Here is a list of all class members with links to the classes they belong to:
- e -
- 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_delta_to_id()
: bdsg::ODGI
- edge_handle()
: bdsg::ODGI
, handlegraph::HandleGraph
- edge_index()
: handlegraph::VectorizableHandleGraph
, vg::Packer
, vg::VG
, xg::XG
- edge_lists_iv
: bdsg::PackedGraph
- edge_locks
: vg::Packer
- edge_max
: PruningParameters
, vg::VariantAdder
- EDGE_NEXT_OFFSET
: bdsg::PackedGraph
- edge_orientation()
: xg::XG
- edge_pileups
: vg::Pileup
- EDGE_RECORD_SIZE
: bdsg::PackedGraph
- edge_relative_offset()
: xg::XG
- edge_support_cache
: vg::CachedPackedTraversalSupportFinder
- edge_supports
: vg::SupportAugmentedGraph
- edge_to_delta()
: bdsg::ODGI
- EDGE_TRAV_OFFSET
: bdsg::PackedGraph
- edge_vector_size()
: vg::Packer
- edge_weight
: vg::FlowSort::WeightedGraph
- edge_weight_callback
: vg::FlowTraversalFinder
- edges
: 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_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_at_position()
: vg::Packer
- eject_deleted_paths()
: bdsg::PackedGraph
- elementary_cycles()
: vg::VG
- embed_transcript_paths()
: vg::Transcriptome
- embedded_alignments
: vg::AugmentedGraph
- emit()
: Vectorizer
, vg::io::TSVAlignmentEmitter
- 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::HTSAlignmentEmitter
, vg::io::AlignmentEmitter
, vg::io::GafAlignmentEmitter
, vg::io::NullAlignmentEmitter
, vg::io::TSVAlignmentEmitter
, vg::io::VGAlignmentEmitter
- emit_mapped_single()
: vg::io::AlignmentEmitter
- emit_mapped_singles()
: vg::HTSAlignmentEmitter
, vg::io::AlignmentEmitter
, vg::io::GafAlignmentEmitter
, vg::io::NullAlignmentEmitter
, vg::io::TSVAlignmentEmitter
, vg::io::VGAlignmentEmitter
- emit_pair()
: vg::io::AlignmentEmitter
- emit_pairs()
: vg::HTSAlignmentEmitter
, vg::io::AlignmentEmitter
, vg::io::GafAlignmentEmitter
, vg::io::NullAlignmentEmitter
, vg::io::TSVAlignmentEmitter
, vg::io::VGAlignmentEmitter
, vg::MultipathAlignmentEmitter
- emit_single()
: vg::io::AlignmentEmitter
- emit_singles()
: vg::HTSAlignmentEmitter
, vg::io::AlignmentEmitter
, vg::io::GafAlignmentEmitter
, vg::io::NullAlignmentEmitter
, vg::io::TSVAlignmentEmitter
, vg::io::VGAlignmentEmitter
, vg::MultipathAlignmentEmitter
- emit_variant()
: vg::MCMCCaller
, vg::VCFOutputCaller
- emitter
: vg::GAFOutputCaller
- emitter_t
: vg::StreamSorter< Message >
- empty()
: haplo::int_itvl_t
, vg::BitString
, vg::GaplessExtension
, vg::MultipathAlignmentGraph
, vg::Option< vector< Item >, Parser >
, vg::Paths
, vg::VG
- empty_edge_ends
: vg::VG
- empty_full_paths
: vg::BandedGlobalAligner< IntType >::AltTracebackStack
- empty_ids
: vg::VG
- empty_score
: vg::BandedGlobalAligner< IntType >::AltTracebackStack
- encode()
: vg::MIPayload
- encode_and_assign_path_name()
: bdsg::PackedGraph
- encode_edge()
: xg::XG
- encode_nucleotide()
: bdsg::PackedGraph
- encode_path_name()
: bdsg::PackedGraph
- encode_traversal()
: bdsg::PackedGraph
- end
: gafkluge::GafStep
, handlegraph::PathForEachSocket
, vg::algorithms::kmer_t
, vg::algorithms::walk_t
, vg::GFFRecord
, 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::walk_t
- end_degree()
: vg::VG
- end_file
: vg::io::BlockedGzipOutputStream
- end_id
: vg::MinimumDistanceIndex::ChainIndex
, vg::MinimumDistanceIndex::SnarlIndex
- END_LEN_OFFSET
: vg::MIPayload
- end_length
: vg::SnarlSeedClusterer::Seed
- end_marker
: xg::XG
- end_self_reachable
: vg::Snarl
- end_sep
: vg::Index
- EndFile()
: vg::io::BlockedGzipOutputStream
- endpoints
: vg::GraphSynchronizer::Lock
- ensure()
: vg::IndexManager
- ensure_distance()
: vg::IndexManager
- ensure_edit_tmpfiles_open()
: vg::Packer
- ensure_gbwt()
: vg::IndexManager
- ensure_gbwtgraph()
: vg::IndexManager
- ensure_graph()
: vg::IndexManager
- ensure_header()
: vg::HTSAlignmentEmitter
- ensure_minimizer()
: vg::IndexManager
- ensure_snarls()
: vg::IndexManager
- entries
: haplo::haplo_DP_column
- entry_to_string()
: vg::Index
- 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
- exact()
: vg::GaplessExtension
- exclude_dist_tree_merges()
: vg::OrientedDistanceClusterer
- exclude_merges()
: vg::OrientedDistanceMeasurer
, vg::PathOrientedDistanceMeasurer
, vg::SnarlOrientedDistanceMeasurer
- exclude_unaligned
: vg::BaseMapper
- excluded_feature
: vg::ReadFilter::Counts
- excluded_features
: vg::ReadFilter
- excluded_refpos_contigs
: vg::ReadFilter
- excluded_samples
: vg::HaplotypeIndexer
- execute()
: vg::AppendHaplotypeCommand
, vg::DeleteHaplotypeCommand
, vg::GenomeState
, vg::GenomeStateCommand
, vg::InsertHaplotypeCommand
, vg::ReplaceLocalHaplotypeCommand
, vg::ReplaceSnarlHaplotypeCommand
, vg::SwapHaplotypesCommand
- Exhaustive
: vg::Genotyper
- ExhaustiveTraversalFinder()
: vg::ExhaustiveTraversalFinder
- exons
: vg::Transcript
- exp_rho
: haplo::haploMath::RRMemo
- expand()
: vg::Funnel
- expand_context()
: vg::Index
, vg::VG
- expand_context_by_length()
: vg::VG
- expand_context_by_steps()
: vg::VG
- expand_path()
: vg::VG
- expanded_subgraph()
: vg::RegionExpander
- expected_depth
: vg::PoissonSupportSnarlCaller::PoissonCallInfo
- expected_separation
: vg::GreedyMinDistanceClusterer
- explicit_exhaustive_traversals()
: vg::Deconstructor
- extend()
: haplo::haplo_DP_column
, haplo::haplo_DP_rectangle
, vg::DozeuInterface
, vg::GaplessExtender
, vg::IncrementalSubgraph
, vg::Paths
, vg::QualAdjXdropAligner
, vg::VG
, vg::XdropAligner
- extend_dist_tree_by_buckets()
: vg::OrientedDistanceClusterer
- extend_dist_tree_by_permutations()
: vg::OrientedDistanceClusterer
- extend_path()
: vg::PhaseUnfolder
- extend_state()
: vg::PhaseUnfolder
- extender
: vg::MinimizerMapper
- extension_score_threshold
: vg::MinimizerMapper
- extension_set_score_threshold
: vg::MinimizerMapper
- extension_to_alignment()
: vg::MinimizerMapper
- external_handle()
: xg::XGPath
- extra_data
: vg::FeatureSet::Feature
- extra_multimaps
: vg::Mapper
- extract_cluster_graph()
: vg::MultipathMapper
- extract_component()
: vg::PathChunker
- extract_encoded_path_name()
: bdsg::PackedGraph
- extract_first()
: vg::io::VPKG
- extract_id_range()
: vg::PathChunker
- extract_left
: vg::IncrementalSubgraph
- extract_linearized_path_graph()
: vg::Surjector
- 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_subgraph()
: vg::PathChunker
- extracted
: vg::IncrementalSubgraph
- extracted_index
: vg::IncrementalSubgraph
- ExtraNodeGraph()
: vg::ExtraNodeGraph