vg
tools for working with variation graphs
Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
vg::GBWTTraversalFinder Class Reference

#include <traversal_finder.hpp>

Inheritance diagram for vg::GBWTTraversalFinder:
vg::TraversalFinder

Public Member Functions

 GBWTTraversalFinder (const HandleGraph &graph, const gbwt::GBWT &gbwt)
 
virtual ~GBWTTraversalFinder ()
 
virtual vector< SnarlTraversalfind_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 HandleGraphgraph
 
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

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