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)
virtual vector< Traversal >	find_traversals (const handle_t &snarl_start, const handle_t &snarl_end)
virtual pair< vector< SnarlTraversal >, vector< vector< gbwt::size_type > > >	find_gbwt_traversals (const Snarl &site, bool return_paths=true)
virtual pair< vector< Traversal >, vector< vector< gbwt::size_type > > >	find_gbwt_traversals (const handle_t &snarl_start, const handle_t &snarl_end, bool return_paths=true)
virtual pair< vector< SnarlTraversal >, vector< gbwt::size_type > >	find_path_traversals (const Snarl &site)
virtual pair< vector< Traversal >, vector< gbwt::size_type > >	find_path_traversals (const handle_t &snarl_start, const handle_t &snarl_end)
const gbwt::GBWT &	get_gbwt ()
Public Member Functions inherited from vg::TraversalFinder
virtual	~TraversalFinder ()=default

Protected Member Functions
vector< pair< vector< gbwt::node_type >, gbwt::SearchState > >	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_gbwt_traversals() [1/2]

pair< vector< Traversal >, vector< vector< gbwt::size_type > > > vg::GBWTTraversalFinder::find_gbwt_traversals ( const handle_t &  snarl_start, const handle_t &  snarl_end, bool  return_paths = true  )

virtual

find_gbwt_traversals() [2/2]

pair< vector< SnarlTraversal >, vector< vector< gbwt::size_type > > > vg::GBWTTraversalFinder::find_gbwt_traversals ( const Snarl &  site, bool  return_paths = true  )

virtual

Return the traversals, paired with their path identifiers in the gbwt. The traversals are unique, but there can be more than one path along each one (hence the vector)

find_path_traversals() [1/2]

pair< vector< Traversal >, vector< gbwt::size_type > > vg::GBWTTraversalFinder::find_path_traversals ( const handle_t &  snarl_start, const handle_t &  snarl_end  )

virtual

find_path_traversals() [2/2]

pair< vector< SnarlTraversal >, vector< gbwt::size_type > > vg::GBWTTraversalFinder::find_path_traversals ( const Snarl &  site )

virtual

Return traversals paired with path identifiers from the GBWT. The traversals are not unique (which is consistent with PathTraversalFinder) To get the sample name from the path identifier id, use gbwtgraph::get_path_sample_name();

find_traversals() [1/2]

vector< Traversal > vg::GBWTTraversalFinder::find_traversals ( const handle_t &  snarl_start, const handle_t &  snarl_end  )

virtual

Reimplemented from vg::TraversalFinder.

find_traversals() [2/2]

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

virtual

Implements vg::TraversalFinder.

get_gbwt()

const gbwt::GBWT& vg::GBWTTraversalFinder::get_gbwt ( )

inline

get_spanning_haplotypes()

vector<pair<vector<gbwt::node_type>, gbwt::SearchState> > 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