fixed a bug in bam_plcmd.c

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 17e5806e6c96db00b88533a4e04ce387a08b512e..cbf6ae8c13754be0c441b311eb14dfb9f04452a3 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -179,7 +179,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
        extern void *bcf_call_add_rg(void *rghash, const char *hdtext, const char *list);
        extern void bcf_call_del_rghash(void *rghash);
        mplp_aux_t **data;
-       int i, tid, pos, *n_plp, tid0 = -1, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid, max_depth, max_indel_depth;
+       int i, tid, pos, *n_plp, tid0 = -1, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid = -1, max_depth, max_indel_depth;
        const bam_pileup1_t **plp;
        bam_mplp_t iter;
        bam_header_t *h = 0;
@@ -276,6 +276,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
        }
        if (tid0 >= 0 && conf->fai) { // region is set
                ref = faidx_fetch_seq(conf->fai, h->target_name[tid0], 0, 0x7fffffff, &ref_len);
+               ref_tid = tid0;
                for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid0;
        } else ref_tid = -1, ref = 0;
        iter = bam_mplp_init(n, mplp_func, (void**)data);