big fix: using samtools view file.bam gibberish returns alignments; iter not checked...

[samtools.git] / bam_aux.c

diff --git a/bam_aux.c b/bam_aux.c
index 2247bdfe9ba15d39d5a1dcf193da9d68cdfab8bf..8727af0d81473bd986cfe272ce6d0db7d5b54a25 100644 (file)
--- a/bam_aux.c
+++ b/bam_aux.c
@@ -59,6 +59,23 @@ int bam_aux_del(bam1_t *b, uint8_t *s)
        return 0;
 }
 
+int bam_aux_drop_other(bam1_t *b, uint8_t *s)
+{
+       if (s) {
+               uint8_t *p, *aux;
+               aux = bam1_aux(b);
+               p = s - 2;
+               __skip_tag(s);
+               memmove(aux, p, s - p);
+               b->data_len -= b->l_aux - (s - p);
+               b->l_aux = s - p;
+       } else {
+               b->data_len -= b->l_aux;
+               b->l_aux = 0;
+       }
+       return 0;
+}
+
 void bam_init_header_hash(bam_header_t *header)
 {
        if (header->hash == 0) {
@@ -124,6 +141,8 @@ int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *be
                        } else s[name_end] = ':', name_end = l;
                }
        } else iter = kh_get(s, h, str);
+        if (iter == kh_end(h))
+          free(s); return -1;
        *ref_id = kh_val(h, iter);
        // parse the interval
        if (name_end < l) {