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Genomic interval overlap queries
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 Dependencies
 Project Readme

bio-cgranges

Gem Version test docs docs

Ruby bindings to lh3/cgranges.

cgranges is a small C library for genomic interval overlap queries

Installation

gem install bio-cgranges

Usage

require "bio/cgranges"

granges = Bio::CGRanges.new
granges.add("chr1", 10, 20, 0)
       .add("chr1", 15, 25, 1)
       .add("chr1", 30, 40, 2)
       .add("chr1", 10, 25, 3)
       .add("chr1", 15, 20, 4)
       .add("chr2", 10, 20, 5)
       .index
0.........5.........10........15........20........25........30........35........40
|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|
                     0-0-0-0-0-0-0-0-0-0
                               1-1-1-1-1-1-1-1-1-1
                                                             2-2-2-2-2-2-2-2-2-2
                     3-3-3-3-3-3-3-3-3-3-3-3-3-3-3
                               4-4-4-4-4
           5-5-5-5-5
|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|
0.........5.........10........15........20........25........30........35........40
granges.overlap("chr1", 12, 22)
# [["chr1", 10, 20, 0],
#  ["chr1", 10, 25, 3],
#  ["chr1", 15, 25, 1],
#  ["chr1", 15, 20, 4]]

granges.contain("chr1", 12, 22)
# [["chr1", 15, 20, 4]]

granges.coverage("chr1", 20, 35)
# [10, 3] # cov, n

granges.coverage("chr1", 12, 22, mode: :contain)
# [5, 1]

See docs for details.

Development

Bug reports and pull requests are welcome on GitHub at https://github.com/ruby-on-bioc/bio-cgranges.

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License

The gem is available as open source under the terms of the MIT License.