- c -

• 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
• candidate_splice_sites() : vg::SpliceRegion
• canonical() : handlegraph::SnarlDecomposition
• chain() : vg::subcommand::GroupedOptionGroup , vg::subcommand::OptionGroup< Receiver > , vg::subcommand::RangeArgSpec< T, Receiver > , vg::subcommand::TickChainLink
• chain_info_to_seed() : vg::MinimizerMapper
• chain_of() : vg::SnarlManager
• chain_orientation_of() : vg::SnarlManager
• chain_rank_of() : vg::SnarlManager
• chains_of() : vg::SnarlManager
• change_sequence() : handlegraph::DeletableHandleGraph , handlegraph::MutablePathDeletableHandleGraph
• 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
• child_info_t() : vg::ZipCodeForest::child_info_t
• children_of() : vg::SnarlManager
• choose_traversals() : vg::Deconstructor
• chop_nodes() : vg::Transcriptome
• 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
• close() : vg::Viz
• close_chain() : vg::ZipCodeForest
• close_edit_tmpfiles() : vg::Packer
• close_fd() : handlegraph::TriviallySerializable
• close_snarl() : vg::ZipCodeForest
• cluster_chain_level() : vg::SnarlDistanceIndexClusterer
• cluster_multiplicity() : vg::MultipathMapper
• cluster_one_chain() : vg::SnarlDistanceIndexClusterer
• cluster_one_node() : vg::SnarlDistanceIndexClusterer
• cluster_one_snarl() : vg::SnarlDistanceIndexClusterer
• cluster_root() : vg::SnarlDistanceIndexClusterer
• cluster_seeds() : vg::SnarlDistanceIndexClusterer
• cluster_seeds_internal() : vg::SnarlDistanceIndexClusterer
• cluster_seeds_on_linear_structure() : vg::SnarlDistanceIndexClusterer
• cluster_snarl_level() : vg::SnarlDistanceIndexClusterer
• ClusterHead() : vg::SnarlDistanceIndexClusterer::ClusterHead
• ClusteringProblem() : vg::SnarlDistanceIndexClusterer::ClusteringProblem
• clusters() : vg::MEMClusterer , vg::MEMClusterer::HitGraph
• clusters_to_drop() : vg::Mapper
• collapse_order_length_runs() : vg::MultipathAlignmentGraph
• collect_coverage() : vg::Packer
• collect_subgraph() : vg::VG
• collect_transcribed_nodes() : vg::Transcriptome
• Colors() : vg::Colors
• 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
• complement_components() : vg::PhaseUnfolder
• completed_indexes() : vg::IndexRegistry
• CompletedTranscriptPath() : vg::CompletedTranscriptPath
• component_topological_order() : vg::MEMClusterer::HitGraph
• ComponentMinDistanceClusterer() : vg::ComponentMinDistanceClusterer
• components() : vg::Haplotypes
• 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
• condense_edits() : vg::Constructor
• ConfigurableParser() : 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_t
• connection_size() : vg::subpath_t
• connection_t() : vg::connection_t
• 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
• contains() : vg::GaplessExtension , vg::SmallBitset
• contains_reversals() : vg::HaplotypePartitioner
• contains_subsequence() : vg::ReadFilter< Read >
• contract() : vg::ContractingGraph
• ContractingGraph() : vg::ContractingGraph
• 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
• copy() : vg::SmallBitset
• count() : vg::HandleGraphNodeSet , vg::SmallBitset
• count_back_inserter() : vg::count_back_inserter< T >
• count_haplotypes() : vg::GenomeState
• count_Ns() : vg::MaximalExactMatch
• count_reachability_edges() : vg::MultipathAlignmentGraph
• Counts() : vg::Counts
• coverage_at_position() : vg::Packer
• coverage_bin_offset() : vg::Packer
• coverage_bin_size() : vg::Packer
• coverage_filter() : vg::Filter
• coverage_size() : vg::Packer
• covered_intervals() : vg::MultipathMapper
• 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
• cumul() : vg::truncated_normal_distribution< T >
• curr_sample_size() : vg::FragmentLengthDistribution
• current_empty_prefix() : vg::BandedGlobalAligner< IntType >::AltTracebackStack
• current_sum() : haplo::haplo_DP_column
• current_traceback_score() : vg::BandedGlobalAligner< IntType >::AltTracebackStack
• cut_anchors() : vg::Surjector
• cycles_in_cactus() : vg::IntegratedSnarlFinder::MergedAdjacencyGraph