ruby-edlib

Edlib - A lightweight and super fast C/C++ library for sequence alignment using edit distance

Installation

sudo apt install edlib-dev
gem install edlib

API

require "edlib"

a = Edlib::Aligner.new(mode: :hw, task: :path)
a.align("AACG", "TCAACCTG")
# => {:edit_distance=>1, :alphabet_length=>4, :locations=>[[2, 4], [2, 5]], :alignment=>[0, 0, 0, 1], :cigar=>"3=1I"}

keyword argument	description
k	edit distance is not larger than k [-1]
mode	global (NW) , prefix (SHW) , infix (HW) ["NW"]
task	DISTANCE, LOC, PATH ["DISTANCE"]
additional_equalities	List of pairs of characters, where each pair defines two characters as equal. [NULL]

Development

• Pull requests welcome

git clone https://github.com/kojix2/ruby-edlib # Please fork repo
cd ruby-edlib
bundle install
bundle exec rake compile
bundle exec rake test