From aa9e32f2f115a81b643b52317d40fc46e79195ef Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 7 Sep 2011 15:48:06 -0400 Subject: [PATCH] Reverting Mark's previous commit as per the open discussion. Now the eval modules check isPolymorphic() before accruing stats when appropriate. Fixed the IndelLengthHistogram module not to error out if the indel isn't simple (that would have been bad). Only integration test that needed to be updated was the tranches one based on a separate commit from Mark. --- .../varianteval/evaluators/CompOverlap.java | 2 +- .../varianteval/evaluators/CountVariants.java | 3 +- .../evaluators/IndelLengthHistogram.java | 15 +-- .../evaluators/IndelStatistics.java | 2 +- .../evaluators/SimpleMetricsByAC.java | 2 +- .../evaluators/ThetaVariantEvaluator.java | 103 +++++++++--------- .../evaluators/TiTvVariantEvaluator.java | 2 +- .../evaluators/ValidationReport.java | 5 +- .../evaluators/VariantQualityScore.java | 2 +- .../varianteval/util/VariantEvalUtils.java | 2 +- .../VariantEvalIntegrationTest.java | 2 +- 11 files changed, 69 insertions(+), 71 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java index 2ea64c49c..5ccacac37 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java @@ -75,7 +75,7 @@ public class CompOverlap extends VariantEvaluator implements StandardEval { } public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - boolean evalIsGood = eval != null && eval.isVariant(); + boolean evalIsGood = eval != null && eval.isPolymorphic(); boolean compIsGood = comp != null && comp.isNotFiltered() && (eval == null || comp.getType() == eval.getType()); if (compIsGood) nCompVariants++; // count the number of comp events diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java index 59ef3d992..2913c97a6 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java @@ -100,11 +100,12 @@ public class CountVariants extends VariantEvaluator implements StandardEval { // So in order to maintain consistency with the previous implementation (and the intention of the original author), I've // added in a proxy check for monomorphic status here. // Protect against case when vc only as no-calls too - can happen if we strafity by sample and sample as a single no-call. - if ( !vc1.isVariant() || (vc1.hasGenotypes() && vc1.getHomRefCount() + vc1.getNoCallCount() == vc1.getNSamples()) ) { + if ( vc1.isMonomorphic() ) { nRefLoci++; } else { switch (vc1.getType()) { case NO_VARIATION: + // shouldn't get here break; case SNP: nVariantLoci++; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java index 35fffd815..ffe7c185f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java @@ -90,18 +90,19 @@ public class IndelLengthHistogram extends VariantEvaluator { public int getComparisonOrder() { return 1; } // need only the evals public String update1(VariantContext vc1, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - if ( ! vc1.isBiallelic() && vc1.isIndel() ) { - //veWalker.getLogger().warn("[IndelLengthHistogram] Non-biallelic indel at "+ref.getLocus()+" ignored."); - return vc1.toString(); // biallelic sites are output - } - if ( vc1.isIndel() ) { + if ( vc1.isIndel() && vc1.isPolymorphic() ) { + + if ( ! vc1.isBiallelic() ) { + //veWalker.getLogger().warn("[IndelLengthHistogram] Non-biallelic indel at "+ref.getLocus()+" ignored."); + return vc1.toString(); // biallelic sites are output + } + + // only count simple insertions/deletions, not complex indels if ( vc1.isSimpleInsertion() ) { indelHistogram.update(vc1.getAlternateAllele(0).length()); } else if ( vc1.isSimpleDeletion() ) { indelHistogram.update(-vc1.getReference().length()); - } else { - throw new ReviewedStingException("Indel type that is not insertion or deletion."); } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java index fc347339d..f70e6c2de 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java @@ -270,7 +270,7 @@ public class IndelStatistics extends VariantEvaluator { public String update1(VariantContext eval, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - if (eval != null ) { + if (eval != null && eval.isPolymorphic()) { if ( indelStats == null ) { indelStats = new IndelStats(eval); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java index d466645ea..203c15a85 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java @@ -166,7 +166,7 @@ public class SimpleMetricsByAC extends VariantEvaluator implements StandardEval } } - if ( eval.isSNP() && eval.isBiallelic() && metrics != null ) { + if ( eval.isSNP() && eval.isBiallelic() && eval.isPolymorphic() && metrics != null ) { metrics.incrValue(eval); } } 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 ec43cbd55..e51623c3c 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 @@ -37,77 +37,74 @@ public class ThetaVariantEvaluator extends VariantEvaluator { } public String update1(VariantContext vc, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - if (vc == null || !vc.isSNP() || !vc.hasGenotypes()) { + if (vc == null || !vc.isSNP() || !vc.hasGenotypes() || vc.isMonomorphic()) { return null; //no interesting sites } - if (vc.hasGenotypes()) { + //this maps allele to a count + ConcurrentMap alleleCounts = new ConcurrentHashMap(); - //this maps allele to a count - ConcurrentMap alleleCounts = new ConcurrentHashMap(); + int numHetsHere = 0; + float numGenosHere = 0; + int numIndsHere = 0; - int numHetsHere = 0; - float numGenosHere = 0; - int numIndsHere = 0; + for (Genotype genotype : vc.getGenotypes().values()) { + numIndsHere++; + if (!genotype.isNoCall()) { + //increment stats for heterozygosity + if (genotype.isHet()) { + numHetsHere++; + } - for (Genotype genotype : vc.getGenotypes().values()) { - numIndsHere++; - if (!genotype.isNoCall()) { - //increment stats for heterozygosity - if (genotype.isHet()) { - numHetsHere++; - } + numGenosHere++; + //increment stats for pairwise mismatches - numGenosHere++; - //increment stats for pairwise mismatches - - for (Allele allele : genotype.getAlleles()) { - if (allele.isNonNull() && allele.isCalled()) { - String alleleString = allele.toString(); - alleleCounts.putIfAbsent(alleleString, 0); - alleleCounts.put(alleleString, alleleCounts.get(alleleString) + 1); - } + for (Allele allele : genotype.getAlleles()) { + if (allele.isNonNull() && allele.isCalled()) { + String alleleString = allele.toString(); + alleleCounts.putIfAbsent(alleleString, 0); + alleleCounts.put(alleleString, alleleCounts.get(alleleString) + 1); } } } - if (numGenosHere > 0) { - //only if have one called genotype at least - this.numSites++; + } + if (numGenosHere > 0) { + //only if have one called genotype at least + this.numSites++; - this.totalHet += numHetsHere / numGenosHere; + this.totalHet += numHetsHere / numGenosHere; - //compute based on num sites - float harmonicFactor = 0; - for (int i = 1; i <= numIndsHere; i++) { - harmonicFactor += 1.0 / i; - } - this.thetaRegionNumSites += 1.0 / harmonicFactor; + //compute based on num sites + float harmonicFactor = 0; + for (int i = 1; i <= numIndsHere; i++) { + harmonicFactor += 1.0 / i; + } + this.thetaRegionNumSites += 1.0 / harmonicFactor; - //now compute pairwise mismatches - float numPairwise = 0; - float numDiffs = 0; - for (String allele1 : alleleCounts.keySet()) { - int allele1Count = alleleCounts.get(allele1); + //now compute pairwise mismatches + float numPairwise = 0; + float numDiffs = 0; + for (String allele1 : alleleCounts.keySet()) { + int allele1Count = alleleCounts.get(allele1); - for (String allele2 : alleleCounts.keySet()) { - if (allele1.compareTo(allele2) < 0) { - continue; - } - if (allele1 .compareTo(allele2) == 0) { - numPairwise += allele1Count * (allele1Count - 1) * .5; + for (String allele2 : alleleCounts.keySet()) { + if (allele1.compareTo(allele2) < 0) { + continue; + } + if (allele1 .compareTo(allele2) == 0) { + numPairwise += allele1Count * (allele1Count - 1) * .5; - } - else { - int allele2Count = alleleCounts.get(allele2); - numPairwise += allele1Count * allele2Count; - numDiffs += allele1Count * allele2Count; - } + } + else { + int allele2Count = alleleCounts.get(allele2); + numPairwise += allele1Count * allele2Count; + numDiffs += allele1Count * allele2Count; } } + } - if (numPairwise > 0) { - this.totalAvgDiffs += numDiffs / numPairwise; - } + if (numPairwise > 0) { + this.totalAvgDiffs += numDiffs / numPairwise; } } 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 be957abd7..1feb37e01 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 @@ -40,7 +40,7 @@ public class TiTvVariantEvaluator extends VariantEvaluator implements StandardEv } public void updateTiTv(VariantContext vc, boolean updateStandard) { - if (vc != null && vc.isSNP() && vc.isBiallelic()) { + if (vc != null && vc.isSNP() && vc.isBiallelic() && vc.isPolymorphic()) { if (VariantContextUtils.isTransition(vc)) { if (updateStandard) nTiInComp++; else nTi++; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java index 9c331b577..307b4f684 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java @@ -117,7 +117,8 @@ public class ValidationReport extends VariantEvaluator implements StandardEval { public SiteStatus calcSiteStatus(VariantContext vc) { if ( vc == null ) return SiteStatus.NO_CALL; if ( vc.isFiltered() ) return SiteStatus.FILTERED; - if ( ! vc.isVariant() ) return SiteStatus.MONO; + if ( vc.isMonomorphic() ) return SiteStatus.MONO; + if ( vc.hasGenotypes() ) return SiteStatus.POLY; // must be polymorphic if isMonomorphic was false and there are genotypes if ( vc.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) ) { int ac = 0; @@ -132,8 +133,6 @@ public class ValidationReport extends VariantEvaluator implements StandardEval { else ac = vc.getAttributeAsInt(VCFConstants.ALLELE_COUNT_KEY); return ac > 0 ? SiteStatus.POLY : SiteStatus.MONO; - } else if ( vc.hasGenotypes() ) { - return vc.isPolymorphic() ? SiteStatus.POLY : SiteStatus.MONO; } else { return TREAT_ALL_SITES_IN_EVAL_VCF_AS_CALLED ? SiteStatus.POLY : SiteStatus.NO_CALL; // we can't figure out what to do //return SiteStatus.NO_CALL; // we can't figure out what to do diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java index b6ad55b18..263227938 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java @@ -232,7 +232,7 @@ public class VariantQualityScore extends VariantEvaluator { public String update1(VariantContext eval, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { final String interesting = null; - if( eval != null && eval.isSNP() && eval.isBiallelic() ) { //BUGBUG: only counting biallelic sites (revisit what to do with triallelic sites) + if( eval != null && eval.isSNP() && eval.isBiallelic() && eval.isPolymorphic() ) { //BUGBUG: only counting biallelic sites (revisit what to do with triallelic sites) if( titvStats == null ) { titvStats = new TiTvStats(); } titvStats.incrValue(eval.getPhredScaledQual(), VariantContextUtils.isTransition(eval)); 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 3cc039141..92e7c6554 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 @@ -277,7 +277,7 @@ public class VariantEvalUtils { * @return a new VariantContext with just the requested samples */ public VariantContext getSubsetOfVariantContext(VariantContext vc, Collection sampleNames) { - VariantContext vcsub = vc.subContextFromGenotypes(vc.getGenotypes(sampleNames).values()); + VariantContext vcsub = vc.subContextFromGenotypes(vc.getGenotypes(sampleNames).values(), vc.getAlleles()); HashMap newAts = new HashMap(vcsub.getAttributes()); 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 3503a2353..7b6d13223 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 @@ -264,7 +264,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { @Test public void testTranches() { String extraArgs = "-T VariantEval -R "+ hg18Reference +" --eval " + validationDataLocation + "GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.optimized.vcf -o %s -EV TiTvVariantEvaluator -L chr1 -noEV -ST CpG -tf " + testDir + "tranches.6.txt"; - WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("984df6e94a546294fc7e0846cbac2dfe")); + WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("6af2b9959aa1778a5b712536de453952")); executeTestParallel("testTranches",spec); }