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
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
tags : GBWTConfig, vg::Haplotypes
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::RecombinatorHaplotype
target : vg::InsufficientInputException
target_alignment_attempts : vg::MinimizerMapper
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
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
text_visit_iteratee_t : vg::algorithms::GFAParser
text_visit_source_t : vg::algorithms::GFAParser
thin_alignment_cutoff : vg::VariantAdder
thread_chunk_inflation_factor : vg::IndexingParameters
thread_extension : vg::Mapper
THREAD_MAX_RETAINED_BYTES : vg::DozeuInterface
THREADS : vg::GAFSorterParameters
threads : HaplotypesConfig, MinimizerConfig, vg::GAFSorterParameters, vg::ReadFilter< Read >
threshold : vg::MinimizerIndexParameters
tick() : vg::Range< Number >, vg::ZipCodeTree::distance_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
timed_out : vg::Watchdog::thread_state_t
timeout : vg::Watchdog
TipAnchoredMaxDistance() : vg::TipAnchoredMaxDistance
tmpfstream_locks : vg::Packer
tmpfstreams : vg::Packer
to : vg::RecombinatorFragment, vg::WFATree
to_alignment() : vg::ReadFilter< Read >
to_anchor : vg::algorithms::transition_info, vg::MinimizerMapper
to_anchors() : vg::MinimizerMapper
to_backing() : vg::SourceSinkOverlay
to_dot() : vg::Funnel, vg::IndexRegistry, vg::IntegratedSnarlFinder::MergedAdjacencyGraph, vg::MultipathAlignmentGraph, vg::VG
to_graph() : vg::Paths
to_idx : vg::MEMClusterer::HitEdge
to_json() : vg::Paths
to_length() : 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::Haplotypes::Subchain
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
top : haplo::int_itvl_t, vg::MatchPos::PathList, vg::ZipCodeTree::distance_iterator
top_border : vg::Viz
top_diag : vg::BandedGlobalAligner< IntType >::BAMatrix
top_down_genotype() : vg::LegacyCaller
top_k : vg::PoissonSupportSnarlCaller
top_level_chains : vg::GrefCover::TopLevelSnarlStats, vg::Haplotypes::Header
top_level_snarl_stats : vg::GrefCover
top_level_snarls : vg::GrefCover::TopLevelSnarlStats, 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_overlap() : vg::Surjector
total_reference_paths() : vg::PrimerFinder
total_seq_length : vg::BaseMapper, vg::NGSSimulator, vg::Sampler
total_size() : vg::IntervalUnion, vg::RebuildJob
total_subchains : vg::Haplotypes::Header
trace() : vg::DozeuInterface, vg::QualAdjXdropAligner, vg::XdropAligner
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_info() : vg::algorithms::transition_info
transition_table : vg::DinucleotideMachine
transitive_reduction() : vg::Surjector
translate() : vg::Translator
translate_back() : vg::algorithms::GFAIDMapInfo, vg::FlatFileBackTranslation
translate_down() : vg::PathSubgraph, vg::TreeSubgraph
translate_node_ids() : vg::JoinedSpliceGraph
translate_snarl_num() : vg::SnarlManager
translation : vg::BackTranslatingAlignmentEmitter, vg::VCFOutputCaller
translations : vg::Translator
Translator() : vg::Translator
translator : vg::AugmentedGraph, vg::Genotyper
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_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
TrivialTraversalFinder() : vg::TrivialTraversalFinder
truncated_normal_distribution() : vg::truncated_normal_distribution< T >
truncation_multiplicity_mq_limit : vg::MultipathMapper
TSVExplainer() : vg::TSVExplainer
tv_path() : vg::TargetValueSearch
tv_path_exists() : vg::TargetValueSearch
tv_path_length() : vg::TargetValueSearch
tv_phase2() : vg::TargetValueSearch
tvs : vg::TVSClusterer
TVSClusterer() : vg::TVSClusterer
two_merge_rounds : vg::GAFSorterParameters
type : ReferenceInterval, vg::GFFRecord, vg::HaplotypePartitioner::Subchain, vg::Haplotypes::Subchain, vg::Range< Number >, vg::ZipCodeForest::child_info_t, vg::ZipCodeTree::tree_item_t
type_as_char() : ReferenceInterval