From 9cba1019c83167c1d56f7e0d2a4d45b7eee1bbec Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Thu, 8 Sep 2011 09:25:13 -0400 Subject: [PATCH] Another fix for genotype given alleles for indels. Expanding the indel integration tests to include multiallelics and indel records that overlap --- .../genotyper/IndelGenotypeLikelihoodsCalculationModel.java | 2 +- .../walkers/genotyper/UnifiedGenotyperIntegrationTest.java | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) 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 41b340058..07f02de57 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 @@ -321,7 +321,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood haplotypeMap.clear(); if (getAlleleListFromVCF) { - for( final VariantContext vc_input : tracker.getValues(UAC.alleles) ) { + for( final VariantContext vc_input : tracker.getValues(UAC.alleles, loc) ) { if( vc_input != null && allowableTypes.contains(vc_input.getType()) && ref.getLocus().getStart() == vc_input.getStart()) { 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 f0164b7c4..185880401 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 @@ -271,9 +271,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2); WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec( - baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation + - "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, - Arrays.asList("408d3aba4d094c067fc00a43992c2292")); + baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2.20101123.indels.sites.vcf -I " + validationDataLocation + + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,080,000", 1, + Arrays.asList("e66b7321e2ac91742ad3ef91040daafd")); executeTest("test MultiSample Pilot2 indels with complicated records", spec3); }