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Small change for Mauricio so that the correct metrics get output when running in GENOTYPE_GIVEN_ALLELES mode. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5327 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-02-27 06:08:32 +00:00
parent 146756de79
commit 54facb2c51
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -159,7 +159,7 @@ public class UnifiedGenotyperEngine {
public VariantCallContext calculateLikelihoodsAndGenotypes(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext) { public VariantCallContext calculateLikelihoodsAndGenotypes(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext) {
Map<String, StratifiedAlignmentContext> stratifiedContexts = getFilteredAndStratifiedContexts(UAC, refContext, rawContext); Map<String, StratifiedAlignmentContext> stratifiedContexts = getFilteredAndStratifiedContexts(UAC, refContext, rawContext);
VariantContext vc = calculateLikelihoods(tracker, refContext, stratifiedContexts, StratifiedAlignmentContext.StratifiedContextType.COMPLETE, null); VariantContext vc = calculateLikelihoods(tracker, refContext, stratifiedContexts, StratifiedAlignmentContext.StratifiedContextType.COMPLETE, null);
if ( vc == null ) if ( vc == null || !vc.hasGenotypes() )
return null; return null;
VariantCallContext vcc = calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc); VariantCallContext vcc = calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc);
@ -195,7 +195,7 @@ public class UnifiedGenotyperEngine {
Allele refAllele = glcm.get().getLikelihoods(tracker, refContext, stratifiedContexts, type, genotypePriors, GLs, alternateAlleleToUse); Allele refAllele = glcm.get().getLikelihoods(tracker, refContext, stratifiedContexts, type, genotypePriors, GLs, alternateAlleleToUse);
if (refAllele != null) if ( refAllele != null )
return createVariantContextFromLikelihoods(refContext, refAllele, GLs); return createVariantContextFromLikelihoods(refContext, refAllele, GLs);
else else
return null; return null;