Here is a list of all class members with links to the classes they belong to:
- e -
- earlier_stage_items : vg::Funnel::Item
- early_stop_number : vg::ComponentMinDistanceClusterer
- easy_sort() : vg::StreamSorter< Message >
- eat_trivial_children : vg::RepresentativeTraversalFinder
- edge : vg::EdgePileup, vg::Graph
- edge_allele_labels() : vg::Genotyper
- edge_by_sides : vg::VG
- edge_cache : vg::Sampler
- edge_count() : vg::VG, xg::XG
- edge_cov_bin_size : vg::Packer
- edge_coverage() : vg::Packer
- edge_coverage_bin_offset() : vg::Packer
- edge_coverage_bin_size() : vg::Packer
- edge_coverage_civ : vg::Packer
- edge_coverage_dynamic : vg::Packer
- edge_handle() : handlegraph::HandleGraph
- edge_index() : handlegraph::VectorizableHandleGraph, vg::Packer, vg::VG, xg::XG
- edge_listeners : vg::algorithms::GFAParser
- edge_locks : vg::Packer
- edge_max : PruningParameters, vg::VariantAdder
- edge_orientation() : xg::XG
- edge_pileups : vg::Pileup
- edge_ref_t : vg::DiagramExplainer
- edge_relative_offset() : xg::XG
- edge_support_cache : vg::CachedPackedTraversalSupportFinder
- edge_supports : vg::SupportAugmentedGraph
- edge_to_snarl_edge() : vg::SnarlGraph
- edge_vector_size() : vg::Packer
- edge_weight : vg::FlowSort::WeightedGraph
- edge_weight_callback : vg::FlowTraversalFinder
- edges : vg::algorithms::Node, vg::DiagramExplainer, vg::PathNode
- edges_end() : vg::VG
- edges_from : vg::MEMClusterer::HitNode, vg::VG
- edges_in_nodes : vg::FlowSort::WeightedGraph
- edges_of() : vg::VG
- edges_of_node() : vg::VG
- edges_of_nodes() : vg::VG
- edges_on_end : vg::VG
- edges_on_start : vg::VG
- edges_out_nodes : vg::FlowSort::WeightedGraph
- edges_start() : vg::VG
- edges_to : vg::MEMClusterer::HitNode, vg::VG
- edit : vg::Mapping, vg::path_mapping_t, vg::VG
- Edit : vg::WFAAlignment
- edit_count : vg::Packer
- edit_csas : vg::Packer
- edit_fast() : vg::VG
- edit_length : vg::BandedGlobalAligner< IntType >::BABuilder, vg::Packer
- edit_read_end_idx : vg::BandedGlobalAligner< IntType >::BABuilder
- edit_size() : vg::path_mapping_t
- edit_t() : vg::edit_t
- edit_tmpfile_names : vg::Packer
- edit_value() : vg::Packer
- EditedTranscriptPath() : vg::EditedTranscriptPath
- edits : vg::WFAAlignment
- edits_at_position() : vg::Packer
- embed_ref_path_snarls() : vg::SnarlGraph
- embed_snarl() : vg::SnarlGraph
- embed_snarls() : vg::SnarlGraph
- embed_transcript_paths() : vg::Transcriptome
- embedded_alignments : vg::AugmentedGraph
- embedded_path_names : vg::TranscriptPath
- emit() : Vectorizer, vg::io::TSVAlignmentEmitter, vg::ReadFilter< Read >
- emit_extra_message() : vg::io::AlignmentEmitter, vg::io::VGAlignmentEmitter
- emit_gaf_traversals() : vg::GAFOutputCaller
- emit_gaf_variant() : vg::GAFOutputCaller
- emit_group() : vg::io::MessageEmitter, vg::io::ProtobufEmitter< T >
- emit_mapped_pair() : vg::io::AlignmentEmitter
- emit_mapped_pairs() : vg::BackTranslatingAlignmentEmitter, vg::HTSAlignmentEmitter, vg::io::AlignmentEmitter, vg::io::GafAlignmentEmitter, vg::io::NullAlignmentEmitter, vg::io::TSVAlignmentEmitter, vg::io::VGAlignmentEmitter, vg::SurjectingAlignmentEmitter
- emit_mapped_single() : vg::io::AlignmentEmitter
- emit_mapped_singles() : vg::BackTranslatingAlignmentEmitter, vg::HTSAlignmentEmitter, vg::io::AlignmentEmitter, vg::io::GafAlignmentEmitter, vg::io::NullAlignmentEmitter, vg::io::TSVAlignmentEmitter, vg::io::VGAlignmentEmitter, vg::SurjectingAlignmentEmitter
- emit_pair() : vg::io::AlignmentEmitter
- emit_pairs() : vg::BackTranslatingAlignmentEmitter, vg::HTSAlignmentEmitter, vg::io::AlignmentEmitter, vg::io::GafAlignmentEmitter, vg::io::NullAlignmentEmitter, vg::io::TSVAlignmentEmitter, vg::io::VGAlignmentEmitter, vg::MultipathAlignmentEmitter, vg::SurjectingAlignmentEmitter
- emit_single() : vg::io::AlignmentEmitter
- emit_singles() : vg::BackTranslatingAlignmentEmitter, vg::HTSAlignmentEmitter, vg::io::AlignmentEmitter, vg::io::GafAlignmentEmitter, vg::io::NullAlignmentEmitter, vg::io::TSVAlignmentEmitter, vg::io::VGAlignmentEmitter, vg::MultipathAlignmentEmitter, vg::SurjectingAlignmentEmitter
- emit_snarl_recursive() : vg::NestedFlowCaller
- emit_tsv() : vg::ReadFilter< Read >
- emit_variant() : vg::MCMCCaller, vg::VCFOutputCaller
- emitter : vg::GAFOutputCaller
- emitter_t : vg::StreamSorter< Message >
- empty() : haplo::int_itvl_t, vg::algorithms::GFAParser, vg::BitString, vg::GaplessExtension, vg::MatchPos, vg::MatchPos::PathList, vg::MultipathAlignmentGraph, vg::Option< vector< Item >, Parser >, vg::Paths, vg::VectorView< Item >, vg::VG, vg::WFAAlignment
- empty_diagonal_range() : vg::WFATree
- empty_edge_ends : vg::VG
- empty_full_paths : vg::BandedGlobalAligner< IntType >::AltTracebackStack
- empty_ids : vg::VG
- empty_score : vg::BandedGlobalAligner< IntType >::AltTracebackStack
- EnableMultiThreading() : vg::io::BlockedGzipInputStream
- encode() : vg::MEMAccelerator, vg::MIPayload
- encode_edge() : xg::XG
- encoding : vg::ParallelKFFReader
- end : gafkluge::GafStep, handlegraph::PathForEachSocket
- END : handlegraph::SnarlDecomposition
- end : ReferenceInterval, vg::algorithms::kmer_t, vg::algorithms::walk_t, vg::GFFRecord, vg::HaplotypePartitioner::Subchain, vg::Haplotypes::Subchain, vg::kmer_t, vg::MaximalExactMatch, vg::NetGraph, vg::Option< vector< Item >, Parser >, vg::PathIndex, vg::PathNode, vg::PhasedGenome, vg::Range< Number >, vg::Region, vg::ShuffledPairs, vg::Snarl, vg::VectorView< Item >
- end_degree() : vg::VG
- end_file : vg::io::BlockedGzipOutputStream
- end_handle() : vg::Haplotypes::Subchain
- end_in : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
- end_self_reachable : vg::Snarl
- EndFile() : vg::io::BlockedGzipOutputStream
- endpoint_t : handlegraph::SnarlDecomposition
- endpoints : vg::GraphSynchronizer::Lock
- ends_at() : handlegraph::SnarlDecomposition
- ends_at_end() : handlegraph::SnarlDecomposition
- ends_at_start() : handlegraph::SnarlDecomposition
- ends_at_tip() : handlegraph::SnarlDecomposition
- ensure_edge() : vg::DiagramExplainer
- ensure_edit_tmpfiles_open() : vg::Packer
- ensure_header() : vg::HTSWriter
- ensure_node() : vg::DiagramExplainer
- ensure_parent_directory() : vg::temp_file::Handler
- entries : haplo::haplo_DP_column, vg::subcommand::Preset
- erase() : vg::SnarlState
- erase_in_out_edges() : vg::FlowSort
- error_model : vg::WFAExtender
- error_on_missing_path : vg::Transcriptome
- escape_delim() : vg::Packer
- escape_delims() : vg::Packer
- establish_strand_consistency() : vg::MultipathMapper
- estimate_batch_size() : vg::Packer
- estimate_bin_count() : vg::Packer
- estimate_data_width() : vg::Packer
- estimate_distribution() : vg::FragmentLengthDistribution
- estimate_edge_score() : vg::MEMClusterer
- estimate_gc_content() : vg::BaseMapper
- estimate_max_possible_mapping_quality() : vg::GSSWAligner, vg::Mapper
- estimate_missed_rescue_multiplicity() : vg::MultipathMapper
- estimate_next_best_score() : vg::GSSWAligner
- evaluate() : vg::WFAExtender::ErrorModel::Event
- exact() : vg::GaplessExtension
- exact_name : vg::ReadFilter< Read >
- exclude_dist_tree_merges() : vg::OrientedDistanceClusterer
- exclude_merges() : vg::OrientedDistanceMeasurer, vg::PathOrientedDistanceMeasurer, vg::SnarlOrientedDistanceMeasurer
- exclude_overlapping_min : vg::MinimizerMapper
- exclude_unaligned : vg::BaseMapper
- excluded_feature : vg::Counts
- excluded_features : vg::ReadFilter< Read >
- excluded_refpos_contigs : vg::ReadFilter< Read >
- excluded_samples : vg::HaplotypeIndexer
- exec : vg::IndexRecipe
- execute() : vg::AppendHaplotypeCommand, vg::DeleteHaplotypeCommand, vg::GenomeState, vg::GenomeStateCommand, vg::IndexRecipe, vg::InsertHaplotypeCommand, vg::JobSchedule, vg::ReplaceLocalHaplotypeCommand, vg::ReplaceSnarlHaplotypeCommand, vg::SwapHaplotypesCommand
- execute_recipe() : vg::IndexRegistry
- Exhaustive : vg::Genotyper
- ExhaustiveTraversalFinder() : vg::ExhaustiveTraversalFinder
- exons : vg::Transcript
- exp_rho : haplo::haploMath::RRMemo
- expand() : vg::Funnel
- expand_context() : vg::VG
- expand_context_by_length() : vg::VG
- expand_context_by_steps() : vg::VG
- expand_for_softclips() : vg::MultipathMapper
- expand_if_necessary() : vg::WFATree
- expand_path() : vg::VG
- expanded() : vg::WFANode
- expanded_subgraph() : vg::RegionExpander
- expected_depth : vg::PoissonSupportSnarlCaller::PoissonCallInfo
- expected_separation : vg::GreedyMinDistanceClusterer
- Explainer() : vg::Explainer
- explanation_number : vg::Explainer
- extend() : haplo::haplo_DP_column, haplo::haplo_DP_rectangle, vg::DozeuInterface, vg::GaplessExtender, vg::IncrementalSubgraph, vg::Paths, vg::QualAdjXdropAligner, vg::RecombinatorHaplotype, vg::VG, vg::WFATree, vg::XdropAligner
- extend_cluster() : vg::MinimizerMapper
- extend_dist_tree_by_buckets() : vg::OrientedDistanceClusterer
- extend_dist_tree_by_permutations() : vg::OrientedDistanceClusterer
- extend_over() : vg::WFATree
- extend_path() : vg::PhaseUnfolder
- extend_state() : vg::PhaseUnfolder
- extender : vg::MinimizerMapper
- extension_score_threshold : vg::MinimizerMapper
- extension_set_min_score : vg::MinimizerMapper
- extension_set_score_threshold : vg::MinimizerMapper
- extension_to_alignment() : vg::MinimizerMapper
- external_handle() : xg::XGPath
- external_id_map : vg::algorithms::GFAParser
- extra_data : vg::FeatureSet::Feature
- extra_multimaps : vg::Mapper
- extra_snarls : vg::HaplotypePartitioner::Subchain
- extract() : vg::algorithms::GFAParser
- extract_cluster_graph() : vg::MultipathMapper
- extract_component() : vg::PathChunker
- extract_id_range() : vg::PathChunker
- extract_left : vg::IncrementalSubgraph
- extract_maximal_graph() : vg::MultipathMapper
- extract_overlapping_paths() : vg::Surjector
- extract_path_component() : vg::PathChunker
- extract_rescue_graph() : vg::MultipathMapper
- extract_restrained_graph() : vg::MultipathMapper
- extract_sequences() : vg::Recombinator
- extract_snarls() : vg::PathChunker
- extract_subgraph() : vg::PathChunker
- extracted : vg::IncrementalSubgraph
- extracting_left() : vg::IncrementalSubgraph
- ExtraNodeGraph() : vg::ExtraNodeGraph