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)
AlignmentChainModelVertex *	max_vertex (void)
vector< Alignment >	traceback (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< AlignmentChainModelVertex >	model
unordered_map< path_handle_t, map< int64_t, vector< vector< AlignmentChainModelVertex >::iterator > > >	positions
set< vector< AlignmentChainModelVertex >::iterator >	redundant_vertexes
vector< Alignment >	unaligned_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

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

• src/mapper.hpp
• src/mapper.cpp