From a471f1918ba52a27987bc9a4e76db25369c7aa95 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Mon, 19 Mar 2012 13:45:09 -0400
Subject: [PATCH] bugfix: long-existing out-of-boundary bug

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

diff --git a/bwase.c b/bwase.c
index 8fa8d45..f05fff9 100644
--- a/bwase.c
+++ b/bwase.c
@@ -245,7 +245,7 @@ char *bwa_cal_md1(int n_cigar, bwa_cigar_t *cigar, int len, bwtint_t pos, ubyte_
 			}
 		}
 	} else { // no gaps
-		for (z = u = 0; z < (bwtint_t)len; ++z) {
+		for (z = u = 0; z < (bwtint_t)len && x+z < l_pac; ++z) {
 			c = pacseq[(x+z)>>2] >> ((~(x+z)&3)<<1) & 3;
 			if (c > 3 || seq[y+z] > 3 || c != seq[y+z]) {
 				ksprintf(str, "%d", u);