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 |