viral_seq 1.0.6 → 1.0.11

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@@ -2,5 +2,6 @@
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  # version info and histroy
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  module ViralSeq
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- VERSION = "1.0.6"
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+ VERSION = "1.0.11"
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+ TCS_VERSION = "2.1.1"
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  end
data/viral_seq.gemspec CHANGED
@@ -26,10 +26,14 @@ Gem::Specification.new do |spec|
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  spec.post_install_message = "Thanks for installing!"
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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 "rake", "~> 13.0"
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  spec.add_development_dependency "rspec", "~> 3.0"
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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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+ # colorize gem required
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+ spec.add_runtime_dependency "colorize", "~> 0.1"
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+
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  spec.requirements << 'R required for some functions'
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  end
metadata CHANGED
@@ -1,7 +1,7 @@
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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: 1.0.6
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+ version: 1.0.11
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  platform: ruby
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  authors:
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  - Shuntai Zhou
@@ -9,7 +9,7 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2019-07-23 00:00:00.000000000 Z
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+ date: 2021-03-02 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: bundler
@@ -31,14 +31,14 @@ dependencies:
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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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+ version: '13.0'
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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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+ version: '13.0'
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  - !ruby/object:Gem::Dependency
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  name: rspec
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  requirement: !ruby/object:Gem::Requirement
@@ -67,6 +67,20 @@ dependencies:
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  - - "~>"
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  - !ruby/object:Gem::Version
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  version: '0.4'
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+ - !ruby/object:Gem::Dependency
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+ name: colorize
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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: '0.1'
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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: '0.1'
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  description: |-
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  A Ruby Gem with bioinformatics tools for processing viral NGS data.
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  Specifically for Primer-ID sequencing and HIV drug resistance analysis.
@@ -75,6 +89,7 @@ email:
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  - clarkmu@gmail.com
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  executables:
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  - locator
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+ - tcs
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  extensions: []
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  extra_rdoc_files: []
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  files:
@@ -88,6 +103,7 @@ files:
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  - README.md
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  - Rakefile
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  - bin/locator
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+ - bin/tcs
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  - lib/viral_seq.rb
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  - lib/viral_seq/constant.rb
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  - lib/viral_seq/enumerable.rb
@@ -98,10 +114,13 @@ files:
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  - lib/viral_seq/pid.rb
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  - lib/viral_seq/ref_seq.rb
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  - lib/viral_seq/rubystats.rb
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+ - lib/viral_seq/sdrm.rb
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  - lib/viral_seq/seq_hash.rb
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  - lib/viral_seq/seq_hash_pair.rb
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  - lib/viral_seq/sequence.rb
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  - lib/viral_seq/string.rb
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+ - lib/viral_seq/tcs_core.rb
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+ - lib/viral_seq/tcs_json.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
@@ -124,7 +143,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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  version: '0'
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  requirements:
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  - R required for some functions
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- rubygems_version: 3.0.3
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+ rubygems_version: 3.2.2
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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.