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; }