Support CIGAR X/= in depad

diff --git a/padding.c b/padding.c
index 17da7582fdc3efd3775c9a16c7fa548c86809e40..4290485131756ef4a77a0e48b01b3933c464350c 100644 (file)
--- a/padding.c
+++ b/padding.c
@@ -37,7 +37,7 @@ static void unpad_seq(bam1_t *b, kstring_t *s)
                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) {