bio-vcf 0.0.2 → 0.0.3

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Files changed (29) hide show
  1. checksums.yaml +4 -4
  2. data/Gemfile +1 -0
  3. data/Gemfile.lock +8 -0
  4. data/README.md +376 -11
  5. data/VERSION +1 -1
  6. data/bin/bio-vcf +172 -39
  7. data/bio-vcf.gemspec +18 -3
  8. data/features/cli.feature +32 -0
  9. data/features/multisample.feature +28 -10
  10. data/features/step_definitions/cli-feature.rb +12 -0
  11. data/features/step_definitions/multisample.rb +64 -18
  12. data/features/support/env.rb +5 -0
  13. data/lib/bio-vcf.rb +2 -0
  14. data/lib/bio-vcf/utils.rb +23 -0
  15. data/lib/bio-vcf/vcfgenotypefield.rb +73 -28
  16. data/lib/bio-vcf/vcfheader.rb +8 -0
  17. data/lib/bio-vcf/vcfline.rb +1 -0
  18. data/lib/bio-vcf/vcfrecord.rb +142 -14
  19. data/lib/bio-vcf/vcfsample.rb +88 -0
  20. data/test/data/input/dbsnp.vcf +200 -0
  21. data/test/data/input/multisample.vcf +2 -2
  22. data/test/data/regression/eval_r.info.dp.ref +150 -0
  23. data/test/data/regression/r.info.dp.ref +147 -0
  24. data/test/data/regression/rewrite.info.sample.ref +150 -0
  25. data/test/data/regression/s.dp.ref +145 -0
  26. data/test/data/regression/seval_s.dp.ref +36 -0
  27. data/test/data/regression/sfilter001.ref +145 -0
  28. data/test/performance/metrics.md +98 -0
  29. metadata +28 -2
data/test/performance/metrics.md ADDED
@@ -0,0 +1,98 @@
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+ Round of testing with
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+
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+ ruby -v
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+ ruby 2.1.0p0 (2013-12-25 revision 44422) [x86_64-linux]
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+
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+ wc test/tmp/test.vcf
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+ 12469 137065 2053314 test/tmp/test.vcf
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+
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+ time ./bin/bio-vcf -i --filter 'r.info.dp>20' --sfilter 's.dp>10' < test/tmp/test.vcf > /dev/null
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+ vcf 0.0.3-pre4 (biogem Ruby 2.1.0) by Pjotr Prins 2014
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+ Options: {:show_help=>false, :ignore_missing=>true, :filter=>"r.info.dp>20", :sfilter=>"s.dp>10"}
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+ real 0m1.215s
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+ user 0m1.208s
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+ sys 0m0.004s
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+
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+ Reload
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+
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+ time ./bin/bio-vcf -i --filter 'r.info.dp>20' --sfilter 's.dp>10' < test/tmp/test.vcf > /dev/null
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+ vcf 0.0.3-pre4 (biogem Ruby 2.1.0) by Pjotr Prins 2014
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+ Options: {:show_help=>false, :ignore_missing=>true, :filter=>"r.info.dp>20", :sfilter=>"s.dp>10"}
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+ real 0m1.194s
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+ user 0m1.172s
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+ sys 0m0.016s
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+
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+ Introduced method caching
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+
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+ real 0m1.190s
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+ user 0m1.180s
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+ sys 0m0.004s
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+
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+ Introduce !!Float test
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+
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+ real 0m1.187s
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+ user 0m1.180s
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+ sys 0m0.004s
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+
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+ Cache sample index
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+
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+ real 0m1.156s
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+ user 0m1.148s
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+ sys 0m0.004s
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+
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+ Run the profiler
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+
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+ ruby -rprofile ./bin/bio-vcf -i --filter 'r.info.dp>20' --sfilter 's.dp>10' < test/tmp/test.vcf > /dev/null
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+ vcf 0.0.3-pre4 (biogem Ruby 2.1.0) by Pjotr Prins 2014
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+ Options: {:show_help=>false, :ignore_missing=>true, :filter=>"r.info.dp>20", :sfilter=>"s.dp>10"}
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+ % cumulative self self total
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+ time seconds seconds calls ms/call ms/call name
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+ 9.45 2.19 2.19 34968 0.06 0.76 Object#parse_line
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+ 7.25 3.87 1.68 75031 0.02 0.03 BioVcf::VcfRecordInfo#[]=
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+ 7.12 5.52 1.65 34968 0.05 0.29 Kernel.eval
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+ 6.86 7.11 1.59 87481 0.02 0.10 BioVcf::VcfRecordInfo#initialize
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+ 5.57 8.40 1.29 35994 0.04 0.47 Array#each
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+ 4.14 9.36 0.96 34253 0.03 0.65 BioVcf::VcfRecord#each_sample
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+ 3.93 10.27 0.91 93880 0.01 0.03 BioVcf::VcfRecordParser.get_format
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+ 3.88 11.17 0.90 145920 0.01 0.01 String#split
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+
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+ Late parsing of info field without split:
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+
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+ real 0m1.124s
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+ user 0m1.120s
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+ sys 0m0.008s
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+
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+ Global sample info caching
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+
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+ real 0m1.032s
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+ user 0m1.020s
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+ sys 0m0.008s
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+
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+ Assign some repeated Hash queries
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+
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+ real 0m1.028s
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+ user 0m1.024s
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+ sys 0m0.000s
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+
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+ Profiler now picking out eval for further optimization
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+
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+ % cumulative self self total
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+ time seconds seconds calls ms/call ms/call name
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+ 10.45 1.80 1.80 34968 0.05 0.59 Object#parse_line
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+ 7.89 3.16 1.36 34968 0.04 0.17 Kernel.eval
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+ 5.69 4.14 0.98 34253 0.03 0.57 BioVcf::VcfRecord#each_sample
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+ 4.93 4.99 0.85 12497 0.07 1.37 nil#
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+
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+ Compiling sample eval
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+
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+ real 0m0.820s
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+ user 0m0.812s
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+ sys 0m0.004s
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+
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+ Compiling record eval
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+
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+ real 0m0.647s
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+ user 0m0.644s
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+ sys 0m0.000s
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+
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+
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: 0.0.2
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+ version: 0.0.3
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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: 2014-03-05 00:00:00.000000000 Z
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+ date: 2014-05-24 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: rspec
@@ -52,6 +52,20 @@ dependencies:
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  - - ">="
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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: regressiontest
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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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+ 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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  description: Smart parser for VCF format
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  email: pjotr.public01@thebird.nl
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  executables:
@@ -70,15 +84,18 @@ files:
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  - VERSION
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  - bin/bio-vcf
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  - bio-vcf.gemspec
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+ - features/cli.feature
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  - features/diff_count.feature
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  - features/multisample.feature
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  - features/somaticsniper.feature
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  - features/step_definitions/bio-vcf_steps.rb
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+ - features/step_definitions/cli-feature.rb
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  - features/step_definitions/diff_count.rb
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  - features/step_definitions/multisample.rb
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  - features/step_definitions/somaticsniper.rb
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  - features/support/env.rb
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  - lib/bio-vcf.rb
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+ - lib/bio-vcf/utils.rb
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  - lib/bio-vcf/variant.rb
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  - lib/bio-vcf/vcf.rb
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  - lib/bio-vcf/vcfgenotypefield.rb
@@ -86,8 +103,17 @@ files:
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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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+ - test/data/input/dbsnp.vcf
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  - test/data/input/multisample.vcf
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  - test/data/input/somaticsniper.vcf
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+ - test/data/regression/eval_r.info.dp.ref
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+ - test/data/regression/r.info.dp.ref
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+ - test/data/regression/rewrite.info.sample.ref
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+ - test/data/regression/s.dp.ref
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+ - test/data/regression/seval_s.dp.ref
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+ - test/data/regression/sfilter001.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:
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  - MIT