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vg
tools for working with variation graphs
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This is the complete list of members for vg::OrientedDistanceClusterer, including all inherited members.
| cluster_t typedef | vg::MEMClusterer | |
| 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) | vg::MEMClusterer | |
| compute_tail_mem_coverage(const Alignment &alignment, const vector< MaximalExactMatch > &mems) | vg::OrientedDistanceClusterer | protected |
| deduplicate_cluster_pairs(vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, int64_t optimal_separation) | vg::MEMClusterer | protected |
| distance_measurer | vg::OrientedDistanceClusterer | protected |
| estimate_edge_score(const MaximalExactMatch *mem_1, const MaximalExactMatch *mem_2, int64_t graph_dist, const GSSWAligner *aligner) const | vg::MEMClusterer | protected |
| exclude_dist_tree_merges(const function< pos_t(size_t)> &get_position, map< pair< size_t, size_t >, size_t > &num_infinite_dists, UnionFind &component_union_find, size_t &num_possible_merges_remaining, int64_t max_failed_distance_probes) | vg::OrientedDistanceClusterer | protected |
| extend_dist_tree_by_buckets(const function< pos_t(size_t)> &get_position, const function< int64_t(size_t)> &get_offset, size_t num_items, unordered_map< pair< size_t, size_t >, int64_t > &recorded_finite_dists, UnionFind &component_union_find, size_t &num_possible_merges_remaining) | vg::OrientedDistanceClusterer | protected |
| extend_dist_tree_by_permutations(const function< pos_t(size_t)> &get_position, const function< int64_t(size_t)> &get_offset, size_t num_items, int64_t max_failed_distance_probes, size_t decrement_frequency, unordered_map< pair< size_t, size_t >, int64_t > &recorded_finite_dists, map< pair< size_t, size_t >, size_t > &num_infinite_dists, UnionFind &component_union_find, size_t &num_possible_merges_remaining) | vg::OrientedDistanceClusterer | protected |
| flatten_distance_tree(size_t num_items, const unordered_map< pair< size_t, size_t >, int64_t > &recorded_finite_dists) | vg::OrientedDistanceClusterer | protected |
| get_on_strand_distance_tree(size_t num_items, const function< pos_t(size_t)> &get_position, const function< int64_t(size_t)> &get_offset) | vg::OrientedDistanceClusterer | protected |
| hit_t typedef | vg::MEMClusterer | |
| make_hit_graph(const Alignment &alignment, const vector< MaximalExactMatch > &mems, const GSSWAligner *aligner, size_t min_mem_length, const match_fanouts_t *fanouts) | vg::OrientedDistanceClusterer | protectedvirtual |
| match_fanouts_t typedef | vg::MEMClusterer | |
| max_expected_dist_approx_error | vg::OrientedDistanceClusterer | protected |
| max_gap | vg::MEMClusterer | |
| MEMClusterer()=default | vg::MEMClusterer | |
| OrientedDistanceClusterer(OrientedDistanceMeasurer &distance_measurer, size_t max_expected_dist_approx_error=8) | vg::OrientedDistanceClusterer | |
| 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) | vg::OrientedDistanceClusterer | virtual |
| unstranded | vg::OrientedDistanceClusterer | protected |
| ~MEMClusterer()=default | vg::MEMClusterer | virtual |
1.8.17