From eeb314edd6ca56b8e134896d87fa04c2bf2015da Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Sat, 24 Feb 2018 09:31:09 -0500
Subject: [PATCH] Release minimap2-2.9 (r720)

---
 NEWS.md    | 23 +++++++++++++++++++++++
 README.md  |  4 ++--
 main.c     |  2 +-
 minimap2.1 |  2 +-
 setup.py   |  4 ++--
 5 files changed, 29 insertions(+), 6 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 6ab5e03..5c32cfa 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,26 @@
+Release 2.9-r720 (23 February 2018)
+-----------------------------------
+
+This release fixed multiple minor bugs.
+
+* Fixed two bugs that lead to incorrect inversion alignment. Also improved the
+  sensitivity to small inversions by using double Z-drop cutoff (#112).
+
+* Fixed an issue that may cause the end of a query sequence unmapped (#104).
+
+* Added a mappy API to retrieve sequences from the index (#126) and to reverse
+  complement DNA sequences. Fixed a bug where the `best_n` parameter did not
+  work (#117).
+
+* Avoided segmentation fault given incorrect FASTQ input (#111).
+
+* Combined all auxiliary javascripts to paftools.js. Fixed several bugs in
+  these scripts at the same time.
+
+(2.9: 24 February 2018, r720)
+
+
+
 Release 2.8-r672 (1 February 2018)
 ----------------------------------
 
diff --git a/README.md b/README.md
index c01fe36..1f8954f 100644
--- a/README.md
+++ b/README.md
@@ -68,9 +68,9 @@ Detailed evaluations are available from the [minimap2 preprint][preprint].
 Minimap2 is optimized for x86-64 CPUs. You can acquire precompiled binaries from
 the [release page][release] with:
 ```sh
-curl -L https://github.com/lh3/minimap2/releases/download/v2.8/minimap2-2.8_x64-linux.tar.bz2 \
+curl -L https://github.com/lh3/minimap2/releases/download/v2.9/minimap2-2.9_x64-linux.tar.bz2 \
   | tar -jxvf -
-./minimap2-2.8_x64-linux/minimap2
+./minimap2-2.9_x64-linux/minimap2
 ```
 If you want to compile from the source, you need to have a C compiler, GNU make
 and zlib development files installed. Then type `make` in the source code
diff --git a/main.c b/main.c
index 00a8948..9b91e69 100644
--- a/main.c
+++ b/main.c
@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "getopt.h"
 
-#define MM_VERSION "2.8-r719-dirty"
+#define MM_VERSION "2.9-r720"
 
 #ifdef __linux__
 #include <sys/resource.h>
diff --git a/minimap2.1 b/minimap2.1
index 1bd735c..6745ffa 100644
--- a/minimap2.1
+++ b/minimap2.1
@@ -1,4 +1,4 @@
-.TH minimap2 1 "1 February 2018" "minimap2-2.8 (r672)" "Bioinformatics tools"
+.TH minimap2 1 "24 February 2018" "minimap2-2.9 (r720)" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences
diff --git a/setup.py b/setup.py
index 0166097..cf2ea8e 100644
--- a/setup.py
+++ b/setup.py
@@ -23,7 +23,7 @@ def readme():
 
 setup(
 	name = 'mappy',
-	version = '2.8',
+	version = '2.9',
 	url = 'https://github.com/lh3/minimap2',
 	description = 'Minimap2 python binding',
 	long_description = readme(),
@@ -43,7 +43,7 @@ setup(
 		include_dirs = ['.'],
 		libraries = ['z', 'm', 'pthread'])],
 	classifiers = [
-		'Development Status :: 4 - Beta',
+		'Development Status :: 5 - Production/Stable',
 		'License :: OSI Approved :: MIT License',
 		'Operating System :: POSIX',
 		'Programming Language :: C',