X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_plcmd.c;h=5bf1ed095096b7cd91fc99d2256467b89e394d33;hp=5d5506fb5630a088f692e6f0c64e8b827f6a5329;hb=4a17fa7e1f91b2fe04ad334a63fc2b0d5e859d8a;hpb=b27e00385f41769d03a8cca4dbd71275fc9fa906

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 5d5506f..5bf1ed0 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -284,7 +284,8 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
 		printf("%d\t%d\t", rms_mapq, n);
 		printf("%s\t%s\t", r->s[0], r->s[1]);
 		//printf("%d\t%d\t", r->gl[0], r->gl[1]);
-		printf("%d\t%d\t%d\n", r->cnt1, r->cnt2, r->cnt_anti);
+		printf("%d\t%d\t%d\t", r->cnt1, r->cnt2, r->cnt_anti);
+		printf("%d\t%d\n", r->cnt_ref, r->cnt_ambi);
 		bam_maqindel_ret_destroy(r);
 	}
 	return 0;
@@ -330,7 +331,7 @@ 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 +357,8 @@ 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);