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_component() : vg::MIPayload, vg::MIPayloadValues, vg::SnarlDistanceIndexClusterer::SeedCache, vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild
- chain_component_end : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
- CHAIN_COMPONENT_MASK : vg::MIPayload
- CHAIN_COMPONENT_OFFSET : vg::MIPayload
- chain_component_start : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
- CHAIN_COMPONENT_WIDTH : vg::MIPayload
- chain_deletions : vg::Constructor
- chain_end : vg::ChainIterator
- chain_end_rewrites : vg::NetGraph
- chain_ends_by_start : vg::NetGraph
- chain_id : HaplotypesConfig
- chain_info_to_seed() : vg::MinimizerMapper
- chain_min_score : vg::MinimizerMapper
- chain_of() : vg::SnarlManager
- chain_orientation_of() : vg::SnarlManager
- chain_rank_of() : vg::SnarlManager
- chain_score_threshold : vg::MinimizerMapper
- chain_start : vg::ChainIterator
- chaining_cluster_distance : vg::MinimizerMapper
- chains : vg::Haplotypes, vg::Recombinator::Statistics
- chains_of() : vg::SnarlManager
- 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_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::MultipathMapper, vg::Surjector
- choose_traversals() : vg::Deconstructor
- chop_nodes() : vg::Transcriptome
- chrom : vg::Transcript
- chrom_length : vg::Transcript
- circular : vg::Paths
- circularize() : vg::VG
- classify_kmers() : vg::Recombinator
- 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_edit_tmpfiles() : vg::Packer
- close_fd() : handlegraph::TriviallySerializable
- 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
- 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
- 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::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_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
- 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_bases : vg::GraphSynchronizer::Lock
- context_length : GBWTConfig
- contig : vg::BREAKPOINT
- contig_name : vg::Haplotypes::TopLevelChain, vg::RecombinatorHaplotype
- contig_prefix : HaplotypesConfig
- 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_reachability_edges() : vg::MultipathAlignmentGraph
- count_threads : GBWTConfig
- 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_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