ngs-ci 0.0.1.a

Sign up to get free protection for your applications and to get access to all the features.
Files changed (29) hide show
  1. checksums.yaml +7 -0
  2. data/.coveralls.yml +1 -0
  3. data/.gitignore +15 -0
  4. data/.rspec +1 -0
  5. data/.travis.yml +19 -0
  6. data/Gemfile +4 -0
  7. data/LICENSE.txt +674 -0
  8. data/README.md +43 -0
  9. data/Rakefile +6 -0
  10. data/TODO.md +31 -0
  11. data/TODO.org +39 -0
  12. data/bin/ngs-ci +125 -0
  13. data/lib/NGSCI/calculator.rb +289 -0
  14. data/lib/NGSCI/cmd.rb +23 -0
  15. data/lib/NGSCI/read.rb +31 -0
  16. data/lib/NGSCI/version.rb +3 -0
  17. data/lib/NGSCI.rb +31 -0
  18. data/ngs-ci.gemspec +35 -0
  19. data/spec/lib/NGSCI_spec.rb +10 -0
  20. data/spec/lib/bin_spec.rb +51 -0
  21. data/spec/lib/calculator_spec.rb +316 -0
  22. data/spec/lib/cmd_spec.rb +17 -0
  23. data/spec/lib/read_spec.rb +35 -0
  24. data/spec/spec_helper.rb +11 -0
  25. data/spec/test_files/empty.bam +0 -0
  26. data/spec/test_files/test.bam +0 -0
  27. data/spec/test_files/test.bam.bai +0 -0
  28. data/spec/test_files/test.fa +2 -0
  29. metadata +209 -0
metadata ADDED
@@ -0,0 +1,209 @@
1
+ --- !ruby/object:Gem::Specification
2
+ name: ngs-ci
3
+ version: !ruby/object:Gem::Version
4
+ version: 0.0.1.a
5
+ platform: ruby
6
+ authors:
7
+ - Matthew Ralston
8
+ autorequire:
9
+ bindir: bin
10
+ cert_chain: []
11
+ date: 2015-10-28 00:00:00.000000000 Z
12
+ dependencies:
13
+ - !ruby/object:Gem::Dependency
14
+ name: trollop
15
+ requirement: !ruby/object:Gem::Requirement
16
+ requirements:
17
+ - - "~>"
18
+ - !ruby/object:Gem::Version
19
+ version: 2.1.2
20
+ type: :runtime
21
+ prerelease: false
22
+ version_requirements: !ruby/object:Gem::Requirement
23
+ requirements:
24
+ - - "~>"
25
+ - !ruby/object:Gem::Version
26
+ version: 2.1.2
27
+ - !ruby/object:Gem::Dependency
28
+ name: bio-samtools
29
+ requirement: !ruby/object:Gem::Requirement
30
+ requirements:
31
+ - - '='
32
+ - !ruby/object:Gem::Version
33
+ version: 2.3.2
34
+ type: :runtime
35
+ prerelease: false
36
+ version_requirements: !ruby/object:Gem::Requirement
37
+ requirements:
38
+ - - '='
39
+ - !ruby/object:Gem::Version
40
+ version: 2.3.2
41
+ - !ruby/object:Gem::Dependency
42
+ name: parallel
43
+ requirement: !ruby/object:Gem::Requirement
44
+ requirements:
45
+ - - "~>"
46
+ - !ruby/object:Gem::Version
47
+ version: '1.4'
48
+ type: :runtime
49
+ prerelease: false
50
+ version_requirements: !ruby/object:Gem::Requirement
51
+ requirements:
52
+ - - "~>"
53
+ - !ruby/object:Gem::Version
54
+ version: '1.4'
55
+ - !ruby/object:Gem::Dependency
56
+ name: yell
57
+ requirement: !ruby/object:Gem::Requirement
58
+ requirements:
59
+ - - ">="
60
+ - !ruby/object:Gem::Version
61
+ version: '0'
62
+ type: :runtime
63
+ prerelease: false
64
+ version_requirements: !ruby/object:Gem::Requirement
65
+ requirements:
66
+ - - ">="
67
+ - !ruby/object:Gem::Version
68
+ version: '0'
69
+ - !ruby/object:Gem::Dependency
70
+ name: ruby-prof
71
+ requirement: !ruby/object:Gem::Requirement
72
+ requirements:
73
+ - - "~>"
74
+ - !ruby/object:Gem::Version
75
+ version: '0.15'
76
+ type: :runtime
77
+ prerelease: false
78
+ version_requirements: !ruby/object:Gem::Requirement
79
+ requirements:
80
+ - - "~>"
81
+ - !ruby/object:Gem::Version
82
+ version: '0.15'
83
+ - !ruby/object:Gem::Dependency
84
+ name: bundler
85
+ requirement: !ruby/object:Gem::Requirement
86
+ requirements:
87
+ - - ">="
88
+ - !ruby/object:Gem::Version
89
+ version: '0'
90
+ type: :development
91
+ prerelease: false
92
+ version_requirements: !ruby/object:Gem::Requirement
93
+ requirements:
94
+ - - ">="
95
+ - !ruby/object:Gem::Version
96
+ version: '0'
97
+ - !ruby/object:Gem::Dependency
98
+ name: rake
99
+ requirement: !ruby/object:Gem::Requirement
100
+ requirements:
101
+ - - "~>"
102
+ - !ruby/object:Gem::Version
103
+ version: '10.0'
104
+ type: :development
105
+ prerelease: false
106
+ version_requirements: !ruby/object:Gem::Requirement
107
+ requirements:
108
+ - - "~>"
109
+ - !ruby/object:Gem::Version
110
+ version: '10.0'
111
+ - !ruby/object:Gem::Dependency
112
+ name: rspec
113
+ requirement: !ruby/object:Gem::Requirement
114
+ requirements:
115
+ - - "~>"
116
+ - !ruby/object:Gem::Version
117
+ version: '3.1'
118
+ type: :development
119
+ prerelease: false
120
+ version_requirements: !ruby/object:Gem::Requirement
121
+ requirements:
122
+ - - "~>"
123
+ - !ruby/object:Gem::Version
124
+ version: '3.1'
125
+ - !ruby/object:Gem::Dependency
126
+ name: coveralls
127
+ requirement: !ruby/object:Gem::Requirement
128
+ requirements:
129
+ - - ">="
130
+ - !ruby/object:Gem::Version
131
+ version: '0'
132
+ type: :development
133
+ prerelease: false
134
+ version_requirements: !ruby/object:Gem::Requirement
135
+ requirements:
136
+ - - ">="
137
+ - !ruby/object:Gem::Version
138
+ version: '0'
139
+ description: Calculated a metric that estimates read complexity at each base for RNA-seq
140
+ BAM files. Alternative to pileup format.
141
+ email:
142
+ - mrals89@gmail.com
143
+ executables:
144
+ - ngs-ci
145
+ extensions: []
146
+ extra_rdoc_files: []
147
+ files:
148
+ - ".coveralls.yml"
149
+ - ".gitignore"
150
+ - ".rspec"
151
+ - ".travis.yml"
152
+ - Gemfile
153
+ - LICENSE.txt
154
+ - README.md
155
+ - Rakefile
156
+ - TODO.md
157
+ - TODO.org
158
+ - bin/ngs-ci
159
+ - lib/NGSCI.rb
160
+ - lib/NGSCI/calculator.rb
161
+ - lib/NGSCI/cmd.rb
162
+ - lib/NGSCI/read.rb
163
+ - lib/NGSCI/version.rb
164
+ - ngs-ci.gemspec
165
+ - spec/lib/NGSCI_spec.rb
166
+ - spec/lib/bin_spec.rb
167
+ - spec/lib/calculator_spec.rb
168
+ - spec/lib/cmd_spec.rb
169
+ - spec/lib/read_spec.rb
170
+ - spec/spec_helper.rb
171
+ - spec/test_files/empty.bam
172
+ - spec/test_files/test.bam
173
+ - spec/test_files/test.bam.bai
174
+ - spec/test_files/test.fa
175
+ homepage: ''
176
+ licenses:
177
+ - GPL v3
178
+ metadata: {}
179
+ post_install_message:
180
+ rdoc_options: []
181
+ require_paths:
182
+ - lib
183
+ required_ruby_version: !ruby/object:Gem::Requirement
184
+ requirements:
185
+ - - ">="
186
+ - !ruby/object:Gem::Version
187
+ version: '0'
188
+ required_rubygems_version: !ruby/object:Gem::Requirement
189
+ requirements:
190
+ - - ">"
191
+ - !ruby/object:Gem::Version
192
+ version: 1.3.1
193
+ requirements: []
194
+ rubyforge_project:
195
+ rubygems_version: 2.4.5
196
+ signing_key:
197
+ specification_version: 4
198
+ summary: Next Generation Sequencing Complexity Index.
199
+ test_files:
200
+ - spec/lib/NGSCI_spec.rb
201
+ - spec/lib/bin_spec.rb
202
+ - spec/lib/calculator_spec.rb
203
+ - spec/lib/cmd_spec.rb
204
+ - spec/lib/read_spec.rb
205
+ - spec/spec_helper.rb
206
+ - spec/test_files/empty.bam
207
+ - spec/test_files/test.bam
208
+ - spec/test_files/test.bam.bai
209
+ - spec/test_files/test.fa