* samtools-0.1.2-22

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 79d0e63b8e75a8c6d55c19f6433d9d4c42d159cc..b85fb866a140f2e3f8e2b83af5cfbb942cb43a1b 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -260,7 +260,7 @@ int bam_pileup(int argc, char *argv[])
                case 'f': fn_fa = strdup(optarg); break;
                case 'T': d->c->theta = atof(optarg); break;
                case 'N': d->c->n_hap = atoi(optarg); break;
-               case 'r': d->c->het_rate = atoi(optarg); break;
+               case 'r': d->c->het_rate = atof(optarg); break;
                case 'c': d->format |= BAM_PLF_CNS; break;
                case 'i': d->format |= BAM_PLF_INDEL_ONLY; break;
                case 'm': d->mask = atoi(optarg); break;
@@ -272,7 +272,7 @@ int bam_pileup(int argc, char *argv[])
        }
        if (optind == argc) {
                fprintf(stderr, "\n");
-               fprintf(stderr, "Usage:  bamtk pileup [options] <in.bam>|<in.sam>\n\n");
+               fprintf(stderr, "Usage:  samtools pileup [options] <in.bam>|<in.sam>\n\n");
                fprintf(stderr, "Option: -s        simple (yet incomplete) pileup format\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);