From f6df8dea863e5216923f81108eb853bd9ecbcf8e Mon Sep 17 00:00:00 2001 From: peterjc Date: Mon, 26 Mar 2012 15:07:17 +0100 Subject: [PATCH] Include leading CIGAR P operators in 'samtools depad' --- padding.c | 3 +++ 1 file changed, 3 insertions(+) diff --git a/padding.c b/padding.c index 2b43275..e2afefb 100644 --- a/padding.c +++ b/padding.c @@ -92,6 +92,9 @@ int bam_pad2unpad(bamFile in, bamFile out) } unpad_seq(b, &q); if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[0]); + /* Include any pads if starts with an insert */ + for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k); + if (k) write_cigar(cigar2, n2, m2, bam_cigar_gen(k, BAM_CPAD)); /* Determine CIGAR operator for each base in the aligned read */ for (i = 0, k = b->core.pos; i < q.l; ++i, ++k) q.s[i] = q.s[i]? (r.s[k]? BAM_CMATCH : BAM_CINS) : (r.s[k]? BAM_CDEL : BAM_CPAD); -- 2.39.2