From b856a286f88f7b4db1b8cd9689664e1ccc6ecc08 Mon Sep 17 00:00:00 2001
From: Lisle Mose <lislemose@gmail.com>
Date: Tue, 3 May 2016 15:59:00 -0400
Subject: [PATCH] Extend assembled contig further into constant region.  Start
 contig in frame.

---
 src/main/c/params.c | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/main/c/params.c b/src/main/c/params.c
index b756158..f9de05c 100644
--- a/src/main/c/params.c
+++ b/src/main/c/params.c
@@ -66,8 +66,8 @@ void set_default_params(params* p) {
 	p->min_source_homology_score = 30;
 	p->filter_read_span = 35;
 	p->filter_mate_span = 48;
-	p->eval_start = 50;
-	p->eval_stop = 390;
+	p->eval_start = 52;
+	p->eval_stop = 411;
 	p->threads = 1;
 	p->window_overlap_check_size = 320;
 }
@@ -92,11 +92,12 @@ void usage() {
 	fprintf(stderr, "\t--ins <expected / median insert length>\n");
 	fprintf(stderr, "\t--rf <read filter floor (default: 1)\n");
 	fprintf(stderr, "\t--k <kmer size (default: 35)>\n");
+	fprintf(stderr, "\t--vk <vregion kmer size (default: 15)>\n");
 	fprintf(stderr, "\t--mrs <min source node homology score (default: 30)\n");
 	fprintf(stderr, "\t--rs <read span distance (default: 35)>\n");
 	fprintf(stderr, "\t--ms <mate span distance (default: 48)>\n");
-	fprintf(stderr, "\t--e0 <start position for contig filtering (default: 50)>\n");
-	fprintf(stderr, "\t--e1 <stop position for contig filtering (default: 390)>\n");
+	fprintf(stderr, "\t--e0 <start position for contig filtering (default: 52)>\n");
+	fprintf(stderr, "\t--e1 <stop position for contig filtering (default: 411)>\n");
 	fprintf(stderr, "\t--wo <window overlap check size>\n");
 }