From 7ec8b5c9e7c77f034925039d69eba20e0470b91f Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Thu, 30 May 2013 16:20:16 -0400
Subject: [PATCH] Release bwa-0.7.5a

---
 NEWS    | 10 ++++++++++
 bwase.c |  4 ++--
 main.c  |  2 +-
 3 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/NEWS b/NEWS
index f53e337..29627f0 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,13 @@
+Release 0.7.5a (30 May, 2013)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Fixed a bug in BWA-backtrack which leads to off-by-one mapping errors in rare
+cases.
+
+(0.7.5a: 30 May 2013, r405)
+
+
+
 Release 0.7.5 (29 May, 2013)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
diff --git a/bwase.c b/bwase.c
index 4c9e0fd..746add5 100644
--- a/bwase.c
+++ b/bwase.c
@@ -182,8 +182,8 @@ bwa_cigar_t *bwa_refine_gapped_core(bwtint_t l_pac, const ubyte_t *pacseq, int l
 	assert(re - rb == rlen);
 	ksw_global(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW, n_cigar, &cigar32);
 	assert(*n_cigar > 0);
-	if ((cigar32[*n_cigar - 1]&0xf) == 1) cigar32[*n_cigar - 1] = (cigar32[*n_cigar - 1]>>4<<4) | 4; // change endding ins to soft clipping
-	if ((cigar32[0]&0xf) == 1) cigar32[0] = (cigar32[0]>>4<<4) | 4; // change beginning ins to soft clipping
+	if ((cigar32[*n_cigar - 1]&0xf) == 1) cigar32[*n_cigar - 1] = (cigar32[*n_cigar - 1]>>4<<4) | 3; // change endding ins to soft clipping
+	if ((cigar32[0]&0xf) == 1) cigar32[0] = (cigar32[0]>>4<<4) | 3; // change beginning ins to soft clipping
 	if ((cigar32[*n_cigar - 1]&0xf) == 2) --*n_cigar; // delete endding del
 	if ((cigar32[0]&0xf) == 2) { // delete beginning del
 		*_rb += cigar32[0]>>4;
diff --git a/main.c b/main.c
index 2c6d08c..662d54f 100644
--- a/main.c
+++ b/main.c
@@ -3,7 +3,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.5-r404"
+#define PACKAGE_VERSION "0.7.5a-r405"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);