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;
    }