#endif
#include "kstring.h"
#include "bam.h"
+#include "sam_header.h"
#include "kseq.h"
#include "khash.h"
bam_header_t *sam_header_read2(const char *fn)
{
bam_header_t *header;
- int c, dret, ret;
+ int c, dret, ret, error = 0;
gzFile fp;
kstream_t *ks;
kstring_t *str;
ks_getuntil(ks, 0, str, &dret);
len = atoi(str->s);
k = kh_put(ref, hash, s, &ret);
+ if (ret == 0) {
+ fprintf(stderr, "[sam_header_read2] duplicated sequence name: %s\n", s);
+ error = 1;
+ }
kh_value(hash, k) = (uint64_t)len<<32 | i;
if (dret != '\n')
while ((c = ks_getc(ks)) != '\n' && c != -1);
gzclose(fp);
free(str->s); free(str);
fprintf(stderr, "[sam_header_read2] %d sequences loaded.\n", kh_size(hash));
+ if (error) return 0;
header = hash2header(hash);
kh_destroy(ref, hash);
return header;
header->text[header->l_text] = 0;
}
-int sam_header_parse_rg(bam_header_t *h)
-{
- kstring_t *rgid, *rglib;
- char *p, *q, *s, *r;
- int n = 0;
-
- // free
- if (h == 0) return 0;
- bam_strmap_destroy(h->rg2lib); h->rg2lib = 0;
- if (h->l_text < 3) return 0;
- // parse @RG lines
- h->rg2lib = bam_strmap_init();
- rgid = calloc(1, sizeof(kstring_t));
- rglib = calloc(1, sizeof(kstring_t));
- s = h->text;
- while ((s = strstr(s, "@RG")) != 0) {
- if (rgid->l && rglib->l) {
- bam_strmap_put(h->rg2lib, rgid->s, rglib->s);
- ++n;
- }
- rgid->l = rglib->l = 0;
- s += 3;
- r = s;
- if ((p = strstr(s, "ID:")) != 0) {
- q = p + 3;
- for (p = q; *p && *p != '\t' && *p != '\r' && *p != '\n'; ++p);
- kputsn(q, p - q, rgid);
- } else {
- fprintf(stderr, "[bam_header_parse] missing ID tag in @RG lines.\n");
- break;
- }
- if (r < p) r = p;
- if ((p = strstr(s, "LB:")) != 0) {
- q = p + 3;
- for (p = q; *p && *p != '\t' && *p != '\r' && *p != '\n'; ++p);
- kputsn(q, p - q, rglib);
- } else {
- fprintf(stderr, "[bam_header_parse] missing LB tag in @RG lines.\n");
- break;
- }
- if (r < p) r = p;
- }
- if (rgid->l && rglib->l) {
- bam_strmap_put(h->rg2lib, rgid->s, rglib->s);
- ++n;
- }
- free(rgid->s); free(rgid);
- free(rglib->s); free(rglib);
- if (n == 0) {
- bam_strmap_destroy(h->rg2lib);
- h->rg2lib = 0;
- }
- return n;
-}
-
int sam_header_parse(bam_header_t *h)
{
+ char **tmp;
int i;
- char *s, *p, *q, *r;
-
- // free
free(h->target_len); free(h->target_name);
h->n_targets = 0; h->target_len = 0; h->target_name = 0;
if (h->l_text < 3) return 0;
- // count number of @SQ
- s = h->text;
- while ((s = strstr(s, "@SQ")) != 0) {
- ++h->n_targets;
- s += 3;
- }
+ if (h->dict == 0) h->dict = sam_header_parse2(h->text);
+ tmp = sam_header2list(h->dict, "SQ", "SN", &h->n_targets);
if (h->n_targets == 0) return 0;
- h->target_len = (uint32_t*)calloc(h->n_targets, 4);
- h->target_name = (char**)calloc(h->n_targets, sizeof(void*));
- // parse @SQ lines
- i = 0;
- s = h->text;
- while ((s = strstr(s, "@SQ")) != 0) {
- s += 3;
- r = s;
- if ((p = strstr(s, "SN:")) != 0) {
- q = p + 3;
- for (p = q; *p && *p != '\t' && *p != '\r' && *p != '\n'; ++p);
- h->target_name[i] = (char*)calloc(p - q + 1, 1);
- strncpy(h->target_name[i], q, p - q);
- } else goto header_err_ret;
- if (r < p) r = p;
- if ((p = strstr(s, "LN:")) != 0) h->target_len[i] = strtol(p + 3, 0, 10);
- else goto header_err_ret;
- if (r < p) r = p;
- s = r + 3;
- ++i;
- }
- sam_header_parse_rg(h);
+ h->target_name = calloc(h->n_targets, sizeof(void*));
+ for (i = 0; i < h->n_targets; ++i)
+ h->target_name[i] = strdup(tmp[i]);
+ free(tmp);
+ tmp = sam_header2list(h->dict, "SQ", "LN", &h->n_targets);
+ h->target_len = calloc(h->n_targets, 4);
+ for (i = 0; i < h->n_targets; ++i)
+ h->target_len[i] = atoi(tmp[i]);
+ free(tmp);
return h->n_targets;
-
-header_err_ret:
- fprintf(stderr, "[bam_header_parse] missing SN or LN tag in @SQ lines.\n");
- free(h->target_len); free(h->target_name);
- h->n_targets = 0; h->target_len = 0; h->target_name = 0;
- return 0;
}
bam_header_t *sam_header_read(tamFile fp)