Public Member Functions
	ClusteringProblem (vector< vector< SeedCache > * > *all_seeds, size_t read_distance_limit, size_t fragment_distance_limit, size_t seed_count)

Public Attributes
vector< vector< SeedCache > * > *	all_seeds

vector< size_t >	seed_count_prefix_sum

size_t	read_distance_limit

size_t	fragment_distance_limit

vector< structures::UnionFind >	read_union_find

structures::UnionFind	fragment_union_find

hash_map< net_handle_t, size_t >	net_handle_to_node_problem_index

vector< SnarlTreeNodeProblem >	all_node_problems

vector< net_handle_t > *	current_chains

vector< net_handle_t > *	parent_chains

vector< net_handle_t >	parent_snarls

vector< pair< net_handle_t, net_handle_t > >	root_children

Constructor & Destructor Documentation

◆ ClusteringProblem()

vg::SnarlDistanceIndexClusterer::ClusteringProblem::ClusteringProblem	(	vector< vector< SeedCache > * > *	all_seeds,
		size_t	read_distance_limit,
		size_t	fragment_distance_limit,
		size_t	seed_count
	)

inline

Member Data Documentation

◆ all_node_problems

vector<SnarlTreeNodeProblem> vg::SnarlDistanceIndexClusterer::ClusteringProblem::all_node_problems

◆ all_seeds

vector<vector<SeedCache>*>* vg::SnarlDistanceIndexClusterer::ClusteringProblem::all_seeds

◆ current_chains

vector<net_handle_t>* vg::SnarlDistanceIndexClusterer::ClusteringProblem::current_chains

◆ fragment_distance_limit

size_t vg::SnarlDistanceIndexClusterer::ClusteringProblem::fragment_distance_limit

◆ fragment_union_find

structures::UnionFind vg::SnarlDistanceIndexClusterer::ClusteringProblem::fragment_union_find

◆ net_handle_to_node_problem_index

hash_map<net_handle_t, size_t> vg::SnarlDistanceIndexClusterer::ClusteringProblem::net_handle_to_node_problem_index

◆ parent_chains

vector<net_handle_t>* vg::SnarlDistanceIndexClusterer::ClusteringProblem::parent_chains

◆ parent_snarls

vector<net_handle_t> vg::SnarlDistanceIndexClusterer::ClusteringProblem::parent_snarls

◆ read_distance_limit

size_t vg::SnarlDistanceIndexClusterer::ClusteringProblem::read_distance_limit

◆ read_union_find

vector<structures::UnionFind> vg::SnarlDistanceIndexClusterer::ClusteringProblem::read_union_find

◆ root_children

vector<pair<net_handle_t, net_handle_t> > vg::SnarlDistanceIndexClusterer::ClusteringProblem::root_children

◆ seed_count_prefix_sum

vector<size_t> vg::SnarlDistanceIndexClusterer::ClusteringProblem::seed_count_prefix_sum

The documentation for this struct was generated from the following file:

src/snarl_seed_clusterer.hpp

Public Member Functions

Public Attributes