From 73272534935626214df3584e6287c3f652f10f32 Mon Sep 17 00:00:00 2001 From: peterjc Date: Mon, 26 Mar 2012 15:35:44 +0100 Subject: [PATCH] Cope with trailing CIGAR H (or S and H) in 'samtools depad' --- padding.c | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/padding.c b/padding.c index 43ff56e..f839c3b 100644 --- a/padding.c +++ b/padding.c @@ -96,7 +96,9 @@ int bam_pad2unpad(bamFile in, bamFile out) 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]); + if (b->core.n_cigar > 2 && 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); @@ -113,6 +115,12 @@ int bam_pad2unpad(bamFile in, bamFile out) } write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op)); if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]); + if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CHARD_CLIP) { + if (b->core.n_cigar > 2 && bam_cigar_op(cigar[b->core.n_cigar-2]) == BAM_CSOFT_CLIP) { + write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-2]); + } + write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]); + } /* Remove redundant P operators between M operators, e.g. 5M2P10M -> 15M */ for (i = 2; i < n2; ++i) if (bam_cigar_op(cigar2[i]) == BAM_CMATCH && bam_cigar_op(cigar2[i-1]) == BAM_CPAD && bam_cigar_op(cigar2[i-2]) == BAM_CMATCH) -- 2.39.2