#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"
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15
};
+unsigned short bam_char2flag_table[256] = {
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,BAM_FREAD1,BAM_FREAD2,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ BAM_FPROPER_PAIR,0,BAM_FMREVERSE,0, 0,BAM_FMUNMAP,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, BAM_FDUP,0,BAM_FQCFAIL,0, 0,0,0,0, 0,0,0,0,
+ BAM_FPAIRED,0,BAM_FREVERSE,BAM_FSECONDARY, 0,BAM_FUNMAP,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0
+};
+
char *bam_nt16_rev_table = "=ACMGRSVTWYHKDBN";
struct __tamFile_t {
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
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;
kh_ref_t *hash;
khiter_t k;
- hash = kh_init(ref);
+ if (fn == 0) return 0;
fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
- assert(fp);
+ if (fp == 0) return 0;
+ hash = kh_init(ref);
ks = ks_init(fp);
str = (kstring_t*)calloc(1, sizeof(kstring_t));
- while (ks_getuntil(ks, 0, str, &dret) >= 0) {
+ while (ks_getuntil(ks, 0, str, &dret) > 0) {
char *s = strdup(str->s);
int len, i;
i = kh_size(hash);
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;
}
static inline void append_text(bam_header_t *header, kstring_t *str)
{
- int x = header->l_text, y = header->l_text + str->l + 2; // 2 = 1 byte dret + 1 byte null
+ size_t x = header->l_text, y = header->l_text + str->l + 2; // 2 = 1 byte dret + 1 byte null
kroundup32(x); kroundup32(y);
- if (x < y) header->text = (char*)realloc(header->text, y);
+ if (x < y)
+ {
+ header->n_text = y;
+ header->text = (char*)realloc(header->text, y);
+ if ( !header->text )
+ {
+ fprintf(stderr,"realloc failed to alloc %ld bytes\n", y);
+ abort();
+ }
+ }
+ // Sanity check
+ if ( header->l_text+str->l+1 >= header->n_text )
+ {
+ fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n", header->l_text+str->l+1,header->n_text,x,y);
+ abort();
+ }
strncpy(header->text + header->l_text, str->s, str->l+1); // we cannot use strcpy() here.
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(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;
+ char **tmp;
+ int i;
+ 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;
+ 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_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;
+}
+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;
memcpy(alloc_data(b, doff + c->l_qname) + doff, str->s, c->l_qname);
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;
+ { // flag
+ long flag;
+ char *s;
+ ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
+ flag = strtol((char*)str->s, &s, 0);
+ if (*s) { // not the end of the string
+ flag = 0;
+ for (s = str->s; *s; ++s)
+ flag |= bam_char2flag_table[(int)*s];
+ }
+ c->flag = flag;
+ }
+ { // tid, pos, qual
+ 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;
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); 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;
+ uint8_t *p = 0;
if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -5; // seq
- 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;
- bzero(p, (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);
+ z += str->l + 1;
+ 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
- if (c->l_qseq != strlen(str->s))
+ 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;
- for (i = 0; i < c->l_qseq; ++i) p[i] = str->s[i] - 33;
+ if (strcmp(str->s, "*") == 0) for (i = 0; i < c->l_qseq; ++i) p[i] = 0xff;
+ else for (i = 0; i < c->l_qseq; ++i) p[i] = str->s[i] - 33;
doff += c->l_qseq + (c->l_qseq+1)/2;
}
doff0 = doff;
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];
*s++ = 'f';
*(float*)s = (float)atof(str->s + 5);
s += 4; doff += 5;
+ } else if (type == 'd') {
+ s = alloc_data(b, doff + 9) + doff;
+ *s++ = 'd';
+ *(float*)s = (float)atof(str->s + 9);
+ s += 8; doff += 9;
} else if (type == 'Z' || type == 'H') {
int size = 1 + (str->l - 5) + 1;
if (type == 'H') { // check whether the hex string is valid
}
b->l_aux = doff - doff0;
b->data_len = doff;
- return 0;
+ return z;
}
tamFile sam_open(const char *fn)
{
tamFile fp;
+ 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));
- fp->fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
+ fp->fp = gzfp;
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;
-}