From 7ed8b4ddb09d648b45df7e4958aedb1da990e1f8 Mon Sep 17 00:00:00 2001 From: carneiro Date: Wed, 4 May 2011 18:04:56 +0000 Subject: [PATCH] Making sure CalculateLikelihoodsAndGenotypes returns an empty variant context when 'EMIT_ALL_SITES' and 'GENOTYPE_GIVEN_ALLELES' are being used, now for indels too! git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5756 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index 2f4ae3e2c..095b51fe9 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -141,12 +141,12 @@ public class UnifiedGenotyperEngine { final GenotypeLikelihoodsCalculationModel.Model model = getCurrentGLModel( rawContext ); if( model == null ) { - return null; + return (UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES && UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ? generateEmptyContext(tracker, refContext, null, rawContext) : null); } Map stratifiedContexts = getFilteredAndStratifiedContexts(UAC, refContext, rawContext, model); if ( stratifiedContexts == null ) { - return (UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES && UAC.GenotypingMode != GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ? generateEmptyContext(tracker, refContext, stratifiedContexts, rawContext) : null); + return (UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES && UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ? generateEmptyContext(tracker, refContext, stratifiedContexts, rawContext) : null); } VariantContext vc = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.COMPLETE, null, true, model);