minimap2 0.2.25.2 → 0.2.26.0
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- checksums.yaml +4 -4
- data/README.md +9 -0
- data/ext/minimap2/NEWS.md +9 -0
- data/ext/minimap2/README.md +2 -2
- data/ext/minimap2/cookbook.md +2 -2
- data/ext/minimap2/minimap.h +1 -1
- data/ext/minimap2/minimap2.1 +1 -1
- data/ext/minimap2/misc/paftools.js +1 -1
- data/ext/minimap2/python/mappy.pyx +1 -1
- data/ext/minimap2/setup.py +22 -32
- data/lib/minimap2/version.rb +1 -1
- metadata +1 -1
checksums.yaml
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@@ -1,7 +1,7 @@
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---
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SHA256:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 20d1a7f791311682922de7fcb3eef581102483c8791fbd63966d42ac1492169c
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data.tar.gz: 58434a8b32467ae6136b80fdaee588d4e7ad62a8a75dcd0c11c4790a13dc3600
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 88ad1f8a20f4541999f348e24ccbd28e94da6163e999965a05b65da2b94cc09c67f070aee05e276bf4578d3e43e6986d376134701da84cf09a58b9e2adbaade1
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data.tar.gz: 4e66f4a5a0b4cfb16c4b592a5de66c0c65b8f7236ded05f6a4f4efdd0a57c3ab0a8440ad7d0bb89126142a49e9a71619e5c95a144f200b43442deb8753cf545b
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data/README.md
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@@ -169,6 +169,15 @@ Run tests.
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bundle exec rake test
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```
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Release a Gem.
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```
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bundle exec rake minimap2:cleanall
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bundle exec rake build
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ls -l pkg # Check the size of the Gem and make sure it does not contain any unused code such as shared libraries or lib/simde.
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bundle exec rake release
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```
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</details>
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ruby-minimap2 is a library under development and there are many points to be improved.
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data/ext/minimap2/NEWS.md
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data/ext/minimap2/README.md
CHANGED
@@ -74,8 +74,8 @@ Detailed evaluations are available from the [minimap2 paper][doi] or the
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Minimap2 is optimized for x86-64 CPUs. You can acquire precompiled binaries from
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the [release page][release] with:
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```sh
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curl -L https://github.com/lh3/minimap2/releases/download/v2.
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./minimap2-2.
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curl -L https://github.com/lh3/minimap2/releases/download/v2.26/minimap2-2.26_x64-linux.tar.bz2 | tar -jxvf -
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./minimap2-2.26_x64-linux/minimap2
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```
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If you want to compile from the source, you need to have a C compiler, GNU make
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and zlib development files installed. Then type `make` in the source code
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data/ext/minimap2/cookbook.md
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@@ -31,8 +31,8 @@ To acquire the data used in this cookbook and to install minimap2 and paftools,
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please follow the command lines below:
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```sh
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# install minimap2 executables
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curl -L https://github.com/lh3/minimap2/releases/download/v2.
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cp minimap2-2.
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curl -L https://github.com/lh3/minimap2/releases/download/v2.26/minimap2-2.26_x64-linux.tar.bz2 | tar jxf -
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cp minimap2-2.26_x64-linux/{minimap2,k8,paftools.js} . # copy executables
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export PATH="$PATH:"`pwd` # put the current directory on PATH
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# download example datasets
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curl -L https://github.com/lh3/minimap2/releases/download/v2.10/cookbook-data.tgz | tar zxf -
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data/ext/minimap2/minimap.h
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#include <stdio.h>
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#include <sys/types.h>
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#define MM_VERSION "2.
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#define MM_VERSION "2.26-r1175"
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#define MM_F_NO_DIAG (0x001LL) // no exact diagonal hit
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#define MM_F_NO_DUAL (0x002LL) // skip pairs where query name is lexicographically larger than target name
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data/ext/minimap2/minimap2.1
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data/ext/minimap2/setup.py
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@@ -1,40 +1,29 @@
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try:
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from setuptools import setup, Extension
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from setuptools.command.build_ext import build_ext
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except ImportError:
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from distutils.core import setup
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from distutils.extension import Extension
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from distutils.command.build_ext import build_ext
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import sys, platform
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import sys, platform
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sys.path.append('python')
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extra_compile_args = ['-DHAVE_KALLOC']
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include_dirs = ["."]
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if platform.machine() in ["aarch64", "arm64"]:
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include_dirs.append("sse2neon/")
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extra_compile_args.extend(['-ftree-vectorize', '-DKSW_SSE2_ONLY', '-D__SSE2__'])
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else:
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extra_compile_args.append('-msse4.1') # WARNING: ancient x86_64 CPUs don't have SSE4
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def readme():
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with open('python/README.rst') as f:
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return f.read()
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-
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class LibMM2Build(build_ext):
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# Uses Makefile to build library, avoids duplicating logic
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# determining which objects to compile but does require
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# end users to have Make (since precompiled wheels are not
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# distributed on PyPI).
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def run(self):
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def compile_libminimap2(*args, **kwargs):
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cmd = ['make', 'libminimap2.a'] + list(args)
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subprocess.check_call(cmd)
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options = []
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if platform.machine() in ["aarch64", "arm64"]:
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options = ["arm_neon=1", "aarch64=1"]
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self.execute(
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compile_libminimap2, options,
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'Compiling libminimap2 using Makefile')
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build_ext.run(self)
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setup(
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name = 'mappy',
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version = '2.
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version = '2.26',
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url = 'https://github.com/lh3/minimap2',
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description = 'Minimap2 python binding',
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long_description = readme(),
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@@ -43,15 +32,16 @@ setup(
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license = 'MIT',
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keywords = 'sequence-alignment',
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scripts = ['python/minimap2.py'],
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ext_modules = [Extension('mappy',
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sources = ['python/mappy.pyx', 'align.c', 'bseq.c', 'lchain.c', 'seed.c', 'format.c', 'hit.c', 'index.c', 'pe.c', 'options.c',
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'ksw2_extd2_sse.c', 'ksw2_exts2_sse.c', 'ksw2_extz2_sse.c', 'ksw2_ll_sse.c',
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'kalloc.c', 'kthread.c', 'map.c', 'misc.c', 'sdust.c', 'sketch.c', 'esterr.c', 'splitidx.c'],
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depends = ['minimap.h', 'bseq.h', 'kalloc.h', 'kdq.h', 'khash.h', 'kseq.h', 'ksort.h',
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'ksw2.h', 'kthread.h', 'kvec.h', 'mmpriv.h', 'sdust.h',
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'python/cmappy.h', 'python/cmappy.pxd'],
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extra_compile_args = extra_compile_args,
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include_dirs = include_dirs,
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libraries = ['z', 'm', 'pthread'])],
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classifiers = [
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'Development Status :: 5 - Production/Stable',
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'License :: OSI Approved :: MIT License',
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data/lib/minimap2/version.rb
CHANGED