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
- 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_mode : GBWTConfig
- thread_names : GBWTConfig
- thread_output : GBWTConfig
- 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, vg::ReadFilter< Read >
- tick() : vg::Range< Number >
- tick_chain() : vg::Range< Number >, vg::subcommand::TickChainLink
- tick_chain_parent : vg::subcommand::TickChainLink
- 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::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_simple_reverse() : vg::FlowSort
- to_simple_reverse_orientation() : vg::FlowSort
- to_string() : ReferenceInterval, vg::BREAKPOINT, vg::Haplotypes::Subchain
- to_swap : vg::SwapHaplotypesCommand
- to_turtle() : vg::VG
- 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
- 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_BITS : vg::BitString
- total_kmers : vg::Haplotypes::Header
- total_node_quality() : vg::Packer
- 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_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
- TreeNode() : vg::TreeNode< T >
- 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
- 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
- type_to_bare_loaders : vg::io::Registry::Tables
- type_to_saver : vg::io::Registry::Tables