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Release minimap2-2.24 (r1122)

This commit is contained in:
Heng Li 2021-12-26 15:14:54 -05:00
parent e25aa5ee74
commit fe35e679e9
8 changed files with 23 additions and 9 deletions
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14
NEWS.md
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@ -1,3 +1,17 @@
Release 2.24-r1122 (26 December 2021)
-------------------------------------
This release improves alignment around long poorly aligned regions. Older
minimap2 may chain through such regions in rare cases which may result in
missing alignments later. The issue has become worse since the the change of
the chaining algorithm in v2.19. v2.23 implements an incomplete remedy. This
release provides a better solution with a X-drop-like heuristic and by enabling
two-bandwidth chaining in the assembly mode.
(2.24: 26 December 2021, r1122)
Release 2.23-r1111 (18 November 2021) Release 2.23-r1111 (18 November 2021)
------------------------------------- -------------------------------------

4
README.md
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@ -74,8 +74,8 @@ Detailed evaluations are available from the [minimap2 paper][doi] or the
Minimap2 is optimized for x86-64 CPUs. You can acquire precompiled binaries from Minimap2 is optimized for x86-64 CPUs. You can acquire precompiled binaries from
the [release page][release] with: the [release page][release] with:
```sh ```sh
curl -L https://github.com/lh3/minimap2/releases/download/v2.23/minimap2-2.23_x64-linux.tar.bz2 | tar -jxvf - curl -L https://github.com/lh3/minimap2/releases/download/v2.24/minimap2-2.24_x64-linux.tar.bz2 | tar -jxvf -
./minimap2-2.23_x64-linux/minimap2 ./minimap2-2.24_x64-linux/minimap2
``` ```
If you want to compile from the source, you need to have a C compiler, GNU make 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 and zlib development files installed. Then type `make` in the source code

4
cookbook.md
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@ -31,8 +31,8 @@ To acquire the data used in this cookbook and to install minimap2 and paftools,
please follow the command lines below: please follow the command lines below:
```sh ```sh
# install minimap2 executables # install minimap2 executables
curl -L https://github.com/lh3/minimap2/releases/download/v2.23/minimap2-2.23_x64-linux.tar.bz2 | tar jxf - curl -L https://github.com/lh3/minimap2/releases/download/v2.24/minimap2-2.24_x64-linux.tar.bz2 | tar jxf -
cp minimap2-2.23_x64-linux/{minimap2,k8,paftools.js} . # copy executables cp minimap2-2.24_x64-linux/{minimap2,k8,paftools.js} . # copy executables
export PATH="$PATH:"`pwd` # put the current directory on PATH export PATH="$PATH:"`pwd` # put the current directory on PATH
# download example datasets # download example datasets
curl -L https://github.com/lh3/minimap2/releases/download/v2.10/cookbook-data.tgz | tar zxf - curl -L https://github.com/lh3/minimap2/releases/download/v2.10/cookbook-data.tgz | tar zxf -

2
main.c
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#include "mmpriv.h" #include "mmpriv.h"
#include "ketopt.h" #include "ketopt.h"
#define MM_VERSION "2.23-r1119-dirty" #define MM_VERSION "2.24-r1122"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #include <sys/resource.h>

2
minimap2.1
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.TH minimap2 1 "18 December 2021" "minimap2-2.24 (r1121)" "Bioinformatics tools" .TH minimap2 1 "18 December 2021" "minimap2-2.24 (r1122)" "Bioinformatics tools"
.SH NAME .SH NAME
.PP .PP
minimap2 - mapping and alignment between collections of DNA sequences minimap2 - mapping and alignment between collections of DNA sequences

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misc/paftools.js
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#!/usr/bin/env k8 #!/usr/bin/env k8
var paftools_version = '2.23-r1111'; var paftools_version = '2.24-r1122';
/***************************** /*****************************
***** Library functions ***** ***** Library functions *****

2
python/mappy.pyx
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@ -3,7 +3,7 @@ from libc.stdlib cimport free
cimport cmappy cimport cmappy
import sys import sys
__version__ = '2.23' __version__ = '2.24'
cmappy.mm_reset_timer() cmappy.mm_reset_timer()

2
setup.py
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@ -23,7 +23,7 @@ def readme():
setup( setup(
name = 'mappy', name = 'mappy',
version = '2.23', version = '2.24',
url = 'https://github.com/lh3/minimap2', url = 'https://github.com/lh3/minimap2',
description = 'Minimap2 python binding', description = 'Minimap2 python binding',
long_description = readme(), long_description = readme(),