vg::GBWTTraversalFinder Class Reference

#include <traversal_finder.hpp>

Inheritance diagram for vg::GBWTTraversalFinder:

Public Member Functions
	GBWTTraversalFinder (const HandleGraph &graph, const gbwt::GBWT &gbwt)
virtual	~GBWTTraversalFinder ()
virtual vector< SnarlTraversal >	find_traversals (const Snarl &site)
Public Member Functions inherited from vg::TraversalFinder
virtual	~TraversalFinder ()=default

Protected Member Functions
vector< vector< gbwt::node_type > >	get_spanning_haplotypes (handle_t start, handle_t end)

Protected Attributes
const HandleGraph &	graph
const gbwt::GBWT &	gbwt

Detailed Description

Rerturn all traversals of a snarl that correspond to haplotypes stored in a GBWT

Constructor & Destructor Documentation

GBWTTraversalFinder()

vg::GBWTTraversalFinder::GBWTTraversalFinder	(	const HandleGraph &	graph,
		const gbwt::GBWT &	gbwt
	)

~GBWTTraversalFinder()

vg::GBWTTraversalFinder::~GBWTTraversalFinder ( )

virtual

Member Function Documentation

find_traversals()

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

virtual

Implements vg::TraversalFinder.

get_spanning_haplotypes()

vector< vector< gbwt::node_type > > vg::GBWTTraversalFinder::get_spanning_haplotypes ( handle_t  start, handle_t  end  )

protected

Breadth first search from the start to the end, only branching if there's a haplotype in the GBWT, and returning all unique haplotypes found.

Member Data Documentation

gbwt

const gbwt::GBWT& vg::GBWTTraversalFinder::gbwt

protected

graph

const HandleGraph& vg::GBWTTraversalFinder::graph

protected

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

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