#include <cluster.hpp>

Inheritance diagram for vg::MinDistanceClusterer:

Public Member Functions
	MinDistanceClusterer (SnarlDistanceIndex *distance_index)

virtual	~MinDistanceClusterer ()=default

vector< pair< pair< size_t, size_t >, int64_t > >	pair_clusters (const Alignment &alignment_1, const Alignment &alignment_2, const vector< cluster_t * > &left_clusters, const vector< cluster_t * > &right_clusters, const vector< pair< size_t, size_t >> &left_alt_cluster_anchors, const vector< pair< size_t, size_t >> &right_alt_cluster_anchors, int64_t optimal_separation, int64_t max_deviation)
	Concrete implementation of virtual method from MEMClusterer. More...

Public Member Functions inherited from vg::MEMClusterer
	MEMClusterer ()=default

virtual	~MEMClusterer ()=default

vector< cluster_t >	clusters (const Alignment &alignment, const vector< MaximalExactMatch > &mems, const GSSWAligner Aligner, size_t min_mem_length=1, int32_t max_qual_score=60, int32_t log_likelihood_approx_factor=0, size_t min_median_mem_coverage_for_split=0, double suboptimal_edge_pruning_factor=.75, double cluster_multiplicity_diff=10.0, const match_fanouts_t fanouts=nullptr)

Protected Member Functions
virtual HitGraph	make_hit_graph (const Alignment &alignment, const vector< MaximalExactMatch > &mems, const GSSWAligner aligner, size_t min_mem_length, const match_fanouts_t fanouts)
	Concrete implementation of virtual method from MEMClusterer. More...

Protected Member Functions inherited from vg::MEMClusterer
int32_t	estimate_edge_score (const MaximalExactMatch mem_1, const MaximalExactMatch mem_2, int64_t graph_dist, const GSSWAligner *aligner) const

void	deduplicate_cluster_pairs (vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, int64_t optimal_separation)

Additional Inherited Members
Public Types inherited from vg::MEMClusterer
using	hit_t = pair< const MaximalExactMatch *, pos_t >

using	cluster_t = pair< vector< hit_t >, double >
	Each cluster is a vector of hits and a paired multiplicity. More...

using	match_fanouts_t = unordered_map< const MaximalExactMatch *, deque< pair< string::const_iterator, char > >>

Public Attributes inherited from vg::MEMClusterer
int64_t	max_gap = numeric_limits<int64_t>::max()
	The largest discrepency we will allow between the read-implied distances and the estimated gap distance. More...

Constructor & Destructor Documentation

◆ MinDistanceClusterer()

vg::MinDistanceClusterer::MinDistanceClusterer ( SnarlDistanceIndex * distance_index )

virtual vg::MinDistanceClusterer::~MinDistanceClusterer ( )

virtualdefault

MEMClusterer::HitGraph vg::MinDistanceClusterer::make_hit_graph	(	const Alignment &	alignment,
		const vector< MaximalExactMatch > &	mems,
		const GSSWAligner *	aligner,
		size_t	min_mem_length,
		const match_fanouts_t *	fanouts
	)

protectedvirtual

Concrete implementation of virtual method from MEMClusterer.

vector< pair< pair< size_t, size_t >, int64_t > > vg::MinDistanceClusterer::pair_clusters	(	const Alignment &	alignment_1,
		const Alignment &	alignment_2,
		const vector< cluster_t * > &	left_clusters,
		const vector< cluster_t * > &	right_clusters,
		const vector< pair< size_t, size_t >> &	left_alt_cluster_anchors,
		const vector< pair< size_t, size_t >> &	right_alt_cluster_anchors,
		int64_t	optimal_separation,
		int64_t	max_deviation
	)

virtual

Concrete implementation of virtual method from MEMClusterer.

SnarlDistanceIndex* vg::MinDistanceClusterer::distance_index

protected

const HandleGraph* vg::MinDistanceClusterer::handle_graph

protected

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