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

Release minimap2-2.20 (r1061)

This commit is contained in:
Heng Li 2021-05-27 15:26:04 -04:00
parent ca19463268
commit 15471bd629
10 changed files with 25 additions and 13 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

14
NEWS.md
View File

@ -1,3 +1,15 @@
Release 2.20-r1061 (27 May 2021)
--------------------------------
This release fixed a bug in the Python module and improves the command-line
compatibiliity with v2.18. In v2.19, if `-r` is specified with an `asm*` preset,
users would get alignments more fragmented than v2.18. This could be an issue
for existing pipelines specifying `-r`. This release resolves this issue.
(2.20: 27 May 2021, r1061)
Release 2.19-r1057 (26 May 2021)
--------------------------------
@ -33,7 +45,7 @@ unimap for contig alignment. Unimap will remain an experimental project and is
no longer recommended over minimap2. Sorry for reverting the recommendation in
short time.
(2.20: 26 May 2021, r1057)
(2.19: 26 May 2021, r1057)

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
the [release page][release] with:
```sh
curl -L https://github.com/lh3/minimap2/releases/download/v2.19/minimap2-2.19_x64-linux.tar.bz2 | tar -jxvf -
./minimap2-2.19_x64-linux/minimap2
curl -L https://github.com/lh3/minimap2/releases/download/v2.20/minimap2-2.20_x64-linux.tar.bz2 | tar -jxvf -
./minimap2-2.20_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

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:
```sh
# install minimap2 executables
curl -L https://github.com/lh3/minimap2/releases/download/v2.19/minimap2-2.19_x64-linux.tar.bz2 | tar jxf -
cp minimap2-2.19_x64-linux/{minimap2,k8,paftools.js} . # copy executables
curl -L https://github.com/lh3/minimap2/releases/download/v2.20/minimap2-2.20_x64-linux.tar.bz2 | tar jxf -
cp minimap2-2.20_x64-linux/{minimap2,k8,paftools.js} . # copy executables
export PATH="$PATH:"`pwd` # put the current directory on PATH
# download example datasets
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 "ketopt.h"
#define MM_VERSION "2.19-r1060-dirty"
#define MM_VERSION "2.20-r1061"
#ifdef __linux__
#include <sys/resource.h>

2
map.c
View File

@ -277,7 +277,7 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
opt->chain_gap_scale * 0.01 * mi->k, 0.0f, is_splice, n_segs, n_a, a, &n_regs0, &u, b->km);
}
if (opt->bw_long > opt->bw && (opt->flag & MM_F_NO_LJOIN) == 0 && n_segs == 1 && n_regs0 > 1) { // re-chain/long-join for long sequences
if (opt->bw_long > opt->bw && (opt->flag & (MM_F_SPLICE|MM_F_SR|MM_F_NO_LJOIN)) == 0 && n_segs == 1 && n_regs0 > 1) { // re-chain/long-join for long sequences
int32_t st = (int32_t)a[0].y, en = (int32_t)a[(int32_t)u[0] - 1].y;
if (qlen_sum - (en - st) > opt->rmq_rescue_size || en - st > qlen_sum * opt->rmq_rescue_ratio) {
int32_t i;

2
minimap2.1
View File

@ -1,4 +1,4 @@
.TH minimap2 1 "26 May 2021" "minimap2-2.19 (r1057)" "Bioinformatics tools"
.TH minimap2 1 "27 May 2021" "minimap2-2.20 (r1061)" "Bioinformatics tools"
.SH NAME
.PP
minimap2 - mapping and alignment between collections of DNA sequences

2
misc/paftools.js
View File

@ -1,6 +1,6 @@
#!/usr/bin/env k8
var paftools_version = '2.19-r1057';
var paftools_version = '2.20-r1061';
/*****************************
***** Library functions *****

4
options.c
View File

@ -75,7 +75,7 @@ void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi)
void mm_mapopt_max_intron_len(mm_mapopt_t *opt, int max_intron_len)
{
if ((opt->flag & MM_F_SPLICE) && max_intron_len > 0)
opt->max_gap_ref = opt->bw = max_intron_len;
opt->max_gap_ref = opt->bw = opt->bw_long = max_intron_len;
}
int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
@ -109,7 +109,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
io->flag = 0, io->k = 19, io->w = 19;
mo->bw = mo->bw_long = 100000;
mo->max_gap = 10000;
mo->flag |= MM_F_RMQ | MM_F_NO_LJOIN;
mo->flag |= MM_F_RMQ;
mo->min_mid_occ = 50, mo->max_mid_occ = 500;
mo->min_dp_max = 200;
mo->best_n = 50;

2
python/mappy.pyx
View File

@ -3,7 +3,7 @@ from libc.stdlib cimport free
cimport cmappy
import sys
__version__ = '2.19'
__version__ = '2.20'
cmappy.mm_reset_timer()

2
setup.py
View File

@ -23,7 +23,7 @@ def readme():
setup(
name = 'mappy',
version = '2.19',
version = '2.20',
url = 'https://github.com/lh3/minimap2',
description = 'Minimap2 python binding',
long_description = readme(),