| addNodesInRange(const HandleGraph *super_graph, int64_t min_distance, int64_t max_distance, SubHandleGraph &sub_graph, vector< tuple< handle_t, int64_t >> &start_nodes, hash_set< pair< id_t, bool >> &seen_nodes) | vg::MinimumDistanceIndex | protected |
| calculateMaxIndex(const HandleGraph *graph, int64_t cap) | vg::MinimumDistanceIndex | protected |
| calculateMinIndex(const HandleGraph *graph, const SnarlManager *snarl_manager, const Chain *chain, size_t parent_id, bool rev_in_parent, bool trivial_chain, size_t depth) | vg::MinimumDistanceIndex | protected |
| chain_assignments | vg::MinimumDistanceIndex | protected |
| chain_indexes | vg::MinimumDistanceIndex | protected |
| chain_ranks | vg::MinimumDistanceIndex | protected |
| ChainIndex class | vg::MinimumDistanceIndex | friend |
| distToCommonAncestor(pair< size_t, bool > common_ancestor, pos_t &pos, bool rev) const | vg::MinimumDistanceIndex | protected |
| file_header | vg::MinimumDistanceIndex | protected |
| getChainAssignment(id_t i) const | vg::MinimumDistanceIndex | inlineprotected |
| getChainRank(id_t i) const | vg::MinimumDistanceIndex | inlineprotected |
| getPrimaryAssignment(id_t i) const | vg::MinimumDistanceIndex | inlineprotected |
| getPrimaryRank(id_t i) const | vg::MinimumDistanceIndex | inlineprotected |
| getSecondaryAssignment(id_t i) const | vg::MinimumDistanceIndex | inlineprotected |
| getSecondaryRank(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_maximum | vg::MinimumDistanceIndex | protected |
| load(istream &in) | vg::MinimumDistanceIndex | |
| max_distances | vg::MinimumDistanceIndex | protected |
| max_node_id | vg::MinimumDistanceIndex | protected |
| maxDistance(pos_t pos1, pos_t pos2) const | vg::MinimumDistanceIndex | |
| min_distances | vg::MinimumDistanceIndex | protected |
| min_node_id | vg::MinimumDistanceIndex | protected |
| minDistance(pos_t pos1, pos_t pos2) const | vg::MinimumDistanceIndex | |
| MinimumDistanceIndex(const HandleGraph *graph, const SnarlManager *snarl_manager, int64_t cap=0) | vg::MinimumDistanceIndex | |
| MinimumDistanceIndex(istream &in) | vg::MinimumDistanceIndex | |
| MinimumDistanceIndex() | vg::MinimumDistanceIndex | |
| minPos(vector< int64_t > vals) | vg::MinimumDistanceIndex | static |
| minPos(int64_t x, int64_t y) | vg::MinimumDistanceIndex | inlinestatic |
| populateSnarlIndex(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) | vg::MinimumDistanceIndex | protected |
| primary_snarl_assignments | vg::MinimumDistanceIndex | protected |
| primary_snarl_ranks | vg::MinimumDistanceIndex | protected |
| printSelf() | vg::MinimumDistanceIndex | |
| printSnarlStats() | 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 |
| subgraphInRange(const Path &path, const HandleGraph *super_graph, int64_t min_distance, int64_t max_distance, SubHandleGraph &sub_graph, bool look_forward) | vg::MinimumDistanceIndex | |
| TestMinDistanceIndex class | vg::MinimumDistanceIndex | friend |
| tree_depth | vg::MinimumDistanceIndex | protected |
