Method: Bio::PolyploidTools::SNP#covered_region

Defined in:

lib/bio/PolyploidTools/SNP.rb

#covered_region ⇒ Object

# File 'lib/bio/PolyploidTools/SNP.rb', line 174

def covered_region
  return @covered_region if @covered_region
  if self.use_reference
     reg = Bio::DB::Fasta::Region.new()
     reg.entry = gene
     reg.orientation = :forward
     reg.start = self.position - self.flanking_size
     reg.end = self.position + self.flanking_size
     reg.start = 1 if reg.start < 1
     return reg
  end
  
  min = @position
  max = @position
  # puts "Calculating covered region for #{self.inspect}"
  # puts "#{@exon_list.inspect}"
  # raise SNPException.new "Exons haven't been loaded for #{self.to_s}" if @exon_list.size == 0
  if @exon_list.size == 0
    min = self.position - self.flanking_size
    min = 1 if min < 1
    max =  self.position + self.flanking_size
  end
  @exon_list.each do | chromosome, exon_arr |
    exon_arr.each do | exon |
      reg = exon.query_region
      min = reg.start if reg.start < min
      max = reg.end if reg.end > max
    end
  end

  reg = Bio::DB::Fasta::Region.new()
  reg.entry = gene
  reg.orientation = :forward
  reg.start = min
  reg.end = max

  @covered_region = reg
  @covered_region
end