* wgsim: added a note

[samtools.git] / misc / wgsim.c

diff --git a/misc/wgsim.c b/misc/wgsim.c
index b7e7b2fe3751170944d3f75fccd5a6e213837333..1ae7572a6a6aff77b04acfea9f6fd194f3ee6f3e 100644 (file)
--- a/misc/wgsim.c
+++ b/misc/wgsim.c
@@ -453,8 +453,9 @@ static int simu_usage()
        fprintf(stderr, "         -R FLOAT      fraction of indels [%.2f]\n", INDEL_FRAC);
        fprintf(stderr, "         -X FLOAT      probability an indel is extended [%.2f]\n", INDEL_EXTEND);
        fprintf(stderr, "         -c            generate reads in color space (SOLiD reads)\n");
-       fprintf(stderr, "         -h            haploid mode\n");
+       fprintf(stderr, "         -h            haplotype mode\n");
        fprintf(stderr, "\n");
+       fprintf(stderr, "Note: For SOLiD reads, the first read is F3 and the second is R3.\n\n");
        return 1;
 }