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Fix in UG for trying to call indels at IUPAC code bases when in EMIT_ALL_SITES mode

This commit is contained in:
Ryan Poplin 2011-08-16 14:17:46 -04:00
parent 9ddbfdcb9f
commit 170d1ff7b6
1 changed files with 4 additions and 3 deletions
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7
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -485,6 +485,9 @@ public class UnifiedGenotyperEngine {
Map<String, AlignmentContext> stratifiedContexts = null; Map<String, AlignmentContext> stratifiedContexts = null;
if ( !BaseUtils.isRegularBase( refContext.getBase() ) )
return null;
if ( model == GenotypeLikelihoodsCalculationModel.Model.INDEL ) { if ( model == GenotypeLikelihoodsCalculationModel.Model.INDEL ) {
if (UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) { if (UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) {
@ -499,6 +502,7 @@ public class UnifiedGenotyperEngine {
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup, UAC.ASSUME_SINGLE_SAMPLE); stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup, UAC.ASSUME_SINGLE_SAMPLE);
} else { } else {
// todo - tmp will get rid of extended events so this wont be needed // todo - tmp will get rid of extended events so this wont be needed
if (!rawContext.hasExtendedEventPileup()) if (!rawContext.hasExtendedEventPileup())
return null; return null;
@ -516,9 +520,6 @@ public class UnifiedGenotyperEngine {
} }
} else if ( model == GenotypeLikelihoodsCalculationModel.Model.SNP ) { } else if ( model == GenotypeLikelihoodsCalculationModel.Model.SNP ) {
if ( !BaseUtils.isRegularBase( refContext.getBase() ) )
return null;
// stratify the AlignmentContext and cut by sample // stratify the AlignmentContext and cut by sample
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(rawContext.getBasePileup(), UAC.ASSUME_SINGLE_SAMPLE); stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(rawContext.getBasePileup(), UAC.ASSUME_SINGLE_SAMPLE);