Updated samtools to 0.1.19

[rsem.git] / sam / faidx.c

diff --git a/sam/faidx.c b/sam/faidx.c
index f0798fccc8057a5e33fdb04afaae1af084badbc9..51c82ac1dfdcd0baf31435a0fe5f8e45c3289d0f 100644 (file)
--- a/sam/faidx.c
+++ b/sam/faidx.c
@@ -337,6 +337,11 @@ char *fai_fetch(const faidx_t *fai, const char *str, int *len)
                        } else s[name_end] = ':', name_end = l;
                }
        } else iter = kh_get(s, h, str);
+       if(iter == kh_end(h)) {
+               fprintf(stderr, "[fai_fetch] Warning - Reference %s not found in FASTA file, returning empty sequence\n", str);
+               free(s);
+               return 0;
+       };
        val = kh_value(h, iter);
        // parse the interval
        if (name_end < l) {