change the command line option of pileup

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 665304f9019621a8734c0651db57a27a26c49fb2..99592276c0bded2906122a09528f5453bdb7ebd3 100644 (file)
--- 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);