Here is a list of all functions with links to the classes they belong to:
- e -
- easy_sort() : vg::StreamSorter< Message >
- edge_allele_labels() : vg::Genotyper
- edge_count() : vg::VG
- edge_coverage() : vg::Packer
- edge_coverage_bin_offset() : vg::Packer
- edge_coverage_bin_size() : vg::Packer
- edge_handle() : handlegraph::HandleGraph
- edge_index() : handlegraph::VectorizableHandleGraph, vg::Packer, xg::XG
- edge_orientation() : xg::XG
- edge_relative_offset() : xg::XG
- edge_to_snarl_edge() : vg::SnarlGraph
- edge_vector_size() : vg::Packer
- edges_end() : vg::VG
- edges_from() : vg::VG
- edges_of() : vg::VG
- edges_of_node() : vg::VG
- edges_of_nodes() : vg::VG
- edges_start() : vg::VG
- edges_to() : vg::VG
- edit() : vg::path_mapping_t, vg::VG
- edit_fast() : vg::VG
- edit_size() : vg::path_mapping_t
- edit_t() : vg::edit_t
- edit_value() : vg::Packer
- EditedTranscriptPath() : vg::EditedTranscriptPath
- edits_at_position() : vg::Packer
- embed_ref_path_snarls() : vg::SnarlGraph
- embed_snarl() : vg::SnarlGraph
- embed_snarls() : vg::SnarlGraph
- embed_transcript_paths() : vg::Transcriptome
- 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
- 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
- EnableMultiThreading() : vg::io::BlockedGzipInputStream
- encode() : vg::MEMAccelerator, vg::MIPayload
- encode_edge() : xg::XG
- end() : handlegraph::PathForEachSocket, vg::Option< vector< Item >, Parser >, vg::PathIndex, vg::PhasedGenome, vg::ShuffledPairs, vg::VectorView< Item >
- end_degree() : vg::VG
- end_handle() : vg::Haplotypes::Subchain
- EndFile() : vg::io::BlockedGzipOutputStream
- 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
- erase() : vg::SnarlState
- erase_in_out_edges() : vg::FlowSort
- 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
- exclude_dist_tree_merges() : vg::OrientedDistanceClusterer
- exclude_merges() : vg::OrientedDistanceMeasurer, vg::PathOrientedDistanceMeasurer, vg::SnarlOrientedDistanceMeasurer
- 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
- ExhaustiveTraversalFinder() : vg::ExhaustiveTraversalFinder
- 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
- Explainer() : 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
- extension_to_alignment() : vg::MinimizerMapper
- external_handle() : xg::XGPath
- extract() : vg::algorithms::GFAParser
- extract_cluster_graph() : vg::MultipathMapper
- extract_component() : vg::PathChunker
- extract_id_range() : vg::PathChunker
- 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
- extracting_left() : vg::IncrementalSubgraph
- ExtraNodeGraph() : vg::ExtraNodeGraph