From b17b6577ac636ebd9642a0d11312b83acc9eea6f Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Wed, 23 Nov 2011 23:30:14 -0500
Subject: [PATCH] removed a useless bwa-sw CMD option

---
 bwtsw2.h      | 2 +-
 bwtsw2_aux.c  | 2 +-
 bwtsw2_main.c | 4 +---
 3 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/bwtsw2.h b/bwtsw2.h
index c13ef9c..8354511 100644
--- a/bwtsw2.h
+++ b/bwtsw2.h
@@ -14,7 +14,7 @@
 typedef struct {
 	int a, b, q, r, t, qr, bw;
 	int z, is, t_seeds, hard_clip;
-	float yita, mask_level, coef;
+	float mask_level, coef;
 	int n_threads, chunk_size;
 } bsw2opt_t;
 
diff --git a/bwtsw2_aux.c b/bwtsw2_aux.c
index 6a283e2..863d23d 100644
--- a/bwtsw2_aux.c
+++ b/bwtsw2_aux.c
@@ -51,7 +51,7 @@ bsw2opt_t *bsw2_init_opt()
 	o->a = 1; o->b = 3; o->q = 5; o->r = 2; o->t = 30;
 	o->bw = 50;
 	o->z = 1; o->is = 3; o->t_seeds = 5; o->hard_clip = 0;
-	o->mask_level = 0.50f; o->yita = 5.5f; o->coef = 5.5f;
+	o->mask_level = 0.50f; o->coef = 5.5f;
 	o->qr = o->q + o->r; o->n_threads = 1; o->chunk_size = 10000000;
 	return o;
 }
diff --git a/bwtsw2_main.c b/bwtsw2_main.c
index 86eddd7..34d3822 100644
--- a/bwtsw2_main.c
+++ b/bwtsw2_main.c
@@ -17,7 +17,7 @@ int bwa_bwtsw2(int argc, char *argv[])
 
 	opt = bsw2_init_opt();
 	srand48(11);
-	while ((c = getopt(argc, argv, "q:r:a:b:t:T:w:d:z:m:y:s:c:N:Hf:")) >= 0) {
+	while ((c = getopt(argc, argv, "q:r:a:b:t:T:w:d:z:m:s:c:N:Hf:")) >= 0) {
 		switch (c) {
 		case 'q': opt->q = atoi(optarg); break;
 		case 'r': opt->r = atoi(optarg); break;
@@ -27,7 +27,6 @@ int bwa_bwtsw2(int argc, char *argv[])
 		case 'T': opt->t = atoi(optarg); break;
 		case 't': opt->n_threads = atoi(optarg); break;
 		case 'z': opt->z = atoi(optarg); break;
-		case 'y': opt->yita = atof(optarg); break;
 		case 's': opt->is = atoi(optarg); break;
 		case 'm': opt->mask_level = atof(optarg); break;
 		case 'c': opt->coef = atof(optarg); break;
@@ -45,7 +44,6 @@ int bwa_bwtsw2(int argc, char *argv[])
 		fprintf(stderr, "         -b INT   mismatch penalty [%d]\n", opt->b);
 		fprintf(stderr, "         -q INT   gap open penalty [%d]\n", opt->q);
 		fprintf(stderr, "         -r INT   gap extension penalty [%d]\n", opt->r);
-//		fprintf(stderr, "         -y FLOAT error recurrence coef. (4..16) [%.1f]\n", opt->yita);
 		fprintf(stderr, "\n");
 		fprintf(stderr, "         -t INT   number of threads [%d]\n", opt->n_threads);
 		fprintf(stderr, "\n");