From 7fd6a11569f84540642071e3c4f39068d586fdbc Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Thu, 10 Jul 2014 10:53:56 -0400
Subject: [PATCH] r788: segfault when the last ref is "weird"

mem_patch_reg() did not check if two hits are on the same strand, which may
lead to an alignment bridging the forward-backward boundary.
---
 bwamem.c | 1 +
 main.c   | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/bwamem.c b/bwamem.c
index c0c7fa9..e9d9304 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -383,6 +383,7 @@ int mem_patch_reg(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac,
 	double r;
 	if (bns == 0 || pac == 0 || query == 0) return 0;
 	assert(a->rid == b->rid && a->rb <= b->rb);
+	if (a->rb < bns->l_pac && b->rb >= bns->l_pac) return 0; // on different strands
 	if (a->qb >= b->qb || a->qe >= b->qe || a->re >= b->re) return 0; // not colinear
 	w = (a->re - b->rb) - (a->qe - b->qb); // required bandwidth
 	w = w > 0? w : -w; // l = abs(l)
diff --git a/main.c b/main.c
index dfa02c2..4be18a2 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.9a-r787-dirty"
+#define PACKAGE_VERSION "0.7.9a-r788-dirty"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);