From ccbf51856ab09dd5cb841326a25364dd470cf03c Mon Sep 17 00:00:00 2001 From: peterjc Date: Mon, 26 Mar 2012 15:28:49 +0100 Subject: [PATCH] Cope with leading CIGAR H (or H and S) in 'samtools depad' --- padding.c | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/padding.c b/padding.c index a3008fc..43ff56e 100644 --- a/padding.c +++ b/padding.c @@ -94,6 +94,10 @@ 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]); + if (bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) { + write_cigar(cigar2, n2, m2, cigar[0]); + if (bam_cigar_op(cigar[1]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[1]); + } /* 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)); -- 2.39.2