diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java index 072f81db9..1eba893fc 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java @@ -348,12 +348,14 @@ public class LikelihoodCalculationEngine { } } } + // add all filtered reads to the NO_CALL list because they weren't given any likelihoods for( final GATKSAMRecord read : perSampleFilteredReadList.get(sample.getKey()) ) { // only count the read if it overlaps the event, otherwise it is not added to the output read list at all if( callLoc.overlapsP(parser.createGenomeLoc(read)) ) { - for( final Allele a : call.getFirst().getAlleles() ) + for( final Allele a : call.getFirst().getAlleles() ) { likelihoodMap.add(read, a, 0.0); + } } } 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 e2ea47d9c..df088a4ad 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 @@ -349,7 +349,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1, - Arrays.asList("beee9457d7cea42006ac45400db5e873")); + Arrays.asList("f3ff7fe0f15f31eadd726c711d6bf3de")); executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2); }