bio-vcf 0.8.1 → 0.8.2

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Files changed (23) hide show
  1. checksums.yaml +4 -4
  2. data/.travis.yml +5 -0
  3. data/Gemfile +4 -4
  4. data/Gemfile.lock +4 -4
  5. data/README.md +32 -11
  6. data/VERSION +1 -1
  7. data/bin/bio-vcf +18 -9
  8. data/bio-vcf.gemspec +25 -17
  9. data/features/cli.feature +11 -1
  10. data/features/step_definitions/cli-feature.rb +1 -1
  11. data/features/step_definitions/vcf_header.rb +48 -0
  12. data/features/vcf_header.feature +35 -0
  13. data/lib/bio-vcf.rb +1 -0
  14. data/lib/bio-vcf/vcfheader.rb +88 -4
  15. data/lib/bio-vcf/vcfheader_line.rb +483 -0
  16. data/lib/bio-vcf/vcfsample.rb +10 -1
  17. data/ragel/gen_vcfheaderline_parser.rb +483 -0
  18. data/ragel/gen_vcfheaderline_parser.rl +122 -0
  19. data/ragel/generate.sh +5 -0
  20. data/template/vcf2json_full_header.erb +23 -0
  21. data/template/vcf2json_use_meta.erb +41 -0
  22. data/test/data/regression/vcf2json_full_header.ref +261 -0
  23. metadata +20 -11
metadata CHANGED
@@ -1,14 +1,14 @@
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  --- !ruby/object:Gem::Specification
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  name: bio-vcf
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  version: !ruby/object:Gem::Version
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- version: 0.8.1
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+ version: 0.8.2
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  platform: ruby
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  authors:
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  - Pjotr Prins
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2014-11-26 00:00:00.000000000 Z
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+ date: 2014-12-28 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: rspec
@@ -16,54 +16,54 @@ dependencies:
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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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+ version: 2.14.0
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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'
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+ version: 2.14.0
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  - !ruby/object:Gem::Dependency
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  name: cucumber
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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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+ version: 1.3.11
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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'
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+ version: 1.3.11
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  - !ruby/object:Gem::Dependency
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  name: jeweler
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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: 2.0.1
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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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+ - - ">="
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  - !ruby/object:Gem::Version
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  version: 2.0.1
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  - !ruby/object:Gem::Dependency
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  name: regressiontest
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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: 0.0.3
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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: 0.0.3
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  description: Smart lazy multi-threaded parser for VCF format with useful filtering
@@ -96,7 +96,9 @@ files:
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  - features/step_definitions/multisample.rb
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  - features/step_definitions/sfilter.rb
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  - features/step_definitions/somaticsniper.rb
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+ - features/step_definitions/vcf_header.rb
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  - features/support/env.rb
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+ - features/vcf_header.feature
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  - lib/bio-vcf.rb
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  - lib/bio-vcf/bedfilter.rb
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  - lib/bio-vcf/template.rb
@@ -105,13 +107,19 @@ files:
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  - lib/bio-vcf/vcf.rb
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  - lib/bio-vcf/vcfgenotypefield.rb
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  - lib/bio-vcf/vcfheader.rb
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+ - lib/bio-vcf/vcfheader_line.rb
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  - lib/bio-vcf/vcfline.rb
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  - lib/bio-vcf/vcfrdf.rb
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  - lib/bio-vcf/vcfrecord.rb
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  - lib/bio-vcf/vcfsample.rb
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  - lib/bio-vcf/vcfstatistics.rb
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+ - ragel/gen_vcfheaderline_parser.rb
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+ - ragel/gen_vcfheaderline_parser.rl
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+ - ragel/generate.sh
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  - template/gatk_vcf2rdf.erb
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  - template/vcf2json.erb
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+ - template/vcf2json_full_header.erb
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+ - template/vcf2json_use_meta.erb
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  - template/vcf2rdf.erb
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  - template/vcf2rdf_header.erb
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  - test/data/input/dbsnp.vcf
@@ -127,6 +135,7 @@ files:
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  - test/data/regression/thread4.ref
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  - test/data/regression/thread4_4.ref
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  - test/data/regression/thread4_4_failed_filter-stderr.ref
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+ - test/data/regression/vcf2json_full_header.ref
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  - test/performance/metrics.md
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  homepage: http://github.com/pjotrp/bioruby-vcf
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  licenses:
@@ -148,7 +157,7 @@ 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: 2.0.3
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  signing_key:
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  specification_version: 4
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  summary: Fast multi-threaded VCF parser