bio-vcf 0.9.0 → 0.9.2
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- checksums.yaml +4 -4
- data/.travis.yml +2 -3
- data/Gemfile.lock +44 -0
- data/README.md +151 -28
- data/VERSION +1 -1
- data/bin/bio-vcf +47 -15
- data/bio-vcf.gemspec +4 -21
- data/features/#cli.feature# +71 -0
- data/features/cli.feature +3 -3
- data/features/filter.feature +12 -0
- data/features/filter.feature~ +35 -0
- data/features/somaticsniper.feature +2 -0
- data/features/step_definitions/cli-feature.rb +5 -0
- data/features/step_definitions/somaticsniper.rb +8 -0
- data/lib/bio-vcf/pcows.rb +123 -36
- data/lib/bio-vcf/vcfgenotypefield.rb +1 -1
- data/lib/bio-vcf/vcfrecord.rb +21 -0
- data/lib/bio-vcf/vcfsample.rb +13 -0
- data/test/data/regression/eval_once-stderr.new +2 -1
- data/test/data/regression/eval_r.info.dp-stderr.new +8 -4
- data/test/data/regression/ifilter_s.dp-stderr.new +8 -4
- data/test/data/regression/pass1-stderr.new +8 -0
- data/test/data/regression/pass1.new +88 -0
- data/test/data/regression/pass1.ref +88 -0
- data/test/data/regression/r.info.dp-stderr.new +8 -4
- data/test/data/regression/rewrite.info.sample-stderr.new +8 -4
- data/test/data/regression/s.dp-stderr.new +8 -4
- data/test/data/regression/seval_s.dp-stderr.new +8 -4
- data/test/data/regression/sfilter_seval_s.dp-stderr.new +8 -4
- data/test/data/regression/thread4-stderr.new +8 -4
- data/test/data/regression/thread4_4-stderr.new +44 -15
- data/test/data/regression/vcf2json_full_header-stderr.new +8 -4
- data/test/data/regression/vcf2json_use_meta-stderr.new +8 -4
- data/test/stress/stress_test.sh +15 -0
- data/test/stress/stress_test.sh~ +8 -0
- metadata +14 -5
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@@ -1,4 +1,8 @@
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bio-vcf 0.9.
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Waiting up to 180 seconds for pid=
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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
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@@ -1,4 +1,8 @@
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bio-vcf 0.9.
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Waiting up to 180 seconds for pid=
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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
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@@ -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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input=test/data/input/multisample.vcf
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filter='--sfilter 's.dp>70' --seval s.dp'
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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
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metadata
CHANGED
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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.
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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:
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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
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@@ -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
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@@ -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
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@@ -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
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@@ -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:
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@@ -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: []
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