fix-trinity-output 1.0.0
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- checksums.yaml +7 -0
- data/.gitignore +48 -0
- data/Gemfile +3 -0
- data/README.md +11 -0
- data/Rakefile +8 -0
- data/bin/fix-trinity-output +42 -0
- data/fix-trinity-output.gemspec +21 -0
- data/lib/fix-trinity-output.rb +1 -0
- data/lib/fix-trinity-output/fix-trinity-output.rb +96 -0
- data/test/helper.rb +8 -0
- data/test/left.fq +888 -0
- data/test/right.fq +880 -0
- data/test/test_test.rb +37 -0
- metadata +150 -0
data/test/test_test.rb
ADDED
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@@ -0,0 +1,37 @@
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1
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#!/usr/bin/env ruby
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2
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3
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require 'helper'
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4
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require 'tmpdir'
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5
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+
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6
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class TestFixer < Test::Unit::TestCase
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7
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+
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8
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context 'fixer' do
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9
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10
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setup do
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11
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@fixer = Fixer.new
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12
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@tmpdir = Dir.mktmpdir
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13
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end
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14
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15
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teardown do
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16
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cmd = "rm -rf #{@tmpdir}"
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17
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`#{cmd}`
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18
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end
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19
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20
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should 'fix pair of fastq files' do
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21
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left = File.join(File.dirname(__FILE__), 'left.fq')
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22
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right = File.join(File.dirname(__FILE__), 'right.fq')
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23
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prefix = "#{@tmpdir}/test"
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24
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@fixer.run left, right, prefix
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25
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assert File.exist?("#{@tmpdir}/test-fixed.1.fastq")
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26
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assert File.exist?("#{@tmpdir}/test-fixed.2.fastq")
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27
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assert File.exist?("#{@tmpdir}/test-fixed.single.fastq")
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28
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lines = `wc -l #{@tmpdir}/test-fixed.1.fastq`
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29
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assert_equal 876, lines.split(/\s+/).first.to_i
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30
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lines = `wc -l #{@tmpdir}/test-fixed.2.fastq`
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31
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assert_equal 876, lines.split(/\s+/).first.to_i
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32
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assert_equal 762, File.size("#{@tmpdir}/test-fixed.single.fastq")
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33
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34
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end
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35
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36
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end
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37
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end
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metadata
ADDED
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@@ -0,0 +1,150 @@
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1
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--- !ruby/object:Gem::Specification
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name: fix-trinity-output
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version: !ruby/object:Gem::Version
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4
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version: 1.0.0
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5
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platform: ruby
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6
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authors:
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7
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- Chris Boursnell
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8
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autorequire:
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9
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bindir: bin
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10
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cert_chain: []
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11
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date: 2014-10-23 00:00:00.000000000 Z
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12
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dependencies:
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13
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- !ruby/object:Gem::Dependency
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14
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name: trollop
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15
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requirement: !ruby/object:Gem::Requirement
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16
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requirements:
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17
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- - "~>"
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18
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- !ruby/object:Gem::Version
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19
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version: '2.0'
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20
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type: :runtime
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21
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prerelease: false
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22
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version_requirements: !ruby/object:Gem::Requirement
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23
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requirements:
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24
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- - "~>"
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25
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+
- !ruby/object:Gem::Version
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26
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version: '2.0'
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27
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- !ruby/object:Gem::Dependency
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28
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name: rake
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29
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requirement: !ruby/object:Gem::Requirement
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30
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requirements:
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31
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- - "~>"
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32
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- !ruby/object:Gem::Version
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33
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version: '10.3'
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34
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- - ">="
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35
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- !ruby/object:Gem::Version
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36
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version: 10.3.2
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37
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type: :development
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38
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prerelease: false
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39
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version_requirements: !ruby/object:Gem::Requirement
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40
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requirements:
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41
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- - "~>"
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42
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- !ruby/object:Gem::Version
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43
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version: '10.3'
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44
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- - ">="
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45
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- !ruby/object:Gem::Version
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46
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version: 10.3.2
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47
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- !ruby/object:Gem::Dependency
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48
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name: turn
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49
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requirement: !ruby/object:Gem::Requirement
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50
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requirements:
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51
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+
- - "~>"
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52
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- !ruby/object:Gem::Version
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53
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version: '0.9'
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54
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- - ">="
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55
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- !ruby/object:Gem::Version
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56
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version: 0.9.7
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57
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type: :development
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58
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prerelease: false
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59
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version_requirements: !ruby/object:Gem::Requirement
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60
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requirements:
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61
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- - "~>"
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62
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- !ruby/object:Gem::Version
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63
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version: '0.9'
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64
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- - ">="
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65
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- !ruby/object:Gem::Version
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66
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version: 0.9.7
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67
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- !ruby/object:Gem::Dependency
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68
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name: simplecov
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69
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requirement: !ruby/object:Gem::Requirement
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70
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requirements:
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71
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- - "~>"
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72
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- !ruby/object:Gem::Version
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73
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version: '0.8'
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74
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- - ">="
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75
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- !ruby/object:Gem::Version
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76
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version: 0.8.2
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77
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type: :development
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78
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prerelease: false
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79
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version_requirements: !ruby/object:Gem::Requirement
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80
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requirements:
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81
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- - "~>"
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82
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- !ruby/object:Gem::Version
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83
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version: '0.8'
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84
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- - ">="
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85
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- !ruby/object:Gem::Version
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86
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version: 0.8.2
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87
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- !ruby/object:Gem::Dependency
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88
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name: shoulda-context
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89
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requirement: !ruby/object:Gem::Requirement
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90
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requirements:
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91
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- - "~>"
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92
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- !ruby/object:Gem::Version
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93
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version: '1.2'
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94
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- - ">="
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95
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- !ruby/object:Gem::Version
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96
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version: 1.2.1
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97
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type: :development
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98
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prerelease: false
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99
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version_requirements: !ruby/object:Gem::Requirement
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100
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requirements:
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101
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- - "~>"
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102
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- !ruby/object:Gem::Version
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103
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version: '1.2'
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104
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- - ">="
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105
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- !ruby/object:Gem::Version
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106
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version: 1.2.1
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107
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description: See readme
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108
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email: cmb211@cam.ac.uk
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109
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executables:
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110
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- fix-trinity-output
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111
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extensions: []
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112
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extra_rdoc_files: []
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113
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files:
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114
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- ".gitignore"
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115
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- Gemfile
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116
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- README.md
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117
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- Rakefile
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118
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- bin/fix-trinity-output
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119
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- fix-trinity-output.gemspec
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120
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- lib/fix-trinity-output.rb
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121
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- lib/fix-trinity-output/fix-trinity-output.rb
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122
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- test/helper.rb
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123
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- test/left.fq
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124
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- test/right.fq
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125
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- test/test_test.rb
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126
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homepage: http://rubygems.org/gems/fix-trinity-output
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127
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licenses:
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128
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- MIT
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129
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metadata: {}
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130
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post_install_message:
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131
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rdoc_options: []
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132
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require_paths:
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133
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- lib
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134
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required_ruby_version: !ruby/object:Gem::Requirement
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135
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requirements:
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136
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- - ">="
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137
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+
- !ruby/object:Gem::Version
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138
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version: '0'
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139
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+
required_rubygems_version: !ruby/object:Gem::Requirement
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140
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requirements:
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141
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+
- - ">="
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142
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+
- !ruby/object:Gem::Version
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143
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version: '0'
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144
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requirements: []
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145
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rubyforge_project:
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146
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rubygems_version: 2.2.2
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147
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signing_key:
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148
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specification_version: 4
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149
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summary: Fix output fastq files from Trinity
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150
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test_files: []
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