Include leading CIGAR P operators in 'samtools depad'

diff --git a/padding.c b/padding.c
index 2b432756d29805b4fe102d376d8ac1810eb38c20..e2afefb4840cd8acca35f07f200501b87990051a 100644 (file)
--- 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);