From 2594fb7e8055fefc08b37a14ad437aa9bafbe837 Mon Sep 17 00:00:00 2001 From: peterjc Date: Mon, 26 Mar 2012 15:22:15 +0100 Subject: [PATCH 1/1] Tolerate CIGAR H operators in 'samtools depad' --- padding.c | 2 ++ 1 file changed, 2 insertions(+) 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 { -- 2.39.2