From 170d1ff7b677fddd2002a86f0bbca29da4b7f076 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Tue, 16 Aug 2011 14:17:46 -0400 Subject: [PATCH] Fix in UG for trying to call indels at IUPAC code bases when in EMIT_ALL_SITES mode --- .../gatk/walkers/genotyper/UnifiedGenotyperEngine.java | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index a10897172..1b72aae25 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -485,6 +485,9 @@ public class UnifiedGenotyperEngine { Map stratifiedContexts = null; + if ( !BaseUtils.isRegularBase( refContext.getBase() ) ) + return null; + if ( model == GenotypeLikelihoodsCalculationModel.Model.INDEL ) { if (UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) { @@ -499,6 +502,7 @@ public class UnifiedGenotyperEngine { stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup, UAC.ASSUME_SINGLE_SAMPLE); } else { + // todo - tmp will get rid of extended events so this wont be needed if (!rawContext.hasExtendedEventPileup()) return null; @@ -516,9 +520,6 @@ public class UnifiedGenotyperEngine { } } else if ( model == GenotypeLikelihoodsCalculationModel.Model.SNP ) { - if ( !BaseUtils.isRegularBase( refContext.getBase() ) ) - return null; - // stratify the AlignmentContext and cut by sample stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(rawContext.getBasePileup(), UAC.ASSUME_SINGLE_SAMPLE);