vg::ReadRestrictedTraversalFinder Class Reference

#include <traversal_finder.hpp>

Inheritance diagram for vg::ReadRestrictedTraversalFinder:

Public Member Functions
	ReadRestrictedTraversalFinder (AugmentedGraph &augmented_graph, SnarlManager &snarl_manager, int min_recurrence=2, int max_path_search_steps=100)
virtual	~ReadRestrictedTraversalFinder ()
virtual vector< SnarlTraversal >	find_traversals (const Snarl &site)
Public Member Functions inherited from vg::TraversalFinder
virtual	~TraversalFinder ()=default
virtual vector< Traversal >	find_traversals (const handle_t &snarl_start, const handle_t &snarl_end)

Private Attributes
AugmentedGraph &	aug
SnarlManager &	snarl_manager
int	min_recurrence
int	max_path_search_steps

Constructor & Destructor Documentation

ReadRestrictedTraversalFinder()

vg::ReadRestrictedTraversalFinder::ReadRestrictedTraversalFinder	(	AugmentedGraph &	augmented_graph,
		SnarlManager &	snarl_manager,
		int	min_recurrence = 2,
		int	max_path_search_steps = 100 )

~ReadRestrictedTraversalFinder()

vg::ReadRestrictedTraversalFinder::~ReadRestrictedTraversalFinder ( )

virtual

Member Function Documentation

find_traversals()

vector< SnarlTraversal > vg::ReadRestrictedTraversalFinder::find_traversals ( const Snarl & site )

virtual

For the given site, emit all traversals with unique sequences that run from start to end, out of the paths in the graph. Uses the map of reads by name to determine if a path is a read or a real named path. Paths through the site supported only by reads are subject to a min recurrence count, while those supported by actual embedded named paths are not.

Implements vg::TraversalFinder.

Member Data Documentation

aug

AugmentedGraph& vg::ReadRestrictedTraversalFinder::aug

private

max_path_search_steps

int vg::ReadRestrictedTraversalFinder::max_path_search_steps

private

min_recurrence

int vg::ReadRestrictedTraversalFinder::min_recurrence

private

snarl_manager

SnarlManager& vg::ReadRestrictedTraversalFinder::snarl_manager

private

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

• src/traversal_finder.hpp
• src/traversal_finder.cpp