bio-bgzf

This library provides support for BGZF (Blocked GZip Format) in Ruby. BGZF, originally defined as part of the SAM/BAM specification, is used to compress record-oriented bioinformatics data in a way that facilitates random access, unlike plain gzip. A BGZF file consists of contatenated 64 KB blocks, each an independent gzip stream. It can be decompressed in its entirety with gzip, but this library enables random access using 'virtual offsets' as defined in SAM/BAM.

A virtual offset is a 64-bit quantity, with a 48-bit block offset giving the position in the file of the start of the block followed by a 16-bit data offset giving a position within the file.

Installation

    gem install bio-bgzf

Usage

    require 'bio-bgzf'

    File.open('example.gz') do |f|
      r = Bio::BGZF::Reader.new(f)
      while true do
        block_vo = r.tell
        block = r.read_block
        break unless block
      end
      block = f.read_block_at(block_vo)
    end

The API doc is online. For more code examples see the test files in the source tree.

Project home page

Information on the source tree, documentation, examples, issues and how to contribute, see

http://github.com/csw/bioruby-bgzf

The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.

Cite

If you use this software, please cite one of

• BioRuby: bioinformatics software for the Ruby programming language
• Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics

Biogems.info

This Biogem is published at #bio-bgzf

Copyright

Copyright (c) 2012 Artem Tarasov and Clayton Wheeler. See LICENSE.txt for further details.