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
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::Range< Number >
range : vg::MaximalExactMatch
range_table : vg::MEMAccelerator
rank : vg::mapping_t, vg::PhasedGenome::iterator, vg::ZipCodeForest::seed_info_t
rank_by_support() : vg::PoissonSupportSnarlCaller
rank_in_chain : vg::FragmentedHaplotypeVisit
rank_in_sequence : vg::FragmentedHaplotypeVisit
RareVariantSimplifier() : vg::RareVariantSimplifier
RatioSupportSnarlCaller() : vg::RatioSupportSnarlCaller
raw_gaf : vg::GAFSorterFile
re_genotype() : vg::LegacyCaller
reachable_with_gap : vg::WFATree::ScoreProperties
read : vg::Counts, vg::GAFSorterFile, vg::MinimizerMapper::alignment_index_t, 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::MinimizerMapper, vg::MultipathAlignmentEmitter
read_interval : vg::GaplessExtension
read_length_prop_disjoint_gap : vg::Surjector
read_line() : vg::GAFSorterRecord
read_log_likelihood() : vg::PhasedGenome
read_mapping() : vg::PhaseUnfolder
read_num : vg::SnarlDistanceIndexClusterer::ClusterHead
read_offset : MappingRun
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() : 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
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::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::AlignmentScorer
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
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 : 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
RegionExpander() : vg::RegionExpander
regions : vg::Funnel::PaintableSpace, vg::HaplotypeIndexer
register_alias() : vg::AliasGraph
register_configurable() : vg::ConfigurableParser
register_fragment_length() : vg::FragmentLengthDistribution
register_generalization() : vg::IndexRegistry
register_index() : vg::IndexRegistry
register_option() : vg::Configurable
register_recipe() : vg::IndexRegistry
register_sampled_position() : vg::NGSSimulator
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
remove() : vg::PhasedGenome
remove_bonuses() : vg::EditAlignmentScorer
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
removed : vg::GAFSorterFile
rename_variants : vg::HaplotypeIndexer
reorder_adjacency_lists() : vg::MultipathAlignmentGraph
reorder_exons() : vg::Transcriptome
rep_match : vg::MappingQualityCalculator
rep_mismatch : vg::MappingQualityCalculator
repeat : vg::Counts
repeat_size : vg::ReadFilter< Read >
repetitiveness() : vg::SeqComplexity< MaxOrder >
replace_mapping() : vg::Paths
replace_occurrence() : vg::PathIndex
report_affinities() : vg::Genotyper
report_allelic_mapq : vg::MultipathMapper
report_group_mapq : vg::MultipathMapper
report_snarl() : vg::Genotyper
report_snarl_traversal() : vg::Genotyper
report_supplementary : vg::Surjector
Representative : vg::Genotyper
RepresentativeTraversalFinder() : vg::RepresentativeTraversalFinder
require() : vg::IndexRegistry
require_distance_index : MinimizerConfig
require_path_payloads : MinimizerConfig
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
rescued_from_first : vg::MinimizerMapper
rescued_from_second : vg::MinimizerMapper
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_along_chain_parent : vg::subcommand::TickChainLink
reset_chain() : vg::subcommand::GroupedOptionGroup, vg::subcommand::OptionGroup< Receiver >, vg::subcommand::TickChainLink
resize_indexes() : vg::VG
resolve_base_path_name() : vg::GrefCover
restore_hard_clips() : vg::Surjector
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
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_seed() : vg::ZipCodeForest::seed_info_t
ReverseGraph() : vg::ReverseGraph
reversing_walk_length : vg::MultipathMapper
RewindPlanException() : vg::RewindPlanException
rewrite_segment() : vg::VG
rgfa_listeners : vg::algorithms::GFAParser
rgfa_path_ranks : vg::algorithms::GFAzParser
rho : haplo::haploMath::RRMemo
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_side : vg::ZipCodeForest::seed_info_t
right_splice_node() : vg::JoinedSpliceGraph
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 : 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