HTSlib

:dna: HTSlib - high-throughput sequencing data manipulation - for Ruby

:apple: Feel free to fork it out if you can develop it!

:bowtie: Just a prototype. Pre-alpha stage.

Requirements

htslib
- Ubuntu : apt install libhts-dev
- macOS : brew install htslib

Installation

gem install htslib

If you installed htslib with Ubuntu/apt or Mac/homebrew, pkg-config will automatically detect the location of the shared library.

Or you can set the environment variable HTSLIBDIR.

export HTSLIBDIR="/your/path/to/htslib" # libhts.so

Usage

HTS::FFI - Low-level API

require 'htslib'

a = HTS::FFI.hts_open("a.bam", "r")
b = HTS::FFI.hts_get_format(a)
p b[:category]
p b[:format]

A high-level API based on hts-python is under development.

require 'htslib'

bam = HTS::Bam.new("a.bam")

bam.each do |aln|
  p name:  aln.qname,
    flag:  aln.flag,
    start: aln.start + 1,
    mpos:  aln.mate_pos + 1,
    mqual: aln.mapping_quality,
    seq:   aln.sequence,
    cigar: aln.cigar.to_s,
    qual:  aln.base_qualities.map { |i| (i + 33).chr }.join
end

Documentation

RubyDoc.info - HTSlib

Development

To get started with development

git clone --recursive https://github.com/kojix2/ruby-htslib
cd ruby-htslib
bundle install
bundle exec rake htslib:build
bundle exec rake test

Contributing

Ruby-htslib is a library under development, so even small improvements like typofix are welcome! Please feel free to send us your pull requests.

Report bugs
Fix bugs and submit pull requests
Write, clarify, or fix documentation
Suggest or add new features

License

MIT License.