Check embedded reference against FASTA if given in 'samtools depad'

diff --git a/padding.c b/padding.c
index d03e5987ab0ca582ca243da8381d3b13a9844d8a..19b95a9fff07a81759343ee165c2abd3f2d4a0e3 100644 (file)
--- a/padding.c
+++ b/padding.c
@@ -89,14 +89,13 @@ int load_unpadded_ref(faidx_t *fai, char *ref_name, int ref_len, kstring_t *seq)
                        // Map gaps to null to match unpad_seq function
                        seq->s[seq->l++] = 0;
                } else {
-                       // Want to map IUPAC bases to upper case, and reject other chars
                        int i = bam_nt16_table[(int)base];
                        if (i == 0 || i==16) { // Equals maps to 0, anything unexpected to 16
                                fprintf(stderr, "[depad] ERROR: Invalid character %c (ASCII %i) in FASTA sequence %s\n", base, (int)base, ref_name);
                                free(fai_ref);
                                return -1;
                        }
-                       seq->s[seq->l++] = bam_nt16_rev_table[i];
+                       seq->s[seq->l++] = i;
                }
        }
        assert(ref_len == seq->l);
@@ -133,23 +132,31 @@ int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
                n2 = 0;
                if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam1_qname(b), h->target_name[b->core.tid]) == 0) {
                        // fprintf(stderr, "[depad] Found embedded reference %s\n", bam1_qname(b));
-                       // TODO - Check this embedded reference matches the FASTA file (if given)
                        r_tid = b->core.tid;
                        unpad_seq(b, &r);
                        if (h->target_len[r_tid] != r.l) {
                                fprintf(stderr, "[depad] ERROR: (Padded) length of %s is %i in BAM header, but %ld in embedded reference\n", bam1_qname(b), h->target_len[r_tid], r.l);
                                return -1;
                        }
+                       if (fai) {
+                               // Check the embedded reference matches the FASTA file
+                               if (load_unpadded_ref(fai, h->target_name[b->core.tid], h->target_len[b->core.tid], &q)) return -1;
+                               assert(r.l == q.l);
+                               int i;
+                               for (i = 0; i < r.l; ++i) {
+                                       if (r.s[i] != q.s[i]) {
+                                               // Show gaps as ASCII 45
+                                               fprintf(stderr, "[depad] ERROR: Embedded sequence and reference FASTA don't match for %s base %i, '%c' vs '%c'\n",
+                                                       h->target_name[b->core.tid], i+1,
+                                                       r.s[i] ? bam_nt16_rev_table[r.s[i]] : 45,
+                                                       q.s[i] ? bam_nt16_rev_table[q.s[i]] : 45);
+                                               return -1;
+                                       }
+                               }
+                       }
                        write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
                        replace_cigar(b, n2, cigar2);
                        posmap = update_posmap(posmap, r);
-                       /*
-                       posmap = realloc(posmap, r.m * sizeof(int));
-                       for (i = k = 0; i < r.l; ++i) {
-                               posmap[i] = k;
-                               if (r.s[i]) ++k;
-                       }
-                       */
                } else if (b->core.n_cigar > 0) {
                        int i, k, op;
                        if (b->core.tid < 0) {