#include <rare_variant_simplifier.hpp>

Inheritance diagram for vg::RareVariantSimplifier:

Public Member Functions
	RareVariantSimplifier (MutablePathDeletableHandleGraph &graph, VcfBuffer &variant_source)
void	simplify ()
	Simplify the graph.
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
double	min_frequency_to_keep = 0
	Keep variants at this total alt allele frequency or higher.
size_t	min_count_to_keep = 0
Public Attributes inherited from vg::Progressive
bool	show_progress = false

Protected Attributes
MutablePathDeletableHandleGraph &	graph
	Holds a reference to the graph we're simplifying.
VcfBuffer &	variant_source
	Holds a reference to the variant buffer we are getting avriants from.

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 removing rare variants' alt and ref paths and their exclusively-used nodes.

Constructor & Destructor Documentation

vg::RareVariantSimplifier::RareVariantSimplifier	(	MutablePathDeletableHandleGraph &	graph,
		VcfBuffer &	variant_source )

Make a simplifier that simplifies the given graph in place, using variants read using the given buffer.

void vg::RareVariantSimplifier::simplify ( )

Simplify the graph.

MutablePathDeletableHandleGraph& vg::RareVariantSimplifier::graph

protected

Holds a reference to the graph we're simplifying.

size_t vg::RareVariantSimplifier::min_count_to_keep = 0

Keep variants with this total alt allele count or higher. AND'd with the frequency condition.

double vg::RareVariantSimplifier::min_frequency_to_keep = 0

Keep variants at this total alt allele frequency or higher.

VcfBuffer& vg::RareVariantSimplifier::variant_source

protected

Holds a reference to the variant buffer we are getting avriants from.

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