Here is a list of all variables 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_engine : vg::MCMCGenotyper
- range : vg::MaximalExactMatch
- 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
- reachable_with_gap : vg::WFATree::ScoreProperties
- read : hFILE_backend, vg::alignment_index_t
- 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_group : vg::Alignment, vg::MinimizerMapper, vg::MultipathAlignment, vg::MultipathAlignmentEmitter
- read_interval : vg::GaplessExtension
- read_mapped : vg::Alignment
- read_num : vg::SnarlDistanceIndexClusterer::ClusterHead
- read_offset : MappingRun
- read_on_reverse_strand : vg::Alignment
- read_paired : vg::Alignment
- read_union_find : vg::SnarlDistanceIndexClusterer::ClusteringProblem
- reader : vg::ParallelKFFReader, vg::WindowedVcfBuffer
- reads_by_name : vg::PathRestrictedTraversalFinder
- realign_indels : vg::Genotyper
- recipe_registry : vg::IndexRegistry
- recoding : vg::ParallelKFFReader
- recombination_penalty : vg::BaseMapper, vg::MultipathMapper
- recombinator_parameters : HaplotypesConfig
- record_bases : vg::Packer
- record_edges : vg::Packer
- record_edits : vg::Packer
- record_offset : vg::MIPayloadValues
- record_qualities : vg::Packer
- redundant_vertexes : vg::AlignmentChainModel, vg::MEMChainModel
- 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_positions : haplo::linear_haplo_structure::SNVvector
- ref_samples : vg::Deconstructor
- ref_steps : vg::ParentGenotypeInfo
- ref_trav_idx : vg::NestedFlowCaller::CallRecord
- ref_traversal : vg::ParentGenotypeInfo
- reference_paths : vg::PhaseUnfolder
- reflect : vg::GraphSynchronizer::Lock
- refpos : vg::Alignment
- regions : vg::Funnel::PaintableSpace, vg::HaplotypeIndexer
- registered_suffixes : vg::IndexRegistry
- registry : vg::IndexingPlan
- regular_aligner : vg::AlignerClient
- remove_failing_edits : vg::Filter
- rename_variants : vg::HaplotypeIndexer
- repeat_size : vg::ReadFilter< Read >
- report_allelic_mapq : vg::MultipathMapper
- report_group_mapq : vg::MultipathMapper
- rescore : vg::ReadFilter< Read >
- rescue_algorithm : vg::MinimizerMapper
- rescue_graph_std_devs : vg::MultipathMapper
- rescue_only_anchor_max : vg::MultipathMapper
- rescue_only_min : vg::MultipathMapper
- rescue_seed_limit : vg::MinimizerMapper
- rescue_subgraph_stdevs : vg::MinimizerMapper
- RESCUED : vg::MultipathMapper
- reseed_search_distance : vg::MinimizerMapper
- reserved : vg::Alignment
- reset_chain_parent : vg::subcommand::TickChainLink
- restrained_graph_extraction : vg::MultipathMapper
- retry_on_Ns : vg::NGSSimulator
- reverse : vg::Support
- reversing_walk_length : vg::MultipathMapper
- rgfa_listeners : vg::algorithms::GFAParser
- rho : haplo::haploMath::RRMemo
- right : vg::Support
- right_ends : vg::ConstructedChunk
- right_full : vg::GaplessExtension
- right_handle_trans : vg::JoinedSpliceGraph
- right_maximal : vg::GaplessExtension
- right_splice_offset : vg::JoinedSpliceGraph
- right_subgraph : vg::JoinedSpliceGraph
- right_telomere_node : vg::PhasedGenome::Haplotype
- 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
- row_idx : vg::BandedGlobalAligner< IntType >::AltTracebackStack::Deflection
- rr_memos : vg::MultipathMapper
- running : vg::Range< Number >
- runs : vg::BenchmarkResult