X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_plcmd.c;h=6804795bd107405982cada8544051cc073fdf55e;hb=aecbff7298d7df0ac206fc5c45aa91d758c1b502;hp=665304f9019621a8734c0651db57a27a26c49fb2;hpb=961c3fe158b5a9777bc8c061425ca3cb15d8687c;p=samtools.git

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 665304f..6804795 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -343,9 +343,10 @@ int bam_pileup(int argc, char *argv[])
 	d->c = bam_maqcns_init();
 	d->c->is_soap = 1; // change the default model
 	d->ido = bam_maqindel_opt_init();
-	while ((c = getopt(argc, argv, "st:f:cT:N:r:l:d:im:gI:G:vM:S2aR:P")) >= 0) {
+	while ((c = getopt(argc, argv, "st:f:cT:N:r:l:d:im:gI:G:vM:S2aR:PA")) >= 0) {
 		switch (c) {
-		case 'a': d->c->is_soap = 0; break;
+		case 'a': d->c->is_soap = 1; break;
+		case 'A': d->c->is_soap = 0; break;
 		case 's': d->format |= BAM_PLF_SIMPLE; break;
 		case 't': fn_list = strdup(optarg); break;
 		case 'l': fn_pos = strdup(optarg); break;
@@ -380,7 +381,7 @@ int bam_pileup(int argc, char *argv[])
 		fprintf(stderr, "Usage:  samtools pileup [options] <in.bam>|<in.sam>\n\n");
 		fprintf(stderr, "Option: -s        simple (yet incomplete) pileup format\n");
 		fprintf(stderr, "        -S        the input is in SAM\n");
-		fprintf(stderr, "        -a        use the MAQ model for SNP calling\n");
+		fprintf(stderr, "        -A        use the MAQ model for SNP calling\n");
 		fprintf(stderr, "        -2        output the 2nd best call and quality\n");
 		fprintf(stderr, "        -i        only show lines/consensus with indels\n");
 		fprintf(stderr, "        -m INT    filtering reads with bits in INT [%d]\n", d->mask);
@@ -389,7 +390,7 @@ int bam_pileup(int argc, char *argv[])
 		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");
+		fprintf(stderr, "        -c        output the SOAPsnp consensus sequence\n");
 		fprintf(stderr, "        -v        print variants only (for -c)\n");
 		fprintf(stderr, "        -g        output in the GLFv3 format (suppressing -c/-i/-s)\n");
 		fprintf(stderr, "        -T FLOAT  theta in maq consensus calling model (for -c/-g) [%f]\n", d->c->theta);