet.empty[FunctionEdge](functionOrdering) readyJobs ++= getReadyJobs @@ -473,7 +473,7 @@ class QGraph extends Logging { logStatusCounts() deleteCleanup(-1) } catch { - case e => + case e: Throwable => logger.error("Uncaught error running jobs.", e) throw e } finally { @@ -662,11 +662,12 @@ class QGraph extends Logging { private def checkRetryJobs(failed: Set[FunctionEdge]) { if (settings.retries > 0) { for (failedJob <- failed) { - if (failedJob.function.jobRestartable && failedJob.retries < settings.retries) { - failedJob.retries += 1 - failedJob.resetToPending(true) + if (failedJob.function.jobRestartable && failedJob.function.retries < settings.retries) { + failedJob.function.retries += 1 + failedJob.function.setupRetry() + failedJob.resetToPending(cleanOutputs = true) logger.info("Reset for retry attempt %d of %d: %s".format( - failedJob.retries, settings.retries, failedJob.function.description)) + failedJob.function.retries, settings.retries, failedJob.function.description)) statusCounts.failed -= 1 statusCounts.pending += 1 } else { @@ -733,7 +734,7 @@ class QGraph extends Logging { private def emailDescription(edge: FunctionEdge) = { val description = new StringBuilder if (settings.retries > 0) - description.append("Attempt %d of %d.%n".format(edge.retries + 1, settings.retries + 1)) + description.append("Attempt %d of %d.%n".format(edge.function.retries + 1, settings.retries + 1)) description.append(edge.function.description) description.toString() } @@ -1077,7 +1078,7 @@ class QGraph extends Logging { runner.checkUnknownStatus() } } catch { - case e => /* ignore */ + case e: Throwable => /* ignore */ } } } @@ -1119,20 +1120,20 @@ class QGraph extends Logging { try { manager.tryStop(managerRunners) } catch { - case e => /* ignore */ + case e: Throwable => /* ignore */ } for (runner <- managerRunners) { try { runner.cleanup() } catch { - case e => /* ignore */ + case e: Throwable => /* ignore */ } } } finally { try { manager.exit() } catch { - case e => /* ignore */ + case e: Throwable => /* ignore */ } } } diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/gridengine/GridEngineJobRunner.scala b/public/scala/src/org/broadinstitute/sting/queue/engine/gridengine/GridEngineJobRunner.scala index 76cefe2a53..0c94e9ecf3 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/engine/gridengine/GridEngineJobRunner.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/engine/gridengine/GridEngineJobRunner.scala @@ -52,13 +52,9 @@ class GridEngineJobRunner(session: Session, function: CommandLineFunction) exten nativeSpec += " -q " + function.jobQueue // If the resident set size is requested pass on the memory request - // NOTE: 12/20/11: depristo commented this out because mem_free isn't - // such a standard feature in SGE (gsa-engineering queue doesn't support it) - // requiring it can make SGE not so usable. It's dangerous to not enforce - // that we have enough memory to run our jobs, but I'd rather be dangerous - // than not be able to run my jobs at all. -// if (function.residentRequest.isDefined) -// nativeSpec += " -l mem_free=%dM".format(function.residentRequest.map(_ * 1024).get.ceil.toInt) + // mem_free is the standard, but may also be virtual_free or even not available + if (function.qSettings.residentRequestParameter != null && function.residentRequest.isDefined) + nativeSpec += " -l %s=%dM".format(function.qSettings.residentRequestParameter, function.residentRequest.map(_ * 1024).get.ceil.toInt) // If the resident set size limit is defined specify the memory limit if (function.residentLimit.isDefined) diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala b/public/scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala index eff4a2ba91..84b625760d 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala @@ -137,12 +137,17 @@ trait CommandLineFunction extends QFunction with Logging { if (residentRequest.isEmpty) residentRequest = memoryLimit - if (residentLimit.isEmpty) - residentLimit = residentRequest.map( _ * 1.2 ) + if (residentLimit.isEmpty || residentLimit == residentRequest) + residentLimit = residentRequest.map(residentLimitBuffer) super.freezeFieldValues() } + /** + * @return A function that decides how much memory cushion to add to the residentRequest to create the residentLimit + */ + def residentLimitBuffer: (Double => Double) = (1.2 * _) + /** * Safely construct a full required command-line argument with consistent quoting, whitespace separation, etc. * @@ -223,7 +228,7 @@ trait CommandLineFunction extends QFunction with Logging { */ protected def conditional( condition: Boolean, param: Any, escape: Boolean = true, format: String = "%s" ): String = { if ( condition ) { - " %s ".format(formatArgument("", param, "", false, escape, format)) + " %s ".format(formatArgument("", param, "", spaceSeparated = false, escape = escape, paramFormat = format)) } else { "" diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala b/public/scala/src/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala index 13448afdd5..b9cb8540f5 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala @@ -54,6 +54,16 @@ trait JavaCommandLineFunction extends CommandLineFunction { */ var javaGCThreads: Option[Int] = None + /** + * Max percent of time spent in garbage collection + */ + var javaGCTimeLimit: Option[Int] = None + + /** + * Min percent of max heap freed during a garbage collection + */ + var javaGCHeapFreeLimit: Option[Int] = None + override def freezeFieldValues() { super.freezeFieldValues() @@ -62,6 +72,37 @@ trait JavaCommandLineFunction extends CommandLineFunction { if (javaMainClass != null && javaClasspath.isEmpty) javaClasspath = JavaCommandLineFunction.currentClasspath + + if (!this.qSettings.disableDefaultJavaGCOptimizations) { + // By default set the GC threads to 4 + if (javaGCThreads.isEmpty) + javaGCThreads = Some(4) + + // By default exit if more than 50% of time in GC + if (javaGCTimeLimit.isEmpty) + javaGCTimeLimit = Some(50) + + // By default exit if GC does not free up 10% of the heap + if (javaGCHeapFreeLimit.isEmpty) + javaGCHeapFreeLimit = Some(10) + } + } + + + override def copySettingsTo(function: QFunction) { + super.copySettingsTo(function) + function match { + case java: JavaCommandLineFunction => + if (java.javaMemoryLimit.isEmpty) + java.javaMemoryLimit = this.javaMemoryLimit + if (java.javaGCThreads.isEmpty) + java.javaGCThreads = this.javaGCThreads + if (java.javaGCTimeLimit.isEmpty) + java.javaGCTimeLimit = this.javaGCTimeLimit + if (java.javaGCHeapFreeLimit.isEmpty) + java.javaGCHeapFreeLimit = this.javaGCHeapFreeLimit + case _ => /* ignore */ + } } /** @@ -77,10 +118,13 @@ trait JavaCommandLineFunction extends CommandLineFunction { null } - def javaOpts = optional("-Xmx", javaMemoryLimit.map(gb => (gb * 1024).ceil.toInt), "m", spaceSeparated=false) + - conditional(javaGCThreads.isDefined, "-XX:+UseParallelOldGC") + - optional("-XX:ParallelGCThreads=", javaGCThreads, spaceSeparated=false) + - required("-Djava.io.tmpdir=", jobTempDir, spaceSeparated=false) + def javaOpts = Array( + optional("-Xmx", javaMemoryLimit.map(gb => (gb * 1024).ceil.toInt), "m", spaceSeparated=false), + conditional(javaGCThreads.isDefined || javaGCTimeLimit.isDefined || javaGCHeapFreeLimit.isDefined, "-XX:+UseParallelOldGC"), + optional("-XX:ParallelGCThreads=", javaGCThreads, spaceSeparated=false), + optional("-XX:GCTimeLimit=", javaGCTimeLimit, spaceSeparated=false), + optional("-XX:GCHeapFreeLimit=", javaGCHeapFreeLimit, spaceSeparated=false), + required("-Djava.io.tmpdir=", jobTempDir, spaceSeparated=false)).mkString("") def commandLine = required("java") + javaOpts + diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala b/public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala index 7d9debbdc6..9f7932d396 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala @@ -112,6 +112,18 @@ trait QFunction extends Logging with QJobReport { /** File to redirect any errors. Defaults to .out */ var jobErrorFile: File = _ + /** Errors (if any) from the last failed run of jobErrorFiles. */ + var jobErrorLines: Seq[String] = Nil + + /** + * The number of times this function has previously been run. + */ + var retries = 0 + + /** Change settings for the next run. Retries will be set to the number of times the function was run and jobErrorLines may contain the error text. */ + def setupRetry() { + } + /** * Description of this command line function. */ diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/RetryMemoryLimit.scala b/public/scala/src/org/broadinstitute/sting/queue/function/RetryMemoryLimit.scala new file mode 100644 index 0000000000..8bba5551ff --- /dev/null +++ b/public/scala/src/org/broadinstitute/sting/queue/function/RetryMemoryLimit.scala @@ -0,0 +1,78 @@ +/* + * 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.queue.function + +/** A mixin that on retry increases the memory limit when certain text is found. */ +trait RetryMemoryLimit extends CommandLineFunction { + + /** How to increase the memory. By default doubles the memory. */ + var retryMemoryFunction: (Double => Double) = (2 * _) + + /** Once the threshold is passed, no more memory will be added to memory limit. */ + var memoryLimitThreshold: Option[Double] = None + + /** Various strings to look for to determine we ran out of memory. */ + var memoryLimitErrorText = Seq("OutOfMemory", "you did not provide enough memory", "TERM_MEMLIMIT") + + override def freezeFieldValues() { + super.freezeFieldValues() + if (this.memoryLimitThreshold.isEmpty) + this.memoryLimitThreshold = this.qSettings.memoryLimitThreshold + } + + override def setupRetry() { + super.setupRetry() + if (this.memoryLimitThreshold.isDefined && this.memoryLimit.isDefined) { + + // NOTE: If we're already at or above the memoryLimit, don't do anything. + if (this.memoryLimit.get < this.memoryLimitThreshold.get) { + updateMemoryLimits() + } + + } else { + updateMemoryLimits() + } + } + + def updateMemoryLimits() { + if (isMemoryError) { + this.memoryLimit = this.memoryLimit.map(this.retryMemoryFunction) + this.residentRequest = this.residentRequest.map(this.retryMemoryFunction) + this.residentLimit = this.residentLimit.map(this.retryMemoryFunction) + + // Rebuffer the memory limit if the limit was set exactly to the request + if (this.residentLimit == this.residentRequest) + this.residentLimit = this.residentRequest.map(this.residentLimitBuffer) + + this match { + case java: JavaCommandLineFunction => + java.javaMemoryLimit = java.javaMemoryLimit.map(this.retryMemoryFunction) + case _ => /* ignore */ + } + } + } + + def isMemoryError = this.jobErrorLines.exists(line => this.memoryLimitErrorText.exists(error => line.contains(error))) +} diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitPipelineTest.scala new file mode 100644 index 0000000000..a9a5928fc2 --- /dev/null +++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitPipelineTest.scala @@ -0,0 +1,44 @@ +/* + * 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.queue.pipeline.examples + +import org.testng.annotations.Test +import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec} +import org.broadinstitute.sting.BaseTest + +class ExampleRetryMemoryLimitPipelineTest { + @Test + def testRetryMemoryLimit() { + val spec = new PipelineTestSpec + spec.name = "RetryMemoryLimit" + spec.args = Array( + " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleRetryMemoryLimit.scala", + " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta", + " -I " + BaseTest.publicTestDir + "exampleBAM.bam", + " -retry 1").mkString + spec.jobRunners = PipelineTest.allJobRunners + PipelineTest.executeTest(spec) + } +} diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleUnifiedGenotyperPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleUnifiedGenotyperPipelineTest.scala index c9d8b59c95..f6fcd7c124 100644 --- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleUnifiedGenotyperPipelineTest.scala +++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleUnifiedGenotyperPipelineTest.scala @@ -24,7 +24,7 @@ package org.broadinstitute.sting.queue.pipeline.examples -import org.testng.annotations.Test +import org.testng.annotations.{DataProvider, Test} import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec} import org.broadinstitute.sting.BaseTest @@ -43,42 +43,53 @@ class ExampleUnifiedGenotyperPipelineTest { PipelineTest.executeTest(spec) } - @Test - def testUnifiedGenotyperWithGatkIntervals() { + @DataProvider(name = "ugIntervals") + def getUnifiedGenotyperIntervals = + Array( + Array("gatk_intervals", BaseTest.validationDataLocation + "intervalTest.intervals"), + Array("bed_intervals", BaseTest.validationDataLocation + "intervalTest.bed"), + Array("vcf_intervals", BaseTest.validationDataLocation + "intervalTest.1.vcf") + ).asInstanceOf[Array[Array[Object]]] + + @Test(dataProvider = "ugIntervals") + def testUnifiedGenotyperWithIntervals(intervalsName: String, intervalsPath: String) { val spec = new PipelineTestSpec - spec.name = "unifiedgenotyper_with_gatk_intervals" + spec.name = "unifiedgenotyper_with_" + intervalsName spec.args = Array( " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala", " -I " + BaseTest.validationDataLocation + "OV-0930.normal.chunk.bam", " -R " + BaseTest.hg18Reference, - " -L " + BaseTest.validationDataLocation + "intervalTest.intervals").mkString + " -L " + intervalsPath).mkString spec.jobRunners = Seq("Lsf706") PipelineTest.executeTest(spec) } @Test - def testUnifiedGenotyperWithBedIntervals() { + def testUnifiedGenotyperNoGCOpt() { val spec = new PipelineTestSpec - spec.name = "unifiedgenotyper_with_bed_intervals" + spec.name = "unifiedgenotyper_no_gc_opt" spec.args = Array( " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala", - " -I " + BaseTest.validationDataLocation + "OV-0930.normal.chunk.bam", - " -R " + BaseTest.hg18Reference, - " -L " + BaseTest.validationDataLocation + "intervalTest.bed").mkString - spec.jobRunners = Seq("Lsf706") + " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta", + " -I " + BaseTest.publicTestDir + "exampleBAM.bam", + " -noGCOpt").mkString + spec.jobRunners = PipelineTest.allJobRunners PipelineTest.executeTest(spec) } - @Test - def testUnifiedGenotyperWithVcfIntervals() { + @DataProvider(name="resMemReqParams") + def getResMemReqParam = Array(Array("mem_free"), Array("virtual_free")).asInstanceOf[Array[Array[Object]]] + + @Test(dataProvider = "resMemReqParams") + def testUnifiedGenotyperResMemReqParam(reqParam: String) { val spec = new PipelineTestSpec - spec.name = "unifiedgenotyper_with_vcf_intervals" + spec.name = "unifiedgenotyper_" + reqParam spec.args = Array( " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala", - " -I " + BaseTest.validationDataLocation + "OV-0930.normal.chunk.bam", - " -R " + BaseTest.hg18Reference, - " -L " + BaseTest.validationDataLocation + "intervalTest.1.vcf").mkString - spec.jobRunners = Seq("Lsf706") + " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta", + " -I " + BaseTest.publicTestDir + "exampleBAM.bam", + " -resMemReqParam " + reqParam).mkString + spec.jobRunners = Seq("GridEngine") PipelineTest.executeTest(spec) } } From b18d7ebc0bb3d84b75f99b6f72b53fd7f4959d8e Mon Sep 17 00:00:00 2001 From: Khalid Shakir Date: Mon, 13 Aug 2012 16:49:27 -0400 Subject: [PATCH 113/176] Removed SelectHeader's --include_reference_name option since the reference is always included. In SelectHeaders instead of including the path to the file, only include the name of the reference since dbGaP does not like paths in headers. --- .../walkers/variantutils/SelectHeaders.java | 12 +----- .../sting/utils/codecs/vcf/VCFUtils.java | 43 ++++++++++++------- 2 files changed, 29 insertions(+), 26 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java index f14f6c2a67..46a3a8cd1d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java @@ -120,12 +120,6 @@ public class SelectHeaders extends RodWalker implements TreeRe @Argument(fullName = "exclude_header_name", shortName = "xl_hn", doc = "Exclude header. Can be specified multiple times", required = false) public Set XLheaderNames; - /** - * Note that reference inclusion takes precedence over other header matching. If set other reference lines may be excluded but the file name will still be added. - */ - @Argument(fullName = "include_reference_name", shortName = "irn", doc = "If set the reference file name minus the file extension will be added to the headers", required = false) - public boolean includeReference; - /** * Note that interval name inclusion takes precedence over other header matching. If set other interval lines may be excluded but the intervals will still be added. */ @@ -162,10 +156,6 @@ public void initialize() { // Select only the headers requested by name or expression. headerLines = new LinkedHashSet(getSelectedHeaders(headerLines)); - // Optionally add in the reference. - if (includeReference && getToolkit().getArguments().referenceFile != null) - headerLines.add(new VCFHeaderLine(VCFHeader.REFERENCE_KEY, FilenameUtils.getBaseName(getToolkit().getArguments().referenceFile.getName()))); - // Optionally add in the intervals. if (includeIntervals && getToolkit().getArguments().intervals != null) { for (IntervalBinding intervalBinding : getToolkit().getArguments().intervals) { @@ -205,7 +195,7 @@ private Set getSelectedHeaders(Set headerLines) { selectedHeaders = ListFileUtils.excludeMatching(selectedHeaders, headerKey, XLheaderNames, true); // always include the contig lines - selectedHeaders = VCFUtils.withUpdatedContigsAsLines(selectedHeaders, getToolkit().getArguments().referenceFile, getToolkit().getMasterSequenceDictionary()); + selectedHeaders = VCFUtils.withUpdatedContigsAsLines(selectedHeaders, getToolkit().getArguments().referenceFile, getToolkit().getMasterSequenceDictionary(), true); return selectedHeaders; } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java index f80b0eae4e..561e8e78d5 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java @@ -27,6 +27,7 @@ import net.sf.samtools.SAMSequenceDictionary; import net.sf.samtools.SAMSequenceRecord; +import org.apache.commons.io.FilenameUtils; import org.apache.log4j.Logger; import org.broad.tribble.Feature; import org.broadinstitute.sting.commandline.RodBinding; @@ -165,12 +166,13 @@ public static Set smartMergeHeaders(Collection headers if ( map.containsKey(key) ) { VCFHeaderLine other = map.get(key); - if ( line.equals(other) ) - continue; - else if ( ! line.getClass().equals(other.getClass()) ) + if ( line.equals(other) ) { + // continue; + } else if ( ! line.getClass().equals(other.getClass()) ) { throw new IllegalStateException("Incompatible header types: " + line + " " + other ); - else if ( line instanceof VCFFilterHeaderLine ) { - String lineName = ((VCFFilterHeaderLine) line).getID(); String otherName = ((VCFFilterHeaderLine) other).getID(); + } else if ( line instanceof VCFFilterHeaderLine ) { + String lineName = ((VCFFilterHeaderLine) line).getID(); + String otherName = ((VCFFilterHeaderLine) other).getID(); if ( ! lineName.equals(otherName) ) throw new IllegalStateException("Incompatible header types: " + line + " " + other ); } else if ( line instanceof VCFCompoundHeaderLine ) { @@ -198,7 +200,7 @@ else if ( line instanceof VCFFilterHeaderLine ) { throw new IllegalStateException("Incompatible header types, collision between these two types: " + line + " " + other ); } } - if ( ! compLine.getDescription().equals(compOther) ) + if ( ! compLine.getDescription().equals(compOther.getDescription()) ) conflictWarner.warn(line, "Allowing unequal description fields through: keeping " + compOther + " excluding " + compLine); } else { // we are not equal, but we're not anything special either @@ -235,7 +237,7 @@ public static String rsIDOfFirstRealVariant(List VCs, VariantCon * @param header the header to update * @param engine the GATK engine containing command line arguments and the master sequence dictionary */ - public final static VCFHeader withUpdatedContigs(final VCFHeader header, final GenomeAnalysisEngine engine) { + public static VCFHeader withUpdatedContigs(final VCFHeader header, final GenomeAnalysisEngine engine) { return VCFUtils.withUpdatedContigs(header, engine.getArguments().referenceFile, engine.getMasterSequenceDictionary()); } @@ -246,11 +248,15 @@ public final static VCFHeader withUpdatedContigs(final VCFHeader header, final G * @param referenceFile the file path to the reference sequence used to generate this vcf * @param refDict the SAM formatted reference sequence dictionary */ - public final static VCFHeader withUpdatedContigs(final VCFHeader oldHeader, final File referenceFile, final SAMSequenceDictionary refDict) { + public static VCFHeader withUpdatedContigs(final VCFHeader oldHeader, final File referenceFile, final SAMSequenceDictionary refDict) { return new VCFHeader(withUpdatedContigsAsLines(oldHeader.getMetaDataInInputOrder(), referenceFile, refDict), oldHeader.getGenotypeSamples()); } - public final static Set withUpdatedContigsAsLines(final Set oldLines, final File referenceFile, final SAMSequenceDictionary refDict) { + public static Set withUpdatedContigsAsLines(final Set oldLines, final File referenceFile, final SAMSequenceDictionary refDict) { + return withUpdatedContigsAsLines(oldLines, referenceFile, refDict, false); + } + + public static Set withUpdatedContigsAsLines(final Set oldLines, final File referenceFile, final SAMSequenceDictionary refDict, boolean referenceNameOnly) { final Set lines = new LinkedHashSet(oldLines.size()); for ( final VCFHeaderLine line : oldLines ) { @@ -264,17 +270,24 @@ public final static Set withUpdatedContigsAsLines(final Set makeContigHeaderLines(final SAMSequenceDictionary refDict, + public static List makeContigHeaderLines(final SAMSequenceDictionary refDict, final File referenceFile) { final List lines = new ArrayList(); final String assembly = referenceFile != null ? getReferenceAssembly(referenceFile.getName()) : null; @@ -283,7 +296,7 @@ public final static List makeContigHeaderLines(final SAMSeq return lines; } - private final static VCFContigHeaderLine makeContigHeaderLine(final SAMSequenceRecord contig, final String assembly) { + private static VCFContigHeaderLine makeContigHeaderLine(final SAMSequenceRecord contig, final String assembly) { final Map map = new LinkedHashMap(3); map.put("ID", contig.getSequenceName()); map.put("length", String.valueOf(contig.getSequenceLength())); @@ -291,7 +304,7 @@ private final static VCFContigHeaderLine makeContigHeaderLine(final SAMSequenceR return new VCFContigHeaderLine(VCFHeader.CONTIG_KEY, map, contig.getSequenceIndex()); } - private final static String getReferenceAssembly(final String refPath) { + private static String getReferenceAssembly(final String refPath) { // This doesn't need to be perfect as it's not a required VCF header line, but we might as well give it a shot String assembly = null; if (refPath.contains("b37") || refPath.contains("v37")) From 0af1be0c4316d545ed8713e693bceb43e186b35d Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 13 Aug 2012 22:55:02 -0400 Subject: [PATCH 114/176] Trivial removal of ununsed variable (mentioned in resolved JIRA entry) --- .../sting/gatk/arguments/GATKArgumentCollection.java | 2 -- 1 file changed, 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java index 1e6920b829..4c9235b58b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java @@ -57,8 +57,6 @@ public class GATKArgumentCollection { public GATKArgumentCollection() { } - public Map walkerArgs = new HashMap(); - // parameters and their defaults @Input(fullName = "input_file", shortName = "I", doc = "SAM or BAM file(s)", required = false) public List samFiles = new ArrayList(); From cd404f6feed3484351686d38742b9f9846976ae1 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Tue, 14 Aug 2012 12:54:31 -0400 Subject: [PATCH 115/176] Two changes to SelectVariants: 1) don't add DP INFO annotation if DP wasn't used in the input VCF (it was adding DP=0 previously). 2) If MLEAC or MLEAF is present in the original VCF and the number of samples decreases, remove those annotations from the VC. --- .../walkers/variantutils/SelectVariants.java | 16 +++++++++--- .../SelectVariantsIntegrationTest.java | 26 +++++++++++++++++++ 2 files changed, 39 insertions(+), 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index cf528de092..1493815ee5 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -730,7 +730,13 @@ private VariantContext subsetRecord(final VariantContext vc, final boolean exclu if ( vc.getAlleles().size() != sub.getAlleles().size() ) newGC = VariantContextUtils.stripPLs(sub.getGenotypes()); - //Remove a fraction of the genotypes if needed + // if we have fewer samples in the selected VC than in the original VC, we need to strip out the MLE tags + if ( vc.getNSamples() != sub.getNSamples() ) { + builder.rmAttribute(VCFConstants.MLE_ALLELE_COUNT_KEY); + builder.rmAttribute(VCFConstants.MLE_ALLELE_FREQUENCY_KEY); + } + + // Remove a fraction of the genotypes if needed if ( fractionGenotypes > 0 ){ ArrayList genotypes = new ArrayList(); for ( Genotype genotype : newGC ) { @@ -767,17 +773,21 @@ private void addAnnotations(final VariantContextBuilder builder, final VariantCo VariantContextUtils.calculateChromosomeCounts(builder, false); + boolean sawDP = false; int depth = 0; for (String sample : originalVC.getSampleNames()) { Genotype g = originalVC.getGenotype(sample); if ( ! g.isFiltered() ) { - if ( g.hasDP() ) + if ( g.hasDP() ) { depth += g.getDP(); + sawDP = true; + } } } - builder.attribute("DP", depth); + if ( sawDP ) + builder.attribute("DP", depth); } private void randomlyAddVariant(int rank, VariantContext vc) { diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java index e25d654659..7a865ddeb8 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java @@ -154,6 +154,32 @@ public void testRegenotype() { executeTest("testRegenotype--" + testFile, spec); } + @Test + public void testRemoveMLE() { + String testFile = privateTestDir + "vcfexample.withMLE.vcf"; + + WalkerTestSpec spec = new WalkerTestSpec( + "-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header", + 1, + Arrays.asList("") + ); + + executeTest("testRegenotype--" + 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("") + ); + + executeTest("testRegenotype--" + testFile, spec); + } + @Test public void testMultipleRecordsAtOnePosition() { String testFile = privateTestDir + "selectVariants.onePosition.vcf"; From a5e48a42b3ad9ef53c7cd9985b6df85b86e3684f Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Tue, 14 Aug 2012 14:21:42 -0400 Subject: [PATCH 116/176] Fixing behavior of the --regenotype argument in SelectVariants to properly run in GenotypeGivenAlleles mode. Added integration tests to cover recent SV changes. --- .../genotyper/UnifiedGenotyperEngine.java | 10 ++++++---- .../walkers/variantutils/SelectVariants.java | 3 ++- .../SelectVariantsIntegrationTest.java | 16 ++++++++-------- 3 files changed, 16 insertions(+), 13 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index f4bd196ae2..f15fa9b999 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -646,15 +646,17 @@ private List getGLModelsToUse(final R // if we're genotyping given alleles and we have a requested SNP at this position, do SNP if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) { - final VariantContext vcInput = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, refContext, rawContext.getLocation(), false, logger, UAC.alleles); - if ( vcInput == null ) + final VariantContext vcInput = getVCFromAllelesRod(tracker, refContext, rawContext.getLocation(), false, logger, UAC.alleles); + if ( vcInput == null ) { + models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix+"SNP")); return models; + } if ( vcInput.isSNP() ) { // ignore SNPs if the user chose INDEL mode only if ( UAC.GLmodel.name().toUpperCase().contains("BOTH") || UAC.GLmodel.name().toUpperCase().contains("SNP") ) models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix+"SNP")); - } + } else if ( vcInput.isIndel() || vcInput.isMixed() ) { // ignore INDELs if the user chose SNP mode only if ( UAC.GLmodel.name().toUpperCase().contains("BOTH") || UAC.GLmodel.name().toUpperCase().contains("INDEL") ) @@ -759,7 +761,7 @@ private static AlleleFrequencyCalculationModel getAlleleFrequencyCalculationObje public static VariantContext getVCFromAllelesRod(RefMetaDataTracker tracker, ReferenceContext ref, GenomeLoc loc, boolean requireSNP, Logger logger, final RodBinding allelesBinding) { if ( tracker == null || ref == null || logger == null ) - throw new ReviewedStingException("Bad arguments: tracker=" + tracker + " ref=" + ref + " logger=" + logger); + return null; VariantContext vc = null; // search for usable record diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index 1493815ee5..0810710c1a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -470,6 +470,7 @@ 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; UAC.NO_SLOD = true; UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY); headerLines.addAll(UnifiedGenotyper.getHeaderInfo(UAC, null, null)); @@ -567,7 +568,7 @@ public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentCo VariantContext sub = subsetRecord(vc, EXCLUDE_NON_VARIANTS); if ( REGENOTYPE && sub.isPolymorphicInSamples() && hasPLs(sub) ) { - final VariantContextBuilder builder = new VariantContextBuilder(UG_engine.calculateGenotypes(tracker, ref, context, sub)).filters(sub.getFiltersMaybeNull()); + final VariantContextBuilder builder = new VariantContextBuilder(UG_engine.calculateGenotypes(null, ref, context, sub)).filters(sub.getFiltersMaybeNull()); addAnnotations(builder, sub); sub = builder.make(); } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java index 7a865ddeb8..e172200f7f 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java @@ -34,7 +34,7 @@ public void testRepeatedLineSelection() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString(" -sn A -sn B -sn C --variant " + testfile), 1, - Arrays.asList("3d98a024bf3aecbd282843e0af89d0e6") + Arrays.asList("125d1c9fa111cd38dfa2ff3900f16b57") ); executeTest("testRepeatedLineSelection--" + testfile, spec); @@ -49,7 +49,7 @@ public void testDiscordance() { + b37hapmapGenotypes + " -disc " + testFile + " -o %s --no_cmdline_in_header -U LENIENT_VCF_PROCESSING", 1, - Arrays.asList("54289033d35d32b8ebbb38c51fbb614c") + Arrays.asList("c0b937edb6a8b6392d477511d4f1ebcf") ); spec.disableShadowBCF(); @@ -135,7 +135,7 @@ public void testUsingDbsnpName() { WalkerTestSpec spec = new WalkerTestSpec( "-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant:dbsnp " + testFile + " -o %s --no_cmdline_in_header", 1, - Arrays.asList("d12ae1617deb38f5ed712dc326935b9a") + Arrays.asList("a554459c9ccafb9812ff6d8c06c11726") ); executeTest("testUsingDbsnpName--" + testFile, spec); @@ -148,7 +148,7 @@ public void testRegenotype() { WalkerTestSpec spec = new WalkerTestSpec( "-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header", 1, - Arrays.asList("c22ad8864d9951403672a24c20d6c3c2") + Arrays.asList("52cb2f150559ca1457e9df7ec153dbb452cb2f150559ca1457e9df7ec153dbb4") ); executeTest("testRegenotype--" + testFile, spec); @@ -161,10 +161,10 @@ public void testRemoveMLE() { WalkerTestSpec spec = new WalkerTestSpec( "-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header", 1, - Arrays.asList("") + Arrays.asList("a554459c9ccafb9812ff6d8c06c11726") ); - executeTest("testRegenotype--" + testFile, spec); + executeTest("testRemoveMLE--" + testFile, spec); } @Test @@ -174,10 +174,10 @@ public void testRemoveMLEAndRegenotype() { WalkerTestSpec spec = new WalkerTestSpec( "-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header", 1, - Arrays.asList("") + Arrays.asList("52cb2f150559ca1457e9df7ec153dbb4") ); - executeTest("testRegenotype--" + testFile, spec); + executeTest("testRemoveMLEAndRegenotype--" + testFile, spec); } @Test From 56aa538af925131feba4aef7e950c3bd6cb8777b Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Tue, 14 Aug 2012 15:02:30 -0400 Subject: [PATCH 117/176] In AlleleCount stratification, check to make sure the AC (or MLEAC) is valid (i.e. not higher than number of chromosomes) and throw a User Error if it isn't. Added a test for bad AC. --- .../varianteval/stratifications/AlleleCount.java | 4 ++++ .../varianteval/VariantEvalIntegrationTest.java | 15 +++++++++++++++ 2 files changed, 19 insertions(+) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java index 158f20b61e..50c5526e49 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java @@ -51,6 +51,10 @@ public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker t AC = Math.max(AC, eval.getCalledChrCount(allele)); } + // make sure that the AC isn't invalid + if ( AC > eval.getCalledChrCount() ) + throw new UserException.MalformedVCF(String.format("The AC or MLEAC value (%d) at position %s:%d is larger than the possible called chromosome count (%d)", AC, eval.getChr(), eval.getStart(), eval.getCalledChrCount())); + return Collections.singletonList((Object) AC); } else { return Collections.emptyList(); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java index 94e52c2b9e..c92d6d4cfb 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java @@ -585,6 +585,21 @@ public void testStandardIndelEval() { executeTest("testStandardIndelEval", spec); } + @Test + public void testBadACValue() { + WalkerTestSpec spec = new WalkerTestSpec( + buildCommandLine( + "-T VariantEval", + "-R " + b37KGReference, + "-eval " + privateTestDir + "vcfexample.withBadAC.vcf", + "-noST -ST AlleleCount", + "-noEV -EV VariantSummary" + ), + 0, + UserException.class); + executeTest("testBadACValue", spec); + } + @Test() public void testIncompatibleEvalAndStrat() { From 611fd1fa1ca29139b8b0186a45f881547c6e02f3 Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Wed, 15 Aug 2012 13:31:45 -0400 Subject: [PATCH 118/176] Updating large-scale validation script to new UG syntax From 5e2db92058c50ca77c487a8a0f1addfc33eaecfe Mon Sep 17 00:00:00 2001 From: David Roazen Date: Wed, 15 Aug 2012 15:56:54 -0400 Subject: [PATCH 119/176] Fix an issue with the classpath for external builds in build.xml Use "path" instead of "pathconvert" to construct the external.gatk.classpath. This allows the path to evolve as the build progresses, instead of being fixed early on to a value that (in some cases) could be incorrect. --- build.xml | 23 +++++++++-------------- 1 file changed, 9 insertions(+), 14 deletions(-) diff --git a/build.xml b/build.xml index 135b9dac7d..2ca48c51be 100644 --- a/build.xml +++ b/build.xml @@ -70,13 +70,18 @@ + + + + - + + @@ -96,8 +101,6 @@ - - @@ -208,19 +211,11 @@ - - - - - - - - - + - + @@ -432,7 +427,7 @@ - + From 3d543e3ef1b7d04781e4cb32ab56f070595d01fe Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Wed, 15 Aug 2012 16:09:51 -0400 Subject: [PATCH 120/176] Reving CoverageByRG to the new GATKReport API From 645c7b6062d8f7ba4612721e71e167dc2d0f8b7c Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Mon, 13 Aug 2012 15:59:35 -0400 Subject: [PATCH 121/176] Removing parallelism bottleneck in the GATK -- GenomeLocParser cache was a major performance bottleneck in parallel GATK performance. With 10 thread > 50% of each thread's time was spent blocking on the MasterSequencingDictionary object. Made this a thread local variable. -- Now we can run the GATK with 48 threads efficiently on GSA4! -- Running -nt 1 => 75 minutes (didn't let is run all of the way through so likely would take longer) -- Running -nt 24 => 3.81 minutes --- .../sting/utils/GenomeLocParser.java | 81 +++++++++++-------- 1 file changed, 48 insertions(+), 33 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java index 4f2b5b2eb7..77ecd295f3 100644 --- a/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java +++ b/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java @@ -43,9 +43,6 @@ /** * Factory class for creating GenomeLocs */ -@Invariant({ - "logger != null", - "contigInfo != null"}) public final class GenomeLocParser { private static Logger logger = Logger.getLogger(GenomeLocParser.class); @@ -54,20 +51,39 @@ public final class GenomeLocParser { // Ugly global variable defining the optional ordering of contig elements // // -------------------------------------------------------------------------------------------------------------- - private final MasterSequenceDictionary contigInfo; + + /** + * This single variable holds the underlying SamSequenceDictionary used by the GATK. We assume + * it is thread safe. + */ + final private SAMSequenceDictionary SINGLE_MASTER_SEQUENCE_DICTIONARY; + + /** + * A thread-local caching contig info + */ + private final ThreadLocal contigInfoPerThread = + new ThreadLocal(); + + /** + * @return a caching sequence dictionary appropriate for this thread + */ + private CachingSequenceDictionary getContigInfo() { + if ( contigInfoPerThread.get() == null ) { + // initialize for this thread + logger.debug("Creating thread-local caching sequence dictionary for thread " + Thread.currentThread().getName()); + contigInfoPerThread.set(new CachingSequenceDictionary(SINGLE_MASTER_SEQUENCE_DICTIONARY)); + } + + assert contigInfoPerThread.get() != null; + + return contigInfoPerThread.get(); + } /** * A wrapper class that provides efficient last used caching for the global - * SAMSequenceDictionary underlying all of the GATK engine capabilities + * SAMSequenceDictionary underlying all of the GATK engine capabilities. */ - // todo -- enable when CoFoJa developers identify the problem (likely thread unsafe invariants) -// @Invariant({ -// "dict != null", -// "dict.size() > 0", -// "lastSSR == null || dict.getSequence(lastContig).getSequenceIndex() == lastIndex", -// "lastSSR == null || dict.getSequence(lastContig).getSequenceName() == lastContig", -// "lastSSR == null || dict.getSequence(lastContig) == lastSSR"}) - private final class MasterSequenceDictionary { + private final class CachingSequenceDictionary { final private SAMSequenceDictionary dict; // cache @@ -76,7 +92,7 @@ private final class MasterSequenceDictionary { int lastIndex = -1; @Requires({"dict != null", "dict.size() > 0"}) - public MasterSequenceDictionary(SAMSequenceDictionary dict) { + public CachingSequenceDictionary(SAMSequenceDictionary dict) { this.dict = dict; } @@ -111,7 +127,6 @@ public synchronized final SAMSequenceRecord getSequence(final int index) { return lastSSR; else return updateCache(null, index); - } @Requires("contig != null") @@ -125,12 +140,12 @@ public synchronized final int getSequenceIndex(final String contig) { } @Requires({"contig != null", "lastContig != null"}) - private final synchronized boolean isCached(final String contig) { + private synchronized boolean isCached(final String contig) { return lastContig.equals(contig); } @Requires({"lastIndex != -1", "index >= 0"}) - private final synchronized boolean isCached(final int index) { + private synchronized boolean isCached(final int index) { return lastIndex == index; } @@ -144,7 +159,7 @@ private final synchronized boolean isCached(final int index) { */ @Requires("contig != null || index >= 0") @Ensures("result != null") - private final synchronized SAMSequenceRecord updateCache(final String contig, int index ) { + private synchronized SAMSequenceRecord updateCache(final String contig, int index ) { SAMSequenceRecord rec = contig == null ? dict.getSequence(index) : dict.getSequence(contig); if ( rec == null ) { throw new ReviewedStingException("BUG: requested unknown contig=" + contig + " index=" + index); @@ -174,7 +189,7 @@ public GenomeLocParser(SAMSequenceDictionary seqDict) { throw new UserException.CommandLineException("Failed to load reference dictionary"); } - contigInfo = new MasterSequenceDictionary(seqDict); + SINGLE_MASTER_SEQUENCE_DICTIONARY = seqDict; logger.debug(String.format("Prepared reference sequence contig dictionary")); for (SAMSequenceRecord contig : seqDict.getSequences()) { logger.debug(String.format(" %s (%d bp)", contig.getSequenceName(), contig.getSequenceLength())); @@ -188,11 +203,11 @@ public GenomeLocParser(SAMSequenceDictionary seqDict) { * @return True if the contig is valid. False otherwise. */ public final boolean contigIsInDictionary(String contig) { - return contig != null && contigInfo.hasContig(contig); + return contig != null && getContigInfo().hasContig(contig); } public final boolean indexIsInDictionary(final int index) { - return index >= 0 && contigInfo.hasContig(index); + return index >= 0 && getContigInfo().hasContig(index); } @@ -208,7 +223,7 @@ public final boolean indexIsInDictionary(final int index) { public final SAMSequenceRecord getContigInfo(final String contig) { if ( contig == null || ! contigIsInDictionary(contig) ) throw new UserException.MalformedGenomeLoc(String.format("Contig %s given as location, but this contig isn't present in the Fasta sequence dictionary", contig)); - return contigInfo.getSequence(contig); + return getContigInfo().getSequence(contig); } /** @@ -226,9 +241,9 @@ public final int getContigIndex(final String contig) { @Requires("contig != null") protected int getContigIndexWithoutException(final String contig) { - if ( contig == null || ! contigInfo.hasContig(contig) ) + if ( contig == null || ! getContigInfo().hasContig(contig) ) return -1; - return contigInfo.getSequenceIndex(contig); + return getContigInfo().getSequenceIndex(contig); } /** @@ -236,7 +251,7 @@ protected int getContigIndexWithoutException(final String contig) { * @return */ public final SAMSequenceDictionary getContigs() { - return contigInfo.dict; + return getContigInfo().dict; } // -------------------------------------------------------------------------------------------------------------- @@ -291,7 +306,7 @@ public GenomeLoc createGenomeLoc(String contig, int index, final int start, fina * @return true if it's valid, false otherwise. If exceptOnError, then throws a UserException if invalid */ private boolean validateGenomeLoc(String contig, int contigIndex, int start, int stop, boolean mustBeOnReference, boolean exceptOnError) { - if ( ! contigInfo.hasContig(contig) ) + if ( ! getContigInfo().hasContig(contig) ) return vglHelper(exceptOnError, String.format("Unknown contig %s", contig)); if (stop < start) @@ -300,8 +315,8 @@ private boolean validateGenomeLoc(String contig, int contigIndex, int start, int if (contigIndex < 0) return vglHelper(exceptOnError, String.format("The contig index %d is less than 0", contigIndex)); - if (contigIndex >= contigInfo.getNSequences()) - return vglHelper(exceptOnError, String.format("The contig index %d is greater than the stored sequence count (%d)", contigIndex, contigInfo.getNSequences())); + if (contigIndex >= getContigInfo().getNSequences()) + return vglHelper(exceptOnError, String.format("The contig index %d is greater than the stored sequence count (%d)", contigIndex, getContigInfo().getNSequences())); if ( mustBeOnReference ) { if (start < 1) @@ -310,7 +325,7 @@ private boolean validateGenomeLoc(String contig, int contigIndex, int start, int if (stop < 1) return vglHelper(exceptOnError, String.format("The stop position %d is less than 1", stop)); - int contigSize = contigInfo.getSequence(contigIndex).getSequenceLength(); + int contigSize = getContigInfo().getSequence(contigIndex).getSequenceLength(); if (start > contigSize || stop > contigSize) return vglHelper(exceptOnError, String.format("The genome loc coordinates %d-%d exceed the contig size (%d)", start, stop, contigSize)); } @@ -558,7 +573,7 @@ public GenomeLoc incPos(GenomeLoc loc, int by) { @Requires("contigName != null") @Ensures("result != null") public GenomeLoc createOverEntireContig(String contigName) { - SAMSequenceRecord contig = contigInfo.getSequence(contigName); + SAMSequenceRecord contig = getContigInfo().getSequence(contigName); return createGenomeLoc(contigName,contig.getSequenceIndex(),1,contig.getSequenceLength(), true); } @@ -573,7 +588,7 @@ public GenomeLoc createGenomeLocAtStart(GenomeLoc loc, int maxBasePairs) { if (GenomeLoc.isUnmapped(loc)) return null; String contigName = loc.getContig(); - SAMSequenceRecord contig = contigInfo.getSequence(contigName); + SAMSequenceRecord contig = getContigInfo().getSequence(contigName); int contigIndex = contig.getSequenceIndex(); int start = loc.getStart() - maxBasePairs; @@ -598,7 +613,7 @@ public GenomeLoc createPaddedGenomeLoc(final GenomeLoc loc, final int padding) { if (GenomeLoc.isUnmapped(loc)) return loc; final String contigName = loc.getContig(); - final SAMSequenceRecord contig = contigInfo.getSequence(contigName); + final SAMSequenceRecord contig = getContigInfo().getSequence(contigName); final int contigIndex = contig.getSequenceIndex(); final int contigLength = contig.getSequenceLength(); @@ -619,7 +634,7 @@ public GenomeLoc createGenomeLocAtStop(GenomeLoc loc, int maxBasePairs) { if (GenomeLoc.isUnmapped(loc)) return null; String contigName = loc.getContig(); - SAMSequenceRecord contig = contigInfo.getSequence(contigName); + SAMSequenceRecord contig = getContigInfo().getSequence(contigName); int contigIndex = contig.getSequenceIndex(); int contigLength = contig.getSequenceLength(); From cc9c1db5b504badbce905e4967ebc558233a7326 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Tue, 14 Aug 2012 08:39:28 -0400 Subject: [PATCH 122/176] GATK performance of time lives -- Cut out CountCovariates and TableRecalibrator (no longer in GATK2) -- Parallelism tests go up to 32 cores by default now -- Only tests 1.6 and 2.0 now -- Useful -justUG option to just run all of the UG performance tests From b5362c58b13c18bddfca0de66aa5b5b0a3886a77 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Tue, 14 Aug 2012 15:02:45 -0400 Subject: [PATCH 123/176] Initial implementation of ThreadFactory that monitors running / blocking / waiting time of threads it creates -- Created makeCombinations utility function (very useful!). Moved template from VariantContextTestProvider -- UnitTests for basic functionality --- .../org/broadinstitute/sting/utils/Utils.java | 30 ++++ .../StateMonitoringThreadFactory.java | 149 ++++++++++++++++ .../StateMonitoringThreadFactoryUnitTest.java | 161 ++++++++++++++++++ .../VariantContextTestProvider.java | 16 +- 4 files changed, 342 insertions(+), 14 deletions(-) create mode 100644 public/java/src/org/broadinstitute/sting/utils/threading/StateMonitoringThreadFactory.java create mode 100755 public/java/test/org/broadinstitute/sting/utils/threading/StateMonitoringThreadFactoryUnitTest.java diff --git a/public/java/src/org/broadinstitute/sting/utils/Utils.java b/public/java/src/org/broadinstitute/sting/utils/Utils.java index 17c145dbf5..14d7177a08 100755 --- a/public/java/src/org/broadinstitute/sting/utils/Utils.java +++ b/public/java/src/org/broadinstitute/sting/utils/Utils.java @@ -732,6 +732,36 @@ public static int nCombinations(final List> options) { } } + /** + * Make all combinations of N size of objects + * + * if objects = [A, B, C] + * if N = 1 => [[A], [B], [C]] + * if N = 2 => [[A, A], [B, A], [C, A], [A, B], [B, B], [C, B], [A, C], [B, C], [C, C]] + * + * @param objects + * @param n + * @param + * @return + */ + public static List> makeCombinations(final List objects, final int n) { + final List> combinations = new ArrayList>(); + + if ( n == 1 ) { + for ( final T o : objects ) + combinations.add(Collections.singletonList(o)); + } else { + final List> sub = makeCombinations(objects, n - 1); + for ( List subI : sub ) { + for ( final T a : objects ) { + combinations.add(Utils.cons(a, subI)); + } + } + } + + return combinations; + } + /** * Convenience function that formats the novelty rate as a %.2f string * diff --git a/public/java/src/org/broadinstitute/sting/utils/threading/StateMonitoringThreadFactory.java b/public/java/src/org/broadinstitute/sting/utils/threading/StateMonitoringThreadFactory.java new file mode 100644 index 0000000000..1e0988bb7d --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/utils/threading/StateMonitoringThreadFactory.java @@ -0,0 +1,149 @@ +/* + * The MIT License + * + * Copyright (c) 2009 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.utils.threading; + +import org.apache.log4j.Logger; + +import java.lang.management.ManagementFactory; +import java.lang.management.ThreadInfo; +import java.lang.management.ThreadMXBean; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.EnumMap; +import java.util.List; +import java.util.concurrent.CountDownLatch; +import java.util.concurrent.ThreadFactory; + +/** + * Create threads, collecting statistics about their running state over time + * + * Uses a ThreadMXBean to capture info via ThreadInfo + * + * User: depristo + * Date: 8/14/12 + * Time: 8:47 AM + */ +public class StateMonitoringThreadFactory implements ThreadFactory { + protected static final boolean DEBUG = false; + private static Logger logger = Logger.getLogger(StateMonitoringThreadFactory.class); + public static final List TRACKED_STATES = Arrays.asList(Thread.State.BLOCKED, Thread.State.RUNNABLE, Thread.State.WAITING); + + final int threadsToCreate; + final List threads; + final EnumMap times = new EnumMap(Thread.State.class); + final ThreadMXBean bean; + final CountDownLatch activeThreads; + + public StateMonitoringThreadFactory(final int threadsToCreate) { + if ( threadsToCreate <= 0 ) throw new IllegalArgumentException("threadsToCreate <= 0: " + threadsToCreate); + + this.threadsToCreate = threadsToCreate; + threads = new ArrayList(threadsToCreate); + for ( final Thread.State state : Thread.State.values() ) + times.put(state, 0l); + bean = ManagementFactory.getThreadMXBean(); + bean.setThreadContentionMonitoringEnabled(true); + bean.setThreadCpuTimeEnabled(true); + activeThreads = new CountDownLatch(threadsToCreate); + } + + public synchronized long getStateTime(final Thread.State state) { + return times.get(state); + } + + public synchronized long getTotalTime() { + long total = 0; + for ( final long time : times.values() ) + total += time; + return total; + } + + public synchronized double getStateFraction(final Thread.State state) { + return getStateTime(state) / (1.0 * getTotalTime()); + } + + public int getNThreads() { + return threads.size(); + } + + public void waitForAllThreadsToComplete() throws InterruptedException { + activeThreads.await(); + } + + @Override + public synchronized String toString() { + final StringBuilder b = new StringBuilder(); + + b.append("total ").append(getTotalTime()).append(" "); + for ( final Thread.State state : TRACKED_STATES ) { + b.append(state).append(" ").append(getStateTime(state)).append(" "); + } + + return b.toString(); + } + + @Override + public synchronized Thread newThread(final Runnable runnable) { + if ( threads.size() >= threadsToCreate ) + throw new IllegalStateException("Attempting to create more threads than allowed by constructor argument threadsToCreate " + threadsToCreate); + + final Thread myThread = new TrackingThread(runnable); + threads.add(myThread); + return myThread; + } + + // TODO -- add polling capability + + private synchronized void updateThreadInfo(final Thread thread, final long runtime) { + if ( DEBUG ) logger.warn("UpdateThreadInfo called"); + final ThreadInfo info = bean.getThreadInfo(thread.getId()); + if ( info != null ) { + if ( DEBUG ) logger.warn("Updating thread total runtime " + runtime + " of which blocked " + info.getBlockedTime() + " and waiting " + info.getWaitedTime()); + incTimes(Thread.State.BLOCKED, info.getBlockedTime()); + incTimes(Thread.State.WAITING, info.getWaitedTime()); + incTimes(Thread.State.RUNNABLE, runtime - info.getWaitedTime() - info.getBlockedTime()); + } + } + + private synchronized void incTimes(final Thread.State state, final long by) { + times.put(state, times.get(state) + by); + } + + private class TrackingThread extends Thread { + private TrackingThread(Runnable runnable) { + super(runnable); + } + + @Override + public void run() { + final long startTime = System.currentTimeMillis(); + super.run(); + final long endTime = System.currentTimeMillis(); + if ( DEBUG ) logger.warn(" Countdown " + activeThreads.getCount() + " in thread " + Thread.currentThread().getName()); + updateThreadInfo(this, endTime - startTime); + activeThreads.countDown(); + if ( DEBUG ) logger.warn(" -> Countdown " + activeThreads.getCount() + " in thread " + Thread.currentThread().getName()); + } + } +} diff --git a/public/java/test/org/broadinstitute/sting/utils/threading/StateMonitoringThreadFactoryUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/threading/StateMonitoringThreadFactoryUnitTest.java new file mode 100755 index 0000000000..6fc852bbff --- /dev/null +++ b/public/java/test/org/broadinstitute/sting/utils/threading/StateMonitoringThreadFactoryUnitTest.java @@ -0,0 +1,161 @@ +/* + * The MIT License + * + * Copyright (c) 2009 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.utils.threading; + +import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.testng.Assert; +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.List; +import java.util.concurrent.*; + +/** + * Tests for the state monitoring thread factory. + */ +public class StateMonitoringThreadFactoryUnitTest extends BaseTest { + private final static long THREAD_TARGET_DURATION_IN_MILLISECOND = 100; + final static Object GLOBAL_LOCK = new Object(); + + private class StateTest extends TestDataProvider { + private final double TOLERANCE = 0.1; // willing to tolerate a 10% error + + final List statesForThreads; + + public StateTest(final List statesForThreads) { + super(StateTest.class); + this.statesForThreads = statesForThreads; + setName("StateTest " + Utils.join(",", statesForThreads)); + } + + public List getStatesForThreads() { + return statesForThreads; + } + + public int getNStates() { return statesForThreads.size(); } + + public double maxStateFraction(final Thread.State state) { return fraction(state) + TOLERANCE; } + public double minStateFraction(final Thread.State state) { return fraction(state) - TOLERANCE; } + + private double fraction(final Thread.State state) { + return Collections.frequency(statesForThreads, state) / (1.0 * statesForThreads.size()); + } + } + + private static class StateTestThread implements Callable { + private final Thread.State stateToImplement; + + private StateTestThread(final Thread.State stateToImplement) { + this.stateToImplement = stateToImplement; + } + + @Override + public Double call() throws Exception { + switch ( stateToImplement ) { + case RUNNABLE: + // do some work until we get to THREAD_TARGET_DURATION_IN_MILLISECOND + double sum = 0.0; + final long startTime = System.currentTimeMillis(); + for ( int i = 1; System.currentTimeMillis() - startTime < (THREAD_TARGET_DURATION_IN_MILLISECOND - 1); i++ ) { + sum += Math.log10(i); + } + return sum; + case WAITING: + Thread.currentThread().sleep(THREAD_TARGET_DURATION_IN_MILLISECOND); + return 0.0; + case BLOCKED: + if ( StateMonitoringThreadFactory.DEBUG ) logger.warn("Blocking..."); + synchronized (GLOBAL_LOCK) { + if ( StateMonitoringThreadFactory.DEBUG ) logger.warn(" ... done blocking"); + } + return 0.0; + default: + throw new ReviewedStingException("Unexpected thread test state " + stateToImplement); + } + } + } + + @DataProvider(name = "StateTest") + public Object[][] createStateTest() { + for ( final int nThreads : Arrays.asList(1, 2, 3, 4, 5) ) { + for (final List states : Utils.makeCombinations(StateMonitoringThreadFactory.TRACKED_STATES, nThreads) ) { + //if ( Collections.frequency(states, Thread.State.BLOCKED) > 0) + new StateTest(states); + } + } + + return StateTest.getTests(StateTest.class); + } + + @Test(enabled = true, dataProvider = "StateTest") + public void testStateTest(final StateTest test) throws InterruptedException { + // allows us to test blocking + final StateMonitoringThreadFactory factory = new StateMonitoringThreadFactory(test.getNStates()); + final ExecutorService threadPool = Executors.newFixedThreadPool(test.getNStates(), factory); + + logger.warn("Running " + test); + synchronized (GLOBAL_LOCK) { + //logger.warn(" Have lock"); + for ( final Thread.State threadToRunState : test.getStatesForThreads() ) + threadPool.submit(new StateTestThread(threadToRunState)); + + // lock has to be here for the whole running of the threads but end before the sleep so the blocked threads + // can block for their allotted time + threadPool.shutdown(); + Thread.sleep(THREAD_TARGET_DURATION_IN_MILLISECOND); + } + //logger.warn(" Releasing lock"); + threadPool.awaitTermination(10, TimeUnit.SECONDS); + //logger.warn(" done awaiting termination"); + //logger.warn(" waiting for all threads to complete"); + factory.waitForAllThreadsToComplete(); + //logger.warn(" done waiting for threads"); + + // make sure we counted everything properly + final long totalTime = factory.getTotalTime(); + final long minTime = (THREAD_TARGET_DURATION_IN_MILLISECOND - 10) * test.getNStates(); + //logger.warn("Testing total time"); + Assert.assertTrue(totalTime >= minTime, "Factory results not properly accumulated: totalTime = " + totalTime + " < minTime = " + minTime); + + for (final Thread.State state : StateMonitoringThreadFactory.TRACKED_STATES ) { + final double min = test.minStateFraction(state); + final double max = test.maxStateFraction(state); + final double obs = factory.getStateFraction(state); + logger.warn(" Checking " + state + + " min " + String.format("%.2f", min) + + " max " + String.format("%.2f", max) + + " obs " + String.format("%.2f", obs) + + " factor = " + factory); + Assert.assertTrue(obs >= min, "Too little time spent in state " + state + " obs " + obs + " min " + min); + Assert.assertTrue(obs <= max, "Too much time spent in state " + state + " obs " + obs + " max " + min); + } + + Assert.assertEquals(factory.getNThreads(), test.getNStates()); + } +} \ No newline at end of file diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java index b95e589b70..dd1985be38 100644 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java @@ -888,20 +888,8 @@ public static void addComplexGenotypesTest() { } } - private static final List> makeAllGenotypes(final List alleles, final int highestPloidy) { - final List> combinations = new ArrayList>(); - if ( highestPloidy == 1 ) { - for ( final Allele a : alleles ) - combinations.add(Collections.singletonList(a)); - } else { - final List> sub = makeAllGenotypes(alleles, highestPloidy - 1); - for ( List subI : sub ) { - for ( final Allele a : alleles ) { - combinations.add(Utils.cons(a, subI)); - } - } - } - return combinations; + private static List> makeAllGenotypes(final List alleles, final int highestPloidy) { + return Utils.makeCombinations(alleles, highestPloidy); } public static void assertEquals(final VCFHeader actual, final VCFHeader expected) { From f1fe90f9c95554a09b257b645e3424be1b917002 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Tue, 14 Aug 2012 16:27:30 -0400 Subject: [PATCH 124/176] Clean, documented implementation of ThreadFactory that monitors running / blocking / waiting time of threads it creates -- Expanded unit tests -- Support for clean logging of results to logger -- Refactored MyTime into AutoFormattingTime in Utils, out of TraversalEngine, for cleanliness and reuse -- Added docs and contracts to StateMonitoringThreadFactory --- .../gatk/traversals/TraversalEngine.java | 67 +----- .../sting/utils/AutoFormattingTime.java | 53 +++++ .../StateMonitoringThreadFactory.java | 198 +++++++++++++++--- .../sting/utils/threading/package-info.java | 2 +- .../StateMonitoringThreadFactoryUnitTest.java | 36 +++- 5 files changed, 260 insertions(+), 96 deletions(-) create mode 100644 public/java/src/org/broadinstitute/sting/utils/AutoFormattingTime.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java index 4ef2555243..2593fc72e3 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java @@ -62,54 +62,6 @@ public ProcessingHistory(double elapsedSeconds, GenomeLoc loc, long unitsProcess } - /** - * Simple utility class that makes it convenient to print unit adjusted times - */ - private static class MyTime { - double t; // in Seconds - int precision; // for format - - public MyTime(double t, int precision) { - this.t = t; - this.precision = precision; - } - - public MyTime(double t) { - this(t, 1); - } - - /** - * Instead of 10000 s, returns 2.8 hours - * @return - */ - public String toString() { - double unitTime = t; - String unit = "s"; - - if ( t > 120 ) { - unitTime = t / 60; // minutes - unit = "m"; - - if ( unitTime > 120 ) { - unitTime /= 60; // hours - unit = "h"; - - if ( unitTime > 100 ) { - unitTime /= 24; // days - unit = "d"; - - if ( unitTime > 20 ) { - unitTime /= 7; // days - unit = "w"; - } - } - } - } - - return String.format("%6."+precision+"f %s", unitTime, unit); - } - } - /** lock object to sure updates to history are consistent across threads */ private static final Object lock = new Object(); LinkedList history = new LinkedList(); @@ -280,20 +232,20 @@ private void printProgress(GenomeLoc loc, ReadMetrics metrics, boolean mustPrint ProcessingHistory last = updateHistory(loc,cumulativeMetrics); - final MyTime elapsed = new MyTime(last.elapsedSeconds); - final MyTime bpRate = new MyTime(secondsPerMillionBP(last)); - final MyTime unitRate = new MyTime(secondsPerMillionElements(last)); + final AutoFormattingTime elapsed = new AutoFormattingTime(last.elapsedSeconds); + final AutoFormattingTime bpRate = new AutoFormattingTime(secondsPerMillionBP(last)); + final AutoFormattingTime unitRate = new AutoFormattingTime(secondsPerMillionElements(last)); final double fractionGenomeTargetCompleted = calculateFractionGenomeTargetCompleted(last); - final MyTime estTotalRuntime = new MyTime(elapsed.t / fractionGenomeTargetCompleted); - final MyTime timeToCompletion = new MyTime(estTotalRuntime.t - elapsed.t); + final AutoFormattingTime estTotalRuntime = new AutoFormattingTime(elapsed.getTimeInSeconds() / fractionGenomeTargetCompleted); + final AutoFormattingTime timeToCompletion = new AutoFormattingTime(estTotalRuntime.getTimeInSeconds() - elapsed.getTimeInSeconds()); if ( printProgress ) { lastProgressPrintTime = curTime; // dynamically change the update rate so that short running jobs receive frequent updates while longer jobs receive fewer updates - if ( estTotalRuntime.t > TWELVE_HOURS_IN_SECONDS ) + if ( estTotalRuntime.getTimeInSeconds() > TWELVE_HOURS_IN_SECONDS ) PROGRESS_PRINT_FREQUENCY = 60 * 1000; // in milliseconds - else if ( estTotalRuntime.t > TWO_HOURS_IN_SECONDS ) + else if ( estTotalRuntime.getTimeInSeconds() > TWO_HOURS_IN_SECONDS ) PROGRESS_PRINT_FREQUENCY = 30 * 1000; // in milliseconds else PROGRESS_PRINT_FREQUENCY = 10 * 1000; // in milliseconds @@ -308,8 +260,9 @@ else if ( estTotalRuntime.t > TWO_HOURS_IN_SECONDS ) lastPerformanceLogPrintTime = curTime; synchronized(performanceLogLock) { performanceLog.printf("%.2f\t%d\t%.2e\t%d\t%.2e\t%.2e\t%.2f\t%.2f%n", - elapsed.t, nRecords, unitRate.t, last.bpProcessed, bpRate.t, - fractionGenomeTargetCompleted, estTotalRuntime.t, timeToCompletion.t); + elapsed.getTimeInSeconds(), nRecords, unitRate.getTimeInSeconds(), last.bpProcessed, + bpRate.getTimeInSeconds(), fractionGenomeTargetCompleted, estTotalRuntime.getTimeInSeconds(), + timeToCompletion.getTimeInSeconds()); } } } diff --git a/public/java/src/org/broadinstitute/sting/utils/AutoFormattingTime.java b/public/java/src/org/broadinstitute/sting/utils/AutoFormattingTime.java new file mode 100644 index 0000000000..8964c16cb8 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/utils/AutoFormattingTime.java @@ -0,0 +1,53 @@ +package org.broadinstitute.sting.utils; + +/** + * Simple utility class that makes it convenient to print unit adjusted times + */ +public class AutoFormattingTime { + double timeInSeconds; // in Seconds + int precision; // for format + + public AutoFormattingTime(double timeInSeconds, int precision) { + this.timeInSeconds = timeInSeconds; + this.precision = precision; + } + + public AutoFormattingTime(double timeInSeconds) { + this(timeInSeconds, 1); + } + + public double getTimeInSeconds() { + return timeInSeconds; + } + + /** + * Instead of 10000 s, returns 2.8 hours + * @return + */ + public String toString() { + double unitTime = timeInSeconds; + String unit = "s"; + + if ( timeInSeconds > 120 ) { + unitTime = timeInSeconds / 60; // minutes + unit = "m"; + + if ( unitTime > 120 ) { + unitTime /= 60; // hours + unit = "h"; + + if ( unitTime > 100 ) { + unitTime /= 24; // days + unit = "d"; + + if ( unitTime > 20 ) { + unitTime /= 7; // days + unit = "w"; + } + } + } + } + + return String.format("%6."+precision+"f %s", unitTime, unit); + } +} diff --git a/public/java/src/org/broadinstitute/sting/utils/threading/StateMonitoringThreadFactory.java b/public/java/src/org/broadinstitute/sting/utils/threading/StateMonitoringThreadFactory.java index 1e0988bb7d..39d5c14978 100644 --- a/public/java/src/org/broadinstitute/sting/utils/threading/StateMonitoringThreadFactory.java +++ b/public/java/src/org/broadinstitute/sting/utils/threading/StateMonitoringThreadFactory.java @@ -23,7 +23,11 @@ */ package org.broadinstitute.sting.utils.threading; +import com.google.java.contract.Ensures; +import com.google.java.contract.Invariant; import org.apache.log4j.Logger; +import org.apache.log4j.Priority; +import org.broadinstitute.sting.utils.AutoFormattingTime; import java.lang.management.ManagementFactory; import java.lang.management.ThreadInfo; @@ -36,7 +40,7 @@ import java.util.concurrent.ThreadFactory; /** - * Create threads, collecting statistics about their running state over time + * Create activeThreads, collecting statistics about their running state over time * * Uses a ThreadMXBean to capture info via ThreadInfo * @@ -44,34 +48,91 @@ * Date: 8/14/12 * Time: 8:47 AM */ +@Invariant({ + "activeThreads.size() <= nThreadsToCreate", + "countDownLatch.getCount() <= nThreadsToCreate", + "nThreadsToCreated <= nThreadsToCreate" +}) public class StateMonitoringThreadFactory implements ThreadFactory { protected static final boolean DEBUG = false; private static Logger logger = Logger.getLogger(StateMonitoringThreadFactory.class); public static final List TRACKED_STATES = Arrays.asList(Thread.State.BLOCKED, Thread.State.RUNNABLE, Thread.State.WAITING); - final int threadsToCreate; - final List threads; + // todo -- it would be nice to not have to specify upfront the number of threads. + // todo -- can we dynamically increment countDownLatch? It seems not... + final int nThreadsToCreate; + final List activeThreads; final EnumMap times = new EnumMap(Thread.State.class); + + int nThreadsToCreated = 0; + + /** + * The bean used to get the thread info about blocked and waiting times + */ final ThreadMXBean bean; - final CountDownLatch activeThreads; - public StateMonitoringThreadFactory(final int threadsToCreate) { - if ( threadsToCreate <= 0 ) throw new IllegalArgumentException("threadsToCreate <= 0: " + threadsToCreate); + /** + * Counts down the number of active activeThreads whose runtime info hasn't been incorporated into + * times. Counts down from nThreadsToCreate to 0, at which point any code waiting + * on the final times is freed to run. + */ + final CountDownLatch countDownLatch; + + /** + * Instead of RUNNABLE we want to print running. This map goes from Thread.State names to human readable ones + */ + final static EnumMap PRETTY_NAMES = new EnumMap(Thread.State.class); + static { + PRETTY_NAMES.put(Thread.State.RUNNABLE, "running"); + PRETTY_NAMES.put(Thread.State.BLOCKED, "blocked"); + PRETTY_NAMES.put(Thread.State.WAITING, "waiting"); + } + + /** + * Create a new factory generating threads whose runtime and contention + * behavior is tracked in this factory. + * + * @param nThreadsToCreate the number of threads we will create in the factory before it's considered complete + * // TODO -- remove argument when we figure out how to implement this capability + */ + public StateMonitoringThreadFactory(final int nThreadsToCreate) { + if ( nThreadsToCreate <= 0 ) throw new IllegalArgumentException("nThreadsToCreate <= 0: " + nThreadsToCreate); - this.threadsToCreate = threadsToCreate; - threads = new ArrayList(threadsToCreate); + this.nThreadsToCreate = nThreadsToCreate; + activeThreads = new ArrayList(nThreadsToCreate); + + // initialize times to 0 for ( final Thread.State state : Thread.State.values() ) times.put(state, 0l); + + // get the bean, and start tracking bean = ManagementFactory.getThreadMXBean(); - bean.setThreadContentionMonitoringEnabled(true); - bean.setThreadCpuTimeEnabled(true); - activeThreads = new CountDownLatch(threadsToCreate); + if ( bean.isThreadContentionMonitoringSupported() ) + bean.setThreadContentionMonitoringEnabled(true); + else + logger.warn("Thread contention monitoring not supported, we cannot track GATK multi-threaded efficiency"); + //bean.setThreadCpuTimeEnabled(true); + + countDownLatch = new CountDownLatch(nThreadsToCreate); } + /** + * Get the time spent in state across all threads created by this factory + * + * @param state on of the TRACKED_STATES + * @return the time in milliseconds + */ + @Ensures({"result >= 0", "TRACKED_STATES.contains(state)"}) public synchronized long getStateTime(final Thread.State state) { return times.get(state); } + /** + * Get the total time spent in all states across all threads created by this factory + * + * @return the time in milliseconds + */ + @Ensures({"result >= 0"}) public synchronized long getTotalTime() { long total = 0; for ( final long time : times.values() ) @@ -79,16 +140,27 @@ public synchronized long getTotalTime() { return total; } + /** + * Get the fraction of time spent in state across all threads created by this factory + * + * @return the fraction (0.0-1.0) of time spent in state over all state times of all threads + */ + @Ensures({"result >= 0.0", "result <= 1.0", "TRACKED_STATES.contains(state)"}) public synchronized double getStateFraction(final Thread.State state) { - return getStateTime(state) / (1.0 * getTotalTime()); + return getStateTime(state) / (1.0 * Math.max(getTotalTime(), 1)); } - public int getNThreads() { - return threads.size(); + /** + * How many threads have been created by this factory so far? + * @return + */ + @Ensures("result >= 0") + public int getNThreadsCreated() { + return nThreadsToCreated; } public void waitForAllThreadsToComplete() throws InterruptedException { - activeThreads.await(); + countDownLatch.await(); } @Override @@ -103,33 +175,108 @@ public synchronized String toString() { return b.toString(); } + /** + * Print usage information about threads from this factory to logger + * with the INFO priority + * + * @param logger + */ + public synchronized void printUsageInformation(final Logger logger) { + printUsageInformation(logger, Priority.INFO); + } + + /** + * Print usage information about threads from this factory to logger + * with the provided priority + * + * @param logger + */ + public synchronized void printUsageInformation(final Logger logger, final Priority priority) { + logger.log(priority, "Number of activeThreads used: " + getNThreadsCreated()); + logger.log(priority, "Total runtime " + new AutoFormattingTime(getTotalTime() / 1000.0)); + for ( final Thread.State state : TRACKED_STATES ) { + logger.log(priority, String.format(" Fraction of time spent %s is %.2f (%s)", + prettyName(state), getStateFraction(state), new AutoFormattingTime(getStateTime(state) / 1000.0))); + } + logger.log(priority, String.format("Efficiency of multi-threading: %.2f%% of time spent doing productive work", + getStateFraction(Thread.State.RUNNABLE) * 100)); + } + + private String prettyName(final Thread.State state) { + return PRETTY_NAMES.get(state); + } + + /** + * Create a new thread from this factory + * + * @param runnable + * @return + */ @Override + @Ensures({ + "activeThreads.size() > old(activeThreads.size())", + "activeThreads.contains(result)", + "nThreadsToCreated == old(nThreadsToCreated) + 1" + }) public synchronized Thread newThread(final Runnable runnable) { - if ( threads.size() >= threadsToCreate ) - throw new IllegalStateException("Attempting to create more threads than allowed by constructor argument threadsToCreate " + threadsToCreate); + if ( activeThreads.size() >= nThreadsToCreate) + throw new IllegalStateException("Attempting to create more activeThreads than allowed by constructor argument nThreadsToCreate " + nThreadsToCreate); + nThreadsToCreated++; final Thread myThread = new TrackingThread(runnable); - threads.add(myThread); + activeThreads.add(myThread); return myThread; } - // TODO -- add polling capability - - private synchronized void updateThreadInfo(final Thread thread, final long runtime) { + /** + * Update the information about completed thread that ran for runtime in milliseconds + * + * This method updates all of the key timing and tracking information in the factory so that + * thread can be retired. After this call the factory shouldn't have a pointer to the thread any longer + * + * @param thread + * @param runtimeInMilliseconds + */ + @Ensures({ + "activeThreads.size() < old(activeThreads.size())", + "! activeThreads.contains(thread)", + "getTotalTime() >= old(getTotalTime())", + "countDownLatch.getCount() < old(countDownLatch.getCount())" + }) + private synchronized void threadIsDone(final Thread thread, final long runtimeInMilliseconds) { + if ( DEBUG ) logger.warn(" Countdown " + countDownLatch.getCount() + " in thread " + Thread.currentThread().getName()); if ( DEBUG ) logger.warn("UpdateThreadInfo called"); + final ThreadInfo info = bean.getThreadInfo(thread.getId()); if ( info != null ) { - if ( DEBUG ) logger.warn("Updating thread total runtime " + runtime + " of which blocked " + info.getBlockedTime() + " and waiting " + info.getWaitedTime()); + if ( DEBUG ) logger.warn("Updating thread total runtime " + runtimeInMilliseconds + " of which blocked " + info.getBlockedTime() + " and waiting " + info.getWaitedTime()); incTimes(Thread.State.BLOCKED, info.getBlockedTime()); incTimes(Thread.State.WAITING, info.getWaitedTime()); - incTimes(Thread.State.RUNNABLE, runtime - info.getWaitedTime() - info.getBlockedTime()); + incTimes(Thread.State.RUNNABLE, runtimeInMilliseconds - info.getWaitedTime() - info.getBlockedTime()); } + + // remove the thread from the list of active activeThreads + if ( ! activeThreads.remove(thread) ) + throw new IllegalStateException("Thread " + thread + " not in list of active activeThreads"); + + // one less thread is live for those blocking on all activeThreads to be complete + countDownLatch.countDown(); + if ( DEBUG ) logger.warn(" -> Countdown " + countDownLatch.getCount() + " in thread " + Thread.currentThread().getName()); } + /** + * Helper function that increments the times counter by by for state + * + * @param state + * @param by + */ private synchronized void incTimes(final Thread.State state, final long by) { times.put(state, times.get(state) + by); } + /** + * A wrapper around Thread that tracks the runtime of the thread and calls threadIsDone() when complete + */ private class TrackingThread extends Thread { private TrackingThread(Runnable runnable) { super(runnable); @@ -140,10 +287,7 @@ public void run() { final long startTime = System.currentTimeMillis(); super.run(); final long endTime = System.currentTimeMillis(); - if ( DEBUG ) logger.warn(" Countdown " + activeThreads.getCount() + " in thread " + Thread.currentThread().getName()); - updateThreadInfo(this, endTime - startTime); - activeThreads.countDown(); - if ( DEBUG ) logger.warn(" -> Countdown " + activeThreads.getCount() + " in thread " + Thread.currentThread().getName()); + threadIsDone(this, endTime - startTime); } } } diff --git a/public/java/src/org/broadinstitute/sting/utils/threading/package-info.java b/public/java/src/org/broadinstitute/sting/utils/threading/package-info.java index dc350920e0..d72dad4714 100644 --- a/public/java/src/org/broadinstitute/sting/utils/threading/package-info.java +++ b/public/java/src/org/broadinstitute/sting/utils/threading/package-info.java @@ -1,4 +1,4 @@ /** - * Provides tools for managing threads, thread pools, and parallelization in general. + * Provides tools for managing activeThreads, thread pools, and parallelization in general. */ package org.broadinstitute.sting.utils.threading; diff --git a/public/java/test/org/broadinstitute/sting/utils/threading/StateMonitoringThreadFactoryUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/threading/StateMonitoringThreadFactoryUnitTest.java index 6fc852bbff..c22b49c237 100755 --- a/public/java/test/org/broadinstitute/sting/utils/threading/StateMonitoringThreadFactoryUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/threading/StateMonitoringThreadFactoryUnitTest.java @@ -23,6 +23,7 @@ */ package org.broadinstitute.sting.utils.threading; +import org.apache.log4j.Priority; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; @@ -30,7 +31,6 @@ import org.testng.annotations.DataProvider; import org.testng.annotations.Test; -import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; import java.util.List; @@ -40,6 +40,7 @@ * Tests for the state monitoring thread factory. */ public class StateMonitoringThreadFactoryUnitTest extends BaseTest { + // the duration of the tests -- 100 ms is tolerable given the number of tests we are doing private final static long THREAD_TARGET_DURATION_IN_MILLISECOND = 100; final static Object GLOBAL_LOCK = new Object(); @@ -68,10 +69,16 @@ private double fraction(final Thread.State state) { } } + /** + * Test helper threading class that puts the thread into RUNNING, BLOCKED, or WAITING state as + * requested for input argument + */ private static class StateTestThread implements Callable { private final Thread.State stateToImplement; private StateTestThread(final Thread.State stateToImplement) { + if ( ! StateMonitoringThreadFactory.TRACKED_STATES.contains(stateToImplement) ) + throw new IllegalArgumentException("Unexpected state " + stateToImplement); this.stateToImplement = stateToImplement; } @@ -92,6 +99,7 @@ public Double call() throws Exception { case BLOCKED: if ( StateMonitoringThreadFactory.DEBUG ) logger.warn("Blocking..."); synchronized (GLOBAL_LOCK) { + // the GLOBAL_LOCK must be held by the unit test itself for this to properly block if ( StateMonitoringThreadFactory.DEBUG ) logger.warn(" ... done blocking"); } return 0.0; @@ -103,7 +111,7 @@ public Double call() throws Exception { @DataProvider(name = "StateTest") public Object[][] createStateTest() { - for ( final int nThreads : Arrays.asList(1, 2, 3, 4, 5) ) { + for ( final int nThreads : Arrays.asList(1, 2, 3, 4) ) { for (final List states : Utils.makeCombinations(StateMonitoringThreadFactory.TRACKED_STATES, nThreads) ) { //if ( Collections.frequency(states, Thread.State.BLOCKED) > 0) new StateTest(states); @@ -125,7 +133,7 @@ public void testStateTest(final StateTest test) throws InterruptedException { for ( final Thread.State threadToRunState : test.getStatesForThreads() ) threadPool.submit(new StateTestThread(threadToRunState)); - // lock has to be here for the whole running of the threads but end before the sleep so the blocked threads + // lock has to be here for the whole running of the activeThreads but end before the sleep so the blocked activeThreads // can block for their allotted time threadPool.shutdown(); Thread.sleep(THREAD_TARGET_DURATION_IN_MILLISECOND); @@ -133,29 +141,35 @@ public void testStateTest(final StateTest test) throws InterruptedException { //logger.warn(" Releasing lock"); threadPool.awaitTermination(10, TimeUnit.SECONDS); //logger.warn(" done awaiting termination"); - //logger.warn(" waiting for all threads to complete"); + //logger.warn(" waiting for all activeThreads to complete"); factory.waitForAllThreadsToComplete(); - //logger.warn(" done waiting for threads"); + //logger.warn(" done waiting for activeThreads"); // make sure we counted everything properly final long totalTime = factory.getTotalTime(); final long minTime = (THREAD_TARGET_DURATION_IN_MILLISECOND - 10) * test.getNStates(); + final long maxTime = (THREAD_TARGET_DURATION_IN_MILLISECOND + 10) * test.getNStates(); //logger.warn("Testing total time"); Assert.assertTrue(totalTime >= minTime, "Factory results not properly accumulated: totalTime = " + totalTime + " < minTime = " + minTime); + Assert.assertTrue(totalTime <= maxTime, "Factory results not properly accumulated: totalTime = " + totalTime + " > maxTime = " + maxTime); for (final Thread.State state : StateMonitoringThreadFactory.TRACKED_STATES ) { final double min = test.minStateFraction(state); final double max = test.maxStateFraction(state); final double obs = factory.getStateFraction(state); - logger.warn(" Checking " + state - + " min " + String.format("%.2f", min) - + " max " + String.format("%.2f", max) - + " obs " + String.format("%.2f", obs) - + " factor = " + factory); +// logger.warn(" Checking " + state +// + " min " + String.format("%.2f", min) +// + " max " + String.format("%.2f", max) +// + " obs " + String.format("%.2f", obs) +// + " factor = " + factory); Assert.assertTrue(obs >= min, "Too little time spent in state " + state + " obs " + obs + " min " + min); Assert.assertTrue(obs <= max, "Too much time spent in state " + state + " obs " + obs + " max " + min); } - Assert.assertEquals(factory.getNThreads(), test.getNStates()); + // we actually ran the expected number of activeThreads + Assert.assertEquals(factory.getNThreadsCreated(), test.getNStates()); + + // should be called to ensure we don't format / NPE on output + factory.printUsageInformation(logger, Priority.INFO); } } \ No newline at end of file From d9fb137993c4d8a589ab81f433389a8b1b1ea133 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Tue, 14 Aug 2012 16:27:57 -0400 Subject: [PATCH 125/176] GATKPerformanceOfTime.R updated to new script outputs From cb9eef528ed3c9314e3fc981258e3860bc2d8822 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Tue, 14 Aug 2012 22:08:49 -0400 Subject: [PATCH 126/176] Enable efficient parallel output of BCF2 -- Previous IO stub was hardcoded to write VCF. So when you ran -nt 2 -o my.bcf you actually created intermediate VCF files that were then encoded single threaded as BCF. Now we emit natively per thread BCF, and use the fast mergeInfo code to read BCF -> write BCF. Upcoming optimizations to avoid decoding genotype data unnecessarily will enable us to really quickly process BCF2 in parallel -- VariantContextWriterStub forces BCF output for intermediate files -- Nicer debug log message in BCF2Codec -- Turn off debug logging of BCF2LazyGenotypesDecoder -- BCF2FieldWriterManager now uses .debug not .info, so you won't see all of that field manager debugging info with BCF2 any longer -- VariantContextWriterFactory.isBCFOutput now has version that accepts just a file path, not path + options --- .../storage/VariantContextWriterStorage.java | 46 +++++++++++-------- .../io/stubs/VariantContextWriterStub.java | 4 ++ .../sting/utils/codecs/bcf2/BCF2Codec.java | 2 +- .../codecs/bcf2/BCF2LazyGenotypesDecoder.java | 5 +- .../writer/BCF2FieldWriterManager.java | 2 +- .../writer/VariantContextWriterFactory.java | 10 ++++ 6 files changed, 45 insertions(+), 24 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java index fb05a6b047..161179f84d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java @@ -27,9 +27,10 @@ import net.sf.samtools.util.BlockCompressedOutputStream; import org.apache.log4j.Logger; import org.broad.tribble.AbstractFeatureReader; +import org.broad.tribble.FeatureCodec; import org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub; +import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager; import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Utils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; @@ -81,6 +82,18 @@ else if ( stub.getOutputStream() != null ) { throw new ReviewedStingException("Unable to create target to which to write; storage was provided with neither a file nor a stream."); } + /** + * Constructs an object which will redirect into a different file. + * @param stub Stub to use when synthesizing file / header info. + * @param tempFile File into which to direct the output data. + */ + public VariantContextWriterStorage(VariantContextWriterStub stub, File tempFile) { + logger.debug("Creating temporary output file " + tempFile.getAbsolutePath() + " for VariantContext output."); + this.file = tempFile; + this.writer = vcfWriterToFile(stub, file, false); + writer.writeHeader(stub.getVCFHeader()); + } + /** * common initialization routine for multiple constructors * @param stub Stub to use when constructing the output file. @@ -139,19 +152,6 @@ public void add(final VariantContext vc) { } } - - /** - * Constructs an object which will redirect into a different file. - * @param stub Stub to use when synthesizing file / header info. - * @param tempFile File into which to direct the output data. - */ - public VariantContextWriterStorage(VariantContextWriterStub stub, File tempFile) { - logger.debug("Creating temporary VCF file " + tempFile.getAbsolutePath() + " for VCF output."); - this.file = tempFile; - this.writer = vcfWriterToFile(stub, file, false); - writer.writeHeader(stub.getVCFHeader()); - } - public void add(VariantContext vc) { writer.add(vc); } @@ -176,12 +176,20 @@ public void close() { public void mergeInto(VariantContextWriterStorage target) { try { - String sourceFilePath = file.getAbsolutePath(); - String targetFilePath = target.file != null ? target.file.getAbsolutePath() : "/dev/stdin"; - logger.debug(String.format("Merging %s into %s",sourceFilePath,targetFilePath)); - AbstractFeatureReader source = AbstractFeatureReader.getFeatureReader(file.getAbsolutePath(), new VCFCodec(), false); + final String targetFilePath = target.file != null ? target.file.getAbsolutePath() : "/dev/stdin"; + logger.debug(String.format("Merging %s into %s",file.getAbsolutePath(),targetFilePath)); + + // use the feature manager to determine the right codec for the tmp file + // that way we don't assume it's a specific type + final FeatureManager.FeatureDescriptor fd = new FeatureManager().getByFiletype(file); + if ( fd == null ) + throw new ReviewedStingException("Unexpectedly couldn't find valid codec for temporary output file " + file); + + final FeatureCodec codec = fd.getCodec(); + final AbstractFeatureReader source = + AbstractFeatureReader.getFeatureReader(file.getAbsolutePath(), codec, false); - for ( VariantContext vc : source.iterator() ) { + for ( final VariantContext vc : source.iterator() ) { target.writer.add(vc); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java index 6ed889eb67..bea7172eac 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java @@ -35,6 +35,7 @@ import org.broadinstitute.sting.utils.variantcontext.writer.Options; import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory; import java.io.File; import java.io.OutputStream; @@ -186,6 +187,9 @@ public EnumSet getWriterOptions(boolean indexOnTheFly) { if ( engine.lenientVCFProcessing() ) options.add(Options.ALLOW_MISSING_FIELDS_IN_HEADER); if ( indexOnTheFly && ! isCompressed() ) options.add(Options.INDEX_ON_THE_FLY); + if ( getFile() != null && VariantContextWriterFactory.isBCFOutput(getFile()) ) + options.add(Options.FORCE_BCF); + return options.isEmpty() ? EnumSet.noneOf(Options.class) : EnumSet.copyOf(options); } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java index 570ca7c1cb..67e189d114 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java @@ -149,7 +149,7 @@ public FeatureCodecHeader readHeader( final PositionalBufferedStream inputStream if ( bcfVersion.getMinorVersion() < MIN_MINOR_VERSION ) error("BCF2Codec can only process BCF2 files with minor version >= " + MIN_MINOR_VERSION + " but this file has minor version " + bcfVersion.getMinorVersion()); - logger.info("BCF version " + bcfVersion); + logger.info("Parsing data stream with BCF version " + bcfVersion); final int headerSizeInBytes = BCF2Type.INT32.read(inputStream); diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2LazyGenotypesDecoder.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2LazyGenotypesDecoder.java index cf34a8b48f..513b9fcb56 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2LazyGenotypesDecoder.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2LazyGenotypesDecoder.java @@ -63,9 +63,8 @@ class BCF2LazyGenotypesDecoder implements LazyGenotypesContext.LazyParser { @Override public LazyGenotypesContext.LazyData parse(final Object data) { - if ( logger.isDebugEnabled() ) - logger.debug("Decoding BCF genotypes for " + nSamples + " samples with " + nFields + " fields each"); - +// if ( logger.isDebugEnabled() ) +// logger.debug("Decoding BCF genotypes for " + nSamples + " samples with " + nFields + " fields each"); try { // load our byte[] data into the decoder diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriterManager.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriterManager.java index 219daf315a..7b8224568c 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriterManager.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriterManager.java @@ -76,7 +76,7 @@ private final void add(final Map map, final String field, final T if ( map.containsKey(field) ) throw new ReviewedStingException("BUG: field " + field + " already seen in VCFHeader while building BCF2 field encoders"); map.put(field, writer); - logger.info(writer); + if ( logger.isDebugEnabled() ) logger.debug(writer); } // ----------------------------------------------------------------- diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWriterFactory.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWriterFactory.java index f23166a026..035aff7d69 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWriterFactory.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWriterFactory.java @@ -84,6 +84,16 @@ public static VariantContextWriter create(final File location, } } + /** + * Should we output a BCF file based solely on the name of the file at location? + * + * @param location + * @return + */ + public static boolean isBCFOutput(final File location) { + return isBCFOutput(location, EnumSet.noneOf(Options.class)); + } + public static boolean isBCFOutput(final File location, final EnumSet options) { return options.contains(Options.FORCE_BCF) || (location != null && location.getName().contains(".bcf")); } From f218769963cd39600cb9f2f191b7d3978086a2ad Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Tue, 14 Aug 2012 22:10:07 -0400 Subject: [PATCH 127/176] Parallel combine variants! -- CombineVariants is now TreeReducible! -- Integration tests running in parallel all pass except one (will fix) due to incorrect use of db=0 flag on input from old VCF format --- .../sting/gatk/walkers/variantutils/CombineVariants.java | 8 +++++++- .../variantutils/CombineVariantsIntegrationTest.java | 2 +- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java index d7dff030f2..d6504e8411 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java @@ -33,6 +33,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.Reference; import org.broadinstitute.sting.gatk.walkers.RodWalker; +import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.gatk.walkers.Window; import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCounts; import org.broadinstitute.sting.utils.SampleUtils; @@ -99,7 +100,7 @@ */ @DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} ) @Reference(window=@Window(start=-50,stop=50)) -public class CombineVariants extends RodWalker { +public class CombineVariants extends RodWalker implements TreeReducible { /** * The VCF files to merge together * @@ -313,5 +314,10 @@ public Integer reduce(Integer counter, Integer sum) { return counter + sum; } + @Override + public Integer treeReduce(Integer lhs, Integer rhs) { + return reduce(lhs, rhs); + } + public void onTraversalDone(Integer sum) {} } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java index c8551657a4..2f28a6dbc3 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java @@ -50,7 +50,7 @@ private static String baseTestString(String args) { private void cvExecuteTest(final String name, final WalkerTestSpec spec) { spec.disableShadowBCF(); - executeTest(name, spec); + executeTestParallel(name, spec); } public void test1InOut(String file, String md5) { From 0fddeb0c80a61e89ff81d60db119fe7af0de2f23 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Tue, 14 Aug 2012 22:10:42 -0400 Subject: [PATCH 128/176] Minor increase in tolerance to sum of states in UnitTest for StateMonitoringThreadFactory --- .../utils/threading/StateMonitoringThreadFactoryUnitTest.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/utils/threading/StateMonitoringThreadFactoryUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/threading/StateMonitoringThreadFactoryUnitTest.java index c22b49c237..87074364a2 100755 --- a/public/java/test/org/broadinstitute/sting/utils/threading/StateMonitoringThreadFactoryUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/threading/StateMonitoringThreadFactoryUnitTest.java @@ -147,8 +147,8 @@ public void testStateTest(final StateTest test) throws InterruptedException { // make sure we counted everything properly final long totalTime = factory.getTotalTime(); - final long minTime = (THREAD_TARGET_DURATION_IN_MILLISECOND - 10) * test.getNStates(); - final long maxTime = (THREAD_TARGET_DURATION_IN_MILLISECOND + 10) * test.getNStates(); + final long minTime = (long)(THREAD_TARGET_DURATION_IN_MILLISECOND * 0.5) * test.getNStates(); + final long maxTime = (long)(THREAD_TARGET_DURATION_IN_MILLISECOND * 1.5) * test.getNStates(); //logger.warn("Testing total time"); Assert.assertTrue(totalTime >= minTime, "Factory results not properly accumulated: totalTime = " + totalTime + " < minTime = " + minTime); Assert.assertTrue(totalTime <= maxTime, "Factory results not properly accumulated: totalTime = " + totalTime + " > maxTime = " + maxTime); From 122b798660b5d1b7f09ba74de2cb2e5a64a31e27 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Tue, 14 Aug 2012 22:11:00 -0400 Subject: [PATCH 129/176] Autoscaling of memory requirements in GATKPerformanceOverTime From 568435ef713b3f6a11a9a6b4bc036df17baf7846 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Wed, 15 Aug 2012 14:26:50 -0400 Subject: [PATCH 130/176] Temporarily disable StateMonitoringThreadTests while I get them reliably working across platforms --- .../utils/threading/StateMonitoringThreadFactoryUnitTest.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/utils/threading/StateMonitoringThreadFactoryUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/threading/StateMonitoringThreadFactoryUnitTest.java index 87074364a2..5a606c50ef 100755 --- a/public/java/test/org/broadinstitute/sting/utils/threading/StateMonitoringThreadFactoryUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/threading/StateMonitoringThreadFactoryUnitTest.java @@ -112,7 +112,7 @@ public Double call() throws Exception { @DataProvider(name = "StateTest") public Object[][] createStateTest() { for ( final int nThreads : Arrays.asList(1, 2, 3, 4) ) { - for (final List states : Utils.makeCombinations(StateMonitoringThreadFactory.TRACKED_STATES, nThreads) ) { + for (final List states : Utils.makePermutations(StateMonitoringThreadFactory.TRACKED_STATES, nThreads, true) ) { //if ( Collections.frequency(states, Thread.State.BLOCKED) > 0) new StateTest(states); } @@ -121,7 +121,7 @@ public Object[][] createStateTest() { return StateTest.getTests(StateTest.class); } - @Test(enabled = true, dataProvider = "StateTest") + @Test(enabled = false, dataProvider = "StateTest") public void testStateTest(final StateTest test) throws InterruptedException { // allows us to test blocking final StateMonitoringThreadFactory factory = new StateMonitoringThreadFactory(test.getNStates()); From 0d0b0001b8ad7045c14a6d26d859010858a364a6 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Wed, 15 Aug 2012 14:36:06 -0400 Subject: [PATCH 131/176] BCF2 optimizations; parallel CombineVariants -- BCF2 now determines whether it can safely write out raw genotype blocks, which is true in the case where the VCF header of the input is a complete, ordered subset of the output header. Added utilities to determine this and extensive unit tests (headerLinesAreOrderedConsistently) -- Cleanup collapseStringList and exploreStringList for new unit tests of BCF2Utils. Fixed bug in edge case that never occurred in practice -- VCFContigHeaderLine now provides its own key (VCFHeader.CONTIG_KEY) directly instead of requiring the user to provide it (and hoping its right) -- More ways to access the data in VCFHeader -- BCF2Writer uses a cache to avoid recomputing unnecessarily whether raw genotype blocks can be emitted directly into the output -- Optimization of fullyDecodeAttributes -- attributes.size() is expensive and unnecessary. We just guess that on average we need ~10 elements for the attribute map -- CombineVariants optimization -- filters are online HashSet but are sorted at the end by creating a TreeSet -- makeCombinations is now makePermutations, and you can request to create the permutations with or without replacement --- .../walkers/variantutils/CombineVariants.java | 6 + .../org/broadinstitute/sting/utils/Utils.java | 13 +- .../sting/utils/codecs/bcf2/BCF2Codec.java | 9 +- .../codecs/bcf2/BCF2LazyGenotypesDecoder.java | 2 +- .../sting/utils/codecs/bcf2/BCF2Utils.java | 65 +++++++- .../utils/codecs/vcf/VCFContigHeaderLine.java | 4 +- .../sting/utils/codecs/vcf/VCFHeader.java | 61 ++++++- .../sting/utils/codecs/vcf/VCFUtils.java | 2 +- .../utils/variantcontext/VariantContext.java | 2 +- .../variantcontext/VariantContextUtils.java | 5 +- .../variantcontext/writer/BCF2Encoder.java | 2 +- .../writer/BCF2FieldEncoder.java | 1 - .../variantcontext/writer/BCF2Writer.java | 47 ++++-- .../utils/codecs/bcf2/BCF2UtilsUnitTest.java | 155 ++++++++++++++++++ .../VariantContextTestProvider.java | 4 +- 15 files changed, 334 insertions(+), 44 deletions(-) create mode 100644 public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2UtilsUnitTest.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java index d6504e8411..8dabd49b88 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java @@ -67,6 +67,12 @@ * VCF and then run SelectVariants to extract the common records with -select 'set == "Intersection"', as worked out * in the detailed example on the wiki. * + * Note that CombineVariants supports multi-threaded parallelism (8/15/12). This is particularly useful + * when converting from VCF to BCF2, which can be expensive. In this case each thread spends CPU time + * doing the conversion, and the GATK engine is smart enough to merge the partial BCF2 blocks together + * efficiency. However, since this merge runs in only one thread, you can quickly reach diminishing + * returns with the number of parallel threads. -nt 4 works well but -nt 8 may be too much. + * *

Input

*

* One or more variant sets to combine. diff --git a/public/java/src/org/broadinstitute/sting/utils/Utils.java b/public/java/src/org/broadinstitute/sting/utils/Utils.java index 14d7177a08..476098ae64 100755 --- a/public/java/src/org/broadinstitute/sting/utils/Utils.java +++ b/public/java/src/org/broadinstitute/sting/utils/Utils.java @@ -32,7 +32,6 @@ import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; -import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.text.TextFormattingUtils; import java.net.InetAddress; @@ -742,19 +741,23 @@ public static int nCombinations(final List> options) { * @param objects * @param n * @param + * @param withReplacement if false, the resulting permutations will only contain unique objects from objects * @return */ - public static List> makeCombinations(final List objects, final int n) { + public static List> makePermutations(final List objects, final int n, final boolean withReplacement) { final List> combinations = new ArrayList>(); - if ( n == 1 ) { + if ( n <= 0 ) + ; + else if ( n == 1 ) { for ( final T o : objects ) combinations.add(Collections.singletonList(o)); } else { - final List> sub = makeCombinations(objects, n - 1); + final List> sub = makePermutations(objects, n - 1, withReplacement); for ( List subI : sub ) { for ( final T a : objects ) { - combinations.add(Utils.cons(a, subI)); + if ( withReplacement || ! subI.contains(a) ) + combinations.add(Utils.cons(a, subI)); } } } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java index 67e189d114..ac6348f808 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java @@ -423,9 +423,8 @@ private void createLazyGenotypesDecoder( final SitesInfoForDecoding siteInfo, final LazyGenotypesContext.LazyParser lazyParser = new BCF2LazyGenotypesDecoder(this, siteInfo.alleles, siteInfo.nSamples, siteInfo.nFormatFields, builders); - LazyGenotypesContext lazy = new LazyGenotypesContext(lazyParser, - new LazyData(siteInfo.nFormatFields, decoder.getRecordBytes()), - header.getNGenotypeSamples()); + final LazyData lazyData = new LazyData(header, siteInfo.nFormatFields, decoder.getRecordBytes()); + final LazyGenotypesContext lazy = new LazyGenotypesContext(lazyParser, lazyData, header.getNGenotypeSamples()); // did we resort the sample names? If so, we need to load the genotype data if ( !header.samplesWereAlreadySorted() ) @@ -436,11 +435,13 @@ private void createLazyGenotypesDecoder( final SitesInfoForDecoding siteInfo, } public static class LazyData { + final public VCFHeader header; final public int nGenotypeFields; final public byte[] bytes; @Requires({"nGenotypeFields > 0", "bytes != null"}) - public LazyData(final int nGenotypeFields, final byte[] bytes) { + public LazyData(final VCFHeader header, final int nGenotypeFields, final byte[] bytes) { + this.header = header; this.nGenotypeFields = nGenotypeFields; this.bytes = bytes; } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2LazyGenotypesDecoder.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2LazyGenotypesDecoder.java index 513b9fcb56..46b1fa6c13 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2LazyGenotypesDecoder.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2LazyGenotypesDecoder.java @@ -39,7 +39,7 @@ * @author Mark DePristo * @since 5/12 */ -class BCF2LazyGenotypesDecoder implements LazyGenotypesContext.LazyParser { +public class BCF2LazyGenotypesDecoder implements LazyGenotypesContext.LazyParser { final protected static Logger logger = Logger.getLogger(BCF2LazyGenotypesDecoder.class); // the essential information for us to use to decode the genotypes data diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java index e6e78d89d6..2ac916db1b 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java @@ -131,17 +131,21 @@ public static byte readByte(final InputStream stream) throws IOException { * @param strings size > 1 list of strings * @return */ - @Requires({"strings != null", "strings.size() > 1"}) + @Requires({"strings != null"}) @Ensures("result != null") public static String collapseStringList(final List strings) { - final StringBuilder b = new StringBuilder(); - for ( final String s : strings ) { - if ( s != null ) { - assert s.indexOf(",") == -1; // no commas in individual strings - b.append(",").append(s); + if ( strings.isEmpty() ) return ""; + else if ( strings.size() == 1 ) return strings.get(0); + else { + final StringBuilder b = new StringBuilder(); + for ( final String s : strings ) { + if ( s != null ) { + assert s.indexOf(",") == -1; // no commas in individual strings + b.append(",").append(s); + } } + return b.toString(); } - return b.toString(); } /** @@ -163,7 +167,7 @@ public static List explodeStringList(final String collapsed) { @Requires("s != null") public static boolean isCollapsedString(final String s) { - return s.charAt(0) == ','; + return s.length() > 0 && s.charAt(0) == ','; } /** @@ -280,4 +284,49 @@ public static List toList(final Object o) { else if ( o instanceof List ) return (List)o; else return Collections.singletonList(o); } + + /** + * Are the elements and their order in the output and input headers consistent so that + * we can write out the raw genotypes block without decoding and recoding it? + * + * If the order of INFO, FILTER, or contrig elements in the output header is different than + * in the input header we must decode the blocks using the input header and then recode them + * based on the new output order. + * + * If they are consistent, we can simply pass through the raw genotypes block bytes, which is + * a *huge* performance win for large blocks. + * + * Many common operations on BCF2 files (merging them for -nt, selecting a subset of records, etc) + * don't modify the ordering of the header fields and so can safely pass through the genotypes + * undecoded. Some operations -- those at add filters or info fields -- can change the ordering + * of the header fields and so produce invalid BCF2 files if the genotypes aren't decoded + */ + public static boolean headerLinesAreOrderedConsistently(final VCFHeader outputHeader, final VCFHeader genotypesBlockHeader) { + // first, we have to have the same samples in the same order + if ( ! nullAsEmpty(outputHeader.getSampleNamesInOrder()).equals(nullAsEmpty(genotypesBlockHeader.getSampleNamesInOrder())) ) + return false; + + final Iterator outputLinesIt = outputHeader.getIDHeaderLines().iterator(); + final Iterator inputLinesIt = genotypesBlockHeader.getIDHeaderLines().iterator(); + + while ( inputLinesIt.hasNext() ) { + if ( ! outputLinesIt.hasNext() ) // missing lines in output + return false; + + final VCFIDHeaderLine outputLine = outputLinesIt.next(); + final VCFIDHeaderLine inputLine = inputLinesIt.next(); + + if ( ! inputLine.getClass().equals(outputLine.getClass()) || ! inputLine.getID().equals(outputLine.getID()) ) + return false; + } + + return true; + } + + private static List nullAsEmpty(List l) { + if ( l == null ) + return Collections.emptyList(); + else + return l; + } } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFContigHeaderLine.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFContigHeaderLine.java index d5d76cab7d..35cc75af23 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFContigHeaderLine.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFContigHeaderLine.java @@ -47,8 +47,8 @@ public VCFContigHeaderLine(final String line, final VCFHeaderVersion version, fi this.contigIndex = contigIndex; } - public VCFContigHeaderLine(final String key, final Map mapping, int contigIndex) { - super(key, mapping, null); + public VCFContigHeaderLine(final Map mapping, int contigIndex) { + super(VCFHeader.CONTIG_KEY, mapping, null); this.contigIndex = contigIndex; } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java index 7a93295834..2663e848f0 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java @@ -53,10 +53,10 @@ public enum HEADER_FIELDS { // the associated meta data private final Set mMetaData = new LinkedHashSet(); - private final Map mInfoMetaData = new HashMap(); - private final Map mFormatMetaData = new HashMap(); - private final Map mFilterMetaData = new HashMap(); - private final Map mOtherMetaData = new HashMap(); + private final Map mInfoMetaData = new LinkedHashMap(); + private final Map mFormatMetaData = new LinkedHashMap(); + private final Map mFilterMetaData = new LinkedHashMap(); + private final Map mOtherMetaData = new LinkedHashMap(); private final List contigMetaData = new ArrayList(); // the list of auxillary tags @@ -101,6 +101,15 @@ public VCFHeader(Set metaData) { loadMetaDataMaps(); } + /** + * Creates a shallow copy of the meta data in VCF header toCopy + * + * @param toCopy + */ + public VCFHeader(final VCFHeader toCopy) { + this(toCopy.mMetaData); + } + /** * create a VCF header, given a list of meta data and auxillary tags * @@ -153,12 +162,39 @@ public void addMetaDataLine(VCFHeaderLine headerLine) { } /** - * @return all of the VCF header lines of the ##contig form in order, or an empty set if none were present + * @return all of the VCF header lines of the ##contig form in order, or an empty list if none were present */ public List getContigLines() { return Collections.unmodifiableList(contigMetaData); } + + /** + * @return all of the VCF FILTER lines in their original file order, or an empty list if none were present + */ + public List getFilterLines() { + final List filters = new ArrayList(); + for ( VCFHeaderLine line : mMetaData ) { + if ( line instanceof VCFFilterHeaderLine ) { + filters.add((VCFFilterHeaderLine)line); + } + } + return filters; + } + + /** + * @return all of the VCF FILTER lines in their original file order, or an empty list if none were present + */ + public List getIDHeaderLines() { + final List filters = new ArrayList(); + for ( VCFHeaderLine line : mMetaData ) { + if ( line instanceof VCFIDHeaderLine ) { + filters.add((VCFIDHeaderLine)line); + } + } + return filters; + } + /** * check our metadata for a VCF version tag, and throw an exception if the version is out of date * or the version is not present @@ -299,10 +335,16 @@ public int getColumnCount() { return HEADER_FIELDS.values().length + (hasGenotypingData() ? mGenotypeSampleNames.size() + 1 : 0); } + /** + * Returns the INFO HeaderLines in their original ordering + */ public Collection getInfoHeaderLines() { return mInfoMetaData.values(); } + /** + * Returns the FORMAT HeaderLines in their original ordering + */ public Collection getFormatHeaderLines() { return mFormatMetaData.values(); } @@ -390,4 +432,13 @@ public ArrayList getSampleNamesInOrder() { public HashMap getSampleNameToOffset() { return sampleNameToOffset; } + + @Override + public String toString() { + final StringBuilder b = new StringBuilder(); + b.append("[VCFHeader:"); + for ( final VCFHeaderLine line : mMetaData ) + b.append("\n\t").append(line); + return b.append("\n]").toString(); + } } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java index 561e8e78d5..be87e7306e 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java @@ -301,7 +301,7 @@ private static VCFContigHeaderLine makeContigHeaderLine(final SAMSequenceRecord map.put("ID", contig.getSequenceName()); map.put("length", String.valueOf(contig.getSequenceLength())); if ( assembly != null ) map.put("assembly", assembly); - return new VCFContigHeaderLine(VCFHeader.CONTIG_KEY, map, contig.getSequenceIndex()); + return new VCFContigHeaderLine(map, contig.getSequenceIndex()); } private static String getReferenceAssembly(final String refPath) { diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java index 2211cfe5e8..1fe6b86522 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java @@ -1351,7 +1351,7 @@ private final void fullyDecodeInfo(final VariantContextBuilder builder, final VC private final Map fullyDecodeAttributes(final Map attributes, final VCFHeader header, final boolean lenientDecoding) { - final Map newAttributes = new HashMap(attributes.size()); + final Map newAttributes = new HashMap(10); for ( final Map.Entry attr : attributes.entrySet() ) { final String field = attr.getKey(); diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java index a8f956413d..e571bb4c1f 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java @@ -504,7 +504,7 @@ public static VariantContext simpleMerge(final GenomeLocParser genomeLocParser, Byte referenceBaseForIndel = null; final Set alleles = new LinkedHashSet(); - final Set filters = new TreeSet(); + final Set filters = new HashSet(); final Map attributes = new TreeMap(); final Set inconsistentAttributes = new HashSet(); final Set variantSources = new HashSet(); // contains the set of sources we found in our set of VCs that are variant @@ -656,7 +656,8 @@ else if ( variantSources.isEmpty() ) // everyone was reference builder.alleles(alleles); builder.genotypes(genotypes); builder.log10PError(log10PError); - builder.filters(filters).attributes(mergeInfoWithMaxAC ? attributesWithMaxAC : attributes); + builder.filters(filters.isEmpty() ? filters : new TreeSet(filters)); + builder.attributes(mergeInfoWithMaxAC ? attributesWithMaxAC : attributes); // Trim the padded bases of all alleles if necessary final VariantContext merged = builder.make(); diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Encoder.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Encoder.java index 01dac7eb69..22acc47879 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Encoder.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Encoder.java @@ -124,7 +124,7 @@ public final void encodeTypedFloat(final double d) throws IOException { @Ensures("encodeStream.size() > old(encodeStream.size())") public final void encodeTyped(List v, final BCF2Type type) throws IOException { if ( type == BCF2Type.CHAR && v.size() != 0 ) { - final String s = v.size() > 1 ? BCF2Utils.collapseStringList((List) v) : (String)v.get(0); + final String s = BCF2Utils.collapseStringList((List) v); v = stringToBytes(s); } diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldEncoder.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldEncoder.java index ddeb4d2842..a91eb216d1 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldEncoder.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldEncoder.java @@ -335,7 +335,6 @@ private String javaStringToBCF2String(final Object value) { else if (value instanceof List) { final List l = (List)value; if ( l.isEmpty() ) return ""; - else if ( l.size() == 1 ) return (String)l.get(0); else return BCF2Utils.collapseStringList(l); } else return (String)value; diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java index a080c4e624..e4c64b26bb 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java @@ -87,14 +87,6 @@ class BCF2Writer extends IndexingVariantContextWriter { public static final int MAJOR_VERSION = 2; public static final int MINOR_VERSION = 1; - /** - * If true, we will write out the undecoded raw bytes for a genotypes block, if it - * is found in the input VC. This can be very dangerous as the genotype encoding - * depends on the exact ordering of the header. - * - * TODO -- enable when the new smart VCF header code is created by Eric Banks - */ - private final static boolean WRITE_UNDECODED_GENOTYPE_BLOCK = false; final protected static Logger logger = Logger.getLogger(BCF2Writer.class); final private static boolean ALLOW_MISSING_CONTIG_LINES = false; @@ -108,6 +100,13 @@ class BCF2Writer extends IndexingVariantContextWriter { private final BCF2Encoder encoder = new BCF2Encoder(); // initialized after the header arrives final BCF2FieldWriterManager fieldManager = new BCF2FieldWriterManager(); + /** + * cached results for whether we can write out raw genotypes data. + */ + private VCFHeader lastVCFHeaderOfUnparsedGenotypes = null; + private boolean canPassOnUnparsedGenotypeDataForLastVCFHeader = false; + + public BCF2Writer(final File location, final OutputStream output, final SAMSequenceDictionary refDict, final boolean enableOnTheFlyIndexing, final boolean doNotWriteGenotypes) { super(writerName(location, output), location, output, refDict, enableOnTheFlyIndexing); this.outputStream = getOutputStream(); @@ -247,13 +246,39 @@ private byte[] buildSitesData( VariantContext vc ) throws IOException { return encoder.getRecordBytes(); } + + /** + * Can we safely write on the raw (undecoded) genotypes of an input VC? + * + * The cache depends on the undecoded lazy data header == lastVCFHeaderOfUnparsedGenotypes, in + * which case we return the previous result. If it's not cached, we use the BCF2Util to + * compare the VC header with our header (expensive) and cache it. + * + * @param lazyData + * @return + */ + private boolean canSafelyWriteRawGenotypesBytes(final BCF2Codec.LazyData lazyData) { + if ( lazyData.header != lastVCFHeaderOfUnparsedGenotypes ) { + // result is already cached + canPassOnUnparsedGenotypeDataForLastVCFHeader = BCF2Utils.headerLinesAreOrderedConsistently(this.header,lazyData.header); + lastVCFHeaderOfUnparsedGenotypes = lazyData.header; + } + + return canPassOnUnparsedGenotypeDataForLastVCFHeader; + } + private BCF2Codec.LazyData getLazyData(final VariantContext vc) { if ( vc.getGenotypes().isLazyWithData() ) { - LazyGenotypesContext lgc = (LazyGenotypesContext)vc.getGenotypes(); - if ( WRITE_UNDECODED_GENOTYPE_BLOCK && lgc.getUnparsedGenotypeData() instanceof BCF2Codec.LazyData ) + final LazyGenotypesContext lgc = (LazyGenotypesContext)vc.getGenotypes(); + + if ( lgc.getUnparsedGenotypeData() instanceof BCF2Codec.LazyData && + canSafelyWriteRawGenotypesBytes((BCF2Codec.LazyData) lgc.getUnparsedGenotypeData())) { + //logger.info("Passing on raw BCF2 genotypes data"); return (BCF2Codec.LazyData)lgc.getUnparsedGenotypeData(); - else + } else { + //logger.info("Decoding raw BCF2 genotypes data"); lgc.decode(); // WARNING -- required to avoid keeping around bad lazy data for too long + } } return null; diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2UtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2UtilsUnitTest.java new file mode 100644 index 0000000000..ae76a374a1 --- /dev/null +++ b/public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2UtilsUnitTest.java @@ -0,0 +1,155 @@ +/* + * 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.utils.codecs.bcf2; + +import org.broad.tribble.readers.PositionalBufferedStream; +import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.codecs.vcf.*; + +import java.io.*; +import java.util.*; +import org.testng.Assert; +import org.testng.annotations.BeforeSuite; +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; + +/** + * Tests for BCF2Utils + */ +public final class BCF2UtilsUnitTest extends BaseTest { + @DataProvider(name = "CollapseExpandTest") + public Object[][] makeCollapseExpandTest() { + List tests = new ArrayList(); + tests.add(new Object[]{Arrays.asList("A"), "A", false}); + tests.add(new Object[]{Arrays.asList("A", "B"), ",A,B", true}); + tests.add(new Object[]{Arrays.asList("AB"), "AB", false}); + tests.add(new Object[]{Arrays.asList("AB", "C"), ",AB,C", true}); + tests.add(new Object[]{Arrays.asList(), "", false}); + return tests.toArray(new Object[][]{}); + } + + @Test(dataProvider = "CollapseExpandTest") + public void testCollapseExpandTest(final List in, final String expectedCollapsed, final boolean isCollapsed) { + final String actualCollapsed = BCF2Utils.collapseStringList(in); + Assert.assertEquals(actualCollapsed, expectedCollapsed); + Assert.assertEquals(BCF2Utils.isCollapsedString(actualCollapsed), isCollapsed); + if ( isCollapsed ) + Assert.assertEquals(BCF2Utils.explodeStringList(actualCollapsed), in); + } + + @DataProvider(name = "HeaderOrderTestProvider") + public Object[][] makeHeaderOrderTestProvider() { + final List inputLines = new ArrayList(); + final List extraLines = new ArrayList(); + + int counter = 0; + inputLines.add(new VCFFilterHeaderLine(String.valueOf(counter++))); + inputLines.add(new VCFFilterHeaderLine(String.valueOf(counter++))); + inputLines.add(new VCFContigHeaderLine(Collections.singletonMap("ID", String.valueOf(counter++)), counter)); + inputLines.add(new VCFContigHeaderLine(Collections.singletonMap("ID", String.valueOf(counter++)), counter)); + inputLines.add(new VCFInfoHeaderLine(String.valueOf(counter++), VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "x")); + inputLines.add(new VCFInfoHeaderLine(String.valueOf(counter++), VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "x")); + inputLines.add(new VCFFormatHeaderLine(String.valueOf(counter++), VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "x")); + inputLines.add(new VCFFormatHeaderLine(String.valueOf(counter++), VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "x")); + final int inputLineCounter = counter; + final VCFHeader inputHeader = new VCFHeader(new LinkedHashSet(inputLines)); + + extraLines.add(new VCFFilterHeaderLine(String.valueOf(counter++))); + extraLines.add(new VCFContigHeaderLine(Collections.singletonMap("ID", String.valueOf(counter++)), counter)); + extraLines.add(new VCFInfoHeaderLine(String.valueOf(counter++), VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "x")); + extraLines.add(new VCFFormatHeaderLine(String.valueOf(counter++), VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "x")); + extraLines.add(new VCFHeaderLine("x", "misc")); + extraLines.add(new VCFHeaderLine("y", "misc")); + + List tests = new ArrayList(); + for ( final int extrasToTake : Arrays.asList(0, 1, 2, 3) ) { + final List empty = Collections.emptyList(); + final List> permutations = extrasToTake == 0 + ? Collections.singletonList(empty) + : Utils.makePermutations(extraLines, extrasToTake, false); + for ( final List permutation : permutations ) { + for ( int i = -1; i < inputLines.size(); i++ ) { + final List allLines = new ArrayList(inputLines); + if ( i >= 0 ) + allLines.remove(i); + allLines.addAll(permutation); + final VCFHeader testHeader = new VCFHeader(new LinkedHashSet(allLines)); + final boolean expectedConsistent = expectedConsistent(testHeader, inputLineCounter); + tests.add(new Object[]{inputHeader, testHeader, expectedConsistent}); + } + } + } + + // sample name tests + final List> sampleNameTests = Arrays.asList( + new ArrayList(), + Arrays.asList("A"), + Arrays.asList("A", "B"), + Arrays.asList("A", "B", "C")); + for ( final List inSamples : sampleNameTests ) { + for ( final List testSamples : sampleNameTests ) { + final VCFHeader inputHeaderWithSamples = new VCFHeader(inputHeader.getMetaDataInInputOrder(), inSamples); + + final List> permutations = testSamples.isEmpty() + ? Collections.singletonList(testSamples) + : Utils.makePermutations(testSamples, testSamples.size(), false); + for ( final List testSamplesPermutation : permutations ) { + final VCFHeader testHeaderWithSamples = new VCFHeader(inputHeader.getMetaDataInInputOrder(), testSamplesPermutation); + final boolean expectedConsistent = testSamples.equals(inSamples); + tests.add(new Object[]{inputHeaderWithSamples, testHeaderWithSamples, expectedConsistent}); + } + } + } + + return tests.toArray(new Object[][]{}); + } + + private static boolean expectedConsistent(final VCFHeader combinationHeader, final int minCounterForInputLines) { + final List ids = new ArrayList(); + for ( final VCFHeaderLine line : combinationHeader.getMetaDataInInputOrder() ) { + if ( line instanceof VCFIDHeaderLine ) { + ids.add(Integer.valueOf(((VCFIDHeaderLine) line).getID())); + } + } + + // as long as the start contains all of the ids up to minCounterForInputLines in order + for ( int i = 0; i < minCounterForInputLines; i++ ) + if ( i >= ids.size() || ids.get(i) != i ) + return false; + + return true; + } + + // + // Test to make sure that we detect correctly the case where we can preserve the genotypes data in a BCF2 + // even when the header file is slightly different + // + @Test(dataProvider = "HeaderOrderTestProvider") + public void testHeaderOrder(final VCFHeader inputHeader, final VCFHeader testHeader, final boolean expectedConsistent) { + final boolean actualOrderConsistency = BCF2Utils.headerLinesAreOrderedConsistently(testHeader, inputHeader); + Assert.assertEquals(actualOrderConsistency, expectedConsistent); + } +} diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java index dd1985be38..26e2dbfbc4 100644 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java @@ -197,7 +197,7 @@ private static void createSyntheticHeader() { addHeaderLine(metaData, "FT", 1, VCFHeaderLineType.String); // prep the header - metaData.add(new VCFContigHeaderLine(VCFHeader.CONTIG_KEY, Collections.singletonMap("ID", "1"), 0)); + metaData.add(new VCFContigHeaderLine(Collections.singletonMap("ID", "1"), 0)); metaData.add(new VCFFilterHeaderLine("FILTER1")); metaData.add(new VCFFilterHeaderLine("FILTER2")); @@ -889,7 +889,7 @@ public static void addComplexGenotypesTest() { } private static List> makeAllGenotypes(final List alleles, final int highestPloidy) { - return Utils.makeCombinations(alleles, highestPloidy); + return Utils.makePermutations(alleles, highestPloidy, true); } public static void assertEquals(final VCFHeader actual, final VCFHeader expected) { From 725ed6ff5db8c4dfaece95f874d567475fcedb87 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Wed, 15 Aug 2012 21:12:21 -0400 Subject: [PATCH 132/176] CombineVariants parallel integration tests -- All tests but one (using old bad VCF3 input) run unmodified with parallel code. -- Disabled UNSAFE_VCF_PROCESSING for all but that test, which changes md5s because the output files have fixed headers -- Minor optimizations to simpleMerge --- .../variantcontext/VariantContextUtils.java | 6 +-- .../CombineVariantsIntegrationTest.java | 46 ++++++++++++------- 2 files changed, 32 insertions(+), 20 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java index e571bb4c1f..5421960b24 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java @@ -505,7 +505,7 @@ public static VariantContext simpleMerge(final GenomeLocParser genomeLocParser, final Set alleles = new LinkedHashSet(); final Set filters = new HashSet(); - final Map attributes = new TreeMap(); + final Map attributes = new LinkedHashMap(); final Set inconsistentAttributes = new HashSet(); final Set variantSources = new HashSet(); // contains the set of sources we found in our set of VCs that are variant final Set rsIDs = new LinkedHashSet(1); // most of the time there's one id @@ -513,7 +513,7 @@ public static VariantContext simpleMerge(final GenomeLocParser genomeLocParser, GenomeLoc loc = getLocation(genomeLocParser,first); int depth = 0; int maxAC = -1; - final Map attributesWithMaxAC = new TreeMap(); + final Map attributesWithMaxAC = new LinkedHashMap(); double log10PError = 1; VariantContext vcWithMaxAC = null; GenotypesContext genotypes = GenotypesContext.create(); @@ -657,7 +657,7 @@ else if ( variantSources.isEmpty() ) // everyone was reference builder.genotypes(genotypes); builder.log10PError(log10PError); builder.filters(filters.isEmpty() ? filters : new TreeSet(filters)); - builder.attributes(mergeInfoWithMaxAC ? attributesWithMaxAC : attributes); + builder.attributes(new TreeMap(mergeInfoWithMaxAC ? attributesWithMaxAC : attributes)); // Trim the padded bases of all alleles if necessary final VariantContext merged = builder.make(); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java index 2f28a6dbc3..9ea751b72c 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java @@ -45,12 +45,16 @@ public class CombineVariantsIntegrationTest extends WalkerTest { // TODO TODO TODO TODO TODO TODO TODO TODO // private static String baseTestString(String args) { - return "-T CombineVariants --no_cmdline_in_header -L 1:1-50,000,000 -o %s -U LENIENT_VCF_PROCESSING -R " + b36KGReference + args; + return "-T CombineVariants --no_cmdline_in_header -L 1:1-50,000,000 -o %s -R " + b36KGReference + args; + //return "-T CombineVariants --no_cmdline_in_header -L 1:1-50,000,000 -o %s -U LENIENT_VCF_PROCESSING -R " + b36KGReference + args; } - private void cvExecuteTest(final String name, final WalkerTestSpec spec) { + private void cvExecuteTest(final String name, final WalkerTestSpec spec, final boolean parallel) { spec.disableShadowBCF(); - executeTestParallel(name, spec); + if ( parallel ) + executeTestParallel(name, spec); + else + executeTest(name, spec); } public void test1InOut(String file, String md5) { @@ -62,15 +66,19 @@ public void test1InOut(String file, String md5, String args) { baseTestString(" -priority v1 -V:v1 " + validationDataLocation + file + args), 1, Arrays.asList(md5)); - cvExecuteTest("testInOut1--" + file, spec); + cvExecuteTest("testInOut1--" + file, spec, true); } public void combine2(String file1, String file2, String args, String md5) { + combine2(file1, file2, args, md5, true); + } + + public void combine2(String file1, String file2, String args, String md5, final boolean parallel) { WalkerTestSpec spec = new WalkerTestSpec( baseTestString(" -priority v1,v2 -V:v1 " + validationDataLocation + file1 + " -V:v2 "+ validationDataLocation + file2 + args), 1, Arrays.asList(md5)); - cvExecuteTest("combine2 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec); + cvExecuteTest("combine2 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec, parallel); } public void combineSites(String args, String md5) { @@ -82,7 +90,7 @@ public void combineSites(String args, String md5) { + " -V:hm3 " + validationDataLocation + file2 + args, 1, Arrays.asList(md5)); - cvExecuteTest("combineSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec); + cvExecuteTest("combineSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec, true); } public void combinePLs(String file1, String file2, String md5) { @@ -90,26 +98,29 @@ public void combinePLs(String file1, String file2, String md5) { "-T CombineVariants --no_cmdline_in_header -o %s -R " + b36KGReference + " -priority v1,v2 -V:v1 " + privateTestDir + file1 + " -V:v2 " + privateTestDir + file2, 1, Arrays.asList(md5)); - cvExecuteTest("combine PLs 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec); + cvExecuteTest("combine PLs 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec, true); } - @Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "6469fce8a5cd5a0f77e5ac5d9e9e192b"); } - @Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "a4cedaa83d54e34cafc3ac4b80acf5b4", " -setKey foo"); } - @Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "ac58a5fde17661e2a19004ca954d9781", " -setKey null"); } + @Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "6469fce8a5cd5a0f77e5ac5d9e9e192b", " -U LENIENT_VCF_PROCESSING"); } + @Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "a4cedaa83d54e34cafc3ac4b80acf5b4", " -setKey foo -U LENIENT_VCF_PROCESSING"); } + @Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "ac58a5fde17661e2a19004ca954d9781", " -setKey null -U LENIENT_VCF_PROCESSING"); } @Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "67a8076e30b4bca0ea5acdc9cd26a4e0"); } // official project VCF files in tabix format @Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "909c6dc74eeb5ab86f8e74073eb0c1d6"); } - @Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "f0c2cb3e3a6160e1ed0ee2fd9b120f55"); } + @Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "381875b3280ba56eef0152e56f64f68d"); } @Test public void combineWithPLs() { combinePLs("combine.3.vcf", "combine.4.vcf", "f0ce3fb83d4ad9ba402d7cb11cd000c3"); } @Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "4efdf983918db822e4ac13d911509576"); } // official project VCF files in tabix format @Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "848d4408ee953053d2307cefebc6bd6d"); } // official project VCF files in tabix format - @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "4159a0c0d7c15852a3a545e0bea6bbc5"); } + @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "5d04f22ef88ed9226cbd7b4483c5cb23"); } - @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "61d0ded244895234ac727391f29f13a8"); } + @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "e54d0dcf14f90d5c8e58b45191dd0219"); } - @Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "0b1815c699e71e143ed129bfadaffbcb"); } + @Test public void uniqueSNPs() { + // parallelism must be disabled because the input VCF is malformed (DB=0) and parallelism actually fixes this which breaks the md5s + combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "acc70f33be741b564f7be9aa3f819dd4", true); + } @Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "def52bcd3942bbe39cd7ebe845c4f206"); } @Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "5f61145949180bf2a0cd342d8e064860"); } @@ -122,11 +133,12 @@ public void combinePLs(String file1, String file2, String md5) { " -V:denovoInfo "+validationDataLocation+"yri_merged_validation_data_240610.annotated.b36.vcf" + " -setKey centerSet" + " -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED" + + " -U LENIENT_VCF_PROCESSING" + " -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" + " -genotypeMergeOptions UNIQUIFY -L 1"), 1, Arrays.asList("3039cfff7abee6aa7fbbafec66a1b019")); - cvExecuteTest("threeWayWithRefs", spec); + cvExecuteTest("threeWayWithRefs", spec, true); } // complex examples with filtering, indels, and multiple alleles @@ -139,7 +151,7 @@ public void combineComplexSites(String args, String md5) { + " -V:two " + privateTestDir + file2 + args, 1, Arrays.asList(md5)); - cvExecuteTest("combineComplexSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec); + cvExecuteTest("combineComplexSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec, true); } @Test public void complexTestFull() { combineComplexSites("", "9d989053826ffe5bef7c4e05ac51bcca"); } @@ -153,6 +165,6 @@ public void combineDBSNPDuplicateSites() { "-T CombineVariants --no_cmdline_in_header -L 1:902000-903000 -o %s -R " + b37KGReference + " -V:v1 " + b37dbSNP132, 1, Arrays.asList("aa926eae333208dc1f41fe69dc95d7a6")); - cvExecuteTest("combineDBSNPDuplicateSites:", spec); + cvExecuteTest("combineDBSNPDuplicateSites:", spec, true); } } \ No newline at end of file From 6e9709ef06aa805ec6f97dd1fe8b08a264cc09fa Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Wed, 15 Aug 2012 21:12:55 -0400 Subject: [PATCH 133/176] Disable general ploidy integration tests because they are running forever From f58b637e02fc32dd2003a1d23cc3e240b121040d Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 15 Aug 2012 21:55:08 -0400 Subject: [PATCH 134/176] Better docs for verbose output of Pileup --- .../org/broadinstitute/sting/gatk/walkers/Pileup.java | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java index 0eb3a628db..2a6ecdb8cb 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java @@ -64,9 +64,17 @@ */ @DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) public class Pileup extends LocusWalker implements TreeReducible { + + private static final String verboseDelimiter = "@"; // it's ugly to use "@" but it's literally the only usable character not allowed in read names + @Output PrintStream out; + /** + * In addition to the standard pileup output, adds 'verbose' output too. The verbose output contains the number of spanning deletions, + * and for each read in the pileup it has the read name, offset in the base string, read length, and read mapping quality. These per + * read items are delimited with an '@' character. + */ @Argument(fullName="showVerbose",shortName="verbose",doc="Add an extra verbose section to the pileup output") public boolean SHOW_VERBOSE = false; @@ -116,8 +124,6 @@ private String getReferenceOrderedData( RefMetaDataTracker tracker ) { return rodString; } - private static final String verboseDelimiter = "@"; // it's ugly to use "@" but it's literally the only usable character not allowed in read names - private static String createVerboseOutput(final ReadBackedPileup pileup) { final StringBuilder sb = new StringBuilder(); boolean isFirst = true; From bd7c09cf49c32513ea6f88662044a941fd5c75dd Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 15 Aug 2012 22:52:56 -0400 Subject: [PATCH 135/176] Implementing support in BaseRecalibrator for SOLiD no call strategies other than throwing an exception. For some reason we never transfered these capabilities into BQSRv2 earlier. --- .../gatk/walkers/bqsr/BaseRecalibrator.java | 2 +- .../sting/utils/recalibration/RecalUtils.java | 83 ++++++++++++------- 2 files changed, 55 insertions(+), 30 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java index f69a02002a..3f35cf8e85 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java @@ -227,7 +227,7 @@ public Long map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentConte if (readNotSeen(read)) { read.setTemporaryAttribute(SEEN_ATTRIBUTE, true); RecalUtils.parsePlatformForRead(read, RAC); - if (RecalUtils.isColorSpaceConsistent(RAC.SOLID_NOCALL_STRATEGY, read)) { + if (!RecalUtils.isColorSpaceConsistent(RAC.SOLID_NOCALL_STRATEGY, read)) { read.setTemporaryAttribute(SKIP_RECORD_ATTRIBUTE, true); continue; } diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java index a605c4649d..2d05877af9 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java @@ -524,46 +524,71 @@ public static void parsePlatformForRead(final GATKSAMRecord read, final Recalibr /** * Parse through the color space of the read and add a new tag to the SAMRecord that says which bases are - * inconsistent with the color space. If there is no call in the color space, this method returns true meaning + * inconsistent with the color space. If there is a no call in the color space, this method returns false meaning * this read should be skipped * * @param strategy the strategy used for SOLID no calls * @param read The SAMRecord to parse - * @return whether or not this read should be skipped + * @return true if this read is consistent or false if this read should be skipped */ public static boolean isColorSpaceConsistent(final SOLID_NOCALL_STRATEGY strategy, final GATKSAMRecord read) { - if (ReadUtils.isSOLiDRead(read)) { // If this is a SOLID read then we have to check if the color space is inconsistent. This is our only sign that SOLID has inserted the reference base - if (read.getAttribute(RecalUtils.COLOR_SPACE_INCONSISTENCY_TAG) == null) { // Haven't calculated the inconsistency array yet for this read - final Object attr = read.getAttribute(RecalUtils.COLOR_SPACE_ATTRIBUTE_TAG); - if (attr != null) { - byte[] colorSpace; - if (attr instanceof String) - colorSpace = ((String) attr).getBytes(); - else - throw new UserException.MalformedBAM(read, String.format("Value encoded by %s in %s isn't a string!", RecalUtils.COLOR_SPACE_ATTRIBUTE_TAG, read.getReadName())); - - byte[] readBases = read.getReadBases(); // Loop over the read and calculate first the inferred bases from the color and then check if it is consistent with the read - if (read.getReadNegativeStrandFlag()) - readBases = BaseUtils.simpleReverseComplement(read.getReadBases()); - - final byte[] inconsistency = new byte[readBases.length]; - int i; - byte prevBase = colorSpace[0]; // The sentinel - for (i = 0; i < readBases.length; i++) { - final byte thisBase = getNextBaseFromColor(read, prevBase, colorSpace[i + 1]); - inconsistency[i] = (byte) (thisBase == readBases[i] ? 0 : 1); - prevBase = readBases[i]; + if (!ReadUtils.isSOLiDRead(read)) // If this is a SOLID read then we have to check if the color space is inconsistent. This is our only sign that SOLID has inserted the reference base + return true; + + if (read.getAttribute(RecalUtils.COLOR_SPACE_INCONSISTENCY_TAG) == null) { // Haven't calculated the inconsistency array yet for this read + final Object attr = read.getAttribute(RecalUtils.COLOR_SPACE_ATTRIBUTE_TAG); + if (attr != null) { + byte[] colorSpace; + if (attr instanceof String) + colorSpace = ((String) attr).getBytes(); + else + throw new UserException.MalformedBAM(read, String.format("Value encoded by %s in %s isn't a string!", RecalUtils.COLOR_SPACE_ATTRIBUTE_TAG, read.getReadName())); + + final boolean badColor = hasNoCallInColorSpace(colorSpace); + if (badColor) { + if (strategy == SOLID_NOCALL_STRATEGY.LEAVE_READ_UNRECALIBRATED) { + return false; // can't recalibrate a SOLiD read with no calls in the color space, and the user wants to skip over them + } + else if (strategy == SOLID_NOCALL_STRATEGY.PURGE_READ) { + read.setReadFailsVendorQualityCheckFlag(true); + return false; } - read.setAttribute(RecalUtils.COLOR_SPACE_INCONSISTENCY_TAG, inconsistency); } - else if (strategy == SOLID_NOCALL_STRATEGY.THROW_EXCEPTION) // if the strategy calls for an exception, throw it - throw new UserException.MalformedBAM(read, "Unable to find color space information in SOLiD read. First observed at read with name = " + read.getReadName() + " Unfortunately this .bam file can not be recalibrated without color space information because of potential reference bias."); - else - return true; // otherwise, just skip the read + byte[] readBases = read.getReadBases(); // Loop over the read and calculate first the inferred bases from the color and then check if it is consistent with the read + if (read.getReadNegativeStrandFlag()) + readBases = BaseUtils.simpleReverseComplement(read.getReadBases()); + + final byte[] inconsistency = new byte[readBases.length]; + int i; + byte prevBase = colorSpace[0]; // The sentinel + for (i = 0; i < readBases.length; i++) { + final byte thisBase = getNextBaseFromColor(read, prevBase, colorSpace[i + 1]); + inconsistency[i] = (byte) (thisBase == readBases[i] ? 0 : 1); + prevBase = readBases[i]; + } + read.setAttribute(RecalUtils.COLOR_SPACE_INCONSISTENCY_TAG, inconsistency); } + else if (strategy == SOLID_NOCALL_STRATEGY.THROW_EXCEPTION) // if the strategy calls for an exception, throw it + throw new UserException.MalformedBAM(read, "Unable to find color space information in SOLiD read. First observed at read with name = " + read.getReadName() + " Unfortunately this .bam file can not be recalibrated without color space information because of potential reference bias."); + + else + return false; // otherwise, just skip the read } - return false; + + return true; + } + + private static boolean hasNoCallInColorSpace(final byte[] colorSpace) { + final int length = colorSpace.length; + for (int i = 1; i < length; i++) { // skip the sentinal + final byte color = colorSpace[i]; + if (color != (byte) '0' && color != (byte) '1' && color != (byte) '2' && color != (byte) '3') { + return true; // There is a bad color in this SOLiD read + } + } + + return false; // There aren't any color no calls in this SOLiD read } /** From 452beba46cf22bb80e55b7f6731c5c7f35dcccd8 Mon Sep 17 00:00:00 2001 From: David Roazen Date: Wed, 15 Aug 2012 22:54:13 -0400 Subject: [PATCH 136/176] Convert external.build.dir and external.dist.dir back to paths The previous push fixed the external classpath issue but broke external builds in a new way by changing the above from paths to properties. This was a mistake, since external builds require absolute, not relative, paths Thanks to akiezun for the bug report and patch --- build.xml | 22 +++++++++++++--------- 1 file changed, 13 insertions(+), 9 deletions(-) diff --git a/build.xml b/build.xml index 2ca48c51be..f681ddafa3 100644 --- a/build.xml +++ b/build.xml @@ -70,10 +70,6 @@ - - - - @@ -211,6 +207,14 @@ + + + + + + + + @@ -425,8 +429,8 @@ - - + + @@ -675,9 +679,9 @@ - - - + + + From 620e1c159b8bf0e352bf4aa317d7b494de8f6eb4 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 15 Aug 2012 23:13:24 -0400 Subject: [PATCH 137/176] Adding tests for the --solid_nocall_strategy argument From 432ae951083d00dc3f5975cc45381b9e63291f45 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 16 Aug 2012 09:28:03 -0400 Subject: [PATCH 138/176] Update md5 in VariantRecalibrationWalkers test for BCF2 -- only encoding differences --- .../VariantRecalibrationWalkersIntegrationTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java index d1ecbb0bf3..b780bcd00c 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java @@ -76,7 +76,7 @@ public void testApplyRecalibration(VRTest params) { VRTest bcfTest = new VRTest(privateTestDir + "vqsr.bcf_test.snps.unfiltered.bcf", "a8ce3cd3dccafdf7d580bcce7d660a9a", // tranches - "1cdf8c9ee77d91d1ba7f002573108bad", // recal file + "74c10fc15f9739a938b7138909fbde04", // recal file "62fda105e14b619a1c263855cf56af1d"); // cut VCF @DataProvider(name = "VRBCFTest") From 1b166538e9e76203730a1a3c121b484e34b18047 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 16 Aug 2012 10:01:10 -0400 Subject: [PATCH 139/176] Meaningful error message and keeping tmp file when mergeInfo fails -- BCF2 is failing for some reason when merging tmp. files with parallel combine variants. ThreadLocalOutputTracker no longer sets deleteOnExit on the tmp file, as this prevents debugging. And it's unnecessary because each mergeInto was deleting files as appropriate -- MergeInfo in VariantContextWriterStorage only deletes the intermediate output if an error occurs --- .../broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java | 2 +- .../sting/gatk/io/storage/VariantContextWriterStorage.java | 3 +++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java b/public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java index 999deddd1f..636787c69f 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java @@ -119,7 +119,7 @@ private File createTempFile( Stub stub ) { try { tempFile = File.createTempFile( stub.getClass().getName(), null ); - tempFile.deleteOnExit(); + //tempFile.deleteOnExit(); } catch( IOException ex ) { throw new UserException.BadTmpDir("Unable to create temporary file for stub: " + stub.getClass().getName() ); diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java index 161179f84d..72f8581dd6 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java @@ -194,6 +194,9 @@ public void mergeInto(VariantContextWriterStorage target) { } source.close(); + file.delete(); // this should be last to aid in debugging when the process fails + } catch (UserException e) { + throw new ReviewedStingException("BUG: intermediate file " + file + " is malformed, got error while reading", e); } catch (IOException e) { throw new UserException.CouldNotReadInputFile(file, "Error reading file in VCFWriterStorage: ", e); } From 0c21fa8aabda0cc8e1e6e797448fdf2964b2e9c8 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 16 Aug 2012 10:53:22 -0400 Subject: [PATCH 140/176] Cleanup BCF2Codec -- Remove FORBID_SYMBOLIC global that is no longer necessary -- all error handling goes via error() function --- .../sting/utils/codecs/bcf2/BCF2Codec.java | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java index ac6348f808..fc0b3c4a9a 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java @@ -51,7 +51,6 @@ */ public final class BCF2Codec implements FeatureCodec { final protected static Logger logger = Logger.getLogger(BCF2Codec.class); - private final static boolean FORBID_SYMBOLICS = false; private final static int ALLOWED_MAJOR_VERSION = 2; private final static int MIN_MINOR_VERSION = 1; @@ -178,7 +177,7 @@ public FeatureCodecHeader readHeader( final PositionalBufferedStream inputStream contigNames.add(contig.getID()); } } else { - throw new UserException.MalformedBCF2("Didn't find any contig lines in BCF2 file header"); + error("Didn't find any contig lines in BCF2 file header"); } // create the string dictionary @@ -271,7 +270,7 @@ private final SitesInfoForDecoding decodeSitesExtendedInfo(final VariantContextB final int nSamples = nFormatSamples & 0x00FFFFF; if ( header.getNGenotypeSamples() != nSamples ) - throw new UserException.MalformedBCF2("GATK currently doesn't support reading BCF2 files with " + + error("GATK currently doesn't support reading BCF2 files with " + "different numbers of samples per record. Saw " + header.getNGenotypeSamples() + " samples in header but have a record with " + nSamples + " samples"); @@ -343,9 +342,6 @@ private List decodeAlleles( final VariantContextBuilder builder, final i if ( isRef ) ref = alleleBases; alleles.add(allele); - - if ( FORBID_SYMBOLICS && allele.isSymbolic() ) - throw new ReviewedStingException("LIMITATION: GATK BCF2 codec does not yet support symbolic alleles"); } assert ref != null; @@ -496,7 +492,7 @@ protected BCF2GenotypeFieldDecoders.Decoder getGenotypeFieldDecoder(final String return gtFieldDecoders.getDecoder(field); } - private final void error(final String message) throws RuntimeException { + private void error(final String message) throws RuntimeException { throw new UserException.MalformedBCF2(String.format("%s, at record %d with position %d:", message, recordNo, pos)); } } From d5dee0b52ec12f70b9d77c0ae69b9396e7067ec0 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 16 Aug 2012 10:54:52 -0400 Subject: [PATCH 141/176] Added -bcf argument to VCFWriter output to force BCF regardless of file extension -- Now possible to do -o /dev/stdout -bcf -l DEBUG > tmp.bcf and create a valid BCF2 file -- Cleanup code to make sure extensions easier by moving to a setX model in VariantContextWriterStub --- .../VCFWriterArgumentTypeDescriptor.java | 53 ++++++++++++++----- .../io/stubs/VariantContextWriterStub.java | 45 +++++++++------- 2 files changed, 66 insertions(+), 32 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java index 09766f1273..5e1132d459 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java @@ -47,6 +47,7 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor { public static final String NO_HEADER_ARG_NAME = "no_cmdline_in_header"; public static final String SITES_ONLY_ARG_NAME = "sites_only"; + public static final String FORCE_BCF = "bcf"; public static final HashSet SUPPORTED_ZIPPED_SUFFIXES = new HashSet(); // @@ -96,7 +97,11 @@ public boolean supports( Class type ) { @Override public List createArgumentDefinitions( ArgumentSource source ) { - return Arrays.asList( createDefaultArgumentDefinition(source), createNoCommandLineHeaderArgumentDefinition(),createSitesOnlyArgumentDefinition()); + return Arrays.asList( + createDefaultArgumentDefinition(source), + createNoCommandLineHeaderArgumentDefinition(), + createSitesOnlyArgumentDefinition(), + createBCFArgumentDefinition() ); } /** @@ -117,7 +122,7 @@ public String typeDefaultDocString(ArgumentSource source) { public Object createTypeDefault(ParsingEngine parsingEngine,ArgumentSource source, Type type) { if(!source.isRequired()) throw new ReviewedStingException("BUG: tried to create type default for argument type descriptor that can't support a type default."); - VariantContextWriterStub stub = new VariantContextWriterStub(engine, defaultOutputStream, false, argumentSources, false, false); + VariantContextWriterStub stub = new VariantContextWriterStub(engine, defaultOutputStream, argumentSources); engine.addOutput(stub); return stub; } @@ -141,15 +146,15 @@ public Object parse( ParsingEngine parsingEngine, ArgumentSource source, Type ty if(writerFile == null && !source.isRequired()) throw new MissingArgumentValueException(defaultArgumentDefinition); - // Should we compress the output stream? - boolean compress = isCompressed(writerFileName); - - boolean skipWritingCmdLineHeader = argumentIsPresent(createNoCommandLineHeaderArgumentDefinition(),matches); - boolean doNotWriteGenotypes = argumentIsPresent(createSitesOnlyArgumentDefinition(),matches); - // Create a stub for the given object. - VariantContextWriterStub stub = (writerFile != null) ? new VariantContextWriterStub(engine, writerFile, compress, argumentSources, skipWritingCmdLineHeader, doNotWriteGenotypes) - : new VariantContextWriterStub(engine, defaultOutputStream, compress, argumentSources, skipWritingCmdLineHeader, doNotWriteGenotypes); + final VariantContextWriterStub stub = (writerFile != null) + ? new VariantContextWriterStub(engine, writerFile, argumentSources) + : new VariantContextWriterStub(engine, defaultOutputStream, argumentSources); + + stub.setCompressed(isCompressed(writerFileName)); + stub.setDoNotWriteGenotypes(argumentIsPresent(createSitesOnlyArgumentDefinition(),matches)); + stub.setSkipWritingCommandLineHeader(argumentIsPresent(createNoCommandLineHeaderArgumentDefinition(),matches)); + stub.setForceBCF(argumentIsPresent(createBCFArgumentDefinition(),matches)); // WARNING: Side effects required by engine! parsingEngine.addTags(stub,getArgumentTags(matches)); @@ -159,8 +164,8 @@ public Object parse( ParsingEngine parsingEngine, ArgumentSource source, Type ty } /** - * Creates the optional compression level argument for the BAM file. - * @return Argument definition for the BAM file itself. Will not be null. + * Creates the optional no_header argument for the VCF file. + * @return Argument definition for the VCF file itself. Will not be null. */ private ArgumentDefinition createNoCommandLineHeaderArgumentDefinition() { return new ArgumentDefinition( ArgumentIOType.ARGUMENT, @@ -179,8 +184,8 @@ private ArgumentDefinition createNoCommandLineHeaderArgumentDefinition() { } /** - * Creates the optional compression level argument for the BAM file. - * @return Argument definition for the BAM file itself. Will not be null. + * Creates the optional sites_only argument definition + * @return Argument definition for the VCF file itself. Will not be null. */ private ArgumentDefinition createSitesOnlyArgumentDefinition() { return new ArgumentDefinition( ArgumentIOType.ARGUMENT, @@ -198,6 +203,26 @@ private ArgumentDefinition createSitesOnlyArgumentDefinition() { null ); } + /** + * Creates the optional bcf argument definition + * @return Argument definition for the VCF file itself. Will not be null. + */ + private ArgumentDefinition createBCFArgumentDefinition() { + return new ArgumentDefinition( ArgumentIOType.ARGUMENT, + boolean.class, + FORCE_BCF, + FORCE_BCF, + "force BCF output, regardless of the file's extension", + false, + true, + false, + true, + null, + null, + null, + null ); + } + /** * Returns true if the file will be compressed. * @param writerFileName Name of the file diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java index bea7172eac..260a7efdaf 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java @@ -79,7 +79,7 @@ public class VariantContextWriterStub implements Stub, Var /** * Should we emit a compressed output stream? */ - private final boolean isCompressed; + private boolean isCompressed = false; /** * A hack: push the argument sources into the VCF header so that the VCF header @@ -90,12 +90,17 @@ public class VariantContextWriterStub implements Stub, Var /** * Should the header be written out? A hidden argument. */ - private final boolean skipWritingCommandLineHeader; + private boolean skipWritingCommandLineHeader = false; /** * Should we not write genotypes even when provided? */ - private final boolean doNotWriteGenotypes; + private boolean doNotWriteGenotypes = false; + + /** + * Should we force BCF writing regardless of the file extension? + */ + private boolean forceBCF = false; /** * Connects this stub with an external stream capable of serving the @@ -108,19 +113,13 @@ public class VariantContextWriterStub implements Stub, Var * * @param engine engine. * @param genotypeFile file to (ultimately) create. - * @param isCompressed should we compress the output stream? * @param argumentSources sources. - * @param skipWritingCommandLineHeader skip writing header. - * @param doNotWriteGenotypes do not write genotypes. */ - public VariantContextWriterStub(GenomeAnalysisEngine engine, File genotypeFile, boolean isCompressed, Collection argumentSources, boolean skipWritingCommandLineHeader, boolean doNotWriteGenotypes) { + public VariantContextWriterStub(GenomeAnalysisEngine engine, File genotypeFile, Collection argumentSources) { this.engine = engine; this.genotypeFile = genotypeFile; this.genotypeStream = null; - this.isCompressed = isCompressed; this.argumentSources = argumentSources; - this.skipWritingCommandLineHeader = skipWritingCommandLineHeader; - this.doNotWriteGenotypes = doNotWriteGenotypes; } /** @@ -128,19 +127,13 @@ public VariantContextWriterStub(GenomeAnalysisEngine engine, File genotypeFile, * * @param engine engine. * @param genotypeStream stream to (ultimately) write. - * @param isCompressed should we compress the output stream? * @param argumentSources sources. - * @param skipWritingCommandLineHeader skip writing header. - * @param doNotWriteGenotypes do not write genotypes. */ - public VariantContextWriterStub(GenomeAnalysisEngine engine, OutputStream genotypeStream, boolean isCompressed, Collection argumentSources, boolean skipWritingCommandLineHeader, boolean doNotWriteGenotypes) { + public VariantContextWriterStub(GenomeAnalysisEngine engine, OutputStream genotypeStream, Collection argumentSources) { this.engine = engine; this.genotypeFile = null; this.genotypeStream = new PrintStream(genotypeStream); - this.isCompressed = isCompressed; this.argumentSources = argumentSources; - this.skipWritingCommandLineHeader = skipWritingCommandLineHeader; - this.doNotWriteGenotypes = doNotWriteGenotypes; } /** @@ -167,6 +160,22 @@ public boolean isCompressed() { return isCompressed; } + public void setCompressed(boolean compressed) { + isCompressed = compressed; + } + + public void setSkipWritingCommandLineHeader(boolean skipWritingCommandLineHeader) { + this.skipWritingCommandLineHeader = skipWritingCommandLineHeader; + } + + public void setDoNotWriteGenotypes(boolean doNotWriteGenotypes) { + this.doNotWriteGenotypes = doNotWriteGenotypes; + } + + public void setForceBCF(boolean forceBCF) { + this.forceBCF = forceBCF; + } + /** * Gets the master sequence dictionary from the engine associated with this stub * @link GenomeAnalysisEngine.getMasterSequenceDictionary @@ -187,7 +196,7 @@ public EnumSet getWriterOptions(boolean indexOnTheFly) { if ( engine.lenientVCFProcessing() ) options.add(Options.ALLOW_MISSING_FIELDS_IN_HEADER); if ( indexOnTheFly && ! isCompressed() ) options.add(Options.INDEX_ON_THE_FLY); - if ( getFile() != null && VariantContextWriterFactory.isBCFOutput(getFile()) ) + if ( forceBCF || (getFile() != null && VariantContextWriterFactory.isBCFOutput(getFile())) ) options.add(Options.FORCE_BCF); return options.isEmpty() ? EnumSet.noneOf(Options.class) : EnumSet.copyOf(options); From 58f303c36482fcf27d4156dd0670adb2c88d6862 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 16 Aug 2012 10:56:07 -0400 Subject: [PATCH 142/176] Make sure the storage writer is closed before running mergeInfo in multi-threaded output management -- It's not clear this is cause of GSA-484 but it will help confirm that it's not the cause --- .../sting/gatk/io/storage/VariantContextWriterStorage.java | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java index 72f8581dd6..0f5290db7a 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java @@ -61,6 +61,7 @@ public class VariantContextWriterStorage implements Storage Date: Thu, 16 Aug 2012 12:39:54 -0400 Subject: [PATCH 143/176] GSA-485: Remove repairVCFHeader from GATK codebase -- Removed half-a*ssed attempt to automatically repair VCF files with bad headers, which allowed users to provide a replacement header overwriting the file's actually header on the fly. Not a good idea, really. Eric has promised to create a utility that walks through a VCF file and creates a meaningful header field based on the file's contents (if this ever becomes a priority) --- .../sting/gatk/GenomeAnalysisEngine.java | 15 ++--------- .../arguments/GATKArgumentCollection.java | 9 ------- .../gatk/refdata/tracks/FeatureManager.java | 8 ++---- .../gatk/refdata/tracks/RMDTrackBuilder.java | 16 +---------- .../sting/utils/codecs/vcf/VCFCodec.java | 27 ------------------- .../variantcontext/writer/VCFWriter.java | 2 +- .../utils/codecs/vcf/VCFIntegrationTest.java | 7 +---- 7 files changed, 7 insertions(+), 77 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index 56fcf0652e..55107833d7 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -849,20 +849,9 @@ private List getReferenceOrderedDataSources(Collecti SAMSequenceDictionary sequenceDictionary, GenomeLocParser genomeLocParser, ValidationExclusion.TYPE validationExclusionType) { - VCFHeader header = null; - if ( getArguments().repairVCFHeader != null ) { - try { - final PositionalBufferedStream pbs = new PositionalBufferedStream(new FileInputStream(getArguments().repairVCFHeader)); - header = (VCFHeader)new VCFCodec().readHeader(pbs).getHeaderValue(); - pbs.close(); - } catch ( IOException e ) { - throw new UserException.CouldNotReadInputFile(getArguments().repairVCFHeader, e); - } - } - - RMDTrackBuilder builder = new RMDTrackBuilder(sequenceDictionary,genomeLocParser, header, validationExclusionType); + final RMDTrackBuilder builder = new RMDTrackBuilder(sequenceDictionary,genomeLocParser, validationExclusionType); - List dataSources = new ArrayList(); + final List dataSources = new ArrayList(); for (RMDTriplet fileDescriptor : referenceMetaDataFiles) dataSources.add(new ReferenceOrderedDataSource(fileDescriptor, builder, diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java index 4c9235b58b..06177868ae 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java @@ -384,14 +384,5 @@ public static DownsamplingMethod getDefaultDownsamplingMethod() { @Hidden public boolean USE_SLOW_GENOTYPES = false; // TODO -- remove all code tagged with TODO -- remove me when argument generateShadowBCF is removed - - /** - * The file pointed to by this argument must be a VCF file. The GATK will read in just the header of this file - * and then use the INFO, FORMAT, and FILTER field values from this file to repair the header file of any other - * VCF file that GATK reads in. This allows us to have in effect a master set of header records and use these - * to fill in any missing ones in input VCF files. - */ - @Argument(fullName="repairVCFHeader", shortName = "repairVCFHeader", doc="If provided, whenever we read a VCF file we will use the header in this file to repair the header of the input VCF files", required=false) - public File repairVCFHeader = null; } diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java index b5d5deedb8..a2fe946412 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java @@ -85,18 +85,16 @@ public int compareTo(FeatureDescriptor o) { private final PluginManager pluginManager; private final Collection featureDescriptors = new TreeSet(); - private final VCFHeader headerForRepairs; private final boolean lenientVCFProcessing; /** * Construct a FeatureManager without a master VCF header */ public FeatureManager() { - this(null, false); + this(false); } - public FeatureManager(final VCFHeader headerForRepairs, final boolean lenientVCFProcessing) { - this.headerForRepairs = headerForRepairs; + public FeatureManager(final boolean lenientVCFProcessing) { this.lenientVCFProcessing = lenientVCFProcessing; pluginManager = new PluginManager(FeatureCodec.class, "Codecs", "Codec"); @@ -255,8 +253,6 @@ public FeatureCodec createCodec(FeatureDescriptor descriptor, String name, Genom ((NameAwareCodec)codex).setName(name); if ( codex instanceof ReferenceDependentFeatureCodec ) ((ReferenceDependentFeatureCodec)codex).setGenomeLocParser(genomeLocParser); - if ( codex instanceof VCFCodec ) - ((VCFCodec)codex).setHeaderForRepairs(headerForRepairs); if ( codex instanceof AbstractVCFCodec && lenientVCFProcessing ) ((AbstractVCFCodec)codex).disableOnTheFlyModifications(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java index e183fe1698..81fe73075d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java @@ -89,17 +89,15 @@ public class RMDTrackBuilder { // extends PluginManager { * please talk through your approach with the SE team. * @param dict Sequence dictionary to use. * @param genomeLocParser Location parser to use. - * @param headerForRepairs a VCF header that should be used to repair VCF headers. Can be null * @param validationExclusionType Types of validations to exclude, for sequence dictionary verification. */ public RMDTrackBuilder(final SAMSequenceDictionary dict, final GenomeLocParser genomeLocParser, - final VCFHeader headerForRepairs, ValidationExclusion.TYPE validationExclusionType) { this.dict = dict; this.validationExclusionType = validationExclusionType; this.genomeLocParser = genomeLocParser; - this.featureManager = new FeatureManager(headerForRepairs, GenomeAnalysisEngine.lenientVCFProcessing(validationExclusionType)); + this.featureManager = new FeatureManager(GenomeAnalysisEngine.lenientVCFProcessing(validationExclusionType)); } /** @@ -111,18 +109,6 @@ public FeatureManager getFeatureManager() { return featureManager; } - /** - * Same as full constructor but makes one without a header for repairs - * @param dict - * @param genomeLocParser - * @param validationExclusionType - */ - public RMDTrackBuilder(final SAMSequenceDictionary dict, - final GenomeLocParser genomeLocParser, - ValidationExclusion.TYPE validationExclusionType) { - this(dict, genomeLocParser, null, validationExclusionType); - } - /** * create a RMDTrack of the specified type * diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java index da5b18831f..4df1efee79 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java @@ -49,13 +49,6 @@ public class VCFCodec extends AbstractVCFCodec { // Our aim is to read in the records and convert to VariantContext as quickly as possible, relying on VariantContext to do the validation of any contradictory (or malformed) record parameters. public final static String VCF4_MAGIC_HEADER = "##fileformat=VCFv4"; - /** - * A VCF header the contains master info/filter/format records that we use to 'fill in' - * any missing records from our input VCF header. This allows us to repair headers on - * the fly - */ - private VCFHeader headerForRepairs = null; - /** * @param reader the line reader to take header lines from * @return the number of header lines @@ -88,8 +81,6 @@ else if (line.startsWith(VCFHeader.HEADER_INDICATOR)) { } headerStrings.add(line); super.parseHeaderFromLines(headerStrings, version); - if ( headerForRepairs != null ) - this.header = repairHeader(this.header, headerForRepairs); return this.header; } else { @@ -103,24 +94,6 @@ else if (line.startsWith(VCFHeader.HEADER_INDICATOR)) { throw new TribbleException.InvalidHeader("We never saw the required CHROM header line (starting with one #) for the input VCF file"); } - private final VCFHeader repairHeader(final VCFHeader readHeader, final VCFHeader masterHeader) { - final Set lines = VCFUtils.smartMergeHeaders(Arrays.asList(readHeader, masterHeader), log); - return new VCFHeader(lines, readHeader.getGenotypeSamples()); - } - - /** - * Tells this VCFCodec to repair the incoming header files with the information in masterHeader - * - * @param headerForRepairs - */ - public void setHeaderForRepairs(final VCFHeader headerForRepairs) { - if ( headerForRepairs != null ) - log.info("Using master VCF header to repair missing files from incoming VCFs"); - this.headerForRepairs = headerForRepairs; - } - - - /** * parse the filter string, first checking to see if we already have parsed it in a previous attempt * diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java index ea968e153a..db74f22630 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java @@ -563,6 +563,6 @@ private final void fieldIsMissingFromHeaderError(final VariantContext vc, final + " at " + vc.getChr() + ":" + vc.getStart() + " but this key isn't defined in the VCFHeader. The GATK now requires all VCFs to have" + " complete VCF headers by default. This error can be disabled with the engine argument" - + " -U LENIENT_VCF_PROCESSING or repair the VCF file header using repairVCFHeader"); + + " -U LENIENT_VCF_PROCESSING"); } } diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java index 71fc1d4642..b2a4ac2dad 100644 --- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java @@ -92,7 +92,7 @@ public void testReadingSamtoolsWExBCFExample() { // // - // Tests to ensure that -U LENIENT_VCF_PROCESS and header repairs are working + // Tests to ensure that -U LENIENT_VCF_PROCESS // // @@ -106,11 +106,6 @@ public void testPassingOnVCFWithoutHeadersWithLenientProcessing() { runVCFWithoutHeaders("-U LENIENT_VCF_PROCESSING", "6de8cb7457154dd355aa55befb943f88", null, true); } - @Test - public void testPassingOnVCFWithoutHeadersRepairingHeaders() { - runVCFWithoutHeaders("-repairVCFHeader " + privateTestDir + "vcfexample2.justHeader.vcf", "ff61e9cad6653c7f93d82d391f7ecdcb", null, false); - } - private void runVCFWithoutHeaders(final String moreArgs, final String expectedMD5, final Class expectedException, final boolean disableBCF) { final String testVCF = privateTestDir + "vcfexample2.noHeader.vcf"; final String baseCommand = "-R " + b37KGReference From 310389acf79d2714258e97b7d8ba1f4ebb84f172 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 16 Aug 2012 13:00:35 -0400 Subject: [PATCH 144/176] GSA-488: MLEAC > AN error when running variant eval fixed --- .../varianteval/stratifications/AlleleCount.java | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java index 50c5526e49..00a5937685 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java @@ -19,6 +19,8 @@ * it computes the AC from the genotypes themselves. If no AC can be computed, 0 is used. */ public class AlleleCount extends VariantStratifier { + int nchrom; + @Override public void initialize() { // we can only work with a single eval VCF, and it must have genotypes @@ -26,7 +28,8 @@ public void initialize() { throw new UserException.BadArgumentValue("AlleleCount", "AlleleCount stratification only works with a single eval vcf"); // There are 2 x n sample chromosomes for diploids - int nchrom = getVariantEvalWalker().getSampleNamesForEvaluation().size() * 2; + // TODO -- generalize to handle multiple ploidy + nchrom = getVariantEvalWalker().getSampleNamesForEvaluation().size() * 2; if ( nchrom < 2 ) throw new UserException.BadArgumentValue("AlleleCount", "AlleleCount stratification requires an eval vcf with at least one sample"); @@ -52,8 +55,10 @@ public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker t } // make sure that the AC isn't invalid - if ( AC > eval.getCalledChrCount() ) - throw new UserException.MalformedVCF(String.format("The AC or MLEAC value (%d) at position %s:%d is larger than the possible called chromosome count (%d)", AC, eval.getChr(), eval.getStart(), eval.getCalledChrCount())); + if ( AC > nchrom ) + throw new UserException.MalformedVCF(String.format("The AC or MLEAC value (%d) at position %s:%d " + + "is larger than the number of chromosomes over all samples (%d)", AC, + eval.getChr(), eval.getStart(), nchrom)); return Collections.singletonList((Object) AC); } else { From 4874fe8c2f4d02acd595489bd7bdcffd6448a81f Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 16 Aug 2012 13:05:17 -0400 Subject: [PATCH 145/176] Fix for performance problem in GGA mode related to previous --regenotype commit. Instead of trying to hack around the determination of the calculation model when it's not needed, just simply overload the calculateGenotypes() method to add one that does simple genotyping. Re-enabling the Pool Caller integration tests. --- .../walkers/genotyper/UnifiedGenotyperEngine.java | 15 +++++++++++---- .../gatk/walkers/variantutils/SelectVariants.java | 2 +- .../SelectVariantsIntegrationTest.java | 2 +- 3 files changed, 13 insertions(+), 6 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index f15fa9b999..c9656dd00f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -38,7 +38,6 @@ import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; @@ -259,6 +258,16 @@ public VariantCallContext calculateGenotypes(RefMetaDataTracker tracker, Referen return calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model); } + /** + * Compute genotypes at a given locus. + * + * @param vc the GL-annotated variant context + * @return the VariantCallContext object + */ + public VariantCallContext calculateGenotypes(VariantContext vc) { + return calculateGenotypes(null, null, null, null, vc, GenotypeLikelihoodsCalculationModel.Model.valueOf("SNP"), false); + } + // --------------------------------------------------------------------------------------------------------- // @@ -647,10 +656,8 @@ private List getGLModelsToUse(final R // if we're genotyping given alleles and we have a requested SNP at this position, do SNP if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) { final VariantContext vcInput = getVCFromAllelesRod(tracker, refContext, rawContext.getLocation(), false, logger, UAC.alleles); - if ( vcInput == null ) { - models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix+"SNP")); + if ( vcInput == null ) return models; - } if ( vcInput.isSNP() ) { // ignore SNPs if the user chose INDEL mode only diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index 0810710c1a..f775c8dd6e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -568,7 +568,7 @@ public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentCo VariantContext sub = subsetRecord(vc, EXCLUDE_NON_VARIANTS); if ( REGENOTYPE && sub.isPolymorphicInSamples() && hasPLs(sub) ) { - final VariantContextBuilder builder = new VariantContextBuilder(UG_engine.calculateGenotypes(null, ref, context, sub)).filters(sub.getFiltersMaybeNull()); + final VariantContextBuilder builder = new VariantContextBuilder(UG_engine.calculateGenotypes(sub)).filters(sub.getFiltersMaybeNull()); addAnnotations(builder, sub); sub = builder.make(); } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java index e172200f7f..bde597fbef 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java @@ -148,7 +148,7 @@ public void testRegenotype() { WalkerTestSpec spec = new WalkerTestSpec( "-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header", 1, - Arrays.asList("52cb2f150559ca1457e9df7ec153dbb452cb2f150559ca1457e9df7ec153dbb4") + Arrays.asList("52cb2f150559ca1457e9df7ec153dbb4") ); executeTest("testRegenotype--" + testFile, spec); From 1db3ed533e81db35cbe7be1d7f39e20fe3119633 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 16 Aug 2012 13:32:44 -0400 Subject: [PATCH 146/176] Killing off some FindBugs 'Usability' issues --- .../sting/commandline/ArgumentDefinitionGroup.java | 6 ++---- .../sting/gatk/walkers/beagle/BeagleOutputToVCF.java | 4 ---- .../gatk/walkers/genotyper/UnifiedGenotyperEngine.java | 4 ++-- .../sting/gatk/walkers/phasing/PhaseByTransmission.java | 2 +- .../gatk/walkers/variantutils/VariantsToBinaryPed.java | 4 ---- .../src/org/broadinstitute/sting/utils/MannWhitneyU.java | 4 ++-- .../java/src/org/broadinstitute/sting/utils/MathUtils.java | 3 +-- public/java/src/org/broadinstitute/sting/utils/Utils.java | 1 - .../sting/utils/codecs/vcf/VCFHeaderLine.java | 2 +- .../sting/utils/help/GenericDocumentationHandler.java | 2 +- .../utils/recalibration/covariates/CycleCovariate.java | 2 +- 11 files changed, 11 insertions(+), 23 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java b/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java index b47677b08e..474225e2a1 100644 --- a/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java +++ b/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java @@ -55,10 +55,8 @@ public ArgumentDefinitionGroup( String groupName, List argum * Does the name of this argument group match the name of another? */ public boolean groupNameMatches( ArgumentDefinitionGroup other ) { - if( this.groupName == null && other.groupName == null ) - return true; - if( this.groupName == null && other.groupName != null ) - return false; + if( this.groupName == null ) + return other.groupName == null; return this.groupName.equals(other.groupName); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java index 9eb0e4dda8..83b10dd91d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java @@ -30,7 +30,6 @@ 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.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.GenomeLoc; @@ -142,9 +141,6 @@ public void initialize() { hInfo.add(new VCFFilterHeaderLine("BGL_RM_WAS_G", "This 'G' site was set to monomorphic by Beagle")); hInfo.add(new VCFFilterHeaderLine("BGL_RM_WAS_T", "This 'T' site was set to monomorphic by Beagle")); - // Open output file specified by output VCF ROD - final List dataSources = this.getToolkit().getRodDataSources(); - if ( comp.isBound() ) { hInfo.add(new VCFInfoHeaderLine("ACH", 1, VCFHeaderLineType.Integer, "Allele Count from Comparison ROD at this site")); hInfo.add(new VCFInfoHeaderLine("ANH", 1, VCFHeaderLineType.Integer, "Allele Frequency from Comparison ROD at this site")); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index c9656dd00f..05e12b43d5 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -183,7 +183,7 @@ public List calculateLikelihoodsAndGenotypes(final RefMetaDa for ( final GenotypeLikelihoodsCalculationModel.Model model : models ) { final Map stratifiedContexts = getFilteredAndStratifiedContexts(UAC, refContext, rawContext, model); if ( stratifiedContexts == null ) { - results.add(UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES && UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ? generateEmptyContext(tracker, refContext, stratifiedContexts, rawContext) : null); + results.add(UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES && UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ? generateEmptyContext(tracker, refContext, null, rawContext) : null); } else { final VariantContext vc = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.COMPLETE, null, true, model); @@ -202,7 +202,7 @@ private List addMissingSamples(final List withAllSamples = new ArrayList(calls.size()); for ( final VariantCallContext call : calls ) { if ( call == null ) - withAllSamples.add(call); + withAllSamples.add(null); else { final VariantContext withoutMissing = VariantContextUtils.addMissingSamples(call, allSamples); withAllSamples.add(new VariantCallContext(withoutMissing, call.confidentlyCalled, call.shouldEmit)); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java index bbd4bf92f3..0dcafb30a2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java @@ -645,7 +645,7 @@ private int phaseTrioGenotypes(Allele ref, Allele alt, Genotype mother, Genotype bestChildGenotype.clear(); bestChildGenotype.add(childGenotype.getKey()); } - else if(configurationLikelihood == bestConfigurationLikelihood) { + else if(MathUtils.compareDoubles(configurationLikelihood, bestConfigurationLikelihood) == 0) { bestFirstParentGenotype.add(firstParentGenotype.getKey()); bestSecondParentGenotype.add(secondParentGenotype.getKey()); bestChildGenotype.add(childGenotype.getKey()); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java index 7e82fc4540..14c811b03f 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java @@ -8,8 +8,6 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.utils.R.RScriptExecutorException; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; @@ -18,7 +16,6 @@ import org.broadinstitute.sting.utils.text.XReadLines; import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import java.io.*; @@ -95,7 +92,6 @@ public void initialize() { // write to the fam file, the first six columns of the standard ped file // first, load data from the input meta data file Map> metaValues = new HashMap>(); - Set samplesToUse = new HashSet(); logger.debug("Reading in metadata..."); try { if ( metaDataFile.getAbsolutePath().endsWith(".fam") ) { diff --git a/public/java/src/org/broadinstitute/sting/utils/MannWhitneyU.java b/public/java/src/org/broadinstitute/sting/utils/MannWhitneyU.java index ecb381e3ff..d1bc755831 100755 --- a/public/java/src/org/broadinstitute/sting/utils/MannWhitneyU.java +++ b/public/java/src/org/broadinstitute/sting/utils/MannWhitneyU.java @@ -199,9 +199,9 @@ public static double calculatePUniformApproximation(int n, int m, long u) { else if ( z > n ) { return 0.0; } else { if ( z > ((double) n) /2 ) { - return 1.0-1/((double)Arithmetic.factorial(n))*uniformSumHelper(z, (int) Math.floor(z), n, 0); + return 1.0-1/(Arithmetic.factorial(n))*uniformSumHelper(z, (int) Math.floor(z), n, 0); } else { - return 1/((double)Arithmetic.factorial(n))*uniformSumHelper(z, (int) Math.floor(z), n, 0); + return 1/(Arithmetic.factorial(n))*uniformSumHelper(z, (int) Math.floor(z), n, 0); } } } diff --git a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java index 96704f0b87..7d1561fc5c 100644 --- a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java @@ -767,7 +767,7 @@ public static byte average(byte[] vals) { for (byte v : vals) { sum += v; } - return (byte) Math.floor(sum / vals.length); + return (byte) (sum / vals.length); } public static double averageDouble(List vals) { @@ -1044,7 +1044,6 @@ public static Comparable orderStatisticSearch(int orderStat, List li // the list is assumed *not* to be sorted final Comparable x = list.get(orderStat); - ListIterator iterator = list.listIterator(); ArrayList lessThanX = new ArrayList(); ArrayList equalToX = new ArrayList(); ArrayList greaterThanX = new ArrayList(); diff --git a/public/java/src/org/broadinstitute/sting/utils/Utils.java b/public/java/src/org/broadinstitute/sting/utils/Utils.java index 476098ae64..a5b5eca6aa 100755 --- a/public/java/src/org/broadinstitute/sting/utils/Utils.java +++ b/public/java/src/org/broadinstitute/sting/utils/Utils.java @@ -563,7 +563,6 @@ public static , V> String sortedString(Map c) { List t = new ArrayList(c.keySet()); Collections.sort(t); - List l = new ArrayList(); List pairs = new ArrayList(); for ( T k : t ) { pairs.add(k + "=" + c.get(k)); diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java index 162c34d80b..83e55cb127 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java @@ -53,7 +53,7 @@ public class VCFHeaderLine implements Comparable { */ public VCFHeaderLine(String key, String value) { if ( key == null ) - throw new IllegalArgumentException("VCFHeaderLine: key cannot be null: key = " + key); + throw new IllegalArgumentException("VCFHeaderLine: key cannot be null"); mKey = key; mValue = value; } diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java index 69d2e7c9e9..dc0668cea7 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java @@ -587,7 +587,7 @@ protected Map docForArgument(FieldDoc fieldDoc, ArgumentSource s private List> docForEnumArgument(Class enumClass) { ClassDoc doc = this.getDoclet().getClassDocForClass(enumClass); if (doc == null) // || ! doc.isEnum() ) - throw new RuntimeException("Tried to get docs for enum " + enumClass + " but got instead: " + doc); + throw new RuntimeException("Tried to get docs for enum " + enumClass + " but got null instead"); List> bindings = new ArrayList>(); for (final FieldDoc field : doc.fields(false)) { diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java index 4f15419c75..cdf12d2848 100755 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java @@ -51,7 +51,7 @@ public class CycleCovariate implements StandardCovariate { private static final int MAXIMUM_CYCLE_VALUE = 1000; private static final int CUSHION_FOR_INDELS = 4; - private static String default_platform = null; + private String default_platform = null; private static final EnumSet DISCRETE_CYCLE_PLATFORMS = EnumSet.of(NGSPlatform.ILLUMINA, NGSPlatform.SOLID, NGSPlatform.PACBIO, NGSPlatform.COMPLETE_GENOMICS); private static final EnumSet FLOW_CYCLE_PLATFORMS = EnumSet.of(NGSPlatform.LS454, NGSPlatform.ION_TORRENT); From ea22eb305819cf2aeb443ceb88e9e45004203406 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 16 Aug 2012 14:00:48 -0400 Subject: [PATCH 147/176] Killing off some FindBugs 'Realiability' issues --- .../sting/alignment/reference/bwt/Bases.java | 8 +++---- .../commandline/ArgumentTypeDescriptor.java | 2 +- .../sting/commandline/ParsingMethod.java | 4 ++-- .../ReadBasedReferenceOrderedView.java | 2 +- .../reference/ReferenceDataSource.java | 3 +-- .../sting/gatk/executive/MicroScheduler.java | 2 +- .../sting/gatk/executive/TreeReducer.java | 4 ++-- .../sting/gatk/phonehome/GATKRunReport.java | 2 +- .../gatk/traversals/TraversalEngine.java | 4 ++-- .../sting/gatk/traversals/TraverseLoci.java | 2 +- .../gatk/traversals/TraverseReadPairs.java | 2 +- .../sting/gatk/traversals/TraverseReads.java | 2 +- .../walkers/annotator/ChromosomeCounts.java | 4 ++-- .../annotator/TandemRepeatAnnotator.java | 4 ++-- .../targets/FindCoveredIntervals.java | 6 ++--- .../gatk/walkers/diffengine/DiffNode.java | 2 +- .../evaluators/ThetaVariantEvaluator.java | 6 ++--- .../walkers/variantutils/SelectVariants.java | 24 ------------------- .../walkers/variantutils/VariantsToTable.java | 2 +- .../broadinstitute/sting/utils/BaseUtils.java | 8 +++---- .../broadinstitute/sting/utils/baq/BAQ.java | 2 +- .../sting/utils/codecs/vcf/VCFHeaderLine.java | 4 ++-- .../sting/utils/pileup/PileupElement.java | 3 ++- .../sting/utils/recalibration/RecalDatum.java | 4 ++-- .../utils/recalibration/RecalDatumNode.java | 2 +- .../utils/sam/GATKSAMReadGroupRecord.java | 2 +- .../sting/utils/sam/ReadUtils.java | 4 ++-- .../utils/variantcontext/GenotypeBuilder.java | 2 +- .../variantcontext/GenotypeLikelihoods.java | 2 +- .../variantcontext/VariantContextUtils.java | 2 +- 30 files changed, 48 insertions(+), 72 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java b/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java index bc0a5b63d6..7cd85cfd8e 100644 --- a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java +++ b/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java @@ -12,10 +12,10 @@ */ public class Bases implements Iterable { - public static byte A = 'A'; - public static byte C = 'C'; - public static byte G = 'G'; - public static byte T = 'T'; + public static final byte A = 'A'; + public static final byte C = 'C'; + public static final byte G = 'G'; + public static final byte T = 'T'; public static final Bases instance = new Bases(); diff --git a/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java index c201e95f04..dd4a151bf1 100644 --- a/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java +++ b/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java @@ -53,7 +53,7 @@ public abstract class ArgumentTypeDescriptor { /** * our log, which we want to capture anything from org.broadinstitute.sting */ - protected static Logger logger = Logger.getLogger(ArgumentTypeDescriptor.class); + protected static final Logger logger = Logger.getLogger(ArgumentTypeDescriptor.class); /** * Fetch the given descriptor from the descriptor repository. diff --git a/public/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java b/public/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java index 26af49e12b..376b6f210a 100755 --- a/public/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java +++ b/public/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java @@ -120,8 +120,8 @@ public static Tags parseTags(String argument, String tagString) { */ private static final String TAG_TEXT = "[\\w\\-\\.\\=]*"; - public static ParsingMethod FullNameParsingMethod = new ParsingMethod(Pattern.compile(String.format("\\s*--(%1$s)(?:\\:(%2$s(?:,%2$s)*))?\\s*",ARGUMENT_TEXT,TAG_TEXT)), + public static final ParsingMethod FullNameParsingMethod = new ParsingMethod(Pattern.compile(String.format("\\s*--(%1$s)(?:\\:(%2$s(?:,%2$s)*))?\\s*",ARGUMENT_TEXT,TAG_TEXT)), ArgumentDefinitions.FullNameDefinitionMatcher) {}; - public static ParsingMethod ShortNameParsingMethod = new ParsingMethod(Pattern.compile(String.format("\\s*-(%1$s)(?:\\:(%2$s(?:,%2$s)*))?\\s*",ARGUMENT_TEXT,TAG_TEXT)), + public static final ParsingMethod ShortNameParsingMethod = new ParsingMethod(Pattern.compile(String.format("\\s*-(%1$s)(?:\\:(%2$s(?:,%2$s)*))?\\s*",ARGUMENT_TEXT,TAG_TEXT)), ArgumentDefinitions.ShortNameDefinitionMatcher) {}; } diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java index 142c8a1785..01e24df671 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java @@ -118,7 +118,7 @@ private void getStates(ShardDataProvider provider, SAMRecord rec) { rec.getAlignmentStart(), stop); states = new ArrayList(); - if (provider != null && provider.getReferenceOrderedData() != null) + if (provider.getReferenceOrderedData() != null) for (ReferenceOrderedDataSource dataSource : provider.getReferenceOrderedData()) states.add(new RMDDataState(dataSource, dataSource.seek(range))); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java index 4ecfe472df..b131e36c10 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java @@ -45,7 +45,6 @@ import java.io.File; import java.util.ArrayList; import java.util.Collections; -import java.util.LinkedList; import java.util.List; /** @@ -56,7 +55,7 @@ public class ReferenceDataSource { private IndexedFastaSequenceFile reference; /** our log, which we want to capture anything from this class */ - protected static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(ReferenceDataSource.class); + protected static final org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(ReferenceDataSource.class); /** * Create reference data source from fasta file diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java index 5080997084..95e39b7c6b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java +++ b/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java @@ -58,7 +58,7 @@ /** Shards and schedules data in manageable chunks. */ public abstract class MicroScheduler implements MicroSchedulerMBean { - protected static Logger logger = Logger.getLogger(MicroScheduler.class); + protected static final Logger logger = Logger.getLogger(MicroScheduler.class); /** * Counts the number of instances of the class that are currently alive. diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java b/public/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java index 632638f64f..390da0cced 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java +++ b/public/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java @@ -66,13 +66,13 @@ public boolean isReadyForReduce() { * @return Result of the reduce. */ public Object call() { - Object result = null; + Object result; final long startTime = System.currentTimeMillis(); try { if( lhs == null ) - result = lhs.get(); + result = null; // todo -- what the hell is this above line? Shouldn't it be the two below? // if( lhs == null ) // throw new IllegalStateException(String.format("Insufficient data on which to reduce; lhs = %s, rhs = %s", lhs, rhs) ); diff --git a/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java b/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java index 4cf5046a24..b60a7845aa 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java +++ b/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java @@ -93,7 +93,7 @@ public class GATKRunReport { /** * our log */ - protected static Logger logger = Logger.getLogger(GATKRunReport.class); + protected static final Logger logger = Logger.getLogger(GATKRunReport.class); @Element(required = false, name = "id") diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java index 2593fc72e3..abc71e5499 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java @@ -92,7 +92,7 @@ public ProcessingHistory(double elapsedSeconds, GenomeLoc loc, long unitsProcess GenomeLocSortedSet targetIntervals = null; /** our log, which we want to capture anything from this class */ - protected static Logger logger = Logger.getLogger(TraversalEngine.class); + protected static final Logger logger = Logger.getLogger(TraversalEngine.class); protected GenomeAnalysisEngine engine; @@ -354,7 +354,7 @@ public void setPerformanceLogFileName(String fileName) { synchronized(performanceLogLock) { // Ignore multiple calls to reset the same lock. - if(performanceLogFile != null && performanceLogFile.equals(fileName)) + if(performanceLogFile != null && performanceLogFile.equals(file)) return; // Close an existing log diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java index 5c9b833120..a5a6919a22 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java +++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java @@ -19,7 +19,7 @@ public class TraverseLoci extends TraversalEngine,Locu /** * our log, which we want to capture anything from this class */ - protected static Logger logger = Logger.getLogger(TraversalEngine.class); + protected static final Logger logger = Logger.getLogger(TraversalEngine.class); @Override protected String getTraversalType() { diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java index dd4402d82f..ebaac40af6 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java +++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java @@ -24,7 +24,7 @@ public class TraverseReadPairs extends TraversalEngine,ReadShardDataProvider> { /** our log, which we want to capture anything from this class */ - protected static Logger logger = Logger.getLogger(TraverseReadPairs.class); + protected static final Logger logger = Logger.getLogger(TraverseReadPairs.class); @Override protected String getTraversalType() { diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java index 24b8ac986b..cb094d29bf 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java +++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java @@ -51,7 +51,7 @@ */ public class TraverseReads extends TraversalEngine,ReadShardDataProvider> { /** our log, which we want to capture anything from this class */ - protected static Logger logger = Logger.getLogger(TraverseReads.class); + protected static final Logger logger = Logger.getLogger(TraverseReads.class); @Override protected String getTraversalType() { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java index 54837baadc..6bdd779c0e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java @@ -53,8 +53,8 @@ */ public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation { - public static final String[] keyNames = { VCFConstants.ALLELE_NUMBER_KEY, VCFConstants.ALLELE_COUNT_KEY, VCFConstants.ALLELE_FREQUENCY_KEY }; - public static final VCFInfoHeaderLine[] descriptions = { + protected static final String[] keyNames = { VCFConstants.ALLELE_NUMBER_KEY, VCFConstants.ALLELE_COUNT_KEY, VCFConstants.ALLELE_FREQUENCY_KEY }; + protected static final VCFInfoHeaderLine[] descriptions = { VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_FREQUENCY_KEY), VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_COUNT_KEY), VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_NUMBER_KEY) }; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java index eced387b36..f220ecbd28 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java @@ -66,8 +66,8 @@ public Map annotate(RefMetaDataTracker tracker, AnnotatorCompati return map; } - public static final String[] keyNames = {STR_PRESENT, REPEAT_UNIT_KEY,REPEATS_PER_ALLELE_KEY }; - public static final VCFInfoHeaderLine[] descriptions = { + protected static final String[] keyNames = {STR_PRESENT, REPEAT_UNIT_KEY,REPEATS_PER_ALLELE_KEY }; + protected static final VCFInfoHeaderLine[] descriptions = { new VCFInfoHeaderLine(STR_PRESENT, 0, VCFHeaderLineType.Flag, "Variant is a short tandem repeat"), new VCFInfoHeaderLine(REPEAT_UNIT_KEY, 1, VCFHeaderLineType.String, "Tandem repeat unit (bases)"), new VCFInfoHeaderLine(REPEATS_PER_ALLELE_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "Number of times tandem repeat unit is repeated, for each allele (including reference)") }; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java index 373c8232e7..e17c6cdb7b 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java @@ -78,9 +78,9 @@ public Long reduceInit() { public Long reduce(final GenomeLoc value, Long reduce) { if (value != null) { out.println(value.toString()); - return ++reduce; - } else - return reduce; + reduce++; + } + return reduce; } @Override diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java index 2f48de2d36..7315fe5033 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java @@ -224,7 +224,7 @@ private static DiffElement fromString(String tree, DiffElement parent) { // X=(A=A B=B C=(D=D)) String[] parts = tree.split("=", 2); if ( parts.length != 2 ) - throw new ReviewedStingException("Unexpected tree structure: " + tree + " parts=" + parts); + throw new ReviewedStingException("Unexpected tree structure: " + tree); String name = parts[0]; String value = parts[1]; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java index a509294ffd..b87a8ee85d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java @@ -41,7 +41,7 @@ public void update1(VariantContext vc, RefMetaDataTracker tracker, ReferenceCont ConcurrentMap alleleCounts = new ConcurrentHashMap(); int numHetsHere = 0; - float numGenosHere = 0; + int numGenosHere = 0; int numIndsHere = 0; for (final Genotype genotype : vc.getGenotypes()) { @@ -68,7 +68,7 @@ public void update1(VariantContext vc, RefMetaDataTracker tracker, ReferenceCont //only if have one called genotype at least this.numSites++; - this.totalHet += numHetsHere / numGenosHere; + this.totalHet += numHetsHere / (double)numGenosHere; //compute based on num sites float harmonicFactor = 0; @@ -79,7 +79,7 @@ public void update1(VariantContext vc, RefMetaDataTracker tracker, ReferenceCont //now compute pairwise mismatches float numPairwise = 0; - float numDiffs = 0; + int numDiffs = 0; for (String allele1 : alleleCounts.keySet()) { int allele1Count = alleleCounts.get(allele1); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index f775c8dd6e..bfd9aa52f6 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -31,7 +31,6 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.samples.Sample; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCounts; @@ -311,10 +310,6 @@ public class SelectVariants extends RodWalker implements TreeR private File rsIDFile = null; - @Hidden - @Argument(fullName="outMVFile", shortName="outMVFile", doc="", required=false) - private String outMVFile = null; - @Hidden @Argument(fullName="fullyDecode", doc="If true, the incoming VariantContext will be fully decoded", required=false) private boolean fullyDecode = false; @@ -369,8 +364,6 @@ public enum NumberAlleleRestriction { private int positionToAdd = 0; private RandomVariantStructure [] variantArray; - private PrintStream outMVFileStream = null; - //Random number generator for the genotypes to remove private Random randomGenotypes = new Random(); @@ -528,23 +521,6 @@ public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentCo if (MENDELIAN_VIOLATIONS && mv.countViolations(this.getSampleDB().getFamilies(samples),vc) < 1) break; - if (outMVFile != null){ - for( String familyId : mv.getViolationFamilies()){ - for(Sample sample : this.getSampleDB().getFamily(familyId)){ - if(sample.getParents().size() > 0){ - outMVFileStream.format("MV@%s:%d. REF=%s, ALT=%s, AC=%d, momID=%s, dadID=%s, childID=%s, momG=%s, momGL=%s, dadG=%s, dadGL=%s, " + - "childG=%s childGL=%s\n",vc.getChr(), vc.getStart(), - vc.getReference().getDisplayString(), vc.getAlternateAllele(0).getDisplayString(), vc.getCalledChrCount(vc.getAlternateAllele(0)), - sample.getMaternalID(), sample.getPaternalID(), sample.getID(), - vc.getGenotype(sample.getMaternalID()).toBriefString(), vc.getGenotype(sample.getMaternalID()).getLikelihoods().getAsString(), - vc.getGenotype(sample.getPaternalID()).toBriefString(), vc.getGenotype(sample.getPaternalID()).getLikelihoods().getAsString(), - vc.getGenotype(sample.getID()).toBriefString(),vc.getGenotype(sample.getID()).getLikelihoods().getAsString() ); - - } - } - } - } - if (DISCORDANCE_ONLY) { Collection compVCs = tracker.getValues(discordanceTrack, context.getLocation()); if (!isDiscordant(vc, compVCs)) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java index b73a498bc2..b9577ca9b2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java @@ -372,7 +372,7 @@ public void onTraversalDone(Integer sum) {} // ---------------------------------------------------------------------------------------------------- public static abstract class Getter { public abstract String get(VariantContext vc); } - public static Map getters = new HashMap(); + public static final Map getters = new HashMap(); static { // #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT diff --git a/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java b/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java index 0065f9258b..13571df789 100644 --- a/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java @@ -67,10 +67,10 @@ private Base(char base, int index) { public static final byte DELETION_INDEX = 4; public static final byte NO_CALL_INDEX = 5; // (this is 'N') - public static int gIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'G'); - public static int cIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'C'); - public static int aIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'A'); - public static int tIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'T'); + public static final int aIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'A'); + public static final int cIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'C'); + public static final int gIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'G'); + public static final int tIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'T'); /// In genetics, a transition is a mutation changing a purine to another purine nucleotide (A <-> G) or // a pyrimidine to another pyrimidine nucleotide (C <-> T). diff --git a/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java b/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java index 439a0d8edd..f37451cbaa 100644 --- a/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java +++ b/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java @@ -68,7 +68,7 @@ public enum ApplicationTime { } // Phred scaled now (changed 1/10/2011) - public static double DEFAULT_GOP = 40; + public static final double DEFAULT_GOP = 40; /* Takes a Phred Scale quality score and returns the error probability. * diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java index 83e55cb127..9b5886c658 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java @@ -38,8 +38,8 @@ * A class representing a key=value entry in the VCF header */ public class VCFHeaderLine implements Comparable { - protected static boolean ALLOW_UNBOUND_DESCRIPTIONS = true; - protected static String UNBOUND_DESCRIPTION = "Not provided in original VCF header"; + protected static final boolean ALLOW_UNBOUND_DESCRIPTIONS = true; + protected static final String UNBOUND_DESCRIPTION = "Not provided in original VCF header"; private String mKey = null; private String mValue = null; diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java index e5cd9f4d59..8cba5ec232 100755 --- a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java +++ b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java @@ -3,6 +3,7 @@ import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; @@ -220,7 +221,7 @@ public int getRepresentativeCount() { if (isDeletion() && (offset + 1 >= read.getReadLength()) ) // deletion in the end of the read throw new UserException.MalformedBAM(read, String.format("Adjacent I/D events in read %s -- cigar: %s", read.getReadName(), read.getCigarString())); - representativeCount = (isDeletion()) ? Math.round((read.getReducedCount(offset) + read.getReducedCount(offset + 1)) / 2) : read.getReducedCount(offset); + representativeCount = (isDeletion()) ? MathUtils.fastRound((read.getReducedCount(offset) + read.getReducedCount(offset + 1)) / 2.0) : read.getReducedCount(offset); } return representativeCount; } diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java index 249422c17a..8c8815b54d 100755 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java @@ -94,8 +94,8 @@ public class RecalDatum { * @param reportedQuality */ public RecalDatum(final long _numObservations, final long _numMismatches, final byte reportedQuality) { - if ( numObservations < 0 ) throw new IllegalArgumentException("numObservations < 0"); - if ( numMismatches < 0 ) throw new IllegalArgumentException("numMismatches < 0"); + if ( _numObservations < 0 ) throw new IllegalArgumentException("numObservations < 0"); + if ( _numMismatches < 0 ) throw new IllegalArgumentException("numMismatches < 0"); if ( reportedQuality < 0 ) throw new IllegalArgumentException("reportedQuality < 0"); numObservations = _numObservations; diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java index 102aa4433c..41e96222c0 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java @@ -21,7 +21,7 @@ */ public class RecalDatumNode { private final static double SMALLEST_CHI2_PVALUE = 1e-300; - protected static Logger logger = Logger.getLogger(RecalDatumNode.class); + protected static final Logger logger = Logger.getLogger(RecalDatumNode.class); /** * fixedPenalty is this value if it's considered fixed diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java index df1ff2a0eb..849a7ddeea 100755 --- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java @@ -13,7 +13,7 @@ */ public class GATKSAMReadGroupRecord extends SAMReadGroupRecord { - public static String LANE_TAG = "LN"; + public static final String LANE_TAG = "LN"; // the SAMReadGroupRecord data we're caching private String mSample = null; diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java index c16470c48c..bd908727f8 100755 --- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java @@ -53,8 +53,8 @@ public class ReadUtils { private ReadUtils() { } - private static int DEFAULT_ADAPTOR_SIZE = 100; - public static int CLIPPING_GOAL_NOT_REACHED = -1; + private static final int DEFAULT_ADAPTOR_SIZE = 100; + public static final int CLIPPING_GOAL_NOT_REACHED = -1; public static int getMeanRepresentativeReadCount(GATKSAMRecord read) { if (!read.isReducedRead()) diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java index e3bef6bc5c..c18f954a29 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java @@ -53,7 +53,7 @@ */ @Invariant({"alleles != null"}) public final class GenotypeBuilder { - public static boolean MAKE_FAST_BY_DEFAULT = true; + public static final boolean MAKE_FAST_BY_DEFAULT = true; private String sampleName = null; private List alleles = Collections.emptyList(); diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java index d644eda7de..7b4256b709 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java @@ -401,7 +401,7 @@ public static GenotypeLikelihoodsAllelePair getAllelePair(final int PLindex) { } // An index conversion from the deprecated PL ordering to the new VCF-based ordering for up to 3 alternate alleles - protected static int[] PLindexConversion = new int[]{0, 1, 3, 6, 2, 4, 7, 5, 8, 9}; + protected static final int[] PLindexConversion = new int[]{0, 1, 3, 6, 2, 4, 7, 5, 8, 9}; /** * get the allele index pair for the given PL using the deprecated PL ordering: diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java index 5421960b24..ff6b0be702 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java @@ -730,7 +730,7 @@ public static Map> separateVariantCont vcList.remove(k); // avoid having empty lists if (vcList.size() == 0) - mappedVCs.remove(vcList); + mappedVCs.remove(type); if ( !mappedVCs.containsKey(vc.getType()) ) mappedVCs.put(vc.getType(), new ArrayList()); mappedVCs.get(vc.getType()).add(otherVC); From bdf716f34cc86e8702c2077249e0a1aca4c86c03 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 16 Aug 2012 14:59:05 -0400 Subject: [PATCH 148/176] One final FindBugs related fix. I think it's safe to consider these changes 'fixes' that are allowed to go in during a code freeze. --- .../sting/gatk/walkers/annotator/ChromosomeCounts.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java index 6bdd779c0e..54837baadc 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java @@ -53,8 +53,8 @@ */ public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation { - protected static final String[] keyNames = { VCFConstants.ALLELE_NUMBER_KEY, VCFConstants.ALLELE_COUNT_KEY, VCFConstants.ALLELE_FREQUENCY_KEY }; - protected static final VCFInfoHeaderLine[] descriptions = { + public static final String[] keyNames = { VCFConstants.ALLELE_NUMBER_KEY, VCFConstants.ALLELE_COUNT_KEY, VCFConstants.ALLELE_FREQUENCY_KEY }; + public static final VCFInfoHeaderLine[] descriptions = { VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_FREQUENCY_KEY), VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_COUNT_KEY), VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_NUMBER_KEY) }; From 4db419d1bd80f32ca7baf7d36c7aa09e42315f42 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 16 Aug 2012 15:07:32 -0400 Subject: [PATCH 149/176] Should've run 'ant clean' instead of just 'ant'. In any event, these are 2 cases where we are setting a class's internal static variable directly. Very dangerous. --- public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java | 2 +- .../sting/utils/variantcontext/GenotypeBuilder.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java b/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java index f37451cbaa..439a0d8edd 100644 --- a/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java +++ b/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java @@ -68,7 +68,7 @@ public enum ApplicationTime { } // Phred scaled now (changed 1/10/2011) - public static final double DEFAULT_GOP = 40; + public static double DEFAULT_GOP = 40; /* Takes a Phred Scale quality score and returns the error probability. * diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java index c18f954a29..e3bef6bc5c 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java @@ -53,7 +53,7 @@ */ @Invariant({"alleles != null"}) public final class GenotypeBuilder { - public static final boolean MAKE_FAST_BY_DEFAULT = true; + public static boolean MAKE_FAST_BY_DEFAULT = true; private String sampleName = null; private List alleles = Collections.emptyList(); From 256773b99e109608ada72ca0c860a224c2f87ac7 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 16 Aug 2012 15:22:10 -0400 Subject: [PATCH 150/176] Removing SlowGenotype object from GATK --- .../sting/gatk/GenomeAnalysisEngine.java | 4 - .../arguments/GATKArgumentCollection.java | 5 - .../utils/variantcontext/FastGenotype.java | 2 +- .../utils/variantcontext/GenotypeBuilder.java | 38 +--- .../utils/variantcontext/SlowGenotype.java | 193 ------------------ 5 files changed, 6 insertions(+), 236 deletions(-) delete mode 100755 public/java/src/org/broadinstitute/sting/utils/variantcontext/SlowGenotype.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index 55107833d7..e76cde43ab 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -233,10 +233,6 @@ public Object execute() { if (args.nonDeterministicRandomSeed) resetRandomGenerator(System.currentTimeMillis()); - // TODO -- REMOVE ME WHEN WE STOP BCF testing - if ( args.USE_SLOW_GENOTYPES ) - GenotypeBuilder.MAKE_FAST_BY_DEFAULT = false; - // if the use specified an input BQSR recalibration table then enable on the fly recalibration if (args.BQSR_RECAL_FILE != null) setBaseRecalibration(args.BQSR_RECAL_FILE, args.quantizationLevels, args.disableIndelQuals, args.PRESERVE_QSCORES_LESS_THAN, args.emitOriginalQuals); diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java index 06177868ae..bbbd96cf1c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java @@ -379,10 +379,5 @@ public static DownsamplingMethod getDefaultDownsamplingMethod() { @Hidden public boolean generateShadowBCF = false; // TODO -- remove all code tagged with TODO -- remove me when argument generateShadowBCF is removed - - @Argument(fullName="useSlowGenotypes",shortName = "useSlowGenotypes",doc="",required=false) - @Hidden - public boolean USE_SLOW_GENOTYPES = false; - // TODO -- remove all code tagged with TODO -- remove me when argument generateShadowBCF is removed } diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/FastGenotype.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/FastGenotype.java index d528bf0e43..4a7df9da44 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/FastGenotype.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/FastGenotype.java @@ -172,7 +172,7 @@ public Map getExtendedAttributes() { * @param values * @return */ - private final static boolean validADorPLField(final int[] values) { + private static boolean validADorPLField(final int[] values) { if ( values != null ) for ( int v : values ) if ( v < 0 ) diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java index e3bef6bc5c..0ee32fa2e2 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java @@ -53,8 +53,6 @@ */ @Invariant({"alleles != null"}) public final class GenotypeBuilder { - public static boolean MAKE_FAST_BY_DEFAULT = true; - private String sampleName = null; private List alleles = Collections.emptyList(); @@ -67,8 +65,6 @@ public final class GenotypeBuilder { private String filters = null; private int initialAttributeMapSize = 5; - private boolean useFast = MAKE_FAST_BY_DEFAULT; - private final static Map NO_ATTRIBUTES = Collections.unmodifiableMap(new HashMap(0)); @@ -78,31 +74,22 @@ public final class GenotypeBuilder { // // ----------------------------------------------------------------- - public final static Genotype create(final String sampleName, final List alleles) { + public static Genotype create(final String sampleName, final List alleles) { return new GenotypeBuilder(sampleName, alleles).make(); } - public final static Genotype create(final String sampleName, + public static Genotype create(final String sampleName, final List alleles, final Map attributes) { return new GenotypeBuilder(sampleName, alleles).attributes(attributes).make(); } - protected final static Genotype create(final String sampleName, + protected static Genotype create(final String sampleName, final List alleles, final double[] gls) { return new GenotypeBuilder(sampleName, alleles).PL(gls).make(); } - public final static Genotype create(final String sampleName, - final List alleles, - final double log10Perror, - final Map attributes) { - return new GenotypeBuilder(sampleName, alleles) - .GQ(log10Perror == SlowGenotype.NO_LOG10_PERROR ? -1 : (int)(log10Perror * -10)) - .attributes(attributes).make(); - } - /** * Create a empty builder. Both a sampleName and alleles must be provided * before trying to make a Genotype from this builder. @@ -182,23 +169,8 @@ public final void reset(final boolean keepSampleName) { */ @Ensures({"result != null"}) public Genotype make() { - if ( useFast ) { - final Map ea = extendedAttributes == null ? NO_ATTRIBUTES : extendedAttributes; - return new FastGenotype(sampleName, alleles, isPhased, GQ, DP, AD, PL, filters, ea); - } else { - final Map attributes = new LinkedHashMap(); - if ( extendedAttributes != null ) attributes.putAll(extendedAttributes); - final double log10PError = GQ == -1 ? SlowGenotype.NO_LOG10_PERROR : (GQ == 0 ? 0 : GQ / -10.0); - if ( DP != -1 ) attributes.put(VCFConstants.DEPTH_KEY, DP); - if ( AD != null ) attributes.put(VCFConstants.GENOTYPE_ALLELE_DEPTHS, AD); - final double[] log10likelihoods = PL != null ? GenotypeLikelihoods.fromPLs(PL).getAsVector() : null; - return new SlowGenotype(sampleName, alleles, log10PError, filters, attributes, isPhased, log10likelihoods); - } - } - - public GenotypeBuilder useFast(boolean useFast) { - this.useFast = useFast; - return this; + final Map ea = extendedAttributes == null ? NO_ATTRIBUTES : extendedAttributes; + return new FastGenotype(sampleName, alleles, isPhased, GQ, DP, AD, PL, filters, ea); } /** diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/SlowGenotype.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/SlowGenotype.java deleted file mode 100755 index c3f027484f..0000000000 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/SlowGenotype.java +++ /dev/null @@ -1,193 +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.utils.variantcontext; - - -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; - -import java.util.*; - -/** - * This class encompasses all the basic information about a genotype. It is immutable. - * - * @author Mark DePristo - */ -@Deprecated -public class SlowGenotype extends Genotype { - protected CommonInfo commonInfo; - public final static double NO_LOG10_PERROR = CommonInfo.NO_LOG10_PERROR; - protected List alleles = null; - protected boolean isPhased = false; - - protected SlowGenotype(final String sampleName, - final List alleles, - final double log10PError, - final String filters, - final Map attributes, - final boolean isPhased, - final double[] log10Likelihoods) { - super(sampleName, filters); - - if ( alleles == null || alleles.isEmpty() ) - this.alleles = Collections.emptyList(); - else - this.alleles = Collections.unmodifiableList(alleles); - commonInfo = new CommonInfo(sampleName, log10PError, Collections.emptySet(), attributes); - if ( log10Likelihoods != null ) - commonInfo.putAttribute(VCFConstants.GENOTYPE_PL_KEY, GenotypeLikelihoods.fromLog10Likelihoods(log10Likelihoods)); - this.isPhased = isPhased; - validate(); - } - - @Override public List getAlleles() { - return alleles; - } - - @Override public Allele getAllele(int i) { - if ( getType() == GenotypeType.UNAVAILABLE ) - throw new ReviewedStingException("Requesting alleles for an UNAVAILABLE genotype"); - return alleles.get(i); - } - - @Override public boolean isPhased() { return isPhased; } - - // - // Useful methods for getting genotype likelihoods for a genotype object, if present - // - @Override public boolean hasLikelihoods() { - return (commonInfo.hasAttribute(VCFConstants.GENOTYPE_PL_KEY) && !commonInfo.getAttribute(VCFConstants.GENOTYPE_PL_KEY).equals(VCFConstants.MISSING_VALUE_v4)) || - (commonInfo.hasAttribute(VCFConstants.GENOTYPE_LIKELIHOODS_KEY) && !commonInfo.getAttribute(VCFConstants.GENOTYPE_LIKELIHOODS_KEY).equals(VCFConstants.MISSING_VALUE_v4)); - } - - @Override public GenotypeLikelihoods getLikelihoods() { - GenotypeLikelihoods x = getLikelihoods(VCFConstants.GENOTYPE_PL_KEY, true); - if ( x != null ) - return x; - else { - x = getLikelihoods(VCFConstants.GENOTYPE_LIKELIHOODS_KEY, false); - return x; - } - } - - private GenotypeLikelihoods getLikelihoods(String key, boolean asPL) { - Object x = commonInfo.getAttribute(key); - if ( x instanceof String ) { - if ( asPL ) - return GenotypeLikelihoods.fromPLField((String)x); - else - return GenotypeLikelihoods.fromGLField((String)x); - } - else if ( x instanceof GenotypeLikelihoods ) return (GenotypeLikelihoods)x; - else return null; - } - - private final void validate() { - if ( alleles.size() == 0) return; - - for ( Allele allele : alleles ) { - if ( allele == null ) - throw new IllegalArgumentException("BUG: allele cannot be null in Genotype"); - } - } - - // --------------------------------------------------------------------------------------------------------- - // - // get routines to access context info fields - // - // --------------------------------------------------------------------------------------------------------- - @Override public boolean hasLog10PError() { return commonInfo.hasLog10PError(); } - @Override public double getLog10PError() { return commonInfo.getLog10PError(); } - - @Override - public boolean hasExtendedAttribute(String key) { return commonInfo.hasAttribute(key); } - - @Override - public Object getExtendedAttribute(String key) { return commonInfo.getAttribute(key); } - - @Override - public Object getExtendedAttribute(String key, Object defaultValue) { - return commonInfo.getAttribute(key, defaultValue); - } - -// public String getAttributeAsString(String key, String defaultValue) { return commonInfo.getAttributeAsString(key, defaultValue); } -// public int getAttributeAsInt(String key, int defaultValue) { return commonInfo.getAttributeAsInt(key, defaultValue); } -// public double getAttributeAsDouble(String key, double defaultValue) { return commonInfo.getAttributeAsDouble(key, defaultValue); } -// public boolean getAttributeAsBoolean(String key, boolean defaultValue) { return commonInfo.getAttributeAsBoolean(key, defaultValue); } - - @Override - public int[] getPL() { - return hasPL() ? getLikelihoods().getAsPLs() : null; - } - - @Override - public boolean hasPL() { - return hasLikelihoods(); - } - - @Override - public int getDP() { - return commonInfo.getAttributeAsInt(VCFConstants.DEPTH_KEY, -1); - } - - @Override - public boolean hasDP() { - return commonInfo.hasAttribute(VCFConstants.DEPTH_KEY); - } - - @Override - public int[] getAD() { - if ( hasAD() ) { - return (int[])commonInfo.getAttribute(VCFConstants.GENOTYPE_ALLELE_DEPTHS); - } else - return null; - } - - @Override - public boolean hasAD() { - return commonInfo.hasAttribute(VCFConstants.GENOTYPE_ALLELE_DEPTHS); - } - - @Override - public int getGQ() { - if ( commonInfo.hasLog10PError() ) - return (int)Math.round(commonInfo.getPhredScaledQual()); - else - return -1; - } - - @Override - public boolean hasGQ() { - return hasLog10PError(); - } - - @Override - public Map getExtendedAttributes() { - final Map ea = new LinkedHashMap(commonInfo.getAttributes()); - for ( final String primary : FastGenotype.PRIMARY_KEYS ) - ea.remove(primary); - return ea; - } -} \ No newline at end of file From efcd56d8427b4478cb0f3eeb524ab09006eb751f Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 16 Aug 2012 15:40:52 -0400 Subject: [PATCH 151/176] FindBugs 'Efficiency' fixes --- .../walkers/beagle/ProduceBeagleInput.java | 2 - .../phasing/PreciseNonNegativeDouble.java | 2 +- .../walkers/phasing/ReadBackedPhasing.java | 2 +- .../sting/utils/SWPairwiseAlignment.java | 53 ------------------- 4 files changed, 2 insertions(+), 57 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java index fdc3336766..d11747766a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java @@ -351,7 +351,6 @@ private void initializeVcfWriter() { } public static class CachingFormatter { - private int maxCacheSize = 0; private String format; private LRUCache cache; @@ -379,7 +378,6 @@ public String format(double value) { } public CachingFormatter(String format, int maxCacheSize) { - this.maxCacheSize = maxCacheSize; this.format = format; this.cache = new LRUCache(maxCacheSize); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java index b68739b48e..d3f4f6266e 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java @@ -86,7 +86,7 @@ public int compareTo(PreciseNonNegativeDouble other) { if (Math.abs(logValDiff) <= EQUALS_THRESH) return 0; // this.equals(other) - return new Double(Math.signum(logValDiff)).intValue(); + return (int)Math.signum(logValDiff); } public boolean equals(PreciseNonNegativeDouble other) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java index f49e8f8c0f..d8ae6b28b0 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java @@ -870,7 +870,7 @@ private List trimWindow(List listHet int useOnLeft, useOnRight; if (numOnLeft <= numOnRight) { - int halfToUse = new Double(Math.floor(numToUse / 2.0)).intValue(); // skimp on the left [floor], and be generous with the right side + int halfToUse = numToUse / 2; // skimp on the left [floor], and be generous with the right side useOnLeft = Math.min(halfToUse, numOnLeft); useOnRight = Math.min(numToUse - useOnLeft, numOnRight); } diff --git a/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java b/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java index bc1158a4d4..500598765a 100755 --- a/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java +++ b/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java @@ -377,59 +377,6 @@ private double wk(int k) { return w_open+(k-1)*w_extend; // gap } - private void print(int[][] s) { - for ( int i = 0 ; i < s.length ; i++) { - for ( int j = 0; j < s[i].length ; j++ ) { - System.out.printf(" %4d",s[i][j]); - } - System.out.println(); - } - } - - private void print(double[][] s) { - for ( int i = 0 ; i < s.length ; i++) { - for ( int j = 0; j < s[i].length ; j++ ) { - System.out.printf(" %4g",s[i][j]); - } - System.out.println(); - } - } - - private void print(int[][] s, String a, String b) { - - System.out.print(" "); - for ( int j = 1 ; j < s[0].length ; j++) System.out.printf(" %4c",b.charAt(j-1)) ; - System.out.println(); - - for ( int i = 0 ; i < s.length ; i++) { - if ( i > 0 ) System.out.print(a.charAt(i-1)); - else System.out.print(' '); - System.out.print(" "); - for ( int j = 0; j < s[i].length ; j++ ) { - System.out.printf(" %4d",s[i][j]); - } - System.out.println(); - } - } - - - private void print(double[][] s, String a, String b) { - - System.out.print(""); - for ( int j = 1 ; j < s[0].length ; j++) System.out.printf(" %4c",b.charAt(j-1)) ; - System.out.println(); - - for ( int i = 0 ; i < s.length ; i++) { - if ( i > 0 ) System.out.print(a.charAt(i-1)); - else System.out.print(' '); - System.out.print(" "); - for ( int j = 0; j < s[i].length ; j++ ) { - System.out.printf(" %2.1f",s[i][j]); - } - System.out.println(); - } - } - private void print(double[] s, byte[] a, byte[] b) { int n = a.length+1; int m = b.length+1; From 550472efa7d537524f8c062052c4f278750284b9 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 16 Aug 2012 15:53:06 -0400 Subject: [PATCH 152/176] FindBugs 'Maintainability' fixes --- .../net/sf/picard/reference/FastaSequenceIndexBuilder.java | 1 + .../gatk/walkers/diagnostics/targets/SampleStatistics.java | 2 +- .../sting/gatk/walkers/diffengine/BAMDiffableReader.java | 4 +++- .../gatk/walkers/diffengine/GATKReportDiffableReader.java | 6 ++++-- .../gatk/walkers/indels/ConstrainedMateFixingManager.java | 2 +- .../gatk/walkers/variantrecalibration/TrancheManager.java | 1 + .../gatk/walkers/variantutils/VariantsToBinaryPed.java | 1 + .../org/broadinstitute/sting/utils/help/ForumAPIUtils.java | 1 + 8 files changed, 13 insertions(+), 5 deletions(-) diff --git a/public/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java b/public/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java index 6c8fe18348..10326ef2ed 100644 --- a/public/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java +++ b/public/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java @@ -208,6 +208,7 @@ else if (basesThisLine != basesPerLine || bytesPerLine != bytesRead - endOfLastL break; } } + in.close(); return sequenceIndex; } catch (IOException e) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatistics.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatistics.java index 0fc2d8929e..9f6258eee3 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatistics.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatistics.java @@ -264,7 +264,7 @@ boolean hasValidMate(GATKSAMRecord read, ThresHolder thresholds) { return false; // different contigs - if (read.getMateReferenceIndex() != read.getReferenceIndex()) + if (!read.getMateReferenceIndex().equals(read.getReferenceIndex())) return false; // unmapped diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java index 2d372ca9f0..0d4db55608 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java @@ -104,7 +104,9 @@ public boolean canRead(File file) { InputStream fstream = new BufferedInputStream(new FileInputStream(file)); if ( !BlockCompressedInputStream.isValidFile(fstream) ) return false; - new BlockCompressedInputStream(fstream).read(buffer, 0, BAM_MAGIC.length); + final BlockCompressedInputStream BCIS = new BlockCompressedInputStream(fstream); + BCIS.read(buffer, 0, BAM_MAGIC.length); + BCIS.close(); return Arrays.equals(buffer, BAM_MAGIC); } catch ( IOException e ) { return false; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java index 480a1fc29c..5e4ea5f813 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java @@ -90,8 +90,10 @@ private DiffNode tableToNode(GATKReportTable table, DiffNode root) { public boolean canRead(File file) { try { final String HEADER = GATKReport.GATKREPORT_HEADER_PREFIX; - char[] buff = new char[HEADER.length()]; - new FileReader(file).read(buff, 0, HEADER.length()); + final char[] buff = new char[HEADER.length()]; + final FileReader FR = new FileReader(file); + FR.read(buff, 0, HEADER.length()); + FR.close(); String firstLine = new String(buff); return firstLine.startsWith(HEADER); } catch (IOException e) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java index 4feba35af6..68365adf7e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java @@ -305,7 +305,7 @@ public boolean iSizeTooBigToMove(SAMRecord read) { } public static boolean iSizeTooBigToMove(SAMRecord read, int maxInsertSizeForMovingReadPairs) { - return ( read.getReadPairedFlag() && ! read.getMateUnmappedFlag() && read.getReferenceName() != read.getMateReferenceName() ) // maps to different chromosomes + return ( read.getReadPairedFlag() && ! read.getMateUnmappedFlag() && !read.getReferenceName().equals(read.getMateReferenceName()) ) // maps to different chromosomes || Math.abs(read.getInferredInsertSize()) > maxInsertSizeForMovingReadPairs; // we won't try to move such a read } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java index d457395289..af07783992 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java @@ -177,6 +177,7 @@ private static void writeTranchesDebuggingInfo(File f, List tranch double runningValue = metric.getRunningMetric(i); out.printf("%.4f %d %.4f%n", d.lod, score, runningValue); } + out.close(); } catch (FileNotFoundException e) { throw new UserException.CouldNotCreateOutputFile(f, e); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java index 14c811b03f..3fba8fa77e 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java @@ -270,6 +270,7 @@ public void onTraversalDone(Integer numSites) { inStream.read(readGenotypes); outBed.write(readGenotypes); } + inStream.close(); } catch (IOException e) { throw new ReviewedStingException("Error reading form temp file for input.",e); } diff --git a/public/java/src/org/broadinstitute/sting/utils/help/ForumAPIUtils.java b/public/java/src/org/broadinstitute/sting/utils/help/ForumAPIUtils.java index 388e7ce450..1dfc4ecc0f 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/ForumAPIUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/ForumAPIUtils.java @@ -135,6 +135,7 @@ private static String httpPost(String data, String URL) { System.out.println(line); } + br.close(); httpClient.getConnectionManager().shutdown(); return output; From 5574196663553faba2751daf15f63f185b8bb520 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 16 Aug 2012 16:23:45 -0400 Subject: [PATCH 153/176] GSA-483: Bug in GATKdocs for Enums -- Fixed to no long show constants in enums as constant values in the gatkdocs --- .../help/GenericDocumentationHandler.java | 39 ++++++++++++++----- 1 file changed, 29 insertions(+), 10 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java index dc0668cea7..ab5181b453 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java @@ -584,20 +584,39 @@ protected Map docForArgument(FieldDoc fieldDoc, ArgumentSource s * @return */ @Requires("enumClass.isEnum()") - private List> docForEnumArgument(Class enumClass) { - ClassDoc doc = this.getDoclet().getClassDocForClass(enumClass); - if (doc == null) // || ! doc.isEnum() ) + private List> docForEnumArgument(final Class enumClass) { + final ClassDoc doc = this.getDoclet().getClassDocForClass(enumClass); + if ( doc == null ) throw new RuntimeException("Tried to get docs for enum " + enumClass + " but got null instead"); - List> bindings = new ArrayList>(); - for (final FieldDoc field : doc.fields(false)) { - bindings.add( - new HashMap() {{ - put("name", field.name()); - put("summary", field.commentText()); - }}); + final Set enumConstantFieldNames = enumConstantsNames(enumClass); + + final List> bindings = new ArrayList>(); + for (final FieldDoc fieldDoc : doc.fields(false)) { + if (enumConstantFieldNames.contains(fieldDoc.name()) ) + bindings.add( + new HashMap() {{ + put("name", fieldDoc.name()); + put("summary", fieldDoc.commentText()); + }}); } return bindings; } + + /** + * Returns the name of the fields that are enum constants according to reflection + * + * @return a non-null set of fields that are enum constants + */ + private Set enumConstantsNames(final Class enumClass) { + final Set enumConstantFieldNames = new HashSet(); + + for ( final Field field : enumClass.getFields() ) { + if ( field.isEnumConstant() ) + enumConstantFieldNames.add(field.getName()); + } + + return enumConstantFieldNames; + } } From 6034f808c9858945b858fcd00307d2bafbfb5bec Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 16 Aug 2012 21:27:07 -0400 Subject: [PATCH 154/176] Better error message for reads that begin/end with a deletion in LIBS --- .../sting/gatk/iterators/LocusIteratorByState.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java index 1606c227de..f970691898 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java +++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java @@ -159,7 +159,7 @@ public CigarOperator stepForwardOnGenome() { return stepForwardOnGenome(); } else { if (curElement != null && curElement.getOperator() == CigarOperator.D) - throw new UserException.MalformedBAM(read, "read ends with deletion. Cigar: " + read.getCigarString() + ". This is an indication of a malformed file, but the SAM spec allows reads ending in deletion. If you are sure you want to use this read, re-run your analysis with the extra option: -rf BadCigar"); + throw new UserException.MalformedBAM(read, "read ends with deletion. Cigar: " + read.getCigarString() + ". Although the SAM spec technically permits such reads, this is often indicative of malformed files. If you are sure you want to use this file, re-run your analysis with the extra option: -rf BadCigar"); // Reads that contain indels model the genomeOffset as the following base in the reference. Because // we fall into this else block only when indels end the read, increment genomeOffset such that the @@ -185,7 +185,7 @@ public CigarOperator stepForwardOnGenome() { break; case D: // deletion w.r.t. the reference if (readOffset < 0) // we don't want reads starting with deletion, this is a malformed cigar string - throw new UserException.MalformedBAM(read, "Read starting with deletion. Cigar: " + read.getCigarString() + ". This is an indication of a malformed file, but the SAM spec allows reads starting in deletion. If you are sure you want to use this read, re-run your analysis with the extra option: -rf BadCigar"); + throw new UserException.MalformedBAM(read, "read starts with deletion. Cigar: " + read.getCigarString() + ". Although the SAM spec technically permits such reads, this is often indicative of malformed files. If you are sure you want to use this file, re-run your analysis with the extra option: -rf BadCigar"); // should be the same as N case genomeOffset++; done = true; From 3945da967e524058a590717ad463bd3a1903d22f Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 16 Aug 2012 21:41:18 -0400 Subject: [PATCH 155/176] Hmm, not good. Fixing the math in PBT resulted in changed MD5s for integration tests that look like significant changes. I am reverting and will report this to Laurent. --- .../sting/gatk/walkers/phasing/PhaseByTransmission.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java index 0dcafb30a2..bbd4bf92f3 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java @@ -645,7 +645,7 @@ private int phaseTrioGenotypes(Allele ref, Allele alt, Genotype mother, Genotype bestChildGenotype.clear(); bestChildGenotype.add(childGenotype.getKey()); } - else if(MathUtils.compareDoubles(configurationLikelihood, bestConfigurationLikelihood) == 0) { + else if(configurationLikelihood == bestConfigurationLikelihood) { bestFirstParentGenotype.add(firstParentGenotype.getKey()); bestSecondParentGenotype.add(secondParentGenotype.getKey()); bestChildGenotype.add(childGenotype.getKey()); From 57dd3abee170f08e20edba40f08e932096ab9af2 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 16 Aug 2012 17:05:25 -0400 Subject: [PATCH 156/176] Improvements to GATKPerformanceOverTime -- CombineVariants parallelism test -- Easy way to ask for specific runs with enum argument -- Update for R to handle new outputs From fd9894a9b1b3b901a41087d93a78ebf2663e8fd9 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 17 Aug 2012 10:13:40 -0400 Subject: [PATCH 157/176] Bugfix for potential SEGFAULT with JNA getting execution hosts for LSF with multiple hosts --- .../sting/queue/engine/lsf/Lsf706JobRunner.scala | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala b/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala index de996d1870..2fbea1497b 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala @@ -35,7 +35,7 @@ import org.broadinstitute.sting.queue.engine.{RunnerStatus, CommandLineJobRunner import java.util.regex.Pattern import java.lang.StringBuffer import java.util.Date -import com.sun.jna.{Structure, StringArray, NativeLong} +import com.sun.jna.{Pointer, Structure, StringArray, NativeLong} import com.sun.jna.ptr.IntByReference /** @@ -295,9 +295,17 @@ object Lsf706JobRunner extends Logging { // the platform LSF startTimes are in seconds, not milliseconds, so convert to the java convention runner.getRunInfo.startTime = new Date(jobInfo.startTime.longValue * 1000) runner.getRunInfo.doneTime = new Date(jobInfo.endTime.longValue * 1000) - val exHostsRaw = jobInfo.exHosts.getStringArray(0) - //logger.warn("exHostsRaw = " + exHostsRaw) - val exHostsList = exHostsRaw.toSeq + + val exHostsList = + if (jobInfo.numExHosts != 1) { + // this is necessary because + val exHostsString = "multipleHosts_" + jobInfo.numExHosts + logger.debug("numExHosts = " + jobInfo.numExHosts + " != 1 for job " + runner.jobId + ", cannot safely get exhosts, setting to " + exHostsString) + List(exHostsString) + } else { + jobInfo.exHosts.getStringArray(0).toSeq + } + //logger.warn("exHostsList = " + exHostsList) val exHosts = exHostsList.reduceLeft(_ + "," + _) //logger.warn("exHosts = " + exHosts) From d6a7df03b5acfee587aa2af36197d41893f44935 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 17 Aug 2012 10:14:19 -0400 Subject: [PATCH 158/176] Proper function call in BCF2Decoder to validateReadBytes --- .../sting/utils/codecs/bcf2/BCF2Decoder.java | 48 ++++++++++++++----- 1 file changed, 37 insertions(+), 11 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java index d7f59632c7..05ba2aa1f8 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java @@ -82,7 +82,7 @@ public void readNextBlock(final int blockSizeInBytes, final InputStream stream) public void skipNextBlock(final int blockSizeInBytes, final InputStream stream) { try { final int bytesRead = (int)stream.skip(blockSizeInBytes); - validateReadBytes(bytesRead, blockSizeInBytes); + validateReadBytes(bytesRead, 1, blockSizeInBytes); } catch ( IOException e ) { throw new UserException.CouldNotReadInputFile("I/O error while reading BCF2 file", e); } @@ -316,17 +316,37 @@ public final int readBlockSize(final InputStream inputStream) throws IOException } /** + * Read all bytes for a BCF record block into a byte[], and return it * - * @param inputStream - * @return + * Is smart about reading from the stream multiple times to fill the buffer, if necessary + * + * @param blockSizeInBytes number of bytes to read + * @param inputStream the stream to read from + * @return a non-null byte[] containing exactly blockSizeInBytes bytes from the inputStream */ - private final static byte[] readRecordBytes(final int blockSizeInBytes, final InputStream inputStream) { + @Requires({"blockSizeInBytes >= 0", "inputStream != null"}) + @Ensures("result != null") + private static byte[] readRecordBytes(final int blockSizeInBytes, final InputStream inputStream) { assert blockSizeInBytes >= 0; final byte[] record = new byte[blockSizeInBytes]; try { - final int bytesRead = inputStream.read(record); - validateReadBytes(bytesRead, blockSizeInBytes); + int bytesRead = 0; + int nReadAttempts = 0; // keep track of how many times we've read + + // because we might not read enough bytes from the file in a single go, do it in a loop until we get EOF + while ( bytesRead < blockSizeInBytes ) { + final int read1 = inputStream.read(record, bytesRead, blockSizeInBytes - bytesRead); + if ( read1 == -1 ) + validateReadBytes(bytesRead, nReadAttempts, blockSizeInBytes); + else + bytesRead += read1; + } + + if ( nReadAttempts > 1 ) // TODO -- remove me + logger.warn("Required multiple read attempts to actually get the entire BCF2 block, unexpected behavior"); + + validateReadBytes(bytesRead, nReadAttempts, blockSizeInBytes); } catch ( IOException e ) { throw new UserException.CouldNotReadInputFile("I/O error while reading BCF2 file", e); } @@ -334,14 +354,20 @@ private final static byte[] readRecordBytes(final int blockSizeInBytes, final In return record; } - private final static void validateReadBytes(final int actuallyRead, final int expected) { + /** + * Make sure we read the right number of bytes, or throw an error + * + * @param actuallyRead + * @param nReadAttempts + * @param expected + */ + private static void validateReadBytes(final int actuallyRead, final int nReadAttempts, final int expected) { assert expected >= 0; if ( actuallyRead < expected ) { - throw new UserException.MalformedBCF2(String.format("Failed to read next complete record: %s", - actuallyRead == -1 ? - "premature end of input stream" : - String.format("expected %d bytes but read only %d", expected, actuallyRead))); + throw new UserException.MalformedBCF2( + String.format("Failed to read next complete record: expected %d bytes but read only %d after %d iterations", + expected, actuallyRead, nReadAttempts)); } } From 1c1d4ae47e0e38aa038da5fd9655ca7cbae9e617 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 17 Aug 2012 10:17:12 -0400 Subject: [PATCH 159/176] Potential fix for GSA-484: Incomplete writing of temp BCF when running CombineVariants in parallel -- Keep reading from BCF2 input stream when read(byte[]) returns < number of needed bytes -- It's possible (I think) that the failure in GSA-484 is due to multi-threading writing/reading of BCF2 records where the underlying stream is not yet flushed so read(byte[]) returns a partial result. No loops until we get all of the needed bytes or EOF is encounted --- .../org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java | 1 + 1 file changed, 1 insertion(+) diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java index fc0b3c4a9a..60fcb65853 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java @@ -118,6 +118,7 @@ public VariantContext decode( final PositionalBufferedStream inputStream ) { final int sitesBlockSize = decoder.readBlockSize(inputStream); final int genotypeBlockSize = decoder.readBlockSize(inputStream); + decoder.readNextBlock(sitesBlockSize, inputStream); decodeSiteLoc(builder); final SitesInfoForDecoding info = decodeSitesExtendedInfo(builder); From a3d200814f1c2296f32d1868b75bce48bd6b13a4 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 17 Aug 2012 10:35:25 -0400 Subject: [PATCH 160/176] Fixed: GSA-392 @arguments with just a short name get the wrong argument bindings -- Now blows up if an argument begins with -. Implementation isn't pretty, as it actually blows up during Queue extension creation with a somewhat obscure error message but at least its something. --- .../sting/commandline/ArgumentDefinition.java | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinition.java b/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinition.java index a5647ec0f9..618120217a 100644 --- a/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinition.java +++ b/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinition.java @@ -26,6 +26,7 @@ package org.broadinstitute.sting.commandline; import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.lang.annotation.Annotation; import java.util.List; @@ -147,6 +148,9 @@ public ArgumentDefinition( ArgumentIOType ioType, this.exclusiveOf = exclusiveOf; this.validation = validation; this.validOptions = validOptions; + + validateName(shortName); + validateName(fullName); } /** @@ -192,6 +196,9 @@ else if( !isFullNameProvided ) else shortName = null; + validateName(shortName); + validateName(fullName); + this.ioType = ioType; this.argumentType = argumentType; this.fullName = fullName; @@ -277,4 +284,14 @@ public static String getValidationRegex( Annotation annotation ) { String validation = (String)CommandLineUtils.getValue(annotation, "validation"); return validation.trim().length() > 0 ? validation.trim() : null; } + + /** + * Make sure the argument's name is valid + * + * @param name + */ + private void validateName(final String name) { + if ( name != null && name.startsWith("-") ) + throw new ReviewedStingException("Invalid argument definition: " + name + " begins with a -"); + } } From 4fbce7193e9f9c635e2201d9af69609e23efa429 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 17 Aug 2012 11:21:49 -0400 Subject: [PATCH 161/176] Fixed GSA-434: GATK should generate error when gzipped FASTA is passed in. -- The GATK sort of handles this now, but only if you have the exactly correct sequence dictionary and FAI files associated with the reference. If you do, the file can be .gz. If not, the GATK will fail on creating the FAI and DICT files. Added an error message that handles this case and clearly says what to do. --- .../reference/ReferenceDataSource.java | 31 ++++++++++--------- .../sting/utils/exceptions/UserException.java | 11 +++++++ 2 files changed, 28 insertions(+), 14 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java index b131e36c10..c02ae7d99b 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java @@ -62,23 +62,24 @@ public class ReferenceDataSource { * @param fastaFile Fasta file to be used as reference */ public ReferenceDataSource(File fastaFile) { - // does the fasta file exist? check that first... if (!fastaFile.exists()) throw new UserException("The fasta file you specified (" + fastaFile.getAbsolutePath() + ") does not exist."); - File indexFile = new File(fastaFile.getAbsolutePath() + ".fai"); - File dictFile; - if (fastaFile.getAbsolutePath().endsWith("fa")) { - dictFile = new File(fastaFile.getAbsolutePath().replace(".fa", ".dict")); - } - else - dictFile = new File(fastaFile.getAbsolutePath().replace(".fasta", ".dict")); + final boolean isGzipped = fastaFile.getAbsolutePath().endsWith(".gz"); + + final File indexFile = new File(fastaFile.getAbsolutePath() + ".fai"); + + // determine the name for the dict file + final String fastaExt = (fastaFile.getAbsolutePath().endsWith("fa") ? ".fa" : ".fasta" ) + (isGzipped ? ".gz" : ""); + final File dictFile = new File(fastaFile.getAbsolutePath().replace(fastaExt, ".dict")); /* - if index file does not exist, create it manually - */ + * if index file does not exist, create it manually + */ if (!indexFile.exists()) { + if ( isGzipped ) throw new UserException.CouldNotCreateReferenceFAIorDictForGzippedRef(fastaFile); + logger.info(String.format("Index file %s does not exist. Trying to create it now.", indexFile.getAbsolutePath())); FSLockWithShared indexLock = new FSLockWithShared(indexFile,true); try { @@ -95,7 +96,7 @@ public ReferenceDataSource(File fastaFile) { } catch(UserException e) { // Rethrow all user exceptions as-is; there should be more details in the UserException itself. - throw e; + throw e; } catch (Exception e) { // If lock creation succeeded, the failure must have been generating the index. @@ -114,6 +115,8 @@ public ReferenceDataSource(File fastaFile) { * This has been filed in trac as (PIC-370) Want programmatic interface to CreateSequenceDictionary */ if (!dictFile.exists()) { + if ( isGzipped ) throw new UserException.CouldNotCreateReferenceFAIorDictForGzippedRef(fastaFile); + logger.info(String.format("Dict file %s does not exist. Trying to create it now.", dictFile.getAbsolutePath())); /* @@ -218,9 +221,9 @@ public Iterable createShardsOverEntireReference(final SAMDataSource reads for(int shardStart = 1; shardStart <= refSequenceRecord.getSequenceLength(); shardStart += maxShardSize) { final int shardStop = Math.min(shardStart+maxShardSize-1, refSequenceRecord.getSequenceLength()); shards.add(new LocusShard(parser, - readsDataSource, - Collections.singletonList(parser.createGenomeLoc(refSequenceRecord.getSequenceName(),shardStart,shardStop)), - null)); + readsDataSource, + Collections.singletonList(parser.createGenomeLoc(refSequenceRecord.getSequenceName(),shardStart,shardStop)), + null)); } } return shards; diff --git a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java index bda03f6752..3130469e5a 100755 --- a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java +++ b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java @@ -340,6 +340,17 @@ public CouldNotCreateReferenceIndexFile(File f, String message, Exception e) { } } + public static class CouldNotCreateReferenceFAIorDictForGzippedRef extends UserException { + public CouldNotCreateReferenceFAIorDictForGzippedRef(final File f) { + super("Although the GATK can process .gz reference sequences, it currently cannot create FAI " + + "or DICT files for them. In order to use the GATK with reference.fasta.gz you will need to " + + "create .dict and .fai files for reference.fasta.gz and name them reference.fasta.gz.fai and " + + "reference.dict. Potentially the easiest way to do this is to uncompress reference.fasta, " + + "run the GATK to create the .dict and .fai files, and copy them to the appropriate location. " + + "Sorry for the inconvenience."); + } + } + public static class CouldNotCreateReferenceIndexFileBecauseOfLock extends UserException.CouldNotCreateReferenceIndexFile { public CouldNotCreateReferenceIndexFileBecauseOfLock(File f) { super(f, "could not be written because an exclusive file lock could not be obtained. " + From 4980f052a7cb9e1140e3cc42406b0a4e6b3eadb3 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 17 Aug 2012 11:41:07 -0400 Subject: [PATCH 162/176] Print to logger not to System.out in CachingIndexFastaSequenceFile when profiling cache performance --- .../sting/utils/fasta/CachingIndexedFastaSequenceFile.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java b/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java index 44b586bcd2..48706543a3 100644 --- a/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java +++ b/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java @@ -41,6 +41,8 @@ * Thread-safe! Uses a lock object to protect write and access to the cache. */ public class CachingIndexedFastaSequenceFile extends IndexedFastaSequenceFile { + protected static final org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(CachingIndexedFastaSequenceFile.class); + /** global enable flag */ private static final boolean USE_CACHE = true; @@ -125,7 +127,7 @@ public CachingIndexedFastaSequenceFile(final File file, long cacheSize ) throws public void printEfficiency() { // comment out to disable tracking if ( (cacheHits + cacheMisses) % PRINT_FREQUENCY == 0 ) { - System.out.printf("### CachingIndexedFastaReader: hits=%d misses=%d efficiency %.6f%%%n", cacheHits, cacheMisses, calcEfficiency()); + logger.info(String.format("### CachingIndexedFastaReader: hits=%d misses=%d efficiency %.6f%%%n", cacheHits, cacheMisses, calcEfficiency())); } } From 30e8b03c8115feef51c21fd306e59af7405cfad6 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 17 Aug 2012 11:48:05 -0400 Subject: [PATCH 163/176] Fix for missing formatter in R 2.15 -- VariantCallQC now works on newest ESP call set --- .../broadinstitute/sting/utils/R/gsalib/R/gsa.variantqc.utils.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.variantqc.utils.R b/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.variantqc.utils.R index 19567e7e6f..45dacd835a 100644 --- a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.variantqc.utils.R +++ b/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.variantqc.utils.R @@ -207,7 +207,7 @@ plotVariantQC <- function(metrics, measures, requestedStrat = "Sample", if ( requestedStrat == "Sample" ) { perSampleGraph <- perSampleGraph + geom_text(aes(label=strat), size=1.5) + geom_blank() # don't display a scale - perSampleGraph <- perSampleGraph + scale_x_discrete("Sample (ordered by nSNPs)", formatter=function(x) "") + perSampleGraph <- perSampleGraph + scale_x_discrete("Sample (ordered by nSNPs)") } else { # by AlleleCount perSampleGraph <- perSampleGraph + geom_point(aes(size=log10(nobs))) #+ geom_smooth(aes(weight=log10(nobs))) perSampleGraph <- perSampleGraph + scale_x_log10("AlleleCount") From 0e168f2fdc0d0f6a7d74ae239b172d9748427b73 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 17 Aug 2012 11:48:43 -0400 Subject: [PATCH 164/176] Add support for CombineVariants nt option in GATKPerformanceOverTime -- Also includes some nicer PDF formatting From a32ba9b87d97b7a76989e9a3472598292e97083f Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Fri, 17 Aug 2012 11:49:53 -0400 Subject: [PATCH 165/176] Put in a sanity check that MLEAC <= AN --- .../walkers/genotyper/UnifiedGenotyperEngine.java | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index 05e12b43d5..67ade390ff 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -38,6 +38,7 @@ import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; @@ -442,10 +443,17 @@ else if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_M // add the MLE AC and AF annotations if ( alleleCountsofMLE.size() > 0 ) { attributes.put(VCFConstants.MLE_ALLELE_COUNT_KEY, alleleCountsofMLE); - final double AN = (double)builder.make().getCalledChrCount(); + final int AN = builder.make().getCalledChrCount(); + + // let's sanity check that we don't have an invalid MLE value in there + for ( int MLEAC : alleleCountsofMLE ) { + if ( MLEAC > AN ) + throw new ReviewedStingException(String.format("MLEAC value (%d) is larger than AN (%d) at position %s:%d", MLEAC, AN, loc.getContig(), loc.getStart())); + } + final ArrayList MLEfrequencies = new ArrayList(alleleCountsofMLE.size()); for ( int AC : alleleCountsofMLE ) - MLEfrequencies.add((double)AC / AN); + MLEfrequencies.add((double)AC / (double)AN); attributes.put(VCFConstants.MLE_ALLELE_FREQUENCY_KEY, MLEfrequencies); } From c656b7ae9b3e32137edb99094f98c01be486dac8 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 17 Aug 2012 14:55:17 -0400 Subject: [PATCH 166/176] Fix GSA-137: Having both DataSource.REFERENCE and DataSource.REFERENCE_BASES is confusing to end users. -- Removed REFERENCE_BASES option. You only have REFERENCE now. There's no efficiency savings for the REFERENCE_BASES option any longer, since the reference bases are loaded lazy so if you don't use them there's effectively no cost to making the RefContext that could load them. --- .../sting/gatk/traversals/TraverseReads.java | 4 +--- .../sting/gatk/walkers/ActiveRegionWalker.java | 2 +- .../sting/gatk/walkers/DataSource.java | 12 +++++++++++- .../sting/gatk/walkers/LocusWalker.java | 2 +- .../sting/gatk/walkers/ReadWalker.java | 2 +- .../broadinstitute/sting/gatk/walkers/RefWalker.java | 2 +- .../sting/gatk/walkers/bqsr/BaseRecalibrator.java | 2 +- 7 files changed, 17 insertions(+), 9 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java index cb094d29bf..d29e9a5f27 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java +++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java @@ -75,8 +75,6 @@ public T traverse(ReadWalker walker, if( !dataProvider.hasReads() ) throw new IllegalArgumentException("Unable to traverse reads; no read data is available."); - boolean needsReferenceBasesP = WalkerManager.isRequired(walker, DataSource.REFERENCE_BASES); - ReadView reads = new ReadView(dataProvider); ReadReferenceView reference = new ReadReferenceView(dataProvider); @@ -91,7 +89,7 @@ public T traverse(ReadWalker walker, ReferenceContext refContext = null; // get the array of characters for the reference sequence, since we're a mapped read - if (needsReferenceBasesP && !read.getReadUnmappedFlag() && dataProvider.hasReference()) + if (!read.getReadUnmappedFlag() && dataProvider.hasReference()) refContext = reference.getReferenceContext(read); // update the number of reads we've seen diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java index aba508b3e9..cbe7913531 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java @@ -28,7 +28,7 @@ */ @By(DataSource.READS) -@Requires({DataSource.READS, DataSource.REFERENCE_BASES}) +@Requires({DataSource.READS, DataSource.REFERENCE}) @PartitionBy(PartitionType.READ) @ActiveRegionExtension(extension=50,maxRegion=1500) @ReadFilters({UnmappedReadFilter.class, NotPrimaryAlignmentFilter.class, DuplicateReadFilter.class, FailsVendorQualityCheckFilter.class, MappingQualityUnavailableFilter.class}) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/DataSource.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/DataSource.java index a152ab1374..1f93c67a62 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/DataSource.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/DataSource.java @@ -16,8 +16,18 @@ * Allow user to choose between a number of different data sources. */ public enum DataSource { + /** + * Does this walker require read (BAM) data to work? + */ READS, + + /** + * Does this walker require reference data to work? + */ REFERENCE, - REFERENCE_BASES, // Do I actually need the reference bases passed to the walker? + + /** + * Does this walker require reference order data (VCF) to work? + */ REFERENCE_ORDERED_DATA } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java index 2a92d8831e..3b18dda44c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java @@ -16,7 +16,7 @@ * To change this template use File | Settings | File Templates. */ @By(DataSource.READS) -@Requires({DataSource.READS,DataSource.REFERENCE, DataSource.REFERENCE_BASES}) +@Requires({DataSource.READS,DataSource.REFERENCE}) @PartitionBy(PartitionType.LOCUS) @ReadFilters({UnmappedReadFilter.class,NotPrimaryAlignmentFilter.class,DuplicateReadFilter.class,FailsVendorQualityCheckFilter.class}) @RemoveProgramRecords diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java index 8933bd73e9..77e3af93f1 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java @@ -12,7 +12,7 @@ * Time: 2:52:28 PM * To change this template use File | Settings | File Templates. */ -@Requires({DataSource.READS, DataSource.REFERENCE_BASES}) +@Requires({DataSource.READS, DataSource.REFERENCE}) @PartitionBy(PartitionType.READ) public abstract class ReadWalker extends Walker { public boolean requiresOrderedReads() { return false; } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/RefWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/RefWalker.java index 1d3debb48f..45bd14d4e6 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/RefWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/RefWalker.java @@ -8,7 +8,7 @@ * To change this template use File | Settings | File Templates. */ @By(DataSource.REFERENCE) -@Requires({DataSource.REFERENCE, DataSource.REFERENCE_BASES}) +@Requires({DataSource.REFERENCE}) @Allows(DataSource.REFERENCE) public abstract class RefWalker extends LocusWalker { } \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java index 3f35cf8e85..e45cad971b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java @@ -107,7 +107,7 @@ @BAQMode(ApplicationTime = BAQ.ApplicationTime.FORBIDDEN) @By(DataSource.READS) @ReadFilters({MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class}) // only look at covered loci, not every loci of the reference file -@Requires({DataSource.READS, DataSource.REFERENCE, DataSource.REFERENCE_BASES}) // filter out all reads with zero or unavailable mapping quality +@Requires({DataSource.READS, DataSource.REFERENCE}) // filter out all reads with zero or unavailable mapping quality @PartitionBy(PartitionType.LOCUS) // this walker requires both -I input.bam and -R reference.fasta public class BaseRecalibrator extends LocusWalker implements TreeReducible { @ArgumentCollection From c018a867076cec334aae36554e206a2ec8c8ab9d Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Fri, 17 Aug 2012 14:20:15 -0400 Subject: [PATCH 167/176] Updated and more thorough version of the BadCigar read filter * No reads with Hard/Soft clips in the middle of the cigar * No reads starting with deletions (with or without preceding clips) * No reads ending in deletions (with or without follow-up clips) * No reads that are fully hard or soft clipped * No reads that have consecutive indels in the cigar (II, DD, ID or DI) Also added systematic test for good cigars and iterative test for bad cigars. --- .../sting/gatk/filters/BadCigarFilter.java | 86 +++++++++++--- .../gatk/filters/BadCigarFilterUnitTest.java | 74 ++++++------ .../utils/clipping/ReadClipperTestUtils.java | 109 +++++++++++++++--- 3 files changed, 206 insertions(+), 63 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java index 9a1455859e..cda7392ae5 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java @@ -29,9 +29,19 @@ import net.sf.samtools.CigarOperator; import net.sf.samtools.SAMRecord; +import java.util.Iterator; + /** * Filter out reads with wonky cigar strings. * + * - No reads with Hard/Soft clips in the middle of the cigar + * - No reads starting with deletions (with or without preceding clips) + * - No reads ending in deletions (with or without follow-up clips) + * - No reads that are fully hard or soft clipped + * - No reads that have consecutive indels in the cigar (II, DD, ID or DI) + * + * ps: apparently an empty cigar is okay... + * * @author ebanks * @version 0.1 */ @@ -40,28 +50,72 @@ public class BadCigarFilter extends ReadFilter { public boolean filterOut(final SAMRecord rec) { final Cigar c = rec.getCigar(); - if( c.isEmpty() ) { return false; } // if there is no Cigar then it can't be bad - boolean previousElementWasIndel = false; - CigarOperator lastOp = c.getCigarElement(0).getOperator(); + // if there is no Cigar then it can't be bad + if( c.isEmpty() ) { + return false; + } + + Iterator elementIterator = c.getCigarElements().iterator(); - if (lastOp == CigarOperator.D) // filter out reads starting with deletion + CigarOperator firstOp = CigarOperator.H; + while (elementIterator.hasNext() && (firstOp == CigarOperator.H || firstOp == CigarOperator.S)) { + CigarOperator op = elementIterator.next().getOperator(); + + // No reads with Hard/Soft clips in the middle of the cigar + if (firstOp != CigarOperator.H && op == CigarOperator.H) { + return true; + } + firstOp = op; + } + + // No reads starting with deletions (with or without preceding clips) + if (firstOp == CigarOperator.D) { return true; - - for (CigarElement ce : c.getCigarElements()) { - CigarOperator op = ce.getOperator(); - if (op == CigarOperator.D || op == CigarOperator.I) { - if (previousElementWasIndel) - return true; // filter out reads with adjacent I/D - - previousElementWasIndel = true; + } + + boolean hasMeaningfulElements = (firstOp != CigarOperator.H && firstOp != CigarOperator.S); + boolean previousElementWasIndel = firstOp == CigarOperator.I; + CigarOperator lastOp = firstOp; + CigarOperator previousOp = firstOp; + + while (elementIterator.hasNext()) { + CigarOperator op = elementIterator.next().getOperator(); + + if (op != CigarOperator.S && op != CigarOperator.H) { + + // No reads with Hard/Soft clips in the middle of the cigar + if (previousOp == CigarOperator.S || previousOp == CigarOperator.H) + return true; + + lastOp = op; + + if (!hasMeaningfulElements && op.consumesReadBases()) { + hasMeaningfulElements = true; + } + + if (op == CigarOperator.I || op == CigarOperator.D) { + + // No reads that have consecutive indels in the cigar (II, DD, ID or DI) + if (previousElementWasIndel) { + return true; + } + previousElementWasIndel = true; + } + else { + previousElementWasIndel = false; + } + } + // No reads with Hard/Soft clips in the middle of the cigar + else if (op == CigarOperator.S && previousOp == CigarOperator.H) { + return true; } - else // this is a regular base (match/mismatch/hard or soft clip) - previousElementWasIndel = false; // reset the previous element - lastOp = op; + previousOp = op; } - return lastOp == CigarOperator.D; + // No reads ending in deletions (with or without follow-up clips) + // No reads that are fully hard or soft clipped + return lastOp == CigarOperator.D || !hasMeaningfulElements; } } \ No newline at end of file diff --git a/public/java/test/org/broadinstitute/sting/gatk/filters/BadCigarFilterUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/filters/BadCigarFilterUnitTest.java index 333d35641e..ff918db68c 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/filters/BadCigarFilterUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/filters/BadCigarFilterUnitTest.java @@ -1,11 +1,14 @@ package org.broadinstitute.sting.gatk.filters; -import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; +import net.sf.samtools.Cigar; +import org.broadinstitute.sting.utils.clipping.ReadClipperTestUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; +import java.util.List; + /** * Checks that the Bad Cigar filter works for all kinds of wonky cigars * @@ -14,6 +17,29 @@ */ public class BadCigarFilterUnitTest { + public static final String[] BAD_CIGAR_LIST = { + "2D4M", // starting with multiple deletions + "4M2D", // ending with multiple deletions + "3M1I1D", // adjacent indels AND ends in deletion + "1M1I1D2M", // adjacent indels I->D + "1M1D2I1M", // adjacent indels D->I + "1M1I2M1D", // ends in single deletion with insertion in the middle + "4M1D", // ends in single deletion + "1D4M", // starts with single deletion + "2M1D1D2M", // adjacent D's + "1M1I1I1M", // adjacent I's + "1H1D4M", // starting with deletion after H + "1S1D3M", // starting with deletion after S + "1H1S1D3M", // starting with deletion after HS + "4M1D1H", // ending with deletion before H + "3M1D1S", // ending with deletion before S + "3M1D1S1H", // ending with deletion before HS + "10M2H10M", // H in the middle + "10M2S10M", // S in the middle + "1H1S10M2S10M1S1H", // deceiving S in the middle + "1H1S10M2H10M1S1H" // deceiving H in the middle + }; + BadCigarFilter filter; @BeforeClass @@ -21,40 +47,20 @@ public void init() { filter = new BadCigarFilter(); } - @Test + @Test(enabled = true) public void testWonkyCigars () { - byte[] bases = {'A', 'A', 'A', 'A'}; - byte[] quals = {30, 30, 30, 30}; - GATKSAMRecord read; - // starting with multiple deletions - read = ArtificialSAMUtils.createArtificialRead(bases, quals, "2D4M"); - Assert.assertTrue(filter.filterOut(read), read.getCigarString()); - - read = ArtificialSAMUtils.createArtificialRead(bases, quals, "4M2D"); // ending with multiple deletions - Assert.assertTrue(filter.filterOut(read), read.getCigarString()); - - read = ArtificialSAMUtils.createArtificialRead(bases, quals, "3M1I1D"); // adjacent indels AND ends in deletion - Assert.assertTrue(filter.filterOut(read), read.getCigarString()); - - read = ArtificialSAMUtils.createArtificialRead(bases, quals, "1M1I1D2M"); // adjacent indels I->D - Assert.assertTrue(filter.filterOut(read), read.getCigarString()); - - read = ArtificialSAMUtils.createArtificialRead(bases, quals, "1M1D2I1M"); // adjacent indels D->I - Assert.assertTrue(filter.filterOut(read), read.getCigarString()); - - read = ArtificialSAMUtils.createArtificialRead(bases, quals, "1M1I2M1D"); // ends in single deletion with insertion in the middle - Assert.assertTrue(filter.filterOut(read), read.getCigarString()); - - read = ArtificialSAMUtils.createArtificialRead(bases, quals, "4M1D"); // ends in single deletion - Assert.assertTrue(filter.filterOut(read), read.getCigarString()); - - read = ArtificialSAMUtils.createArtificialRead(bases, quals, "1D4M"); // starts with single deletion - Assert.assertTrue(filter.filterOut(read), read.getCigarString()); - - read = ArtificialSAMUtils.createArtificialRead(bases, quals, "2M1D1D2M"); // adjacent D's - Assert.assertTrue(filter.filterOut(read), read.getCigarString()); + for (String cigarString : BAD_CIGAR_LIST) { + GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigarString); + Assert.assertTrue(filter.filterOut(read), read.getCigarString()); + } + } - read = ArtificialSAMUtils.createArtificialRead(bases, quals, "1M1I1I1M"); // adjacent I's - Assert.assertTrue(filter.filterOut(read), read.getCigarString()); + @Test(enabled = true) + public void testGoodCigars() { + List cigarList = ReadClipperTestUtils.generateCigarList(10); + for (Cigar cigar : cigarList) { + GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar); + Assert.assertFalse(filter.filterOut(read), read.getCigarString()); + } } } diff --git a/public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperTestUtils.java b/public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperTestUtils.java index baa2f6218f..208c14fbd0 100644 --- a/public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperTestUtils.java +++ b/public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperTestUtils.java @@ -4,6 +4,7 @@ import net.sf.samtools.CigarElement; import net.sf.samtools.CigarOperator; import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.testng.Assert; @@ -37,17 +38,22 @@ public static GATKSAMRecord makeReadFromCigar(Cigar cigar) { return ArtificialSAMUtils.createArtificialRead(Utils.arrayFromArrayWithLength(BASES, cigar.getReadLength()), Utils.arrayFromArrayWithLength(QUALS, cigar.getReadLength()), cigar.toString()); } - /** - * This function generates every valid permutation of cigar strings with a given length. - * - * A valid cigar object obeys the following rules: - * - No Hard/Soft clips in the middle of the read - * - No deletions in the beginning / end of the read - * - No repeated adjacent element (e.g. 1M2M -> this should be 3M) - * - * @param maximumLength the maximum number of elements in the cigar - * @return a list with all valid Cigar objects - */ + public static GATKSAMRecord makeReadFromCigar(String cigarString) { + return makeReadFromCigar(cigarFromString(cigarString)); + } + + /** + * This function generates every valid permutation of cigar strings with a given length. + * + * A valid cigar object obeys the following rules: + * - No Hard/Soft clips in the middle of the read + * - No deletions in the beginning / end of the read + * - No repeated adjacent element (e.g. 1M2M -> this should be 3M) + * - No consecutive I/D elements + * + * @param maximumLength the maximum number of elements in the cigar + * @return a list with all valid Cigar objects + */ public static List generateCigarList(int maximumLength) { int numCigarElements = cigarElements.length; LinkedList cigarList = new LinkedList(); @@ -137,7 +143,10 @@ private static Cigar combineAdjacentCigarElements(Cigar rawCigar) { CigarElement lastElement = null; int lastElementLength = 0; for (CigarElement cigarElement : rawCigar.getCigarElements()) { - if (lastElement != null && lastElement.getOperator() == cigarElement.getOperator()) + if (lastElement != null && + ((lastElement.getOperator() == cigarElement.getOperator()) || + (lastElement.getOperator() == CigarOperator.I && cigarElement.getOperator() == CigarOperator.D) || + (lastElement.getOperator() == CigarOperator.D && cigarElement.getOperator() == CigarOperator.I))) lastElementLength += cigarElement.getLength(); else { @@ -191,7 +200,7 @@ public static Cigar invertCigar (Cigar cigar) { /** * Checks whether or not the read has any cigar element that is not H or S * - * @param read + * @param read the read * @return true if it has any M, I or D, false otherwise */ public static boolean readHasNonClippedBases(GATKSAMRecord read) { @@ -201,5 +210,79 @@ public static boolean readHasNonClippedBases(GATKSAMRecord read) { return false; } + public static Cigar cigarFromString(String cigarString) { + Cigar cigar = new Cigar(); + + boolean isNumber = false; + int number = 0; + for (int i = 0; i < cigarString.length(); i++) { + char x = cigarString.charAt(i); + + if (x >= '0' && x <='9') { + if (isNumber) { + number *= 10; + } + else { + isNumber = true; + } + number += x - '0'; + } + + else { + CigarElement e; + switch (x) { + case 'M': + case 'm': + e = new CigarElement(number, CigarOperator.M); + break; + + case 'I': + case 'i': + e = new CigarElement(number, CigarOperator.I); + break; + + case 'D': + case 'd': + e = new CigarElement(number, CigarOperator.D); + break; + + case 'S': + case 's': + e = new CigarElement(number, CigarOperator.S); + break; + + case 'N': + case 'n': + e = new CigarElement(number, CigarOperator.N); + break; + + case 'H': + case 'h': + e = new CigarElement(number, CigarOperator.H); + break; + + case 'P': + case 'p': + e = new CigarElement(number, CigarOperator.P); + break; + + case '=': + e = new CigarElement(number, CigarOperator.EQ); + break; + + case 'X': + case 'x': + e = new CigarElement(number, CigarOperator.X); + break; + + default: + throw new ReviewedStingException("Unrecognized cigar operator: " + x + " (number: " + number + ")"); + } + cigar.add(e); + } + } + return cigar; + } + } From 9db35953d4a97ca660a34c39ced09a19e6817a89 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Sat, 18 Aug 2012 18:46:52 -0400 Subject: [PATCH 168/176] Cleanup and expansion of GATKPerformanceOfTime -- Does BQSR parallelism test -- Does CountLoci parallelism test -- Updated R script From 5df70f7332e28f31f120548fd23a78e932031cda Mon Sep 17 00:00:00 2001 From: David Roazen Date: Sat, 18 Aug 2012 21:06:57 -0400 Subject: [PATCH 169/176] Bring bamboo performance test runner script under version control From f82e0830e52eeabd5bf0833ffe2b76732ebc773f Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Sun, 19 Aug 2012 10:29:38 -0400 Subject: [PATCH 170/176] CombineVariants outputs the first non-MISSING qual, not the maximum -- When merging multiple VCF records at a site, the combined VCF record has the QUAL of the first VCF record with a non-MISSING QUAL value. The previous behavior was to take the max QUAL, which resulted in sometime strange downstream confusion. --- .../sting/gatk/walkers/variantutils/CombineVariants.java | 7 +++++++ .../sting/utils/variantcontext/VariantContextUtils.java | 6 ++++-- .../variantutils/CombineVariantsIntegrationTest.java | 6 +++--- 3 files changed, 14 insertions(+), 5 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java index 8dabd49b88..555999bdb6 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java @@ -73,6 +73,13 @@ * efficiency. However, since this merge runs in only one thread, you can quickly reach diminishing * returns with the number of parallel threads. -nt 4 works well but -nt 8 may be too much. * + * Some fine details about the merging algorithm: + *
    + *
  • As of GATK 2.1, when merging multiple VCF records at a site, the combined VCF record has the QUAL of + * the first VCF record with a non-MISSING QUAL value. The previous behavior was to take the + * max QUAL, which resulted in sometime strange downstream confusion
    • + *
+ * *

Input

*

* One or more variant sets to combine. diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java index ff6b0be702..d7e4a71358 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java @@ -514,7 +514,7 @@ public static VariantContext simpleMerge(final GenomeLocParser genomeLocParser, int depth = 0; int maxAC = -1; final Map attributesWithMaxAC = new LinkedHashMap(); - double log10PError = 1; + double log10PError = CommonInfo.NO_LOG10_PERROR; VariantContext vcWithMaxAC = null; GenotypesContext genotypes = GenotypesContext.create(); @@ -542,7 +542,9 @@ public static VariantContext simpleMerge(final GenomeLocParser genomeLocParser, mergeGenotypes(genotypes, vc, alleleMapping, genotypeMergeOptions == GenotypeMergeType.UNIQUIFY); - log10PError = Math.min(log10PError, vc.isVariant() ? vc.getLog10PError() : 1); + // We always take the QUAL of the first VC with a non-MISSING qual for the combined value + if ( log10PError == CommonInfo.NO_LOG10_PERROR ) + log10PError = vc.getLog10PError(); filters.addAll(vc.getFilters()); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java index 9ea751b72c..c32d77f824 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java @@ -113,13 +113,13 @@ public void combinePLs(String file1, String file2, String md5) { @Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "4efdf983918db822e4ac13d911509576"); } // official project VCF files in tabix format @Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "848d4408ee953053d2307cefebc6bd6d"); } // official project VCF files in tabix format - @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "5d04f22ef88ed9226cbd7b4483c5cb23"); } + @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "629656bfef7713c23f3a593523503b2f"); } @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "e54d0dcf14f90d5c8e58b45191dd0219"); } @Test public void uniqueSNPs() { // parallelism must be disabled because the input VCF is malformed (DB=0) and parallelism actually fixes this which breaks the md5s - combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "acc70f33be741b564f7be9aa3f819dd4", true); + combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "e5ea6ac3905bd9eeea1a2ef5d2cb5af7", true); } @Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "def52bcd3942bbe39cd7ebe845c4f206"); } @@ -137,7 +137,7 @@ public void combinePLs(String file1, String file2, String md5) { " -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" + " -genotypeMergeOptions UNIQUIFY -L 1"), 1, - Arrays.asList("3039cfff7abee6aa7fbbafec66a1b019")); + Arrays.asList("e5f0e7a80cd392172ebf5ddb06b91a00")); cvExecuteTest("threeWayWithRefs", spec, true); } From 121ffa7ba0c1f4e828593fc7e40d38b946709ce0 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Sun, 19 Aug 2012 10:32:55 -0400 Subject: [PATCH 171/176] Print "Parsing data stream with BCF version BCFx.y" in BCF2 codec as .debug not .info --- .../org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java index 60fcb65853..c221b8fba1 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java @@ -149,7 +149,7 @@ public FeatureCodecHeader readHeader( final PositionalBufferedStream inputStream if ( bcfVersion.getMinorVersion() < MIN_MINOR_VERSION ) error("BCF2Codec can only process BCF2 files with minor version >= " + MIN_MINOR_VERSION + " but this file has minor version " + bcfVersion.getMinorVersion()); - logger.info("Parsing data stream with BCF version " + bcfVersion); + logger.debug("Parsing data stream with BCF version " + bcfVersion); final int headerSizeInBytes = BCF2Type.INT32.read(inputStream); From e2c3bbcd16406ca52a06f372c84e6ba4e41ebe46 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 20 Aug 2012 01:16:23 -0400 Subject: [PATCH 172/176] Thanks to Guillermo I was able to isolate an instance of where the MLEAC > AN. It turns out that this is valid, e.g. when PLs are all 0s for a sample we no-call it but it's allowed to factor into the MLE (since that's the contract with the exact model). Removing the check in UG and instead protecting for it in the AlleleCount stratification. --- .../gatk/walkers/genotyper/UnifiedGenotyperEngine.java | 10 ++-------- .../varianteval/stratifications/AlleleCount.java | 5 +++-- 2 files changed, 5 insertions(+), 10 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index 67ade390ff..3d9724ffb1 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -444,16 +444,10 @@ else if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_M if ( alleleCountsofMLE.size() > 0 ) { attributes.put(VCFConstants.MLE_ALLELE_COUNT_KEY, alleleCountsofMLE); final int AN = builder.make().getCalledChrCount(); - - // let's sanity check that we don't have an invalid MLE value in there - for ( int MLEAC : alleleCountsofMLE ) { - if ( MLEAC > AN ) - throw new ReviewedStingException(String.format("MLEAC value (%d) is larger than AN (%d) at position %s:%d", MLEAC, AN, loc.getContig(), loc.getStart())); - } - final ArrayList MLEfrequencies = new ArrayList(alleleCountsofMLE.size()); + // the MLEAC is allowed to be larger than the AN (e.g. in the case of all PLs being 0, the GT is ./. but the exact model may arbitrarily choose an AC>1) for ( int AC : alleleCountsofMLE ) - MLEfrequencies.add((double)AC / (double)AN); + MLEfrequencies.add(Math.min(1.0, (double)AC / (double)AN)); attributes.put(VCFConstants.MLE_ALLELE_FREQUENCY_KEY, MLEfrequencies); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java index 00a5937685..2b1bd9c62c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java @@ -46,7 +46,8 @@ public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker t int AC = 0; // by default, the site is considered monomorphic if ( eval.hasAttribute(VCFConstants.MLE_ALLELE_COUNT_KEY) && eval.isBiallelic() ) { - AC = eval.getAttributeAsInt(VCFConstants.MLE_ALLELE_COUNT_KEY, 0); + // the MLEAC is allowed to be larger than the AN (e.g. in the case of all PLs being 0, the GT is ./. but the exact model may arbitrarily choose an AC>1) + AC = Math.min(eval.getAttributeAsInt(VCFConstants.MLE_ALLELE_COUNT_KEY, 0), nchrom); } else if ( eval.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) && eval.isBiallelic() ) { AC = eval.getAttributeAsInt(VCFConstants.ALLELE_COUNT_KEY, 0); } else if ( eval.isVariant() ) { @@ -56,7 +57,7 @@ public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker t // make sure that the AC isn't invalid if ( AC > nchrom ) - throw new UserException.MalformedVCF(String.format("The AC or MLEAC value (%d) at position %s:%d " + + throw new UserException.MalformedVCF(String.format("The AC value (%d) at position %s:%d " + "is larger than the number of chromosomes over all samples (%d)", AC, eval.getChr(), eval.getStart(), nchrom)); From db3dc55717ecd6703d0b03f92004074bd4491ce2 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 20 Aug 2012 12:43:17 -0400 Subject: [PATCH 173/176] Temporarily disabling multi-threaded usage of BaseRecalibrator for performance reasons. --- .../sting/gatk/walkers/bqsr/BaseRecalibrator.java | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java index e45cad971b..91d982f201 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java @@ -136,6 +136,10 @@ public class BaseRecalibrator extends LocusWalker implements TreeRed */ public void initialize() { + // TODO -- remove me after the 2.1 release + if ( getToolkit().getArguments().numberOfThreads > 1 ) + throw new UserException("We have temporarily disabled the ability to run BaseRecalibrator multi-threaded for performance reasons. We hope to have this fixed for the next GATK release (2.2) and apologize for the inconvenience."); + // check for unsupported access if (getToolkit().isGATKLite() && !getToolkit().getArguments().disableIndelQuals) throw new UserException.NotSupportedInGATKLite("base insertion/deletion recalibration is not supported, please use the --disable_indel_quals argument"); From 997d23b3daa13014c8edb5a511af3c51e4f9d96a Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Mon, 20 Aug 2012 13:41:08 -0400 Subject: [PATCH 174/176] Bug fix in HaplotypeCaller for non-regular bases in the reference or reads. Those events don't get created any more. Bug fix for advanced GenotypeFullActiveRegion mode: custom variant annotations created by the HC don't make sense when in this mode so don't try to calculate them. --- .../walkers/genotyper/UnifiedArgumentCollection.java | 1 - .../src/org/broadinstitute/sting/utils/BaseUtils.java | 11 +++++++++-- 2 files changed, 9 insertions(+), 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java index e755a1e366..f11f1e5995 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java @@ -181,7 +181,6 @@ Generalized ploidy argument (debug only): squash all reads into a single pileup Generalized ploidy argument (debug only): When building site error models, ignore lane information and build only sample-level error model */ - @Argument(fullName = "ignoreLaneInfo", shortName = "ignoreLane", doc = "Ignore lane when building error model, error model is then per-site", required = false) public boolean IGNORE_LANE_INFO = false; diff --git a/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java b/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java index 13571df789..2d7f51c3fb 100644 --- a/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java @@ -227,14 +227,21 @@ static public int extendedBaseToBaseIndex(byte base) { } @Deprecated - static public boolean isRegularBase(char base) { + static public boolean isRegularBase( final char base ) { return simpleBaseToBaseIndex(base) != -1; } - static public boolean isRegularBase(byte base) { + static public boolean isRegularBase( final byte base ) { return simpleBaseToBaseIndex(base) != -1; } + static public boolean isAllRegularBases( final byte[] bases ) { + for( final byte base : bases) { + if( !isRegularBase(base) ) { return false; } + } + return true; + } + static public boolean isNBase(byte base) { return base == 'N' || base == 'n'; } From bda26632d4678e981fc4b13a997018375326a982 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 20 Aug 2012 15:10:24 -0400 Subject: [PATCH 175/176] Fixing the docs for DP and AD --- .../gatk/walkers/annotator/DepthOfCoverage.java | 17 ++++------------- .../annotator/DepthPerAlleleBySample.java | 12 ++++++------ 2 files changed, 10 insertions(+), 19 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java index 28ca77f183..39b5e84dca 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java @@ -22,19 +22,10 @@ /** * Total (unfiltered) depth over all samples. * - * This and AD are complementary fields that are two important ways of thinking about the depth of the data for this sample - * at this site. The DP field describe the total depth of reads that passed the Unified Genotypers internal - * quality control metrics (like MAPQ > 17, for example), whatever base was present in the read at this site. - * The AD values (one for each of REF and ALT fields) is the count of all reads that carried with them the - * REF and ALT alleles. The reason for this distinction is that the DP is in some sense reflective of the - * power I have to determine the genotype of the sample at this site, while the AD tells me how many times - * I saw each of the REF and ALT alleles in the reads, free of any bias potentially introduced by filtering - * the reads. If, for example, I believe there really is a an A/T polymorphism at a site, then I would like - * to know the counts of A and T bases in this sample, even for reads with poor mapping quality that would - * normally be excluded from the statistical calculations going into GQ and QUAL. - * - * Note that the DP is affected by downsampling (-dcov) though, so the max value one can obtain for N samples with - * -dcov D is N * D + * While the sample-level (FORMAT) DP field describes the total depth of reads that passed the Unified Genotyper's + * internal quality control metrics (like MAPQ > 17, for example), the INFO field DP represents the unfiltered depth + * over all samples. Note though that the DP is affected by downsampling (-dcov), so the max value one can obtain for + * N samples with -dcov D is N * D */ public class DepthOfCoverage extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java index a9edab752f..5d83ddd510 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java @@ -24,10 +24,10 @@ /** * The depth of coverage of each VCF allele in this sample. * - * This and DP are complementary fields that are two important ways of thinking about the depth of the data for this sample - * at this site. The DP field describe the total depth of reads that passed the Unified Genotypers internal - * quality control metrics (like MAPQ > 17, for example), whatever base was present in the read at this site. - * The AD values (one for each of REF and ALT fields) is the count of all reads that carried with them the + * The AD and DP are complementary fields that are two important ways of thinking about the depth of the data for this + * sample at this site. While the sample-level (FORMAT) DP field describes the total depth of reads that passed the + * Unified Genotyper's internal quality control metrics (like MAPQ > 17, for example), the AD values (one for each of + * REF and ALT fields) is the unfiltered count of all reads that carried with them the * REF and ALT alleles. The reason for this distinction is that the DP is in some sense reflective of the * power I have to determine the genotype of the sample at this site, while the AD tells me how many times * I saw each of the REF and ALT alleles in the reads, free of any bias potentially introduced by filtering @@ -35,10 +35,10 @@ * to know the counts of A and T bases in this sample, even for reads with poor mapping quality that would * normally be excluded from the statistical calculations going into GQ and QUAL. Please note, however, that * the AD isn't necessarily calculated exactly for indels (it counts as non-reference only those indels that - * are actually present and correctly left-aligned in the alignments themselves). Because of this fact and + * are unambiguously informative about the alternate allele). Because of this fact and * because the AD includes reads and bases that were filtered by the Unified Genotyper, one should not base * assumptions about the underlying genotype based on it; instead, the genotype likelihoods (PLs) are what - * determine the genotype calls (see below). + * determine the genotype calls. */ public class DepthPerAlleleBySample extends GenotypeAnnotation implements StandardAnnotation { From 94eeb79d1b4e35788d27eb945b516a726a98ed84 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Mon, 20 Aug 2012 15:28:39 -0400 Subject: [PATCH 176/176] Pulling out common caller arguments into its own StandardCallerArgumentCollection base class so that every caller isn't exposed to the unused arguments from every other caller. --- .../StandardCallerArgumentCollection.java | 62 +++++++++++++++++++ .../genotyper/UnifiedArgumentCollection.java | 60 +++++------------- 2 files changed, 76 insertions(+), 46 deletions(-) create mode 100644 public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java new file mode 100644 index 0000000000..f30fc03160 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java @@ -0,0 +1,62 @@ +package org.broadinstitute.sting.gatk.arguments; + +import org.broadinstitute.sting.commandline.Advanced; +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Input; +import org.broadinstitute.sting.commandline.RodBinding; +import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel; +import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine; +import org.broadinstitute.sting.utils.variantcontext.VariantContext; + +/** + * Created with IntelliJ IDEA. + * User: rpoplin + * Date: 8/20/12 + * A collection of arguments that are common to the various callers. + * This is pulled out so that every caller isn't exposed to the arguments from every other caller. + */ + +public class StandardCallerArgumentCollection { + /** + * The expected heterozygosity value used to compute prior likelihoods for any locus. The default priors are: + * het = 1e-3, P(hom-ref genotype) = 1 - 3 * het / 2, P(het genotype) = het, P(hom-var genotype) = het / 2 + */ + @Argument(fullName = "heterozygosity", shortName = "hets", doc = "Heterozygosity value used to compute prior likelihoods for any locus", required = false) + public Double heterozygosity = UnifiedGenotyperEngine.HUMAN_SNP_HETEROZYGOSITY; + + @Argument(fullName = "genotyping_mode", shortName = "gt_mode", doc = "Specifies how to determine the alternate alleles to use for genotyping", required = false) + public GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.DISCOVERY; + + @Argument(fullName = "output_mode", shortName = "out_mode", doc = "Specifies which type of calls we should output", required = false) + public UnifiedGenotyperEngine.OUTPUT_MODE OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_VARIANTS_ONLY; + + /** + * The minimum phred-scaled Qscore threshold to separate high confidence from low confidence calls. Only genotypes with + * confidence >= this threshold are emitted as called sites. A reasonable threshold is 30 for high-pass calling (this + * is the default). + */ + @Argument(fullName = "standard_min_confidence_threshold_for_calling", shortName = "stand_call_conf", doc = "The minimum phred-scaled confidence threshold at which variants should be called", required = false) + public double STANDARD_CONFIDENCE_FOR_CALLING = 30.0; + + /** + * This argument allows you to emit low quality calls as filtered records. + */ + @Argument(fullName = "standard_min_confidence_threshold_for_emitting", shortName = "stand_emit_conf", doc = "The minimum phred-scaled confidence threshold at which variants should be emitted (and filtered with LowQual if less than the calling threshold)", required = false) + public double STANDARD_CONFIDENCE_FOR_EMITTING = 30.0; + + /** + * When the UnifiedGenotyper is put into GENOTYPE_GIVEN_ALLELES mode it will genotype the samples using only the alleles provide in this rod binding + */ + @Input(fullName="alleles", shortName = "alleles", doc="The set of alleles at which to genotype when --genotyping_mode is GENOTYPE_GIVEN_ALLELES", required=false) + public RodBinding alleles; + + /** + * If there are more than this number of alternate alleles presented to the genotyper (either through discovery or GENOTYPE_GIVEN ALLELES), + * then only this many alleles will be used. Note that genotyping sites with many alternate alleles is both CPU and memory intensive and it + * scales exponentially based on the number of alternate alleles. Unless there is a good reason to change the default value, we highly recommend + * that you not play around with this parameter. + */ + @Advanced + @Argument(fullName = "max_alternate_alleles", shortName = "maxAltAlleles", doc = "Maximum number of alternate alleles to genotype", required = false) + public int MAX_ALTERNATE_ALLELES = 3; +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java index f11f1e5995..30c0f3e18d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java @@ -26,11 +26,12 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; import org.broadinstitute.sting.commandline.*; +import org.broadinstitute.sting.gatk.arguments.StandardCallerArgumentCollection; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; -public class UnifiedArgumentCollection { +public class UnifiedArgumentCollection extends StandardCallerArgumentCollection { @Argument(fullName = "genotype_likelihoods_model", shortName = "glm", doc = "Genotype likelihoods calculation model to employ -- SNP is the default option, while INDEL is also available for calling indels and BOTH is available for calling both together", required = false) public GenotypeLikelihoodsCalculationModel.Model GLmodel = GenotypeLikelihoodsCalculationModel.Model.SNP; @@ -42,13 +43,6 @@ public class UnifiedArgumentCollection { @Argument(fullName = "p_nonref_model", shortName = "pnrm", doc = "Non-reference probability calculation model to employ", required = false) protected AlleleFrequencyCalculationModel.Model AFmodel = AlleleFrequencyCalculationModel.Model.EXACT; - /** - * The expected heterozygosity value used to compute prior likelihoods for any locus. The default priors are: - * het = 1e-3, P(hom-ref genotype) = 1 - 3 * het / 2, P(het genotype) = het, P(hom-var genotype) = het / 2 - */ - @Argument(fullName = "heterozygosity", shortName = "hets", doc = "Heterozygosity value used to compute prior likelihoods for any locus", required = false) - public Double heterozygosity = UnifiedGenotyperEngine.HUMAN_SNP_HETEROZYGOSITY; - /** * The PCR error rate is independent of the sequencing error rate, which is necessary because we cannot necessarily * distinguish between PCR errors vs. sequencing errors. The practical implication for this value is that it @@ -57,26 +51,6 @@ public class UnifiedArgumentCollection { @Argument(fullName = "pcr_error_rate", shortName = "pcr_error", doc = "The PCR error rate to be used for computing fragment-based likelihoods", required = false) public Double PCR_error = DiploidSNPGenotypeLikelihoods.DEFAULT_PCR_ERROR_RATE; - @Argument(fullName = "genotyping_mode", shortName = "gt_mode", doc = "Specifies how to determine the alternate alleles to use for genotyping", required = false) - public GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.DISCOVERY; - - @Argument(fullName = "output_mode", shortName = "out_mode", doc = "Specifies which type of calls we should output", required = false) - public UnifiedGenotyperEngine.OUTPUT_MODE OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_VARIANTS_ONLY; - - /** - * The minimum phred-scaled Qscore threshold to separate high confidence from low confidence calls. Only genotypes with - * confidence >= this threshold are emitted as called sites. A reasonable threshold is 30 for high-pass calling (this - * is the default). - */ - @Argument(fullName = "standard_min_confidence_threshold_for_calling", shortName = "stand_call_conf", doc = "The minimum phred-scaled confidence threshold at which variants should be called", required = false) - public double STANDARD_CONFIDENCE_FOR_CALLING = 30.0; - - /** - * This argument allows you to emit low quality calls as filtered records. - */ - @Argument(fullName = "standard_min_confidence_threshold_for_emitting", shortName = "stand_emit_conf", doc = "The minimum phred-scaled confidence threshold at which variants should be emitted (and filtered with LowQual if less than the calling threshold)", required = false) - public double STANDARD_CONFIDENCE_FOR_EMITTING = 30.0; - /** * Note that calculating the SLOD increases the runtime by an appreciable amount. */ @@ -90,12 +64,6 @@ public class UnifiedArgumentCollection { @Argument(fullName = "annotateNDA", shortName = "nda", doc = "If provided, we will annotate records with the number of alternate alleles that were discovered (but not necessarily genotyped) at a given site", required = false) public boolean ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED = false; - /** - * When the UnifiedGenotyper is put into GENOTYPE_GIVEN_ALLELES mode it will genotype the samples using only the alleles provide in this rod binding - */ - @Input(fullName="alleles", shortName = "alleles", doc="The set of alleles at which to genotype when --genotyping_mode is GENOTYPE_GIVEN_ALLELES", required=false) - public RodBinding alleles; - /** * The minimum confidence needed in a given base for it to be used in variant calling. Note that the base quality of a base * is capped by the mapping quality so that bases on reads with low mapping quality may get filtered out depending on this value. @@ -107,16 +75,6 @@ public class UnifiedArgumentCollection { @Argument(fullName = "max_deletion_fraction", shortName = "deletions", doc = "Maximum fraction of reads with deletions spanning this locus for it to be callable [to disable, set to < 0 or > 1; default:0.05]", required = false) public Double MAX_DELETION_FRACTION = 0.05; - /** - * If there are more than this number of alternate alleles presented to the genotyper (either through discovery or GENOTYPE_GIVEN ALLELES), - * then only this many alleles will be used. Note that genotyping sites with many alternate alleles is both CPU and memory intensive and it - * scales exponentially based on the number of alternate alleles. Unless there is a good reason to change the default value, we highly recommend - * that you not play around with this parameter. - */ - @Advanced - @Argument(fullName = "max_alternate_alleles", shortName = "maxAltAlleles", doc = "Maximum number of alternate alleles to genotype", required = false) - public int MAX_ALTERNATE_ALLELES = 3; - @Hidden @Argument(fullName = "cap_max_alternate_alleles_for_indels", shortName = "capMaxAltAllelesForIndels", doc = "Cap the maximum number of alternate alleles to genotype for indel calls at 2; overrides the --max_alternate_alleles argument; GSA production use only", required = false) public boolean CAP_MAX_ALTERNATE_ALLELES_FOR_INDELS = false; @@ -139,7 +97,6 @@ public class UnifiedArgumentCollection { @Argument(fullName = "min_indel_fraction_per_sample", shortName = "minIndelFrac", doc = "Minimum fraction of all reads at a locus that must contain an indel (of any allele) for that sample to contribute to the indel count for alleles", required = false) public double MIN_INDEL_FRACTION_PER_SAMPLE = 0.25; - /** * This argument informs the prior probability of having an indel at a site. */ @@ -274,5 +231,16 @@ public UnifiedArgumentCollection clone() { return uac; } - + public UnifiedArgumentCollection() { } + + public UnifiedArgumentCollection( final StandardCallerArgumentCollection SCAC ) { + super(); + this.alleles = SCAC.alleles; + this.GenotypingMode = SCAC.GenotypingMode; + this.heterozygosity = SCAC.heterozygosity; + this.MAX_ALTERNATE_ALLELES = SCAC.MAX_ALTERNATE_ALLELES; + this.OutputMode = SCAC.OutputMode; + this.STANDARD_CONFIDENCE_FOR_CALLING = SCAC.STANDARD_CONFIDENCE_FOR_CALLING; + this.STANDARD_CONFIDENCE_FOR_EMITTING = SCAC.STANDARD_CONFIDENCE_FOR_EMITTING; + } }