augref.hpp File Reference

#include <optional>
#include "handle.hpp"
#include "snarls.hpp"
#include "traversal_finder.hpp"

Classes
class	vg::AugRefCover
struct	vg::AugRefCover::RankedFragment

Namespaces
	vg

Detailed Description

Interface for computing and querying augmented reference path covers.

An augref cover is a set of path fragments (stored as separate paths) in the graph. They are always relative to an existing reference sample (ie GRCh38 or CHM13). Unlike rGFA paths which use complex metadata embedding, augref paths use a simple naming scheme: {base_path_name}_{N}_alt

For example, if the reference path is "CHM13#0#chr1", augref paths would be named:

• CHM13#0#chr1_1_alt
• CHM13#0#chr1_2_alt
• etc.

The data structures used in this class are always relative to the original paths in the graph. The REFERENCE-sense fragments that are used to serialize the cover can be created and loaded, but they are not used beyond that.