minimap2 0.0.1 → 0.0.2
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- checksums.yaml +4 -4
- data/README.md +93 -13
- data/lib/minimap2.rb +9 -9
- data/lib/minimap2/aligner.rb +87 -51
- data/lib/minimap2/alignment.rb +53 -9
- data/lib/minimap2/ffi.rb +4 -4
- data/lib/minimap2/ffi/functions.rb +7 -7
- data/lib/minimap2/ffi/mappy.rb +2 -2
- data/lib/minimap2/ffi_helper.rb +1 -1
- data/lib/minimap2/version.rb +1 -1
- metadata +2 -3
- data/vendor/libminimap2.so +0 -0
checksums.yaml
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SHA256:
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metadata.gz:
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data.tar.gz:
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metadata.gz: '09e4267638f072ee219b2af3ef1afd3938c3a6d02f5370aa9454b25b871652b7'
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data.tar.gz: ab035c12eb6d6bda353ffab1b5f5923ec8327fea9a4552259b01b02523b7f934
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metadata.gz:
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metadata.gz: 8f24c1f2d8e07e1be825fbc2a67049d378c1e1d5f3d23312d474e796fa7968b7d85b58b061226dbf4a14e637c27708667a5737da246e4874f03cadf9df4f013e
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data.tar.gz: 5e92b4c08e02416b0385c9a5a6b6c7b46381469ae70447fea80a9269a06e1ac11155a06de3d3a4a97995880f542d8adf9cd6063afa2c133be474644dd6d3245f
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data/README.md
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# Minimap2
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[![Gem Version](https://img.shields.io/gem/v/minimap2?color=brightgreen)](https://rubygems.org/gems/minimap2)
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[![CI](https://github.com/kojix2/ruby-minimap2/workflows/CI/badge.svg)](https://github.com/kojix2/ruby-minimap2/actions)
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[![The MIT License](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE.txt)
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[![Docs Latest](https://img.shields.io/badge/docs-stable-blue.svg)](https://rubydoc.info/gems/minimap2)
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:dna: [minimap2](https://github.com/lh3/minimap2) - the long-read mapper - for [Ruby](https://github.com/ruby/ruby)
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## Installation
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You need to install
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-
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You need to install ruby-minimap2 from the source code. Because you need to build minimap2 and create a shared library. Open your terminal and type the following commands in order.
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Build
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```sh
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git clone --recurse-submodules https://github.com/kojix2/ruby-minimap2
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cd ruby-minimap2
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bundle install
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bundle exec rake minimap2:build
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bundle exec rake install
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```
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-
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Install
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```
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bundle exec rake
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bundle exec rake install
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```
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Ruby-minimap2 is tested on Ubuntu and macOS.
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## Quick Start
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```ruby
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@@ -37,40 +42,115 @@ seq = aligner.seq("MT_human", 100, 200)
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# mapping
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aligner.align(seq) do |h|
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pp h.to_h
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# {:ctg => "MT_human",
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# :ctg_len => 16569,
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# :r_st => 100,
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# :r_en => 200,
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# :strand => 1,
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# :trans_strand => 0,
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# :blen => 100,
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# :mlen => 100,
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# :nm => 0,
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# :primary => 1,
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# :q_st => 0,
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# :q_en => 100,
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# :mapq => 60,
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# :cigar => [[100, 0]],
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# :read_num => 1,
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# :cs => "",
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# :md => "",
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# :cigar_str => "100M"}
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end
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```
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## APIs
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## APIs Overview
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See
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* [Mappy: Minimap2 Python Binding](https://github.com/lh3/minimap2/tree/master/python)
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See the [RubyDoc.info document](https://rubydoc.info/gems/minimap2) for details.
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```markdown
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* Minimap2 module
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- fastx_read
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- revcomp
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* Aligner class
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* attributes
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- index
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- idx_opt
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- map_opt
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* methods
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- new(path, preset: nil)
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- align
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* Alignment class
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* attributes
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- ctg
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- ctg_len
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- r_st
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- r_en
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- strand
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- trans_strand
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- blen
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- mlen
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- nm
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- primary
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- q_st
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- q_en
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- mapq
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- cigar
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- read_num
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- cs
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- md
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- cigar_str
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* methods
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- to_h
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- to_s
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* FFI module
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* IdxOpt class
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* MapOpt class
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```
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The ruby-minimap2 API is compliant with mappy, the official Python binding for Minimap2. However, there are a few differences. For example, the `map` method has been renamed to `align` since map is the common name for iterators in Ruby.
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* [Mappy: Minimap2 Python Binding](https://github.com/lh3/minimap2/tree/master/python)
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ruby-minimap2 is built on top of [Ruby-FFI](https://github.com/ffi/ffi). Native functions can be called from the FFI module, which also provides a way to access some C structs such as IdxOpt and MapOpt.
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## Development
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Fork your repository and clone.
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```sh
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git clone --recurse-submodules https://github.com/kojix2/ruby-minimap2
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# git clone https://github.com/kojix2/ruby-minimap2
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# cd ruby-minimap2
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# git submodule update -i
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```
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Build.
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```sh
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cd ruby-minimap2
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bundle install
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bundle install # Install dependent packages including Ruby-FFI
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bundle exec rake minimap2:build
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```
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Run tests.
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```
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bundle exec rake test
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```
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## Contributing
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ruby-minimap2 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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ruby-minimap2 is a library under development and there are many points to be improved. Please feel free to send us your pull request.
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* [Report bugs](https://github.com/kojix2/ruby-minimap2/issues)
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* Fix bugs and [submit pull requests](https://github.com/kojix2/ruby-minimap2/pulls)
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* Write, clarify, or fix documentation
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* Suggest or add new features
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* Create tools based on ruby-minimap2
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* Update minimap2 in github submodule
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## License
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data/lib/minimap2.rb
CHANGED
@@ -1,15 +1,15 @@
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# frozen_string_literal: true
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3
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# dependencies
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require
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require 'ffi'
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6
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# bit fields
|
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require_relative
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require_relative 'minimap2/ffi_helper'
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# modules
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require_relative
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require_relative
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require_relative
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require_relative 'minimap2/aligner'
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require_relative 'minimap2/alignment'
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require_relative 'minimap2/version'
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# Minimap2 mapper for long read sequences
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# https://github.com/lh3/minimap2
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@@ -22,15 +22,15 @@ module Minimap2
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22
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attr_accessor :ffi_lib
|
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end
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24
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-
lib_name = ::FFI.map_library_name(
|
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-
self.ffi_lib = if ENV[
|
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-
File.expand_path(lib_name, ENV[
|
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lib_name = ::FFI.map_library_name('minimap2')
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self.ffi_lib = if ENV['MINIMAPDIR']
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File.expand_path(lib_name, ENV['MINIMAPDIR'])
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else
|
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File.expand_path("../vendor/#{lib_name}", __dir__)
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end
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# friendlier error message
|
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autoload :FFI,
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autoload :FFI, 'minimap2/ffi'
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# methods from mappy
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class << self
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data/lib/minimap2/aligner.rb
CHANGED
@@ -2,10 +2,34 @@
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2
2
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3
3
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module Minimap2
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class Aligner
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attr_reader :
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attr_reader :idx_opt, :map_opt, :index
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# Create a new aligner
|
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#
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# @param fn_idx_in [String] index or sequence file name.
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# @param seq [String] a single sequence to index.
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# @param preset [String] minimap2 preset.
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# @param k [Integer] k-mer length, no larger than 28.
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# @param w [Integer] minimizer window size, no larger than 255.
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# @param min_cnt [Integer] mininum number of minimizers on a chain.
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# @param min_chain_score [Integer] minimum chaing score.
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# @param min_dp_score
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# @param bw [Integer] chaining and alignment band width.
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# @param best_n [Integer] max number of alignments to return.
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# @param n_threads [Integer] number of indexing threads.
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# @param fn_idx_out [String] name of file to which the index is written.
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# This parameter has no effect if seq is set.
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# @param max_frag_len [Integer]
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# @param extra_flags [Integer] additional flags defined in minimap.h.
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# @param scoring [Array] scoring system.
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# It is a tuple/list consisting of 4, 6 or 7 positive integers.
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# The first 4 elements specify match scoring, mismatch penalty, gap open and gap extension penalty.
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# The 5th and 6th elements, if present, set long-gap open and long-gap extension penalty.
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# The 7th sets a mismatch penalty involving ambiguous bases.
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7
30
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def initialize(
|
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-
fn_idx_in
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fn_idx_in = nil,
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seq: nil,
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preset: nil,
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k: nil,
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w: nil,
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@@ -18,76 +42,81 @@ module Minimap2
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fn_idx_out: nil,
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max_frag_len: nil,
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extra_flags: nil,
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seq: nil,
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scoring: nil
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)
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-
@
|
26
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-
@
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@idx_opt = FFI::IdxOpt.new
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+
@map_opt = FFI::MapOpt.new
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27
50
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|
28
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-
|
29
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-
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30
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-
else
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# set the default options
|
32
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-
FFI.mm_set_opt(0, index_options, map_options)
|
33
|
-
end
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51
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+
r = FFI.mm_set_opt(preset, idx_opt, map_opt)
|
52
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+
raise ArgumentError, "Unknown preset name: #{preset}" if r == -1
|
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|
35
54
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# always perform alignment
|
36
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-
|
37
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-
|
55
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map_opt[:flag] |= 4
|
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idx_opt[:batch_size] = 0x7fffffffffffffff
|
38
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|
39
58
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# override preset options
|
40
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-
|
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-
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-
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-
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-
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-
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-
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47
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-
|
48
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-
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59
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idx_opt[:k] = k if k
|
60
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+
idx_opt[:w] = w if w
|
61
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map_opt[:min_cnt] = min_cnt if min_cnt
|
62
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map_opt[:min_chain_score] = min_chain_score if min_chain_score
|
63
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+
map_opt[:min_dp_max] = min_dp_score if min_dp_score
|
64
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map_opt[:bw] = bw if bw
|
65
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map_opt[:best_n] = best_n if best_n
|
66
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map_opt[:max_frag_len] = max_frag_len if max_frag_len
|
67
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+
map_opt[:flag] |= extra_flags if extra_flags
|
49
68
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if scoring && scoring.size >= 4
|
50
|
-
|
51
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-
|
52
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-
|
53
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-
|
54
|
-
|
55
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-
|
69
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+
map_opt[:a] = scoring[0]
|
70
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+
map_opt[:b] = scoring[1]
|
71
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+
map_opt[:q] = scoring[2]
|
72
|
+
map_opt[:e] = scoring[3]
|
73
|
+
map_opt[:q2] = map_opt.q
|
74
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+
map_opt[:e2] = map_opt.e
|
56
75
|
if scoring.size >= 6
|
57
|
-
|
58
|
-
|
59
|
-
|
76
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+
map_opt[:q2] = scoring[4]
|
77
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+
map_opt[:e2] = scoring[5]
|
78
|
+
map_opt[:sc_ambi] = scoring[6] if scoring.size >= 7
|
60
79
|
end
|
61
80
|
end
|
62
81
|
|
63
|
-
if
|
64
|
-
|
65
|
-
|
66
|
-
index_options.bucket_bits, seq, seq.size
|
67
|
-
)
|
68
|
-
FFI.mm_mapopt_update(map_options, index)
|
69
|
-
map_options.mid_occ = 1000 # don't filter high-occ seeds
|
70
|
-
else
|
71
|
-
reader = FFI.mm_idx_reader_open(fn_idx_in, index_options, fn_idx_out)
|
82
|
+
if fn_idx_in
|
83
|
+
warn "Since fn_idx_in is specified, the seq argument will be ignored." if seq
|
84
|
+
reader = FFI.mm_idx_reader_open(fn_idx_in, idx_opt, fn_idx_out)
|
72
85
|
|
73
86
|
# The Ruby version raises an error here
|
74
87
|
raise "Cannot open : #{fn_idx_in}" if reader.null?
|
75
88
|
|
76
89
|
@index = FFI.mm_idx_reader_read(reader, n_threads)
|
77
90
|
FFI.mm_idx_reader_close(reader)
|
78
|
-
FFI.mm_mapopt_update(
|
91
|
+
FFI.mm_mapopt_update(map_opt, index)
|
79
92
|
FFI.mm_idx_index_name(index)
|
93
|
+
elsif seq
|
94
|
+
@index = FFI.mappy_idx_seq(
|
95
|
+
idx_opt[:w], idx_opt[:k], idx_opt[:flag] & 1,
|
96
|
+
idx_opt[:bucket_bits], seq, seq.size
|
97
|
+
)
|
98
|
+
FFI.mm_mapopt_update(map_opt, index)
|
99
|
+
map_opt[:mid_occ] = 1000 # don't filter high-occ seeds
|
80
100
|
end
|
81
101
|
end
|
82
102
|
|
83
|
-
#
|
84
|
-
def
|
103
|
+
# Explicitly releases the memory of the index object.
|
104
|
+
def free_index
|
85
105
|
FFI.mm_idx_destroy(index) unless index.null?
|
86
106
|
end
|
87
107
|
|
88
|
-
#
|
89
|
-
#
|
90
|
-
#
|
108
|
+
# @param seq [String]
|
109
|
+
# @param seq2 [String]
|
110
|
+
# @param buf [FFI::TBuf]
|
111
|
+
# @param cs [true, false]
|
112
|
+
# @param md [true, false]
|
113
|
+
# @param max_frag_len [Integer]
|
114
|
+
# @param extra_flags [Integer]
|
115
|
+
# @note Name change: map -> align
|
116
|
+
# In the Ruby language, the name map means iterator.
|
117
|
+
# The original name is map, but here I use the method name align.
|
118
|
+
# @note The use of Enumerator is being considered. The method names may change again.
|
119
|
+
|
91
120
|
def align(
|
92
121
|
seq, seq2 = nil,
|
93
122
|
buf: nil,
|
@@ -99,14 +128,14 @@ module Minimap2
|
|
99
128
|
|
100
129
|
return if index.null?
|
101
130
|
|
102
|
-
|
103
|
-
|
131
|
+
map_opt.max_frag_len = max_frag_len if max_frag_len
|
132
|
+
map_opt.flag |= extra_flags if extra_flags
|
104
133
|
|
105
134
|
buf ||= FFI::TBuf.new
|
106
135
|
km = FFI.mm_tbuf_get_km(buf)
|
107
136
|
n_regs_ptr = ::FFI::MemoryPointer.new :int
|
108
137
|
|
109
|
-
ptr = FFI.mm_map_aux(index, seq, seq2, n_regs_ptr, buf,
|
138
|
+
ptr = FFI.mm_map_aux(index, seq, seq2, n_regs_ptr, buf, map_opt)
|
110
139
|
n_regs = n_regs_ptr.read_int
|
111
140
|
|
112
141
|
regs = Array.new(n_regs) { |i| FFI::Reg1.new(ptr + i * FFI::Reg1.size) }
|
@@ -124,13 +153,13 @@ module Minimap2
|
|
124
153
|
# convert the 32-bit CIGAR encoding to Ruby array
|
125
154
|
cigar = c.map { |x| [x >> 4, x & 0xf] }
|
126
155
|
|
127
|
-
_cs =
|
156
|
+
_cs = ''
|
128
157
|
if cs
|
129
158
|
l_cs_str = FFI.mm_gen_cs(km, cs_str, m_cs_str, @index, regs[i], seq, 1)
|
130
159
|
_cs = cs_str.read_pointer.read_string(l_cs_str)
|
131
160
|
end
|
132
161
|
|
133
|
-
_md =
|
162
|
+
_md = ''
|
134
163
|
if md
|
135
164
|
l_cs_str = FFI.mm_gen_md(km, cs_str, m_cs_str, @index, regs[i], seq)
|
136
165
|
_md = cs_str.read_pointer.read_string(l_cs_str)
|
@@ -149,6 +178,11 @@ module Minimap2
|
|
149
178
|
end
|
150
179
|
end
|
151
180
|
|
181
|
+
# retrieve a subsequence from the index.
|
182
|
+
# @params name
|
183
|
+
# @params start
|
184
|
+
# @params stop
|
185
|
+
|
152
186
|
def seq(name, start = 0, stop = 0x7fffffff)
|
153
187
|
lp = ::FFI::MemoryPointer.new(:int)
|
154
188
|
s = FFI.mappy_fetch_seq(index, name, start, stop, lp)
|
@@ -158,10 +192,12 @@ module Minimap2
|
|
158
192
|
s.read_string(l)
|
159
193
|
end
|
160
194
|
|
195
|
+
# k-mer length, no larger than 28
|
161
196
|
def k
|
162
197
|
index[:k]
|
163
198
|
end
|
164
199
|
|
200
|
+
# minimizer window size, no larger than 255
|
165
201
|
def w
|
166
202
|
index[:w]
|
167
203
|
end
|
data/lib/minimap2/alignment.rb
CHANGED
@@ -1,13 +1,57 @@
|
|
1
1
|
# frozen_string_literal: true
|
2
2
|
|
3
3
|
module Minimap2
|
4
|
+
# Alignment result
|
5
|
+
#
|
6
|
+
# @!attribute ctg
|
7
|
+
# @return [String] name of the reference sequence the query is mapped to.
|
8
|
+
# @!attribute ctg_len
|
9
|
+
# @return [Integer] total length of the reference sequence.
|
10
|
+
# @!attribute r_st
|
11
|
+
# @return [Integer] start positions on the reference.
|
12
|
+
# @!attribute r_en
|
13
|
+
# @return [Integer] end positions on the reference.
|
14
|
+
# @!attribute strand
|
15
|
+
# @return [Integer] +1 if on the forward strand; -1 if on the reverse strand.
|
16
|
+
# @!attribute trans_strand
|
17
|
+
# @return [Integer] transcript strand.
|
18
|
+
# +1 if on the forward strand; -1 if on the reverse strand; 0 if unknown.
|
19
|
+
# @!attribute blen
|
20
|
+
# @return [Integer] length of the alignment, including both alignment matches and gaps
|
21
|
+
# but excluding ambiguous bases.
|
22
|
+
# @!attribute mlen
|
23
|
+
# @return [Integer] length of the matching bases in the alignment,
|
24
|
+
# excluding ambiguous base matches.
|
25
|
+
# @!attribute nm
|
26
|
+
# @return [Integer] number of mismatches, gaps and ambiguous poistions in the alignment.
|
27
|
+
# @!attribute primary
|
28
|
+
# @return [Integer] if the alignment is primary (typically the best and the first to generate)
|
29
|
+
# @!attribute q_st
|
30
|
+
# @return [Integer] start positions on the query.
|
31
|
+
# @!attribute q_en
|
32
|
+
# @return [Integer] end positions on the query.
|
33
|
+
# @!attribute mapq
|
34
|
+
# @return [Integer] mapping quality.
|
35
|
+
# @!attribute cigar
|
36
|
+
# @return [Array] CIGAR returned as an array of shape (n_cigar,2).
|
37
|
+
# The two numbers give the length and the operator of each CIGAR operation.
|
38
|
+
# @!attribute read_num
|
39
|
+
# @return [Integer] read number that the alignment corresponds to;
|
40
|
+
# 1 for the first read and 2 for the second read.
|
41
|
+
# @!attribute cs
|
42
|
+
# @return [String] the cs tag.
|
43
|
+
# @!attribute md
|
44
|
+
# @return [String] the MD tag as in the SAM format.
|
45
|
+
# It is an empty string unless the md argument is applied when calling Aligner#align.
|
46
|
+
# @!attribute cigar_str
|
47
|
+
# @return [String] CIGAR string.
|
48
|
+
|
4
49
|
class Alignment
|
5
50
|
def self.keys
|
6
51
|
%i[ctg ctg_len r_st r_en strand trans_strand blen mlen nm primary
|
7
52
|
q_st q_en mapq cigar read_num cs md cigar_str]
|
8
53
|
end
|
9
54
|
|
10
|
-
# Read only
|
11
55
|
attr_reader(*keys)
|
12
56
|
|
13
57
|
def initialize(h, cigar, cs = nil, md = nil)
|
@@ -29,7 +73,7 @@ module Minimap2
|
|
29
73
|
@cs = cs
|
30
74
|
@md = md
|
31
75
|
|
32
|
-
@cigar_str = cigar.map { |x| x[0].to_s +
|
76
|
+
@cigar_str = cigar.map { |x| x[0].to_s + 'MIDNSH'[x[1]] }.join
|
33
77
|
end
|
34
78
|
|
35
79
|
def primary?
|
@@ -42,19 +86,19 @@ module Minimap2
|
|
42
86
|
|
43
87
|
def to_s
|
44
88
|
strand = if @strand.positive?
|
45
|
-
|
89
|
+
'+'
|
46
90
|
elsif @strand.negative?
|
47
|
-
|
91
|
+
'-'
|
48
92
|
else
|
49
|
-
|
93
|
+
'?'
|
50
94
|
end
|
51
|
-
tp = @primary != 0 ?
|
95
|
+
tp = @primary != 0 ? 'tp:A:P' : 'tp:A:S'
|
52
96
|
ts = if @trans_strand.positive?
|
53
|
-
|
97
|
+
'ts:A:+'
|
54
98
|
elsif @trans_strand.negative?
|
55
|
-
|
99
|
+
'ts:A:-'
|
56
100
|
else
|
57
|
-
|
101
|
+
'ts:A:.'
|
58
102
|
end
|
59
103
|
a = [@q_st, @q_en, strand, @ctg, @ctg_len, @r_st, @r_en,
|
60
104
|
@mlen, @blen, @mapq, tp, ts, "cg:Z:#{@cigar_str}"]
|
data/lib/minimap2/ffi.rb
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
# frozen_string_literal: true
|
2
2
|
|
3
3
|
# bit fields
|
4
|
-
require_relative
|
4
|
+
require_relative 'ffi_helper'
|
5
5
|
|
6
6
|
module Minimap2
|
7
7
|
# Native APIs
|
@@ -22,6 +22,6 @@ module Minimap2
|
|
22
22
|
end
|
23
23
|
end
|
24
24
|
|
25
|
-
require_relative
|
26
|
-
require_relative
|
27
|
-
require_relative
|
25
|
+
require_relative 'ffi/constants'
|
26
|
+
require_relative 'ffi/functions'
|
27
|
+
require_relative 'ffi/mappy'
|
@@ -6,15 +6,15 @@ module Minimap2
|
|
6
6
|
:mm_set_opt_raw, :mm_set_opt,
|
7
7
|
[:pointer, IdxOpt.by_ref, MapOpt.by_ref],
|
8
8
|
:int
|
9
|
-
|
9
|
+
|
10
10
|
private_class_method :mm_set_opt_raw
|
11
|
-
|
11
|
+
|
12
12
|
def self.mm_set_opt(preset, io, mo)
|
13
|
-
if preset
|
14
|
-
|
15
|
-
|
16
|
-
|
17
|
-
|
13
|
+
ptr = if preset
|
14
|
+
::FFI::MemoryPointer.from_string(preset.to_s)
|
15
|
+
else
|
16
|
+
::FFI::Pointer.new(:int, 0)
|
17
|
+
end
|
18
18
|
mm_set_opt_raw(ptr, io, mo)
|
19
19
|
end
|
20
20
|
|
data/lib/minimap2/ffi/mappy.rb
CHANGED
@@ -38,7 +38,7 @@ module Minimap2
|
|
38
38
|
:seq, KString,
|
39
39
|
:qual, KString,
|
40
40
|
:last_char, :int,
|
41
|
-
:f, :pointer #
|
41
|
+
:f, :pointer # KStream
|
42
42
|
end
|
43
43
|
|
44
44
|
attach_function \
|
@@ -88,7 +88,7 @@ module Minimap2
|
|
88
88
|
|
89
89
|
attach_function \
|
90
90
|
:mappy_idx_seq,
|
91
|
-
%i[int int int int
|
91
|
+
%i[int int int int string int],
|
92
92
|
Idx.by_ref
|
93
93
|
|
94
94
|
attach_function \
|
data/lib/minimap2/ffi_helper.rb
CHANGED
data/lib/minimap2/version.rb
CHANGED
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: minimap2
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.0.
|
4
|
+
version: 0.0.2
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- kojix2
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2021-03-
|
11
|
+
date: 2021-03-14 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: ffi
|
@@ -112,7 +112,6 @@ files:
|
|
112
112
|
- lib/minimap2/ffi/mappy.rb
|
113
113
|
- lib/minimap2/ffi_helper.rb
|
114
114
|
- lib/minimap2/version.rb
|
115
|
-
- vendor/libminimap2.so
|
116
115
|
homepage: https://github.com/kojix2/ruby-minimap2
|
117
116
|
licenses:
|
118
117
|
- MIT
|
data/vendor/libminimap2.so
DELETED
Binary file
|