#include <cluster.hpp>
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| ComponentMinDistanceClusterer (SnarlDistanceIndex *distance_index) |
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| ~ComponentMinDistanceClusterer ()=default |
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| MinDistanceClusterer (SnarlDistanceIndex *distance_index) |
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virtual | ~MinDistanceClusterer ()=default |
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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.
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| MEMClusterer ()=default |
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virtual | ~MEMClusterer ()=default |
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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) |
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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.
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int32_t | estimate_edge_score (const MaximalExactMatch *mem_1, const MaximalExactMatch *mem_2, int64_t graph_dist, const GSSWAligner *aligner) const |
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void | deduplicate_cluster_pairs (vector< pair< pair< size_t, size_t >, int64_t > > &cluster_pairs, int64_t optimal_separation) |
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using | hit_t = pair< const MaximalExactMatch *, pos_t > |
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using | cluster_t = pair< vector< hit_t >, double > |
| Each cluster is a vector of hits and a paired multiplicity.
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using | match_fanouts_t = unordered_map< const MaximalExactMatch *, deque< pair< string::const_iterator, char > > > |
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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.
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◆ ComponentMinDistanceClusterer()
vg::ComponentMinDistanceClusterer::ComponentMinDistanceClusterer |
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SnarlDistanceIndex * |
distance_index | ) |
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◆ ~ComponentMinDistanceClusterer()
vg::ComponentMinDistanceClusterer::~ComponentMinDistanceClusterer |
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default |
◆ make_hit_graph()
◆ early_stop_number
const int64_t vg::ComponentMinDistanceClusterer::early_stop_number = 2 |
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protected |
The number of connections from one hit in a component to another that we will consider (0 for no maximum)
◆ min_read_separation
const int64_t vg::ComponentMinDistanceClusterer::min_read_separation = 0 |
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protected |
Minimum distance between two seeds on the read.
The documentation for this class was generated from the following files: