Release minimap2-2.4 (r555)

NEWS.md

@@ -1,3 +1,41 @@
+Release 2.4-r555 (6 November 2017)
+----------------------------------
+
+As is planned, this release focuses on fine tuning the base algorithm. Notable
+changes include
+
+ * Changed the mapping quality scale to match the scale of BWA-MEM. This makes
+   minimap2 and BWA-MEM achieve similar sensitivity-specificity balance on real
+   short-read data.
+
+ * Improved the accuracy of splice alignment by modeling one additional base
+   close to the GT-AG signal. This model is used by default with `-x splice`.
+   For SIRV control data, however, it is recommended to add `--splice-flank=no`
+   to disable this feature as the SIRV splice signals are slightly different.
+
+ * Tuned the parameters for Nanopore Direct RNA reads. The recommended command
+   line is `-axsplice -k14 -uf` (#46).
+
+ * Fixed a segmentation fault when aligning PacBio reads (#47 and #48). This
+   bug is very rare but it affects all versions of minimap2. It is also
+   recommended to re-index reference genomes created with `map-pb`. For human,
+   two minimizers in an old index are wrong.
+
+ * Changed option `-L` in sync with the final decision of hts-specs: a fake
+   CIGAR takes the form of `<readLen>S<refLen>N`. Note that `-L` only enables
+   future tools to recognize long CIGARs. It is not possible for older tools to
+   work with such alignments in BAM (#43 and #51).
+
+ * Fixed a tiny issue whereby minimap2 may waste 8 bytes per candidate
+   alignment.
+
+The minimap2 technical note hosted at arXiv has also been updated to reflect
+recent changes.
+
+(2.4: 6 November 2017, r555)
+
+
+
 Release 2.3-r531 (22 October 2017)
 ----------------------------------
 
@@ -26,7 +64,7 @@ This release come with many improvements and bug fixes:
 
 This release has implemented all the major features I planned five months ago,
 with the addition of spliced long-read alignment. The next couple of releases
-will focus on fine tuning of base algorithms.
+will focus on fine tuning of the base algorithms.
 
 (2.3: 22 October 2017, r531)
 

README.md

@@ -1,10 +1,10 @@
-[![Release](https://img.shields.io/badge/Release-v2.3-blue.svg?style=flat)](https://github.com/lh3/minimap2/releases)
+[![Release](https://img.shields.io/badge/Release-v2.4-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)
 [![License](https://img.shields.io/badge/License-MIT-blue.svg?style=flat)](LICENSE.txt)
 [![Build Status](https://travis-ci.org/lh3/minimap2.svg?branch=master)](https://travis-ci.org/lh3/minimap2)
-<!-- [![Downloads](https://img.shields.io/github/downloads/lh3/minimap2/total.svg?style=flat)](https://github.com/lh3/minimap2/releases) -->
+[![Downloads](https://img.shields.io/github/downloads/lh3/minimap2/total.svg?style=flat)](https://github.com/lh3/minimap2/releases)
 ## <a name="started"></a>Getting Started
 ```sh
 git clone https://github.com/lh3/minimap2
@@ -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/v2.3/minimap2-2.3_x64-linux.tar.bz2 \
+wget --no-check-certificate -O- https://github.com/lh3/minimap2/releases/download/v2.4/minimap2-2.4_x64-linux.tar.bz2 \
   | tar -jxvf -
-./minimap2-2.3_x64-linux/minimap2
+./minimap2-2.4_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 "2.3-r552-dirty"
+#define MM_VERSION "2.4-r555"
 
 #ifdef __linux__
 #include <sys/resource.h>

minimap2.1

@@ -1,4 +1,4 @@
-.TH minimap2 1 "27 October 2017" "minimap2-2.3-dirty (r537)" "Bioinformatics tools"
+.TH minimap2 1 "6 November 2017" "minimap2-2.4 (r555)" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences

python/cmappy.pxd

@@ -22,7 +22,6 @@ cdef extern from "minimap.h":
 		float mask_level
 		float pri_ratio
 		int best_n
-		float min_iden
 		int max_join_long, max_join_short
 		int min_join_flank_sc
 		int a, b, q, e, q2, e2

setup.py

@@ -23,7 +23,7 @@ def readme():
 
 setup(
 	name = 'mappy',
-	version = '2.3',
+	version = '2.4',
 	url = 'https://github.com/lh3/minimap2',
 	description = 'Minimap2 python binding',
 	long_description = readme(),