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vg
tools for working with variation graphs
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This is the complete list of members for vg::GreedyMinDistanceClusterer, 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 | |
| deduplicate_cluster_pairs(vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, int64_t optimal_separation) | vg::MEMClusterer | protected |
| distance_index | vg::MinDistanceClusterer | protected |
| estimate_edge_score(const MaximalExactMatch *mem_1, const MaximalExactMatch *mem_2, int64_t graph_dist, const GSSWAligner *aligner) const | vg::MEMClusterer | protected |
| expected_separation | vg::GreedyMinDistanceClusterer | protected |
| forward_multiplier | vg::GreedyMinDistanceClusterer | protected |
| GreedyMinDistanceClusterer(SnarlDistanceIndex *distance_index) | vg::GreedyMinDistanceClusterer | |
| handle_graph | vg::MinDistanceClusterer | 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::GreedyMinDistanceClusterer | protectedvirtual |
| match_fanouts_t typedef | vg::MEMClusterer | |
| max_gap | vg::MEMClusterer | |
| max_separation | vg::GreedyMinDistanceClusterer | protected |
| MEMClusterer()=default | vg::MEMClusterer | |
| min_separation | vg::GreedyMinDistanceClusterer | protected |
| MinDistanceClusterer(SnarlDistanceIndex *distance_index) | vg::MinDistanceClusterer | |
| 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::MinDistanceClusterer | virtual |
| ~GreedyMinDistanceClusterer()=default | vg::GreedyMinDistanceClusterer | |
| ~MEMClusterer()=default | vg::MEMClusterer | virtual |
| ~MinDistanceClusterer()=default | vg::MinDistanceClusterer | virtual |
1.8.17