X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=padding.c;h=e2afefb4840cd8acca35f07f200501b87990051a;hb=f6df8dea863e5216923f81108eb853bd9ecbcf8e;hp=2b432756d29805b4fe102d376d8ac1810eb38c20;hpb=bb67db90fd5100502c29fbd96461b93f1ff20591;p=samtools.git

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);