ruby-minigraph 0.0.20.0 → 0.0.20.1
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- checksums.yaml +4 -4
- data/README.md +38 -6
- data/lib/minigraph/ffi/constants.rb +1 -1
- data/lib/minigraph/ffi/functions.rb +56 -2
- data/lib/minigraph/version.rb +1 -1
- data/lib/minigraph.rb +1 -0
- metadata +5 -5
checksums.yaml
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data/README.md
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## Installation
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-
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```sh
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gem install ruby-minigraph
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```
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<details>
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<summary><b>Compiling from source</b></summary>
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```sh
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git clone --recursive https://github.com/kojix2/ruby-minigraph
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@@ -22,20 +27,47 @@ bundle exec rake minigraph:build
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bundle exec rake install
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```
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-
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-
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```
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bundle exec rake test
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```
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</details>
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## Quick Start
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```ruby
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require "minigraph"
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Minigraph.execute("--version")
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```
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## APIs
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Only low-level functions are provided at this time.
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```ruby
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require "minigraph"
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MG = Minigraph
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n_threads = 4
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target = "ext/minigraph/test/MT-human.fa"
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queries = ["ext/minigraph/test/MT-orangeA.fa"]
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opt = MG::FFI::MapOpt.new
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ipt = MG::FFI::IdxOpt.new
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gpt = MG::FFI::GGOpt.new
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MG::FFI.mg_opt_set(0, ipt, opt, gpt)
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g = MG::FFI.gfa_read(target)
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ptr = FFI::MemoryPointer.new(:pointer, queries.length)
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ptrs = queries.map{ FFI::MemoryPointer.from_string(_1) }
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ptr.write_array_of_pointer(ptrs)
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MG::FFI.mg_map_files(g, 1, ptr, ipt, opt, n_threads)
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MG::FFI.gfa_destroy(g)
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```
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## Development
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```sh
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# options
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attach_function \
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:mg_opt_set,
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[:
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:mg_opt_set_raw, :mg_opt_set,
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[:pointer, IdxOpt.by_ref, MapOpt.by_ref, GGOpt.by_ref],
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:int
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private_class_method :mg_opt_set_raw
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def self.mg_opt_set(preset, io, mo, go)
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ptr = case preset
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when 0, nil
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::FFI::Pointer.new(:int, 0)
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else
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::FFI::MemoryPointer.from_string(preset.to_s)
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end
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mg_opt_set_raw(ptr, io, mo, go)
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end
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attach_function \
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:mg_opt_check,
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[IdxOpt.by_ref, MapOpt.by_ref, GGOpt.by_ref],
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:mg_ggen,
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[:pointer, :int32, :pointer, IdxOpt.by_ref, MapOpt.by_ref, GGOpt.by_ref, :int], # FIXME: gfa_t
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:int
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attach_function \
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:mg_idxopt_init,
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[IdxOpt.by_ref],
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:void
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attach_function \
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:mg_mapopt_init,
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[MapOpt.by_ref],
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:void
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attach_function \
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:mg_ggopt_init,
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[GGOpt.by_ref],
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:void
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# gfa.h
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attach_function \
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:gfa_init,
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[:void],
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:pointer # gfa_t *
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attach_function \
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:gfa_destroy,
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[:pointer], # gfa_t *
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:void
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attach_function \
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:gfa_read,
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[:string],
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:pointer # gfa_t *
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attach_function \
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:gfa_print,
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%i[pointer pointer int],
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:void
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attach_function \
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:gfa_sort_ref_arc,
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[:pointer], # gfa_t *
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:void
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end
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end
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data/lib/minigraph/version.rb
CHANGED
data/lib/minigraph.rb
CHANGED
@@ -10,6 +10,7 @@ require_relative "minigraph/version"
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# https://github.com/lh3/minigraph
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# Li, H., Feng, X. & Chu, C. The design and construction of reference pangenome graphs
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# with minigraph. Genome Biol 21, 265 (2020). https://doi.org/10.1186
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module Minigraph
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class Error < StandardError; end
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metadata
CHANGED
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--- !ruby/object:Gem::Specification
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name: ruby-minigraph
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version: !ruby/object:Gem::Version
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version: 0.0.20.
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version: 0.0.20.1
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platform: ruby
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authors:
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- kojix2
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autorequire:
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2023-
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date: 2023-06-07 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: ffi
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@@ -137,7 +137,7 @@ homepage: https://github.com/kojix2/ruby-minigraph
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licenses:
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- MIT
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metadata: {}
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post_install_message:
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post_install_message:
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rdoc_options: []
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require_paths:
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- lib
|
@@ -153,7 +153,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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version: '0'
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requirements: []
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rubygems_version: 3.4.10
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signing_key:
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signing_key:
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specification_version: 4
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summary: Ruby bindings for minigraph
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test_files: []
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