- r -

• radix_sort_zipcodes() : vg::ZipCodeForest
• random() : vg::Colors , vg::Pictographs
• random_match_length() : vg::BaseMapper
• random_match_p_value() : vg::MultipathMapper
• random_read() : vg::VG
• range() : vg::io::MessageIterator , vg::io::ProtobufIterator< T >
• Range() : vg::Range< Number >
• 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
• read() : vg::GAFSorterFile , vg::ParallelKFFReader
• read_end() : vg::algorithms::Anchor
• read_exclusion_end() : vg::algorithms::Anchor
• read_exclusion_start() : vg::algorithms::Anchor
• read_line() : vg::GAFSorterRecord
• read_log_likelihood() : vg::PhasedGenome
• read_mapping() : vg::PhaseUnfolder
• read_start() : vg::algorithms::Anchor
• ReadMasker() : vg::ReadMasker
• ReadRestrictedTraversalFinder() : vg::ReadRestrictedTraversalFinder
• 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
• Recombinator() : vg::Recombinator
• RecombinatorFragment() : vg::RecombinatorFragment
• RecombinatorHaplotype() : vg::RecombinatorHaplotype
• record() : vg::SnarlManager
• record_fanouts() : vg::MultipathMapper
• record_fragment_configuration() : vg::FragmentLengthStatistics
• record_read_pair_quality() : vg::NGSSimulator
• record_read_quality() : vg::NGSSimulator
• record_transition() : vg::NGSSimulator::MarkovDistribution< From, To >
• recover_log_base() : vg::GSSWAligner
• recursively_emit_snarls() : vg::CactusSnarlFinder
• reduce_to_single_path() : vg::MultipathMapper
• reencode_old_g_vector() : xg::XG
• ref_position() : haplo::linear_haplo_structure::SNVvector
• refactor_split_alignment() : vg::Filter
• reference_transcript_paths() : vg::Transcriptome
• RegionExpander() : vg::RegionExpander
• 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
• 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_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
• rename_path() : handlegraph::MutablePathHandleGraph
• rend() : vg::ZipCodeTree
• reorder_adjacency_lists() : vg::MultipathAlignmentGraph
• reorder_exons() : vg::Transcriptome
• 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_snarl() : vg::Genotyper
• report_snarl_traversal() : vg::Genotyper
• RepresentativeTraversalFinder() : vg::RepresentativeTraversalFinder
• require() : vg::IndexRegistry
• rescue_high_count_order_length_mems() : vg::BaseMapper
• resect_snarls_from_paths() : vg::MultipathAlignmentGraph
• 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_chain() : vg::subcommand::GroupedOptionGroup , vg::subcommand::OptionGroup< Receiver > , vg::subcommand::TickChainLink
• resize_indexes() : vg::VG
• restore_paths() : vg::PhaseUnfolder
• retry_pairing_spliced_alignments() : vg::MultipathMapper
• reverse() : vg::NodeTraversal
• 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
• RewindPlanException() : vg::RewindPlanException
• rewrite_segment() : handlegraph::MutablePathHandleGraph , vg::VG
• right_degree() : vg::VG
• right_seed_node() : vg::JoinedSpliceGraph
• right_splice_node() : vg::JoinedSpliceGraph
• 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
• round_outward() : vg::PathIndex
• RRMemo() : haplo::haploMath::RRMemo
• run() : vg::Genotyper
• run_dp() : vg::DeletionAligner
• run_genotype() : vg::MCMCGenotyper