X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=padding.c;h=43ff56e5bb33ef24e27a1016319e8105887b0a2a;hb=ccbf51856ab09dd5cb841326a25364dd470cf03c;hp=a3008fc54a531093200dd1b61960bf040a48cee8;hpb=2594fb7e8055fefc08b37a14ad437aa9bafbe837;p=samtools.git

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));