From 9f26bfcc7780753129b60717ecab0ebba6f04b7c Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Mon, 23 Oct 2017 13:10:17 -0400
Subject: [PATCH] Released bwa-0.7.17 (r1188)

---
 NEWS.md | 11 +++++++++++
 bwa.1   |  9 +++++++--
 main.c  |  2 +-
 3 files changed, 19 insertions(+), 3 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 02a1c0ce..151e024b 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,14 @@
+Release 0.7.17 (23 October 2017)
+--------------------------------
+
+This release adds option -q to preserve the mapping quality of split alignment
+with a lower alignment score than the primary alignment. Option -5
+automatically applies -q as well.
+
+(0.7.17: 23 October 2017, r1188)
+
+
+
 Release 0.7.16 (30 July 2017)
 -----------------------------
 
diff --git a/bwa.1 b/bwa.1
index 94c2c58e..d30ac331 100644
--- a/bwa.1
+++ b/bwa.1
@@ -1,4 +1,4 @@
-.TH bwa 1 "30 July 2017" "bwa-0.7.16-r1180" "Bioinformatics tools"
+.TH bwa 1 "23 October 2017" "bwa-0.7.17-r1188" "Bioinformatics tools"
 .SH NAME
 .PP
 bwa - Burrows-Wheeler Alignment Tool
@@ -303,9 +303,14 @@ For compatibility with other BWA commands, this option may also be given as
 .IR FILE .
 [standard ouptut]
 .TP
+.B -q
+ Don't reduce the mapping quality of split alignment of lower alignment score.
+.TP
 .B -5
 For split alignment, mark the segment with the smallest coordinate as the
-primary. This option may help some Hi-C pipelines. By default, BWA-MEM marks
+primary. It automatically applies option
+.B -q
+as well. This option may help some Hi-C pipelines. By default, BWA-MEM marks
 highest scoring segment as primary.
 .TP
 .B -K \ INT
diff --git a/main.c b/main.c
index 063384e7..50ae755e 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.16a-r1187-dirty"
+#define PACKAGE_VERSION "0.7.17-r1188"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);