Here is a list of all class members with links to the classes they belong to:
- r -
- R
: haplo::haplo_DP_rectangle
- r_iv
: xg::XG
- random()
: vg::Colors
, vg::Pictographs
, vg::ReadFilter::Counts
- 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 >
- rank
: vg::Mapping
, vg::mapping_t
, vg::PhasedGenome::iterator
- rank_by_support()
: vg::PoissonSupportSnarlCaller
- rank_in_parent()
: vg::SnarlSeedClusterer::NetgraphNode
- RANK_MASK
: vg::MIPayload
- RANK_OFFSET
: vg::MIPayload
- rank_to_handle()
: handlegraph::RankedHandleGraph
- rank_to_id()
: bdsg::ODGI
, handlegraph::RankedHandleGraph
, xg::XG
- rank_to_path()
: bdsg::ODGI
- RANK_WIDTH
: vg::MIPayload
- RareVariantSimplifier()
: vg::RareVariantSimplifier
- RatioSupportSnarlCaller()
: vg::RatioSupportSnarlCaller
- re_genotype()
: vg::LegacyCaller
- read
: hFILE_backend
, vg::ReadFilter::Counts
- read_best_left
: vg::SnarlSeedClusterer::NodeClusters
- read_best_right
: vg::SnarlSeedClusterer::NodeClusters
- read_cluster_dists
: vg::SnarlSeedClusterer::TreeState
- read_cluster_heads
: vg::SnarlSeedClusterer::NodeClusters
- read_coverage()
: vg::MultipathMapper
- read_coverage_z_score()
: vg::MultipathMapper
- read_distance_limit
: vg::SnarlSeedClusterer::TreeState
- read_group
: vg::Alignment
, vg::MinimizerMapper
, vg::MultipathAlignment
, vg::MultipathAlignmentEmitter
- read_index_offsets
: vg::SnarlSeedClusterer::TreeState
- read_interval
: vg::GaplessExtension
- read_log_likelihood()
: vg::PhasedGenome
- read_mapped
: vg::Alignment
- read_mapping()
: vg::PhaseUnfolder
- read_on_reverse_strand
: vg::Alignment
- read_paired
: vg::Alignment
- read_union_find
: vg::SnarlSeedClusterer::TreeState
- reader
: vg::WindowedVcfBuffer
- 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()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::MutableHandleGraph
, vg::VG
- rebuild_edge_indexes()
: vg::VG
- rebuild_indexes()
: vg::VG
- rebuild_mapping_aux()
: vg::Paths
- rebuild_node_mapping()
: vg::Paths
- recombination_penalty
: vg::BaseMapper
, vg::MultipathMapper
- 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_qualities
: vg::Packer
- record_read_pair_quality()
: vg::NGSSimulator
- record_read_quality()
: vg::NGSSimulator
- record_transition()
: vg::NGSSimulator::MarkovDistribution< From, To >
- 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_names
: vg::SRPE
- ref_offset
: vg::DozeuInterface::graph_pos_s
- ref_offsets
: vg::FlowCaller
, vg::LegacyCaller
, vg::MCMCCaller
- ref_path
: vg::FlowSort::Growth
- ref_path_handle
: haplo::linear_haplo_structure
- ref_path_lengths
: vg::MCMCCaller
- ref_path_offsets
: vg::MCMCCaller
- ref_path_set
: vg::FlowCaller
- ref_paths
: vg::Deconstructor
, vg::FlowCaller
, vg::GAFOutputCaller
, vg::LegacyCaller
, vg::MCMCCaller
- ref_position()
: haplo::linear_haplo_structure::SNVvector
- ref_positions
: haplo::linear_haplo_structure::SNVvector
- ref_span
: haplo::linear_haplo_structure
- refactor_split_alignment()
: vg::Filter
- reference_origin
: vg::TranscriptPath
- reference_paths
: vg::PhaseUnfolder
- reflect
: vg::GraphSynchronizer::Lock
- refpos
: vg::Alignment
- RegionExpander()
: vg::RegionExpander
- regions
: vg::HaplotypeIndexer
- register_bare_loader()
: vg::io::Registry
- register_bare_loader_saver()
: vg::io::Registry
- register_bare_loader_saver_with_magic()
: vg::io::Registry
- register_bare_loader_saver_with_magics()
: 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_loader()
: vg::io::Registry
- register_loader_saver()
: vg::io::Registry
- register_option()
: vg::Configurable
- register_protobuf()
: vg::io::Registry
- register_sampled_position()
: vg::NGSSimulator
- register_saver()
: vg::io::Registry
- regular_aligner
: vg::AlignerClient
- regularize()
: vg::SnarlManager
- release()
: json_autoptr
- remap()
: vg::Filter
, vg::Homogenizer
- remember_kmer_size()
: vg::Index
- remove()
: bdsg::HashGraph::path_t
, vg::PhasedGenome
- remove_bonuses()
: vg::GSSWAligner
- remove_clipped_portion()
: vg::Filter
- remove_duplicated_in()
: vg::VG
- remove_duplicates()
: vg::VG
- remove_edge()
: vg::FlowSort
- remove_edge_reference()
: bdsg::PackedGraph
- 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()
: 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_transitive_edges()
: vg::MultipathAlignmentGraph
- rename_variants
: vg::HaplotypeIndexer
- reorder_adjacency_lists()
: vg::MultipathAlignmentGraph
- reorder_exons()
: vg::Transcriptome
- repeat
: vg::ReadFilter::Counts
- repeat_size
: vg::ReadFilter
- replace_local_haplotype()
: vg::GenomeState
- replace_mapping()
: vg::Paths
- replace_occurrence()
: vg::PathIndex
- replace_snarl_haplotype()
: vg::GenomeState
- report_affinities()
: vg::Genotyper
- report_group_mapq
: vg::MultipathMapper
- report_memory()
: bdsg::PackedGraph
- report_snarl()
: vg::Genotyper
- report_snarl_traversal()
: vg::Genotyper
- Representative
: vg::Genotyper
- RepresentativeTraversalFinder()
: vg::RepresentativeTraversalFinder
- rescore
: vg::ReadFilter
- rescue_algorithm
: vg::MinimizerMapper
- rescue_dozeu
: vg::MinimizerMapper
- rescue_graph_std_devs
: vg::MultipathMapper
- rescue_gssw
: vg::MinimizerMapper
- rescue_haplotypes
: 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_subgraph_stdevs
: vg::MinimizerMapper
- RescueAlgorithm
: vg::MinimizerMapper
- resect_snarls_from_paths()
: vg::MultipathAlignmentGraph
- reserved
: vg::Alignment
- reset()
: vg::discrete_distribution< T >
, vg::normal_distribution< T >
, vg::Range< Number >
, vg::ReadFilter::Counts
, vg::uniform_int_distribution< T >
, vg::uniform_real_distribution< T >
- reset_chain()
: vg::Range< Number >
- reset_chain_parent
: vg::Range< Number >
- reset_options()
: vg::Index
- resize_indexes()
: vg::VG
- restore_paths()
: vg::PhaseUnfolder
- restrained_graph_extraction
: vg::MultipathMapper
- result_type
: vg::discrete_distribution< T >
, vg::normal_distribution< T >
, vg::uniform_int_distribution< T >
, vg::uniform_real_distribution< T >
, vg::WideningPRNG< PRNG, OutType >
- retry_on_Ns
: vg::NGSSimulator
- rev_in_chain
: vg::SnarlSeedClusterer::Seed
- rev_in_parent
: vg::MinimumDistanceIndex::ChainIndex
, vg::MinimumDistanceIndex::SnarlIndex
- REV_OFFSET
: vg::MIPayload
- reverse()
: vg::NodeTraversal
, vg::Support
- reverse_adjacencies()
: vg::Surjector
- 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_self_edge_records
: bdsg::PackedGraph
- reversing_walk_length
: vg::MultipathMapper
- rewrite_segment()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::MutablePathHandleGraph
, vg::VG
- rho
: haplo::haploMath::RRMemo
- right
: vg::Support
- right_degree()
: vg::VG
- right_edges
: bdsg::HashGraph::node_t
- 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::Pictographs
, vg::Sampler
- robust_estimation_fraction
: vg::FragmentLengthDistribution
- root
: vg::BitStringTree< Item >
, vg::Tree< T >
- root_chains
: vg::SnarlManager
- 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_genotype()
: vg::MCMCGenotyper
- running
: vg::Range< Number >
- runs
: vg::BenchmarkResult