Class: VCF::Variant

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

Constant Summary collapse

CASTING = 
lambda do |string, type|
  case type
  when 'Integer'
    return string.to_i
  when 'Float'
    return string.to_f
  else
    return string.to_s
  end
end

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(str) ⇒ Variant

Returns a new instance of Variant.



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# File 'lib/exodb/vcf.rb', line 80

def initialize(str)
  @str = str
end

Instance Attribute Details

#alt ⇒ Object (readonly)

Returns the value of attribute alt.



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# File 'lib/exodb/vcf.rb', line 67

def alt
  @alt
end

#chrom ⇒ Object (readonly)

Returns the value of attribute chrom.



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# File 'lib/exodb/vcf.rb', line 67

def chrom
  @chrom
end

#filter ⇒ Object (readonly)

Returns the value of attribute filter.



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# File 'lib/exodb/vcf.rb', line 67

def filter
  @filter
end

#id ⇒ Object (readonly)

Returns the value of attribute id.



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# File 'lib/exodb/vcf.rb', line 67

def id
  @id
end

#info ⇒ Object (readonly)

Returns the value of attribute info.



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# File 'lib/exodb/vcf.rb', line 67

def info
  @info
end

#pos ⇒ Object (readonly)

Returns the value of attribute pos.



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# File 'lib/exodb/vcf.rb', line 67

def pos
  @pos
end

#qual ⇒ Object (readonly)

Returns the value of attribute qual.



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# File 'lib/exodb/vcf.rb', line 67

def qual
  @qual
end

#ref ⇒ Object (readonly)

Returns the value of attribute ref.



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# File 'lib/exodb/vcf.rb', line 67

def ref
  @ref
end

#sample_data ⇒ Object (readonly)

Returns the value of attribute sample_data.



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# File 'lib/exodb/vcf.rb', line 67

def sample_data
  @sample_data
end

#str ⇒ Object (readonly)

Returns the value of attribute str.



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# File 'lib/exodb/vcf.rb', line 67

def str
  @str
end

Instance Method Details

#parse!(info_attr, format_attr) ⇒ Object 



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# File 'lib/exodb/vcf.rb', line 84

def parse!(info_attr, format_attr)
  
  if @str
    splited = str.split(/\s+/)
    @chrom = splited[0]
    @pos = splited[1].to_i
    @id = splited[2]
    @ref = splited[3]
    @alt = splited[4]
    @qual = splited[5]
    @filter = splited[6]
    @info = {}
    parse_info(splited[7], info_attr)
    
    @formats = splited[8].split(/:/)
    @sample_data = []
    splited[9..-1].each {|data| @sample_data.push(parse_format(data, @formats, format_attr))}
    @str = nil
  end
  
end