gistfile1.txt

    def run_thread
      input   = @options[:input]  || []
      output  = @options[:output]
      threads = []

      @commands[1 .. -1].reverse.each do |command|
        io_read, io_write = BioPieces::Stream.pipe

        threads << Thread.new(command, io_read, output) do |cmd, iin, iout|
          cmd.run(iin, iout)
        end

        output = io_write
      end

      @commands.first.run(input, output)

      threads.reverse.each { |t| t.join }
    end