for (k = 0; k < c->n_cigar; ++k) {
int op = cigar[k] & BAM_CIGAR_MASK;
int l = cigar[k] >> BAM_CIGAR_SHIFT;
for (k = 0; k < c->n_cigar; ++k) {
int op = cigar[k] & BAM_CIGAR_MASK;
int l = cigar[k] >> BAM_CIGAR_SHIFT;
for (j = 0; j < l; ++j)
if (x + j >= left && x + j < right)
cns[x+j-left] += (bam1_seqi(seq, y+j) == ref0[x+j-left])? 1 : 0x10000;
for (j = 0; j < l; ++j)
if (x + j >= left && x + j < right)
cns[x+j-left] += (bam1_seqi(seq, y+j) == ref0[x+j-left])? 1 : 0x10000;