bio-vcf 0.0.1

data/Gemfile

@@ -0,0 +1,16 @@
+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "minitest", "~> 5.0.7" 
+  gem "rspec", "~> 2.8.0"
+  gem "cucumber", ">= 0"
+  gem "jeweler", "~> 1.8.4", :git => "https://github.com/technicalpickles/jeweler.git"
+  gem "bundler", ">= 1.0.21"
+  # gem "bio", ">= 1.4.2"
+  gem "rdoc", "~> 3.12"
+end

data/Gemfile.lock

@@ -0,0 +1,78 @@
+GIT
+  remote: https://github.com/technicalpickles/jeweler.git
+  revision: f7e0a55a207d83f56637dd8fbabf26a803410faf
+  specs:
+    jeweler (1.8.7)
+      builder
+      bundler (~> 1.0)
+      git (>= 1.2.5)
+      github_api (= 0.10.1)
+      highline (>= 1.6.15)
+      nokogiri (= 1.5.10)
+      rake
+      rdoc
+
+GEM
+  remote: http://rubygems.org/
+  specs:
+    addressable (2.3.5)
+    builder (3.2.2)
+    cucumber (1.3.2)
+      builder (>= 2.1.2)
+      diff-lcs (>= 1.1.3)
+      gherkin (~> 2.12.0)
+      multi_json (~> 1.3)
+    diff-lcs (1.1.3)
+    faraday (0.8.8)
+      multipart-post (~> 1.2.0)
+    gherkin (2.12.1)
+      multi_json (~> 1.3)
+    git (1.2.6)
+    github_api (0.10.1)
+      addressable
+      faraday (~> 0.8.1)
+      hashie (>= 1.2)
+      multi_json (~> 1.4)
+      nokogiri (~> 1.5.2)
+      oauth2
+    hashie (2.0.5)
+    highline (1.6.19)
+    httpauth (0.2.0)
+    json (1.8.0)
+    jwt (0.1.8)
+      multi_json (>= 1.5)
+    minitest (5.0.7)
+    multi_json (1.8.0)
+    multi_xml (0.5.5)
+    multipart-post (1.2.0)
+    nokogiri (1.5.10)
+    oauth2 (0.9.2)
+      faraday (~> 0.8)
+      httpauth (~> 0.2)
+      jwt (~> 0.1.4)
+      multi_json (~> 1.0)
+      multi_xml (~> 0.5)
+      rack (~> 1.2)
+    rack (1.5.2)
+    rake (10.1.0)
+    rdoc (3.12.2)
+      json (~> 1.4)
+    rspec (2.8.0)
+      rspec-core (~> 2.8.0)
+      rspec-expectations (~> 2.8.0)
+      rspec-mocks (~> 2.8.0)
+    rspec-core (2.8.0)
+    rspec-expectations (2.8.0)
+      diff-lcs (~> 1.1.2)
+    rspec-mocks (2.8.0)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler (>= 1.0.21)
+  cucumber
+  jeweler (~> 1.8.4)!
+  minitest (~> 5.0.7)
+  rdoc (~> 3.12)
+  rspec (~> 2.8.0)

data/LICENSE.txt

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+Copyright (c) 2013 Pjotr Prins
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# bio-vcf
+
+[![Build Status](https://secure.travis-ci.org/pjotrp/bioruby-vcf.png)](http://travis-ci.org/pjotrp/bioruby-vcf) 
+
+Yet another VCF parser. This one may give better performance and
+useful command line filtering.
+
+The VCF format is commonly used for variant calling between NGS
+samples. The fast parser needs to carry some state, recorded for each
+file in VcfHeader, which contains the VCF file header. Individual
+lines (variant calls) first go through a raw parser returning an array
+of fields. Further (lazy) parsing is handled through VcfRecord.
+
+Health warning: Early days, your mileage may vary because I add
+features as I go along! If something is not working, check out the
+code. It is easy to add features.
+
+## Installation
+
+```sh
+gem install bio-vcf
+```
+
+## Quick start
+
+## Command line interface (CLI)
+
+Get the version of the VCF file
+
+```ruby
+  bio-vcf -q --eval-once header.version < file.vcf
+  4.1
+```
+
+Get the column headers
+
+```ruby
+  bio-vcf -q -eval-once 'header.column_names.join(",")' < file.vcf
+  CHROM,POS,ID,REF,ALT,QUAL,FILTER,INFO,FORMAT,NORMAL,TUMOR
+```
+
+The 'fields' array contains unprocessed data (strings).  Print first
+five raw fields
+
+```ruby
+  bio-vcf --eval 'fields[0..4].join("\t")' < file.vcf 
+```
+
+Add a filter to display the fields on chromosome 12
+
+```ruby
+  bio-vcf --filter 'fields[0]=="12"' --eval 'fields[0..4].join("\t")' < file.vcf 
+```
+
+It gets better when we start using processed data, represented by an
+object named 'rec'. Position is a value, so we can filter a range
+
+```ruby
+  bio-vcf --filter 'rec.chrom=="12" and rec.pos>96_641_270 and rec.pos<96_641_276' < file.vcf 
+```
+
+With subfields defined by rec.format
+
+```ruby
+  bio-vcf --filter 'rec.tumor.ss != 2' < file.vcf 
+```
+
+Output
+
+```ruby
+  bio-vcf --filter 'rec.tumor.gq>30' --eval '[rec.ref,rec.alt,rec.tumor.bcount,rec.tumor.gq,rec.normal.gq].join("\t")' < file.vcf
+```
+
+Show the count of the bases that were scored as somatic
+
+```ruby
+  bio-vcf --eval 'rec.alt+"\t"+rec.tumor.bcount.split(",")[["A","C","G","T"].index(rec.alt)]+"\t"+rec.tumor.gq.to_s' < file.vcf
+```
+
+Actually, we have a convenience implementation for bcount, so this is the same
+
+```ruby
+  bio-vcf --eval 'rec.alt+"\t"+rec.tumor.bcount[rec.alt].to_s+"\t"+rec.tumor.gq.to_s' < file.vcf
+```
+
+Filter on the somatic results that were scored at least 4 times
+ 
+```ruby
+  bio-vcf --filter 'rec.alt.size==1 and rec.tumor.bcount[rec.alt]>4' < test.vcf 
+```
+
+Similar for base quality scores
+
+```ruby
+  bio-vcf --filter 'rec.alt.size==1 and rec.tumor.amq[rec.alt]>30' < test.vcf 
+```
+
+
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/pjotrp/bioruby-vcf
+
+## Cite
+
+If you use this software, please cite one of
+  
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+## Biogems.info
+
+This Biogem is published at (http://biogems.info/index.html#bio-vcf)
+
+## Copyright
+
+Copyright (c) 2014 Pjotr Prins. See LICENSE.txt for further details.
+

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-vcf"
+  gem.homepage = "http://github.com/pjotrp/bioruby-vcf"
+  gem.license = "MIT"
+  gem.summary = %Q{VCF parser}
+  gem.description = %Q{Smart parser for VCF format}
+  gem.email = "pjotr.public01@thebird.nl"
+  gem.authors = ["Pjotr Prins"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+# require 'rspec/core'
+# require 'rspec/core/rake_task'
+# RSpec::Core::RakeTask.new(:spec) do |spec|
+#   spec.pattern = FileList['spec/**/*_spec.rb']
+# end
+
+# RSpec::Core::RakeTask.new(:rcov) do |spec|
+#   spec.pattern = 'spec/**/*_spec.rb'
+#   spec.rcov = true
+# end
+
+require 'rake/testtask'
+
+Rake::TestTask.new do |t|
+  t.pattern = "spec/*_spec.rb"
+end
+
+require 'cucumber/rake/task'
+Cucumber::Rake::Task.new(:features)
+
+task :default => :spec
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-vcf #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.1

data/bin/bio-vcf

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+#!/usr/bin/env ruby
+#
+# BioRuby vcf plugin 
+# Author:: Pjotr Prins
+#
+# Copyright (C) 2014 Pjotr Prins <pjotr.prins@thebird.nl>
+
+USAGE = "Vcf parser"
+
+gempath = File.dirname(File.dirname(__FILE__))
+$: << File.join(gempath,'lib')
+
+VERSION_FILENAME=File.join(gempath,'VERSION')
+version = File.new(VERSION_FILENAME).read.chomp
+
+require 'bio-vcf'
+require 'optparse'
+
+# Uncomment when using the bio-logger 
+# require 'bio-logger'
+# log = Bio::Log::LoggerPlus.new 'vcf'
+# log.outputters = Bio::Log::Outputter.stderr 
+# Bio::Log::CLI.logger('stderr')
+# Bio::Log::CLI.trace('info')
+
+options = { show_help: false}
+opts = OptionParser.new do |o|
+  o.banner = "Usage: #{File.basename($0)} [options] filename\ne.g.  #{File.basename($0)} --rdf < test/data/input/somaticsniper.vcf"
+
+  o.on_tail('--filter cmd',String, 'Evaluate filter on each record') do |cmd|
+    options[:filter] = cmd
+  end
+  o.on_tail('-e cmd', '--eval cmd',String, 'Evaluate command on each record') do |cmd|
+    options[:eval] = cmd
+  end
+  o.on_tail('--eval-once cmd',String, 'Evaluate command once') do |cmd|
+    options[:eval_once] = true
+    options[:eval] = cmd
+  end
+  o.on("--rdf", "Generate RDF") do |b|
+    options[:rdf] = true
+  end
+ 
+  # Uncomment the following when using the bio-logger 
+  # o.separator ""
+  # o.on("--logger filename",String,"Log to file (default stderr)") do | name |
+  #   Bio::Log::CLI.logger(name)
+  # end
+  #
+  # o.on("--trace options",String,"Set log level (default INFO, see bio-logger)") do | s |
+  #   Bio::Log::CLI.trace(s)
+  # end
+  # 
+  o.on("-q", "--quiet", "Run quietly") do |q|
+    # Bio::Log::CLI.trace('error')
+    options[:quiet] = true
+  end
+  # 
+  # o.on("-v", "--verbose", "Run verbosely") do |v|
+  #   Bio::Log::CLI.trace('info')
+  # end
+  # 
+  # o.on("--debug", "Show debug messages") do |v|
+  #   Bio::Log::CLI.trace('debug')
+  # end
+
+  o.separator ""
+  o.on_tail('-h', '--help', 'display this help and exit') do
+    options[:show_help] = true
+  end
+end
+
+include BioVcf
+
+begin
+  opts.parse!(ARGV)
+
+  $stderr.print "vcf #{version} (biogem Ruby #{RUBY_VERSION}) by Pjotr Prins 2014\n" if !options[:quiet]
+
+
+  if options[:show_help] 
+    print opts 
+    print USAGE
+    exit 1
+  end
+
+  $stderr.print "Options: ",options,"\n" if !options[:quiet]
+
+  header = VcfHeader.new
+
+  STDIN.each_line do | line |
+    if line =~ /^##fileformat=/
+      # ---- We have a new file header
+      header = VcfHeader.new
+      header.add(line)
+      STDIN.each_line do | headerline |
+        if headerline !~ /^#/
+          line = headerline
+          break # end of header
+        end
+        header.add(headerline)
+      end
+    end
+    # ---- Parse VCF record line
+    # fields = VcfLine.parse(line,header.columns)
+    fields = VcfLine.parse(line)
+    rec = VcfRecord.new(fields,header)
+    if !options[:filter] or (options[:filter] and eval(options[:filter]))
+      if options[:eval] 
+        print eval(options[:eval]) 
+        exit(1) if options[:eval_once]
+      else
+        # Default behaviour
+        print fields.join("\t")
+      end
+      print "\n"
+    end
+  end
+
+end
+

data/features/support/env.rb

@@ -0,0 +1,13 @@
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+
+$LOAD_PATH.unshift(File.dirname(__FILE__) + '/../../lib')
+require 'bio-vcf'
+
+require 'rspec/expectations'

data/lib/bio-vcf.rb

@@ -0,0 +1,15 @@
+# Please require your code below, respecting the naming conventions in the
+# bioruby directory tree.
+#
+# For example, say you have a plugin named bio-plugin, the only uncommented
+# line in this file would be 
+#
+#   require 'bio/bio-plugin/plugin'
+#
+# In this file only require other files. Avoid other source code.
+
+require 'bio-vcf/vcf'
+require 'bio-vcf/vcfheader'
+require 'bio-vcf/vcfline'
+require 'bio-vcf/vcfgenotypefield'
+require 'bio-vcf/vcfrecord'

data/lib/bio-vcf/vcf.rb

@@ -0,0 +1,3 @@
+
+module BioVcf
+end

data/lib/bio-vcf/vcfgenotypefield.rb

@@ -0,0 +1,43 @@
+module BioVcf
+
+  class VcfNucleotides 
+    def initialize list
+      @list = list
+    end
+  
+    def [] idx
+      idx = ["A","C","G","T"].index(idx) if idx.kind_of?(String)
+      return 0 if idx == nil
+      @list[idx].to_i
+    end
+  end
+
+  class VcfGenotypeField
+    def initialize s, format, header
+      @values = s.split(/:/)
+      @format = format
+      @header = header
+    end
+
+    def bcount
+      VcfNucleotides.new(@values[@format['BCOUNT']].split(','))
+    end
+
+    def bq
+      VcfNucleotides.new(@values[@format['BQ']].split(','))
+    end
+
+    def amq
+      VcfNucleotides.new(@values[@format['AMQ']].split(','))
+    end
+
+
+    def method_missing(m, *args, &block)  
+      v = @values[@format[m.to_s.upcase]]
+      v = v.to_i if v =~ /^\d+$/
+      v = v.to_f if v =~ /^\d+\.\d+$/
+      v
+    end  
+
+  end
+end

data/lib/bio-vcf/vcfheader.rb

@@ -0,0 +1,42 @@
+
+module BioVcf
+
+  module VcfHeaderParser
+    def VcfHeaderParser.get_column_names(lines)
+      lines.each do | line |
+        if line =~ /^#[^#]/
+          names = line.split
+          names[0].sub!(/^#/,'')
+          return names
+        end
+      end
+      nil
+    end
+  end
+
+  class VcfHeader
+
+    attr_reader :lines
+
+    def initialize
+      @lines = []
+    end
+
+    def add line
+      @lines << line.strip
+    end
+
+    def version
+      @version ||= lines[0].scan(/##fileformat=VCFv(\d+\.\d+)/)[0][0]
+    end
+
+    def column_names
+      @column_names ||= VcfHeaderParser::get_column_names(@lines)
+    end
+
+    def columns
+      @column ||= column_names.size
+    end
+  end
+
+end

data/lib/bio-vcf/vcfline.rb

@@ -0,0 +1,11 @@
+module BioVcf
+  module VcfLine
+
+    # Split a line into fields and check size
+    def VcfLine.parse line,expected_size=nil
+      fields = line.strip.split(/\t/)
+      raise "Expected #{expected_size} fields but got #{fields.size} in "+fields.to_s if expected_size and fields.size != expected_size
+      fields
+    end
+  end
+end

data/lib/bio-vcf/vcfrecord.rb

@@ -0,0 +1,55 @@
+module BioVcf
+
+  module VcfRecordParser
+    def VcfRecordParser.get_format s
+      h = {}
+      s.split(/:/).each_with_index { |v,i| h[v] = i }
+      h
+    end
+  end
+
+  class VcfRecord
+
+    def initialize fields, header
+      @header = header
+      @fields = fields
+    end
+     
+    def chrom
+      @fields[0]
+    end
+
+    def pos
+      @pos ||= @fields[1].to_i
+    end
+
+    def ids 
+      @ids ||= @fields[2].split(';')
+    end
+
+    def id
+      ids[0]
+    end
+
+    def ref
+      @refs ||= @fields[3]
+    end
+
+    def alt
+      @alt ||= @fields[4]
+    end
+
+    def format
+      @format ||= VcfRecordParser.get_format(@fields[8])
+    end
+
+    def normal
+      @normal ||= VcfGenotypeField.new(@fields[9],format,@header)
+    end
+
+    def tumor
+      @tumor ||= VcfGenotypeField.new(@fields[10],format,@header)
+    end
+
+  end
+end

data/test/data/input/somaticsniper.vcf

@@ -0,0 +1,87 @@
+##fileformat=VCFv4.1
+##fileDate=20140121
+##phasing=none
+##reference=file:///data/GENOMES/human_GATK_GRCh37/GRCh37_gatk.fasta
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=IGT,Number=1,Type=String,Description="Genotype when called independently (only filled if called in joint prior mode)">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total read depth">
+##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description="Occurrence count for each base at this site (A,C,G,T)">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
+##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description="Joint genotype quality (only filled if called in join prior mode)">
+##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description="Variant allele quality">
+##FORMAT=<ID=BQ,Number=.,Type=Integer,Description="Average base quality">
+##FORMAT=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality across all reads">
+##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description="Average mapping quality for each allele present in the genotype">
+##FORMAT=<ID=SS,Number=1,Type=Integer,Description="Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown">
+##FORMAT=<ID=SSC,Number=1,Type=Integer,Description="Somatic Score">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR
+1	1636394	.	C	T	.	.	.	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:17:12,5,0,0:0,17,0,0:75:36:0:56:37:37:0:.	0/1:0/1:6:3,1,1,1:0,4,0,2:29:36:29:60,60:37:37,37:2:36
+1	36217006	.	C	T	.	.	.	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:21:9,12,0,0:0,21,0,0:90:31:0:60:37:37:0:.	0/1:0/1:6:2,2,0,2:0,4,0,2:24:31:24:60,53:37:37,37:2:31
+1	46527674	.	G	A	.	.	.	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:9:6,3,0,0:0,0,9,0:54:37:0:60:37:37:0:.	0/1:0/1:4:2,0,0,2:2,0,2,0:30:37:30:60,60:37:37,37:2:34
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metadata

@@ -0,0 +1,163 @@
+--- !ruby/object:Gem::Specification
+name: bio-vcf
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+  prerelease: 
+platform: ruby
+authors:
+- Pjotr Prins
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-01-23 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 5.0.7
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 5.0.7
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.8.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.8.0
+- !ruby/object:Gem::Dependency
+  name: cucumber
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.4
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.4
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+description: Smart parser for VCF format
+email: pjotr.public01@thebird.nl
+executables:
+- bio-vcf
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+files:
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.md
+- Rakefile
+- VERSION
+- bin/bio-vcf
+- features/step_definitions/bio-vcf_steps.rb
+- features/support/env.rb
+- lib/bio-vcf.rb
+- lib/bio-vcf/vcf.rb
+- lib/bio-vcf/vcfgenotypefield.rb
+- lib/bio-vcf/vcfheader.rb
+- lib/bio-vcf/vcfline.rb
+- lib/bio-vcf/vcfrecord.rb
+- test/data/input/somaticsniper.vcf
+homepage: http://github.com/pjotrp/bioruby-vcf
+licenses:
+- MIT
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: 751802321492035161
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.23
+signing_key: 
+specification_version: 3
+summary: VCF parser
+test_files: []