dna_hamming 0.1.0

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data/.gitignore ADDED
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+ /.bundle/
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+ /.yardoc
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+ /Gemfile.lock
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+ /_yardoc/
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+ /coverage/
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+ /doc/
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+ /pkg/
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+ /spec/reports/
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+ /tmp/
data/.travis.yml ADDED
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+ language: ruby
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+ rvm:
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+ - 2.2.3
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+ before_install: gem install bundler -v 1.10.6
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+ # Contributor Code of Conduct
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+
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+ For you, brethren, have been called to liberty; only do not use liberty as an opportunity for the flesh, but through love serve one another. For all the law is fulfilled in one word, even in this: “You shall love your neighbor as yourself.” But if you bite and devour one another, beware lest you be consumed by one another! - [Galatians 5:13-15](https://www.biblegateway.com/passage/?search=Gal.5.13-Gal.5.15&version=NKJV)
data/Gemfile ADDED
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+ source 'https://rubygems.org'
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+
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+ # Specify your gem's dependencies in dna_hamming.gemspec
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+ gemspec
data/LICENSE.txt ADDED
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+ The MIT License (MIT)
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+
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+ Copyright (c) 2015 Daniel P. Clark
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy
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+ of this software and associated documentation files (the "Software"), to deal
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+ in the Software without restriction, including without limitation the rights
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+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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+ copies of the Software, and to permit persons to whom the Software is
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+ furnished to do so, subject to the following conditions:
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+
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+ The above copyright notice and this permission notice shall be included in
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+ all copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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+ THE SOFTWARE.
data/README.md ADDED
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+ # DnaHamming
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+
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+ My solution to computing DNA Hamming.
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+
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+ ## License
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+
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+ The gem is available as open source under the terms of the [MIT License](http://opensource.org/licenses/MIT).
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+
data/Rakefile ADDED
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+ require "bundler/gem_tasks"
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+ require "rake/testtask"
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+
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+ Rake::TestTask.new(:test) do |t|
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+ t.libs << "test"
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+ t.libs << "lib"
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+ t.test_files = FileList['test/**/*_test.rb']
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+ end
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+
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+ task :default => :test
data/bin/console ADDED
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+ #!/usr/bin/env ruby
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+
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+ require "bundler/setup"
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+ require "dna_hamming"
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+
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+ # You can add fixtures and/or initialization code here to make experimenting
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+ # with your gem easier. You can also use a different console, if you like.
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+
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+ # (If you use this, don't forget to add pry to your Gemfile!)
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+ # require "pry"
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+ # Pry.start
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+
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+ require "irb"
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+ IRB.start
data/bin/setup ADDED
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+ #!/bin/bash
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+ set -euo pipefail
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+ IFS=$'\n\t'
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+
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+ bundle install
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+
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+ # Do any other automated setup that you need to do here
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+ # coding: utf-8
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+ lib = File.expand_path('../lib', __FILE__)
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+ $LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
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+ require 'dna_hamming/version'
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+
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+ Gem::Specification.new do |spec|
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+ spec.name = "dna_hamming"
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+ spec.version = DNAHamming::VERSION
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+ spec.authors = ["Daniel P. Clark"]
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+ spec.email = ["6ftdan@gmail.com"]
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+
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+ spec.summary = %q{My solution to the DNA Hamming computation.}
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+ spec.description = %q{DNA Hamming. Compute the difference between two DNA strands as represented by strings.}
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+ spec.homepage = "http://github.com/danielpclark/dna_hamming"
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+ spec.license = "MIT"
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+ spec.files = `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
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+ spec.bindir = "exe"
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+ spec.executables = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
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+ spec.require_paths = ["lib"]
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+
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+ spec.add_development_dependency "bundler", "~> 1.10"
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+ spec.add_development_dependency "rake", "~> 10.0"
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+ spec.add_development_dependency "minitest", "~> 5.8"
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+ end
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+ require "dna_hamming/version"
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+ require "dna_hamming/hamming"
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+ require "dna_hamming/pair"
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+
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+ module DNAHamming
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+ ::DNAPair = ->a,b{Pair.new(a, b)}
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+ end
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+ module Hamming
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+ def self.compute(pair)
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+ set_strand_position_by_length(pair) unless pair.same?
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+ count_the_distance(pair)
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+ end
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+
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+ private
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+ def self.count_the_distance(pair)
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+ pair.entries.map(&:chars).inject(:zip).select{|a,b| a!=b}.count
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+ end
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+
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+ def self.set_strand_position_by_length(pair)
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+ pair.swap! if pair.inject{|a,b|a.length>b.length}
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+ end
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+ end
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+
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+ module DNAHamming
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+ class Pair < Struct.new(:first, :second)
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+ def same?
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+ inject(:eql?)
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+ end
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+
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+ def swap!
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+ members.zip(entries.reverse) {|a,b| self[a] = b}
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+ end
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+ end
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+ end
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+
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+ module DNAHamming
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+ VERSION = "0.1.0"
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+ end
metadata ADDED
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+ --- !ruby/object:Gem::Specification
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+ name: dna_hamming
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+ version: !ruby/object:Gem::Version
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+ version: 0.1.0
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+ platform: ruby
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+ authors:
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+ - Daniel P. Clark
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+ autorequire:
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+ bindir: exe
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+ cert_chain: []
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+ date: 2015-12-11 00:00:00.000000000 Z
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+ dependencies:
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+ - !ruby/object:Gem::Dependency
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+ name: bundler
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '1.10'
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+ type: :development
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '1.10'
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+ - !ruby/object:Gem::Dependency
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+ name: rake
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '10.0'
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+ type: :development
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '10.0'
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+ - !ruby/object:Gem::Dependency
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+ name: minitest
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '5.8'
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+ type: :development
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '5.8'
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+ description: DNA Hamming. Compute the difference between two DNA strands as represented
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+ by strings.
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+ email:
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+ - 6ftdan@gmail.com
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+ executables: []
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+ extensions: []
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+ extra_rdoc_files: []
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+ files:
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+ - ".gitignore"
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+ - ".travis.yml"
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+ - CODE_OF_CONDUCT.md
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+ - Gemfile
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+ - LICENSE.txt
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+ - README.md
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+ - Rakefile
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+ - bin/console
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+ - bin/setup
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+ - dna_hamming.gemspec
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+ - lib/dna_hamming.rb
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+ - lib/dna_hamming/hamming.rb
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+ - lib/dna_hamming/pair.rb
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+ - lib/dna_hamming/version.rb
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+ homepage: http://github.com/danielpclark/dna_hamming
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+ licenses:
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+ - MIT
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+ metadata: {}
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+ post_install_message:
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+ rdoc_options: []
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+ require_paths:
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+ - lib
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+ required_ruby_version: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ required_rubygems_version: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ requirements: []
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+ rubyforge_project:
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+ rubygems_version: 2.5.0
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+ signing_key:
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+ specification_version: 4
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+ summary: My solution to the DNA Hamming computation.
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+ test_files: []