vg::MEMClusterer::HitGraph Class Reference

#include <cluster.hpp>

Public Member Functions
	HitGraph (const vector< MaximalExactMatch > &mems, const Alignment &alignment, const GSSWAligner *aligner, size_t min_mem_length=1, bool track_components=false, const match_fanouts_t *fanouts=nullptr)
	Initializes nodes in the hit graph, but does not add edges.
void	add_edge (size_t from, size_t to, int32_t weight, int64_t distance)
	Add an edge.
vector< cluster_t >	clusters (const Alignment &alignment, const GSSWAligner *aligner, int32_t max_qual_score, int32_t log_likelihood_approx_factor, size_t min_median_mem_coverage_for_split, double suboptimal_edge_pruning_factor, double cluster_multiplicity_diff)
	Returns the top scoring connected components.

Public Attributes
vector< HitNode >	nodes

Private Member Functions
void	connected_components (vector< vector< size_t > > &components_out) const
	Identify weakly connected components in the graph.
void	prune_low_scoring_edges (vector< vector< size_t > > &components, size_t component_idx, double score_factor)
void	perform_dp ()
	Perform dynamic programming and store scores in nodes.
void	identify_sources_and_sinks (vector< size_t > &sources_out, vector< size_t > &sinks_out) const
	Fills input vectors with indices of source and sink nodes.
void	topological_order (vector< size_t > &order_out) const
	Fills the input vector with the indices of a topological sort.
void	component_topological_order (const vector< size_t > &component, vector< size_t > &order_out) const
	Computes the topological order of.
size_t	median_mem_coverage (const vector< size_t > &component, const Alignment &aln) const

Private Attributes
bool	track_components
	Should we actively keep track of connected components?
UnionFind	components
	Keeps track of the connected components.

Constructor & Destructor Documentation

HitGraph()

vg::MEMClusterer::HitGraph::HitGraph	(	const vector< MaximalExactMatch > &	mems,
		const Alignment &	alignment,
		const GSSWAligner *	aligner,
		size_t	min_mem_length = 1,
		bool	track_components = false,
		const match_fanouts_t *	fanouts = nullptr )

Initializes nodes in the hit graph, but does not add edges.

Member Function Documentation

add_edge()

void vg::MEMClusterer::HitGraph::add_edge	(	size_t	from,
		size_t	to,
		int32_t	weight,
		int64_t	distance )

Add an edge.

clusters()

vector< MEMClusterer::cluster_t > vg::MEMClusterer::HitGraph::clusters	(	const Alignment &	alignment,
		const GSSWAligner *	aligner,
		int32_t	max_qual_score,
		int32_t	log_likelihood_approx_factor,
		size_t	min_median_mem_coverage_for_split,
		double	suboptimal_edge_pruning_factor,
		double	cluster_multiplicity_diff )

Returns the top scoring connected components.

component_topological_order()

void vg::MEMClusterer::HitGraph::component_topological_order ( const vector< size_t > & component, vector< size_t > & order_out ) const

private

Computes the topological order of.

connected_components()

void vg::MEMClusterer::HitGraph::connected_components ( vector< vector< size_t > > & components_out ) const

private

Identify weakly connected components in the graph.

identify_sources_and_sinks()

void vg::MEMClusterer::HitGraph::identify_sources_and_sinks ( vector< size_t > & sources_out, vector< size_t > & sinks_out ) const

private

Fills input vectors with indices of source and sink nodes.

median_mem_coverage()

size_t vg::MEMClusterer::HitGraph::median_mem_coverage ( const vector< size_t > & component, const Alignment & aln ) const

private

Returns the median coverage of bases in the reads by bases in the cluster, attempts to remove apparent redundant sub-MEMs

perform_dp()

void vg::MEMClusterer::HitGraph::perform_dp ( )

private

Perform dynamic programming and store scores in nodes.

prune_low_scoring_edges()

void vg::MEMClusterer::HitGraph::prune_low_scoring_edges ( vector< vector< size_t > > & components, size_t component_idx, double score_factor )

private

Prune edges that are not on any traceback that scores highly compared to the best score in the component, splits up the components (adding some to the end of the vector) if doing so splits a component

topological_order()

void vg::MEMClusterer::HitGraph::topological_order ( vector< size_t > & order_out ) const

private

Fills the input vector with the indices of a topological sort.

Member Data Documentation

components

UnionFind vg::MEMClusterer::HitGraph::components

private

Keeps track of the connected components.

nodes

vector<HitNode> vg::MEMClusterer::HitGraph::nodes

track_components

bool vg::MEMClusterer::HitGraph::track_components

private

Should we actively keep track of connected components?

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The documentation for this class was generated from the following files:

• src/cluster.hpp
• src/cluster.cpp