Class: HTS::VCF::Variant

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

Instance Method Summary collapse

Constructor Details

#initialize(bcf_t, vcf) ⇒ Variant

Returns a new instance of Variant.



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# File 'lib/hts/vcf/variant.rb', line 6

def initialize(bcf_t, vcf)
  @c = bcf_t
  FFI.bcf_unpack(@c, HTS::FFI::BCF_UN_ALL) # FIXME
  @vcf = vcf
end

Instance Method Details

#formats ⇒ Object

def inspect; end



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# File 'lib/hts/vcf/variant.rb', line 14

def formats; end

#genotypes ⇒ Object 



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# File 'lib/hts/vcf/variant.rb', line 16

def genotypes; end

#id ⇒ Object 



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# File 'lib/hts/vcf/variant.rb', line 30

def id
  @c[:d][:id]
end

#pos ⇒ Object 



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# File 'lib/hts/vcf/variant.rb', line 18

def pos
  @c[:pos] + 1 # FIXME
end

#qual ⇒ Object 



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# File 'lib/hts/vcf/variant.rb', line 34

def qual
  @c[:qual]
end

#ref ⇒ Object 



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# File 'lib/hts/vcf/variant.rb', line 38

def ref
  @c[:d][:allele].get_pointer(0).read_string
end

#start ⇒ Object 



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# File 'lib/hts/vcf/variant.rb', line 22

def start
  @c[:pos]
end

#stop ⇒ Object 



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# File 'lib/hts/vcf/variant.rb', line 26

def stop
  @c[:pos] + @c[:rlen]
end