Cope with trailing CIGAR H (or S and H) in 'samtools depad'

diff --git a/padding.c b/padding.c
index 43ff56e5bb33ef24e27a1016319e8105887b0a2a..f839c3bc57d37fc153880fb12a17230dcdb8b0f1 100644 (file)
--- 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)