diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java index 84a4a3120..cbf536e4f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java @@ -47,7 +47,7 @@ import java.util.Map; public class SampleList extends InfoFieldAnnotation { public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { - if ( vc.isMonomorphic() || !vc.hasGenotypes() ) + if ( vc.isMonomorphicInSamples() || !vc.hasGenotypes() ) return null; StringBuffer samples = new StringBuffer(); 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 088c4ddc4..b27bef265 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 @@ -260,7 +260,7 @@ public class ValidationAmplicons extends RodWalker { } } } else /* (mask != null && validate == null ) */ { - if ( ! mask.isSNP() && ! mask.isFiltered() && ( ! filterMonomorphic || ! mask.isMonomorphic() )) { + if ( ! mask.isSNP() && ! mask.isFiltered() && ( ! filterMonomorphic || ! mask.isMonomorphicInSamples() )) { logger.warn("Mask Variant Context on the following warning line is not a SNP. Currently we can only mask out SNPs. This probe will not be designed."); logger.warn(String.format("%s:%d-%d\t%s\t%s",mask.getChr(),mask.getStart(),mask.getEnd(),mask.isSimpleInsertion() ? "INS" : "DEL", Utils.join(",",mask.getAlleles()))); sequenceInvalid = true; @@ -281,7 +281,7 @@ public class ValidationAmplicons extends RodWalker { sequence.append('N'); indelCounter--; rawSequence.append(Character.toUpperCase((char)ref.getBase())); - } else if ( ! mask.isFiltered() && ( ! filterMonomorphic || ! mask.isMonomorphic() )){ + } else if ( ! mask.isFiltered() && ( ! filterMonomorphic || ! mask.isMonomorphicInSamples() )){ logger.debug("SNP in mask found at " + ref.getLocus().toString()); if ( lowerCaseSNPs ) { 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 9facb11b5..b3695921a 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 @@ -72,7 +72,7 @@ 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.isPolymorphic(); + boolean evalIsGood = eval != null && eval.isPolymorphicInSamples(); boolean compIsGood = comp != null && comp.isNotFiltered(); if (evalIsGood) nEvalVariants++; // count the number of eval 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 a134ef5aa..d8413573a 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 @@ -103,7 +103,7 @@ 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.isMonomorphic() ) { + if ( vc1.isMonomorphicInSamples() ) { nRefLoci++; } else { switch (vc1.getType()) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/G1KPhaseITable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/G1KPhaseITable.java index 417e340b8..ff8f6307c 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/G1KPhaseITable.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/G1KPhaseITable.java @@ -30,7 +30,6 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.VariantContext; @@ -103,7 +102,7 @@ public class G1KPhaseITable extends VariantEvaluator { } public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - if ( eval == null || eval.isMonomorphic() ) return null; + if ( eval == null || eval.isMonomorphicInSamples() ) return null; switch (eval.getType()) { case SNP: 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 ffe7c185f..ccec9af12 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 @@ -91,7 +91,7 @@ public class IndelLengthHistogram extends VariantEvaluator { public String update1(VariantContext vc1, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - if ( vc1.isIndel() && vc1.isPolymorphic() ) { + if ( vc1.isIndel() && vc1.isPolymorphicInSamples() ) { if ( ! vc1.isBiallelic() ) { //veWalker.getLogger().warn("[IndelLengthHistogram] Non-biallelic indel at "+ref.getLocus()+" ignored."); 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 f70e6c2de..87b453ae3 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 @@ -8,11 +8,9 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType; import org.broadinstitute.sting.utils.IndelUtils; -import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.ArrayList; -import java.util.HashMap; /* * Copyright (c) 2010 The Broad Institute @@ -270,7 +268,7 @@ public class IndelStatistics extends VariantEvaluator { public String update1(VariantContext eval, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - if (eval != null && eval.isPolymorphic()) { + if (eval != null && eval.isPolymorphicInSamples()) { 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 2d0163206..27e8e7c86 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 @@ -118,7 +118,7 @@ public class SimpleMetricsByAC extends VariantEvaluator implements StandardEval int ac = -1; if ( eval.hasGenotypes() ) - ac = eval.getChromosomeCount(eval.getAlternateAllele(0)); + ac = eval.getCalledChrCount(eval.getAlternateAllele(0)); else if ( eval.hasAttribute("AC") ) { ac = eval.getAttributeAsInt("AC", -1); } @@ -166,7 +166,7 @@ public class SimpleMetricsByAC extends VariantEvaluator implements StandardEval } } - if ( eval.isSNP() && eval.isBiallelic() && eval.isPolymorphic() && metrics != null ) { + if ( eval.isSNP() && eval.isBiallelic() && eval.isPolymorphicInSamples() && 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 e1069d2d2..bb7843361 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 @@ -37,7 +37,7 @@ public class ThetaVariantEvaluator extends VariantEvaluator { } public String update1(VariantContext vc, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - if (vc == null || !vc.isSNP() || !vc.hasGenotypes() || vc.isMonomorphic()) { + if (vc == null || !vc.isSNP() || !vc.hasGenotypes() || vc.isMonomorphicInSamples()) { return null; //no interesting sites } 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 9b6e145e6..17d7171b8 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() && vc.isPolymorphic()) { + if (vc != null && vc.isSNP() && vc.isBiallelic() && vc.isPolymorphicInSamples()) { 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 3b4967cad..1a0591e9d 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 @@ -11,7 +11,6 @@ import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.Collection; -import java.util.Set; /** * The Broad Institute @@ -118,8 +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.isMonomorphic() ) return SiteStatus.MONO; - if ( vc.hasGenotypes() ) return SiteStatus.POLY; // must be polymorphic if isMonomorphic was false and there are genotypes + if ( vc.isMonomorphicInSamples() ) return SiteStatus.MONO; + if ( vc.hasGenotypes() ) return SiteStatus.POLY; // must be polymorphic if isMonomorphicInSamples was false and there are genotypes if ( vc.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) ) { int ac = 0; 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 263227938..ce9e45c9b 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 @@ -232,14 +232,14 @@ 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() && eval.isPolymorphic() ) { //BUGBUG: only counting biallelic sites (revisit what to do with triallelic sites) + if( eval != null && eval.isSNP() && eval.isBiallelic() && eval.isPolymorphicInSamples() ) { //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)); if( alleleCountStats == null ) { alleleCountStats = new AlleleCountStats(); } int alternateAlleleCount = 0; for (final Allele a : eval.getAlternateAlleles()) { - alternateAlleleCount += eval.getChromosomeCount(a); + alternateAlleleCount += eval.getCalledChrCount(a); } alleleCountStats.incrValue(eval.getPhredScaledQual(), alternateAlleleCount); } 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 c7bea93b2..2f342e120 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 @@ -47,7 +47,7 @@ public class AlleleCount extends VariantStratifier { AC = eval.getAttributeAsInt("AC", 0); } else if ( eval.isVariant() ) { for (Allele allele : eval.getAlternateAlleles()) - AC = Math.max(AC, eval.getChromosomeCount(allele)); + AC = Math.max(AC, eval.getCalledChrCount(allele)); } else // by default, the site is considered monomorphic AC = 0; 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 e04bfab76..a2782fe34 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 @@ -26,7 +26,6 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration; import org.apache.log4j.Logger; -import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.utils.GenomeLoc; @@ -38,7 +37,6 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.io.PrintStream; import java.util.ArrayList; import java.util.Collections; -import java.util.HashMap; import java.util.List; /** @@ -284,7 +282,7 @@ public class VariantDataManager { private boolean isValidVariant( final VariantContext evalVC, final VariantContext trainVC, final boolean TRUST_ALL_POLYMORPHIC) { return trainVC != null && trainVC.isNotFiltered() && trainVC.isVariant() && ((evalVC.isSNP() && trainVC.isSNP()) || ((evalVC.isIndel()||evalVC.isMixed()) && (trainVC.isIndel()||trainVC.isMixed()))) && - (TRUST_ALL_POLYMORPHIC || !trainVC.hasGenotypes() || trainVC.isPolymorphic()); + (TRUST_ALL_POLYMORPHIC || !trainVC.hasGenotypes() || trainVC.isPolymorphicInSamples()); } public void writeOutRecalibrationTable( final PrintStream RECAL_FILE ) { 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 be9a193d3..9c24360c5 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 @@ -488,7 +488,7 @@ public class SelectVariants extends RodWalker { if (outMVFile != null) 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.getChromosomeCount(vc.getAlternateAllele(0)), + vc.getReference().getDisplayString(), vc.getAlternateAllele(0).getDisplayString(), vc.getCalledChrCount(vc.getAlternateAllele(0)), mv.getSampleMom(), mv.getSampleDad(), mv.getSampleChild(), vc.getGenotype(mv.getSampleMom()).toBriefString(), vc.getGenotype(mv.getSampleMom()).getLikelihoods().getAsString(), vc.getGenotype(mv.getSampleDad()).toBriefString(), vc.getGenotype(mv.getSampleMom()).getLikelihoods().getAsString(), @@ -520,7 +520,7 @@ public class SelectVariants extends RodWalker { continue; VariantContext sub = subsetRecord(vc, samples); - if ( (sub.isPolymorphic() || !EXCLUDE_NON_VARIANTS) && (!sub.isFiltered() || !EXCLUDE_FILTERED) ) { + if ( (sub.isPolymorphicInSamples() || !EXCLUDE_NON_VARIANTS) && (!sub.isFiltered() || !EXCLUDE_FILTERED) ) { for ( VariantContextUtils.JexlVCMatchExp jexl : jexls ) { if ( !VariantContextUtils.match(sub, jexl) ) { return 0; @@ -677,11 +677,11 @@ public class SelectVariants extends RodWalker { if (KEEP_ORIGINAL_CHR_COUNTS) { if ( sub.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) ) - builder.attribute("AC_Orig",sub.getAttribute(VCFConstants.ALLELE_COUNT_KEY)); + builder.attribute("AC_Orig", sub.getAttribute(VCFConstants.ALLELE_COUNT_KEY)); if ( sub.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY) ) - builder.attribute("AF_Orig",sub.getAttribute(VCFConstants.ALLELE_FREQUENCY_KEY)); + builder.attribute("AF_Orig", sub.getAttribute(VCFConstants.ALLELE_FREQUENCY_KEY)); if ( sub.hasAttribute(VCFConstants.ALLELE_NUMBER_KEY) ) - builder.attribute("AN_Orig",sub.getAttribute(VCFConstants.ALLELE_NUMBER_KEY)); + builder.attribute("AN_Orig", sub.getAttribute(VCFConstants.ALLELE_NUMBER_KEY)); } Map attributes = new HashMap(builder.make().getAttributes()); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java index 79bbea29d..31aa8963b 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java @@ -233,17 +233,17 @@ public class VariantValidationAssessor extends RodWalker numRecords++; // add the info fields - builder.attribute("NoCallPct", String.format("%.1f", 100.0*noCallProp)); - builder.attribute("HomRefPct", String.format("%.1f", 100.0*homRefProp)); - builder.attribute("HomVarPct", String.format("%.1f", 100.0*homVarProp)); - builder.attribute("HetPct", String.format("%.1f", 100.0*hetProp)); + builder.attribute("NoCallPct", String.format("%.1f", 100.0 * noCallProp)); + builder.attribute("HomRefPct", String.format("%.1f", 100.0 * homRefProp)); + builder.attribute("HomVarPct", String.format("%.1f", 100.0 * homVarProp)); + builder.attribute("HetPct", String.format("%.1f", 100.0 * hetProp)); builder.attribute("HW", String.format("%.2f", hwScore)); Collection altAlleles = vContext.getAlternateAlleles(); - int altAlleleCount = altAlleles.size() == 0 ? 0 : vContext.getChromosomeCount(altAlleles.iterator().next()); + int altAlleleCount = altAlleles.size() == 0 ? 0 : vContext.getCalledChrCount(altAlleles.iterator().next()); if ( !isViolation && altAlleleCount > 0 ) numTrueVariants++; builder.attribute(VCFConstants.ALLELE_COUNT_KEY, String.format("%d", altAlleleCount)); - builder.attribute(VCFConstants.ALLELE_NUMBER_KEY, String.format("%d", vContext.getChromosomeCount())); + builder.attribute(VCFConstants.ALLELE_NUMBER_KEY, String.format("%d", vContext.getCalledChrCount())); return builder.make(); } 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 ba138a9da..e6e4aa8ce 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 @@ -98,7 +98,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec, headerStrings.add(line); Set metaData = new TreeSet(); - Set auxTags = new LinkedHashSet(); + Set sampleNames = new LinkedHashSet(); // iterate over all the passed in strings for ( String str : headerStrings ) { if ( !str.startsWith(VCFHeader.METADATA_INDICATOR) ) { @@ -126,9 +126,9 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec, } while ( arrayIndex < strings.length ) - auxTags.add(strings[arrayIndex++]); + sampleNames.add(strings[arrayIndex++]); - if ( sawFormatTag && auxTags.size() == 0 ) + if ( sawFormatTag && sampleNames.size() == 0 ) throw new UserException.MalformedVCFHeader("The FORMAT field was provided but there is no genotype/sample data"); } else { @@ -152,7 +152,8 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec, } } - header = new VCFHeader(metaData, auxTags); + header = new VCFHeader(metaData, sampleNames); + header.buildVCFReaderMaps(new ArrayList(sampleNames)); return header; } 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 53b3d5fd4..42c224fe9 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 @@ -151,7 +151,7 @@ public class VCFCodec extends AbstractVCFCodec { int nParts = ParsingUtils.split(str, genotypeParts, VCFConstants.FIELD_SEPARATOR_CHAR); - GenotypesContext genotypes = GenotypesContext.create(nParts); + ArrayList genotypes = new ArrayList(nParts); // get the format keys int nGTKeys = ParsingUtils.split(genotypeParts[0], genotypeKeyArray, VCFConstants.GENOTYPE_FIELD_SEPARATOR_CHAR); @@ -215,7 +215,7 @@ public class VCFCodec extends AbstractVCFCodec { } } - return genotypes; + return GenotypesContext.create(genotypes, header.sampleNameToOffset, header.sampleNamesInOrder); } @Override 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 66e11bc1e..5c5df15ab 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 @@ -2,6 +2,7 @@ package org.broadinstitute.sting.utils.codecs.vcf; import org.broad.tribble.util.ParsingUtils; +import org.broadinstitute.sting.utils.variantcontext.Genotype; import java.util.*; @@ -38,6 +39,10 @@ public class VCFHeader { // were the input samples sorted originally (or are we sorting them)? private boolean samplesWereAlreadySorted = true; + // cache for efficient conversion of VCF -> VariantContext + protected ArrayList sampleNamesInOrder = null; + protected HashMap sampleNameToOffset = null; + /** * create a VCF header, given a list of meta data and auxillary tags @@ -69,6 +74,27 @@ public class VCFHeader { samplesWereAlreadySorted = ParsingUtils.isSorted(genotypeSampleNames); } + /** + * Tell this VCF header to use pre-calculated sample name ordering and the + * sample name -> offset map. This assumes that all VariantContext created + * using this header (i.e., read by the VCFCodec) will have genotypes + * occurring in the same order + * + */ + + protected void buildVCFReaderMaps(List genotypeSampleNamesInAppearenceOrder) { + sampleNamesInOrder = new ArrayList(genotypeSampleNamesInAppearenceOrder.size()); + sampleNameToOffset = new HashMap(genotypeSampleNamesInAppearenceOrder.size()); + + int i = 0; + for ( final String name : genotypeSampleNamesInAppearenceOrder ) { + sampleNamesInOrder.add(name); + sampleNameToOffset.put(name, i++); + } + Collections.sort(sampleNamesInOrder); + } + + /** * Adds a header line to the header metadata. * diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypesContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypesContext.java index 77a02874d..671066d24 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypesContext.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypesContext.java @@ -85,6 +85,12 @@ public class GenotypesContext implements List { return new GenotypesContext(nGenotypes, false); } + public static final GenotypesContext create(final ArrayList genotypes, + final Map sampleNameToOffset, + final List sampleNamesInOrder) { + return new GenotypesContext(genotypes, sampleNameToOffset, sampleNamesInOrder, false); + } + public static final GenotypesContext create(final ArrayList genotypes) { return genotypes == null ? NO_GENOTYPES : new GenotypesContext(genotypes, false); } @@ -101,6 +107,8 @@ public class GenotypesContext implements List { return toCopy == null ? NO_GENOTYPES : create(new ArrayList(toCopy)); } + + // public static final GenotypeMap create(final Collection genotypes) { // if ( genotypes == null ) // return null; // todo -- really should return an empty map 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 455a9b997..9875680b0 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java @@ -131,17 +131,17 @@ import java.util.*; * * 
  * vc.hasGenotypes()
- * vc.isMonomorphic()
- * vc.isPolymorphic()
+ * vc.isMonomorphicInSamples()
+ * vc.isPolymorphicInSamples()
  * vc.getSamples().size()
  *
  * vc.getGenotypes()
  * vc.getGenotypes().get("g1")
  * vc.hasGenotype("g1")
  *
- * vc.getChromosomeCount()
- * vc.getChromosomeCount(Aref)
- * vc.getChromosomeCount(T)
+ * vc.getCalledChrCount()
+ * vc.getCalledChrCount(Aref)
+ * vc.getCalledChrCount(T)
  *
* * === NO_CALL alleles === @@ -374,72 +374,17 @@ public class VariantContext implements Feature { // to enable tribble intergrati // // --------------------------------------------------------------------------------------------------------- -// /** -// * Returns a context identical to this (i.e., filter, qual are all the same) but containing only the Genotype -// * genotype and alleles in genotype. This is the right way to test if a single genotype is actually -// * variant or not. -// * -// * @param genotype genotype -// * @return vc subcontext -// * @deprecated replaced by {@link #subContextFromSample(String)} -// */ -// public VariantContext subContextFromGenotypes(Genotype genotype) { -// return subContextFromGenotypes(Arrays.asList(genotype)); -// } -// -// -// /** -// * Returns a context identical to this (i.e., filter, qual are all the same) but containing only the Genotypes -// * genotypes and alleles in these genotypes. This is the right way to test if a single genotype is actually -// * variant or not. -// * -// * @param genotypes genotypes -// * @return vc subcontext -// * @deprecated replaced by {@link #subContextFromSamples(java.util.Collection)} -// */ -// public VariantContext subContextFromGenotypes(Collection genotypes) { -// return subContextFromGenotypes(genotypes, allelesOfGenotypes(genotypes)) ; -// } -// -// /** -// * Returns a context identical to this (i.e., filter, qual are all the same) but containing only the Genotypes -// * genotypes. Also, the resulting variant context will contain the alleles provided, not only those found in genotypes -// * -// * @param genotypes genotypes -// * @param alleles the set of allele segregating alleles at this site. Must include those in genotypes, but may be more -// * @return vc subcontext -// * @deprecated replaced by {@link #subContextFromSamples(java.util.Collection, java.util.Collection)} -// */ -// @Deprecated -// public VariantContext subContextFromGenotypes(Collection genotypes, Collection alleles) { -// return new VariantContext(getSource(), contig, start, stop, alleles, -// GenotypeCollection.create(genotypes), -// getNegLog10PError(), -// filtersWereApplied() ? getFilters() : null, -// getAttributes(), -// getReferenceBaseForIndel()); -// } - public VariantContext subContextFromSamples(Set sampleNames, Collection alleles) { loadGenotypes(); - GenotypesContext newGenotypes = genotypes.subsetToSamples(sampleNames); - return new VariantContext(getSource(), getID(), contig, start, stop, alleles, - newGenotypes, - getNegLog10PError(), - filtersWereApplied() ? getFilters() : null, - getAttributes(), - getReferenceBaseForIndel()); + VariantContextBuilder builder = new VariantContextBuilder(this); + return builder.genotypes(genotypes.subsetToSamples(sampleNames)).make(); } public VariantContext subContextFromSamples(Set sampleNames) { loadGenotypes(); + VariantContextBuilder builder = new VariantContextBuilder(this); GenotypesContext newGenotypes = genotypes.subsetToSamples(sampleNames); - return new VariantContext(getSource(), getID(), contig, start, stop, allelesOfGenotypes(newGenotypes), - newGenotypes, - getNegLog10PError(), - filtersWereApplied() ? getFilters() : null, - getAttributes(), - getReferenceBaseForIndel()); + return builder.genotypes(newGenotypes).alleles(allelesOfGenotypes(newGenotypes)).make(); } public VariantContext subContextFromSample(String sampleName) { @@ -451,12 +396,12 @@ public class VariantContext implements Feature { // to enable tribble intergrati * @param genotypes genotypes * @return allele set */ - private Set allelesOfGenotypes(Collection genotypes) { - Set alleles = new HashSet(); + private final Set allelesOfGenotypes(Collection genotypes) { + final Set alleles = new HashSet(); boolean addedref = false; - for ( Genotype g : genotypes ) { - for ( Allele a : g.getAlleles() ) { + for ( final Genotype g : genotypes ) { + for ( final Allele a : g.getAlleles() ) { addedref = addedref || a.isReference(); if ( a.isCalled() ) alleles.add(a); @@ -938,7 +883,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati * * @return chromosome count */ - public int getChromosomeCount() { + public int getCalledChrCount() { int n = 0; for ( final Genotype g : getGenotypes() ) { @@ -955,7 +900,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati * @param a allele * @return chromosome count */ - public int getChromosomeCount(Allele a) { + public int getCalledChrCount(Allele a) { int n = 0; for ( final Genotype g : getGenotypes() ) { @@ -971,9 +916,9 @@ public class VariantContext implements Feature { // to enable tribble intergrati * * @return true if it's monomorphic */ - public boolean isMonomorphic() { + public boolean isMonomorphicInSamples() { if ( monomorphic == null ) - monomorphic = ! isVariant() || (hasGenotypes() && getChromosomeCount(getReference()) == getChromosomeCount()); + monomorphic = ! isVariant() || (hasGenotypes() && getCalledChrCount(getReference()) == getCalledChrCount()); return monomorphic; } @@ -983,8 +928,8 @@ public class VariantContext implements Feature { // to enable tribble intergrati * * @return true if it's polymorphic */ - public boolean isPolymorphic() { - return ! isMonomorphic(); + public boolean isPolymorphicInSamples() { + return ! isMonomorphicInSamples(); } private void calculateGenotypeCounts() { @@ -1119,19 +1064,28 @@ public class VariantContext implements Feature { // to enable tribble intergrati } public void validateChromosomeCounts() { - Map observedAttrs = calculateChromosomeCounts(); - // AN if ( hasAttribute(VCFConstants.ALLELE_NUMBER_KEY) ) { int reportedAN = Integer.valueOf(getAttribute(VCFConstants.ALLELE_NUMBER_KEY).toString()); - int observedAN = (Integer)observedAttrs.get(VCFConstants.ALLELE_NUMBER_KEY); + int observedAN = getCalledChrCount(); if ( reportedAN != observedAN ) throw new TribbleException.InternalCodecException(String.format("the Allele Number (AN) tag is incorrect for the record at position %s:%d, %d vs. %d", getChr(), getStart(), reportedAN, observedAN)); } // AC if ( hasAttribute(VCFConstants.ALLELE_COUNT_KEY) ) { - List observedACs = (List)observedAttrs.get(VCFConstants.ALLELE_COUNT_KEY); + ArrayList observedACs = new ArrayList(); + + // if there are alternate alleles, record the relevant tags + if ( getAlternateAlleles().size() > 0 ) { + for ( Allele allele : getAlternateAlleles() ) { + observedACs.add(getCalledChrCount(allele)); + } + } + else { // otherwise, set them to 0 + observedACs.add(0); + } + if ( getAttribute(VCFConstants.ALLELE_COUNT_KEY) instanceof List ) { Collections.sort(observedACs); List reportedACs = (List)getAttribute(VCFConstants.ALLELE_COUNT_KEY); @@ -1152,31 +1106,6 @@ public class VariantContext implements Feature { // to enable tribble intergrati } } - private Map calculateChromosomeCounts() { - Map attributes = new HashMap(); - - attributes.put(VCFConstants.ALLELE_NUMBER_KEY, getChromosomeCount()); - ArrayList alleleFreqs = new ArrayList(); - ArrayList alleleCounts = new ArrayList(); - - // if there are alternate alleles, record the relevant tags - if ( getAlternateAlleles().size() > 0 ) { - for ( Allele allele : getAlternateAlleles() ) { - alleleCounts.add(getChromosomeCount(allele)); - alleleFreqs.add((double)getChromosomeCount(allele) / (double)getChromosomeCount()); - } - } - // otherwise, set them to 0 - else { - alleleCounts.add(0); - alleleFreqs.add(0.0); - } - - attributes.put(VCFConstants.ALLELE_COUNT_KEY, alleleCounts); - attributes.put(VCFConstants.ALLELE_FREQUENCY_KEY, alleleFreqs); - return attributes; - } - // --------------------------------------------------------------------------------------------------------- // // validation: the normal validation routines are called automatically upon creation of the VC @@ -1399,7 +1328,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati Allele best = null; int maxAC1 = 0; for (Allele a:this.getAlternateAlleles()) { - int ac = this.getChromosomeCount(a); + int ac = this.getCalledChrCount(a); if (ac >=maxAC1) { maxAC1 = ac; best = a; 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 d9057ea8f..972f70689 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java @@ -63,7 +63,7 @@ public class VariantContextUtils { */ public static void calculateChromosomeCounts(VariantContext vc, Map attributes, boolean removeStaleValues) { // if everyone is a no-call, remove the old attributes if requested - if ( vc.getChromosomeCount() == 0 && removeStaleValues ) { + if ( vc.getCalledChrCount() == 0 && removeStaleValues ) { if ( attributes.containsKey(VCFConstants.ALLELE_COUNT_KEY) ) attributes.remove(VCFConstants.ALLELE_COUNT_KEY); if ( attributes.containsKey(VCFConstants.ALLELE_FREQUENCY_KEY) ) @@ -74,15 +74,15 @@ public class VariantContextUtils { } if ( vc.hasGenotypes() ) { - attributes.put(VCFConstants.ALLELE_NUMBER_KEY, vc.getChromosomeCount()); + attributes.put(VCFConstants.ALLELE_NUMBER_KEY, vc.getCalledChrCount()); // if there are alternate alleles, record the relevant tags if ( vc.getAlternateAlleles().size() > 0 ) { ArrayList alleleFreqs = new ArrayList(); ArrayList alleleCounts = new ArrayList(); - double totalChromosomes = (double)vc.getChromosomeCount(); + double totalChromosomes = (double)vc.getCalledChrCount(); for ( Allele allele : vc.getAlternateAlleles() ) { - int altChromosomes = vc.getChromosomeCount(allele); + int altChromosomes = vc.getCalledChrCount(allele); alleleCounts.add(altChromosomes); String freq = String.format(makePrecisionFormatStringFromDenominatorValue(totalChromosomes), ((double)altChromosomes / totalChromosomes)); alleleFreqs.add(freq); @@ -320,7 +320,7 @@ public class VariantContextUtils { } public static double computeHardyWeinbergPvalue(VariantContext vc) { - if ( vc.getChromosomeCount() == 0 ) + if ( vc.getCalledChrCount() == 0 ) return 0.0; return HardyWeinbergCalculation.hwCalculate(vc.getHomRefCount(), vc.getHetCount(), vc.getHomVarCount()); } 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 38c4f84ab..200f3859b 100755 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java @@ -12,7 +12,6 @@ import org.testng.annotations.DataProvider; import org.testng.annotations.Test; import org.testng.Assert; -import java.lang.reflect.Array; import java.util.*; @@ -260,12 +259,12 @@ public class VariantContextUnitTest extends BaseTest { Assert.assertTrue(vc.isSNP()); Assert.assertEquals(vc.getNAlleles(), 2); Assert.assertTrue(vc.hasGenotypes()); - Assert.assertFalse(vc.isMonomorphic()); - Assert.assertTrue(vc.isPolymorphic()); + Assert.assertFalse(vc.isMonomorphicInSamples()); + Assert.assertTrue(vc.isPolymorphicInSamples()); Assert.assertEquals(vc.getGenotype("foo"), g); - Assert.assertEquals(vc.getChromosomeCount(), 1); // we only have 1 called chromosomes, we exclude the NO_CALL one isn't called - Assert.assertEquals(vc.getChromosomeCount(Aref), 0); - Assert.assertEquals(vc.getChromosomeCount(C), 1); + Assert.assertEquals(vc.getCalledChrCount(), 1); // we only have 1 called chromosomes, we exclude the NO_CALL one isn't called + Assert.assertEquals(vc.getCalledChrCount(Aref), 0); + Assert.assertEquals(vc.getCalledChrCount(C), 1); Assert.assertFalse(vc.getGenotype("foo").isHet()); Assert.assertFalse(vc.getGenotype("foo").isHom()); Assert.assertFalse(vc.getGenotype("foo").isNoCall()); @@ -332,8 +331,8 @@ public class VariantContextUnitTest extends BaseTest { .genotypes(g1, g2, g3).make(); Assert.assertTrue(vc.hasGenotypes()); - Assert.assertFalse(vc.isMonomorphic()); - Assert.assertTrue(vc.isPolymorphic()); + Assert.assertFalse(vc.isMonomorphicInSamples()); + Assert.assertTrue(vc.isPolymorphicInSamples()); Assert.assertEquals(vc.getSampleNames().size(), 3); Assert.assertEquals(vc.getGenotypes().size(), 3); @@ -352,9 +351,9 @@ public class VariantContextUnitTest extends BaseTest { Assert.assertFalse(vc.hasGenotype("at")); Assert.assertFalse(vc.hasGenotype("tt")); - Assert.assertEquals(vc.getChromosomeCount(), 6); - Assert.assertEquals(vc.getChromosomeCount(Aref), 3); - Assert.assertEquals(vc.getChromosomeCount(T), 3); + Assert.assertEquals(vc.getCalledChrCount(), 6); + Assert.assertEquals(vc.getCalledChrCount(Aref), 3); + Assert.assertEquals(vc.getCalledChrCount(T), 3); } @Test @@ -372,17 +371,17 @@ public class VariantContextUnitTest extends BaseTest { .genotypes(g1, g2, g3, g4, g5, g6).make(); Assert.assertTrue(vc.hasGenotypes()); - Assert.assertFalse(vc.isMonomorphic()); - Assert.assertTrue(vc.isPolymorphic()); + Assert.assertFalse(vc.isMonomorphicInSamples()); + Assert.assertTrue(vc.isPolymorphicInSamples()); Assert.assertEquals(vc.getGenotypes().size(), 6); Assert.assertEquals(3, vc.getGenotypes(Arrays.asList("AA", "Td", "dd")).size()); - Assert.assertEquals(10, vc.getChromosomeCount()); - Assert.assertEquals(3, vc.getChromosomeCount(Aref)); - Assert.assertEquals(4, vc.getChromosomeCount(T)); - Assert.assertEquals(3, vc.getChromosomeCount(del)); - Assert.assertEquals(2, vc.getChromosomeCount(Allele.NO_CALL)); + 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(2, vc.getCalledChrCount(Allele.NO_CALL)); } @Test @@ -398,14 +397,14 @@ public class VariantContextUnitTest extends BaseTest { .genotypes(g1, g2, g3).make(); Assert.assertTrue(vc.hasGenotypes()); - Assert.assertTrue(vc.isMonomorphic()); - Assert.assertFalse(vc.isPolymorphic()); + Assert.assertTrue(vc.isMonomorphicInSamples()); + Assert.assertFalse(vc.isPolymorphicInSamples()); Assert.assertEquals(vc.getGenotypes().size(), 3); - Assert.assertEquals(4, vc.getChromosomeCount()); - Assert.assertEquals(4, vc.getChromosomeCount(Aref)); - Assert.assertEquals(0, vc.getChromosomeCount(T)); - Assert.assertEquals(2, vc.getChromosomeCount(Allele.NO_CALL)); + Assert.assertEquals(4, vc.getCalledChrCount()); + Assert.assertEquals(4, vc.getCalledChrCount(Aref)); + Assert.assertEquals(0, vc.getCalledChrCount(T)); + Assert.assertEquals(2, vc.getCalledChrCount(Allele.NO_CALL)); } } @@ -452,12 +451,12 @@ public class VariantContextUnitTest extends BaseTest { VariantContext vc14 = vc.subContextFromSamples(new HashSet(Arrays.asList(g1.getSampleName(), g4.getSampleName()))); VariantContext vc5 = vc.subContextFromSamples(new HashSet(Arrays.asList(g5.getSampleName()))); - Assert.assertTrue(vc12.isPolymorphic()); - Assert.assertTrue(vc23.isPolymorphic()); - Assert.assertTrue(vc1.isMonomorphic()); - Assert.assertTrue(vc4.isMonomorphic()); - Assert.assertTrue(vc14.isMonomorphic()); - Assert.assertTrue(vc5.isPolymorphic()); + 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()); @@ -484,12 +483,12 @@ public class VariantContextUnitTest extends BaseTest { Assert.assertTrue(vc5.isVariant()); Assert.assertTrue(vc5.isBiallelic()); - Assert.assertEquals(3, vc12.getChromosomeCount(Aref)); - Assert.assertEquals(1, vc23.getChromosomeCount(Aref)); - Assert.assertEquals(2, vc1.getChromosomeCount(Aref)); - Assert.assertEquals(0, vc4.getChromosomeCount(Aref)); - Assert.assertEquals(2, vc14.getChromosomeCount(Aref)); - Assert.assertEquals(0, vc5.getChromosomeCount(Aref)); + 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() { @@ -827,14 +826,14 @@ public class VariantContextUnitTest extends BaseTest { VariantContext vc = new VariantContextBuilder("genotypes", snpLoc, snpLocStart, snpLocStop, Arrays.asList(Aref, T)).genotypes(gc).make(); Assert.assertEquals(vc.getNSamples(), nSamples); if ( nSamples > 0 ) { - Assert.assertEquals(vc.isPolymorphic(), nT > 0); - Assert.assertEquals(vc.isMonomorphic(), nT == 0); + Assert.assertEquals(vc.isPolymorphicInSamples(), nT > 0); + Assert.assertEquals(vc.isMonomorphicInSamples(), nT == 0); } - Assert.assertEquals(vc.getChromosomeCount(), nA + nT); + Assert.assertEquals(vc.getCalledChrCount(), nA + nT); - Assert.assertEquals(vc.getChromosomeCount(Allele.NO_CALL), nNoCallAlleles); - Assert.assertEquals(vc.getChromosomeCount(Aref), nA); - Assert.assertEquals(vc.getChromosomeCount(T), nT); + Assert.assertEquals(vc.getCalledChrCount(Allele.NO_CALL), nNoCallAlleles); + Assert.assertEquals(vc.getCalledChrCount(Aref), nA); + Assert.assertEquals(vc.getCalledChrCount(T), nT); Assert.assertEquals(vc.getNoCallCount(), nNoCall); Assert.assertEquals(vc.getHomRefCount(), nHomRef);