module BioVcf::VcfRecordCall

Public Instance Methods

call_diff() click to toggle source
# File lib/bio-vcf/vcfrecord.rb, line 89
def call_diff
  Variant.diff(normal.bcount.to_ary,tumor.bcount.to_ary)
end
call_normal_count() click to toggle source
# File lib/bio-vcf/vcfrecord.rb, line 114
def call_normal_count
  normal.bcount.to_ary[index()]
end
call_nuc() click to toggle source
# File lib/bio-vcf/vcfrecord.rb, line 93
def call_nuc
  ['A','C','G','T'][index()]
end
call_tumor_count() click to toggle source
# File lib/bio-vcf/vcfrecord.rb, line 106
def call_tumor_count
  tumor.bcount.to_ary[index()]
end
call_tumor_relative_count() click to toggle source
# File lib/bio-vcf/vcfrecord.rb, line 110
def call_tumor_relative_count
  Variant.relative_diff(normal.bcount.to_ary,tumor.bcount.to_ary)[index()]
end
get_gt(index) click to toggle source

Get the GT when 0 is REF and >0 is ALT

# File lib/bio-vcf/vcfrecord.rb, line 98
def get_gt(index)
  if index == 0
    ref()
  else
    alt[index-1]
  end
end
index() click to toggle source
# File lib/bio-vcf/vcfrecord.rb, line 118
def index
  Variant.index(self.normal.bcount.to_ary,self.tumor.bcount.to_ary)
end