From 95a79afe719011c14c11736b7a239b2e78e848b4 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Fri, 8 Feb 2013 22:11:44 -0500
Subject: [PATCH] command-line prompt

---
 fastmap.c | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/fastmap.c b/fastmap.c
index e31b0a5..990f442 100644
--- a/fastmap.c
+++ b/fastmap.c
@@ -33,7 +33,10 @@ int main_mem(int argc, char *argv[])
 	}
 	if (optind + 1 >= argc) {
 		fprintf(stderr, "\n");
-		fprintf(stderr, "Usage: bwa mem [options] <idxbase> <in1.fq> [in2.fq]\n");
+		fprintf(stderr, "Usage:   bwa mem [options] <idxbase> <in.fq>\n");
+		fprintf(stderr, "Options: -k INT     minimum seed length [%d]\n", opt->min_seed_len);
+		fprintf(stderr, "         -c INT     skip seeds with more than INT occurrences [%d]\n", opt->max_occ);
+		fprintf(stderr, "         -s INT     look for internal seeds inside a seed with less than INT occ [%d]\n", opt->split_width);
 		fprintf(stderr, "\n");
 		free(opt);
 		return 1;