Check current reference sequence matches RNAME in samtools depad

diff --git a/padding.c b/padding.c
index 4290485131756ef4a77a0e48b01b3933c464350c..ad68728b28761d114c99ef0ebcbad339102d99b9 100644 (file)
--- a/padding.c
+++ b/padding.c
@@ -45,7 +45,7 @@ static void unpad_seq(bam1_t *b, kstring_t *s)
                } else if (op == BAM_CDEL) {
                        for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
                 } else {
-                       fprintf(stderr, "[unpad_seq] Didn't expect CIGAR op %c in %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
+                       fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
                         assert(-1);
                }
        }
@@ -56,6 +56,7 @@ int bam_pad2unpad(bamFile in, bamFile out)
        bam_header_t *h;
        bam1_t *b;
        kstring_t r, q;
+        int r_tid = -1;
        uint32_t *cigar2 = 0;
        int n2 = 0, m2 = 0, *posmap = 0;
 
@@ -68,6 +69,10 @@ int bam_pad2unpad(bamFile in, bamFile out)
                n2 = 0;
                if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam1_qname(b), h->target_name[b->core.tid]) == 0) {
                        int i, k;
+                       /*
+                       fprintf(stderr, "[depad] Found embedded reference %s\n", bam1_qname(b));
+                       */
+                       r_tid = b->core.tid;
                        unpad_seq(b, &r);
                        write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
                        replace_cigar(b, n2, cigar2);
@@ -76,8 +81,15 @@ int bam_pad2unpad(bamFile in, bamFile out)
                                posmap[i] = k; // note that a read should NOT start at a padding
                                if (r.s[i]) ++k;
                        }
-               } else {
+               } else if (b->core.n_cigar > 0) {
                        int i, k, op;
+                       if (b->core.tid < 0) {
+                               fprintf(stderr, "[depad] ERROR: Read %s has CIGAR but no RNAME\n", bam1_qname(b));
+                               return -1;
+                       } else if (b->core.tid != r_tid) {
+                               fprintf(stderr, "[depad] ERROR: Missing %s embedded reference sequence\n", h->target_name[b->core.tid]);
+                               return -1;
+                       }
                        unpad_seq(b, &q);
                        if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[0]);
                        for (i = 0, k = b->core.pos; i < q.l; ++i, ++k)
@@ -110,13 +122,14 @@ int bam_pad2unpad(bamFile in, bamFile out)
 int main_pad2unpad(int argc, char *argv[])
 {
        bamFile in, out;
+        int result=0;
        if (argc == 1) {
                fprintf(stderr, "Usage: samtools depad <in.bam>\n");
                return 1;
        }
        in = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r");
        out = bam_dopen(fileno(stdout), "w");
-       bam_pad2unpad(in, out);
+       result = bam_pad2unpad(in, out);
        bam_close(in); bam_close(out);
-       return 0;
+       return result;
 }