Class: HTS::Bcf::Format::GenotypeView

Inherits:
Object
  • Object
show all
Includes:
Enumerable
Defined in:
lib/hts/bcf/format.rb

Instance Method Summary collapse

Instance Method Details

#each_allele ⇒ Object Also known as: each 



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# File 'lib/hts/bcf/format.rb', line 61

def each_allele
  return to_enum(__method__) unless block_given?

  ensure_valid!
  @values.each_with_index do |encoded, index|
    break if encoded == GT_VECTOR_END

    missing = gt_missing?(encoded)
    # The phase bit describes the separator before this allele. It has
    # no semantic meaning for the first allele, and HTSlib versions do
    # not consistently clear it while parsing VCF text.
    phased = index.positive? && gt_phased?(encoded)
    yield(missing ? nil : gt_allele(encoded), phased, missing)
  end
  self
end

#reset(values, buffer, generation) ⇒ Object 



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# File 'lib/hts/bcf/format.rb', line 54

def reset(values, buffer, generation)
  @values = values
  @buffer = buffer
  @generation = generation
  self
end

#to_s ⇒ Object 



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# File 'lib/hts/bcf/format.rb', line 78

def to_s
  result = +""
  each_allele.with_index do |(allele, phased, missing), index|
    result << (phased && index.positive? ? "|" : "/") if index.positive?
    result << (missing ? "." : allele.to_s)
  end
  result
end