ruby-htslib

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Ruby-htslib is the Ruby bindings to HTSlib, a C library for high-throughput sequencing data formats. It allows you to read and write file formats commonly used in genomics, such as SAM, BAM, VCF, and BCF in the Ruby language.

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

:bowtie: alpha stage.

Requirements

  • Ruby 3.1 or above.
  • HTSlib
    • Ubuntu : apt install libhts-dev
    • macOS : brew install htslib
    • Build from source code (see Development section)

Installation

gem install htslib

If you have installed htslib with apt on Ubuntu or homebrew on Mac, pkg-config will automatically detect the location of the shared library. If pkg-config does not work well, set PKG_CONFIG_PATH. Alternatively, you can specify the directory of the shared library by setting the environment variable HTSLIBDIR.

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

Overview

High level API

Read SAM / BAM / CRAM - Sequence Alignment Map file

require 'htslib'

bam = HTS::Bam.open("test/fixtures/moo.bam")

bam.each do |r|
  pp name: r.qname,
     flag: r.flag,
     chrm: r.chrom,
     strt: r.pos + 1,
     mapq: r.mapq,
     cigr: r.cigar.to_s,
     mchr: r.mate_chrom,
     mpos: r.mpos + 1,
     isiz: r.isize,
     seqs: r.seq,
     qual: r.qual.map { |i| (i + 33).chr }.join,
     MC:   r.aux("MC")
end

bam.close

Read VCF / BCF - Variant Call Format file

bcf = HTS::Bcf.open("b.bcf")

bcf.each do |r|
  p chrom:  r.chrom,
    pos:    r.pos,
    id:     r.id,
    qual:   r.qual.round(2),
    ref:    r.ref,
    alt:    r.alt,
    filter: r.filter,
    info:   r.info.to_h,
    format: r.format.to_h
end

bcf.close

Low level API

HTS::LibHTS provides native C functions. 

require 'htslib'

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

Note: htslib makes extensive use of macro functions for speed. you cannot use C macro functions in Ruby if they are not reimplemented in ruby-htslib. Only small number of C structs are implemented with FFI's ManagedStruct, which frees memory when Ruby's garbage collection fires. Other structs will need to be freed manually.

Need more speed?

Try Crystal. htslib.cr is implemented in Crystal language and provides an API compatible with ruby-htslib. Crsytal language is not as flexible as Ruby language. You can not use eval methods, and you must always be careful with the data types. Writing one-time scripts in Crystal or playing with REPL may not be as much fun. However, if you have a clear idea of what you want to do in your mind, have already written code in Ruby, and need to run them over and over, try creating a command line tool in Crystal. The Crystal language is fast, as fast as the Rust and C languages. It will give you great power to create tools.

Documentation

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

GNU Autotools is required to compile htslib.

Many macro functions are used in HTSlib. Since these macro functions cannot be called using FFI, they must be reimplemented in Ruby.

  • Use the new version of Ruby to take full advantage of Ruby's potential.
    • This is possible because we have a small number of users. What a deal!
  • Remain compatibile with htslib.cr.
    • The most difficult part is the return value. In the Crystal language, methods are expected to return only one type. On the other hand, in the Ruby language, methods that return multiple classes are very common. For example, in the Crystal language, the compiler gets confused if the return value is one of six types: Int32, Int64, Float32, Float64, Nil, or String. In fact Crystal can do this. But the code gets a little messy. In Ruby, this is very common and doesn't cause any problems.

In the script directory, there are several tools to help implement ruby-htslib. These tools may be forked into independent repository in the future.

FFI Extensions

  • ffi-bitfield : Extension of Ruby-FFI to support bitfields.

Automatic generation or automatic validation (Future plan)

  • c2ffi is a tool to create JSON format metadata from C header files. It is planned to use c2ffi to automatically generate bindings or tests.

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.

# Ownership and Commitment Rights

Do you need commit rights to ruby-htslib repository?
Do you want to get admin rights and take over the project?
If so, please feel free to contact us @kojix2.

Why do you implement htslib in a language like Ruby, which is not widely used in the bioinformatics?

One of the greatest joys of using a minor language like Ruby in bioinformatics is that there is nothing stopping you from reinventing the wheel. Reinventing the wheel can be fun. But with languages like Python and R, where many bioinformatics masters work, there is no chance left for beginners to create htslib bindings. Bioinformatics file formats, libraries and tools are very complex and I don't know how to understand them. So I wanted to implement the HTSLib binding myself to better understand how the pioneers of bioinformatics felt when establishing the file format and how they created their tools. I hope one day we can work on bioinformatics using Ruby and Crystal languages, not to replace other languages such as Python and R, but to add new power and value to this advancing field.

Funding support

This work was supported partially by Ruby Association Grant 2020.

License

MIT License.