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 , vg::PrimerFinder
• r_index_name : GBWTConfig , HaplotypesConfig
• r_iv : xg::XG
• radix_sort_zipcodes() : vg::ZipCodeForest
• 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_in_chain : vg::FragmentedHaplotypeVisit
• rank_in_sequence : vg::FragmentedHaplotypeVisit
• rank_to_handle() : handlegraph::RankedHandleGraph
• rank_to_id() : handlegraph::RankedHandleGraph , xg::XG
• RareVariantSimplifier() : vg::RareVariantSimplifier
• RatioSupportSnarlCaller() : vg::RatioSupportSnarlCaller
• raw_gaf : vg::GAFSorterFile
• re_genotype() : vg::LegacyCaller
• reachable_with_gap : vg::WFATree::ScoreProperties
• read : hFILE_backend , vg::alignment_index_t , vg::Counts , vg::GAFSorterFile , 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_exclusion_end() : vg::algorithms::Anchor
• read_exclusion_start() : vg::algorithms::Anchor
• read_group : vg::Alignment , vg::MinimizerMapper , vg::MultipathAlignment , vg::MultipathAlignmentEmitter
• read_interval : vg::GaplessExtension
• read_line() : vg::GAFSorterRecord
• 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_TOO_SHORT : vg::AlignmentValidity
• 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 : vg::RecombinatorHaplotype
• recombinator_parameters : HaplotypesConfig
• RecombinatorFragment() : vg::RecombinatorFragment
• RecombinatorHaplotype() : vg::RecombinatorHaplotype
• 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::ZipCode::snarl_code_t
• record_qualities : vg::Packer
• record_read_pair_quality() : vg::NGSSimulator
• record_read_quality() : vg::NGSSimulator
• record_transition() : vg::NGSSimulator::MarkovDistribution< From, To >
• records : vg::GAFSorterFile
• RECORDS_PER_FILE : vg::GAFSorterParameters
• records_per_file : vg::GAFSorterParameters
• 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_sample : HaplotypesConfig
• 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_samples : HaplotypesConfig
• 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
• REGULAR_SNARL : vg::ZipCode
• REGULAR_SNARL_IS_REVERSED_OFFSET : vg::ZipCode
• REGULAR_SNARL_SIZE : vg::ZipCode
• regularize() : vg::SnarlManager
• release() : json_autoptr
• remaining_tree() : vg::ZipCodeTree::iterator
• 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_temporary() : vg::GAFSorterFile
• remove_transitive_edges() : vg::MultipathAlignmentGraph
• removed : vg::GAFSorterFile
• rename_path() : handlegraph::MutablePathHandleGraph
• rename_variants : vg::HaplotypeIndexer
• rend() : vg::ZipCodeTree , vg::ZipCodeTree::reverse_iterator
• 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_likelihood_limit : vg::MinimizerMapper
• 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
• 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_along_chain() : vg::Range< Number > , vg::subcommand::TickChainLink
• reset_along_chain_parent : vg::subcommand::TickChainLink
• reset_chain() : vg::subcommand::GroupedOptionGroup , vg::subcommand::OptionGroup< Receiver > , 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
• reverse_iterator() : vg::ZipCodeTree::reverse_iterator
• 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_primer : vg::PrimerPair
• 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_CHAIN : vg::ZipCode
• ROOT_CHAIN_COMPONENT_COUNT_OFFSET : vg::ZipCode
• ROOT_CHAIN_SIZE : vg::ZipCode
• root_chains : vg::SnarlManager
• root_children : vg::SnarlDistanceIndexClusterer::ClusteringProblem
• ROOT_IDENTIFIER_OFFSET : vg::ZipCode
• ROOT_IS_CHAIN_OFFSET : vg::ZipCode
• ROOT_NODE : vg::ZipCode
• ROOT_NODE_LENGTH_OFFSET : vg::ZipCode
• ROOT_NODE_OR_CHAIN_CONNECTIVITY_OR_LENGTH_OFFSET : vg::ZipCode
• ROOT_NODE_SIZE : vg::ZipCode
• ROOT_SNARL : vg::ZipCode
• ROOT_SNARL_SIZE : vg::ZipCode
• 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