vg
tools for working with variation graphs
Public Member Functions | Protected Member Functions | List of all members
vg::NullClusterer Class Reference

#include <cluster.hpp>

Inheritance diagram for vg::NullClusterer:
vg::MEMClusterer

Public Member Functions

 NullClusterer ()=default
 
virtual ~NullClusterer ()=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_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)
 
- 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

◆ NullClusterer()

vg::NullClusterer::NullClusterer ( )
default

◆ ~NullClusterer()

virtual vg::NullClusterer::~NullClusterer ( )
virtualdefault

Member Function Documentation

◆ make_hit_graph()

MEMClusterer::HitGraph vg::NullClusterer::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 Note: ignores the min_mem_length parameter

Implements vg::MEMClusterer.

◆ pair_clusters()

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


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