#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 {
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) {
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_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)
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); z += str->l + 1; c->flag = atoi(str->s);
+ { // 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) {
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;
- 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);
+ 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))
memcpy(s, str->s + 5, str->l - 5);
s[str->l - 5] = 0;
doff += size;
+ } else if (type == 'B') {
+ int32_t n = 0, Bsize, k = 0, size;
+ char *p;
+ if (str->l < 8) parse_error(fp->n_lines, "too few values in aux type B");
+ Bsize = bam_aux_type2size(str->s[5]); // the size of each element
+ for (p = (char*)str->s + 6; *p; ++p) // count the number of elements in the array
+ if (*p == ',') ++n;
+ p = str->s + 7; // now p points to the first number in the array
+ size = 6 + Bsize * n; // total number of bytes allocated to this tag
+ s = alloc_data(b, doff + 6 * Bsize * n) + doff; // allocate memory
+ *s++ = 'B'; *s++ = str->s[5];
+ memcpy(s, &n, 4); s += 4; // write the number of elements
+ if (str->s[5] == 'c') while (p < str->s + str->l) ((int8_t*)s)[k++] = (int8_t)strtol(p, &p, 0), ++p;
+ else if (str->s[5] == 'C') while (p < str->s + str->l) ((uint8_t*)s)[k++] = (uint8_t)strtol(p, &p, 0), ++p;
+ else if (str->s[5] == 's') while (p < str->s + str->l) ((int16_t*)s)[k++] = (int16_t)strtol(p, &p, 0), ++p; // FIXME: avoid unaligned memory
+ else if (str->s[5] == 'S') while (p < str->s + str->l) ((uint16_t*)s)[k++] = (uint16_t)strtol(p, &p, 0), ++p;
+ else if (str->s[5] == 'i') while (p < str->s + str->l) ((int32_t*)s)[k++] = (int32_t)strtol(p, &p, 0), ++p;
+ else if (str->s[5] == 'I') while (p < str->s + str->l) ((uint32_t*)s)[k++] = (uint32_t)strtol(p, &p, 0), ++p;
+ else if (str->s[5] == 'f') while (p < str->s + str->l) ((float*)s)[k++] = (float)strtod(p, &p), ++p;
+ else parse_error(fp->n_lines, "unrecognized array type");
+ s += Bsize * n; doff += size;
} else parse_error(fp->n_lines, "unrecognized type");
if (dret == '\n' || dret == '\r') break;
}
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);
return fp;
}
projects / samtools.git / blobdiff