From 133a2bfbb2fecea980ed3764bd9d5953ddc19110 Mon Sep 17 00:00:00 2001
From: peterjc
Date: Thu, 22 Mar 2012 17:49:15 +0000
Subject: [PATCH] Support CIGAR X/= in depad
---
padding.c | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
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) {
--
2.39.2