def _command_list(self):
        """ build the command list """
        cmd = [
            self.params.binary, 
            "-f", str(self.params.f), 
            "-T", str(self.params.T), 
            "-m", str(self.params.m),
            "-n", str(self.params.n),
            "-w", str(self.params.w),
            "-s", str(self.params.s),
            "-p", str(self.params.p),
        ]
        if 'N' in self.params:
            cmd += ["-N", str(self.params.N)]
        if "x" in self.params:
            cmd += ["-x", str(self.params.x)]

        # ultrafast boostrap and mapping with -f d
        # If no bootstraps then run -f D not -f a, and drop -x and -N 
        #        if "-f D":

        # add ougroups
        if 'o' in self.params:
            cmd += ["-o"]
            cmd += [",".join(self.params.o)]
        return cmd