bb92e31118cd0342077ce1ef29d20fcca11cca58,java/src/org/broadinstitute/sting/utils/AlignmentUtils.java,AlignmentUtils,mismatchesInRefWindow,#PileupElement#ReferenceContext#boolean#,179

Before Change



        int mismatches = 0;

        GenomeLoc window = ref.getWindow();
        char[] refBases = ref.getBases();
        byte[] readBases = p.getRead().getReadBases();
        Cigar c = p.getRead().getCigar();

        int readIndex = 0;
        int currentPos = p.getRead().getAlignmentStart();
        int refIndex = Math.max(0, currentPos - (int)window.getStart());

        for (int i = 0 ; i < c.numCigarElements() ; i++) {
            CigarElement ce = c.getCigarElement(i);

After Change



        int mismatches = 0;

        int windowStart = (int)ref.getWindow().getStart();
        int windowStop = (int)ref.getWindow().getStop();
        char[] refBases = ref.getBases();
        byte[] readBases = p.getRead().getReadBases();