Class: BioVcf::VcfGenotypeField

Inherits:
Object
  • Object
show all
Defined in:
lib/bio-vcf/vcfgenotypefield.rb

Instance Method Summary collapse

Constructor Details

#initialize(s, format, header, alt) ⇒ VcfGenotypeField

Returns a new instance of VcfGenotypeField.



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# File 'lib/bio-vcf/vcfgenotypefield.rb', line 89

def initialize s, format, header, alt
  @values = s.split(/:/)
  @format = format
  @header = header
  @alt = alt
end

Dynamic Method Handling

This class handles dynamic methods through the method_missing method

#method_missing(m, *args, &block) ⇒ Object 



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# File 'lib/bio-vcf/vcfgenotypefield.rb', line 120

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

Instance Method Details

#ad ⇒ Object 



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# File 'lib/bio-vcf/vcfgenotypefield.rb', line 100

def ad
  @values[@format['AD']].split(',').map{|i| i.to_i}
end

#amq ⇒ Object 



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# File 'lib/bio-vcf/vcfgenotypefield.rb', line 116

def amq
  VcfAltInfo.new(@alt,@values[@format['AMQ']].split(','))
end

#bcount ⇒ Object 



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# File 'lib/bio-vcf/vcfgenotypefield.rb', line 108

def bcount
  VcfNucleotides.new(@alt,@values[@format['BCOUNT']].split(','))
end

#bq ⇒ Object 



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# File 'lib/bio-vcf/vcfgenotypefield.rb', line 112

def bq
  VcfAltInfo.new(@alt,@values[@format['BQ']].split(','))
end

#dp4 ⇒ Object 



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# File 'lib/bio-vcf/vcfgenotypefield.rb', line 96

def dp4
  @values[@format['DP4']].split(',').map{|i| i.to_i}
end

#pl ⇒ Object 



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# File 'lib/bio-vcf/vcfgenotypefield.rb', line 104

def pl
  @values[@format['PL']].split(',').map{|i| i.to_i}
end