mem.hpp File Reference

#include <gcsa/gcsa.h>
#include <gcsa/lcp.h>
#include "position.hpp"
#include "utility.hpp"
#include <functional>
#include <string>
#include <vector>
#include <map>

Classes
class	vg::MaximalExactMatch

Namespaces
	vg

Functions
const string	vg::mems_to_json (const vector< MaximalExactMatch > &mems)
vector< string::const_iterator >	vg::cluster_cover (const vector< MaximalExactMatch > &cluster)
int	vg::cluster_coverage (const vector< MaximalExactMatch > &cluster)
bool	vg::mems_overlap (const MaximalExactMatch &mem1, const MaximalExactMatch &mem2)
int	vg::mems_overlap_length (const MaximalExactMatch &mem1, const MaximalExactMatch &mem2)
bool	vg::clusters_overlap_in_read (const vector< MaximalExactMatch > &cluster1, const vector< MaximalExactMatch > &cluster2)
bool	vg::clusters_overlap_in_graph (const vector< MaximalExactMatch > &cluster1, const vector< MaximalExactMatch > &cluster2)
int	vg::clusters_overlap_length (const vector< MaximalExactMatch > &cluster1, const vector< MaximalExactMatch > &cluster2)
vector< pos_t >	vg::cluster_nodes (const vector< MaximalExactMatch > &cluster)
vector< MaximalExactMatch >	vg::translate_mems (const vector< MaximalExactMatch > &mems, const unordered_map< id_t, pair< id_t, bool > > &trans)
pair< int64_t, int64_t >	vg::mem_min_oriented_distances (const MaximalExactMatch &m1, const MaximalExactMatch &m2)

Detailed Description

Maximal Exact Matches (MEMs) header