Here is a list of all class members with links to the classes they belong to:
- r -
- R : haplo::haplo_DP_rectangle
- r_index : vg::HaplotypePartitioner
- r_index_name : GBWTConfig, HaplotypesConfig
- r_iv : xg::XG
- random() : vg::Colors, vg::Counts, vg::Pictographs
- random_engine : vg::MCMCGenotyper
- random_match_length() : vg::BaseMapper
- random_match_p_value() : vg::MultipathMapper
- random_read() : vg::VG
- range() : vg::io::MessageIterator, vg::io::ProtobufIterator< T >, vg::MaximalExactMatch
- Range() : vg::Range< Number >
- RANGE_END_MATCH : handlegraph::PathMetadata
- RANGE_END_SEPARATOR : handlegraph::PathMetadata
- RANGE_START_MATCH : handlegraph::PathMetadata
- RANGE_START_SEPARATOR : handlegraph::PathMetadata
- range_table : vg::MEMAccelerator
- RANGE_TERMINATOR : handlegraph::PathMetadata
- rank : vg::Mapping, vg::mapping_t, vg::PhasedGenome::iterator
- rank_by_support() : vg::PoissonSupportSnarlCaller
- rank_to_handle() : handlegraph::RankedHandleGraph
- rank_to_id() : handlegraph::RankedHandleGraph, xg::XG
- RareVariantSimplifier() : vg::RareVariantSimplifier
- RatioSupportSnarlCaller() : vg::RatioSupportSnarlCaller
- re_genotype() : vg::LegacyCaller
- reachable_with_gap : vg::WFATree::ScoreProperties
- read : hFILE_backend, vg::alignment_index_t, vg::Counts, vg::ParallelKFFReader
- read_1_adapter : vg::MultipathMapper
- read_1_adapter_lps : vg::MultipathMapper
- read_2_adapter : vg::MultipathMapper
- read_2_adapter_lps : vg::MultipathMapper
- read_best_left : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
- read_best_right : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
- read_cluster_heads : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
- read_distance_limit : vg::SnarlDistanceIndexClusterer::ClusteringProblem
- read_end() : vg::algorithms::Anchor
- read_group : vg::Alignment, vg::MinimizerMapper, vg::MultipathAlignment, vg::MultipathAlignmentEmitter
- read_interval : vg::GaplessExtension
- read_log_likelihood() : vg::PhasedGenome
- read_mapped : vg::Alignment
- read_mapping() : vg::PhaseUnfolder
- read_num : vg::SnarlDistanceIndexClusterer::ClusterHead
- read_offset : MappingRun
- read_on_reverse_strand : vg::Alignment
- read_paired : vg::Alignment
- read_start() : vg::algorithms::Anchor
- read_union_find : vg::SnarlDistanceIndexClusterer::ClusteringProblem
- reader : vg::ParallelKFFReader, vg::WindowedVcfBuffer
- ReadMasker() : vg::ReadMasker
- ReadRestrictedTraversalFinder() : vg::ReadRestrictedTraversalFinder
- Reads : vg::Genotyper
- reads_by_name : vg::PathRestrictedTraversalFinder
- realign_indels : vg::Genotyper
- realigning_surject() : vg::Surjector
- reassign_node() : vg::Paths
- reassign_node_ids() : handlegraph::MutableHandleGraph, vg::VG
- reassign_split_clusters() : vg::MultipathMapper
- rebuild_edge_indexes() : vg::VG
- rebuild_indexes() : vg::VG
- rebuild_mapping_aux() : vg::Paths
- rebuild_node_mapping() : vg::Paths
- recipe_registry : vg::IndexRegistry
- recoding : vg::ParallelKFFReader
- recombination_penalty : vg::BaseMapper, vg::MultipathMapper
- Recombinator() : vg::Recombinator
- recombinator_parameters : HaplotypesConfig
- record() : vg::SnarlManager
- record_bases : vg::Packer
- record_edges : vg::Packer
- record_edits : vg::Packer
- record_fanouts() : vg::MultipathMapper
- record_fragment_configuration() : vg::FragmentLengthStatistics
- record_offset() : vg::MIPayload, vg::MIPayloadValues
- record_qualities : vg::Packer
- record_read_pair_quality() : vg::NGSSimulator
- record_read_quality() : vg::NGSSimulator
- record_transition() : vg::NGSSimulator::MarkovDistribution< From, To >
- recover_log_base() : vg::GSSWAligner
- RecurseAlways : vg::GraphCaller
- RecurseNever : vg::GraphCaller
- RecurseOnFail : vg::GraphCaller
- RecurseType : vg::GraphCaller
- recursively_emit_snarls() : vg::CactusSnarlFinder
- reduce_to_single_path() : vg::MultipathMapper
- redundant_vertexes : vg::AlignmentChainModel, vg::MEMChainModel
- reencode_old_g_vector() : xg::XG
- reestimation_frequency : vg::FragmentLengthDistribution
- ref_base : vg::BasePileup
- ref_offset : vg::DozeuInterface::graph_pos_s
- ref_offsets : vg::FlowCaller, vg::LegacyCaller, vg::MCMCCaller, vg::NestedFlowCaller
- ref_path : vg::FlowSort::Growth
- ref_path_handle : haplo::linear_haplo_structure
- ref_path_handles : vg::MultipathMapper
- ref_path_interval : vg::NestedFlowCaller::CallRecord
- ref_path_lengths : vg::MCMCCaller
- ref_path_name : vg::NestedFlowCaller::CallRecord
- ref_path_offsets : vg::MCMCCaller
- ref_path_set : vg::FlowCaller, vg::NestedFlowCaller
- ref_paths : vg::Deconstructor, vg::FlowCaller, vg::GAFOutputCaller, vg::LegacyCaller, vg::MCMCCaller, vg::NestedFlowCaller, vg::Recombinator::Statistics
- ref_ploidies : vg::FlowCaller, vg::LegacyCaller, vg::NestedFlowCaller
- ref_position() : haplo::linear_haplo_structure::SNVvector
- ref_positions : haplo::linear_haplo_structure::SNVvector
- ref_samples : vg::Deconstructor
- ref_span : haplo::linear_haplo_structure
- ref_steps : vg::ParentGenotypeInfo
- ref_trav_idx : vg::NestedFlowCaller::CallRecord
- ref_traversal : vg::ParentGenotypeInfo
- refactor_split_alignment() : vg::Filter
- reference : vg::count_back_inserter< T >, vg::VectorView< Item >::const_iterator
- reference_paths : vg::PhaseUnfolder
- reference_transcript_paths() : vg::Transcriptome
- reflect : vg::GraphSynchronizer::Lock
- refpos : vg::Alignment
- RegionExpander() : vg::RegionExpander
- regions : vg::Funnel::PaintableSpace, vg::HaplotypeIndexer
- register_alias() : vg::AliasGraph
- register_bare_loader() : vg::io::Registry
- register_bare_loader_saver() : vg::io::Registry
- register_bare_loader_saver_with_header_check() : vg::io::Registry
- register_bare_loader_saver_with_magic() : vg::io::Registry
- register_bare_loader_saver_with_magic_and_filename() : vg::io::Registry
- register_bare_loader_saver_with_magics() : vg::io::Registry
- register_bare_loader_with_filename() : vg::io::Registry
- register_barrier() : vg::io::StreamMultiplexer
- register_breakpoint() : vg::io::StreamMultiplexer
- register_configurable() : vg::ConfigurableParser
- register_everything() : vg::io::Registry
- register_fragment_length() : vg::FragmentLengthDistribution
- register_generalization() : vg::IndexRegistry
- register_index() : vg::IndexRegistry
- register_loader() : vg::io::Registry
- register_loader_saver() : vg::io::Registry
- register_option() : vg::Configurable
- register_protobuf() : vg::io::Registry
- register_recipe() : vg::IndexRegistry
- register_sampled_position() : vg::NGSSimulator
- register_saver() : vg::io::Registry
- registered_suffixes : vg::IndexRegistry
- registry : vg::IndexingPlan
- regular_aligner : vg::AlignerClient
- regularize() : vg::SnarlManager
- release() : json_autoptr
- remap() : vg::Filter
- remove() : vg::PhasedGenome
- remove_bonuses() : vg::GSSWAligner
- remove_clipped_portion() : vg::Filter
- remove_directory() : vg::temp_file::Handler
- remove_dominated_chunks() : vg::Surjector
- remove_duplicated_in() : vg::VG
- remove_duplicates() : vg::VG
- remove_edge() : vg::FlowSort
- remove_edit_tmpfiles() : vg::Packer
- remove_failing_edits : vg::Filter
- remove_full_length_bonuses() : vg::Mapper
- remove_inverting_edges() : vg::VG
- remove_mapping() : vg::Paths
- remove_node() : vg::Paths
- remove_node_forwarding_edges() : vg::VG
- remove_non_path() : vg::VG
- remove_non_transcribed_nodes() : vg::Transcriptome
- remove_null_nodes() : vg::VG
- remove_null_nodes_forwarding_edges() : vg::VG
- remove_orphan_edges() : vg::VG
- remove_path() : vg::Paths, vg::VG
- remove_paths() : vg::Paths
- remove_redundant_transcript_paths() : vg::Transcriptome
- remove_transitive_edges() : vg::MultipathAlignmentGraph
- rename_path() : handlegraph::MutablePathHandleGraph
- rename_variants : vg::HaplotypeIndexer
- reorder_adjacency_lists() : vg::MultipathAlignmentGraph
- reorder_exons() : vg::Transcriptome
- repeat : vg::Counts
- repeat_size : vg::ReadFilter< Read >
- repetitiveness() : vg::SeqComplexity< MaxOrder >
- replace_local_haplotype() : vg::GenomeState
- replace_mapping() : vg::Paths
- replace_occurrence() : vg::PathIndex
- replace_snarl_haplotype() : vg::GenomeState
- report_affinities() : vg::Genotyper
- report_allelic_mapq : vg::MultipathMapper
- report_group_mapq : vg::MultipathMapper
- report_snarl() : vg::Genotyper
- report_snarl_traversal() : vg::Genotyper
- Representative : vg::Genotyper
- RepresentativeTraversalFinder() : vg::RepresentativeTraversalFinder
- require() : vg::IndexRegistry
- rescore : vg::ReadFilter< Read >
- rescue_algorithm : vg::MinimizerMapper
- rescue_dozeu : vg::MinimizerMapper
- rescue_graph_std_devs : vg::MultipathMapper
- rescue_gssw : vg::MinimizerMapper
- rescue_high_count_order_length_mems() : vg::BaseMapper
- rescue_none : vg::MinimizerMapper
- rescue_only_anchor_max : vg::MultipathMapper
- rescue_only_min : vg::MultipathMapper
- rescue_seed_limit : vg::MinimizerMapper
- rescue_subgraph_stdevs : vg::MinimizerMapper
- RescueAlgorithm : vg::MinimizerMapper
- RESCUED : vg::MultipathMapper
- resect_snarls_from_paths() : vg::MultipathAlignmentGraph
- reseed_between() : vg::MinimizerMapper
- reseed_search_distance : vg::MinimizerMapper
- reserved : vg::Alignment
- reset() : vg::Counts, vg::discrete_distribution< T >, vg::IndexFile, vg::IndexRegistry, vg::normal_distribution< T >, vg::Range< Number >, vg::truncated_normal_distribution< T >, vg::uniform_int_distribution< T >, vg::uniform_real_distribution< T >
- reset_chain() : vg::Range< Number >, vg::subcommand::TickChainLink
- reset_chain_parent : vg::subcommand::TickChainLink
- resize_indexes() : vg::VG
- restore_paths() : vg::PhaseUnfolder
- restrained_graph_extraction : vg::MultipathMapper
- result_type : vg::discrete_distribution< T >, vg::normal_distribution< T >, vg::truncated_normal_distribution< T >, vg::uniform_int_distribution< T >, vg::uniform_real_distribution< T >, vg::WideningPRNG< PRNG, OutType >
- retry_on_Ns : vg::NGSSimulator
- retry_pairing_spliced_alignments() : vg::MultipathMapper
- Reverse : vg::MultipathMapper
- reverse() : vg::NodeTraversal, vg::Support
- reverse_adjacencies() : vg::Surjector
- reverse_alignment() : vg::MultipathAlignmentGraph
- reverse_complement_graph() : vg::VG
- reverse_edge() : vg::FlowSort
- reverse_from_start_to_end_edge() : vg::FlowSort
- ReverseGraph() : vg::ReverseGraph
- reversing_filter() : vg::Filter
- reversing_walk_length : vg::MultipathMapper
- RewindPlanException() : vg::RewindPlanException
- rewrite_segment() : handlegraph::MutablePathHandleGraph, vg::VG
- rgfa_listeners : vg::algorithms::GFAParser
- rho : haplo::haploMath::RRMemo
- right : vg::Support
- right_degree() : vg::VG
- right_ends : vg::ConstructedChunk
- right_full : vg::GaplessExtension
- right_handle_trans : vg::JoinedSpliceGraph
- right_maximal : vg::GaplessExtension
- right_seed_node() : vg::JoinedSpliceGraph
- right_splice_node() : vg::JoinedSpliceGraph
- right_splice_offset : vg::JoinedSpliceGraph
- right_subgraph : vg::JoinedSpliceGraph
- right_telomere_node : vg::PhasedGenome::Haplotype
- ring_buffer_empty() : vg::io::StreamMultiplexer
- ring_buffer_full() : vg::io::StreamMultiplexer
- ring_buffer_peek() : vg::io::StreamMultiplexer
- ring_buffer_pop() : vg::io::StreamMultiplexer
- ring_buffer_push() : vg::io::StreamMultiplexer
- RING_BUFFER_SIZE : vg::io::StreamMultiplexer
- rng : vg::Colors, vg::LazyRNG, vg::Pictographs, vg::Sampler
- robust_estimation_fraction : vg::FragmentLengthDistribution
- root : vg::BitStringTree< Item >, vg::Tree< T >
- root_chains : vg::SnarlManager
- root_children : vg::SnarlDistanceIndexClusterer::ClusteringProblem
- root_trim : vg::TreeSubgraph
- roots : vg::SnarlManager
- round_outward() : vg::PathIndex
- row_idx : vg::BandedGlobalAligner< IntType >::AltTracebackStack::Deflection
- rr_memos : vg::MultipathMapper
- RRMemo() : haplo::haploMath::RRMemo
- run() : vg::Genotyper
- run_dp() : vg::DeletionAligner
- run_genotype() : vg::MCMCGenotyper
- running : vg::Range< Number >
- runs : vg::BenchmarkResult