vardetect-vc 0.0.2 → 0.0.3
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- data/lib/vardetect-vc.rb +60 -1
- data/lib/vardetect-vc/version.rb +1 -1
- data/vardetect-vc.gemspec +2 -1
- metadata +4 -4
data/lib/vardetect-vc.rb
CHANGED
@@ -1,7 +1,66 @@
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1
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require "vardetect-vc/version"
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2
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+
require "vardetect-vc/lib"
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require 'ffi'
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4
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require "bio/db/sam"
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5
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require "bio/db/sam/sam"
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6
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require "bio/db/pileup"
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require "bio/db/vcf"
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8
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9
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# tasks :
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10
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# 1. include indel mutation detection
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11
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# 2. include base call quality => completed
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12
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# 3. recalling
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13
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# 4. known snp
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14
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# 5. snv function
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# 6. interactive
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# 7. workflow
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module Vardetect
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module Vc
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-
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20
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def self.hi
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puts 'hello inside '
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end
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# command params options
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# variance call
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def self.exec args
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params = parse_params args.join(' ')
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puts params.inspect
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29
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cmd = params[:cmd]
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case cmd
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when 'snv'
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call_snv params
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when 'snv-range'
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call_snv_range params
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when 'prepare-st'
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call_prepare_st params
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when 'prepare-snp'
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48
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call_prepare_snp params
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when 'prepare-vc'
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call_prepare_vc params
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when 'combine-all'
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call_combine_all params
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when 'analyse-combine'
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call_analyse_combine params
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62
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end
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63
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64
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end
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65
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end
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66
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end
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data/lib/vardetect-vc/version.rb
CHANGED
data/vardetect-vc.gemspec
CHANGED
@@ -13,11 +13,12 @@ Gem::Specification.new do |gem|
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gem.homepage = ""
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gem.files = `git ls-files`.split($/)
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gem.executables = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
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+
gem.default_executable = 'bin/vardetect-vc'
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gem.test_files = gem.files.grep(%r{^(test|spec|features)/})
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gem.require_paths = ["lib"]
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-
gem.add_development_dependency "bio-samtools"
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gem.add_development_dependency "ffi"
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+
gem.add_development_dependency "bio-samtools"
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gem.add_runtime_dependency "ffi"
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gem.add_runtime_dependency "bio-samtools"
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end
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metadata
CHANGED
@@ -1,7 +1,7 @@
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--- !ruby/object:Gem::Specification
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name: vardetect-vc
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version: !ruby/object:Gem::Version
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-
version: 0.0.
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version: 0.0.3
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prerelease:
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platform: ruby
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authors:
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@@ -9,10 +9,10 @@ authors:
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autorequire:
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10
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bindir: bin
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cert_chain: []
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-
date: 2012-11-
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+
date: 2012-11-20 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name:
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name: ffi
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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@@ -28,7 +28,7 @@ dependencies:
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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:
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name: bio-samtools
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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