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) {