Index

D

DistanceGraph (C++ class) DistanceGraph::add_link (C++ function) DistanceGraph::are_connected (C++ function) DistanceGraph::copy_links (C++ function) DistanceGraph::disconnect_node (C++ function) DistanceGraph::dump_to_text (C++ function) DistanceGraph::find_all_paths_between (C++ function) DistanceGraph::find_bubbles (C++ function) DistanceGraph::fw_neighbours_by_distance (C++ function) DistanceGraph::fw_reached_nodes (C++ function) DistanceGraph::get_all_lines (C++ function) DistanceGraph::get_all_nodeviews (C++ function) DistanceGraph::get_bw_links (C++ function)

DistanceGraph::get_connected_nodes (C++ function) DistanceGraph::get_fw_links (C++ function) DistanceGraph::get_link (C++ function) DistanceGraph::get_next_nodes (C++ function) DistanceGraph::get_nodeview (C++ function) DistanceGraph::get_prev_nodes (C++ function) DistanceGraph::links (C++ member) DistanceGraph::load_from_text (C++ function) DistanceGraph::remove_link (C++ function) DistanceGraph::remove_transitive_links (C++ function) DistanceGraph::report_connectivity (C++ function) DistanceGraph::stats_by_kci (C++ function) DistanceGraph::write_to_gfa1 (C++ function) DistanceGraph::write_to_gfa2 (C++ function)

L

LinkageMaker (C++ class) LinkageMaker::filter_mappings_with_linked_reads (C++ function) LinkageMaker::make_long10x_multilinkage (C++ function) LinkageMaker::make_paired_linkage (C++ function) LinkageMaker::make_topology_linkage (C++ function) LinkedReadsMapper (C++ class) LinkedReadsMapper::compute_all_tag_neighbours (C++ function) LinkedReadsMapper::get_node_tags (C++ function) LinkedReadsMapper::ls (C++ function) LinkedReadsMapper::map_reads (C++ function) LinkedReadsMapper::map_reads63 (C++ function) LinkedReadsMapper::operator= (C++ function) LinkedReadsMapper::path_reads (C++ function) LinkedReadsMapper::populate_orientation (C++ function) LinkedReadsMapper::print_status (C++ function) LinkedReadsMapper::read_direction_in_node (C++ member) LinkedReadsMapper::read_to_node (C++ member) LinkedReadsMapper::reads_in_node (C++ member) LinkedReadsMapper::remap_all_reads (C++ function) LinkedReadsMapper::remap_all_reads63 (C++ function) LinkedReadsMapper::tag_neighbours (C++ member) LinkView (C++ class) LinkView::distance (C++ function) LinkView::node (C++ function) LinkView::support (C++ function) LongReadsMapper (C++ class) LongReadsMapper::alignment_blocks (C++ function)

LongReadsMapper::all_paths_between (C++ member) LongReadsMapper::count_candidates (C++ function) LongReadsMapper::datastore (C++ member) LongReadsMapper::filter_and_chain_matches_by_offset_group (C++ function) LongReadsMapper::filter_blocks (C++ function) LongReadsMapper::get_all_kmer_matches (C++ function) LongReadsMapper::get_raw_mappings_from_read (C++ function) LongReadsMapper::get_sat_kmer_matches (C++ function) LongReadsMapper::improve_read_mappings (C++ function) LongReadsMapper::k (C++ member) LongReadsMapper::LongReadsMapper (C++ function) LongReadsMapper::ls (C++ function) LongReadsMapper::map_reads (C++ function) LongReadsMapper::map_reads_to_best_nodes (C++ function) LongReadsMapper::map_sequence (C++ function) LongReadsMapper::mappings (C++ member) LongReadsMapper::max_delta_change (C++ member) LongReadsMapper::max_hits_to_candidate (C++ member) LongReadsMapper::max_index_freq (C++ member) LongReadsMapper::max_jump (C++ member) LongReadsMapper::min_chain (C++ member) LongReadsMapper::min_number_of_node_occurrences (C++ member) LongReadsMapper::min_size (C++ member) LongReadsMapper::reads_in_node (C++ member) LongReadsMapper::remove_shadowed_matches (C++ function) LongReadsMapper::set_params (C++ function) LongReadsMapper::update_indexes (C++ function)

N

NodeView (C++ class) NodeView::fw_neighbours_by_distance (C++ function) NodeView::get_linked_mappings (C++ function) NodeView::get_linked_reads (C++ function) NodeView::get_linked_tags (C++ function) NodeView::get_long_mappings (C++ function) NodeView::get_long_reads (C++ function) NodeView::get_paired_mappings (C++ function)

NodeView::get_paired_reads (C++ function) NodeView::kmer_coverage (C++ function), [1] NodeView::next (C++ function) NodeView::node_id (C++ function) NodeView::parallels (C++ function) NodeView::prev (C++ function) NodeView::rc (C++ function) NodeView::sequence (C++ function) NodeView::size (C++ function)

P

PairedReadsMapper (C++ class) PairedReadsMapper::frdist (C++ member) PairedReadsMapper::get_node_readpairs_ids (C++ function) PairedReadsMapper::ls (C++ function) PairedReadsMapper::map_reads (C++ function) PairedReadsMapper::map_reads63 (C++ function) PairedReadsMapper::path_fw (C++ function) PairedReadsMapper::path_reads (C++ function) PairedReadsMapper::path_reads63 (C++ function)

PairedReadsMapper::populate_orientation (C++ function) PairedReadsMapper::print_status (C++ function) PairedReadsMapper::read_direction_in_node (C++ member) PairedReadsMapper::read_paths (C++ member) PairedReadsMapper::read_to_node (C++ member) PairedReadsMapper::reads_in_node (C++ member) PairedReadsMapper::remap_all_reads (C++ function) PairedReadsMapper::remap_all_reads63 (C++ function) PairedReadsMapper::rfdist (C++ member) PairedReadsMapper::size_distribution (C++ function)

S

SequenceDistanceGraph (C++ class) SequenceDistanceGraph::add_node (C++ function), [1] SequenceDistanceGraph::expand_node (C++ function) SequenceDistanceGraph::filename (C++ member) SequenceDistanceGraph::get_all_bubbly_subgraphs (C++ function) SequenceDistanceGraph::get_all_unitigs (C++ function) SequenceDistanceGraph::is_sane (C++ function) SequenceDistanceGraph::join_path (C++ function)

SequenceDistanceGraph::load_from_gfa (C++ function) SequenceDistanceGraph::nodeID_to_name (C++ function) SequenceDistanceGraph::oldnames (C++ member) SequenceDistanceGraph::oldnames_to_ids (C++ member) SequenceDistanceGraph::oldnames_to_nodes (C++ function) SequenceDistanceGraph::print_bubbly_subgraph_stats (C++ function) SequenceDistanceGraph::remove_node (C++ function) SequenceDistanceGraph::write (C++ function) SequenceDistanceGraph::ws (C++ member)

W

WorkSpace (C++ class) WorkSpace::add_distance_graph (C++ function) WorkSpace::add_kmer_counter (C++ function), [1] WorkSpace::add_linked_reads_datastore (C++ function) WorkSpace::add_long_reads_datastore (C++ function) WorkSpace::add_paired_reads_datastore (C++ function) WorkSpace::dump_to_disk (C++ function)

WorkSpace::get_distance_graph (C++ function) WorkSpace::get_kmer_counter (C++ function) WorkSpace::get_linked_reads_datastore (C++ function) WorkSpace::get_long_reads_datastore (C++ function) WorkSpace::get_paired_reads_datastore (C++ function) WorkSpace::load_from_disk (C++ function) WorkSpace::ls (C++ function)