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

#include <cluster.hpp>

Public Member Functions

 MEMChainModel (const vector< size_t > &aln_lengths, const vector< vector< MaximalExactMatch > > &matches, const function< int64_t(pos_t)> &approx_position, const function< unordered_map< path_handle_t, vector< pair< size_t, bool > > >(pos_t)> &path_position, const function< double(const MaximalExactMatch &, const MaximalExactMatch &)> &transition_weight, int band_width=10, int position_depth=1, int max_connections=20)
 
void score (const unordered_set< MEMChainModelVertex * > &exclude)
 
MEMChainModelVertexmax_vertex (void)
 
vector< vector< MaximalExactMatch > > traceback (int alt_alns, bool paired, bool debug)
 
void display (ostream &out)
 
void display_dot (ostream &out, vector< MEMChainModelVertex * > vertex_trace)
 
void clear_scores (void)
 

Public Attributes

vector< MEMChainModelVertexmodel
 
unordered_map< path_handle_t, map< int64_t, vector< vector< MEMChainModelVertex >::iterator > > > positions
 
set< vector< MEMChainModelVertex >::iterator > redundant_vertexes
 

Constructor & Destructor Documentation

◆ MEMChainModel()

vg::MEMChainModel::MEMChainModel ( const vector< size_t > & aln_lengths,
const vector< vector< MaximalExactMatch > > & matches,
const function< int64_t(pos_t)> & approx_position,
const function< unordered_map< path_handle_t, vector< pair< size_t, bool > > >(pos_t)> & path_position,
const function< double(const MaximalExactMatch &, const MaximalExactMatch &)> & transition_weight,
int band_width = 10,
int position_depth = 1,
int max_connections = 20 )

Member Function Documentation

◆ clear_scores()

void vg::MEMChainModel::clear_scores ( void )

◆ display()

void vg::MEMChainModel::display ( ostream & out)

◆ display_dot()

void vg::MEMChainModel::display_dot ( ostream & out,
vector< MEMChainModelVertex * > vertex_trace )

◆ max_vertex()

MEMChainModelVertex * vg::MEMChainModel::max_vertex ( void )

◆ score()

void vg::MEMChainModel::score ( const unordered_set< MEMChainModelVertex * > & exclude)

◆ traceback()

vector< vector< MaximalExactMatch > > vg::MEMChainModel::traceback ( int alt_alns,
bool paired,
bool debug )

Member Data Documentation

◆ model

vector<MEMChainModelVertex> vg::MEMChainModel::model

◆ positions

unordered_map<path_handle_t, map<int64_t, vector<vector<MEMChainModelVertex>::iterator> > > vg::MEMChainModel::positions

◆ redundant_vertexes

set<vector<MEMChainModelVertex>::iterator> vg::MEMChainModel::redundant_vertexes

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