From: peterjc <p.j.a.cock@googlemail.com>
Date: Mon, 26 Mar 2012 14:22:15 +0000 (+0100)
Subject: Tolerate CIGAR H operators in 'samtools depad'
X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=2594fb7e8055fefc08b37a14ad437aa9bafbe837

Tolerate CIGAR H operators in 'samtools depad'
---

diff --git a/padding.c b/padding.c
index e2afefb..a3008fc 100644
--- a/padding.c
+++ b/padding.c
@@ -41,6 +41,8 @@ static void unpad_seq(bam1_t *b, kstring_t *s)
 			for (i = 0; i < ol; ++i, ++j) s->s[s->l++] = bam1_seqi(seq, j);
 		} else if (op == BAM_CSOFT_CLIP) {
 			j += ol;
+		} else if (op == BAM_CHARD_CLIP) {
+			/* do nothing */
 		} else if (op == BAM_CDEL || op == BAM_CPAD) {
 			for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
                 } else {