222cd42ceb8e2162e6824f7f986d57ab9c1cfdb3,java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperEngine.java,UnifiedGenotyperEngine,calculateLikelihoods,#RefMetaDataTracker#ReferenceContext#AlignmentContext#,158

Before Change


     */
    public VariantContext calculateLikelihoods(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext) {
        Map<String, StratifiedAlignmentContext> stratifiedContexts = getFilteredAndStratifiedContexts(UAC, refContext, rawContext);
        return calculateLikelihoods(tracker, refContext, stratifiedContexts, StratifiedAlignmentContext.StratifiedContextType.COMPLETE);
    }

    private VariantContext calculateLikelihoods(RefMetaDataTracker tracker, ReferenceContext refContext, Map<String, StratifiedAlignmentContext> stratifiedContexts, StratifiedAlignmentContext.StratifiedContextType type) {

After Change


     */
    public VariantContext calculateLikelihoods(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext) {
        Map<String, StratifiedAlignmentContext> stratifiedContexts = getFilteredAndStratifiedContexts(UAC, refContext, rawContext);
        VariantContext vc = calculateLikelihoods(tracker, refContext, stratifiedContexts, StratifiedAlignmentContext.StratifiedContextType.COMPLETE);
        return GLsToPLs(vc);
    }

    private VariantContext calculateLikelihoods(RefMetaDataTracker tracker, ReferenceContext refContext, Map<String, StratifiedAlignmentContext> stratifiedContexts, StratifiedAlignmentContext.StratifiedContextType type) {