e28fc2164286ce39249b8dbf42469eae6726b08b,java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/modules/casecontrol/MateOtherContig.java,MateOtherContig,map,#ReadBackedPileup#,18

Before Change


        int tot = 0;
        int otherCon = 0;
        for ( PileupElement e : pileup ) {
            if ( e.getRead().getReadPairedFlag() ) {
                ++tot;
                if ( ! e.getRead().getMateReferenceIndex().equals(e.getRead().getReferenceIndex()) ) {
                    ++otherCon;

After Change


        int tot = 0;
        int otherCon = 0;
        for ( PileupElement e : pileup ) {
            if ( e.getRead().getReadPairedFlag() && e.getRead().getMappingQuality() >= MAPQ_THRESHOLD ) {
                ++tot;
                if ( ! e.getRead().getMateReferenceIndex().equals(e.getRead().getReferenceIndex()) ) {
                    ++otherCon;