From: peterjc <p.j.a.cock@googlemail.com>
Date: Thu, 22 Mar 2012 17:49:15 +0000 (+0000)
Subject: Support CIGAR X/= in depad
X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=133a2bfbb2fecea980ed3764bd9d5953ddc19110

Support CIGAR X/= in depad
---

diff --git a/padding.c b/padding.c
index 17da758..4290485 100644
--- 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) {