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