From af7b4d89808f1c48f320f4a2f76d3466d6ff50bc Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Fri, 8 Mar 2013 12:45:50 -0500
Subject: [PATCH] gcc wrongly thinks a variable may be uninitialized

It should always be initialized. To avoid a warning, made a change.
---
 bwamem.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bwamem.c b/bwamem.c
index 766227d..40b481a 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -612,7 +612,7 @@ void bwa_hit2sam(kstring_t *str, const int8_t mat[25], int q, int r, int w, cons
 #define is_mapped(x) ((x)->rb >= 0 && (x)->rb < (x)->re && (x)->re <= bns->l_pac<<1)
 	int score, n_cigar, is_rev = 0, rid, mid, copy_mate = 0, NM = -1;
 	uint32_t *cigar = 0;
-	int64_t pos;
+	int64_t pos = -1;
 	bwahit_t ptmp, *p = &ptmp;
 
 	if (!p_) { // in this case, generate an unmapped alignment