Sorry. The old Makefile is for PDCurses...

[samtools.git] / bam_aux.c

diff --git a/bam_aux.c b/bam_aux.c
index a63e2aeadccf35e95b786097cd33394cb31a7a06..7482500ef08a53f3471858793112d9c72263e33a 100644 (file)
--- a/bam_aux.c
+++ b/bam_aux.c
@@ -19,12 +19,12 @@ void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *d
        b->data[ori_len + 2] = type;
        memcpy(b->data + ori_len + 3, data, len);
 }
-/*
+
 uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2])
 {
        return bam_aux_get(b, tag);
 }
-*/
+
 uint8_t *bam_aux_get(const bam1_t *b, const char tag[2])
 {
        uint8_t *s;
@@ -39,7 +39,7 @@ uint8_t *bam_aux_get(const bam1_t *b, const char tag[2])
                else if (type == 'S') s += 2;
                else if (type == 'I' || type == 'F') s += 4;
                else if (type == 'D') s += 8;
-               else if (type == 'Z' || type == 'H') { while (*s) putchar(*s++); ++s; }
+               else if (type == 'Z' || type == 'H') { while (*s) ++s; ++s; }
        }
        return 0;
 }
@@ -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)