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_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::MultipathAlignmentGraph | private |
clear_reachability_edges() | vg::MultipathAlignmentGraph | |
collapse_order_length_runs(const HandleGraph &graph, gcsa::GCSA *gcsa) | vg::MultipathAlignmentGraph | private |
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, 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::MultipathAlignmentGraph | private |
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::MultipathAlignmentGraph | private |
create_projector(const unordered_map< id_t, pair< id_t, bool >> &projection_trans) | vg::MultipathAlignmentGraph | static |
empty() | vg::MultipathAlignmentGraph | |
get_connected_components() const | vg::MultipathAlignmentGraph | |
has_reachability_edges | vg::MultipathAlignmentGraph | private |
into_cutting_snarl(id_t node_id, bool is_rev, SnarlManager *snarl_manager, MinimumDistanceIndex *dist_index) | vg::MultipathAlignmentGraph | private |
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_nodes | vg::MultipathAlignmentGraph | private |
pessimistic_tail_gap(int64_t tail_length, double multiplier) | vg::MultipathAlignmentGraph | private |
pessimistic_tail_gap_memo | vg::MultipathAlignmentGraph | privatestatic |
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::MultipathAlignmentGraph | private |
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_size | vg::MultipathAlignmentGraph | privatestatic |
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 | privatestatic |
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 |