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vg
tools for working with variation graphs
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This is the complete list of members for vg::MultipathAlignmentGraph, including all inherited members.
| add_decomposed_tail_alignments(const Alignment &alignment, const HandleGraph &align_graph, multipath_alignment_t &multipath_aln_out, unordered_set< size_t > &prohibited_merges, vector< pair< path_t, int32_t >> &shared_tail_alns, vector< vector< pair< path_t, int32_t >>> &unshared_tail_alns, size_t attachment_idx, bool to_left, size_t unmergeable_len, const GSSWAligner *aligner, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function< pair< id_t, bool >(id_t)> *project=nullptr) | vg::MultipathAlignmentGraph | protected |
| add_reachability_edges(const HandleGraph &vg, const function< pair< id_t, bool >(id_t)> &project, const unordered_multimap< id_t, pair< id_t, bool >> &injection_trans, vector< size_t > *path_node_provenance=nullptr) | vg::MultipathAlignmentGraph | |
| align(const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, bool score_anchors_as_matches, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, size_t max_tail_length, bool simplify_topologies, size_t unmergeable_len, size_t band_padding, multipath_alignment_t &multipath_aln_out, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function< pair< id_t, bool >(id_t)> *project=nullptr, bool allow_negative_scores=false, bool align_in_reverse=false) | vg::MultipathAlignmentGraph | |
| align(const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, bool score_anchors_as_matches, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, size_t max_tail_length, bool simplify_topologies, size_t unmergeable_len, const function< size_t(const Alignment &, const HandleGraph &)> &band_padding_function, multipath_alignment_t &multipath_aln_out, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function< pair< id_t, bool >(id_t)> *project=nullptr, bool allow_negative_scores=false, bool align_in_reverse=false) | vg::MultipathAlignmentGraph | |
| align_tails(const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, size_t min_paths, size_t max_tail_length, unordered_set< size_t > *sources=nullptr) | vg::MultipathAlignmentGraph | protected |
| clear_reachability_edges() | vg::MultipathAlignmentGraph | |
| collapse_order_length_runs(const HandleGraph &graph, gcsa::GCSA *gcsa, vector< size_t > &path_node_provenance) | vg::MultipathAlignmentGraph | protected |
| count_reachability_edges() const | vg::MultipathAlignmentGraph | |
| create_identity_projection_trans(const HandleGraph &graph) | vg::MultipathAlignmentGraph | static |
| create_injection_trans(const unordered_map< id_t, pair< id_t, bool >> &projection_trans) | vg::MultipathAlignmentGraph | static |
| create_injection_trans(const HandleGraph &graph, const function< pair< id_t, bool >(id_t)> &project) | vg::MultipathAlignmentGraph | static |
| create_match_nodes(const HandleGraph &graph, MultipathMapper::memcluster_t &hits, const function< pair< id_t, bool >(id_t)> &project, const unordered_multimap< id_t, pair< id_t, bool >> &injection_trans, vector< size_t > &path_node_provenance, int64_t max_branch_trim_length, const MultipathMapper::match_fanouts_t *fanout_breaks) | vg::MultipathAlignmentGraph | protected |
| create_path_chunk_nodes(const HandleGraph &graph, const vector< pair< pair< string::const_iterator, string::const_iterator >, path_t >> &path_chunks, const Alignment &alignment, const function< pair< id_t, bool >(id_t)> &project, const unordered_multimap< id_t, pair< id_t, bool >> &injection_trans, vector< size_t > *path_node_provenance=nullptr) | vg::MultipathAlignmentGraph | protected |
| create_projector(const unordered_map< id_t, pair< id_t, bool >> &projection_trans) | vg::MultipathAlignmentGraph | static |
| decompose_alignments(const vector< pair< path_t, int32_t >> &alt_alns, const Alignment &alignment, const HandleGraph &align_graph, string::const_iterator begin, const GSSWAligner *aligner) | vg::MultipathAlignmentGraph | protectedstatic |
| deduplicate_alt_alns(vector< pair< path_t, int32_t >> &alt_alns, bool leftward, bool rightward) | vg::MultipathAlignmentGraph | protectedstatic |
| empty() const | vg::MultipathAlignmentGraph | |
| get_connected_components() const | vg::MultipathAlignmentGraph | |
| get_cut_segments(path_t &path, SnarlManager *cutting_snarls, SnarlDistanceIndex *dist_index, const function< pair< id_t, bool >(id_t)> &project, int64_t max_snarl_cut_size) const | vg::MultipathAlignmentGraph | protected |
| has_reachability_edges | vg::MultipathAlignmentGraph | protected |
| into_cutting_snarl(id_t node_id, bool is_rev, SnarlManager *snarl_manager, SnarlDistanceIndex *dist_index) const | vg::MultipathAlignmentGraph | protected |
| jitter_homopolymer_ends(const HandleGraph &graph, vector< size_t > &path_node_provenance, const MultipathMapper::memcluster_t &hits, int64_t max_branch_trim_length) | vg::MultipathAlignmentGraph | protected |
| max_shift() const | vg::MultipathAlignmentGraph | |
| merge_partially_redundant_match_nodes(const unordered_map< int64_t, vector< int64_t >> &node_matches, vector< size_t > &path_node_provenance) | vg::MultipathAlignmentGraph | protected |
| MultipathAlignmentGraph(const HandleGraph &graph, MultipathMapper::memcluster_t &hits, const function< pair< id_t, bool >(id_t)> &project, const unordered_multimap< id_t, pair< id_t, bool >> &injection_trans, vector< size_t > &path_node_provenance, size_t max_branch_trim_length=0, gcsa::GCSA *gcsa=nullptr, const MultipathMapper::match_fanouts_t *fanout_breaks=nullptr) | vg::MultipathAlignmentGraph | |
| MultipathAlignmentGraph(const HandleGraph &graph, MultipathMapper::memcluster_t &hits, const unordered_map< id_t, pair< id_t, bool >> &projection_trans, vector< size_t > &path_node_provenance, size_t max_branch_trim_length=0, gcsa::GCSA *gcsa=nullptr, const MultipathMapper::match_fanouts_t *fanout_breaks=nullptr) | vg::MultipathAlignmentGraph | |
| MultipathAlignmentGraph(const HandleGraph &graph, MultipathMapper::memcluster_t &hits, const function< pair< id_t, bool >(id_t)> &project, vector< size_t > &path_node_provenance, size_t max_branch_trim_length=0, gcsa::GCSA *gcsa=nullptr, const MultipathMapper::match_fanouts_t *fanout_breaks=nullptr) | vg::MultipathAlignmentGraph | |
| MultipathAlignmentGraph(const HandleGraph &graph, const vector< pair< pair< string::const_iterator, string::const_iterator >, path_t >> &path_chunks, const Alignment &alignment, const function< pair< id_t, bool >(id_t)> &project, const unordered_multimap< id_t, pair< id_t, bool >> &injection_trans, bool realign_Ns=true, bool preserve_tail_anchors=false, vector< size_t > *path_node_provenance=nullptr) | vg::MultipathAlignmentGraph | |
| MultipathAlignmentGraph(const HandleGraph &graph, const vector< pair< pair< string::const_iterator, string::const_iterator >, path_t >> &path_chunks, const Alignment &alignment, const unordered_map< id_t, pair< id_t, bool >> &projection_trans, bool realign_Ns=true, bool preserve_tail_anchors=false, vector< size_t > *path_node_provenance=nullptr) | vg::MultipathAlignmentGraph | |
| MultipathAlignmentGraph(const HandleGraph &graph, const vector< pair< pair< string::const_iterator, string::const_iterator >, path_t >> &path_chunks, const Alignment &alignment, const function< pair< id_t, bool >(id_t)> &project, bool realign_Ns=true, bool preserve_tail_anchors=false, vector< size_t > *path_node_provenance=nullptr) | vg::MultipathAlignmentGraph | |
| MultipathAlignmentGraph(const HandleGraph &graph, const Alignment &alignment, SnarlManager *snarl_manager, SnarlDistanceIndex *dist_index, size_t max_snarl_cut_size, const function< pair< id_t, bool >(id_t)> &project, const unordered_multimap< id_t, pair< id_t, bool >> &injection_trans) | vg::MultipathAlignmentGraph | |
| MultipathAlignmentGraph(const HandleGraph &graph, const Alignment &alignment, SnarlManager *snarl_manager, SnarlDistanceIndex *dist_index, size_t max_snarl_cut_size, const unordered_map< id_t, pair< id_t, bool >> &projection_trans) | vg::MultipathAlignmentGraph | |
| MultipathAlignmentGraph(const HandleGraph &graph, const Alignment &alignment, SnarlManager *snarl_manager, SnarlDistanceIndex *dist_index, size_t max_snarl_cut_size, const function< pair< id_t, bool >(id_t)> &project) | vg::MultipathAlignmentGraph | |
| path_nodes | vg::MultipathAlignmentGraph | protected |
| pessimistic_tail_gap(int64_t tail_length, double multiplier) | vg::MultipathAlignmentGraph | protected |
| pessimistic_tail_gap_memo | vg::MultipathAlignmentGraph | protectedstatic |
| prune_high_shift_edges(size_t prune_diff, bool prohibit_new_sources, bool prohibit_new_sinks) | vg::MultipathAlignmentGraph | |
| prune_to_high_scoring_paths(const Alignment &alignment, const GSSWAligner *aligner, double max_suboptimal_score_ratio, const vector< size_t > &topological_order, vector< size_t > &path_node_provenance) | vg::MultipathAlignmentGraph | |
| remove_transitive_edges(const vector< size_t > &topological_order) | vg::MultipathAlignmentGraph | |
| reorder_adjacency_lists(const vector< size_t > &order) | vg::MultipathAlignmentGraph | protected |
| resect_snarls_from_paths(SnarlManager *cutting_snarls, SnarlDistanceIndex *dist_index, const function< pair< id_t, bool >(id_t)> &project, int64_t max_snarl_cut_size=5) | vg::MultipathAlignmentGraph | |
| reverse_alignment(Alignment &aln) const | vg::MultipathAlignmentGraph | protected |
| size() const | vg::MultipathAlignmentGraph | |
| synthesize_tail_anchors(const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, size_t min_anchor_size, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier) | vg::MultipathAlignmentGraph | |
| tail_gap_memo_max_size | vg::MultipathAlignmentGraph | protectedstatic |
| to_dot(ostream &out, const Alignment *alignment=nullptr) const | vg::MultipathAlignmentGraph | |
| topological_sort(vector< size_t > &order_out) | vg::MultipathAlignmentGraph | |
| trim_and_check_for_empty(const Alignment &alignment, bool trim_Ns, PathNode &path_node, bool preserve_tail_anchors, int64_t *removed_start_from_length=nullptr, int64_t *removed_end_from_length=nullptr) | vg::MultipathAlignmentGraph | protectedstatic |
| trim_hanging_indels(const Alignment &alignment, bool trim_Ns=true, bool preserve_tail_anchors=false) | vg::MultipathAlignmentGraph | |
| trim_to_branch_points(const HandleGraph *graph, size_t max_trim_length=1) | vg::MultipathAlignmentGraph | |
| zip_alignments(vector< pair< path_t, int32_t >> &alt_alns, bool from_left, const Alignment &alignment, const HandleGraph &align_graph, string::const_iterator begin, const GSSWAligner *aligner) | vg::MultipathAlignmentGraph | protectedstatic |
| ~MultipathAlignmentGraph() | vg::MultipathAlignmentGraph |
1.8.17