From 8977f07269bd7fd57959927e2b7ddcff9362043e Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Tue, 27 Jun 2017 14:50:31 -0400
Subject: [PATCH] r88: fixed an out-of-boundary bug in ksw2

---
 ksw2_extz2_sse.c | 4 ++++
 main.c           | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/ksw2_extz2_sse.c b/ksw2_extz2_sse.c
index 05167cc..1fedb40 100644
--- a/ksw2_extz2_sse.c
+++ b/ksw2_extz2_sse.c
@@ -102,6 +102,10 @@ void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 		if (en > r) en = r;
 		if (st < (r-wr+1)>>1) st = (r-wr+1)>>1; // take the ceil
 		if (en > (r+wl)>>1) en = (r+wl)>>1; // take the floor
+		if (st > en) {
+			ez->zdropped = 1;
+			break;
+		}
 		st0 = st, en0 = en;
 		st = st / 16 * 16, en = (en + 16) / 16 * 16 - 1;
 		// set boundary conditions
diff --git a/main.c b/main.c
index 1094c69..1d3bcbd 100644
--- a/main.c
+++ b/main.c
@@ -10,7 +10,7 @@
 #include "minimap.h"
 #include "mmpriv.h"
 
-#define MM_VERSION "2.0-r87-pre"
+#define MM_VERSION "2.0-r88-pre"
 
 void liftrlimit()
 {