* samtools-0.1.6-13 (r479)

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 5bf1ed095096b7cd91fc99d2256467b89e394d33..fff42f7c582b0f40947616723e3c3fc15ca630c9 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -299,8 +299,9 @@ int bam_pileup(int argc, char *argv[])
        d->tid = -1; d->mask = BAM_DEF_MASK;
        d->c = bam_maqcns_init();
        d->ido = bam_maqindel_opt_init();
-       while ((c = getopt(argc, argv, "st:f:cT:N:r:l:im:gI:G:vM:S2")) >= 0) {
+       while ((c = getopt(argc, argv, "st:f:cT:N:r:l:im:gI:G:vM:S2a")) >= 0) {
                switch (c) {
+               case 'a': d->c->is_soap = 1; break;
                case 's': d->format |= BAM_PLF_SIMPLE; break;
                case 't': fn_list = strdup(optarg); break;
                case 'l': fn_pos = strdup(optarg); break;
@@ -327,6 +328,7 @@ 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 SOAPsnp 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);