return k == kh_end(h)? -1 : kh_value(h, k);
}
-void bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end)
+int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end)
{
char *s, *p;
int i, l, k;
iter = kh_get(s, h, s); /* get the ref_id */
if (iter == kh_end(h)) { // name not found
*ref_id = -1; free(s);
- return;
+ return -1;
}
*ref_id = kh_value(h, iter);
if (i == k) { /* dump the whole sequence */
*begin = 0; *end = 1<<29; free(s);
- return;
+ return -1;
}
for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break;
*begin = atoi(p);
*end = atoi(p);
} else *end = 1<<29;
if (*begin > 0) --*begin;
- assert(*begin <= *end);
free(s);
+ if (*begin > *end) {
+ fprintf(stderr, "[bam_parse_region] invalid region.\n");
+ return -1;
+ }
+ return 0;
}
int32_t bam_aux2i(const uint8_t *s)