ruby-minigraph 0.0.20.0
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- checksums.yaml +7 -0
- data/LICENSE.txt +21 -0
- data/README.md +62 -0
- data/ext/Rakefile +56 -0
- data/ext/cmappy/cmappy.c +7 -0
- data/ext/cmappy/cmappy.h +8 -0
- data/ext/minigraph/LICENSE.txt +23 -0
- data/ext/minigraph/Makefile +66 -0
- data/ext/minigraph/NEWS.md +317 -0
- data/ext/minigraph/README.md +207 -0
- data/ext/minigraph/algo.c +194 -0
- data/ext/minigraph/algo.h +33 -0
- data/ext/minigraph/asm-call.c +147 -0
- data/ext/minigraph/bseq.c +133 -0
- data/ext/minigraph/bseq.h +76 -0
- data/ext/minigraph/cal_cov.c +139 -0
- data/ext/minigraph/doc/example1.png +0 -0
- data/ext/minigraph/doc/example2.png +0 -0
- data/ext/minigraph/doc/examples.graffle +0 -0
- data/ext/minigraph/format.c +241 -0
- data/ext/minigraph/galign.c +140 -0
- data/ext/minigraph/gchain1.c +532 -0
- data/ext/minigraph/gcmisc.c +223 -0
- data/ext/minigraph/gfa-aug.c +260 -0
- data/ext/minigraph/gfa-base.c +526 -0
- data/ext/minigraph/gfa-bbl.c +372 -0
- data/ext/minigraph/gfa-ed.c +617 -0
- data/ext/minigraph/gfa-io.c +395 -0
- data/ext/minigraph/gfa-priv.h +154 -0
- data/ext/minigraph/gfa.h +166 -0
- data/ext/minigraph/ggen.c +182 -0
- data/ext/minigraph/ggen.h +21 -0
- data/ext/minigraph/ggsimple.c +570 -0
- data/ext/minigraph/gmap.c +211 -0
- data/ext/minigraph/index.c +230 -0
- data/ext/minigraph/kalloc.c +224 -0
- data/ext/minigraph/kalloc.h +82 -0
- data/ext/minigraph/kavl.h +414 -0
- data/ext/minigraph/kdq.h +134 -0
- data/ext/minigraph/ketopt.h +116 -0
- data/ext/minigraph/khashl.h +348 -0
- data/ext/minigraph/krmq.h +474 -0
- data/ext/minigraph/kseq.h +256 -0
- data/ext/minigraph/ksort.h +164 -0
- data/ext/minigraph/kstring.h +165 -0
- data/ext/minigraph/kthread.c +159 -0
- data/ext/minigraph/kthread.h +15 -0
- data/ext/minigraph/kvec-km.h +105 -0
- data/ext/minigraph/kvec.h +110 -0
- data/ext/minigraph/lchain.c +441 -0
- data/ext/minigraph/main.c +301 -0
- data/ext/minigraph/map-algo.c +500 -0
- data/ext/minigraph/mgpriv.h +128 -0
- data/ext/minigraph/minigraph.1 +359 -0
- data/ext/minigraph/minigraph.h +176 -0
- data/ext/minigraph/miniwfa.c +834 -0
- data/ext/minigraph/miniwfa.h +95 -0
- data/ext/minigraph/misc/mgutils.js +1451 -0
- data/ext/minigraph/misc.c +12 -0
- data/ext/minigraph/options.c +134 -0
- data/ext/minigraph/shortk.c +251 -0
- data/ext/minigraph/sketch.c +109 -0
- data/ext/minigraph/sys.c +147 -0
- data/ext/minigraph/sys.h +20 -0
- data/ext/minigraph/test/MT-chimp.fa +277 -0
- data/ext/minigraph/test/MT-human.fa +239 -0
- data/ext/minigraph/test/MT-orangA.fa +276 -0
- data/ext/minigraph/test/MT.gfa +19 -0
- data/ext/minigraph/tex/Makefile +13 -0
- data/ext/minigraph/tex/minigraph.bib +676 -0
- data/ext/minigraph/tex/minigraph.tex +986 -0
- data/ext/minigraph/tex/plots/CHM13-f1-90.bb.anno.gp +42 -0
- data/ext/minigraph/tex/plots/CHM13-f1-90.bb.anno.tbl +13 -0
- data/ext/minigraph/tex/plots/CHM13-f1-90.bb.mini-inter-none.win.gp +269 -0
- data/ext/minigraph/tex/plots/CHM13-f1-90.bb.mini-inter-none.win.sh +7 -0
- data/ext/minigraph/tex/plots/CHM13v1.cen.bed +23 -0
- data/ext/minigraph/tex/plots/CHM13v1.size +23 -0
- data/ext/minigraph/tex/plots/anno2tbl.js +40 -0
- data/ext/minigraph/tex/plots/bedutils.js +367 -0
- data/ext/minigraph/tex/plots/chr-plot.js +130 -0
- data/ext/minigraph/tex/plots/gen-anno.mak +24 -0
- data/ext/minigraph.patch +21 -0
- data/lib/minigraph/ffi/constants.rb +230 -0
- data/lib/minigraph/ffi/functions.rb +70 -0
- data/lib/minigraph/ffi/mappy.rb +8 -0
- data/lib/minigraph/ffi.rb +27 -0
- data/lib/minigraph/version.rb +5 -0
- data/lib/minigraph.rb +72 -0
- metadata +159 -0
checksums.yaml
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---
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SHA256:
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metadata.gz: 49f58deab3da3bede2c3097c3f1cd2c246adc9f327b2c1f4dce099d60b4ddddb
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data.tar.gz: e877833193973c617c12247901cc4ea18f1718dbce408f877052b702da533d94
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SHA512:
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metadata.gz: c185b325b680d528d55c069e9b9f0697cdde2dd73bbe7f8cce68215e07a1c32335c633217656592c0c33fdc5b97570f33768cb8208338ccbb3288d981f12ee83
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data.tar.gz: a3d3787cd6534192f9366b1c4b1eb9cba0a0520904e583a21d7fd6251eb1958e0bdfa22e586ae8bb5a9223a3fc11218a0c68c830ab54c8e027f4e6f15b0a1bf6
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data/LICENSE.txt
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The MIT License (MIT)
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Copyright (c) 2020 kojix2
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in
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all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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THE SOFTWARE.
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data/README.md
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# ruby-minigraph
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[![Gem Version](https://badge.fury.io/rb/ruby-minigraph.svg)](https://badge.fury.io/rb/ruby-minigraph)
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[![test](https://github.com/kojix2/ruby-minigraph/actions/workflows/ci.yml/badge.svg)](https://github.com/kojix2/ruby-minigraph/actions/workflows/ci.yml)
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[![Docs Latest](https://img.shields.io/badge/docs-latest-blue.svg)](https://kojix2.github.io/ruby-minigraph/)
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[![The MIT License](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE.txt)
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[![DOI](https://zenodo.org/badge/339645970.svg)](https://zenodo.org/badge/latestdoi/339645970)
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:curly_loop: [minigraph](https://github.com/lh3/minigraph) - the sequence-to-graph mapper - for [Ruby](https://github.com/ruby/ruby)
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:construction: under development
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## Installation
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You need to install it from the source code. Because you need to build minigraph and create a shared library. Open your terminal and type the following commands in order.
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```sh
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git clone --recursive https://github.com/kojix2/ruby-minigraph
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cd ruby-minigraph
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bundle install
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bundle exec rake minigraph:build
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bundle exec rake install
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```
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You can run tests to see if the installation was successful.
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```
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bundle exec rake test
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```
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## Quick Start
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```ruby
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require "minigraph"
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```
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## APIs
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## Development
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```sh
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git clone --recursive https://github.com/kojix2/ruby-minigraph
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# git clone https://github.com/kojix2/ruby-minigraph
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# cd ruby-minigraph
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# git submodule update -i
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cd ruby-minigraph
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bundle install
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bundle exec rake minigraph:build
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bundle exec rake test
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```
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## Contributing
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ruby-minigraph is a library under development and there are many points to be improved.
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If you improve the source code, please feel free to send us your pull request.
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Typo corrections are also welcome.
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Bug reports and pull requests are welcome on GitHub at https://github.com/kojix2/ruby-minigraph.
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## License
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[MIT License](https://opensource.org/licenses/MIT).
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data/ext/Rakefile
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# frozen_string_literal: true
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require "rake"
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require "fileutils"
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require "ffi"
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minigraph_dir = File.expand_path("minigraph", __dir__)
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target_dir = "../../vendor"
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target_fname = FFI.map_library_name("minigraph")
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target_path = File.join(target_dir, target_fname)
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task default: ["minigraph:build", "minigraph:clean"]
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namespace :minigraph do
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desc "Compile Minigraph"
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task :build do
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Dir.chdir(minigraph_dir) do
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# Add -fPIC option to Makefile
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sh "git apply ../minigraph.patch"
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sh "cp ../cmappy/cmappy.h ../cmappy/cmappy.c ."
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# case RbConfig::CONFIG["host_cpu"]
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sh "make"
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# end
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case RbConfig::CONFIG["host_os"]
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when /mswin|msys|mingw|cygwin|bccwin|wince|emc/
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warn "windows not supported"
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sh "cc *.o -shared -o #{target_fname} -lm -lz -lpthread"
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when /darwin|mac os/
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sh "clang -dynamiclib -undefined dynamic_lookup -o #{target_fname} *.o -lm -lz -lpthread"
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sh "otool -L #{target_fname}"
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else
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sh "cc *.o -shared -o #{target_fname} -lm -lz -lpthread"
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sh "ldd -r #{target_fname}"
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end
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sh "rm cmappy.h cmappy.c"
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sh "git apply -R ../minigraph.patch"
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FileUtils.mkdir_p(target_dir)
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warn "mkdir -p #{target_dir}"
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sh "mv #{target_fname} #{target_path}"
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end
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end
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desc "make clean"
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task :clean do
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Dir.chdir(minigraph_dir) do
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sh "make clean"
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end
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end
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desc "`make clean` and remove shared lib"
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task cleanall: [:clean] do
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Dir.chdir(minigraph_dir) do
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sh "rm #{target_path}" if File.exist?(target_path)
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end
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end
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end
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data/ext/cmappy/cmappy.c
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data/ext/cmappy/cmappy.h
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The MIT License
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Copyright (c) 2019- Dana-Farber Cancer Institute
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
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BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
|
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ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
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CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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CC= gcc
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CFLAGS= -g -Wall -Wc++-compat -std=c99 -msse4 -O3
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CPPFLAGS=
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INCLUDES=
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OBJS= kalloc.o kthread.o algo.o sys.o gfa-base.o gfa-io.o gfa-aug.o gfa-bbl.o gfa-ed.o \
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sketch.o misc.o bseq.o options.o shortk.o miniwfa.o \
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index.o lchain.o gchain1.o galign.o gcmisc.o map-algo.o cal_cov.o \
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format.o gmap.o ggsimple.o ggen.o asm-call.o
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PROG= minigraph
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LIBS= -lz -lpthread -lm
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ifneq ($(asan),)
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CFLAGS+=-fsanitize=address
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LIBS+=-fsanitize=address -ldl
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endif
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.SUFFIXES:.c .o
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.PHONY:all clean depend
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.c.o:
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$(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
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all:$(PROG)
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minigraph:$(OBJS) main.o
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$(CC) $(CFLAGS) $^ -o $@ $(LIBS)
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clean:
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rm -fr gmon.out *.o a.out $(PROG) *~ *.a *.dSYM
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depend:
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(LC_ALL=C; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) -- *.c)
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# DO NOT DELETE
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algo.o: kalloc.h algo.h miniwfa.h kvec-km.h ksort.h
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asm-call.o: mgpriv.h minigraph.h gfa.h ggen.h bseq.h gfa-priv.h algo.h
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bseq.o: bseq.h kvec-km.h kalloc.h kseq.h
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cal_cov.o: mgpriv.h minigraph.h gfa.h gfa-priv.h algo.h kalloc.h
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format.o: kalloc.h mgpriv.h minigraph.h gfa.h
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galign.o: mgpriv.h minigraph.h gfa.h kalloc.h miniwfa.h
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gchain1.o: mgpriv.h minigraph.h gfa.h ksort.h khashl.h kalloc.h gfa-priv.h
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gcmisc.o: mgpriv.h minigraph.h gfa.h kalloc.h
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gfa-aug.o: gfa-priv.h gfa.h ksort.h
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gfa-base.o: gfa-priv.h gfa.h kstring.h khashl.h kalloc.h ksort.h
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gfa-bbl.o: gfa-priv.h gfa.h kalloc.h ksort.h kvec.h
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gfa-ed.o: gfa-priv.h gfa.h kalloc.h ksort.h khashl.h kdq.h kvec-km.h
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gfa-io.o: kstring.h gfa-priv.h gfa.h kseq.h
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ggen.o: kthread.h kalloc.h sys.h bseq.h ggen.h minigraph.h gfa.h mgpriv.h
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ggen.o: gfa-priv.h
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ggsimple.o: mgpriv.h minigraph.h gfa.h gfa-priv.h kalloc.h bseq.h algo.h
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ggsimple.o: sys.h ggen.h kvec-km.h
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gmap.o: kthread.h kalloc.h bseq.h sys.h mgpriv.h minigraph.h gfa.h gfa-priv.h
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index.o: mgpriv.h minigraph.h gfa.h khashl.h kalloc.h kthread.h kvec-km.h
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index.o: sys.h
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kalloc.o: kalloc.h
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kthread.o: kthread.h
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lchain.o: mgpriv.h minigraph.h gfa.h kalloc.h krmq.h
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main.o: mgpriv.h minigraph.h gfa.h gfa-priv.h sys.h ketopt.h
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map-algo.o: kalloc.h mgpriv.h minigraph.h gfa.h khashl.h ksort.h
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miniwfa.o: miniwfa.h kalloc.h
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misc.o: mgpriv.h minigraph.h gfa.h ksort.h
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options.o: mgpriv.h minigraph.h gfa.h sys.h
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shortk.o: mgpriv.h minigraph.h gfa.h ksort.h kavl.h algo.h khashl.h kalloc.h
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sketch.o: kvec-km.h kalloc.h mgpriv.h minigraph.h gfa.h
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sys.o: sys.h
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Release 0.20-r559 (20 November 2022)
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------------------------------------
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This release fixes several assertion failures (#78, #79 and #80) caused by
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recent changes in graph chaining. It also fixes an integer overflow that may
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happen to chromosomes longer than 256 Mb (#76). Results remain the same.
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(20 November 2022, r559)
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Release 0.19-r551 (12 June 2022)
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--------------------------------
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14
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15
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This release fixes a segmental fault if minigraph is compiled with certain
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compiler-libc combinations. This is apparently caused by memcpy(0,0,0).
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Minigraph is otherwise identical v0.18.
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(12 June 2022, r551)
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Release 0.18-r538 (9 May 2022)
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------------------------------
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This release uses heuristics to speed up base alignment in long divergent
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regions. The heuristics does not guarantee optimal alignment but it reliably
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produces alignment close to the optimal except in centromeres where the
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algorithmically optimal alignment may not represent true evolution in biology.
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The new version is 10-700% faster than v0.17 depending on input data and
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parameters in use.
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(9 May 2022, r538)
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Release 0.17-r524 (29 April 2022)
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---------------------------------
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This release adds base alignment to minigraph. It represents the first major
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improvement to minigraph. Specifically, this release attempts to connect linear
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chains with the graph wavefront alignemnt algorithm (GWFA) and produces the
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final alignment with miniwfa under the 2-piece gap penalty. Graph generation
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also considers base alignment. This gives more accurate graph alignment and
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generally simpler graph topology. Note that minigraph still focuses on
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structural variations and does not generate base-level graphs. To endusers,
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minigraph remains similar feature wise.
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+
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Notable changes:
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* New feature: option `-c` for base alignment and graph generation. In the
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alignment mode, the option adds the `cg:Z` CIGAR tag like minimap2. Graph
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generation still works without `-c` but applying this option is generally
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recommended now.
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+
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It should be noted that the base alignment is currently slow for species of
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high diversity. This will be addressed in the next couple of releases.
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(29 April 2022, r524)
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Release 0.16-r436 (21 February 2022)
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------------------------------------
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65
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+
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66
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Notable changes:
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* Improvement: 2-level chaining. This is a feature backported from minimap2.
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It speeds up graph generation for human graphs.
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+
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* Improvement: break a chain at poorly aligned regions, another recent
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minimap2 feature.
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* Added the script for generating figures in the minigraph paper.
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(21 February 2022, r436)
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Release 0.15-r426 (21 March 2021)
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+
---------------------------------
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Fixed a bug in bubble identification around inversions. This version should be
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used together with the latest gfatools for consistency.
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+
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(21 March 2021, r426)
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Release 0.14-r415 (19 December 2020)
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+
------------------------------------
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+
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93
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+
Notable changes:
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+
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95
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* Added the `--call` option to find the allele/walk in each bubble.
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+
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* Reduced the default minimum variant length (option `-L`) from 100 to 50 for
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the consistency with the SV community.
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(19 December 2020, r415)
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+
Release 0.13-r397 (3 December 2020)
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-----------------------------------
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+
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+
Notable change:
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+
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* Fixed incorrect anchors in linear chains. In older versions, a linear chain
|
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may contain two anchors with identical reference or query coordinates.
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+
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(3 December 2020, r397)
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+
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Release 0.12-r389 (26 October 2020)
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+
-----------------------------------
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+
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+
Notable changes:
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+
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* Improve alignments towards ends of graph segments. If there is an SV close to
|
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the ends but not at the ends, older versions may produce an excessively
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large bubble including high-identity matches.
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+
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* Heuristically accelerates alignment in complex subgraphs by skipping
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many unnecessary sequence-aware graph traversals. This speeds up graph
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generation for CHM13 by three folds without obviously affecting accuracy.
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+
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* Added option --inv to optionally disable inversions. Graph traversal is hard
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+
with inversions.
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+
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* Fixed the bug that prevents large -K.
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* Apply option -K4g to the asm preset.
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+
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* Added option --write-mz to output the positions of minimizer anchors.
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+
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+
(26 October 2020, r389)
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+
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+
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+
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+
Release 0.11-r371 (13 September 2020)
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+
-------------------------------------
|
144
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+
|
145
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+
Notable changes:
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+
|
147
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+
* Added option --max-rmq-size to limit the max RMQ size, which is set 100k by
|
148
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+
default. This heuristic reduces the long running time for aligning long
|
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centromeric sequences. The accuracy might be affected in rare cases.
|
150
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+
|
151
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+
* Cap the max k-mer occurrence to 250 by default. For maize genomes, the
|
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+
current heuristic may choose an occurrence cutoff larger than 1000. This
|
153
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+
makes minigraph too slow to be practical.
|
154
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+
|
155
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+
* Added option -S to output more detailed information about linear chains.
|
156
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+
|
157
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+
* Added option -D to ignore diagonal minimizer anchors. This is useful to
|
158
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+
mapping a sequence against itself.
|
159
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+
|
160
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+
(13 September 2020, r371)
|
161
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+
|
162
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+
|
163
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+
|
164
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+
Release 0.10-r356 (14 February 2020)
|
165
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+
------------------------------------
|
166
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+
|
167
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+
Notable changes:
|
168
|
+
|
169
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+
* Older releases miss a small fraction of INDELs involving repeats. This
|
170
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+
release fixes this issue.
|
171
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+
|
172
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+
* Added the "stableGaf" command to mgutils.js to convert unstable GAF (e.g. by
|
173
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+
GraphAligner) to stable GAF.
|
174
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+
|
175
|
+
(14 February 2020, r356)
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176
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+
|
177
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+
|
178
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+
|
179
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+
Release 0.9-r343 (31 December 2019)
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180
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+
-----------------------------------
|
181
|
+
|
182
|
+
Notable changes:
|
183
|
+
|
184
|
+
* RMQ based linear chaining. The chaining accuracy should be higher for large
|
185
|
+
events. The speed remains similar.
|
186
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+
|
187
|
+
* Use ksw2 to check the sequence divergence of events to be inserted.
|
188
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+
|
189
|
+
* Treat inversions as special events. Don't insert them as long substitutions.
|
190
|
+
|
191
|
+
(31 December 2019, r343)
|
192
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+
|
193
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+
|
194
|
+
|
195
|
+
Release 0.8-r316 (11 December 2019)
|
196
|
+
-----------------------------------
|
197
|
+
|
198
|
+
This release reduces suboptimal chains caused by the chaining heuristics. It
|
199
|
+
generates slightly simpler human graphs.
|
200
|
+
|
201
|
+
(11 December 2019, r316)
|
202
|
+
|
203
|
+
|
204
|
+
|
205
|
+
Release 0.7-r310 (21 November 2019)
|
206
|
+
-----------------------------------
|
207
|
+
|
208
|
+
Notable changes:
|
209
|
+
|
210
|
+
* Increased the default maximum INDEL/event length from 10kb to 100kb for
|
211
|
+
assembly mapping and graph generation.
|
212
|
+
|
213
|
+
* Decreased the default minimum INDEL/event length from 250bp to 100bp.
|
214
|
+
|
215
|
+
* Accelerated graph mapping by pre-filtering isolated anchors and disconnected
|
216
|
+
linear chains. This triples the performance when long gaps are desired.
|
217
|
+
|
218
|
+
Due to the change of default parameters, this release generates graphs
|
219
|
+
different from the previous versions.
|
220
|
+
|
221
|
+
(21 November 2019, r310)
|
222
|
+
|
223
|
+
|
224
|
+
|
225
|
+
Release 0.6-r302 (17 November 2019)
|
226
|
+
-----------------------------------
|
227
|
+
|
228
|
+
Notable changes:
|
229
|
+
|
230
|
+
* Assign weight to seeds based on their repetitiveness. This helps chaining in
|
231
|
+
repetitive regions a little bit.
|
232
|
+
|
233
|
+
* For short-read mapping, prefer the reference path if the alternate path is
|
234
|
+
not much better.
|
235
|
+
|
236
|
+
Major changes may be coming in the next release.
|
237
|
+
|
238
|
+
(17 November 2019, r302)
|
239
|
+
|
240
|
+
|
241
|
+
|
242
|
+
Release 0.5-r285 (8 September 2019)
|
243
|
+
-----------------------------------
|
244
|
+
|
245
|
+
Notable changes:
|
246
|
+
|
247
|
+
* Fixed a bug that leads to wrong mapping positions in GAF.
|
248
|
+
|
249
|
+
* Fixed two bugs related to graph chaining.
|
250
|
+
|
251
|
+
* Added option `-j` to set expected sequence divergence and to adjust other
|
252
|
+
chaining parameters accordingly.
|
253
|
+
|
254
|
+
* Increased the k-mer thresholds for fast divergence estimate. This improves
|
255
|
+
the alignment around low-complexity regions.
|
256
|
+
|
257
|
+
* Tuned the default parameters to add highly divergent events only.
|
258
|
+
|
259
|
+
* Warn about duplicated sequence names in graph construction (#3).
|
260
|
+
|
261
|
+
This version generates graphs different from the previous versions. The mapping
|
262
|
+
accuracy is improved due to the bug fixes and parameter tuning.
|
263
|
+
|
264
|
+
(8 September 2019, r285)
|
265
|
+
|
266
|
+
|
267
|
+
|
268
|
+
Release 0.4-r267 (22 August 2019)
|
269
|
+
---------------------------------
|
270
|
+
|
271
|
+
Notable changes:
|
272
|
+
|
273
|
+
* Support paired-end mapping for short reads.
|
274
|
+
|
275
|
+
* Remap and calculate coverage (see the new --cov option in the manpage).
|
276
|
+
|
277
|
+
* Fixed multiple edges in the generated graphs. The v0.3 14-genome graph
|
278
|
+
contains one multiple edge.
|
279
|
+
|
280
|
+
* Use dynamic minimizer occurrence cutoff. For human data, the dynamic cutoff
|
281
|
+
is around 137, higher than the default cutoff 100 used in earlier versions.
|
282
|
+
As a result, graph generations will become a little slower.
|
283
|
+
|
284
|
+
Due to the last two changes, graphs generated with this version are different
|
285
|
+
from the previous versions.
|
286
|
+
|
287
|
+
(22 August 2019, r267)
|
288
|
+
|
289
|
+
|
290
|
+
|
291
|
+
Release 0.3-r243 (7 August 2019)
|
292
|
+
--------------------------------
|
293
|
+
|
294
|
+
This release generates graphs with SR tags on L-lines. The topology of the
|
295
|
+
graph is identical to the one generated with v0.2.
|
296
|
+
|
297
|
+
(7 August 2019, r243)
|
298
|
+
|
299
|
+
|
300
|
+
|
301
|
+
Release 0.2-r235 (19 July 2019)
|
302
|
+
-------------------------------
|
303
|
+
|
304
|
+
This release fixes multiple minor bugs. It also considers k-mer matches and
|
305
|
+
improves the accuracy of graph chaining. Nonetheless, the old chaining
|
306
|
+
algorithm, albeit simple, works quite well. The improvement is marginal.
|
307
|
+
|
308
|
+
(19 July 2019, r235)
|
309
|
+
|
310
|
+
|
311
|
+
|
312
|
+
Release 0.1-r191 (6 July 2019)
|
313
|
+
------------------------------
|
314
|
+
|
315
|
+
Initial proof-of-concept release.
|
316
|
+
|
317
|
+
(6 July 2019, r191)
|