Index C | F | G | I | K | L | M | O | R | S | W C circuit_from_the_starter_forward() (in module khloraascaf.ilp.pulp_circuit) combine_repeat_scaffolding() (in module khloraascaf.scaffolding_methods) combine_scaffolding_problems() (in module khloraascaf.scaffolding_methods) combine_singlecopy_scaffolding() (in module khloraascaf.scaffolding_methods) CONTIGS_OF_REGIONS_EXT (in module khloraascaf.outputs) CONTIGS_OF_REGIONS_PREFIX (in module khloraascaf.outputs) F flow_definition() (in module khloraascaf.ilp.pulp_circuit) fmt_contigs_of_regions_filename() (in module khloraascaf.outputs) fmt_map_of_regions_filename() (in module khloraascaf.outputs) fmt_solver_log_name() (in module khloraascaf.ilp.pulp_to_solver) G generate_output_directory() (in module khloraascaf.outputs) I intermediate_in_circuit() (in module khloraascaf.ilp.pulp_circuit) K khloraascaf.ilp.pulp_circuit module khloraascaf.ilp.pulp_to_solver module khloraascaf.outputs module khloraascaf.scaffolding_methods module L LOG_EXT (in module khloraascaf.ilp.pulp_to_solver) M MAP_OF_REGIONS_EXT (in module khloraascaf.outputs) MAP_OF_REGIONS_PREFIX (in module khloraascaf.outputs) module khloraascaf.ilp.pulp_circuit khloraascaf.ilp.pulp_to_solver khloraascaf.outputs khloraascaf.scaffolding_methods O ORC_ID_IND (in module khloraascaf.outputs) ORC_OR_IND (in module khloraascaf.outputs) OrCT (in module khloraascaf.outputs) ORIENT_INT_STR (in module khloraascaf.outputs) R read_contigs_of_regions() (in module khloraascaf.outputs) read_map_of_regions() (in module khloraascaf.outputs) S scaffolding() (in module khloraascaf.scaffolding_methods) scaffolding_region() (in module khloraascaf.scaffolding_methods) solve_pulp_problem() (in module khloraascaf.ilp.pulp_to_solver) SOLVER_LOG_PREFIX (in module khloraascaf.ilp.pulp_to_solver) W write_contigs_of_regions() (in module khloraascaf.outputs) write_map_of_regions() (in module khloraascaf.outputs)