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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
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14
NEWS.md
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@ -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) 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 no longer recommended over minimap2. Sorry for reverting the recommendation in
short time. short time.
(2.20: 26 May 2021, r1057) (2.19: 26 May 2021, r1057)

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/v2.19/minimap2-2.19_x64-linux.tar.bz2 | tar -jxvf - curl -L https://github.com/lh3/minimap2/releases/download/v2.20/minimap2-2.20_x64-linux.tar.bz2 | tar -jxvf -
./minimap2-2.19_x64-linux/minimap2 ./minimap2-2.20_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/v2.19/minimap2-2.19_x64-linux.tar.bz2 | tar jxf - curl -L https://github.com/lh3/minimap2/releases/download/v2.20/minimap2-2.20_x64-linux.tar.bz2 | tar jxf -
cp minimap2-2.19_x64-linux/{minimap2,k8,paftools.js} . # copy executables cp minimap2-2.20_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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@ -7,7 +7,7 @@
#include "mmpriv.h" #include "mmpriv.h"
#include "ketopt.h" #include "ketopt.h"
#define MM_VERSION "2.19-r1060-dirty" #define MM_VERSION "2.20-r1061"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #include <sys/resource.h>

2
map.c
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@ -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); 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; 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) { if (qlen_sum - (en - st) > opt->rmq_rescue_size || en - st > qlen_sum * opt->rmq_rescue_ratio) {
int32_t i; int32_t i;

2
minimap2.1
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@ -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 .SH NAME
.PP .PP
minimap2 - mapping and alignment between collections of DNA sequences minimap2 - mapping and alignment between collections of DNA sequences

2
misc/paftools.js
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@ -1,6 +1,6 @@
#!/usr/bin/env k8 #!/usr/bin/env k8
var paftools_version = '2.19-r1057'; var paftools_version = '2.20-r1061';
/***************************** /*****************************
***** Library functions ***** ***** Library functions *****

4
options.c
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@ -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) void mm_mapopt_max_intron_len(mm_mapopt_t *opt, int max_intron_len)
{ {
if ((opt->flag & MM_F_SPLICE) && max_intron_len > 0) 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) 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; io->flag = 0, io->k = 19, io->w = 19;
mo->bw = mo->bw_long = 100000; mo->bw = mo->bw_long = 100000;
mo->max_gap = 10000; 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_mid_occ = 50, mo->max_mid_occ = 500;
mo->min_dp_max = 200; mo->min_dp_max = 200;
mo->best_n = 50; mo->best_n = 50;

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__ = '2.19' __version__ = '2.20'
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 = '2.19', version = '2.20',
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(),