Here is a list of all functions with links to the classes they belong to:
- r -
- 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::ParallelKFFReader
- read_end() : vg::algorithms::Anchor
- 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
- record() : vg::SnarlManager
- record_fanouts() : vg::MultipathMapper
- record_fragment_configuration() : vg::FragmentLengthStatistics
- record_offset() : vg::MIPayload
- 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
- 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_transitive_edges() : vg::MultipathAlignmentGraph
- rename_path() : handlegraph::MutablePathHandleGraph
- 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
- reseed_between() : vg::MinimizerMapper
- 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_chain() : vg::Range< Number >, 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
- 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