vg::PathRestrictedTraversalFinder Class Reference

#include <traversal_finder.hpp>

Inheritance diagram for vg::PathRestrictedTraversalFinder:

Public Member Functions
	PathRestrictedTraversalFinder (VG &graph, SnarlManager &snarl_manager, map< string, const Alignment * > &reads_by_name, int min_recurrence=2, int max_path_search_steps=100, bool allow_duplicates=false)
virtual	~PathRestrictedTraversalFinder ()
virtual vector< SnarlTraversal >	find_traversals (const Snarl &site)
virtual pair< vector< SnarlTraversal >, vector< string > >	find_named_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
VG &	graph
SnarlManager &	snarl_manager
map< string, const Alignment * > &	reads_by_name
int	min_recurrence
int	max_path_search_steps
bool	allow_duplicates

Detailed Description

Like ReadRestrictedTraversal finder, but works on paths in the graph. As with the former, it's been cut out of Genotyper and moved here.

I'm not sure what PathBasedTraversalFinder (see below) does, but it does not work as a drop-in replacement for this class, so keep the two implementations at least for now.

DEPRECATED: Use PathTraversalFinder instead

Constructor & Destructor Documentation

PathRestrictedTraversalFinder()

vg::PathRestrictedTraversalFinder::PathRestrictedTraversalFinder	(	VG &	graph,
		SnarlManager &	snarl_manager,
		map< string, const Alignment * > &	reads_by_name,
		int	min_recurrence = 2,
		int	max_path_search_steps = 100,
		bool	allow_duplicates = false
	)

~PathRestrictedTraversalFinder()

vg::PathRestrictedTraversalFinder::~PathRestrictedTraversalFinder ( )

virtual

Member Function Documentation

find_named_traversals()

pair< vector< SnarlTraversal >, vector< string > > vg::PathRestrictedTraversalFinder::find_named_traversals ( const Snarl &  site )

virtual

Like above, but return the path name corresponding to each traversal

find_traversals()

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

virtual

For the given site, emit all subpaths 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 snarl 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

allow_duplicates

bool vg::PathRestrictedTraversalFinder::allow_duplicates

private

graph

VG& vg::PathRestrictedTraversalFinder::graph

private

max_path_search_steps

int vg::PathRestrictedTraversalFinder::max_path_search_steps

private

min_recurrence

int vg::PathRestrictedTraversalFinder::min_recurrence

private

reads_by_name

map<string, const Alignment*>& vg::PathRestrictedTraversalFinder::reads_by_name

private

snarl_manager

SnarlManager& vg::PathRestrictedTraversalFinder::snarl_manager

private

---

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

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