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First round of critical fixes to indel genotyper (more to come tomorrow): 

a) Avoid complete crash of caller that broke due to a recent refactoring by someone who must not be named <cough>EB<cough>... an integration test to avoid this in the future coming soon.
b) Fixed up strand bias computation for indels





git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4779 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel 2010-12-03 02:48:09 +00:00
parent c7dbf66d41
commit da6a07ad3b
2 changed files with 6 additions and 2 deletions
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3
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DindelGenotypeLikelihoodsCalculationModel.java
View File

@ -88,7 +88,8 @@ public class DindelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoo
if (!vc.isIndel()) if (!vc.isIndel())
return null; return null;
if (sitesVisited.contains(new Integer(vc.getStart()))) if (sitesVisited.contains(new Integer(vc.getStart())) &&
contextType.equals(StratifiedAlignmentContext.StratifiedContextType.COMPLETE))
return null; return null;
sitesVisited.add(new Integer(vc.getStart())); sitesVisited.add(new Integer(vc.getStart()));

3
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -177,7 +177,10 @@ public class UnifiedGenotyperEngine {
Map<String, BiallelicGenotypeLikelihoods> GLs = new HashMap<String, BiallelicGenotypeLikelihoods>(); Map<String, BiallelicGenotypeLikelihoods> GLs = new HashMap<String, BiallelicGenotypeLikelihoods>();
Allele refAllele = glcm.get().getLikelihoods(tracker, refContext, stratifiedContexts, type, genotypePriors, GLs); Allele refAllele = glcm.get().getLikelihoods(tracker, refContext, stratifiedContexts, type, genotypePriors, GLs);
if (refAllele != null)
return createVariantContextFromLikelihoods(refContext, refAllele, GLs); return createVariantContextFromLikelihoods(refContext, refAllele, GLs);
else
return null;
} }
private VariantContext createVariantContextFromLikelihoods(ReferenceContext refContext, Allele refAllele, Map<String, BiallelicGenotypeLikelihoods> GLs) { private VariantContext createVariantContextFromLikelihoods(ReferenceContext refContext, Allele refAllele, Map<String, BiallelicGenotypeLikelihoods> GLs) {