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++;