| chain_distance(pair< size_t, bool > start, pair< size_t, bool > end, int64_t startLen, int64_t endLen, bool check_loop=false) const | vg::MinimumDistanceIndex::ChainIndex | |
| chain_length() const | vg::MinimumDistanceIndex::ChainIndex | inline |
| chain_to_json() | vg::MinimumDistanceIndex::ChainIndex | |
| ChainIndex(id_t parent_id, id_t id_in_parent, id_t end_id, bool rev_in_parent, bool loops, size_t length) | vg::MinimumDistanceIndex::ChainIndex | |
| ChainIndex() | vg::MinimumDistanceIndex::ChainIndex | |
| end_id | vg::MinimumDistanceIndex::ChainIndex | protected |
| id_in_parent | vg::MinimumDistanceIndex::ChainIndex | protected |
| is_looping_chain | vg::MinimumDistanceIndex::ChainIndex | protected |
| load(istream &in) | vg::MinimumDistanceIndex::ChainIndex | |
| loop_distance(pair< size_t, bool > start, pair< size_t, bool > end, int64_t startLen, int64_t endLen) const | vg::MinimumDistanceIndex::ChainIndex | protected |
| loop_fd | vg::MinimumDistanceIndex::ChainIndex | protected |
| loop_rev | vg::MinimumDistanceIndex::ChainIndex | protected |
| max_width | vg::MinimumDistanceIndex::ChainIndex | protected |
| MinimumDistanceIndex class | vg::MinimumDistanceIndex::ChainIndex | friend |
| parent_id | vg::MinimumDistanceIndex::ChainIndex | protected |
| prefix_sum | vg::MinimumDistanceIndex::ChainIndex | protected |
| print_self() const | vg::MinimumDistanceIndex::ChainIndex | |
| rev_in_parent | vg::MinimumDistanceIndex::ChainIndex | protected |
| serialize(ostream &out) const | vg::MinimumDistanceIndex::ChainIndex | |
| SnarlSeedClusterer class | vg::MinimumDistanceIndex::ChainIndex | friend |
