From b5b50ac8da72bfe06810bbe24055dfb1218f83e3 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Thu, 7 Mar 2013 21:35:57 -0500
Subject: [PATCH] r341: bugfix - wrong mate position

when one end is mapped with a score less than -T. Caused by the -T option.
---
 bwamem_pair.c | 2 +-
 main.c        | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/bwamem_pair.c b/bwamem_pair.c
index 9ff12b3..49e9ad2 100644
--- a/bwamem_pair.c
+++ b/bwamem_pair.c
@@ -303,7 +303,7 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
 
 no_pairing:
 	for (i = 0; i < 2; ++i) {
-		if (a[i].n) {
+		if (a[i].n && a[i].a[0].score >= opt->T) {
 			mem_alnreg2hit(&a[i].a[0], &h[i]);
 			bwa_fix_xref(opt->mat, opt->q, opt->r, opt->w, bns, pac, (uint8_t*)s[i].seq, &h[i].qb, &h[i].qe, &h[i].rb, &h[i].re);
 		} else h[i].rb = h[i].re = -1;
diff --git a/main.c b/main.c
index da986a7..a772e3b 100644
--- a/main.c
+++ b/main.c
@@ -3,7 +3,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.0-r340-beta"
+#define PACKAGE_VERSION "0.7.0-r341-beta"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);