* samtools-0.1.4-21 (r368)

[samtools.git] / bam_aux.c

diff --git a/bam_aux.c b/bam_aux.c
index a63e2aeadccf35e95b786097cd33394cb31a7a06..9b918424eeaf046719105956ea7baaef29b6cd03 100644 (file)
--- a/bam_aux.c
+++ b/bam_aux.c
@@ -72,7 +72,7 @@ int32_t bam_get_tid(const bam_header_t *header, const char *seq_name)
        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;
@@ -93,12 +93,12 @@ void bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *b
        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);
@@ -107,8 +107,12 @@ void bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *b
                *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)