From ea5a0cd17da3752d396473c56f074a3ab5ede613 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Sun, 17 Sep 2017 20:08:47 -0400
Subject: [PATCH] Release minimap2-2.2 (r409)

---
 NEWS.md           | 29 +++++++++++++++++++++++++++++
 main.c            |  2 +-
 minimap2.1        |  2 +-
 python/README.rst |  4 ++--
 setup.py          |  2 +-
 5 files changed, 34 insertions(+), 5 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 7b04ab6e..566ae2aa 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,32 @@
+Release 2.2-r409 (17 September 2017)
+------------------------------------
+
+This is a feature release. It improves single-end short-read alignment and
+comes with Python bindings. Detailed changes include:
+
+ * Added the **sr** preset for single-end short-read alignment. In this mode,
+   minimap2 runs faster than BWA-MEM, but is slightly less accurate on
+   simulated data sets. Paired-end alignment is not supported as of now.
+
+ * Improved mapping quality estimate with more accurate identification of
+   repetitive hits. This mainly helps short-read alignment.
+
+ * Implemented **mappy**, a Python binding for minimap2, which is available
+   from PyPI and can be installed with `pip install --user mappy`. Python users
+   can perform read alignment without the minimap2 executable.
+
+ * Restructured the indexing APIs and documented key minimap2 APIs in the
+   header file minimap.h. Updated example.c with the new APIs. Old APIs still
+   work but may become deprecated in future.
+
+This release may output alignments different from the previous version, though
+the overall alignment statistics, such as the number of aligned bases and long
+gaps, remain close.
+
+(2.2: 17 September 2017, r409)
+
+
+
 Release 2.1.1-r341 (6 September 2017)
 -------------------------------------
 
diff --git a/main.c b/main.c
index 58c3bfea..49f2a221 100644
--- a/main.c
+++ b/main.c
@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "getopt.h"
 
-#define MM_VERSION "2.1.1-r402-dirty"
+#define MM_VERSION "2.2-r409"
 
 #ifdef __linux__
 #include <sys/resource.h>
diff --git a/minimap2.1 b/minimap2.1
index 877b51c9..dee97d17 100644
--- a/minimap2.1
+++ b/minimap2.1
@@ -1,4 +1,4 @@
-.TH minimap2 1 "17 September 2017" "minimap2-2.1.1-r402-dirty" "Bioinformatics tools"
+.TH minimap2 1 "17 September 2017" "minimap2-2.2 (r409)" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences
diff --git a/python/README.rst b/python/README.rst
index 1d8d17f1..8629c222 100644
--- a/python/README.rst
+++ b/python/README.rst
@@ -16,7 +16,7 @@ Mappy depends on `zlib <http://zlib.net>`_. It can be installed with `pip
 
 	pip install --user mappy
 
-or from the minimap2 github repo:
+or from the minimap2 github repo (`Cython <http://cython.org>`_ required):
 
 .. code:: shell
 
@@ -27,7 +27,7 @@ or from the minimap2 github repo:
 Usage
 -----
 
-The following Python program shows the key functionality of mappy:
+The following Python script demonstrates the key functionality of mappy:
 
 .. code:: python
 
diff --git a/setup.py b/setup.py
index d9b4e82f..69ec2318 100644
--- a/setup.py
+++ b/setup.py
@@ -23,7 +23,7 @@ def readme():
 
 setup(
 	name = 'mappy',
-	version = '2.2rc1',
+	version = '2.2',
 	url = 'https://github.com/lh3/minimap2',
 	description = 'Minimap2 python binding',
 	long_description = readme(),