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, vg::PrimerFinder
r_index_name : GBWTConfig, HaplotypesConfig
random_engine : vg::MCMCGenotyper
range : vg::MaximalExactMatch
range_table : vg::MEMAccelerator
rank : vg::mapping_t, vg::PhasedGenome::iterator, vg::ZipCodeForest::seed_info_t
rank_in_chain : vg::FragmentedHaplotypeVisit
rank_in_sequence : vg::FragmentedHaplotypeVisit
raw_gaf : vg::GAFSorterFile
reachable_with_gap : vg::WFATree::ScoreProperties
read : vg::MinimizerMapper::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::MinimizerMapper, vg::MultipathAlignmentEmitter
read_interval : vg::GaplessExtension
read_length_prop_disjoint_gap : vg::Surjector
read_num : vg::SnarlDistanceIndexClusterer::ClusterHead
read_offset : MappingRun
read_union_find : vg::SnarlDistanceIndexClusterer::ClusteringProblem
reader : vg::ParallelKFFReader, vg::WindowedVcfBuffer
reads_by_name : vg::PathRestrictedTraversalFinder
realign_indels : vg::Genotyper
rec_consistency_bonus : vg::MinimizerMapper
rec_intervals : vg::algorithms::ChainWithRec
rec_num : vg::algorithms::TracedScore
rec_penalty : vg::MinimizerMapper
rec_penalty_aln : vg::MinimizerMapper
rec_positions : vg::algorithms::ChainWithRec
recipe_registry : vg::IndexRegistry
recoding : vg::ParallelKFFReader
recombination_penalty : vg::algorithms::ChainScoringScheme, vg::BaseMapper, vg::MultipathMapper
recombinator : vg::RecombinatorHaplotype
recombinator_parameters : HaplotypesConfig
record_bases : vg::Packer
record_edges : vg::Packer
record_edits : vg::Packer
record_offset : vg::ZipCode::snarl_code_t
record_qualities : vg::Packer
records : vg::GAFSorterFile
RECORDS_PER_FILE : vg::GAFSorterParameters
records_per_file : vg::GAFSorterParameters
redundant_vertexes : vg::AlignmentChainModel, vg::MEMChainModel
reestimation_frequency : vg::FragmentLengthDistribution
ref_len : vg::VCFOutputCaller::SuppressedRef
ref_offset : vg::DozeuInterface::graph_pos_s
ref_offsets : vg::FlowCaller, vg::LegacyCaller, vg::MCMCCaller, vg::NestedFlowCaller
ref_path : vg::FlowSort::Growth
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_sample : HaplotypesConfig
ref_samples : vg::Deconstructor
ref_steps : vg::ParentGenotypeInfo
ref_trav_idx : vg::NestedFlowCaller::CallRecord
ref_traversal : vg::ParentGenotypeInfo
reference_paths : vg::PhaseUnfolder
reference_samples : HaplotypesConfig
reflect : vg::GraphSynchronizer::Lock
regions : vg::Funnel::PaintableSpace, vg::HaplotypeIndexer
registered_suffixes : vg::IndexRegistry
registry : vg::IndexingPlan
regular_aligner : vg::AlignerClient
REGULAR_SNARL_IS_REVERSED_OFFSET : vg::ZipCode
REGULAR_SNARL_SIZE : vg::ZipCode
removed : vg::GAFSorterFile
rename_variants : vg::HaplotypeIndexer
rep_match : vg::MappingQualityCalculator
rep_mismatch : vg::MappingQualityCalculator
repeat_size : vg::ReadFilter< Read >
report_allelic_mapq : vg::MultipathMapper
report_group_mapq : vg::MultipathMapper
report_supplementary : vg::Surjector
require_distance_index : MinimizerConfig
require_path_payloads : MinimizerConfig
rescore : vg::ReadFilter< Read >
rescue_algorithm : vg::MinimizerMapper
rescue_graph_std_devs : vg::MultipathMapper
rescue_likelihood_limit : vg::MinimizerMapper
rescue_only_anchor_max : vg::MultipathMapper
rescue_only_min : vg::MultipathMapper
rescue_seed_limit : vg::MinimizerMapper
rescue_subgraph_stdevs : vg::MinimizerMapper
RESCUED : vg::MultipathMapper
reset_along_chain_parent : vg::subcommand::TickChainLink
restrained_graph_extraction : vg::MultipathMapper
retry_on_Ns : vg::NGSSimulator
reversing_walk_length : vg::MultipathMapper
rgfa_listeners : vg::algorithms::GFAParser
rgfa_path_ranks : vg::algorithms::GFAzParser
rho : haplo::haploMath::RRMemo
right_ends : vg::ConstructedChunk
right_full : vg::GaplessExtension
right_handle_trans : vg::JoinedSpliceGraph
right_maximal : vg::GaplessExtension
right_primer : vg::PrimerPair
right_side : vg::ZipCodeForest::seed_info_t
right_splice_offset : vg::JoinedSpliceGraph
right_subgraph : vg::JoinedSpliceGraph
right_telomere_node : vg::PhasedGenome::Haplotype
right_to_left : vg::ZipCodeTree::distance_iterator::iteration_position, vg::ZipCodeTree::seed_iterator
rng : vg::Colors, vg::LazyRNG, vg::Pictographs, vg::Sampler
robust_estimation_fraction : vg::FragmentLengthDistribution
root : vg::BitStringTree< Item >, vg::Tree< T >
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_LENGTH_OFFSET : vg::ZipCode
ROOT_NODE_OR_CHAIN_CONNECTIVITY_OR_LENGTH_OFFSET : vg::ZipCode
ROOT_NODE_SIZE : vg::ZipCode
ROOT_SNARL_SIZE : vg::ZipCode
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