API to work with the fai format produced to samtools. Useful if you don't want to rely on all the samtools component. Can query sequences from the fasta file. At the minute, it uses bio-samtools, but the idea is to make this self-sufficient.
gem install bio-faidxrequire 'bio-faidx'The API doc is online. For more code examples see the test files in the source tree.
Information on the source tree, documentation, examples, issues and how to contribute, see
http://github.com/homonecloco/bioruby-faidx
The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
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
This Biogem is published at (http://biogems.info/index.html#bio-faidx)
Copyright (c) 2014 homonecloco. See LICENSE.txt for further details.