bam_header_t *sam_header_read2(const char *fn)
{
bam_header_t *header;
int c, dret, ret;
gzFile fp;
kstream_t *ks;
kstring_t *str;
kh_ref_t *hash;
khiter_t k;
hash = kh_init(ref);
fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
assert(fp);
ks = ks_init(fp);
str = (kstring_t*)calloc(1, sizeof(kstring_t));
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);
kh_value(hash, k) = (uint64_t)len<<32 | i;
if (dret != '\n')
while ((c = ks_getc(ks)) != '\n' && c != -1);
}
ks_destroy(ks);
gzclose(fp);
free(str->s); free(str);
fprintf(stderr, "[sam_header_read2] %d sequences loaded.\n", kh_size(hash));
header = hash2header(hash);
kh_destroy(ref, hash);
return header;
}
bam_header_t *sam_header_read2(const char *fn)
{
bam_header_t *header;
int c, dret, ret, error = 0;
gzFile fp;
kstream_t *ks;
kstring_t *str;
kh_ref_t *hash;
khiter_t k;
if (fn == 0) return 0;
fp = gzopen(fn, "r");
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) {
char *s = malloc(strlen(str->s) + 1);
strcpy(s,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) {
Rprintf("[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);
}
ks_destroy(ks);
gzclose(fp);
free(str->s); free(str);
Rprintf("[sam_header_read2] %d sequences loaded.\n", kh_size(hash));
if (error) return 0;
header = hash2header(hash);
kh_destroy(ref, hash);
return header;
}
