vg
tools for working with variation graphs
Loading...
Searching...
No Matches
vg::AlignmentChainModel Class Reference

#include <mapper.hpp>

Public Member Functions

 AlignmentChainModel (vector< vector< Alignment > > &bands, Mapper *mapper, const function< double(const Alignment &, const Alignment &, const unordered_map< path_handle_t, vector< pair< size_t, bool > > > &, const unordered_map< path_handle_t, vector< pair< size_t, bool > > > &, int64_t)> &transition_weight, int vertex_band_width=10, int position_depth=1, int max_connections=30)
 
void score (const unordered_set< AlignmentChainModelVertex * > &exclude)
 
AlignmentChainModelVertexmax_vertex (void)
 
vector< Alignmenttraceback (const Alignment &read, int alt_alns, bool paired, bool debug)
 
void display (ostream &out)
 
void display_dot (ostream &out, vector< AlignmentChainModelVertex * > vertex_trace)
 
void clear_scores (void)
 

Public Attributes

vector< AlignmentChainModelVertexmodel
 
unordered_map< path_handle_t, map< int64_t, vector< vector< AlignmentChainModelVertex >::iterator > > > positions
 
set< vector< AlignmentChainModelVertex >::iterator > redundant_vertexes
 
vector< Alignmentunaligned_bands
 

Constructor & Destructor Documentation

◆ AlignmentChainModel()

vg::AlignmentChainModel::AlignmentChainModel ( vector< vector< Alignment > > & bands,
Mapper * mapper,
const function< double(const Alignment &, const Alignment &, const unordered_map< path_handle_t, vector< pair< size_t, bool > > > &, const unordered_map< path_handle_t, vector< pair< size_t, bool > > > &, int64_t)> & transition_weight,
int vertex_band_width = 10,
int position_depth = 1,
int max_connections = 30 )

Member Function Documentation

◆ clear_scores()

void vg::AlignmentChainModel::clear_scores ( void )

◆ display()

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

◆ display_dot()

void vg::AlignmentChainModel::display_dot ( ostream & out,
vector< AlignmentChainModelVertex * > vertex_trace )

◆ max_vertex()

AlignmentChainModelVertex * vg::AlignmentChainModel::max_vertex ( void )

◆ score()

void vg::AlignmentChainModel::score ( const unordered_set< AlignmentChainModelVertex * > & exclude)

◆ traceback()

vector< Alignment > vg::AlignmentChainModel::traceback ( const Alignment & read,
int alt_alns,
bool paired,
bool debug )

Member Data Documentation

◆ model

vector<AlignmentChainModelVertex> vg::AlignmentChainModel::model

◆ positions

unordered_map<path_handle_t, map<int64_t, vector<vector<AlignmentChainModelVertex>::iterator> > > vg::AlignmentChainModel::positions

◆ redundant_vertexes

set<vector<AlignmentChainModelVertex>::iterator> vg::AlignmentChainModel::redundant_vertexes

◆ unaligned_bands

vector<Alignment> vg::AlignmentChainModel::unaligned_bands

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