From: peterjc <p.j.a.cock@googlemail.com>
Date: Mon, 26 Mar 2012 13:23:37 +0000 (+0100)
Subject: Record actual sequence in unpad_seq (fixes apparently harmless bug)
X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=bb67db90fd5100502c29fbd96461b93f1ff20591

Record actual sequence in unpad_seq (fixes apparently harmless bug)
---

diff --git a/padding.c b/padding.c
index 6c8b31f..2b43275 100644
--- a/padding.c
+++ b/padding.c
@@ -38,8 +38,7 @@ static void unpad_seq(bam1_t *b, kstring_t *s)
 		op = bam_cigar_op(cigar[k]);
 		ol = bam_cigar_oplen(cigar[k]);
 		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;
+			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_CDEL || op == BAM_CPAD) {