Here is a list of all class members with links to the classes they belong to:

- t -

• T : vg::subcommand::FlagArgSpec< Receiver >
• tag : vg::Funnel::Item , vg::Funnel::Stage , vg::Funnel , vg::io::ProtobufEmitter< T >
• tag_correct() : vg::Funnel
• tag_length : vg::Funnel::Item
• tag_list_t : vg::algorithms::GFAParser
• tag_seeds() : vg::MinimizerMapper
• tag_space : vg::Funnel::Stage
• tag_start : vg::Funnel::Item
• tag_to_loader : vg::io::Registry::Tables
• tag_to_protobuf : vg::io::Registry::Tables
• TaggedMessage : vg::io::MessageIterator
• tags : GBWTConfig
• tags_to_set : GBWTConfig
• tail_gap_memo_max_size : vg::MultipathAlignmentGraph
• tail_nodes() : vg::VG
• tail_offset() : vg::GaplessExtension
• tail_position() : vg::GaplessExtension
• take() : vg::io::MessageIterator , vg::io::ProtobufIterator< T > , vg::RecombinatorHaplotype
• target : vg::InsufficientInputException
• TARGET_LENGTH : vg::WFANode
• target_memory_usage() : vg::IndexingPlan , vg::IndexRegistry
• target_offset : vg::WFANode , vg::WFAPoint
• targets : vg::IndexingPlan
• TargetValueSearch() : vg::TargetValueSearch
• task_name : vg::Watchdog::thread_state_t
• Tell() : vg::io::BlockedGzipInputStream , vg::io::BlockedGzipOutputStream
• tell_group() : vg::io::MessageIterator , vg::io::ProtobufIterator< T >
• telomere_pair : vg::SwapHaplotypesCommand
• telomeres : vg::GenomeState
• template_feature : vg::PrimerPair
• template_position : vg::PrimerPair
• temporary : vg::GAFSorterFile
• test_mean : vg::BenchmarkResult
• test_splice_candidates() : vg::MultipathMapper
• test_stddev : vg::BenchmarkResult
• TestMinimizerMapper : vg::MinimizerMapper
• thin_alignment_cutoff : vg::VariantAdder
• thread_breakpoint_cursors : vg::io::StreamMultiplexer
• thread_chunk_inflation_factor : vg::IndexingParameters
• thread_extension : vg::Mapper
• THREAD_MAX_RETAINED_BYTES : vg::DozeuInterface
• thread_queue_byte_counts : vg::io::StreamMultiplexer
• thread_queue_empty_slots : vg::io::StreamMultiplexer
• thread_queue_filled_slots : vg::io::StreamMultiplexer
• thread_queue_mutexes : vg::io::StreamMultiplexer
• thread_queues : vg::io::StreamMultiplexer
• thread_streams : vg::io::StreamMultiplexer
• threads : HaplotypesConfig
• THREADS : vg::GAFSorterParameters
• threads : vg::GAFSorterParameters , vg::ReadFilter< Read >
• tick() : vg::Range< Number > , vg::ZipCodeTree::reverse_iterator
• tick_along_chain() : vg::Range< Number > , vg::subcommand::TickChainLink
• tick_along_chain_parent : vg::subcommand::TickChainLink
• tick_chain() : vg::subcommand::GroupedOptionGroup , vg::subcommand::OptionGroup< Receiver > , vg::subcommand::TickChainLink
• TickChainLink() : vg::subcommand::TickChainLink
• time : vg::MinimizerMapper::aligner_stats_t
• time_point : vg::Funnel , vg::Watchdog
• time_used : vg::Alignment
• timed_out : vg::Watchdog::thread_state_t
• timeout : vg::Watchdog
• TIP : handlegraph::SnarlDecomposition
• TipAnchoredMaxDistance() : vg::TipAnchoredMaxDistance
• tmpfstream_locks : vg::Packer
• tmpfstreams : vg::Packer
• to : vg::Alignment , vg::Edge , vg::RecombinatorFragment , vg::Translation , vg::WFATree
• to_alignment() : vg::ReadFilter< Read >
• to_anchor() : vg::MinimizerMapper
• to_anchors() : vg::MinimizerMapper
• to_backing() : vg::ExtraNodeGraph , vg::SourceSinkOverlay
• to_big_endian() : vg::endianness< IntType >
• to_correct : vg::Alignment
• to_dot() : vg::Funnel , vg::IndexRegistry , vg::IntegratedSnarlFinder::MergedAdjacencyGraph , vg::MultipathAlignmentGraph , vg::VG
• to_end : vg::Edge
• to_gfa() : xg::XG
• to_graph() : vg::Paths
• to_idx : vg::MEMClusterer::HitEdge
• to_json() : vg::Paths
• to_length : vg::Edit , vg::edit_t
• to_mapping() : vg::mapping_t
• to_matrix : vg::BandedGlobalAligner< IntType >::AltTracebackStack::Deflection
• to_node_id : vg::BandedGlobalAligner< IntType >::AltTracebackStack::Deflection
• to_number() : vg::BitString
• to_path() : vg::GaplessExtension , vg::MinimizerMapper , vg::WFAAlignment
• to_remove : GBWTConfig
• to_seed() : vg::GaplessExtender
• to_sequence() : vg::FragmentedHaplotypeVisit
• to_simple_reverse() : vg::FlowSort
• to_simple_reverse_orientation() : vg::FlowSort
• to_string() : ReferenceInterval , vg::BREAKPOINT , vg::Haplotypes::Subchain , vg::str_view
• to_swap : vg::SwapHaplotypesCommand
• to_turtle() : vg::VG
• to_vector() : vg::varint_vector_t , vg::ZipCode
• to_visit() : vg::NodeSide
• to_wfa_alignment() : vg::MinimizerMapper
• to_xg() : vg::VGset
• toggle_bit() : handlegraph::number_bool_packing
• top : haplo::int_itvl_t , vg::MatchPos::PathList , vg::ZipCodeTree::reverse_iterator
• top_border : vg::Viz
• top_diag : vg::BandedGlobalAligner< IntType >::BAMatrix
• top_down_genotype() : vg::LegacyCaller
• top_k : vg::PoissonSupportSnarlCaller
• top_level_chains : vg::Haplotypes::Header
• top_level_snarls() : vg::SnarlManager
• top_m : vg::PoissonSupportSnarlCaller
• top_tracebacks : vg::MultipathMapper
• topological_order : vg::BandedGlobalAligner< IntType > , vg::MEMClusterer::HitGraph
• topological_sort() : vg::MultipathAlignmentGraph
• total() : vg::MinimizerMapper::aligner_stats_t::stat_collection_t
• TOTAL_BITS : vg::BitString
• total_kmers : vg::Haplotypes::Header
• total_node_quality() : vg::Packer
• total_reference_paths() : vg::PrimerFinder
• total_seq_length : vg::BaseMapper , vg::NGSSimulator , vg::Sampler
• total_size : vg::RebuildJob
• total_subchains : vg::Haplotypes::Header
• total_supports() : vg::BREAKPOINT
• trace() : vg::DozeuInterface , vg::QualAdjXdropAligner , vg::SnarlState , vg::XdropAligner
• trace_haplotype() : vg::GenomeState
• trace_to_alignment() : vg::DeletionAligner
• traceback() : vg::AlignmentChainModel , vg::BandedGlobalAligner< IntType >::BAMatrix , vg::BandedGlobalAligner< IntType > , vg::DeletionAligner , vg::MEMChainModel
• traceback_over_edge() : vg::BandedGlobalAligner< IntType >::BAMatrix
• track_components : vg::MEMClusterer::HitGraph
• track_correctness : vg::MinimizerMapper
• track_position : vg::MinimizerMapper
• track_provenance : vg::MinimizerMapper
• Transcript() : vg::Transcript
• transcript_names : vg::TranscriptPath
• transcript_paths() : vg::Transcriptome
• transcript_tag : vg::Transcriptome
• Transcriptome() : vg::Transcriptome
• TranscriptPath() : vg::TranscriptPath
• transform() : vg::VGset
• transition_distrs_1 : vg::NGSSimulator
• transition_distrs_2 : vg::NGSSimulator
• transition_table : vg::DinucleotideMachine
• transitive_reduction() : vg::Surjector
• translate() : vg::Translator
• translate_back() : handlegraph::NamedNodeBackTranslation , vg::algorithms::GFAIDMapInfo , vg::FlatFileBackTranslation
• translate_down() : vg::PathSubgraph , vg::TreeSubgraph
• translate_node_ids() : vg::JoinedSpliceGraph
• translate_snarl_num() : vg::SnarlManager
• translate_through : vg::io::GafAlignmentEmitter
• translation : vg::BackTranslatingAlignmentEmitter , vg::VCFOutputCaller
• translations : vg::Translator
• translator : vg::AugmentedGraph , vg::Genotyper
• Translator() : vg::Translator
• trav : vg::MCMCCaller
• trav_padding : vg::GAFOutputCaller
• trav_sequence() : vg::VG
• trav_string() : vg::VCFOutputCaller
• traversal : vg::mapping_t
• traversal_alg : vg::Genotyper
• traversal_finder : vg::FlowCaller , vg::LegacyCaller , vg::NestedFlowCaller , vg::SmallSnarlSimplifier , vg::VCFGenotyper
• TraversalAlg : vg::Genotyper
• traversals_only : vg::FlowCaller , vg::NestedFlowCaller , vg::VCFGenotyper
• TraversalSupportFinder() : vg::TraversalSupportFinder
• traverse_computed_decomposition() : vg::IntegratedSnarlFinder
• traverse_decomposition() : vg::HandleGraphSnarlFinder , vg::IntegratedSnarlFinder
• traverse_edge_handle() : handlegraph::HandleGraph
• traverse_in_order() : vg::BitStringTree< Item > , vg::BitStringTree< Item >::TreeNode
• traverse_left() : vg::Paths
• traverse_right() : vg::Paths
• traverse_up() : vg::BitStringTree< Item > , vg::BitStringTree< Item >::TreeNode
• travs : vg::NestedFlowCaller::CallRecord
• travs_from() : vg::VG
• travs_of() : vg::VG
• travs_to() : vg::VG
• Tree() : vg::Tree< T >
• tree : vg::TreeSubgraph
• tree_item_t : vg::ZipCodeForest , vg::ZipCodeTree::tree_item_t
• tree_item_type_t : vg::ZipCodeForest , vg::ZipCodeTree
• TreeNode() : vg::TreeNode< T >
• trees : vg::ZipCodeForest
• TreeSubgraph() : vg::TreeSubgraph
• trim() : vg::WFATree
• trim_ambiguous_end() : vg::ReadFilter< Read >
• trim_ambiguous_ends() : vg::ReadFilter< Read >
• trim_and_check_for_empty() : vg::MultipathAlignmentGraph
• trim_hanging_indels() : vg::MultipathAlignmentGraph
• trim_indels : vg::Constructor
• trim_to_branch_points() : vg::MultipathAlignmentGraph
• trim_to_variable() : vg::Constructor
• TriviallySerializable() : handlegraph::TriviallySerializable
• TrivialTraversalFinder() : vg::TrivialTraversalFinder
• truncate_handle() : handlegraph::DeletableHandleGraph
• truncated_normal_distribution() : vg::truncated_normal_distribution< T >
• truncation_multiplicity_mq_limit : vg::MultipathMapper
• try_load_bare() : vg::io::VPKG
• try_load_encapsulated() : vg::io::VPKG
• try_load_first() : vg::io::VPKG
• try_load_first_bare() : vg::io::VPKG
• try_load_first_encapsulated() : vg::io::VPKG
• try_load_one() : vg::io::VPKG
• TSVAlignmentEmitter() : vg::io::TSVAlignmentEmitter
• TSVExplainer() : vg::TSVExplainer
• tumor_supports : vg::BREAKPOINT
• tv_path() : vg::TargetValueSearch
• tv_path_exists() : vg::TargetValueSearch
• tv_path_length() : vg::TargetValueSearch
• tv_phase2() : vg::TargetValueSearch
• tvs : vg::TVSClusterer
• TVSClusterer() : vg::TVSClusterer
• type : handlegraph::return_type_of< Returns(*)(Args...)> , handlegraph::return_type_of< Returns(Owner::*)(Args...) const > , handlegraph::return_type_of< Returns(Owner::*)(Args...)> , ReferenceInterval , vg::GFFRecord , vg::HaplotypePartitioner::Subchain , vg::Haplotypes::Subchain , vg::Range< Number > , vg::Snarl , vg::ZipCodeForest::child_info_t , vg::ZipCodeTree::tree_item_t
• type_as_char() : ReferenceInterval
• type_to_bare_loaders : vg::io::Registry::Tables
• type_to_saver : vg::io::Registry::Tables