Should update POS on unmapped reads in 'samtools depad'

Previously unmapped reads with a POS entry (e.g. those reads with
a mate which was mapped) were not being updated.

This has passed my testing with some non-trivial de novo MIRA 3.9
assemblies, coupled with the new 'samtools index' BIN verification.

diff --git a/padding.c b/padding.c
index 71dfc25957bf38214e899cbd92b653bd729f3373..3ee8087d4d054768f0f7d317e24acd208ac18683 100644 (file)
--- a/padding.c
+++ b/padding.c
@@ -195,7 +195,6 @@ int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
                        write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
                        replace_cigar(b, n2, cigar2);
                        posmap = update_posmap(posmap, r);
-                       b->core.bin = bam_reg2bin(0, bam_calend(&b->core, bam1_cigar(b)));
                } else if (b->core.n_cigar > 0) {
                        int i, k, op;
                        if (b->core.tid < 0) {
@@ -272,41 +271,43 @@ int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
                                if (cigar2[i]) cigar2[k++] = cigar2[i];
                        n2 = k;
                        replace_cigar(b, n2, cigar2);
-                       b->core.pos = posmap[b->core.pos];
-                       b->core.bin = bam_reg2bin(b->core.pos, bam_calend(&b->core.pos, bam1_cigar(b)));
-                       if (b->core.mtid < 0 || b->core.mpos < 0) {
-                               /* Nice case, no mate to worry about*/
-                               // fprintf(stderr, "[depad] Read '%s' mate not mapped\n", bam1_qname(b));
-                               /* TODO - Warning if FLAG says mate should be mapped? */
-                               /* Clean up funny input where mate position is given but mate reference is missing: */
-                               b->core.mtid = -1;
-                               b->core.mpos = -1;
-                       } else if (b->core.mtid == b->core.tid) {
-                               /* Nice case, same reference */
-                               // fprintf(stderr, "[depad] Read '%s' mate mapped to same ref\n", bam1_qname(b));
-                               b->core.mpos = posmap[b->core.mpos];
-                       } else {
-                               /* Nasty case, Must load alternative posmap */
-                               // fprintf(stderr, "[depad] Loading reference '%s' temporarily\n", h->target_name[b->core.mtid]);
-                               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);
+               }
+               /* Even unmapped reads can have a POS value, e.g. if their mate was mapped */
+               if (b->core.pos != -1) b->core.pos = posmap[b->core.pos];
+               if (b->core.mtid < 0 || b->core.mpos < 0) {
+                       /* Nice case, no mate to worry about*/
+                       // fprintf(stderr, "[depad] Read '%s' mate not mapped\n", bam1_qname(b));
+                       /* TODO - Warning if FLAG says mate should be mapped? */
+                       /* Clean up funny input where mate position is given but mate reference is missing: */
+                       b->core.mtid = -1;
+                       b->core.mpos = -1;
+               } else if (b->core.mtid == b->core.tid) {
+                       /* Nice case, same reference */
+                       // fprintf(stderr, "[depad] Read '%s' mate mapped to same ref\n", bam1_qname(b));
+                       b->core.mpos = posmap[b->core.mpos];
+               } else {
+                       /* Nasty case, Must load alternative posmap */
+                       // fprintf(stderr, "[depad] Loading reference '%s' temporarily\n", h->target_name[b->core.mtid]);
+                       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);
                }
+               /* Most reads will have been moved so safest to always recalculate the BIN value */
+               b->core.bin = bam_reg2bin(b->core.pos, bam_calend(&b->core, bam1_cigar(b)));
                samwrite(out, b);
        }
        if (read_ret < -1) {