vg::SmallSnarlSimplifier Class Reference

#include <small_snarl_simplifier.hpp>

Inheritance diagram for vg::SmallSnarlSimplifier:

Public Member Functions
	SmallSnarlSimplifier (VG &graph)
	Make a simplifier that simplifies the given graph in place.
pair< size_t, size_t >	simplify_once (size_t iteration=0)
void	simplify ()
Public Member Functions inherited from vg::Progressive
void	preload_progress (const string &message)
void	create_progress (const string &message, long count)
void	create_progress (long count)
void	ensure_progress (long count)
void	update_progress (long i)
void	increment_progress ()
void	destroy_progress (void)

Public Attributes
size_t	min_size = 10
size_t	max_iterations = 10
	How many iterations of simplification should we allow in a simplify() call?
bool	drop_hairpin_paths = false
FeatureSet *	features = nullptr
Public Attributes inherited from vg::Progressive
bool	show_progress = false

Protected Attributes
VG &	graph
	Holds a reference to the graph we're simplifying.
SnarlManager	site_manager
	This keeps track of the sites to simplify.
TrivialTraversalFinder	traversal_finder
	This is used to find traversals of those sites.

Additional Inherited Members
Static Public Member Functions inherited from vg::Progressive
static void	with_progress (bool show_progress, const std::string &task, const std::function< void(const std::function< void(size_t, size_t)> &progress)> &callback)

Detailed Description

A class that can be used to simplify a graph, by repeatedly popping leaf bubbles under a certain size. Keeps graph paths and an optional set of BED- like features up to date. TODO: doesn't handle path start and end positions within nodes.

Constructor & Destructor Documentation

SmallSnarlSimplifier()

vg::SmallSnarlSimplifier::SmallSnarlSimplifier

(

VG &

graph

)

Make a simplifier that simplifies the given graph in place.

Member Function Documentation

simplify()

void vg::SmallSnarlSimplifier::simplify

(

)

Simplify the graph until material stops being deleted or the maximum iteration count is reached.

simplify_once()

pair< size_t, size_t > vg::SmallSnarlSimplifier::simplify_once

(

size_t

iteration = 0

)

Simplify the graph by one step. Returns the number of nodes deleted and the number of edges deleted. Can be passed an iteration for its progress messages.

Member Data Documentation

drop_hairpin_paths

bool vg::SmallSnarlSimplifier::drop_hairpin_paths = false

Should we simplify bubbles where paths come in and leave through the enterance node (and delete those paths) (true)? Or should we leave those bubbles unsimplified?

features

FeatureSet* vg::SmallSnarlSimplifier::features = nullptr

If the user points this to a FeatureSet, that FeatureSet will get its features updated with changes to the graph as simplification proceeds. The user should load the features in and pull them out. TODO: Replace this with an on_path_edit event on this object that can be listened on.

graph

VG& vg::SmallSnarlSimplifier::graph

protected

Holds a reference to the graph we're simplifying.

max_iterations

size_t vg::SmallSnarlSimplifier::max_iterations = 10

How many iterations of simplification should we allow in a simplify() call?

min_size

size_t vg::SmallSnarlSimplifier::min_size = 10

What's the miniumum size of a bubble to keep, in involved bases? Everything smaller will get squished away.

site_manager

SnarlManager vg::SmallSnarlSimplifier::site_manager

protected

This keeps track of the sites to simplify.

traversal_finder

TrivialTraversalFinder vg::SmallSnarlSimplifier::traversal_finder

protected

This is used to find traversals of those sites.

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

• src/small_snarl_simplifier.hpp
• src/small_snarl_simplifier.cpp