ece694d0af6b384a816f818ebbd718eaff9d4ce4,java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java,MappingQualityZero,annotate,#RefMetaDataTracker#ReferenceContext#Map#VariantContext#,23
Before Change
int mq0 = 0;
for ( Map.Entry<String, StratifiedAlignmentContext> sample : stratifiedContexts.entrySet() ) {
ReadBackedPileup pileup = sample.getValue().getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup();
for (PileupElement p : pileup ) {
if ( p.getMappingQual() == 0 )
mq0++;
After Change
int mq0 = 0;
for ( Map.Entry<String, StratifiedAlignmentContext> sample : stratifiedContexts.entrySet() ) {
AlignmentContext context = sample.getValue().getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE);
ReadBackedPileup pileup = null;
if (context.hasExtendedEventPileup())
pileup = context.getExtendedEventPileup();
else if (context.hasBasePileup())
pileup = context.getBasePileup();
if (pileup != null) {
for (PileupElement p : pileup ) {
if ( p.getMappingQual() == 0 )
mq0++;