* samtools-0.1.5-16 (r421)

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 5d5506fb5630a088f692e6f0c64e8b827f6a5329..391767ab134833f5dcc5ea914866fd7f10b97718 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -330,7 +330,7 @@ int bam_pileup(int argc, char *argv[])
                fprintf(stderr, "        -i        only show lines/consensus with indels\n");
                fprintf(stderr, "        -m INT    filtering reads with bits in INT [%d]\n", d->mask);
                fprintf(stderr, "        -M INT    cap mapping quality at INT [%d]\n", d->c->cap_mapQ);
-               fprintf(stderr, "        -t FILE   list of reference sequences (assume the input is in SAM)\n");
+               fprintf(stderr, "        -t FILE   list of reference sequences (force -S)\n");
                fprintf(stderr, "        -l FILE   list of sites at which pileup is output\n");
                fprintf(stderr, "        -f FILE   reference sequence in the FASTA format\n\n");
                fprintf(stderr, "        -c        output the maq consensus sequence\n");
@@ -356,6 +356,8 @@ int bam_pileup(int argc, char *argv[])
        }
        if (d->fai == 0 && (d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)))
                fprintf(stderr, "[bam_pileup] indels will not be called when -f is absent.\n");
+       if (fn_fa && is_SAM && fn_list == 0) fn_list = samfaipath(fn_fa);
+
        {
                samfile_t *fp;
                fp = is_SAM? samopen(argv[optind], "r", fn_list) : samopen(argv[optind], "rb", 0);