diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java index 221d623de..dd3c70a18 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java @@ -10,7 +10,7 @@ import java.util.ArrayList; public class AlleleBalance extends StandardVariantAnnotation { - public Pair annotate(ReferenceContext ref, ReadBackedPileup pileup, List genotypes) { + public Pair annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List genotypes) { if ( genotypes.size() == 0 ) return null; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java index 77ffd714e..e48e3ec0f 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java @@ -4,13 +4,14 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.Pair; import org.broadinstitute.sting.utils.ReadBackedPileup; import org.broadinstitute.sting.utils.genotype.Genotype; +import org.broadinstitute.sting.utils.genotype.Variation; import java.util.List; public class DepthOfCoverage extends StandardVariantAnnotation { - public Pair annotate(ReferenceContext ref, ReadBackedPileup pileup, List genotypes) { + public Pair annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List genotypes) { int depth = pileup.getReads().size(); return new Pair("DoC", String.format("%d", depth)); } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java index 338f63a51..3c3ca7ca2 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java @@ -5,6 +5,7 @@ import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.Pair; import org.broadinstitute.sting.utils.ReadBackedPileup; import org.broadinstitute.sting.utils.genotype.Genotype; +import org.broadinstitute.sting.utils.genotype.Variation; import net.sf.samtools.SAMRecord; import cern.jet.math.Arithmetic; @@ -13,7 +14,7 @@ import java.util.List; public class FisherStrand extends StandardVariantAnnotation { - public Pair annotate(ReferenceContext ref, ReadBackedPileup pileup, List genotypes) { + public Pair annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List genotypes) { // this test doesn't make sense for homs Genotype genotype = VariantAnnotator.getFirstHetVariant(genotypes); diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java index 6bb34b7de..b809ef8cb 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java @@ -5,25 +5,19 @@ import org.broadinstitute.sting.utils.Pair; import org.broadinstitute.sting.utils.ReadBackedPileup; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.genotype.Genotype; +import org.broadinstitute.sting.utils.genotype.Variation; import java.util.List; public class HomopolymerRun extends StandardVariantAnnotation { - public Pair annotate(ReferenceContext ref, ReadBackedPileup pileup, List genotypes) { + public Pair annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List genotypes) { - Genotype genotype = VariantAnnotator.getFirstVariant(ref.getBase(), genotypes); - if ( genotype == null ) + if ( !variation.isBiallelic() || !variation.isSNP() ) return null; - final String genotypeStr = genotype.getBases().toUpperCase(); - if ( genotypeStr.length() != 2 ) - return null; - - char altAllele = (genotypeStr.charAt(0) != ref.getBase() ? genotypeStr.charAt(0) : genotypeStr.charAt(1)); - - int run = computeHomopolymerRun(altAllele, ref); + int run = computeHomopolymerRun(variation.getAlternativeBaseForSNP(), ref); return new Pair("HomopolymerRun", String.format("%d", run)); } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java index 3b31bac47..3af98798d 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java @@ -4,6 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.Pair; import org.broadinstitute.sting.utils.ReadBackedPileup; import org.broadinstitute.sting.utils.genotype.Genotype; +import org.broadinstitute.sting.utils.genotype.Variation; import net.sf.samtools.SAMRecord; import java.util.List; @@ -11,7 +12,7 @@ import java.util.List; public class MappingQualityZero extends StandardVariantAnnotation { - public Pair annotate(ReferenceContext ref, ReadBackedPileup pileup, List genotypes) { + public Pair annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List genotypes) { List reads = pileup.getReads(); int MQ0Count = 0; for (int i=0; i < reads.size(); i++) { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/OnOffGenotype.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/OnOffGenotype.java deleted file mode 100755 index 801dac6cd..000000000 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/OnOffGenotype.java +++ /dev/null @@ -1,135 +0,0 @@ -package org.broadinstitute.sting.gatk.walkers.annotator; - -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.*; -import org.broadinstitute.sting.utils.genotype.Genotype; -import org.broadinstitute.sting.utils.genotype.ReadBacked; -import org.broadinstitute.sting.utils.genotype.PosteriorsBacked; -import org.broadinstitute.sting.utils.genotype.DiploidGenotype; - -import java.util.List; -import java.util.ArrayList; - -public class OnOffGenotype extends StandardVariantAnnotation { - - public Pair annotate(ReferenceContext ref, ReadBackedPileup pileup, List genotypes) { - - if ( genotypes.size() == 0 ) - return null; - - double ratio; - Genotype g = genotypes.get(0); - if ( g instanceof ReadBacked && g instanceof PosteriorsBacked) { - Pair weightedBalance = computeWeightedBalance(ref.getBase(), genotypes, pileup); - if ( weightedBalance.second == 0 ) - return null; - ratio = weightedBalance.first; - } else { - Genotype genotype = VariantAnnotator.getFirstVariant(ref.getBase(), genotypes); - if ( genotype == null ) - return null; - - final String genotypeStr = genotype.getBases().toUpperCase(); - if ( genotypeStr.length() != 2 ) - return null; - - final String bases = pileup.getBasesAsString().toUpperCase(); - if ( bases.length() == 0 ) - return null; - - ratio = computeSingleBalance(genotypeStr, bases); - } - - return new Pair("OnOffGenotype", String.format("%.2f", ratio)); - } - - private double computeSingleBalance(final String genotypeStr, final String bases) { - - int on = 0, off = 0; - for ( char base : BaseUtils.BASES ) { - int count = BasicPileup.countBase(base, bases); - if ( Utils.countOccurrences(base, genotypeStr) > 0 ) - on += count; - else - off += count; - } - - double ratio = (double)on / (double)(on + off); - return ratio; - } - - private Pair computeWeightedBalance(char ref, List genotypes, ReadBackedPileup pileup) { - - ArrayList onOffBalances = new ArrayList(); - ArrayList weights = new ArrayList(); - - // accumulate ratios and weights - for ( Genotype g : genotypes ) { - - if ( !(g instanceof ReadBacked) || !(g instanceof PosteriorsBacked) ) - continue; - - final String genotypeStr = g.getBases().toUpperCase(); - if ( genotypeStr.length() != 2 ) - continue; - - DiploidGenotype bestGenotype = DiploidGenotype.unorderedValueOf(genotypeStr); - - // we care only about non-ref calls - if ( bestGenotype.isHomRef(ref) ) - continue; - - char a = genotypeStr.charAt(0); - char b = genotypeStr.charAt(1); - - // get the base counts at this pileup (minus deletions) - ReadBackedPileup myPileup = ((ReadBacked)g).getPileup(); - - // if the pileup is null, we'll just have to use the full pileup (it's better than nothing) - if ( myPileup == null ) - myPileup = pileup; - - int[] counts = myPileup.getBasePileupAsCounts(); - int onCount = counts[BaseUtils.simpleBaseToBaseIndex(a)]; - if ( a != b ) - onCount += counts[BaseUtils.simpleBaseToBaseIndex(b)]; - int totalCount = 0; - for (int i = 0; i < counts.length; i++) - totalCount += counts[i]; - - // sanity check - if ( totalCount == 0 ) - continue; - - double[] posteriors = ((PosteriorsBacked)g).getPosteriors(); - posteriors = MathUtils.normalizeFromLog10(posteriors); - double weight = posteriors[bestGenotype.ordinal()]; - - // sanity check - if ( MathUtils.compareDoubles(weight, 0.0) == 0 ) - continue; - - weights.add(weight); - onOffBalances.add((double)onCount / (double)totalCount); - } - - double ratio = 0.0; - - if ( weights.size() > 0 ) { - // normalize the weights - double sum = 0.0; - for (int i = 0; i < weights.size(); i++) - sum += weights.get(i); - for (int i = 0; i < weights.size(); i++) - weights.set(i, weights.get(i) / sum); - - // calculate total weighted ratios - for (int i = 0; i < weights.size(); i++) - ratio += weights.get(i) * onOffBalances.get(i); - } - - return new Pair(ratio, weights.size()); - } - - public boolean useZeroQualityReads() { return false; } -} diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/PrimaryBaseSecondaryBaseSymmetry.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/PrimaryBaseSecondaryBaseSymmetry.java index 2f653eec6..fb42106f9 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/PrimaryBaseSecondaryBaseSymmetry.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/PrimaryBaseSecondaryBaseSymmetry.java @@ -4,6 +4,7 @@ import org.broadinstitute.sting.utils.Pair; import org.broadinstitute.sting.utils.ReadBackedPileup; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.genotype.Genotype; +import org.broadinstitute.sting.utils.genotype.Variation; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.apache.log4j.Logger; @@ -34,7 +35,7 @@ public class PrimaryBaseSecondaryBaseSymmetry implements VariantAnnotation{ public boolean useZeroQualityReads() { return USE_ZERO_QUALITY_READS; } - public Pair annotate(ReferenceContext ref, ReadBackedPileup pileup, List genotypes) { + public Pair annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List genotypes) { Pair refSecondBasePair = getProportionOfReferenceSecondBasesThatSupportAlt(ref, pileup, genotypes); Pair nonrefPrimaryBasePair = getProportionOfPrimaryNonrefBasesThatSupportAlt(ref, pileup, genotypes); if ( refSecondBasePair == null || nonrefPrimaryBasePair == null ) { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java index ba1df8824..4ea995c55 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java @@ -5,6 +5,7 @@ import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.Pair; import org.broadinstitute.sting.utils.ReadBackedPileup; import org.broadinstitute.sting.utils.genotype.Genotype; +import org.broadinstitute.sting.utils.genotype.Variation; import net.sf.samtools.SAMRecord; import java.util.List; @@ -12,7 +13,7 @@ import java.util.List; public class RMSMappingQuality extends StandardVariantAnnotation { - public Pair annotate(ReferenceContext ref, ReadBackedPileup pileup, List genotypes) { + public Pair annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List genotypes) { List reads = pileup.getReads(); int[] qualities = new int[reads.size()]; for (int i=0; i < reads.size(); i++) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ResidualQuality.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ResidualQuality.java index dbda3c2c6..3bfd666d4 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ResidualQuality.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ResidualQuality.java @@ -4,6 +4,7 @@ import org.broadinstitute.sting.utils.Pair; import org.broadinstitute.sting.utils.ReadBackedPileup; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.genotype.Genotype; +import org.broadinstitute.sting.utils.genotype.Variation; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import java.util.List; @@ -21,7 +22,7 @@ public class ResidualQuality implements VariantAnnotation{ public boolean useZeroQualityReads() { return true; } // for robustness - public Pair annotate( ReferenceContext ref, ReadBackedPileup p, List genotypes) { + public Pair annotate( ReferenceContext ref, ReadBackedPileup p, Variation variation, List genotypes) { Character snp = getSNPChar(ref, genotypes); if ( snp == null ) { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java index 02d3ce84b..c807cbec3 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java @@ -5,6 +5,7 @@ import org.broadinstitute.sting.utils.ReadBackedPileup; import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.genotype.Genotype; +import org.broadinstitute.sting.utils.genotype.Variation; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import java.util.List; @@ -26,7 +27,7 @@ public class SecondBaseSkew implements VariantAnnotation{ public boolean useZeroQualityReads() { return USE_ZERO_QUALITY_READS; } - public Pair annotate(ReferenceContext ref, ReadBackedPileup pileup, List genotypes) { + public Pair annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List genotypes) { double chi_square; Pair depthProp = getSecondaryPileupNonrefEstimator(pileup,genotypes); if ( depthProp == null ) { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java index 80dcb36fa..e879ac947 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java @@ -4,19 +4,20 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.Pair; import org.broadinstitute.sting.utils.ReadBackedPileup; import org.broadinstitute.sting.utils.genotype.Genotype; +import org.broadinstitute.sting.utils.genotype.Variation; import java.util.List; public class SpanningDeletions extends StandardVariantAnnotation { - public Pair annotate(ReferenceContext ref, ReadBackedPileup pileup, List genotypes) { + public Pair annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List genotypes) { int deletions = 0; for (Integer offset : pileup.getOffsets() ) { if ( offset == -1 ) deletions++; } - return new Pair("SpanningDeletions", String.format("%d", deletions)); + return new Pair("SpanningDeletionFraction", String.format("%.2f", (double)deletions/(double)pileup.getReads().size())); } public boolean useZeroQualityReads() { return false; } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotation.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotation.java index 8146c4a82..cc00c41fc 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotation.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotation.java @@ -4,12 +4,13 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.Pair; import org.broadinstitute.sting.utils.ReadBackedPileup; import org.broadinstitute.sting.utils.genotype.Genotype; +import org.broadinstitute.sting.utils.genotype.Variation; import java.util.List; public interface VariantAnnotation { - public Pair annotate(ReferenceContext ref, ReadBackedPileup pileup, List genotypes); + public Pair annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List genotypes); public boolean useZeroQualityReads(); } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java index 3ea563229..6a1c37354 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java @@ -169,7 +169,7 @@ public class VariantAnnotator extends RodWalker { variant instanceof VariantBackedByGenotype ) { final List genotypes = ((VariantBackedByGenotype)variant).getGenotypes(); if ( genotypes != null ) - annotations = getAnnotations(ref, context, genotypes, requestedAnnotations); + annotations = getAnnotations(ref, context, variant, genotypes, requestedAnnotations); } writeVCF(tracker, ref, context, variant, annotations); @@ -177,13 +177,13 @@ public class VariantAnnotator extends RodWalker { return 1; } - public static Map getAnnotations(ReferenceContext ref, AlignmentContext context, List genotypes) { + public static Map getAnnotations(ReferenceContext ref, AlignmentContext context, Variation variation, List genotypes) { if ( standardAnnotations == null ) determineAllAnnotations(); - return getAnnotations(ref, context, genotypes, standardAnnotations.values()); + return getAnnotations(ref, context, variation, genotypes, standardAnnotations.values()); } - public static Map getAnnotations(ReferenceContext ref, AlignmentContext context, List genotypes, Collection annotations) { + public static Map getAnnotations(ReferenceContext ref, AlignmentContext context, Variation variation, List genotypes, Collection annotations) { // set up the pileup for the full collection of reads at this position ReadBackedPileup fullPileup = new ReadBackedPileup(ref.getBase(), context); @@ -208,7 +208,7 @@ public class VariantAnnotator extends RodWalker { HashMap results = new HashMap(); for ( VariantAnnotation annotator : annotations) { - Pair annot = annotator.annotate(ref, (annotator.useZeroQualityReads() ? fullPileup : MQ0freePileup), genotypes); + Pair annot = annotator.annotate(ref, (annotator.useZeroQualityReads() ? fullPileup : MQ0freePileup), variation, genotypes); if ( annot != null ) { // System.out.println("Annotating: First="+annot.getFirst()+" Second="+annot.getSecond()); results.put(annot.first, annot.second); diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java index 9a6f7c03b..1eab5838b 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java @@ -175,7 +175,7 @@ public class UnifiedGenotyper extends LocusWalker, GenotypeL // annotate the call, if possible if ( call != null && call.second != null && call.second instanceof ArbitraryFieldsBacked ) { - Map annotations = VariantAnnotator.getAnnotations(refContext, fullContext, call.first); + Map annotations = VariantAnnotator.getAnnotations(refContext, fullContext, call.second, call.first); ((ArbitraryFieldsBacked)call.second).setFields(annotations); } diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java index 3939d534c..592793c3e 100644 --- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java @@ -124,7 +124,7 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter { params.setLocations(locusdata.getLocation(), locusdata.getReference().charAt(0)); // if there is no genotype data, we'll also need to set an alternate allele - if ( locusdata.isSNP() && locusdata.isBiallelic() ) + if ( locusdata.isBiallelic() && locusdata.isSNP() ) params.addAlternateBase(new VCFGenotypeEncoding(locusdata.getAlternateAlleleList().get(0))); } else { params.setLocations(genotypes.get(0).getLocation(), genotypes.get(0).getReference()); diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java index 46fb9cccb..3a875febd 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -66,7 +66,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testHasAnnotsAsking1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -all -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("3b54731a929134410f167630ec434310")); + Arrays.asList("aa4fd832eab85123b97c7961c9c8402a")); executeTest("test file has annotations, asking for annotations, #1", spec); } @@ -74,7 +74,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testHasAnnotsAsking2() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -all -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample3.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, - Arrays.asList("c713d6d6cf922eab4150737f51f13abc")); + Arrays.asList("1f757921997fb5db79e2c4a79082e6d1")); executeTest("test file has annotations, asking for annotations, #2", spec); } @@ -98,7 +98,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoAnnotsAsking1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -all -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2empty.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("0feb1dd8aae945ce5f05c1156acadd3c")); + Arrays.asList("ad3945cab44444d3b1c0bd35307814f7")); executeTest("test file doesn't have annotations, asking for annotations, #1", spec); } @@ -106,7 +106,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoAnnotsAsking2() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -all -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample3empty.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, - Arrays.asList("b15b965af6d204cbb2926f59f68d987c")); + Arrays.asList("417917556d3a0f7da0eb3830e6b33c71")); executeTest("test file doesn't have annotations, asking for annotations, #2", spec); } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index dc1c703c9..278c478e7 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -47,7 +47,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultiSamplePilot1PointEM() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,400-10,024,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1, - Arrays.asList("fbb3ae6e835df5cf9b99dae5bf1fa8e5")); + Arrays.asList("90072e7f935357695f8f48c40ff6e7a4")); executeTest("testMultiSamplePilot1 - Point Estimate EM", spec); } @@ -55,7 +55,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultiSamplePilot2PointEM() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,010,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1, - Arrays.asList("98495e6f75a63558996ed45f7a1f062a")); + Arrays.asList("72bcbd0786bb94803d1ad867becf12e2")); executeTest("testMultiSamplePilot2 - Point Estimate EM", spec); } @@ -68,7 +68,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testPooled1() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,000-10,024,000 -bm empirical -gm POOLED -ps 60 -confidence 30", 1, - Arrays.asList("80fcd214108b4f4145ae585e5f119460")); + Arrays.asList("cdbda4a455f11f75fa666e9317139f22")); executeTest("testPooled1", spec); } @@ -81,7 +81,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultiSamplePilot1Joint() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,022,000-10,025,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1, - Arrays.asList("e1a206a49982f7db5c3f4b65aa910b3a")); + Arrays.asList("415f4a276005cad7fea0a8fcc3b8c3b5")); executeTest("testMultiSamplePilot1 - Joint Estimate", spec); } @@ -89,7 +89,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultiSamplePilot2Joint() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,050,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1, - Arrays.asList("7eb10aec21497da727eeb67bb5c5a743")); + Arrays.asList("8673c7dbe8dc4e93726706bd9276afc3")); executeTest("testMultiSamplePilot2 - Joint Estimate", spec); } @@ -97,7 +97,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testSingleSamplePilot2Joint() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1, - Arrays.asList("0cd57b2b6272202db0eca45376fdb01d")); + Arrays.asList("3d9bcf0f5525014f06b68fa006ef3fa3")); executeTest("testSingleSamplePilot2 - Joint Estimate", spec); }