vg
tools for working with variation graphs
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vg::TVSClusterer Class Reference

#include <cluster.hpp>

Inheritance diagram for vg::TVSClusterer:
vg::MEMClusterer

Public Member Functions

 TVSClusterer (const HandleGraph *handle_graph, SnarlDistanceIndex *distance_index)
 
 ~TVSClusterer ()=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.
 
- Public Member Functions inherited from vg::MEMClusterer
 MEMClusterer ()=default
 
virtual ~MEMClusterer ()=default
 
vector< cluster_tclusters (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

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.
 
- 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)
 

Protected Attributes

TargetValueSearch tvs
 

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.
 
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.
 

Constructor & Destructor Documentation

◆ TVSClusterer()

vg::TVSClusterer::TVSClusterer ( const HandleGraph * handle_graph,
SnarlDistanceIndex * distance_index )

◆ ~TVSClusterer()

vg::TVSClusterer::~TVSClusterer ( )
default

Member Function Documentation

◆ make_hit_graph()

MEMClusterer::HitGraph vg::TVSClusterer::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.

Implements vg::MEMClusterer.

◆ pair_clusters()

vector< pair< pair< size_t, size_t >, int64_t > > vg::TVSClusterer::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.

Implements vg::MEMClusterer.

Member Data Documentation

◆ tvs

TargetValueSearch vg::TVSClusterer::tvs
protected

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