From 87664941b09d8ded9705ccdb5af7b375751d5187 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Mon, 24 Jan 2011 22:00:24 -0500
Subject: [PATCH] Release bwa-0.5.9 (r16)

---
 NEWS   | 27 +++++++++++++++++++++++++++
 README |  2 +-
 bwa.1  |  2 +-
 main.c |  2 +-
 4 files changed, 30 insertions(+), 3 deletions(-)

diff --git a/NEWS b/NEWS
index 027beec0..a49db00d 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,30 @@
+Beta Release 0.5.9 (24 January, 2011)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes:
+
+ * Feature: barcode support via the `-B' option.
+
+ * Feature: Illumina 1.3+ read format support via the `-I' option.
+
+ * Bugfix: RG tags are not attached to unmapped reads.
+
+ * Bugfix: very rare bwasw mismappings
+
+ * Recommend options for PacBio reads in bwasw help message.
+
+
+Also, since January 13, the BWA master repository has been moved to github:
+
+  https://github.com/lh3/bwa
+
+The revision number has been reset. All recent changes will be first
+committed to this repository.
+
+(0.5.9: 24 January 2011, r16)
+
+
+
 Beta Release Candidate 0.5.9rc1 (10 December, 2010)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
diff --git a/README b/README
index d92563da..f398cec5 100644
--- a/README
+++ b/README
@@ -23,7 +23,7 @@ Publications (Open Access):
   http://www.ncbi.nlm.nih.gov/pubmed/20080505
   http://www.ncbi.nlm.nih.gov/pubmed/19451168
 
-Part of citations (via HubMed.org):
+Incomplete list of citations (via HubMed.org):
 
   http://www.hubmed.org/references.cgi?uids=20080505
   http://www.hubmed.org/references.cgi?uids=19451168
diff --git a/bwa.1 b/bwa.1
index d6af7a03..c82fdc7a 100644
--- a/bwa.1
+++ b/bwa.1
@@ -1,4 +1,4 @@
-.TH bwa 1 "10 December 2010" "bwa-0.5.9rc1" "Bioinformatics tools"
+.TH bwa 1 "24 January 2011" "bwa-0.5.9" "Bioinformatics tools"
 .SH NAME
 .PP
 bwa - Burrows-Wheeler Alignment Tool
diff --git a/main.c b/main.c
index a87d1a10..39902964 100644
--- a/main.c
+++ b/main.c
@@ -3,7 +3,7 @@
 #include "main.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.5.9rc1-r15"
+#define PACKAGE_VERSION "0.5.9-r16"
 #endif
 
 static int usage()