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Release minimap2-2.14 (r883)

This commit is contained in:
Heng Li 2018-11-06 00:03:16 -05:00
parent 5e55e397e9
commit 59f23f7579
8 changed files with 24 additions and 15 deletions
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16
NEWS.md
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@ -1,22 +1,26 @@
Release 2.14-r8xx (yy November 2018) Release 2.14-r883 (5 November 2018)
------------------------------------ -----------------------------------
Changes to minimap2: Notable changes:
* Fixed two minor bugs caused by typos (#254 and #266). * Fixed two minor bugs caused by typos (#254 and #266).
* Fixed a bug that made minimap2 abort when -L was used with --MD/--cs (#257). * Fixed a bug that made minimap2 abort when --eqx was used together with --MD
or --cs (#257).
* Added --cap-sw-mem to cap the size of DP matrices (#259). Base alignment may * Added --cap-sw-mem to cap the size of DP matrices (#259). Base alignment may
take a lot of memory in the splicing mode. This may lead to issues when we take a lot of memory in the splicing mode. This may lead to issues when we
run minimap2 on a cluster with a hard memory limit. The new option avoids run minimap2 on a cluster with a hard memory limit. The new option avoids
unlimited memory usage at the cost of missing a few long introns. unlimited memory usage at the cost of missing a few long introns.
* Conforming to C99 and C11 if possible (#261). * Conforming to C99 and C11 when possible (#261).
* Warn about malformatted FASTA or FASTQ (#252 and #255). * Warn about malformatted FASTA or FASTQ (#252 and #255).
(2.14: yy November 2018, r8xx) This release occasionally produces base alignments different from v2.13. The
overall alignment accuracy remain similar.
(2.14: 5 November 2018, r883)

4
README.md
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@ -71,8 +71,8 @@ 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/v2.13/minimap2-2.13_x64-linux.tar.bz2 | tar -jxvf - curl -L https://github.com/lh3/minimap2/releases/download/v2.14/minimap2-2.14_x64-linux.tar.bz2 | tar -jxvf -
./minimap2-2.13_x64-linux/minimap2 ./minimap2-2.14_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/v2.13/minimap2-2.13_x64-linux.tar.bz2 | tar jxf - curl -L https://github.com/lh3/minimap2/releases/download/v2.14/minimap2-2.14_x64-linux.tar.bz2 | tar jxf -
cp minimap2-2.13_x64-linux/{minimap2,k8,paftools.js} . # copy executables cp minimap2-2.14_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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@ -6,7 +6,7 @@
#include "mmpriv.h" #include "mmpriv.h"
#include "ketopt.h" #include "ketopt.h"
#define MM_VERSION "2.13-r882-dirty" #define MM_VERSION "2.14-r883"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #include <sys/resource.h>

2
minimap2.1
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@ -1,4 +1,4 @@
.TH minimap2 1 "11 October 2018" "minimap2-2.13 (r850)" "Bioinformatics tools" .TH minimap2 1 "5 November 2018" "minimap2-2.14 (r883)" "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

7
misc/paftools.js
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@ -1,6 +1,6 @@
#!/usr/bin/env k8 #!/usr/bin/env k8
var paftools_version = '2.13-r872-dirty'; var paftools_version = '2.14-r883';
/***************************** /*****************************
***** Library functions ***** ***** Library functions *****
@ -781,6 +781,10 @@ function paf_asmgene(args)
var n_fn = args.length - getopt.ind; var n_fn = args.length - getopt.ind;
if (n_fn < 2) { if (n_fn < 2) {
print("Usage: paftools.js asmgene [options] <ref-splice.paf> <asm-splice.paf> [...]"); print("Usage: paftools.js asmgene [options] <ref-splice.paf> <asm-splice.paf> [...]");
print("Options:");
print(" -i FLOAT min identity [" + opt.min_iden + "]");
print(" -c FLOAT min coverage [" + opt.min_cov + "]");
print(" -e print fragmented/missing genes");
exit(1); exit(1);
} }
@ -2339,6 +2343,7 @@ function main(args)
print(""); print("");
print(" stat collect basic mapping information in PAF/SAM"); print(" stat collect basic mapping information in PAF/SAM");
print(" asmstat collect basic assembly information"); print(" asmstat collect basic assembly information");
print(" asmgene evaluate gene completeness (EXPERIMENTAL)");
print(" liftover simplistic liftOver"); print(" liftover simplistic liftOver");
print(" call call variants from asm-to-ref alignment with the cs tag"); print(" call call variants from asm-to-ref alignment with the cs tag");
print(" bedcov compute the number of bases covered"); print(" bedcov compute the number of bases covered");

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__ = '2.13' __version__ = '2.14'
cmappy.mm_reset_timer() cmappy.mm_reset_timer()

2
setup.py
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@ -33,7 +33,7 @@ def readme():
setup( setup(
name = 'mappy', name = 'mappy',
version = '2.13', version = '2.14',
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(),