From bcd53f36006f4864b238fa1b31a46f8a177fd5d7 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Fri, 2 Mar 2012 18:14:51 -0500
Subject: [PATCH] bugfix: wrong score for KSW_XBYTE

---
 ksw.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ksw.c b/ksw.c
index 400a81f..3f0fea8 100644
--- a/ksw.c
+++ b/ksw.c
@@ -198,7 +198,7 @@ end_loop16:
 		}
 		S = H1; H1 = H0; H0 = S; // swap H0 and H1
 	}
-	r.score = gmax + q->shift < 255? gmax + q->shift : 255;
+	r.score = gmax + q->shift < 255? gmax : 255;
 	r.te = te;
 	if (r.score != 255) { // get a->qe, the end of query match; find the 2nd best score
 		int max = -1, low, high, qlen = slen * 16;
-- 
2.47.3