viral_seq 0.3.0

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+ # lib/version.rb
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+ # version info and histroy
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+
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+ module ViralSeq
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+ VERSION = "0.3.0"
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+ end
data/lib/viral_seq.rb ADDED
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+ # Copyright (c) 2019 Shuntai Zhou (shuntai.zhou@gmail.com)
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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.
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+
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+ # viral_seq main
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+ module ViralSeq; end
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+
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+ # load all modules
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+
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+ require "viral_seq/version"
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+ require "viral_seq/sequence"
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+ require "viral_seq/math"
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+ require "viral_seq/fasta"
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+ require "viral_seq/misc"
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+ require "viral_seq/refseq"
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+ require "viral_seq/locator"
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+ require "viral_seq/muscle"
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+ require "viral_seq/tcs_core.rb"
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+ require "viral_seq/poisson_cutoff"
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+ require "viral_seq/a3g"
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+ require "viral_seq/sdrm_core"
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+ require "viral_seq/hcv_dr"
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+ require "viral_seq/nt_variation"
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+
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+ require "muscle_bio"
data/viral_seq.gemspec ADDED
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+
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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 "viral_seq/version"
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+
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+ Gem::Specification.new do |spec|
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+ spec.name = "viral_seq"
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+ spec.version = ViralSeq::VERSION
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+ spec.authors = ["Shuntai Zhou", "Michael Clark"]
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+ spec.email = ["shuntai.zhou@gmail.com", "clarkmu@gmail.com"]
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+
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+ spec.summary = %q{A Ruby Gem containing bioinformatics tools for processing viral NGS data.}
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+ spec.description = %q{Specifically for Primer-ID sequencing and HIV drug resistance analysis.}
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+ spec.homepage = "https://github.com/ViralSeq/viral_seq"
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+ spec.license = "MIT"
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+
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+ # Specify which files should be added to the gem when it is released.
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+ # The `git ls-files -z` loads the files in the RubyGem that have been added into git.
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+ spec.files = Dir.chdir(File.expand_path('..', __FILE__)) do
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+ `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
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+ end
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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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+ spec.post_install_message = "Thanks for installing!"
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+
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+ spec.add_development_dependency "bundler", "~> 2.0"
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+ spec.add_development_dependency "rake", "~> 10.0"
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+ spec.add_development_dependency "rspec", "~> 3.0"
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+
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+ # muscle_bio gem required
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+ spec.add_runtime_dependency "muscle_bio", "~> 0.4"
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+
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+
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+ spec.requirements << 'MUSCLE (http://www.drive5.com/muscle) required for some functions'
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+ spec.requirements << 'R required for some functions'
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+ end
metadata ADDED
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+ --- !ruby/object:Gem::Specification
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+ name: viral_seq
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+ version: !ruby/object:Gem::Version
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+ version: 0.3.0
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+ platform: ruby
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+ authors:
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+ - Shuntai Zhou
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+ - Michael Clark
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+ autorequire:
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+ bindir: exe
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+ cert_chain: []
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+ date: 2019-06-21 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: '2.0'
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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: '2.0'
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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: rspec
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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: '3.0'
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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: '3.0'
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+ - !ruby/object:Gem::Dependency
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+ name: muscle_bio
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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: '0.4'
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+ type: :runtime
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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: '0.4'
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+ description: Specifically for Primer-ID sequencing and HIV drug resistance analysis.
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+ email:
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+ - shuntai.zhou@gmail.com
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+ - clarkmu@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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+ - ".rspec"
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+ - ".travis.yml"
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+ - CODE_OF_CONDUCT.md
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+ - Gemfile
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+ - Gemfile.lock
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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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+ - lib/viral_seq.rb
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+ - lib/viral_seq/a3g.rb
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+ - lib/viral_seq/fasta.rb
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+ - lib/viral_seq/hcv_dr.rb
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+ - lib/viral_seq/locator.rb
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+ - lib/viral_seq/math.rb
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+ - lib/viral_seq/misc.rb
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+ - lib/viral_seq/muscle.rb
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+ - lib/viral_seq/nt_variation.rb
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+ - lib/viral_seq/poisson_cutoff.rb
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+ - lib/viral_seq/refseq.rb
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+ - lib/viral_seq/sdrm_core.rb
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+ - lib/viral_seq/sequence.rb
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+ - lib/viral_seq/tcs_core.rb
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+ - lib/viral_seq/version.rb
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+ - viral_seq.gemspec
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+ homepage: https://github.com/ViralSeq/viral_seq
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+ licenses:
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+ - MIT
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+ metadata: {}
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+ post_install_message: Thanks for installing!
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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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+ - MUSCLE (http://www.drive5.com/muscle) required for some functions
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+ - R required for some functions
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+ rubygems_version: 3.0.3
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+ signing_key:
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+ specification_version: 4
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+ summary: A Ruby Gem containing bioinformatics tools for processing viral NGS data.
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+ test_files: []