- 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
• candidate_node : vg::WFATree
• candidate_point : vg::WFATree
• candidates_per_window : vg::MinimizerMapper::Minimizer
• category : vg::subcommand::Subcommand
• 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_rewrites : vg::NetGraph
• chain_ends_by_start : vg::NetGraph
• CHAIN_LENGTH_OFFSET : vg::ZipCode
• chain_order : vg::ZipCodeForest::sort_value_t
• CHAIN_RANK_IN_SNARL_OFFSET : vg::ZipCode
• chain_score_threshold : vg::MinimizerMapper
• CHAIN_SIZE : vg::ZipCode
• chain_start : vg::ChainIterator
• chains : vg::Haplotypes , vg::Recombinator::Statistics
• char_count : vg::Pictographs
• chars : vg::Pictographs
• checkin_high_water_kb : vg::Watchdog::thread_state_t
• child_chains : vg::SnarlManager::SnarlRecord
• child_count : vg::ZipCode::snarl_code_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
• choose_band_padding : vg::MinimizerMapper , vg::MultipathMapper , vg::Surjector
• chrom : vg::Transcript
• chrom_length : vg::Transcript
• chromosome_name : vg::PrimerPair
• chroms : vg::PrimerFinder
• circular : vg::Paths
• close : hFILE_backend
• cluster_coverage_threshold : vg::MinimizerMapper
• cluster_num : vg::SnarlDistanceIndexClusterer::ClusterHead
• cluster_score_threshold : vg::MinimizerMapper
• cluster_threshold : vg::Deconstructor
• clusterer : vg::MinimizerMapper
• code_type : vg::ZipCode::snarl_code_t , vg::ZipCodeForest::interval_state_t , vg::ZipCodeForest::sort_value_t
• codenames : vg::Version
• codes_by_option : vg::ConfigurableParser
• cohort : haplo::linear_haplo_structure
• col_idx : vg::BandedGlobalAligner< IntType >::AltTracebackStack::Deflection
• colors : vg::Colors
• column_number : vg::algorithms::GFAFormatError
• column_of : vg::NGSSimulator::MarkovDistribution< From, To >
• COMPILER : vg::Version
• complement : vg::ChainIterator , vg::ReverseGraph
• complement_filter : vg::ReadFilter< Read >
• component_min_dist : vg::MultipathMapper
• component_params : vg::SpliceStats
• component_path_set_of_path : vg::PathComponentIndex
• component_path_sets : vg::PathComponentIndex
• components : vg::MEMClusterer::HitGraph
• compressed : vg::GAFSorterFile , vg::GBWTHandler
• cond_distrs : vg::NGSSimulator::MarkovDistribution< From, To >
• configurables : vg::ConfigurableParser
• connection : vg::Subpath
• connections : vg::Recombinator::Statistics
• connectivity : vg::NetGraph , vg::ZipCode::chain_code_t
• consistent : vg::Genotyper::Affinity
• construction_jobs : vg::Haplotypes::Header
• containing_net_handle : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
• 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
• control_mean : vg::BenchmarkResult
• control_stddev : vg::BenchmarkResult
• coordinates : vg::Exon
• copy_id : vg::TranscriptPath
• correct : vg::Alignment
• correctly_mapped : vg::Alignment
• count : vg::count_back_inserter< T >
• count_of_max : vg::SummaryStatistics
• count_paths : GBWTConfig
• counts : vg::Counts
• cov_bin_size : vg::Packer
• COVERAGE : vg::Recombinator
• coverage : vg::Recombinator::Parameters , vg::SnarlDistanceIndexClusterer::Cluster
• coverage_civ : vg::Packer
• coverage_dynamic : vg::Packer
• cr : vg::Viz
• crossing_edges : vg::PhaseUnfolder
• 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_traceback : vg::BandedGlobalAligner< IntType >::AltTracebackStack
• current : vg::IncrementIter , vg::WindowedVcfBuffer
• current_chains : vg::SnarlDistanceIndexClusterer::ClusteringProblem
• 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_VERSION : xg::XG
• cursor_pool : vg::IndexedVG
• cursor_pool_mutex : vg::IndexedVG
• cursor_streams : vg::IndexedVG