cluster.hpp File Reference

#include <gcsa/gcsa.h>
#include <gcsa/lcp.h>
#include <structures/union_find.hpp>
#include "position.hpp"
#include "aligner.hpp"
#include "mem.hpp"
#include "handle.hpp"
#include "snarl_distance_index.hpp"
#include "snarl_seed_clusterer.hpp"
#include "path_component_index.hpp"
#include "bdsg/hash_graph.hpp"
#include <functional>
#include <string>
#include <vector>
#include <map>

Classes
class	vg::ShuffledPairs
class	vg::ShuffledPairs::iterator
class	vg::MEMChainModelVertex
class	vg::MEMChainModel
class	vg::MEMClusterer
class	vg::MEMClusterer::HitGraph
class	vg::MEMClusterer::HitNode
class	vg::MEMClusterer::HitEdge
struct	vg::MEMClusterer::DPScoreComparator
class	vg::NullClusterer
class	vg::OrientedDistanceMeasurer
class	vg::PathOrientedDistanceMeasurer
class	vg::SnarlOrientedDistanceMeasurer
class	vg::OrientedDistanceClusterer
class	vg::DistanceHeuristic
class	vg::SnarlMinDistance
class	vg::TipAnchoredMaxDistance
class	vg::TargetValueSearch
class	vg::TVSClusterer
class	vg::MinDistanceClusterer
class	vg::GreedyMinDistanceClusterer
class	vg::ComponentMinDistanceClusterer

Namespaces
	vg

Functions
vector< pair< gcsa::node_type, size_t > >	vg::mem_node_start_positions (const HandleGraph &graph, const vg::MaximalExactMatch &mem)
	get the handles that a mem covers More...
bdsg::HashGraph	vg::cluster_subgraph_containing (const HandleGraph &base, const Alignment &aln, const vector< vg::MaximalExactMatch > &cluster, const GSSWAligner *aligner)
	return a containing subgraph connecting the mems More...
bdsg::HashGraph	vg::cluster_subgraph_walk (const HandleGraph &base, const Alignment &aln, const vector< vg::MaximalExactMatch > &mems, double expansion)

Detailed Description

Chaining and clustering tools to work with maximal exact matches.