bio-vcf 0.9.0 → 0.9.2

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Files changed (36) hide show
  1. checksums.yaml +4 -4
  2. data/.travis.yml +2 -3
  3. data/Gemfile.lock +44 -0
  4. data/README.md +151 -28
  5. data/VERSION +1 -1
  6. data/bin/bio-vcf +47 -15
  7. data/bio-vcf.gemspec +4 -21
  8. data/features/#cli.feature# +71 -0
  9. data/features/cli.feature +3 -3
  10. data/features/filter.feature +12 -0
  11. data/features/filter.feature~ +35 -0
  12. data/features/somaticsniper.feature +2 -0
  13. data/features/step_definitions/cli-feature.rb +5 -0
  14. data/features/step_definitions/somaticsniper.rb +8 -0
  15. data/lib/bio-vcf/pcows.rb +123 -36
  16. data/lib/bio-vcf/vcfgenotypefield.rb +1 -1
  17. data/lib/bio-vcf/vcfrecord.rb +21 -0
  18. data/lib/bio-vcf/vcfsample.rb +13 -0
  19. data/test/data/regression/eval_once-stderr.new +2 -1
  20. data/test/data/regression/eval_r.info.dp-stderr.new +8 -4
  21. data/test/data/regression/ifilter_s.dp-stderr.new +8 -4
  22. data/test/data/regression/pass1-stderr.new +8 -0
  23. data/test/data/regression/pass1.new +88 -0
  24. data/test/data/regression/pass1.ref +88 -0
  25. data/test/data/regression/r.info.dp-stderr.new +8 -4
  26. data/test/data/regression/rewrite.info.sample-stderr.new +8 -4
  27. data/test/data/regression/s.dp-stderr.new +8 -4
  28. data/test/data/regression/seval_s.dp-stderr.new +8 -4
  29. data/test/data/regression/sfilter_seval_s.dp-stderr.new +8 -4
  30. data/test/data/regression/thread4-stderr.new +8 -4
  31. data/test/data/regression/thread4_4-stderr.new +44 -15
  32. data/test/data/regression/vcf2json_full_header-stderr.new +8 -4
  33. data/test/data/regression/vcf2json_use_meta-stderr.new +8 -4
  34. data/test/stress/stress_test.sh +15 -0
  35. data/test/stress/stress_test.sh~ +8 -0
  36. metadata +14 -5
data/test/data/regression/vcf2json_full_header-stderr.new CHANGED
@@ -1,4 +1,8 @@
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- bio-vcf 0.9.0-pre2 (biogem Ruby 2.2.2 with pcows) by Pjotr Prins 2015
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- Waiting up to 180 seconds for pid=3688 to complete
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- OK pid=3688, processing /tmp/bio-vcf_20150816-3685-12epvot/000001-bio-vcf
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- Processing /tmp/bio-vcf_20150816-3685-12epvot/000001-bio-vcf
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+ bio-vcf 0.9.2 (biogem Ruby 2.2.4 with pcows) by Pjotr Prins 2015
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+ Waiting up to 180 seconds for pid=9418 to complete /tmp/bio-vcf_20160122-9416-1txay4y/000001-bio-vcf
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+ Processing remaining output...
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+ Trying: [[9418, 1, "/tmp/bio-vcf_20160122-9416-1txay4y/000001-bio-vcf"]]
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+ Set lock on [[9418, 1, "/tmp/bio-vcf_20160122-9416-1txay4y/000001-bio-vcf"]]
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+ Processing output file /tmp/bio-vcf_20160122-9416-1txay4y/000001-bio-vcf (blocking)
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+ Removing /tmp/bio-vcf_20160122-9416-1txay4y/000001-bio-vcf
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+ Removing dir /tmp/bio-vcf_20160122-9416-1txay4y
data/test/data/regression/vcf2json_use_meta-stderr.new CHANGED
@@ -1,4 +1,8 @@
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- bio-vcf 0.9.0-pre2 (biogem Ruby 2.2.2 with pcows) by Pjotr Prins 2015
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- Waiting up to 180 seconds for pid=3696 to complete
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- OK pid=3696, processing /tmp/bio-vcf_20150816-3694-162o65x/000001-bio-vcf
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- Processing /tmp/bio-vcf_20150816-3694-162o65x/000001-bio-vcf
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+ bio-vcf 0.9.2 (biogem Ruby 2.2.4 with pcows) by Pjotr Prins 2015
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+ Waiting up to 180 seconds for pid=9427 to complete /tmp/bio-vcf_20160122-9425-l2fs1h/000001-bio-vcf
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+ Processing remaining output...
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+ Trying: [[9427, 1, "/tmp/bio-vcf_20160122-9425-l2fs1h/000001-bio-vcf"]]
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+ Set lock on [[9427, 1, "/tmp/bio-vcf_20160122-9425-l2fs1h/000001-bio-vcf"]]
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+ Processing output file /tmp/bio-vcf_20160122-9425-l2fs1h/000001-bio-vcf (blocking)
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+ Removing /tmp/bio-vcf_20160122-9425-l2fs1h/000001-bio-vcf
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+ Removing dir /tmp/bio-vcf_20160122-9425-l2fs1h
data/test/stress/stress_test.sh ADDED
@@ -0,0 +1,15 @@
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+ #! /bin/bash
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+ #
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+ # Stress test bio-vcf by running it on large files and comparing
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+ # results using threads
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+
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+ input=test/data/input/multisample.vcf
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+ filter='--sfilter 's.dp>70' --seval s.dp'
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+
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+ echo "cat $input | ./bin/bio-vcf --num-threads 1 $filter > stress_simple01.vcf"
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+ cat $input | ./bin/bio-vcf --num-threads 1 $filter > stress_simple01.vcf
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+ cat $input | ./bin/bio-vcf --num-threads 2 $filter > stress_simple02.vcf
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+ cat $input | ./bin/bio-vcf --num-threads 4 $filter > stress_simple03.vcf
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+ cat $input | ./bin/bio-vcf $filter > stress_simple04.vcf
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+ cat $input | ./bin/bio-vcf --thread-lines 3 $filter > stress_simple05.vcf
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+ cat $input | ./bin/bio-vcf --thread-lines 1 $filter > stress_simple06.vcf
data/test/stress/stress_test.sh~ ADDED
@@ -0,0 +1,8 @@
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+ #! /bin/bash
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+ #
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+ # Stress test bio-vcf by running it on large files and comparing
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+ # results using threads
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+
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+ input=test/data/input/multisample.vcf
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+
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+ cat $input | ./bin/bio-vcf --num-threads 1 > stress_simple01.vcf
metadata CHANGED
@@ -1,17 +1,17 @@
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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: 0.9.0
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+ version: 0.9.2
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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: 2015-08-16 00:00:00.000000000 Z
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+ date: 2016-01-22 00:00:00.000000000 Z
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  dependencies: []
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  description: Smart lazy multi-threaded parser for VCF format with useful filtering
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- and output rewriting
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+ and output rewriting (JSON, RDF etc.)
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  email: pjotr.public01@thebird.nl
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  executables:
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  - bio-vcf
@@ -22,6 +22,7 @@ extra_rdoc_files:
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  files:
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  - ".travis.yml"
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  - Gemfile
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+ - Gemfile.lock
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  - LICENSE.txt
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  - README.md
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  - Rakefile
@@ -29,8 +30,11 @@ 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/cli.feature
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  - features/diff_count.feature
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+ - features/filter.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
@@ -81,6 +85,9 @@ files:
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  - test/data/regression/ifilter_s.dp-stderr.new
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  - test/data/regression/ifilter_s.dp.new
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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
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  - test/data/regression/r.info.dp.ref
@@ -112,6 +119,8 @@ files:
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  - test/data/regression/vcf2json_use_meta.new
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  - test/data/regression/vcf2json_use_meta.ref
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  - test/performance/metrics.md
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+ - test/stress/stress_test.sh
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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/pjotrp/bioruby-vcf
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  licenses:
@@ -133,8 +142,8 @@ 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: 2.4.5
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+ rubygems_version: 2.4.5.1
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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: []