| add_nodes_in_range(const HandleGraph *super_graph, int64_t min_distance, int64_t max_distance, std::unordered_set< id_t > &sub_graph, vector< tuple< handle_t, int64_t >> &start_nodes, hash_set< pair< id_t, bool >> &seen_nodes) | vg::MinimumDistanceIndex | protected |
| calculate_max_index(const HandleGraph *graph, int64_t cap) | vg::MinimumDistanceIndex | protected |
| calculate_min_index(const HandleGraph *graph, const SnarlManager *snarl_manager, const Chain *chain, size_t parent_id, bool rev_in_parent, bool trivial_chain, size_t depth, size_t component_num) | vg::MinimumDistanceIndex | protected |
| chain_assignments | vg::MinimumDistanceIndex | protected |
| chain_indexes | vg::MinimumDistanceIndex | protected |
| chain_ranks | vg::MinimumDistanceIndex | protected |
| ChainIndex class | vg::MinimumDistanceIndex | friend |
| component_to_chain_index | vg::MinimumDistanceIndex | protected |
| component_to_chain_length | vg::MinimumDistanceIndex | protected |
| dist_to_common_ancestor(pair< size_t, bool > common_ancestor, pos_t &pos, bool rev) const | vg::MinimumDistanceIndex | protected |
| file_header | vg::MinimumDistanceIndex | protected |
| get_chain_assignment(id_t i) const | vg::MinimumDistanceIndex | inlineprotected |
| get_chain_rank(id_t i) const | vg::MinimumDistanceIndex | inlineprotected |
| get_connected_component(id_t node_id) | vg::MinimumDistanceIndex | |
| get_minimizer_distances(pos_t pos) | vg::MinimumDistanceIndex | |
| get_primary_assignment(id_t i) const | vg::MinimumDistanceIndex | inlineprotected |
| get_primary_rank(id_t i) const | vg::MinimumDistanceIndex | inlineprotected |
| get_secondary_assignment(id_t i) const | vg::MinimumDistanceIndex | inlineprotected |
| get_secondary_rank(id_t i) const | vg::MinimumDistanceIndex | inlineprotected |
| has_chain | vg::MinimumDistanceIndex | protected |
| has_chain_bv | vg::MinimumDistanceIndex | protected |
| has_secondary_snarl | vg::MinimumDistanceIndex | protected |
| has_secondary_snarl_bv | vg::MinimumDistanceIndex | protected |
| include_component | vg::MinimumDistanceIndex | protected |
| include_maximum | vg::MinimumDistanceIndex | protected |
| into_which_snarl(id_t node_id, bool reverse) const | vg::MinimumDistanceIndex | |
| load(istream &in) | vg::MinimumDistanceIndex | |
| max_distance(pos_t pos1, pos_t pos2) const | vg::MinimumDistanceIndex | |
| max_distances | vg::MinimumDistanceIndex | protected |
| max_node_id | vg::MinimumDistanceIndex | protected |
| min_distance(pos_t pos1, pos_t pos2) const | vg::MinimumDistanceIndex | |
| min_distances | vg::MinimumDistanceIndex | protected |
| min_node_id | vg::MinimumDistanceIndex | protected |
| min_pos(vector< int64_t > vals) | vg::MinimumDistanceIndex | static |
| min_pos(int64_t x, int64_t y) | vg::MinimumDistanceIndex | inlinestatic |
| MinimumDistanceIndex(const HandleGraph *graph, const SnarlManager *snarl_manager, int64_t cap=0) | vg::MinimumDistanceIndex | |
| MinimumDistanceIndex(istream &in) | vg::MinimumDistanceIndex | |
| MinimumDistanceIndex() | vg::MinimumDistanceIndex | |
| node_length(id_t id) const | vg::MinimumDistanceIndex | |
| node_to_component | vg::MinimumDistanceIndex | protected |
| populate_snarl_index(const HandleGraph *graph, const SnarlManager *snarl_manager, const NetGraph &ng, const Snarl *snarl, bool snarl_rev_in_chain, size_t snarl_assignment, hash_set< pair< id_t, bool >> &all_nodes, size_t depth, size_t component_num) | vg::MinimumDistanceIndex | protected |
| primary_snarl_assignments | vg::MinimumDistanceIndex | protected |
| primary_snarl_ranks | vg::MinimumDistanceIndex | protected |
| print_self() const | vg::MinimumDistanceIndex | |
| print_snarl_stats() | vg::MinimumDistanceIndex | |
| secondary_snarl_assignments | vg::MinimumDistanceIndex | protected |
| secondary_snarl_ranks | vg::MinimumDistanceIndex | protected |
| serialize(ostream &out) const | vg::MinimumDistanceIndex | |
| snarl_indexes | vg::MinimumDistanceIndex | protected |
| SnarlIndex class | vg::MinimumDistanceIndex | friend |
| SnarlSeedClusterer class | vg::MinimumDistanceIndex | friend |
| subgraph_in_range(const Path &path, const HandleGraph *super_graph, int64_t min_distance, int64_t max_distance, std::unordered_set< id_t > &sub_graph, bool look_forward) | vg::MinimumDistanceIndex | |
| top_level_chain_length(id_t node_id) | vg::MinimumDistanceIndex | |
| tree_depth | vg::MinimumDistanceIndex | protected |
| write_snarls_to_json() | vg::MinimumDistanceIndex | |
