From 56a18659b6d2caa5218a2d2f3e08f9f10ab2be0a Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Sat, 12 Nov 2011 16:53:53 -0500
Subject: [PATCH] crash under non-typical setting (by John Marshall)

---
 bwape.c | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/bwape.c b/bwape.c
index 30cba12..63783c8 100644
--- a/bwape.c
+++ b/bwape.c
@@ -346,7 +346,8 @@ int bwa_cal_pac_pos_pe(const bntseq_t *bns, const char *prefix, bwt_t *const _bw
 			&& (p[1]->type == BWA_TYPE_UNIQUE || p[1]->type == BWA_TYPE_REPEAT))
 		{ // only when both ends mapped
 			b128_t x;
-			int j, k, n_occ[2];
+			int j, k;
+			long long n_occ[2];
 			for (j = 0; j < 2; ++j) {
 				n_occ[j] = 0;
 				for (k = 0; k < d->aln[j].n; ++k)