int op, ol;
op = bam_cigar_op(cigar[k]);
ol = bam_cigar_oplen(cigar[k]);
- if (op == BAM_CMATCH) {
+ if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
for (i = 0; i < ol; ++i) s->s[s->l++] = bam1_seqi(seq, j);
++j;
} else if (op == BAM_CSOFT_CLIP) {