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

- c -

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
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_internal() : vg::FlowCaller
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
canonicalize_subrange() : vg::MultipathAlignmentEmitter
category : vg::subcommand::Subcommand
cerrWrapper() : vg::cerrWrapper
CHAIN : vg::ZipCode
chain() : vg::subcommand::GroupedOptionGroup, vg::subcommand::OptionGroup< Receiver >, vg::subcommand::RangeArgSpec< T, Receiver >, vg::subcommand::TickChainLink
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_COUNT : vg::ZipCodeTree
chain_deletions : vg::Constructor
CHAIN_END : vg::ZipCodeTree
chain_end : vg::ChainIterator
chain_end_rewrites : vg::NetGraph
chain_ends_by_start : vg::NetGraph
chain_info_to_seed() : vg::MinimizerMapper
CHAIN_LENGTH_OFFSET : vg::ZipCode
chain_numbers : vg::ZipCodeTree::distance_iterator::iteration_position, vg::ZipCodeTree::seed_iterator
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::ZipCodeTree
chain_start : vg::ChainIterator
chains : vg::algorithms::ChainsResult, vg::Haplotypes, vg::Recombinator::Statistics
chains_of() : vg::SnarlManager
ChainsConfig() : ChainsConfig
change_index_to() : vg::ZipCodeTree::distance_iterator
char_count : vg::Pictographs
chars : vg::Pictographs
chars_t : vg::algorithms::GFAParser
check_alignment() : vg::Mapper
check_files : vg::IndexRegistry
check_for_read_in() : vg::MinimizerMapper::read_alignment_index_t
check_in() : vg::Watchdog
check_lengths() : vg::WFAAlignment
check_max_trav_cutoff() : vg::VCFTraversalFinder
check_out() : vg::Watchdog
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_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_primary() : vg::Surjector
choose_primary_internal() : vg::Surjector
choose_primary_strand() : vg::Surjector
choose_traversals() : vg::Deconstructor
chop_nodes() : vg::Transcriptome
chrom : vg::Transcript, vg::VCFOutputCaller::SuppressedRef
chrom_length : vg::Transcript
chromosome_name : vg::PrimerPair
chroms : vg::PrimerFinder
circular : vg::Paths
circularize() : vg::VG
clear() : GraphHandler, vg::Annotation< T, Enabled >, vg::AugmentedGraph, vg::GBWTHandler, vg::GrefCover, vg::IntervalUnion, vg::Packer, vg::Paths, vg::SmallBitset, vg::SupportAugmentedGraph, vg::VG
clear_annotation() : vg::multipath_alignment_t
clear_connection() : vg::subpath_t
clear_context() : vg::Explainer
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::algorithms::Anchor, 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
clone() : vg::subcommand::BaseValuation, vg::subcommand::Valuation< T >
close() : vg::Viz
close_chain() : vg::ZipCodeForest
close_edit_tmpfiles() : vg::Packer
close_snarl() : vg::ZipCodeForest
Cluster : vg::MinimizerMapper
cluster_chain_level() : vg::SnarlDistanceIndexClusterer
cluster_coverage_threshold : vg::MinimizerMapper
cluster_min_allele_len : vg::Deconstructor
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
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_size() : vg::IntervalUnion
component_topological_order() : vg::MEMClusterer::HitGraph
ComponentMinDistanceClusterer() : vg::ComponentMinDistanceClusterer
components() : vg::Haplotypes, vg::MEMClusterer::HitGraph
compressed : vg::GAFSorterFile
compressed_external : vg::GBWTHandler
compressed_owned : vg::GBWTHandler
compute() : vg::GrefCover
compute_all_mapping_qualities() : vg::MappingQualityCalculator
compute_borders_and_dimensions() : vg::Viz
compute_chains() : vg::SnarlManager
compute_cluster_mapping_quality() : vg::Mapper
compute_disjoint_path_intervals() : vg::Surjector
compute_divergence() : vg::LoggedGapAlignmentScorer
compute_first_mapping_quality() : vg::MappingQualityCalculator
compute_group_mapping_quality() : vg::MappingQualityCalculator
compute_mapping_qualities() : vg::Mapper
compute_mapping_quality() : vg::MappingQualityCalculator
compute_mapq_caps() : vg::MinimizerMapper
compute_max_mapping_quality() : vg::MappingQualityCalculator
compute_paired_mapping_quality() : vg::MappingQualityCalculator
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_t
connection_size() : vg::subpath_t
connection_t() : vg::connection_t
connections : vg::Recombinator::Statistics
connectivity : vg::NetGraph, vg::ZipCode::chain_code_t
consistency_bonus : vg::algorithms::ChainScoringScheme
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 : vg::SubHandleGraph
context : vg::Logger, vg::zstd_compress_buf, vg::zstd_decompress_buf
context_bases : vg::GraphSynchronizer::Lock
context_length : GBWTConfig
contig_name : vg::Haplotypes::TopLevelChain, vg::RecombinatorHaplotype
contigs : GBWTConfig
continue_snarl() : vg::ZipCodeTree::distance_iterator
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
copied_paths : vg::Recombinator::Statistics
copy() : vg::SmallBitset
copy_base_paths_to_gref() : vg::GrefCover
copy_chain() : vg::Recombinator
copy_id : vg::TranscriptPath
count : vg::count_back_inserter< T >, vg::HandleGraphNodeSet, vg::SmallBitset
count_alignment_operations() : vg::LoggedGapAlignmentScorer
count_back_inserter() : vg::count_back_inserter< T >
count_mismatches() : vg::Surjector
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_size() : vg::Packer
covered_intervals() : vg::MultipathMapper
cr : vg::Viz
CRAM : vg::MultipathAlignmentEmitter
create_alignment_shim() : vg::MultipathAlignmentEmitter
create_edge() : vg::VG
create_gssw_graph() : vg::GSSWAligner
create_handle() : 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() : vg::Paths, vg::VG
create_path_chunk_nodes() : vg::MultipathAlignmentGraph
create_path_handle() : vg::VG
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_context : vg::Explainer
current_empty_prefix() : vg::BandedGlobalAligner< IntType >::AltTracebackStack
current_id : vg::VG
current_item : vg::ZipCodeTree::distance_iterator, vg::ZipCodeTree::seed_iterator
current_node_id : vg::BandedGlobalAligner< IntType >::BABuilder
current_node_sequence : vg::BandedGlobalAligner< IntType >::BABuilder
current_seeds : vg::ZipCodeTree::seed_iterator
current_sum() : haplo::haplo_DP_column
current_traceback_score() : vg::BandedGlobalAligner< IntType >::AltTracebackStack
cursor_t : vg::algorithms::GFAParser, vg::StreamIndex< Message >, vg::StreamSorter< Message >
cut_anchors() : vg::Surjector
cycles_in_cactus() : vg::IntegratedSnarlFinder::MergedAdjacencyGraph
CYCLIC_SNARL : vg::ZipCode
cyclic_snarl_nestedness : vg::ZipCodeTree::seed_iterator