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