#include "sam_header.h"
#include "sam.h"
#include "bam.h"
+#include "faidx.h"
static void replace_cigar(bam1_t *b, int n, uint32_t *cigar)
{
assert(length == s->l);
}
-int bam_pad2unpad(samfile_t *in, samfile_t *out)
+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 {
+ 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++] = 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;
bam1_t *b;
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));
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 = realloc(posmap, r.m * sizeof(int));
- for (i = k = 0; i < r.l; ++i) {
- posmap[i] = k;
- if (r.s[i]) ++k;
- }
+ posmap = update_posmap(posmap, r);
} 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);
int main_pad2unpad(int argc, char *argv[])
{
samfile_t *in = 0, *out = 0;
+ 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;
+ char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0;
int ret=0;
/* parse command-line options */
strcpy(in_mode, "r"); strcpy(out_mode, "w");
- while ((c = getopt(argc, argv, "Sso:u1?")) >= 0) {
+ while ((c = getopt(argc, argv, "Sso:u1T:?")) >= 0) {
switch (c) {
case 'S': is_bamin = 0; break;
case 's': assert(compress_level == -1); is_bamout = 0; break;
case 'o': fn_out = strdup(optarg); break;
case 'u': assert(is_bamout == 1); compress_level = 0; break;
case '1': assert(is_bamout == 1); compress_level = 1; break;
+ case 'T': fn_ref = strdup(optarg); is_bamin = 0; break;
case '?': is_long_help = 1; break;
default: return usage(is_long_help);
}
strcat(out_mode, tmp);
}
+ // Load FASTA reference (also needed for SAM -> BAM if missing header)
+ if (fn_ref) {
+ fn_list = samfaipath(fn_ref);
+ fai = fai_load(fn_ref);
+ }
// open file handlers
if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {
- fprintf(stderr, "[depad] fail to open \"%s\" for reading.\n", argv[optind]);
+ fprintf(stderr, "[depad] failed to open \"%s\" for reading.\n", argv[optind]);
ret = 1;
goto depad_end;
}
if (in->header == 0) {
- fprintf(stderr, "[depad] fail to read the header from \"%s\".\n", argv[optind]);
+ fprintf(stderr, "[depad] failed to read the header from \"%s\".\n", argv[optind]);
ret = 1;
goto depad_end;
}
/* TODO - The reference sequence lengths in the BAM + SAM headers should be updated */
if ((out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
- fprintf(stderr, "[depad] fail to open \"%s\" for writing.\n", fn_out? fn_out : "standard output");
+ fprintf(stderr, "[depad] failed to open \"%s\" for writing.\n", fn_out? fn_out : "standard output");
ret = 1;
goto depad_end;
}
// Do the depad
- ret = bam_pad2unpad(in, out);
+ ret = bam_pad2unpad(in, out, fai);
depad_end:
// close files, free and return
free(fn_list); free(fn_out);
samclose(in);
samclose(out);
+ fai_destroy(fai);
return ret;
}
fprintf(stderr, " -S input is SAM (default is BAM)\n");
fprintf(stderr, " -u uncompressed BAM output (can't use with -s)\n");
fprintf(stderr, " -1 fast compression BAM output (can't use with -s)\n");
- //TODO - These are the arguments I think make sense to support:
- //fprintf(stderr, " -@ INT number of BAM compression threads [0]\n");
- //fprintf(stderr, " -T FILE reference sequence file (force -S) [null]\n");
+ fprintf(stderr, " -T FILE reference sequence file [null]\n");
fprintf(stderr, " -o FILE output file name [stdout]\n");
fprintf(stderr, " -? longer help\n");
fprintf(stderr, "\n");
if (is_long_help)
fprintf(stderr, "Notes:\n\
\n\
- 1. Requires embedded reference sequences (before the reads for that reference).\n\
+ 1. Requires embedded reference sequences (before the reads for that reference),\n\
+ with the future aim to also support a FASTA padded reference sequence file.\n\
\n\
2. The input padded alignment read's CIGAR strings must not use P or I operators.\n\
\n");
projects / samtools.git / blobdiff