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Release minimap2-2.30 (r1287)

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Heng Li
2025-06-15 17:54:11 -04:00
parent ea4c8935bd
commit 79c9cc186b
8 changed files with 24 additions and 9 deletions
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NEWS.md
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Release 2.30-r1287 (15 June 2025)
---------------------------------
Notable changes:
* Improvement: consolidated `--spsc`.
* Deprecation: subcommands `splice2bed`, `gff2bed`, `gff2junc`, `junceval` and
`exoneval` in `paftools.js` are deprecated by minigff. They will remain
indefinitely for backward compatibility.
(2.30: 15 June 2025, r1287)
Release 2.29-r1283 (18 April 2025) Release 2.29-r1283 (18 April 2025)
---------------------------------- ----------------------------------
README.md
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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/v2.29/minimap2-2.29_x64-linux.tar.bz2 | tar -jxvf - curl -L https://github.com/lh3/minimap2/releases/download/v2.30/minimap2-2.30_x64-linux.tar.bz2 | tar -jxvf -
./minimap2-2.29_x64-linux/minimap2 ./minimap2-2.30_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
cookbook.md
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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/v2.29/minimap2-2.29_x64-linux.tar.bz2 | tar jxf - curl -L https://github.com/lh3/minimap2/releases/download/v2.30/minimap2-2.30_x64-linux.tar.bz2 | tar jxf -
cp minimap2-2.29_x64-linux/{minimap2,k8,paftools.js} . # copy executables cp minimap2-2.30_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 -
minimap.h
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#include <stdio.h> #include <stdio.h>
#include <sys/types.h> #include <sys/types.h>
#define MM_VERSION "2.29-r1285-dirty" #define MM_VERSION "2.30-r1287"
#define MM_F_NO_DIAG (0x001LL) // no exact diagonal hit #define MM_F_NO_DIAG (0x001LL) // no exact diagonal hit
#define MM_F_NO_DUAL (0x002LL) // skip pairs where query name is lexicographically larger than target name #define MM_F_NO_DUAL (0x002LL) // skip pairs where query name is lexicographically larger than target name
minimap2.1
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.TH minimap2 1 "18 April 2025" "minimap2-2.29 (r1283)" "Bioinformatics tools" .TH minimap2 1 "15 June 2025" "minimap2-2.30 (r1287)" "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
misc/paftools.js
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#!/usr/bin/env k8 #!/usr/bin/env k8
var paftools_version = '2.29-r1283'; var paftools_version = '2.30-r1287';
/***************************** /*****************************
***** Library functions ***** ***** Library functions *****
python/mappy.pyx
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cimport cmappy cimport cmappy
import sys import sys
__version__ = '2.29' __version__ = '2.30'
cmappy.mm_reset_timer() cmappy.mm_reset_timer()
setup.py
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setup( setup(
name = 'mappy', name = 'mappy',
version = '2.29', version = '2.30',
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(),