Run a Picard command with the provided option pairs.

def run(self, command, options, pipe=False, get_stdout=False, memscale=None):
        """Run a Picard command with the provided option pairs.
        """
        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)