vg::CactusSnarlFinder Class Reference

#include <cactus_snarl_finder.hpp>

Inheritance diagram for vg::CactusSnarlFinder:

Public Member Functions
	CactusSnarlFinder (const PathHandleGraph &graph, const string &hint_path="")
virtual SnarlManager	find_snarls ()
virtual SnarlManager	find_snarls_parallel ()
Public Member Functions inherited from vg::SnarlFinder
virtual	~SnarlFinder ()=default

Protected Member Functions
const Snarl *	recursively_emit_snarls (const Visit &start, const Visit &end, const Visit &parent_start, const Visit &parent_end, stList *chains_list, stList *unary_snarls_list, SnarlManager &destination)
virtual SnarlManager	find_snarls_impl (bool known_single_component, bool finish_index)

Protected Attributes
const PathHandleGraph *	graph
	Holds the vg graph we are looking for sites in. More...
unordered_set< string >	hint_paths
	Holds the names of reference path hints. More...

Detailed Description

Class for finding all snarls using the base-level Cactus snarl decomposition interface.

Constructor & Destructor Documentation

CactusSnarlFinder()

vg::CactusSnarlFinder::CactusSnarlFinder	(	const PathHandleGraph &	graph,
		const string &	hint_path = ""
	)

Make a new CactusSnarlFinder to find snarls in the given graph. We can't filter trivial bubbles because that would break our chains.

Optionally takes a hint path name.

Member Function Documentation

find_snarls()

SnarlManager vg::CactusSnarlFinder::find_snarls ( )

virtual

Find all the snarls with Cactus, and put them into a SnarlManager.

Implements vg::SnarlFinder.

find_snarls_impl()

SnarlManager vg::CactusSnarlFinder::find_snarls_impl ( bool  known_single_component, bool  finish_index  )

protectedvirtual

Find all the snarls with Cactus, and put them into a SnarlManager. Skip breaking into connected components if "known_single_component" is true Skip making the snarl manager index if finish_index is false

find_snarls_parallel()

SnarlManager vg::CactusSnarlFinder::find_snarls_parallel ( )

virtual

Find all the snarls of weakly connected components in parallel. Even single-threaded, this may be worth using as it will use less memory by only considering each component in the context of itself.

Reimplemented from vg::SnarlFinder.

recursively_emit_snarls()

const Snarl * vg::CactusSnarlFinder::recursively_emit_snarls ( const Visit &  start, const Visit &  end, const Visit &  parent_start, const Visit &  parent_end, stList *  chains_list, stList *  unary_snarls_list, SnarlManager &  destination  )

protected

Create a snarl in the given SnarlManager with the given start and end, containing the given child snarls in the list of chains of children and the given list of unary children. Recursively creates snarls in the SnarlManager for the children. Returns a pointer to the finished snarl in the SnarlManager. Start and end may be empty visits, in which case no snarl is created, all the child chains are added as root chains, and null is returned. If parent_start and parent_end are empty Visits, no parent() is added to the produced snarl.

Member Data Documentation

graph

const PathHandleGraph* vg::CactusSnarlFinder::graph

protected

Holds the vg graph we are looking for sites in.

hint_paths

unordered_set<string> vg::CactusSnarlFinder::hint_paths

protected

Holds the names of reference path hints.

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

• src/cactus_snarl_finder.hpp
• src/cactus_snarl_finder.cpp