Method: Exodb::Utils.load_variant_from_merge

Defined in:
lib/exodb/rositza/load.rb

.load_variant_from_merge(mergefile, normal = false, assembly = Exodb::DEFAULTASSEMBLY) ⇒ Object 



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# File 'lib/exodb/rositza/load.rb', line 96

def load_variant_from_merge(mergefile, normal = false, assembly = Exodb::DEFAULTASSEMBLY)
	
	File.open(mergefile).each do |line|
		record = line.chomp.split("\t")
		
		header = record[0..15]
		
		list = record[16..-1]
		
		until list.empty?
			if normal
				snv = Exodb::Variant.where(oid: "#{header[2]}:#{header[3]}:#{assembly}:#{sampledata[0]}").first
				snv.pileupn = sampledata[6] if snv != nil
			else
				sampledata = list.shift(7)
				snv = Exodb::Variant.new()
				snv.location=("#{header[2]}:#{header[3]}:#{assembly}")
				snv.reference = header[10]
				snv.pileupt = sampledata[6]
				snv.temp = {} if snv.temp.blank?
				snv.add_to_sample(sampledata[0])
				p snv.save!
			end
		end
	end
	
end