#include <feature_set.hpp>

Classes
struct	Feature

Public Member Functions
void	load_bed (istream &in)

void	save_bed (ostream &out) const

void	on_path_edit (const string &path, size_t start, size_t old_length, size_t new_length)

const vector< Feature > &	get_features (const string &path) const

Private Attributes
map< string, vector< Feature > >	features
	Stores all the loaded features by path name. More...

Detailed Description

Stores a bunch of features defined on paths, as would be found in a BED file, and listens for messages describing edits to the paths that the features are on. Edit operations are of the form "On path X, range Y to Z has been replaced with a segment of length W". Updates the positions and boundaries of features appropriately.

Originally designed to allow BED files to be carried through "vg simplify", but could be used for other annotation liftover tasks.

Member Function Documentation

◆ get_features()

const vector< FeatureSet::Feature > & vg::FeatureSet::get_features ( const string & path ) const

Get the features on a path. Generally used for testing.

◆ load_bed()

void vg::FeatureSet::load_bed ( istream & in )

Read features from the given BED stream. Adds them to the collection of loaded features.

◆ on_path_edit()

void vg::FeatureSet::on_path_edit	(	const string &	path,
		size_t	start,
		size_t	old_length,
		size_t	new_length
	)

Notify the FeatureSet that, at the given path, from the given start position, the given number of bases bave been replaced with the other given number of bases. Can handle pure inserts, pure deletions, length- preserving substitutions, and general length-changing substitutions.

Updates the contained features that need to change.

Note that this is currently O(n) in features on the path. TODO: come up with a truly efficient algorithm to back this using some kind of skip list or rope or something.

◆ save_bed()

void vg::FeatureSet::save_bed ( ostream & out ) const

Save features to the given BED stream.

Member Data Documentation

◆ features

map<string, vector<Feature> > vg::FeatureSet::features

private

Stores all the loaded features by path name.

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

src/feature_set.hpp
src/feature_set.cpp

Classes

Public Member Functions

Private Attributes