-khash_t(set64) *bcf_load_pos(const char *fn, bcf_hdr_t *_h)
-{
- void *str2id;
- gzFile fp;
- kstream_t *ks;
- int ret, dret, lineno = 1;
- kstring_t *str;
- khash_t(set64) *hash = 0;
-
- hash = kh_init(set64);
- str2id = bcf_build_refhash(_h);
- str = calloc(1, sizeof(kstring_t));
- fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
- ks = ks_init(fp);
- while (ks_getuntil(ks, 0, str, &dret) >= 0) {
- int tid = bcf_str2id(str2id, str->s);
- if (tid >= 0 && dret != '\n') {
- if (ks_getuntil(ks, 0, str, &dret) >= 0) {
- uint64_t x = (uint64_t)tid<<32 | (atoi(str->s) - 1);
- kh_put(set64, hash, x, &ret);
- } else break;
- } else fprintf(stderr, "[%s] %s is not a reference name (line %d).\n", __func__, str->s, lineno);
- if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n');
- if (dret < 0) break;
- ++lineno;
- }
- bcf_str2id_destroy(str2id);
- ks_destroy(ks);
- gzclose(fp);
- free(str->s); free(str);
- return hash;
-}
+void *bed_read(const char *fn);
+void bed_destroy(void *_h);
+int bed_overlap(const void *_h, const char *chr, int beg, int end);