#include <sampler.hpp>

Inheritance diagram for vg::AbstractReadSampler:

Public Member Functions
virtual	~AbstractReadSampler ()=default

	AbstractReadSampler (PathPositionHandleGraph &graph)
	Make a new sampler using the given graph. More...

Public Attributes
bool	multi_position_annotations = false

size_t	max_tries = 100
	What limit should we use for retry loops before giving up or failing? More...

std::unique_ptr< std::function< bool(const path_handle_t &)> >	annotation_path_filter

Protected Member Functions
void	annotate_with_path_positions (Alignment &aln)

Protected Attributes
PathPositionHandleGraph &	graph
	The graph being simulated against. More...

Detailed Description

Interface for shared functionality for things that sample reads.

Constructor & Destructor Documentation

◆ ~AbstractReadSampler()

virtual vg::AbstractReadSampler::~AbstractReadSampler ( )

virtualdefault

◆ AbstractReadSampler()

vg::AbstractReadSampler::AbstractReadSampler ( PathPositionHandleGraph & graph )

inline

Make a new sampler using the given graph.

Member Function Documentation

◆ annotate_with_path_positions()

void vg::AbstractReadSampler::annotate_with_path_positions ( Alignment & aln )

protected

Annotate the given alignment with the appropriate type of path positions.

Member Data Documentation

◆ annotation_path_filter

std::unique_ptr<std::function<bool(const path_handle_t&)> > vg::AbstractReadSampler::annotation_path_filter

Set to a filter function that returns true if a given path in the graph is allowed to be used as an annotation path.

◆ graph

PathPositionHandleGraph& vg::AbstractReadSampler::graph

protected

The graph being simulated against.

◆ max_tries

size_t vg::AbstractReadSampler::max_tries = 100

What limit should we use for retry loops before giving up or failing?

◆ multi_position_annotations

bool vg::AbstractReadSampler::multi_position_annotations = false

If true, annotate alignments with multiple positions along reference paths. If false, annotate them with minimum visited positions along reference paths.

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

src/sampler.hpp
src/sampler.cpp

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes