vg::GreedyMinDistanceClusterer Class Reference

#include <cluster.hpp>

Inheritance diagram for vg::GreedyMinDistanceClusterer:

Public Member Functions
	GreedyMinDistanceClusterer (SnarlDistanceIndex *distance_index)
	~GreedyMinDistanceClusterer ()=default
Public Member Functions inherited from vg::MinDistanceClusterer
	MinDistanceClusterer (SnarlDistanceIndex *distance_index)
virtual	~MinDistanceClusterer ()=default
vector< pair< pair< size_t, size_t >, int64_t > >	pair_clusters (const Alignment &alignment_1, const Alignment &alignment_2, const vector< cluster_t * > &left_clusters, const vector< cluster_t * > &right_clusters, const vector< pair< size_t, size_t >> &left_alt_cluster_anchors, const vector< pair< size_t, size_t >> &right_alt_cluster_anchors, int64_t optimal_separation, int64_t max_deviation)
	Concrete implementation of virtual method from MEMClusterer. More...
Public Member Functions inherited from vg::MEMClusterer
	MEMClusterer ()=default
virtual	~MEMClusterer ()=default
vector< cluster_t >	clusters (const Alignment &alignment, const vector< MaximalExactMatch > &mems, const GSSWAligner *Aligner, size_t min_mem_length=1, int32_t max_qual_score=60, int32_t log_likelihood_approx_factor=0, size_t min_median_mem_coverage_for_split=0, double suboptimal_edge_pruning_factor=.75, double cluster_multiplicity_diff=10.0, const match_fanouts_t *fanouts=nullptr)

Protected Member Functions
HitGraph	make_hit_graph (const Alignment &alignment, const vector< MaximalExactMatch > &mems, const GSSWAligner *aligner, size_t min_mem_length, const match_fanouts_t *fanouts)
	Concrete implementation of virtual method from MEMClusterer, overides the inherited one from MinDistanceClusterer. More...
Protected Member Functions inherited from vg::MEMClusterer
int32_t	estimate_edge_score (const MaximalExactMatch *mem_1, const MaximalExactMatch *mem_2, int64_t graph_dist, const GSSWAligner *aligner) const
void	deduplicate_cluster_pairs (vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, int64_t optimal_separation)

Protected Attributes
const int64_t	expected_separation = 20
	How far apart do we expect the seeds to be on the read? More...
const int64_t	forward_multiplier = 3
const int64_t	min_separation = -10
	Minimum distance between two seeds on the read. More...
const int64_t	max_separation = 250
	Maximum distance between two seeds on the read. More...
Protected Attributes inherited from vg::MinDistanceClusterer
const HandleGraph *	handle_graph
SnarlDistanceIndex *	distance_index

Additional Inherited Members
Public Types inherited from vg::MEMClusterer
using	hit_t = pair< const MaximalExactMatch *, pos_t >
using	cluster_t = pair< vector< hit_t >, double >
	Each cluster is a vector of hits and a paired multiplicity. More...
using	match_fanouts_t = unordered_map< const MaximalExactMatch *, deque< pair< string::const_iterator, char > >>
Public Attributes inherited from vg::MEMClusterer
int64_t	max_gap = numeric_limits<int64_t>::max()
	The largest discrepency we will allow between the read-implied distances and the estimated gap distance. More...

Constructor & Destructor Documentation

GreedyMinDistanceClusterer()

vg::GreedyMinDistanceClusterer::GreedyMinDistanceClusterer

(

SnarlDistanceIndex *

distance_index

)

~GreedyMinDistanceClusterer()

vg::GreedyMinDistanceClusterer::~GreedyMinDistanceClusterer ( )

default

Member Function Documentation

make_hit_graph()

MEMClusterer::HitGraph vg::GreedyMinDistanceClusterer::make_hit_graph ( const Alignment &  alignment, const vector< MaximalExactMatch > &  mems, const GSSWAligner *  aligner, size_t  min_mem_length, const match_fanouts_t *  fanouts  )

protectedvirtual

Concrete implementation of virtual method from MEMClusterer, overides the inherited one from MinDistanceClusterer.

Reimplemented from vg::MinDistanceClusterer.

Member Data Documentation

expected_separation

const int64_t vg::GreedyMinDistanceClusterer::expected_separation = 20

protected

How far apart do we expect the seeds to be on the read?

forward_multiplier

const int64_t vg::GreedyMinDistanceClusterer::forward_multiplier = 3

protected

How more bases would we search forward to find the next seed before we think it's worth searching 1 base backward?

max_separation

const int64_t vg::GreedyMinDistanceClusterer::max_separation = 250

protected

Maximum distance between two seeds on the read.

min_separation

const int64_t vg::GreedyMinDistanceClusterer::min_separation = -10

protected

Minimum distance between two seeds on the read.

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

• src/cluster.hpp
• src/cluster.cpp