Use FASTA file when no embedded reference in 'samtools depad'

diff --git a/padding.c b/padding.c
index 9f8bca7e0fe13992aba557b176090936a34cb34a..d03e5987ab0ca582ca243da8381d3b13a9844d8a 100644 (file)
--- a/padding.c
+++ b/padding.c
@@ -69,6 +69,52 @@ static void unpad_seq(bam1_t *b, kstring_t *s)
        assert(length == s->l);
 }
 
+int load_unpadded_ref(faidx_t *fai, char *ref_name, int ref_len, kstring_t *seq)
+{
+       char base;
+       char *fai_ref = 0;
+       int fai_ref_len = 0, k;
+
+       fai_ref = fai_fetch(fai, ref_name, &fai_ref_len);
+       if (fai_ref_len != ref_len) {
+               fprintf(stderr, "[depad] ERROR: FASTA sequence %s length %i, expected %i\n", ref_name, fai_ref_len, ref_len);
+               free(fai_ref);
+               return -1;
+       }
+       ks_resize(seq, ref_len);
+       seq->l = 0;
+       for (k = 0; k < ref_len; ++k) {
+               base = fai_ref[k];
+               if (base == '-' || base == '*') {
+                       // 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];
+               }
+       }
+       assert(ref_len == seq->l);
+       free(fai_ref);
+       return 0;
+}
+
+inline int * update_posmap(int *posmap, kstring_t ref)
+{
+       int i, k;
+       posmap = realloc(posmap, ref.m * sizeof(int));
+       for (i = k = 0; i < ref.l; ++i) {
+               posmap[i] = k;
+               if (ref.s[i]) ++k;
+       }
+       return posmap;
+}
+
 int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
 {
        bam_header_t *h;
@@ -86,10 +132,8 @@ int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
                uint32_t *cigar = bam1_cigar(b);
                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));
-                       */
+                       // 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) {
@@ -98,18 +142,28 @@ 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);
+                       /*
                        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) {
                                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]);
+                       } else if (b->core.tid == r_tid) {
+                               ; // good case, reference available
+                       } else if (fai) {
+                               if (load_unpadded_ref(fai, h->target_name[b->core.tid], h->target_len[b->core.tid], &r)) return -1;
+                               posmap = update_posmap(posmap, r);
+                               r_tid = b->core.tid;
+                               // fprintf(stderr, "[depad] Loaded %s from FASTA file\n", h->target_name[b->core.tid]);
+                       } else {                                
+                               fprintf(stderr, "[depad] ERROR: Missing %s embedded reference sequence (and no FASTA file)\n", h->target_name[b->core.tid]);
                                return -1;
                        }
                        unpad_seq(b, &q);
@@ -186,7 +240,7 @@ static int usage(int is_long_help);
 int main_pad2unpad(int argc, char *argv[])
 {
        samfile_t *in = 0, *out = 0;
-       faidx_t *fai;
+       faidx_t *fai = 0;
        int c, is_bamin = 1, compress_level = -1, is_bamout = 1, is_long_help = 0;
        char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0;
         int ret=0;