From c404f49569fa2d606b652418ffa4b9743bcaf641 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Thu, 10 Jan 2019 12:34:45 -0500
Subject: [PATCH] Release minimap2-2.15 (r905)

---
 NEWS.md          | 36 ++++++++++++++++++++++++++++++++++++
 README.md        |  4 ++--
 cookbook.md      |  4 ++--
 main.c           |  2 +-
 minimap2.1       |  2 +-
 misc/paftools.js |  2 +-
 python/mappy.pyx |  2 +-
 setup.py         |  2 +-
 8 files changed, 45 insertions(+), 9 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index e5060bc..e540e50 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,39 @@
+Release 2.15-r905 (10 January 2019)
+-----------------------------------
+
+Changes to minimap2:
+
+ * Fixed a rare segmentation fault when option -H is in use (#307). This may
+   happen when there are very long homopolymers towards the 5'-end of a read.
+
+ * Fixed wrong CIGARs when option --eqx is used (#266).
+
+ * Fixed a typo in the base encoding table (#264). This should have no
+   practical effect.
+
+ * Fixed a typo in the example code (#265).
+
+ * Improved the C++ compatibility by removing "register" (#261). However,
+   minimap2 still can't be compiled in the pedantic C++ mode (#306).
+
+ * Output a new "de" tag for gap-compressed sequence divergence.
+
+Changes to paftools.js:
+
+ * Added "asmgene" to evaluate the completeness of an assembly by measuring the
+   uniquely mapped single-copy genes. This command learns the idea of BUSCO.
+
+ * Added "vcfpair" to call a phased VCF from phased whole-genome assemblies. An
+   earlier version of this script is used to produce the ground truth for the
+   syndip benchmark [PMID:30013044].
+
+This release produces identical alignment coordinates and CIGARs in comparison
+to v2.14. Users are advised to upgrade due to the several bug fixes.
+
+(2.15: 10 Janurary 2019, r905)
+
+
+
 Release 2.14-r883 (5 November 2018)
 -----------------------------------
 
diff --git a/README.md b/README.md
index d3ba33f..3fe3387 100644
--- a/README.md
+++ b/README.md
@@ -71,8 +71,8 @@ Detailed evaluations are available from the [minimap2 paper][doi] or the
 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/v2.14/minimap2-2.14_x64-linux.tar.bz2 | tar -jxvf -
-./minimap2-2.14_x64-linux/minimap2
+curl -L https://github.com/lh3/minimap2/releases/download/v2.15/minimap2-2.15_x64-linux.tar.bz2 | tar -jxvf -
+./minimap2-2.15_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/cookbook.md b/cookbook.md
index d43d190..6345f0e 100644
--- a/cookbook.md
+++ b/cookbook.md
@@ -31,8 +31,8 @@ To acquire the data used in this cookbook and to install minimap2 and paftools,
 please follow the command lines below:
 ```sh
 # install minimap2 executables
-curl -L https://github.com/lh3/minimap2/releases/download/v2.14/minimap2-2.14_x64-linux.tar.bz2 | tar jxf -
-cp minimap2-2.14_x64-linux/{minimap2,k8,paftools.js} .  # copy executables
+curl -L https://github.com/lh3/minimap2/releases/download/v2.15/minimap2-2.15_x64-linux.tar.bz2 | tar jxf -
+cp minimap2-2.15_x64-linux/{minimap2,k8,paftools.js} .  # copy executables
 export PATH="$PATH:"`pwd`                               # put the current directory on PATH
 # download example datasets
 curl -L https://github.com/lh3/minimap2/releases/download/v2.10/cookbook-data.tgz | tar zxf -
diff --git a/main.c b/main.c
index 9f52bb7..9481685 100644
--- a/main.c
+++ b/main.c
@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "ketopt.h"
 
-#define MM_VERSION "2.14-r904-dirty"
+#define MM_VERSION "2.15-r905"
 
 #ifdef __linux__
 #include <sys/resource.h>
diff --git a/minimap2.1 b/minimap2.1
index b9badbb..ffb8158 100644
--- a/minimap2.1
+++ b/minimap2.1
@@ -1,4 +1,4 @@
-.TH minimap2 1 "12 December 2018" "minimap2-2.14-dirty (r894)" "Bioinformatics tools"
+.TH minimap2 1 "10 January 2019" "minimap2-2.15 (r905)" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences
diff --git a/misc/paftools.js b/misc/paftools.js
index c84ffa8..77e3c94 100755
--- a/misc/paftools.js
+++ b/misc/paftools.js
@@ -1,6 +1,6 @@
 #!/usr/bin/env k8
 
-var paftools_version = '2.14-r895-dirty';
+var paftools_version = '2.15-r905';
 
 /*****************************
  ***** Library functions *****
diff --git a/python/mappy.pyx b/python/mappy.pyx
index b9e703f..8d55fca 100644
--- a/python/mappy.pyx
+++ b/python/mappy.pyx
@@ -3,7 +3,7 @@ from libc.stdlib cimport free
 cimport cmappy
 import sys
 
-__version__ = '2.14'
+__version__ = '2.15'
 
 cmappy.mm_reset_timer()
 
diff --git a/setup.py b/setup.py
index 1760057..bf689f4 100644
--- a/setup.py
+++ b/setup.py
@@ -33,7 +33,7 @@ def readme():
 
 setup(
 	name = 'mappy',
-	version = '2.14',
+	version = '2.15',
 	url = 'https://github.com/lh3/minimap2',
 	description = 'Minimap2 python binding',
 	long_description = readme(),