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[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 20c5632b80d7c6a5c6c333ca2760af5a6f5dab6b..358e9f99daea56c43dec513f82e64dacc13bd843 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -561,7 +561,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                data[i]->min_mq = conf->min_mq;
                data[i]->flag = conf->flag;
                data[i]->capQ_thres = conf->capQ_thres;
-               data[i]->fp = bam_open(fn[i], "r");
+               data[i]->fp = strcmp(fn[i], "-") == 0? bam_dopen(fileno(stdin), "r") : bam_open(fn[i], "r");
                h_tmp = bam_header_read(data[i]->fp);
                bam_smpl_add(sm, fn[i], h_tmp->text);
                if (conf->reg) {