https://github.com/kojix2/ruby-minimap2
Powerful long read aligner for Ruby
https://github.com/kojix2/ruby-minimap2
bioinformatics genomics minimap2 ruby
Last synced: about 1 year ago
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Powerful long read aligner for Ruby
- Host: GitHub
- URL: https://github.com/kojix2/ruby-minimap2
- Owner: kojix2
- License: mit
- Created: 2020-12-31T04:13:33.000Z (over 5 years ago)
- Default Branch: main
- Last Pushed: 2025-01-17T03:32:13.000Z (over 1 year ago)
- Last Synced: 2025-03-27T12:52:44.572Z (about 1 year ago)
- Topics: bioinformatics, genomics, minimap2, ruby
- Language: Ruby
- Homepage: https://kojix2.github.io/ruby-minimap2/
- Size: 497 KB
- Stars: 14
- Watchers: 2
- Forks: 1
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- Funding: .github/FUNDING.yml
- License: LICENSE.txt
Awesome Lists containing this project
README
# ruby-minimap2
[](https://rubygems.org/gems/minimap2)
[](https://github.com/kojix2/ruby-minimap2/actions/workflows/ci.yml)
[](https://rubydoc.info/gems/minimap2)
[](https://kojix2.github.io/ruby-minimap2/)
[](LICENSE.txt)
[](https://zenodo.org/badge/latestdoi/325711305)
:dna: [minimap2](https://github.com/lh3/minimap2) - the long-read mapper - for [Ruby](https://github.com/ruby/ruby)
## Installation
```
gem install minimap2
```
Compiling from source
git clone --recursive https://github.com/kojix2/ruby-minimap2
cd ruby-minimap2
bundle install
bundle exec rake minimap2:build
bundle exec rake install
## Quick Start
```ruby
require "minimap2"
aligner = Minimap2::Aligner.new("ext/minimap2/test/MT-human.fa")
seq = aligner.seq("MT_human", 100, 200)
hits = aligner.align(seq)
pp hits
```
```
[#]
```
## APIs Overview
```markdown
* Minimap2 module
- fastx_read Read fasta/fastq file.
- revcomp Reverse complement sequence.
- execute Calls the main function of Minimap2 with arguments. `Minimap2.execute("--version")`
* Aligner class
* attributes
- index Returns the value of attribute index.
- idx_opt Returns the value of attribute idx_opt.
- map_opt Returns the value of attribute map_opt.
* methods
- new(path, preset: nil) Create a new aligner. (presets: sr, map-pb, map-out, map-hifi, splice, asm5, etc.)
- align Maps and returns alignments.
- seq Retrieve a subsequence from the index.
* Alignment class
* attributes
- ctg Returns name of the reference sequence the query is mapped to.
- ctg_len Returns total length of the reference sequence.
- r_st Returns start positions on the reference.
- r_en Returns end positions on the reference.
- strand Returns +1 if on the forward strand; -1 if on the reverse strand.
- trans_strand Returns transcript strand. +1 if on the forward strand; -1 if on the reverse strand; 0 if unknown.
- blen Returns length of the alignment, including both alignment matches and gaps but excluding ambiguous bases.
- mlen Returns length of the matching bases in the alignment, excluding ambiguous base matches.
- nm Returns number of mismatches, gaps and ambiguous positions in the alignment.
- primary Returns if the alignment is primary (typically the best and the first to generate).
- q_st Returns start positions on the query.
- q_en Returns end positions on the query.
- mapq Returns mapping quality.
- cigar Returns CIGAR returned as an array of shape (n_cigar,2). The two numbers give the length and the operator of each CIGAR operation.
- read_num Returns read number that the alignment corresponds to; 1 for the first read and 2 for the second read.
- cs Returns the cs tag.
- md Returns the MD tag as in the SAM format. It is an empty string unless the md argument is applied when calling Aligner#align.
- cigar_str Returns CIGAR string.
* methods
- to_h Convert Alignment to hash.
- to_s Convert to the PAF format without the QueryName and QueryLength columns.
## FFI module
* IdxOpt class Indexing options.
* MapOpt class Mapping options.
```
- API is based on [Mappy](https://github.com/lh3/minimap2/tree/master/python), the official Python binding for Minimap2.
- `Aligner#map` has been changed to `align`, because `map` means iterator in Ruby.
- See [documentation](https://kojix2.github.io/ruby-minimap2/) for details.
C Structures and Functions
### FFI
- Ruby-Minimap2 is built on top of [Ruby-FFI](https://github.com/ffi/ffi).
- Native C functions can be called from the `Minimap2::FFI` module.
- Native C structure members can be accessed.
- Bitfields are supported by [ffi-bitfield](https://github.com/kojix2/ffi-bitfield) gems.
```ruby
aligner.idx_opt.members
# => [:k, :w, :flag, :bucket_bits, :mini_batch_size, :batch_size]
aligner.kds_opt.values
# => [15, 10, 0, 14, 50000000, 9223372036854775807]
aligner.idx_opt[:k]
# => 15
aligner.idx_opt[:k] = 14
aligner.idx_opt[:k]
# => 14
```
## Contributing
Development
Fork your repository.
then clone.
```sh
git clone --recursive https://github.com/kojix2/ruby-minimap2
# git clone https://github.com/kojix2/ruby-minimap2
# cd ruby-minimap2
# git submodule update -i
```
Build Minimap2 and Mappy.
```sh
cd ruby-minimap2
bundle install # Install dependent packages including Ruby-FFI
bundle exec rake minimap2:build
```
A shared library will be created in the vendor directory.
```
└── vendor
└── libminimap2.so
```
Run tests.
```
bundle exec rake test
```
Release a Gem.
```
bundle exec rake minimap2:cleanall
bundle exec rake build
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.
bundle exec rake release
```
ruby-minimap2 is a library under development and there are many points to be improved.
Please feel free to report [bugs](https://github.com/kojix2/ruby-minimap2/issues) and [pull requests](https://github.com/kojix2/ruby-minimap2/pulls)!
Many OSS projects become abandoned because only the founder has commit rights to the original repository.
If you need commit rights to ruby-minimap2 repository or want to get admin rights and take over the project, please feel free to contact me @kojix2.
## License
[MIT License](https://opensource.org/licenses/MIT).
## Acknowledgements
I would like to thank Heng Li for making Minimap2, and all the readers who read the README to the end.