Ruby bindings to lh3/cgranges.
cgranges is a small C library for genomic interval overlap queries
gem install bio-cgrangesrequire "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)
.index0.........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
git clone https://github.com/kojix2/bio-cgranges
bundle install
bundle exec rake compile
bundle exec rake testBug reports and pull requests are welcome on GitHub at https://github.com/kojix2/bio-cgranges.
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The gem is available as open source under the terms of the MIT License.
