RubyGems - bio-sambamba - Versions diffs - 0.0.1 - Mend

bio-sambamba 0.0.1

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Files changed (38) hide show

data/.document +5 -0
data/.travis.yml +12 -0
data/Gemfile +11 -0
data/LICENSE.txt +20 -0
data/README.md +68 -0
data/Rakefile +47 -0
data/VERSION +1 -0
data/features/iterate-alignments.feature +40 -0
data/features/random-access.feature +10 -0
data/features/sam-header.feature +23 -0
data/features/step_definitions/iterate-alignments_steps.rb +83 -0
data/features/step_definitions/random-access_steps.rb +22 -0
data/features/step_definitions/sam-header_steps.rb +56 -0
data/features/step_definitions/validation-steps.rb +34 -0
data/features/support/env.rb +13 -0
data/features/syntax-sugar.feature +17 -0
data/features/validation.feature +16 -0
data/lib/bio-sambamba.rb +8 -0
data/lib/bio-sambamba/alignment.rb +131 -0
data/lib/bio-sambamba/alignmentiterator.rb +45 -0
data/lib/bio-sambamba/bamfile.rb +45 -0
data/lib/bio-sambamba/samfile.rb +25 -0
data/lib/bio-sambamba/samheader.rb +194 -0
data/test/data/bins.bam +0 -0
data/test/data/bins.bam.bai +0 -0
data/test/data/c1215_fixmate.bam +0 -0
data/test/data/corrupted_zlib_archive.bam +0 -0
data/test/data/duplicated_block_size.bam +0 -0
data/test/data/ex1_header.bam +0 -0
data/test/data/ex1_header.bam.bai +0 -0
data/test/data/ex1_header.sam +3273 -0
data/test/data/ex1_header.uncompressed.bam +0 -0
data/test/data/no_block_size.bam +0 -0
data/test/data/tags.bam +0 -0
data/test/data/tags.bam.bai +0 -0
data/test/data/wrong_bc_subfield_length.bam +0 -0
data/test/data/wrong_extra_gzip_length.bam +0 -0
metadata +184 -0

data/test/data/ex1_header.uncompressed.bam ADDED Viewed

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data/test/data/wrong_bc_subfield_length.bam ADDED Viewed

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data/test/data/wrong_extra_gzip_length.bam ADDED Viewed

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metadata ADDED Viewed

@@ -0,0 +1,184 @@
+--- !ruby/object:Gem::Specification
+name: bio-sambamba
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+  prerelease:
+platform: ruby
+authors:
+- Artem Tarasov
+autorequire:
+bindir: bin
+cert_chain: []
+date: 2012-06-27 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+- !ruby/object:Gem::Dependency
+  name: oj
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.2.9
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.2.9
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.1.4
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.1.4
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.3
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.3
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.7.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.7.0
+- !ruby/object:Gem::Dependency
+  name: cucumber
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.2.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.2.0
+description: New Sambamba library comes with a command-line tool for working with
+  SAM/BAM files. This gem brings some of its functionality to Ruby.
+email: lomereiter@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+files:
+- .document
+- .travis.yml
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- VERSION
+- features/iterate-alignments.feature
+- features/random-access.feature
+- features/sam-header.feature
+- features/step_definitions/iterate-alignments_steps.rb
+- features/step_definitions/random-access_steps.rb
+- features/step_definitions/sam-header_steps.rb
+- features/step_definitions/validation-steps.rb
+- features/support/env.rb
+- features/syntax-sugar.feature
+- features/validation.feature
+- lib/bio-sambamba.rb
+- lib/bio-sambamba/alignment.rb
+- lib/bio-sambamba/alignmentiterator.rb
+- lib/bio-sambamba/bamfile.rb
+- lib/bio-sambamba/samfile.rb
+- lib/bio-sambamba/samheader.rb
+- test/data/bins.bam
+- test/data/bins.bam.bai
+- test/data/c1215_fixmate.bam
+- test/data/corrupted_zlib_archive.bam
+- test/data/duplicated_block_size.bam
+- test/data/ex1_header.bam
+- test/data/ex1_header.bam.bai
+- test/data/ex1_header.sam
+- test/data/ex1_header.uncompressed.bam
+- test/data/no_block_size.bam
+- test/data/tags.bam
+- test/data/tags.bam.bai
+- test/data/wrong_bc_subfield_length.bam
+- test/data/wrong_extra_gzip_length.bam
+homepage: http://github.com/lomereiter/bioruby-sambamba
+licenses:
+- MIT
+post_install_message:
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: 3091856073334228890
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project:
+rubygems_version: 1.8.24
+signing_key:
+specification_version: 3
+summary: Ruby wrapper for Sambamba tool
+test_files: []