vg
tools for working with variation graphs
vg::MultipathAlignmentGraph Member List

This is the complete list of members for vg::MultipathAlignmentGraph, including all inherited members.

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)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 band_padding, multipath_alignment_t &multipath_aln_out, bool allow_negative_scores=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, function< size_t(const Alignment &, const HandleGraph &)> band_padding_function, multipath_alignment_t &multipath_aln_out, bool allow_negative_scores=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, unordered_set< size_t > *sources=nullptr)vg::MultipathAlignmentGraphprivate
clear_reachability_edges()vg::MultipathAlignmentGraph
collapse_order_length_runs(const HandleGraph &graph, gcsa::GCSA *gcsa)vg::MultipathAlignmentGraphprivate
create_identity_projection_trans(const HandleGraph &graph)vg::MultipathAlignmentGraphstatic
create_injection_trans(const unordered_map< id_t, pair< id_t, bool >> &projection_trans)vg::MultipathAlignmentGraphstatic
create_injection_trans(const HandleGraph &graph, const function< pair< id_t, bool >(id_t)> &project)vg::MultipathAlignmentGraphstatic
create_match_nodes(const HandleGraph &graph, const MultipathMapper::memcluster_t &hits, const function< pair< id_t, bool >(id_t)> &project, const unordered_multimap< id_t, pair< id_t, bool >> &injection_trans, const MultipathMapper::match_fanouts_t *fanout_breaks)vg::MultipathAlignmentGraphprivate
create_path_chunk_nodes(const HandleGraph &graph, const vector< pair< pair< string::const_iterator, string::const_iterator >, Path >> &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)vg::MultipathAlignmentGraphprivate
create_projector(const unordered_map< id_t, pair< id_t, bool >> &projection_trans)vg::MultipathAlignmentGraphstatic
empty()vg::MultipathAlignmentGraph
get_connected_components() constvg::MultipathAlignmentGraph
has_reachability_edgesvg::MultipathAlignmentGraphprivate
into_cutting_snarl(id_t node_id, bool is_rev, SnarlManager *snarl_manager, MinimumDistanceIndex *dist_index)vg::MultipathAlignmentGraphprivate
MultipathAlignmentGraph(const HandleGraph &graph, const MultipathMapper::memcluster_t &hits, const function< pair< id_t, bool >(id_t)> &project, const unordered_multimap< id_t, pair< id_t, bool >> &injection_trans, 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 MultipathMapper::memcluster_t &hits, const unordered_map< id_t, pair< id_t, bool >> &projection_trans, 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 MultipathMapper::memcluster_t &hits, const function< pair< id_t, bool >(id_t)> &project, 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 >> &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)vg::MultipathAlignmentGraph
MultipathAlignmentGraph(const HandleGraph &graph, const vector< pair< pair< string::const_iterator, string::const_iterator >, Path >> &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)vg::MultipathAlignmentGraph
MultipathAlignmentGraph(const HandleGraph &graph, const vector< pair< pair< string::const_iterator, string::const_iterator >, Path >> &path_chunks, const Alignment &alignment, const function< pair< id_t, bool >(id_t)> &project, bool realign_Ns=true, bool preserve_tail_anchors=false)vg::MultipathAlignmentGraph
MultipathAlignmentGraph(const HandleGraph &graph, const Alignment &alignment, SnarlManager *snarl_manager, MinimumDistanceIndex *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, MinimumDistanceIndex *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, MinimumDistanceIndex *dist_index, size_t max_snarl_cut_size, const function< pair< id_t, bool >(id_t)> &project)vg::MultipathAlignmentGraph
path_nodesvg::MultipathAlignmentGraphprivate
pessimistic_tail_gap(int64_t tail_length, double multiplier)vg::MultipathAlignmentGraphprivate
pessimistic_tail_gap_memovg::MultipathAlignmentGraphprivatestatic
prune_to_high_scoring_paths(const Alignment &alignment, const GSSWAligner *aligner, double max_suboptimal_score_ratio, const vector< size_t > &topological_order)vg::MultipathAlignmentGraph
remove_transitive_edges(const vector< size_t > &topological_order)vg::MultipathAlignmentGraph
reorder_adjacency_lists(const vector< size_t > &order)vg::MultipathAlignmentGraphprivate
resect_snarls_from_paths(SnarlManager *cutting_snarls, MinimumDistanceIndex *dist_index, const function< pair< id_t, bool >(id_t)> &project, int64_t max_snarl_cut_size=5)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_sizevg::MultipathAlignmentGraphprivatestatic
to_dot(ostream &out, const Alignment *alignment=nullptr) constvg::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::MultipathAlignmentGraphprivatestatic
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
~MultipathAlignmentGraph()vg::MultipathAlignmentGraph