#include <stdlib.h>
#include <unistd.h>
#include <assert.h>
+#include "kstring.h"
#include "bam.h"
#include "kseq.h"
#include "khash.h"
kstream_t *ks;
kstring_t *str;
uint64_t n_lines;
+ int is_first;
};
char **__bam_get_lines(const char *fn, int *_n) // for bam_plcmd.c only
header->l_text += str->l + 1;
header->text[header->l_text] = 0;
}
-int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
+
+int sam_header_parse_rg(bam_header_t *h)
{
- int ret, doff, doff0, dret;
- bam1_core_t *c = &b->core;
- kstring_t *str = fp->str;
- kstream_t *ks = fp->ks;
+ kstring_t *rgid, *rglib;
+ char *p, *q, *s, *r;
+ int n = 0;
+
+ // free
+ 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)
+{
+ 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->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);
+ 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)
+{
+ int ret, dret;
+ bam_header_t *header = bam_header_init();
+ kstring_t *str = fp->str;
while ((ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret)) >= 0 && str->s[0] == '@') { // skip header
str->s[str->l] = dret; // note that str->s is NOT null terminated!!
append_text(header, str);
}
++fp->n_lines;
}
- while (ret == 0) ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret); // special consideration for "\r\n"
+ sam_header_parse(header);
+ bam_init_header_hash(header);
+ fp->is_first = 1;
+ return header;
+}
+
+int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
+{
+ int ret, doff, doff0, dret, z = 0;
+ bam1_core_t *c = &b->core;
+ kstring_t *str = fp->str;
+ kstream_t *ks = fp->ks;
+
+ if (fp->is_first) {
+ fp->is_first = 0;
+ ret = str->l;
+ } else {
+ do { // special consideration for empty lines
+ ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret);
+ if (ret >= 0) z += str->l + 1;
+ } while (ret == 0);
+ }
if (ret < 0) return -1;
++fp->n_lines;
doff = 0;
doff += c->l_qname;
}
{ // flag, tid, pos, qual
- ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); c->flag = atoi(str->s);
- ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); c->tid = bam_get_tid(header, str->s);
- ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); c->pos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
- ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); c->qual = isdigit(str->s[0])? atoi(str->s) : 0;
+ ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->flag = atoi(str->s);
+ ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->tid = bam_get_tid(header, str->s);
+ if (c->tid < 0 && strcmp(str->s, "*")) {
+ if (header->n_targets == 0) {
+ fprintf(stderr, "[sam_read1] missing header? Abort!\n");
+ exit(1);
+ } else fprintf(stderr, "[sam_read1] reference '%s' is recognized as '*'.\n", str->s);
+ }
+ ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->pos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
+ ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->qual = isdigit(str->s[0])? atoi(str->s) : 0;
if (ret < 0) return -2;
}
{ // cigar
long x;
c->n_cigar = 0;
if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -3;
+ z += str->l + 1;
if (str->s[0] != '*') {
for (s = str->s; *s; ++s) {
if (isalpha(*s)) ++c->n_cigar;
} else c->bin = bam_reg2bin(c->pos, c->pos + 1);
}
{ // mtid, mpos, isize
- ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); c->mtid = strcmp(str->s, "=")? bam_get_tid(header, str->s) : c->tid;
- ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); c->mpos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
- ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); c->isize = (str->s[0] == '-' || isdigit(str->s[0]))? atoi(str->s) : 0;
+ ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
+ c->mtid = strcmp(str->s, "=")? bam_get_tid(header, str->s) : c->tid;
+ ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
+ c->mpos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
+ ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
+ c->isize = (str->s[0] == '-' || isdigit(str->s[0]))? atoi(str->s) : 0;
if (ret < 0) return -4;
}
{ // seq and qual
int i;
uint8_t *p;
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");
for (i = 0; i < c->l_qseq; ++i)
p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2);
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))
parse_error(fp->n_lines, "sequence and quality are inconsistent");
p += (c->l_qseq+1)/2;
if (dret != '\n' && dret != '\r') { // aux
while (ks_getuntil(ks, KS_SEP_TAB, str, &dret) >= 0) {
uint8_t *s, type, key[2];
+ z += str->l + 1;
if (str->l < 6 || str->s[2] != ':' || str->s[4] != ':')
parse_error(fp->n_lines, "missing colon in auxiliary data");
key[0] = str->s[0]; key[1] = str->s[1];
}
b->l_aux = doff - doff0;
b->data_len = doff;
- return 0;
+ return z;
}
tamFile sam_open(const char *fn)
fp->str = (kstring_t*)calloc(1, sizeof(kstring_t));
fp->fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
fp->ks = ks_init(fp->fp);
- fp->n_lines = 0;
return fp;
}
free(fp);
}
}
-
-static void taf2baf_core(const char *fntaf, const char *fnbaf, bam_header_t *header)
-{
- bamFile fpbaf;
- bam1_t *b;
- tamFile fp;
- int ret;
-
- b = (bam1_t*)calloc(1, sizeof(bam1_t));
- fpbaf = (strcmp(fnbaf, "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(fnbaf, "w");
- fp = sam_open(fntaf);
- ret = sam_read1(fp, header, b);
- bam_header_write(fpbaf, header);
- if (ret >= 0) {
- bam_write1(fpbaf, b);
- while (sam_read1(fp, header, b) >= 0) bam_write1(fpbaf, b);
- }
- bam_close(fpbaf);
- free(b->data); free(b);
- sam_close(fp);
-}
-
-int bam_taf2baf(int argc, char *argv[])
-{
- int c;
- bam_header_t *header;
-
- while ((c = getopt(argc, argv, "")) >= 0) {
- }
- if (optind + 3 > argc) {
- fprintf(stderr, "Usage: bamtk import <in.ref_list> <in.sam> <out.bam>\n");
- return 1;
- }
- header = sam_header_read2(argv[optind]);
- taf2baf_core(argv[optind+1], argv[optind+2], header);
- bam_header_destroy(header);
- return 0;
-}
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