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();