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"c Cst}t}|r3tjj}tjj} n|} |} |j|\t_} tjjdk r| rx(tjj D]} |j id| 6q}W|j|\t_} n| rd}|j |dj | n|r|tj_| tj_nt tj|| dtjkr1tjj}n t}ttj||||| ||}tjjrztjddfSt||||tjtj||fS(NsIPlease specify option (e.g. -1, -2, -s, etc)) for the following paths: %ss, RF(R;RRR#R~RuRRtRRZt set_defaultsRRRRFR<R"RR(RRRtsecondary_fillingRtRRRRtold_output_dirtold_stop_afterRRRRVtmsgRF((sr/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.4-Linux/share/spades/spades_pipeline/options_parser.pyt parse_args\s8      cCst}|jdS(N(Rt print_help(R%t show_hiddenRRR((sr/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.4-Linux/share/spades/spades_pipeline/options_parser.pyR5s cCstjjdkr$tjtj_ntjjdkr{tjritt tj tjtj_q{tj tj_ntjj dkrt tj_ ntjj dkrt tj_ ntjjdkrt tj_ntjjdkrt tj_ntjjdkr dtj_ntjjdkrAt tj_ntjjdkrbt tj_ntjjdkrdtj_ntjjdkrdtj_ntjjdkrtjjtjjtjtj_ntjjdkrt tj_ntjjdkrt tj_ntjjdkr@t tj_ntjjdkrat tj_ntjjdkrt tj_ndS(NtnoneR]Rl( RR#RRRRRJtget_available_memoryR`tminRRRRRRRRRRkRoRRRRR~tTMP_DIRRRRRR(((sr/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.4-Linux/share/spades/spades_pipeline/options_parser.pyRsH ''cCsCtjttjt_dtj_dtj_dtj_ dS(N( Rt NamespacetvarsRR#trestartRRRtR~(((sr/oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.15.4-Linux/share/spades/spades_pipeline/options_parser.pyRs  cCsdtjkrltjjrltjjt_tjjdkrKdtj_ntjjtj_dtj_nxGtjjD]9}tjj|dk rytjj|tjj| sZ      $   &       - N 6 p M @ x   K Z s* (