bio-vcf 0.8.0 → 0.9.4
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- checksums.yaml +5 -5
- data/.travis.yml +1 -11
- data/Gemfile +4 -5
- data/Gemfile.lock +28 -65
- data/LICENSE.txt +1 -1
- data/README.md +387 -107
- data/RELEASE_NOTES.md +20 -0
- data/RELEASE_NOTES.md~ +11 -0
- data/Rakefile +3 -40
- data/TAGS +115 -0
- data/VERSION +1 -1
- data/bin/bio-vcf +176 -109
- data/bio-vcf.gemspec +14 -70
- data/features/cli.feature +22 -4
- data/features/diff_count.feature +0 -1
- data/features/filter.feature +12 -0
- data/features/multisample.feature +25 -0
- data/features/somaticsniper.feature +2 -0
- data/features/step_definitions/cli-feature.rb +15 -6
- data/features/step_definitions/diff_count.rb +1 -1
- data/features/step_definitions/multisample.rb +19 -0
- data/features/step_definitions/somaticsniper.rb +9 -1
- data/features/step_definitions/vcf_header.rb +48 -0
- data/features/support/env.rb +0 -9
- data/features/vcf_header.feature +35 -0
- data/lib/bio-vcf.rb +2 -0
- data/lib/bio-vcf/bedfilter.rb +43 -0
- data/lib/bio-vcf/pcows.rb +303 -0
- data/lib/bio-vcf/template.rb +75 -0
- data/lib/bio-vcf/vcffile.rb +46 -0
- data/lib/bio-vcf/vcfgenotypefield.rb +25 -20
- data/lib/bio-vcf/vcfheader.rb +146 -6
- data/lib/bio-vcf/vcfheader_line.rb +778 -0
- data/lib/bio-vcf/vcfrecord.rb +56 -18
- data/lib/bio-vcf/vcfsample.rb +27 -3
- data/ragel/gen_vcfheaderline_parser.rl +165 -0
- data/ragel/generate.sh +8 -0
- data/template/vcf2json.erb +19 -7
- data/template/vcf2json_full_header.erb +22 -0
- data/template/vcf2json_use_meta.erb +41 -0
- data/template/vcf2rdf_header.erb +24 -0
- data/test/data/input/empty.vcf +2 -0
- data/test/data/input/gatk_exome.vcf +237 -0
- data/test/data/input/gatk_wgs.vcf +1000 -0
- data/test/data/input/test.bed +632 -0
- data/test/data/regression/empty-stderr.new +12 -0
- data/test/data/regression/empty.new +2 -0
- data/test/data/regression/empty.ref +2 -0
- data/test/data/regression/eval_once-stderr.new +2 -0
- data/test/data/regression/eval_once.new +1 -0
- data/test/data/regression/eval_once.ref +1 -0
- data/test/data/regression/eval_r.info.dp-stderr.new +10 -0
- data/test/data/regression/eval_r.info.dp.new +150 -0
- data/test/data/regression/ifilter_s.dp-stderr.new +34 -0
- data/test/data/regression/ifilter_s.dp.new +31 -0
- data/test/data/regression/pass1-stderr.new +10 -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 +4 -0
- data/test/data/regression/r.info.dp.new +114 -0
- data/test/data/regression/rewrite.info.sample-stderr.new +10 -0
- data/test/data/regression/rewrite.info.sample.new +150 -0
- data/test/data/regression/s.dp-stderr.new +18 -0
- data/test/data/regression/s.dp.new +145 -0
- data/test/data/regression/seval_s.dp-stderr.new +10 -0
- data/test/data/regression/seval_s.dp.new +36 -0
- data/test/data/regression/sfilter_seval_s.dp-stderr.new +18 -0
- data/test/data/regression/sfilter_seval_s.dp.new +31 -0
- data/test/data/regression/thread4-stderr.new +10 -0
- data/test/data/regression/thread4.new +150 -0
- data/test/data/regression/thread4_4-stderr.new +25 -0
- data/test/data/regression/thread4_4.new +130 -0
- data/test/data/regression/thread4_4_failed_filter-stderr.new +5 -0
- data/test/data/regression/thread4_4_failed_filter-stderr.ref +5 -1
- data/test/data/regression/thread4_4_failed_filter.new +110 -0
- data/test/data/regression/vcf2json_full_header-stderr.new +10 -0
- data/test/data/regression/vcf2json_full_header.new +225 -0
- data/test/data/regression/vcf2json_full_header.ref +225 -0
- data/test/data/regression/vcf2json_use_meta-stderr.new +10 -0
- data/test/data/regression/vcf2json_use_meta.new +4697 -0
- data/test/data/regression/vcf2json_use_meta.ref +4697 -0
- data/test/performance/metrics.md +18 -1
- data/test/stress/stress_test.sh +15 -0
- data/test/tmp/test.vcf +12469 -0
- metadata +65 -64
metadata
CHANGED
@@ -1,73 +1,17 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: bio-vcf
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3
3
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version: !ruby/object:Gem::Version
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4
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-
version: 0.
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4
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+
version: 0.9.4
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5
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platform: ruby
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6
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authors:
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7
7
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- Pjotr Prins
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8
8
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autorequire:
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9
9
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bindir: bin
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10
10
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cert_chain: []
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-
date:
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12
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-
dependencies:
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13
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-
- !ruby/object:Gem::Dependency
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name: rspec
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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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- !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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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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-
- !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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-
- !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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-
- !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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-
- !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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-
- !ruby/object:Gem::Version
|
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-
version: 0.0.3
|
11
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+
date: 2020-12-22 00:00:00.000000000 Z
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12
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+
dependencies: []
|
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13
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description: Smart lazy multi-threaded parser for VCF format with useful filtering
|
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-
and output rewriting
|
14
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+
and output rewriting (JSON, RDF etc.)
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71
15
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email: pjotr.public01@thebird.nl
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executables:
|
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- bio-vcf
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@@ -81,12 +25,16 @@ files:
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- Gemfile.lock
|
82
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- LICENSE.txt
|
83
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- README.md
|
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+
- RELEASE_NOTES.md
|
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+
- RELEASE_NOTES.md~
|
84
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- Rakefile
|
31
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+
- TAGS
|
85
32
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- VERSION
|
86
33
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- bin/bio-vcf
|
87
34
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- bio-vcf.gemspec
|
88
35
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- features/cli.feature
|
89
36
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- features/diff_count.feature
|
37
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+
- features/filter.feature
|
90
38
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- features/multisample.feature
|
91
39
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- features/sfilter.feature
|
92
40
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- features/somaticsniper.feature
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@@ -96,36 +44,89 @@ files:
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96
44
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- features/step_definitions/multisample.rb
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97
45
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- features/step_definitions/sfilter.rb
|
98
46
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- features/step_definitions/somaticsniper.rb
|
47
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+
- features/step_definitions/vcf_header.rb
|
99
48
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- features/support/env.rb
|
49
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+
- features/vcf_header.feature
|
100
50
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- lib/bio-vcf.rb
|
51
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+
- lib/bio-vcf/bedfilter.rb
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52
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+
- lib/bio-vcf/pcows.rb
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53
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+
- lib/bio-vcf/template.rb
|
101
54
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- lib/bio-vcf/utils.rb
|
102
55
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- lib/bio-vcf/variant.rb
|
103
56
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- lib/bio-vcf/vcf.rb
|
57
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+
- lib/bio-vcf/vcffile.rb
|
104
58
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- lib/bio-vcf/vcfgenotypefield.rb
|
105
59
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- lib/bio-vcf/vcfheader.rb
|
60
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+
- lib/bio-vcf/vcfheader_line.rb
|
106
61
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- lib/bio-vcf/vcfline.rb
|
107
62
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- lib/bio-vcf/vcfrdf.rb
|
108
63
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- lib/bio-vcf/vcfrecord.rb
|
109
64
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- lib/bio-vcf/vcfsample.rb
|
110
65
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- lib/bio-vcf/vcfstatistics.rb
|
66
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+
- ragel/gen_vcfheaderline_parser.rl
|
67
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+
- ragel/generate.sh
|
111
68
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- template/gatk_vcf2rdf.erb
|
112
69
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- template/vcf2json.erb
|
70
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+
- template/vcf2json_full_header.erb
|
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+
- template/vcf2json_use_meta.erb
|
113
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- template/vcf2rdf.erb
|
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+
- template/vcf2rdf_header.erb
|
114
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- test/data/input/dbsnp.vcf
|
75
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+
- test/data/input/empty.vcf
|
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+
- test/data/input/gatk_exome.vcf
|
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+
- test/data/input/gatk_wgs.vcf
|
115
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- test/data/input/multisample.vcf
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116
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- test/data/input/somaticsniper.vcf
|
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+
- test/data/input/test.bed
|
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+
- test/data/regression/empty-stderr.new
|
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+
- test/data/regression/empty.new
|
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+
- test/data/regression/empty.ref
|
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+
- test/data/regression/eval_once-stderr.new
|
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+
- test/data/regression/eval_once.new
|
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+
- test/data/regression/eval_once.ref
|
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- test/data/regression/eval_r.info.dp-stderr.new
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- test/data/regression/eval_r.info.dp.new
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- test/data/regression/eval_r.info.dp.ref
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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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- test/data/regression/rewrite.info.sample-stderr.new
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- test/data/regression/rewrite.info.sample.new
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- test/data/regression/rewrite.info.sample.ref
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- test/data/regression/s.dp-stderr.new
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- test/data/regression/s.dp.new
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- test/data/regression/s.dp.ref
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- test/data/regression/seval_s.dp-stderr.new
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- test/data/regression/seval_s.dp.new
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- test/data/regression/seval_s.dp.ref
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- test/data/regression/sfilter_seval_s.dp-stderr.new
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- test/data/regression/sfilter_seval_s.dp.new
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- test/data/regression/sfilter_seval_s.dp.ref
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- test/data/regression/thread4-stderr.new
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- test/data/regression/thread4.new
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- test/data/regression/thread4.ref
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- test/data/regression/thread4_4-stderr.new
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- test/data/regression/thread4_4.new
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- test/data/regression/thread4_4.ref
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- test/data/regression/thread4_4_failed_filter-stderr.new
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- test/data/regression/thread4_4_failed_filter-stderr.ref
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+
- test/data/regression/thread4_4_failed_filter.new
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+
- test/data/regression/vcf2json_full_header-stderr.new
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- test/data/regression/vcf2json_full_header.new
|
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- test/data/regression/vcf2json_full_header.ref
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- test/data/regression/vcf2json_use_meta-stderr.new
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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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-
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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/vcflib/bio-vcf
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licenses:
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- MIT
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metadata: {}
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@@ -137,7 +138,7 @@ required_ruby_version: !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:
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version: 2.0.0
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required_rubygems_version: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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@@ -145,8 +146,8 @@ 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.
|
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+
rubygems_version: 2.7.6.2
|
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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: []
|