Class: VCF

Inherits:
Object
  • Object
show all
Defined in:
lib/exodb/vcf.rb

Defined Under Namespace

Classes: Variant

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ VCF

Returns a new instance of VCF.



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# File 'lib/exodb/vcf.rb', line 7

def initialize()
  @info_attr = {}
  @filter_attr = {}
  @format_attr = {}
  @alt_attr = {}
  @meta = {}
  @contig = {}
  @variants = []

end

Instance Attribute Details

#alt_attr ⇒ Object (readonly)

Returns the value of attribute alt_attr.



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# File 'lib/exodb/vcf.rb', line 5

def alt_attr
  @alt_attr
end

#contig ⇒ Object (readonly)

Returns the value of attribute contig.



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# File 'lib/exodb/vcf.rb', line 5

def contig
  @contig
end

#filter_attr ⇒ Object (readonly)

Returns the value of attribute filter_attr.



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# File 'lib/exodb/vcf.rb', line 5

def filter_attr
  @filter_attr
end

#format_attr ⇒ Object (readonly)

Returns the value of attribute format_attr.



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# File 'lib/exodb/vcf.rb', line 5

def format_attr
  @format_attr
end

#info_attr ⇒ Object (readonly)

Returns the value of attribute info_attr.



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# File 'lib/exodb/vcf.rb', line 5

def info_attr
  @info_attr
end

#meta ⇒ Object (readonly)

Returns the value of attribute meta.



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# File 'lib/exodb/vcf.rb', line 5

def meta
  @meta
end

#samples ⇒ Object (readonly)

Returns the value of attribute samples.



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# File 'lib/exodb/vcf.rb', line 5

def samples
  @samples
end

#variants ⇒ Object (readonly)

Returns the value of attribute variants.



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# File 'lib/exodb/vcf.rb', line 5

def variants
  @variants
end

Instance Method Details

#fileformat ⇒ Object 



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# File 'lib/exodb/vcf.rb', line 44

def fileformat
  return @meta[:fileformat]
end

#open(filename) ⇒ Object 



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# File 'lib/exodb/vcf.rb', line 18

def open(filename)
  
  File.open(filename).each do |line|
    case line
    when /^##INFO/
      parse_info(line.chomp)
    when /^##FORMAT/
      parse_format(line.chomp)
    when /^##FILTER/
      parse_filter(line.chomp)
    when /^##contig/
      parse_contig(line.chomp)
    when /^##ALT/
      parse_alt(line.chomp)
    when /^##/
      parse_meta(line.chomp)
    when /^#/
      @samples = line.split(/\s+/)[9..-1]
    else
      @variants.push(Variant.new(line.chomp))
    end
    
  end
  
end

#parse(line = 4000) ⇒ Object 



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# File 'lib/exodb/vcf.rb', line 48

def parse(line = 4000)
  @variants.each_index do |ind|
    break if ind > line
    Thread.new (ind) {
      @variants[ind].parse!(@info_attr, @format_attr)
    }
  end
end

#sample_num ⇒ Object 



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# File 'lib/exodb/vcf.rb', line 57

def sample_num
  return @samples.length
end

#variant_num ⇒ Object 



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# File 'lib/exodb/vcf.rb', line 61

def variant_num
  return @variants.length
end