Release minimap2-2.5 (r572)

Author: lh3

NEWS.md

@@ -1,3 +1,26 @@
+Release 2.5-r572 (11 November 2017)
+-----------------------------------
+
+This release fixes several bugs and brings a couple of minor improvements:
+
+ * Fixed a severe bug that leads to incorrect mapping coordinates in rare
+   corner cases.
+
+ * Fixed underestimated mapping quality for chimeric alignments when the whole
+   query sequence contain many repetitive minimizers, and for chimeric
+   alignments caused by Z-drop.
+
+ * Fixed two bugs in Python binding: incorrect strand field (#57) and incorrect
+   sequence names for Python3 (#55).
+
+ * Improved mapping accuracy for highly overlapping paired ends.
+
+ * Added option -Y to use soft clipping for supplementary alignments (#56).
+
+(2.5: 11 November 2017, r572)
+
+
+
 Release 2.4-r555 (6 November 2017)
 ----------------------------------
 

README.md

@@ -1,4 +1,4 @@
-[![Release](https://img.shields.io/badge/Release-v2.4-blue.svg?style=flat)](https://github.com/lh3/minimap2/releases)
+[![Release](https://img.shields.io/badge/Release-v2.5-blue.svg?style=flat)](https://github.com/lh3/minimap2/releases)
 [![BioConda](https://img.shields.io/conda/vn/bioconda/minimap2.svg?style=flat)](https://anaconda.org/bioconda/minimap2)
 [![PyPI](https://img.shields.io/pypi/v/mappy.svg?style=flat)](https://pypi.python.org/pypi/mappy)
 [![Python Version](https://img.shields.io/pypi/pyversions/mappy.svg?style=flat)](https://pypi.python.org/pypi/mappy)
@@ -71,9 +71,9 @@ Detailed evaluations are available from the [minimap2 preprint][preprint].
 Minimap2 only works on x86-64 CPUs. You can acquire precompiled binaries from
 the [release page][release] with:
 ```sh
-wget --no-check-certificate -O- https://github.com/lh3/minimap2/releases/download/v2.4/minimap2-2.4_x64-linux.tar.bz2 \
+curl -L https://github.com/lh3/minimap2/releases/download/v2.5/minimap2-2.5_x64-linux.tar.bz2 \
   | tar -jxvf -
-./minimap2-2.4_x64-linux/minimap2
+./minimap2-2.5_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

main.c

@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "getopt.h"
 
-#define MM_VERSION "2.4-r569-dirty"
+#define MM_VERSION "2.5-r572"
 
 #ifdef __linux__
 #include <sys/resource.h>

minimap2.1

@@ -1,4 +1,4 @@
-.TH minimap2 1 "6 November 2017" "minimap2-2.4 (r555)" "Bioinformatics tools"
+.TH minimap2 1 "11 November 2017" "minimap2-2.5 (r572)" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences

setup.py

@@ -23,7 +23,7 @@ def readme():
 
 setup(
 	name = 'mappy',
-	version = '2.4',
+	version = '2.5',
 	url = 'https://github.com/lh3/minimap2',
 	description = 'Minimap2 python binding',
 	long_description = readme(),