Here is a list of all class members with links to the classes they belong to:

- c -

• cache_mutex : vg::IndexedVG
• cached_fragment_direction : vg::FragmentLengthStatistics
• cached_fragment_length_mean : vg::FragmentLengthStatistics
• cached_fragment_length_stdev : vg::FragmentLengthStatistics
• cached_fragment_orientation_same : vg::FragmentLengthStatistics
• cached_genotypes : vg::WindowedVcfBuffer
• CachedPackedTraversalSupportFinder() : vg::CachedPackedTraversalSupportFinder
• CacheEntry() : vg::IndexedVG::CacheEntry
• CactusSnarlFinder() : vg::CactusSnarlFinder
• calculate_and_save_alignment() : vg::DozeuInterface
• calculate_consistency() : vg::ConsistencyCalculator , vg::SimpleConsistencyCalculator
• calculate_I() : haplo::haplo_DP_rectangle
• calculate_log_likelihood() : vg::GenotypeLikelihoodCalculator
• calculate_log_prior() : vg::FixedGenotypePriorCalculator , vg::GenotypePriorCalculator
• calculate_max_position() : vg::DozeuInterface
• calculate_seed_position() : vg::DozeuInterface
• calculate_supports() : vg::SimpleTraversalSupportCalculator , vg::TraversalSupportCalculator
• calibrate_mismapping_detection() : vg::MultipathMapper
• call_snarl() : vg::FlowCaller , vg::GraphCaller , vg::LegacyCaller , vg::MCMCCaller , vg::NestedFlowCaller , vg::VCFGenotyper
• call_snarl_recursive() : vg::NestedFlowCaller
• call_top_level_chains() : vg::GraphCaller
• call_top_level_snarls() : vg::GraphCaller , vg::MCMCCaller
• CallTable : vg::NestedFlowCaller
• candidate_id_t : vg::MultipathMapper
• candidate_node : vg::WFATree
• candidate_point : vg::WFATree
• candidate_splice_sites() : vg::SpliceRegion
• candidates_per_window : vg::MinimizerMapper::Minimizer
• canonical() : handlegraph::SnarlDecomposition
• category : vg::subcommand::Subcommand
• chain() : vg::subcommand::GroupedOptionGroup , vg::subcommand::OptionGroup< Receiver > , vg::subcommand::RangeArgSpec< T, Receiver > , vg::subcommand::TickChainLink
• CHAIN : vg::ZipCode
• chain_component : vg::MIPayload , vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild , vg::ZipCode::node_code_t , vg::ZipCode::snarl_code_t , vg::ZipCodeForest::child_info_t , vg::ZipCodeForest::sort_value_t
• CHAIN_COMPONENT_COUNT_OFFSET : vg::ZipCode
• chain_component_end : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
• chain_component_start : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
• chain_deletions : vg::Constructor
• chain_end : vg::ChainIterator
• CHAIN_END : vg::ZipCodeTree
• chain_end_rewrites : vg::NetGraph
• chain_ends_by_start : vg::NetGraph
• chain_info_to_seed() : vg::MinimizerMapper
• CHAIN_LENGTH_OFFSET : vg::ZipCode
• chain_of() : vg::SnarlManager
• chain_order : vg::ZipCodeForest::sort_value_t
• chain_orientation_of() : vg::SnarlManager
• CHAIN_RANK_IN_SNARL_OFFSET : vg::ZipCode
• chain_rank_of() : vg::SnarlManager
• chain_score_threshold : vg::MinimizerMapper
• CHAIN_SIZE : vg::ZipCode
• chain_start : vg::ChainIterator
• CHAIN_START : vg::ZipCodeTree
• chains : vg::Haplotypes , vg::Recombinator::Statistics
• chains_of() : vg::SnarlManager
• change_sequence() : handlegraph::DeletableHandleGraph , handlegraph::MutablePathDeletableHandleGraph
• char_count : vg::Pictographs
• chars : vg::Pictographs
• chars_t : vg::algorithms::GFAParser
• check_alignment() : vg::Mapper
• check_for_read_in() : vg::read_alignment_index_t
• check_in() : vg::Watchdog
• check_lengths() : vg::WFAAlignment
• check_max_trav_cutoff() : vg::VCFTraversalFinder
• check_out() : vg::Watchdog
• check_protobuf_tag() : vg::io::Registry
• check_status() : vg::Viz
• checkin_high_water_kb : vg::Watchdog::thread_state_t
• child_chains : vg::SnarlManager::SnarlRecord
• child_count : vg::ZipCode::snarl_code_t
• child_info_t() : vg::ZipCodeForest::child_info_t
• child_snarls : vg::Deconstructor::NestingInfo
• child_support_map : vg::NestedCachedPackedTraversalSupportFinder
• children : vg::BitStringTree< Item >::TreeNode , vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem , vg::SnarlManager::SnarlRecord , vg::TreeNode< T > , vg::TreeSubgraph , vg::WFANode
• children_of() : vg::SnarlManager
• choose_band_padding : vg::MinimizerMapper , vg::MultipathMapper , vg::Surjector
• choose_traversals() : vg::Deconstructor
• chop_nodes() : vg::Transcriptome
• chrom : vg::Transcript
• chrom_length : vg::Transcript
• chromosome_name : vg::PrimerPair
• chroms : vg::PrimerFinder
• circular : vg::Paths
• circularize() : vg::VG
• clear() : GraphHandler , handlegraph::DeletableHandleGraph , vg::Annotation< T, Enabled > , vg::AugmentedGraph , vg::GBWTHandler , vg::Packer , vg::Paths , vg::SmallBitset , vg::SupportAugmentedGraph , vg::VG
• clear_annotation() : vg::multipath_alignment_t
• clear_connection() : vg::subpath_t
• clear_edge_indexes() : vg::VG
• clear_edge_indexes_no_resize() : vg::VG
• clear_indexes() : vg::VG
• clear_indexes_no_resize() : vg::VG
• clear_mapping() : vg::path_t
• clear_mapping_ranks() : vg::Paths
• clear_next() : vg::subpath_t
• clear_node_indexes() : vg::VG
• clear_node_indexes_no_resize() : vg::VG
• clear_paths() : vg::VG
• clear_reachability_edges() : vg::MultipathAlignmentGraph
• clear_scores() : vg::AlignmentChainModel , vg::MEMChainModel
• clear_start() : vg::multipath_alignment_t
• clear_subpath() : vg::multipath_alignment_t
• clock : vg::Funnel , vg::Watchdog
• close : hFILE_backend , vg::Viz
• close_chain() : vg::ZipCodeForest
• close_edit_tmpfiles() : vg::Packer
• close_fd() : handlegraph::TriviallySerializable
• close_snarl() : vg::ZipCodeForest
• Cluster : vg::MinimizerMapper
• cluster_chain_level() : vg::SnarlDistanceIndexClusterer
• cluster_coverage_threshold : vg::MinimizerMapper
• cluster_multiplicity() : vg::MultipathMapper
• cluster_num : vg::SnarlDistanceIndexClusterer::ClusterHead
• cluster_one_chain() : vg::SnarlDistanceIndexClusterer
• cluster_one_node() : vg::SnarlDistanceIndexClusterer
• cluster_one_snarl() : vg::SnarlDistanceIndexClusterer
• cluster_root() : vg::SnarlDistanceIndexClusterer
• cluster_score_threshold : vg::MinimizerMapper
• cluster_seeds() : vg::SnarlDistanceIndexClusterer
• cluster_seeds_internal() : vg::SnarlDistanceIndexClusterer
• cluster_seeds_on_linear_structure() : vg::SnarlDistanceIndexClusterer
• cluster_snarl_level() : vg::SnarlDistanceIndexClusterer
• cluster_t : vg::MEMClusterer
• cluster_threshold : vg::Deconstructor
• cluster_type : vg::GaplessExtender
• clusterer : vg::MinimizerMapper
• clustergraph_t : vg::MultipathMapper
• ClusterHead() : vg::SnarlDistanceIndexClusterer::ClusterHead
• ClusteringProblem() : vg::SnarlDistanceIndexClusterer::ClusteringProblem
• clusters() : vg::MEMClusterer , vg::MEMClusterer::HitGraph
• clusters_to_drop() : vg::Mapper
• code_type : vg::MIPayload , vg::ZipCode , vg::ZipCode::snarl_code_t , vg::ZipCodeForest::interval_state_t , vg::ZipCodeForest::sort_value_t
• code_type_t : vg::ZipCode
• codenames : vg::Version
• codes_by_option : vg::ConfigurableParser
• cohort : haplo::linear_haplo_structure
• col_idx : vg::BandedGlobalAligner< IntType >::AltTracebackStack::Deflection
• collapse_order_length_runs() : vg::MultipathAlignmentGraph
• collect_coverage() : vg::Packer
• collect_subgraph() : vg::VG
• collect_transcribed_nodes() : vg::Transcriptome
• Colors() : vg::Colors
• colors : vg::Colors
• column_number : vg::algorithms::GFAFormatError
• column_of : vg::NGSSimulator::MarkovDistribution< From, To >
• combine() : vg::Recombinator::Statistics , vg::VG
• combine_qualities() : vg::Packer
• comma() : vg::ProblemDumpExplainer
• common_ancestor_next() : vg::VG
• common_ancestor_prev() : vg::VG
• common_bin() : vg::StreamIndexBase
• common_prefix_length() : vg::BitString
• compact_ids() : vg::VG
• compact_ranks() : vg::Paths
• compact_sequence_type : vg::Haplotypes
• compare() : ReferenceInterval
• compare_and_combine_cluster_on_child_structures() : vg::SnarlDistanceIndexClusterer
• compare_and_combine_cluster_on_one_child() : vg::SnarlDistanceIndexClusterer
• COMPILER : vg::Version
• complement : vg::ChainIterator , vg::ReverseGraph
• complement_components() : vg::PhaseUnfolder
• complement_filter : vg::ReadFilter< Read >
• completed_indexes() : vg::IndexRegistry
• CompletedTranscriptPath() : vg::CompletedTranscriptPath
• component_min_dist : vg::MultipathMapper
• component_params : vg::SpliceStats
• component_path_set_of_path : vg::PathComponentIndex
• component_path_sets : vg::PathComponentIndex
• component_topological_order() : vg::MEMClusterer::HitGraph
• ComponentMinDistanceClusterer() : vg::ComponentMinDistanceClusterer
• components() : vg::Haplotypes , vg::MEMClusterer::HitGraph
• compressed : vg::GAFSorterFile , vg::GBWTHandler
• compute_all_mapping_qualities() : vg::GSSWAligner
• compute_borders_and_dimensions() : vg::Viz
• compute_chains() : vg::SnarlManager
• compute_cluster_mapping_quality() : vg::Mapper
• compute_first_mapping_quality() : vg::GSSWAligner
• compute_group_mapping_quality() : vg::GSSWAligner
• compute_mapping_qualities() : vg::Mapper
• compute_mapping_quality() : vg::GSSWAligner
• compute_mapq_caps() : vg::MinimizerMapper
• compute_max_mapping_quality() : vg::GSSWAligner
• compute_paired_mapping_quality() : vg::GSSWAligner
• compute_path_interval() : vg::Surjector
• compute_quality() : vg::Packer
• compute_raw_mapping_qualities_from_scores() : vg::MultipathMapper
• compute_tail_mem_coverage() : vg::OrientedDistanceClusterer
• compute_uniqueness() : vg::Mapper
• concat_mappings_for_node_pair() : vg::VG
• cond_distrs : vg::NGSSimulator::MarkovDistribution< From, To >
• condense_edits() : vg::Constructor
• ConfigurableParser() : vg::ConfigurableParser
• configurables : vg::ConfigurableParser
• connect() : vg::RecombinatorHaplotype , vg::WFAExtender
• connect_consistently() : vg::MinimizerMapper
• connect_node_to_nodes() : vg::VG
• connect_nodes_to_node() : vg::VG
• connect_to_position_file() : vg::NGSSimulator
• connected_components() : vg::MEMClusterer::HitGraph , vg::Surjector
• connection : vg::Subpath , vg::subpath_t
• connection_size() : vg::subpath_t
• connection_t() : vg::connection_t
• connections : vg::Recombinator::Statistics
• connectivity : vg::NetGraph , vg::ZipCode::chain_code_t
• consistent : vg::Genotyper::Affinity
• const_iterator : vg::ShuffledPairs
• construct() : vg::FlowSort::WeightedGraph
• construct_chunk() : vg::Constructor
• construct_completed_transcript_paths() : vg::Transcriptome
• construct_graph() : vg::Constructor
• construct_reference_transcript_paths_embedded() : vg::Transcriptome
• construct_reference_transcript_paths_embedded_callback() : vg::Transcriptome
• construct_reference_transcript_paths_gbwt() : vg::Transcriptome
• construct_reference_transcript_paths_gbwt_callback() : vg::Transcriptome
• construction_jobs : vg::Haplotypes::Header
• containing_net_handle : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
• contains() : vg::GaplessExtension , vg::SmallBitset
• contains_reversals() : vg::HaplotypePartitioner
• contains_subsequence() : vg::ReadFilter< Read >
• content : vg::BitStringTree< Item >::TreeNode
• contents : handlegraph::algorithms::SubHandleGraph , vg::SubHandleGraph
• context : vg::zstd_compress_buf , vg::zstd_decompress_buf
• context_bases : vg::GraphSynchronizer::Lock
• context_length : GBWTConfig
• contig : vg::BREAKPOINT
• contig_name : vg::Haplotypes::TopLevelChain , vg::RecombinatorHaplotype
• contigs : GBWTConfig
• contract() : vg::ContractingGraph
• ContractingGraph() : vg::ContractingGraph
• control_mean : vg::BenchmarkResult
• control_stddev : vg::BenchmarkResult
• convert() : vg::VcfRecordConverter
• convert_alignment() : vg::HTSAlignmentEmitter , vg::SplicedHTSAlignmentEmitter
• convert_paired() : vg::HTSAlignmentEmitter
• convert_to_alignment() : vg::MultipathAlignmentEmitter
• convert_to_hts_paired() : vg::MultipathAlignmentEmitter
• convert_to_hts_unpaired() : vg::MultipathAlignmentEmitter
• convert_unpaired() : vg::HTSAlignmentEmitter
• coordinates : vg::Exon
• copy() : vg::SmallBitset
• copy_id : vg::TranscriptPath
• correct : vg::Alignment
• correctly_mapped : vg::Alignment
• count : vg::count_back_inserter< T > , vg::HandleGraphNodeSet , vg::SmallBitset
• count_back_inserter() : vg::count_back_inserter< T >
• count_haplotypes() : vg::GenomeState
• count_Ns() : vg::MaximalExactMatch
• count_of_max : vg::SummaryStatistics
• count_paths : GBWTConfig
• count_reachability_edges() : vg::MultipathAlignmentGraph
• Counts() : vg::Counts
• counts : vg::Counts
• cov_bin_size : vg::Packer
• COVERAGE : vg::Recombinator
• coverage : vg::Recombinator::Parameters , vg::SnarlDistanceIndexClusterer::Cluster
• coverage_at_position() : vg::Packer
• coverage_bin_offset() : vg::Packer
• coverage_bin_size() : vg::Packer
• coverage_civ : vg::Packer
• coverage_dynamic : vg::Packer
• coverage_filter() : vg::Filter
• coverage_size() : vg::Packer
• covered_intervals() : vg::MultipathMapper
• cr : vg::Viz
• CRAM : vg::MultipathAlignmentEmitter
• create_alignment_shim() : vg::MultipathAlignmentEmitter
• create_edge() : handlegraph::MutableHandleGraph , vg::VG
• create_gssw_graph() : vg::GSSWAligner
• create_handle() : handlegraph::MutableHandleGraph , vg::VG
• create_identity_projection_trans() : vg::MultipathAlignmentGraph
• create_injection_trans() : vg::MultipathAlignmentGraph
• create_item() : vg::Funnel
• create_match_nodes() : vg::MultipathAlignmentGraph
• create_node() : vg::VG
• create_path() : handlegraph::MutablePathMetadata , vg::Paths , vg::VG
• create_path_chunk_nodes() : vg::MultipathAlignmentGraph
• create_path_handle() : handlegraph::MutablePathHandleGraph , handlegraph::MutablePathMetadata , vg::VG
• create_path_name() : handlegraph::PathMetadata
• create_progress() : vg::Progressive
• create_projector() : vg::MultipathAlignmentGraph
• create_state() : vg::PhaseUnfolder
• create_variant_index() : vg::VCFTraversalFinder
• crossing_edges : vg::PhaseUnfolder
• cumul() : vg::truncated_normal_distribution< T >
• cumulative_seq_len : vg::BandedGlobalAligner< IntType >::BAMatrix
• curr : vg::algorithms::kmer_t , vg::algorithms::walk_t , vg::kmer_t , vg::PathBranch
• curr_deflxn : vg::BandedGlobalAligner< IntType >::AltTracebackStack
• curr_sample_size() : vg::FragmentLengthDistribution
• curr_traceback : vg::BandedGlobalAligner< IntType >::AltTracebackStack
• current : vg::IncrementIter , vg::WindowedVcfBuffer
• current_chains : vg::SnarlDistanceIndexClusterer::ClusteringProblem
• current_empty_prefix() : vg::BandedGlobalAligner< IntType >::AltTracebackStack
• current_id : vg::VG
• current_node_id : vg::BandedGlobalAligner< IntType >::BABuilder
• current_node_sequence : vg::BandedGlobalAligner< IntType >::BABuilder
• current_state : vg::ZipCodeTree::reverse_iterator
• current_sum() : haplo::haplo_DP_column
• current_traceback_score() : vg::BandedGlobalAligner< IntType >::AltTracebackStack
• CURRENT_VERSION : xg::XG
• cursor_pool : vg::IndexedVG
• cursor_pool_mutex : vg::IndexedVG
• cursor_streams : vg::IndexedVG
• cursor_t : vg::algorithms::GFAParser , vg::IndexedVG , vg::StreamIndex< Message > , vg::StreamSorter< Message >
• cut_anchors() : vg::Surjector
• cycles_in_cactus() : vg::IntegratedSnarlFinder::MergedAdjacencyGraph
• CYCLIC_SNARL : vg::ZipCode