First attempt at updating MPOS in 'samtools depad'

diff --git a/padding.c b/padding.c
index 88945e2ca5c54c1a592a45899358996ddd810ece..ad8bf5c480d97642dd433ac740059b1d6e45e1e5 100644 (file)
--- a/padding.c
+++ b/padding.c
@@ -271,6 +271,31 @@ int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
                        n2 = k;
                        replace_cigar(b, n2, cigar2);
                        b->core.pos = posmap[b->core.pos];
+                       if (b->core.mpos < 0) {
+                               /* Nice case, no mate to worry about*/
+                       } else if (b->core.mtid == b->core.tid) {
+                               /* Nice case, same reference */
+                               b->core.mpos = posmap[b->core.mpos];
+                       } else {
+                               /* Nasty case, Must load alternative posmap */
+                               if (!fai) {
+                                       fprintf(stderr, "[depad] ERROR: Needed reference %s sequence for mate (and no FASTA file)\n", h->target_name[b->core.mtid]);
+                                       return -1;
+                               }
+                               /* Temporarily load the other reference sequence */
+                               if (load_unpadded_ref(fai, h->target_name[b->core.mtid], h->target_len[b->core.mtid], &r)) {
+                                       fprintf(stderr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", h->target_name[b->core.mtid]);
+                                       return -1;
+                               }
+                               posmap = update_posmap(posmap, r);
+                               b->core.mpos = posmap[b->core.mpos];
+                               /* Restore the reference and posmap*/
+                               if (load_unpadded_ref(fai, h->target_name[b->core.tid], h->target_len[b->core.tid], &r)) {
+                                       fprintf(stderr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", h->target_name[b->core.tid]);
+                                       return -1;
+                               }
+                               posmap = update_posmap(posmap, r);
+                       }
                }
                samwrite(out, b);
        }