bio-vcf 0.8.1 → 0.9.5

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Files changed (84) hide show
  1. checksums.yaml +5 -5
  2. data/.travis.yml +1 -11
  3. data/Gemfile +2 -8
  4. data/LICENSE.txt +1 -1
  5. data/README.md +467 -129
  6. data/RELEASE_NOTES.md +27 -0
  7. data/RELEASE_NOTES.md~ +11 -0
  8. data/Rakefile +9 -42
  9. data/TAGS +115 -0
  10. data/VERSION +1 -1
  11. data/bin/bio-vcf +156 -108
  12. data/bio-vcf.gemspec +13 -75
  13. data/features/cli.feature +22 -4
  14. data/features/diff_count.feature +0 -1
  15. data/features/filter.feature +12 -0
  16. data/features/multisample.feature +12 -0
  17. data/features/somaticsniper.feature +2 -0
  18. data/features/step_definitions/cli-feature.rb +15 -6
  19. data/features/step_definitions/diff_count.rb +1 -1
  20. data/features/step_definitions/multisample.rb +19 -0
  21. data/features/step_definitions/somaticsniper.rb +9 -1
  22. data/features/step_definitions/vcf_header.rb +48 -0
  23. data/features/support/env.rb +1 -11
  24. data/features/vcf_header.feature +35 -0
  25. data/lib/bio-vcf.rb +1 -0
  26. data/lib/bio-vcf/pcows.rb +303 -0
  27. data/lib/bio-vcf/vcffile.rb +46 -0
  28. data/lib/bio-vcf/vcfgenotypefield.rb +19 -19
  29. data/lib/bio-vcf/vcfheader.rb +137 -5
  30. data/lib/bio-vcf/vcfheader_line.rb +778 -0
  31. data/lib/bio-vcf/vcfrecord.rb +56 -18
  32. data/lib/bio-vcf/vcfsample.rb +26 -2
  33. data/lib/regressiontest.rb +11 -0
  34. data/lib/regressiontest/cli_exec.rb +101 -0
  35. data/ragel/gen_vcfheaderline_parser.rl +165 -0
  36. data/ragel/generate.sh +8 -0
  37. data/template/vcf2json.erb +16 -16
  38. data/template/vcf2json_full_header.erb +22 -0
  39. data/template/vcf2json_use_meta.erb +41 -0
  40. data/test/data/input/empty.vcf +2 -0
  41. data/test/data/input/gatk_exome.vcf +237 -0
  42. data/test/data/input/gatk_wgs.vcf +1000 -0
  43. data/test/data/input/test.bed +632 -0
  44. data/test/data/regression/empty-stderr.new +12 -0
  45. data/test/data/regression/empty.new +2 -0
  46. data/test/data/regression/empty.ref +2 -0
  47. data/test/data/regression/eval_once-stderr.new +2 -0
  48. data/test/data/regression/eval_once.new +1 -0
  49. data/test/data/regression/eval_once.ref +1 -0
  50. data/test/data/regression/eval_r.info.dp-stderr.new +10 -0
  51. data/test/data/regression/eval_r.info.dp.new +150 -0
  52. data/test/data/regression/ifilter_s.dp-stderr.new +34 -0
  53. data/test/data/regression/ifilter_s.dp.new +31 -0
  54. data/test/data/regression/pass1-stderr.new +10 -0
  55. data/test/data/regression/pass1.new +88 -0
  56. data/test/data/regression/pass1.ref +88 -0
  57. data/test/data/regression/r.info.dp-stderr.new +4 -0
  58. data/test/data/regression/r.info.dp.new +114 -0
  59. data/test/data/regression/rewrite.info.sample-stderr.new +10 -0
  60. data/test/data/regression/rewrite.info.sample.new +150 -0
  61. data/test/data/regression/s.dp-stderr.new +18 -0
  62. data/test/data/regression/s.dp.new +145 -0
  63. data/test/data/regression/seval_s.dp-stderr.new +10 -0
  64. data/test/data/regression/seval_s.dp.new +36 -0
  65. data/test/data/regression/sfilter_seval_s.dp-stderr.new +18 -0
  66. data/test/data/regression/sfilter_seval_s.dp.new +31 -0
  67. data/test/data/regression/thread4-stderr.new +10 -0
  68. data/test/data/regression/thread4.new +150 -0
  69. data/test/data/regression/thread4_4-stderr.new +25 -0
  70. data/test/data/regression/thread4_4.new +130 -0
  71. data/test/data/regression/thread4_4_failed_filter-stderr.new +5 -0
  72. data/test/data/regression/thread4_4_failed_filter-stderr.ref +5 -2
  73. data/test/data/regression/thread4_4_failed_filter.new +110 -0
  74. data/test/data/regression/vcf2json_full_header-stderr.new +10 -0
  75. data/test/data/regression/vcf2json_full_header.new +225 -0
  76. data/test/data/regression/vcf2json_full_header.ref +225 -0
  77. data/test/data/regression/vcf2json_use_meta-stderr.new +10 -0
  78. data/test/data/regression/vcf2json_use_meta.new +4697 -0
  79. data/test/data/regression/vcf2json_use_meta.ref +4697 -0
  80. data/test/performance/metrics.md +18 -1
  81. data/test/stress/stress_test.sh +15 -0
  82. data/test/tmp/test.vcf +12469 -0
  83. metadata +63 -64
  84. data/Gemfile.lock +0 -81
metadata CHANGED
@@ -1,73 +1,17 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: bio-vcf
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.8.1
4
+ version: 0.9.5
5
5
  platform: ruby
6
6
  authors:
7
7
  - Pjotr Prins
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2014-11-26 00:00:00.000000000 Z
12
- dependencies:
13
- - !ruby/object:Gem::Dependency
14
- name: rspec
15
- requirement: !ruby/object:Gem::Requirement
16
- requirements:
17
- - - ">="
18
- - !ruby/object:Gem::Version
19
- version: '0'
20
- type: :development
21
- prerelease: false
22
- version_requirements: !ruby/object:Gem::Requirement
23
- requirements:
24
- - - ">="
25
- - !ruby/object:Gem::Version
26
- version: '0'
27
- - !ruby/object:Gem::Dependency
28
- name: cucumber
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- requirement: !ruby/object:Gem::Requirement
30
- requirements:
31
- - - ">="
32
- - !ruby/object:Gem::Version
33
- version: '0'
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- type: :development
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- prerelease: false
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- version_requirements: !ruby/object:Gem::Requirement
37
- requirements:
38
- - - ">="
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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: jeweler
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- requirement: !ruby/object:Gem::Requirement
44
- requirements:
45
- - - "~>"
46
- - !ruby/object:Gem::Version
47
- version: 2.0.1
48
- type: :development
49
- prerelease: false
50
- version_requirements: !ruby/object:Gem::Requirement
51
- requirements:
52
- - - "~>"
53
- - !ruby/object:Gem::Version
54
- version: 2.0.1
55
- - !ruby/object:Gem::Dependency
56
- name: regressiontest
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- requirement: !ruby/object:Gem::Requirement
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- requirements:
59
- - - "~>"
60
- - !ruby/object:Gem::Version
61
- version: 0.0.3
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- type: :development
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- prerelease: false
64
- version_requirements: !ruby/object:Gem::Requirement
65
- requirements:
66
- - - "~>"
67
- - !ruby/object:Gem::Version
68
- version: 0.0.3
11
+ date: 2021-01-18 00:00:00.000000000 Z
12
+ dependencies: []
69
13
  description: Smart lazy multi-threaded parser for VCF format with useful filtering
70
- and output rewriting
14
+ and output rewriting (JSON, RDF etc.)
71
15
  email: pjotr.public01@thebird.nl
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16
  executables:
73
17
  - bio-vcf
@@ -78,15 +22,18 @@ extra_rdoc_files:
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  files:
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23
  - ".travis.yml"
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  - Gemfile
81
- - Gemfile.lock
82
25
  - LICENSE.txt
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26
  - README.md
27
+ - RELEASE_NOTES.md
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+ - RELEASE_NOTES.md~
84
29
  - Rakefile
30
+ - TAGS
85
31
  - VERSION
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32
  - bin/bio-vcf
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33
  - bio-vcf.gemspec
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34
  - features/cli.feature
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  - features/diff_count.feature
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+ - features/filter.feature
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  - features/multisample.feature
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  - features/sfilter.feature
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  - features/somaticsniper.feature
@@ -96,39 +43,91 @@ files:
96
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  - features/step_definitions/multisample.rb
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  - features/step_definitions/sfilter.rb
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45
  - features/step_definitions/somaticsniper.rb
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+ - features/step_definitions/vcf_header.rb
99
47
  - features/support/env.rb
48
+ - features/vcf_header.feature
100
49
  - lib/bio-vcf.rb
101
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  - lib/bio-vcf/bedfilter.rb
51
+ - lib/bio-vcf/pcows.rb
102
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  - lib/bio-vcf/template.rb
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  - lib/bio-vcf/utils.rb
104
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  - lib/bio-vcf/variant.rb
105
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  - lib/bio-vcf/vcf.rb
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+ - lib/bio-vcf/vcffile.rb
106
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  - lib/bio-vcf/vcfgenotypefield.rb
107
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  - lib/bio-vcf/vcfheader.rb
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+ - lib/bio-vcf/vcfheader_line.rb
108
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  - lib/bio-vcf/vcfline.rb
109
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  - lib/bio-vcf/vcfrdf.rb
110
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  - lib/bio-vcf/vcfrecord.rb
111
63
  - lib/bio-vcf/vcfsample.rb
112
64
  - lib/bio-vcf/vcfstatistics.rb
65
+ - lib/regressiontest.rb
66
+ - lib/regressiontest/cli_exec.rb
67
+ - ragel/gen_vcfheaderline_parser.rl
68
+ - ragel/generate.sh
113
69
  - template/gatk_vcf2rdf.erb
114
70
  - template/vcf2json.erb
71
+ - template/vcf2json_full_header.erb
72
+ - template/vcf2json_use_meta.erb
115
73
  - template/vcf2rdf.erb
116
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  - template/vcf2rdf_header.erb
117
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  - test/data/input/dbsnp.vcf
76
+ - test/data/input/empty.vcf
77
+ - test/data/input/gatk_exome.vcf
78
+ - test/data/input/gatk_wgs.vcf
118
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  - test/data/input/multisample.vcf
119
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  - test/data/input/somaticsniper.vcf
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+ - test/data/input/test.bed
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+ - test/data/regression/empty-stderr.new
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+ - test/data/regression/empty.new
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+ - test/data/regression/empty.ref
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+ - test/data/regression/eval_once-stderr.new
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+ - test/data/regression/eval_once.new
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+ - test/data/regression/eval_once.ref
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+ - test/data/regression/eval_r.info.dp-stderr.new
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+ - test/data/regression/eval_r.info.dp.new
120
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  - test/data/regression/eval_r.info.dp.ref
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+ - test/data/regression/ifilter_s.dp-stderr.new
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+ - test/data/regression/ifilter_s.dp.new
121
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  - test/data/regression/ifilter_s.dp.ref
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+ - test/data/regression/pass1-stderr.new
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+ - test/data/regression/pass1.new
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+ - test/data/regression/pass1.ref
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+ - test/data/regression/r.info.dp-stderr.new
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+ - test/data/regression/r.info.dp.new
122
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  - test/data/regression/r.info.dp.ref
100
+ - test/data/regression/rewrite.info.sample-stderr.new
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+ - test/data/regression/rewrite.info.sample.new
123
102
  - test/data/regression/rewrite.info.sample.ref
103
+ - test/data/regression/s.dp-stderr.new
104
+ - test/data/regression/s.dp.new
124
105
  - test/data/regression/s.dp.ref
106
+ - test/data/regression/seval_s.dp-stderr.new
107
+ - test/data/regression/seval_s.dp.new
125
108
  - test/data/regression/seval_s.dp.ref
109
+ - test/data/regression/sfilter_seval_s.dp-stderr.new
110
+ - test/data/regression/sfilter_seval_s.dp.new
126
111
  - test/data/regression/sfilter_seval_s.dp.ref
112
+ - test/data/regression/thread4-stderr.new
113
+ - test/data/regression/thread4.new
127
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  - test/data/regression/thread4.ref
115
+ - test/data/regression/thread4_4-stderr.new
116
+ - test/data/regression/thread4_4.new
128
117
  - test/data/regression/thread4_4.ref
118
+ - test/data/regression/thread4_4_failed_filter-stderr.new
129
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  - test/data/regression/thread4_4_failed_filter-stderr.ref
120
+ - test/data/regression/thread4_4_failed_filter.new
121
+ - test/data/regression/vcf2json_full_header-stderr.new
122
+ - test/data/regression/vcf2json_full_header.new
123
+ - test/data/regression/vcf2json_full_header.ref
124
+ - test/data/regression/vcf2json_use_meta-stderr.new
125
+ - test/data/regression/vcf2json_use_meta.new
126
+ - test/data/regression/vcf2json_use_meta.ref
130
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  - test/performance/metrics.md
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- homepage: http://github.com/pjotrp/bioruby-vcf
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+ - test/stress/stress_test.sh
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+ - test/tmp/test.vcf
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+ homepage: http://github.com/vcflib/bio-vcf
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  licenses:
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  - MIT
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  metadata: {}
@@ -148,8 +147,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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  version: '0'
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  requirements: []
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  rubyforge_project:
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- rubygems_version: 2.2.2
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+ rubygems_version: 2.7.6.2
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  signing_key:
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  specification_version: 4
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- summary: Fast multi-threaded VCF parser
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+ summary: Fast multi-purpose multi-threaded VCF parser
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  test_files: []
data/Gemfile.lock DELETED
@@ -1,81 +0,0 @@
1
- GEM
2
- remote: http://rubygems.org/
3
- specs:
4
- addressable (2.3.5)
5
- builder (3.2.2)
6
- cucumber (1.3.11)
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- builder (>= 2.1.2)
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- diff-lcs (>= 1.1.3)
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- gherkin (~> 2.12)
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- multi_json (>= 1.7.5, < 2.0)
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- multi_test (>= 0.0.2)
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- descendants_tracker (0.0.3)
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- diff-lcs (1.2.5)
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- faraday (0.9.0)
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- multipart-post (>= 1.2, < 3)
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- gherkin (2.12.2)
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- multi_json (~> 1.3)
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- gherkin (2.12.2-java)
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- multi_json (~> 1.3)
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- git (1.2.6)
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- github_api (0.11.3)
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- addressable (~> 2.3)
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- descendants_tracker (~> 0.0.1)
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- faraday (~> 0.8, < 0.10)
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- hashie (>= 1.2)
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- multi_json (>= 1.7.5, < 2.0)
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- nokogiri (~> 1.6.0)
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- oauth2
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- hashie (2.0.5)
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- highline (1.6.21)
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- jeweler (2.0.1)
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- builder
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- bundler (>= 1.0)
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- git (>= 1.2.5)
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- github_api
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- highline (>= 1.6.15)
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- nokogiri (>= 1.5.10)
38
- rake
39
- rdoc
40
- json (1.8.1)
41
- json (1.8.1-java)
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- jwt (0.1.11)
43
- multi_json (>= 1.5)
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- mini_portile (0.5.2)
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- multi_json (1.9.0)
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- multi_test (0.0.3)
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- multi_xml (0.5.5)
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- multipart-post (2.0.0)
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- nokogiri (1.6.1)
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- mini_portile (~> 0.5.0)
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- nokogiri (1.6.1-java)
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- mini_portile (~> 0.5.0)
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- oauth2 (0.9.3)
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- faraday (>= 0.8, < 0.10)
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- jwt (~> 0.1.8)
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- multi_json (~> 1.3)
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- multi_xml (~> 0.5)
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- rack (~> 1.2)
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- rack (1.5.2)
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- rake (10.1.1)
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- rdoc (4.1.1)
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- json (~> 1.4)
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- regressiontest (0.0.3)
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- rspec (2.14.1)
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- rspec-core (~> 2.14.0)
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- rspec-expectations (~> 2.14.0)
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- rspec-mocks (~> 2.14.0)
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- rspec-core (2.14.8)
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- rspec-expectations (2.14.5)
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- diff-lcs (>= 1.1.3, < 2.0)
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- rspec-mocks (2.14.6)
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-
73
- PLATFORMS
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- java
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- ruby
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-
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- DEPENDENCIES
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- cucumber
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- jeweler (~> 2.0.1)
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- regressiontest (~> 0.0.3)
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- rspec