zzh
/
minimap2
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Release minimap2-2.21 (r1071)

This commit is contained in:
Heng Li 2021-07-06 13:18:55 -04:00
parent 52dbd439bc
commit 581f2d7123
8 changed files with 22 additions and 11 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

11
NEWS.md
View File

@ -1,3 +1,14 @@
Release 2.21-r1071 (6 July 2021)
--------------------------------
This release fixed a regression in short-read mapping introduced in v2.19
(#776). It also fixed invalid comparisons of uninitialized variables, though
these are harmless (#752). Long-read alignment should be identical to v2.20.
(2.21: 6 July 2021)
Release 2.20-r1061 (27 May 2021) Release 2.20-r1061 (27 May 2021)
-------------------------------- --------------------------------

4
README.md
View File

@ -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/v2.20/minimap2-2.20_x64-linux.tar.bz2 | tar -jxvf - curl -L https://github.com/lh3/minimap2/releases/download/v2.21/minimap2-2.21_x64-linux.tar.bz2 | tar -jxvf -
./minimap2-2.20_x64-linux/minimap2 ./minimap2-2.21_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
View File

@ -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/v2.20/minimap2-2.20_x64-linux.tar.bz2 | tar jxf - curl -L https://github.com/lh3/minimap2/releases/download/v2.21/minimap2-2.21_x64-linux.tar.bz2 | tar jxf -
cp minimap2-2.20_x64-linux/{minimap2,k8,paftools.js} . # copy executables cp minimap2-2.21_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
View File

@ -7,7 +7,7 @@
#include "mmpriv.h" #include "mmpriv.h"
#include "ketopt.h" #include "ketopt.h"
#define MM_VERSION "2.20-r1080-dirty" #define MM_VERSION "2.21-r1071"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #include <sys/resource.h>

6
minimap2.1
View File

@ -1,4 +1,4 @@
.TH minimap2 1 "27 May 2021" "minimap2-2.20 (r1061)" "Bioinformatics tools" .TH minimap2 1 "6 July 2021" "minimap2-2.21 (r1071)" "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
@ -592,8 +592,8 @@ Long-read splice alignment for PacBio CCS reads
.B sr .B sr
Short single-end reads without splicing Short single-end reads without splicing
.RB ( -k21 .RB ( -k21
.B -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20 .B -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -r100 -p.5 -N20 -f1000,5000 -n2 -m20
.B -s40 -g200 -2K50m --heap-sort=yes .B -s40 -g100 -2K50m --heap-sort=yes
.BR --secondary=no ). .BR --secondary=no ).
.TP .TP
.B ava-pb .B ava-pb

2
misc/paftools.js
View File

@ -1,6 +1,6 @@
#!/usr/bin/env k8 #!/usr/bin/env k8
var paftools_version = '2.20-r1061'; var paftools_version = '2.21-r1071';
/***************************** /*****************************
***** Library functions ***** ***** Library functions *****

2
python/mappy.pyx
View File

@ -3,7 +3,7 @@ from libc.stdlib cimport free
cimport cmappy cimport cmappy
import sys import sys
__version__ = '2.20' __version__ = '2.21'
cmappy.mm_reset_timer() cmappy.mm_reset_timer()

2
setup.py
View File

@ -23,7 +23,7 @@ def readme():
setup( setup(
name = 'mappy', name = 'mappy',
version = '2.20', version = '2.21',
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(),