222cd42ceb8e2162e6824f7f986d57ab9c1cfdb3,java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperEngine.java,UnifiedGenotyperEngine,calculateLikelihoodsAndGenotypes,#RefMetaDataTracker#ReferenceContext#AlignmentContext#,144
Before Change
public VariantCallContext calculateLikelihoodsAndGenotypes(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext) {
Map<String, StratifiedAlignmentContext> stratifiedContexts = getFilteredAndStratifiedContexts(UAC, refContext, rawContext);
VariantContext vc = calculateLikelihoods(tracker, refContext, stratifiedContexts, StratifiedAlignmentContext.StratifiedContextType.COMPLETE);
return vc == null ? null : calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc);
}
/**
After Change
if ( vc == null )
return null;
VariantCallContext vcc = calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc);
vcc.vc = GLsToPLs(vcc.vc);
return vcc;
}