#include <stdlib.h>
#include <unistd.h>
#include <assert.h>
+#ifdef _WIN32
+#include <fcntl.h>
+#endif
#include "kstring.h"
#include "bam.h"
+#include "sam_header.h"
#include "kseq.h"
#include "khash.h"
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;
- s = r + 3;
- }
- 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)
for (i = 0, s = str->s; i != c->n_cigar; ++i) {
x = strtol(s, &t, 10);
op = toupper(*t);
- if (op == 'M') op = BAM_CMATCH;
+ if (op == 'M' || op == '=' || op == 'X') op = BAM_CMATCH;
else if (op == 'I') op = BAM_CINS;
else if (op == 'D') op = BAM_CDEL;
else if (op == 'N') op = BAM_CREF_SKIP;
if (*s) parse_error(fp->n_lines, "unmatched CIGAR operation");
c->bin = bam_reg2bin(c->pos, bam_calend(c, bam1_cigar(b)));
doff += c->n_cigar * 4;
- } else c->bin = bam_reg2bin(c->pos, c->pos + 1);
+ } else {
+ if (!(c->flag&BAM_FUNMAP)) {
+ fprintf(stderr, "Parse warning at line %lld: mapped sequence without CIGAR\n", (long long)fp->n_lines);
+ c->flag |= BAM_FUNMAP;
+ }
+ c->bin = bam_reg2bin(c->pos, c->pos + 1);
+ }
}
{ // mtid, mpos, isize
ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
}
{ // seq and qual
int i;
- uint8_t *p;
+ uint8_t *p = 0;
if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -5; // seq
z += str->l + 1;
- c->l_qseq = strlen(str->s);
- if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b)))
- parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
- p = (uint8_t*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff;
- memset(p, 0, (c->l_qseq+1)/2);
- for (i = 0; i < c->l_qseq; ++i)
- p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2);
+ if (strcmp(str->s, "*")) {
+ c->l_qseq = strlen(str->s);
+ if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b)))
+ parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
+ p = (uint8_t*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff;
+ memset(p, 0, (c->l_qseq+1)/2);
+ for (i = 0; i < c->l_qseq; ++i)
+ p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2);
+ } else c->l_qseq = 0;
if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -6; // qual
z += str->l + 1;
if (strcmp(str->s, "*") && c->l_qseq != strlen(str->s))
tamFile sam_open(const char *fn)
{
tamFile fp;
- gzFile gzfp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
+ gzFile gzfp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "rb") : gzopen(fn, "rb");
if (gzfp == 0) return 0;
fp = (tamFile)calloc(1, sizeof(struct __tamFile_t));
fp->str = (kstring_t*)calloc(1, sizeof(kstring_t));
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