Class: SamMutationCLI

Inherits:
Thor
  • Object
show all
Defined in:
bin/sam-mutation

Instance Method Summary collapse

Instance Method Details

#tag(file_name) ⇒ Object 



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# File 'bin/sam-mutation', line 8

def tag (file_name)
  File.open(file_name).each do |line|
    next if line.match(/^@/)
    sam = Bio::DB::Alignment.new(line)
    if sam.mutations
      new_tag = Bio::DB::Tag.new("YH:m:"+sam.mutations.to_hgvs)
      puts sam.add_tag(new_tag)
    end
  end
end