From 220fc39e9daf3569ca328a76f5075da50f85c968 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Fri, 8 Feb 2013 14:51:24 -0500
Subject: [PATCH] the previous change does not work... Fixed.

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

diff --git a/bwamem.c b/bwamem.c
index b2f61a4..b4283fd 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -402,8 +402,8 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
 			if (t->rbeg + t->len > a->re || t->qbeg + t->len > a->qe)
 				break;
 		}
+		if (a->score >= best.score) csub = best.score, best = *a;
 		if (i >= c->n) break; // all seeds are included; no need to proceed
-		if (a->score > best.score) csub = best.score, best = *a;
 		k = i;
 	}
 	if (a->score < best.score) *a = best;