crb-blast 0.3 → 0.3.1

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Files changed (3) hide show
  1. checksums.yaml +4 -4
  2. data/lib/crb-blast.rb +7 -0
  3. metadata +60 -30
checksums.yaml CHANGED
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data/lib/crb-blast.rb CHANGED
@@ -192,6 +192,9 @@ class CRB_Blast
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  cat_cmd << blasts.join(" ")
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  cat_cmd << " > #{@output1}"
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  `#{cat_cmd}`
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+ files.each do |file|
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+ File.delete(file) if File.exist?(file)
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+ end
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  blasts.each do |b|
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  File.delete(b) # delete intermediate blast output files
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  end
@@ -213,6 +216,9 @@ class CRB_Blast
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  cat_cmd << blasts.join(" ")
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  cat_cmd << " > #{@output2}"
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  `#{cat_cmd}`
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+ files.each do |file|
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+ File.delete(file) if File.exist?(file)
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+ end
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  blasts.each do |b|
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  File.delete(b) # delete intermediate blast output files
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  end
@@ -240,6 +246,7 @@ class CRB_Blast
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  output_files=[]
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  pieces.times do |n|
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  outfile = "#{filename}_chunk_#{n}.fasta"
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+ outfile = File.expand_path(outfile)
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  outputs[n] = File.open("#{outfile}", "w")
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  output_files[n] = "#{outfile}"
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  end
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: crb-blast
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  version: !ruby/object:Gem::Version
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- version: '0.3'
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+ version: 0.3.1
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  platform: ruby
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  authors:
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  - Chris Boursnell
@@ -9,36 +9,22 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2014-04-28 00:00:00.000000000 Z
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+ date: 2014-07-18 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: trollop
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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'
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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'
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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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+ - - "~>"
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  - !ruby/object:Gem::Version
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- version: '0'
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+ version: '2.0'
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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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+ - - "~>"
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  - !ruby/object:Gem::Version
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- version: '0'
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+ version: '2.0'
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  - !ruby/object:Gem::Dependency
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  name: bio
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  requirement: !ruby/object:Gem::Requirement
@@ -78,6 +64,9 @@ dependencies:
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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: '0.2'
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+ - - ">="
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  - !ruby/object:Gem::Version
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  version: 0.2.0
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  type: :runtime
@@ -85,6 +74,9 @@ dependencies:
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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: '0.2'
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+ - - ">="
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  - !ruby/object:Gem::Version
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  version: 0.2.0
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  - !ruby/object:Gem::Dependency
@@ -107,62 +99,100 @@ dependencies:
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  - - ">="
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  - !ruby/object:Gem::Version
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  version: 0.0.7
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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: '10.3'
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: 10.3.2
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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: '10.3'
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: 10.3.2
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  - !ruby/object:Gem::Dependency
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  name: turn
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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: '0.9'
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: '0'
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+ version: 0.9.7
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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: '0.9'
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: '0'
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+ version: 0.9.7
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  - !ruby/object:Gem::Dependency
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  name: simplecov
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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: '0.8'
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: '0'
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+ version: 0.8.2
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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: '0.8'
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: '0'
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+ version: 0.8.2
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  - !ruby/object:Gem::Dependency
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  name: shoulda-context
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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: '1.2'
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: '0'
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+ version: 1.2.1
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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: '1.2'
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: '0'
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+ version: 1.2.1
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  - !ruby/object:Gem::Dependency
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  name: coveralls
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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- - - ">="
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+ - - "~>"
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  - !ruby/object:Gem::Version
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- version: 0.6.7
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+ version: '0.7'
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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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+ - - "~>"
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  - !ruby/object:Gem::Version
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- version: 0.6.7
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+ version: '0.7'
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  description: See summary
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  email: cmb211@cam.ac.uk
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  executables: