code: def run(self, command, options, pipe=False, get_stdout=False, memscale=None):
          
          cl = self.cl_picard(command, options, memscale=memscale)
          if pipe:
              subprocess.Popen(cl)
          elif get_stdout:
              p = subprocess.Popen(cl, stdout=subprocess.PIPE)
              stdout = p.stdout.read()
              p.wait()
              p.stdout.close()
              return stdout
          else:
              do.run(cl, "Picard {0}".format(command), None)
docs: Run a Picard command with the provided option pairs.