vg
tools for working with variation graphs
vg::MinimumDistanceIndex Member List

This is the complete list of members for vg::MinimumDistanceIndex, including all inherited members.

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::MinimumDistanceIndexprotected
calculate_max_index(const HandleGraph *graph, int64_t cap)vg::MinimumDistanceIndexprotected
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::MinimumDistanceIndexprotected
chain_assignmentsvg::MinimumDistanceIndexprotected
chain_indexesvg::MinimumDistanceIndexprotected
chain_ranksvg::MinimumDistanceIndexprotected
ChainIndex classvg::MinimumDistanceIndexfriend
component_to_chain_indexvg::MinimumDistanceIndexprotected
component_to_chain_lengthvg::MinimumDistanceIndexprotected
dist_to_common_ancestor(pair< size_t, bool > common_ancestor, pos_t &pos, bool rev) constvg::MinimumDistanceIndexprotected
file_headervg::MinimumDistanceIndexprotected
get_chain_assignment(id_t i) constvg::MinimumDistanceIndexinlineprotected
get_chain_rank(id_t i) constvg::MinimumDistanceIndexinlineprotected
get_connected_component(id_t node_id)vg::MinimumDistanceIndex
get_minimizer_distances(pos_t pos)vg::MinimumDistanceIndex
get_primary_assignment(id_t i) constvg::MinimumDistanceIndexinlineprotected
get_primary_rank(id_t i) constvg::MinimumDistanceIndexinlineprotected
get_secondary_assignment(id_t i) constvg::MinimumDistanceIndexinlineprotected
get_secondary_rank(id_t i) constvg::MinimumDistanceIndexinlineprotected
has_chainvg::MinimumDistanceIndexprotected
has_chain_bvvg::MinimumDistanceIndexprotected
has_secondary_snarlvg::MinimumDistanceIndexprotected
has_secondary_snarl_bvvg::MinimumDistanceIndexprotected
include_componentvg::MinimumDistanceIndexprotected
include_maximumvg::MinimumDistanceIndexprotected
into_which_snarl(id_t node_id, bool reverse) constvg::MinimumDistanceIndex
load(istream &in)vg::MinimumDistanceIndex
max_distance(pos_t pos1, pos_t pos2) constvg::MinimumDistanceIndex
max_distancesvg::MinimumDistanceIndexprotected
max_node_idvg::MinimumDistanceIndexprotected
min_distance(pos_t pos1, pos_t pos2) constvg::MinimumDistanceIndex
min_distancesvg::MinimumDistanceIndexprotected
min_node_idvg::MinimumDistanceIndexprotected
min_pos(vector< int64_t > vals)vg::MinimumDistanceIndexstatic
min_pos(int64_t x, int64_t y)vg::MinimumDistanceIndexinlinestatic
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) constvg::MinimumDistanceIndex
node_to_componentvg::MinimumDistanceIndexprotected
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::MinimumDistanceIndexprotected
primary_snarl_assignmentsvg::MinimumDistanceIndexprotected
primary_snarl_ranksvg::MinimumDistanceIndexprotected
print_self() constvg::MinimumDistanceIndex
print_snarl_stats()vg::MinimumDistanceIndex
secondary_snarl_assignmentsvg::MinimumDistanceIndexprotected
secondary_snarl_ranksvg::MinimumDistanceIndexprotected
serialize(ostream &out) constvg::MinimumDistanceIndex
snarl_indexesvg::MinimumDistanceIndexprotected
SnarlIndex classvg::MinimumDistanceIndexfriend
SnarlSeedClusterer classvg::MinimumDistanceIndexfriend
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_depthvg::MinimumDistanceIndexprotected
write_snarls_to_json()vg::MinimumDistanceIndex