* 0.1.16-dev (r969:252)

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 0aa44f5853e3126d8d403b05b1f9d45335081b61..487080529a6820d0540e2bb10a6161b84a221698 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -287,7 +287,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                if (conf->bed && tid >= 0 && !bed_overlap(conf->bed, h->target_name[tid], pos, pos+1)) continue;
                if (tid != ref_tid) {
                        free(ref); ref = 0;
-                       if (conf->fai) ref = fai_fetch(conf->fai, h->target_name[tid], &ref_len);
+                       if (conf->fai) ref = faidx_fetch_seq(conf->fai, h->target_name[tid], 0, 0x7fffffff, &ref_len);
                        for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid;
                        ref_tid = tid;
                }