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_index()
: vg::MinimumDistanceIndex
- calculate_max_position()
: vg::DozeuInterface
- calculate_min_index()
: vg::MinimumDistanceIndex
- 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::VCFGenotyper
- call_svs()
: vg::SRPE
- call_svs_paired_end()
: vg::SRPE
- call_svs_split_read()
: vg::SRPE
- call_top_level_chains()
: vg::GraphCaller
- call_top_level_snarls()
: vg::GraphCaller
, vg::MCMCCaller
- can_get()
: vg::IndexManager
- can_get_distance()
: vg::IndexManager
- can_get_gbwt()
: vg::IndexManager
- can_get_gbwtgraph()
: vg::IndexManager
- can_get_graph()
: vg::IndexManager
- can_get_minimizer()
: vg::IndexManager
- can_get_snarls()
: vg::IndexManager
- candidate_splice_sites()
: vg::SpliceRegion
- candidates_per_window
: vg::MinimizerMapper::Minimizer
- canonicalize_edge()
: bdsg::ODGI
- category
: vg::subcommand::Subcommand
- chain()
: vg::Range< Number >
- CHAIN
: vg::SnarlSeedClusterer
- chain_assignments
: vg::MinimumDistanceIndex
- chain_deletions
: vg::Constructor
- chain_distance()
: vg::MinimumDistanceIndex::ChainIndex
- chain_end
: vg::ChainIterator
- chain_end_rewrites
: vg::NetGraph
- chain_ends_by_start
: vg::NetGraph
- chain_indexes
: vg::MinimumDistanceIndex
- chain_length()
: vg::MinimumDistanceIndex::ChainIndex
- chain_of()
: vg::SnarlManager
- chain_orientation_of()
: vg::SnarlManager
- chain_rank_of()
: vg::SnarlManager
- chain_ranks
: vg::MinimumDistanceIndex
- chain_start
: vg::ChainIterator
- chain_to_json()
: vg::MinimumDistanceIndex::ChainIndex
- chain_to_snarls
: vg::SnarlSeedClusterer::TreeState
- ChainIndex
: vg::MinimumDistanceIndex
, vg::MinimumDistanceIndex::ChainIndex
- chains_of()
: vg::SnarlManager
- char_assignment
: bdsg::PackedGraph
- char_count
: vg::Pictographs
- chars
: vg::Pictographs
- check_alignment()
: vg::Mapper
- check_in()
: vg::Watchdog
- check_max_nodes()
: vg::Deconstructor
- check_max_trav_cutoff()
: vg::VCFTraversalFinder
- check_out()
: vg::Watchdog
- check_protobuf_tag()
: vg::io::Registry
- checkin_high_water_kb
: vg::Watchdog::thread_state_t
- child_chains
: vg::SnarlManager::SnarlRecord
- ChildNodeType
: vg::SnarlSeedClusterer
- children
: vg::BitStringTree< Item >::TreeNode
, vg::SnarlManager::SnarlRecord
, vg::TreeNode< T >
, vg::TreeSubgraph
- children_of()
: vg::SnarlManager
- choose_traversals()
: vg::Deconstructor
- chrom
: vg::Transcript
- chrom_length
: vg::Transcript
- circular
: vg::Paths
- circularize()
: vg::VG
- clear()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::DeletableHandleGraph
, vg::Annotation< T, Enabled >
, vg::AugmentedGraph
, 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()
: bdsg::ODGI
, 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::Watchdog
- close
: hFILE_backend
, vg::Index
, vg::Viz
- close_edit_tmpfiles()
: vg::Packer
- Cluster
: vg::MinimizerMapper
- cluster_chain_level()
: vg::SnarlSeedClusterer
- cluster_coverage_threshold
: vg::MinimizerMapper
- cluster_multiplicity()
: vg::MultipathMapper
- cluster_one_chain()
: vg::SnarlSeedClusterer
- cluster_one_node()
: vg::SnarlSeedClusterer
- cluster_one_snarl()
: vg::SnarlSeedClusterer
- cluster_only_top_level_chain_seeds()
: vg::SnarlSeedClusterer
- cluster_score_threshold
: vg::MinimizerMapper
- cluster_seeds()
: vg::SnarlSeedClusterer
- cluster_seeds_internal()
: vg::SnarlSeedClusterer
- cluster_simple_snarl()
: vg::SnarlSeedClusterer
- cluster_snarl_level()
: vg::SnarlSeedClusterer
- cluster_t
: vg::MEMClusterer
- cluster_type
: vg::GaplessExtender
- clusterer
: vg::MinimizerMapper
- clustergraph_t
: vg::MultipathMapper
- 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
- collapse_transcript_paths
: vg::Transcriptome
- collect_coverage()
: vg::Packer
- collect_subgraph()
: vg::VG
- Colors()
: vg::Colors
- colors
: vg::Colors
- column_family_options
: vg::Index
- column_of
: vg::NGSSimulator::MarkovDistribution< From, To >
- combine()
: vg::VG
- combine_handles()
: bdsg::ODGI
- combine_qualities()
: vg::Packer
- common_ancestor_next()
: vg::VG
- common_ancestor_prev()
: vg::VG
- common_bin()
: vg::StreamIndexBase
- common_prefix_length()
: vg::BitString
- compact()
: vg::Index
- compact_ids()
: bdsg::PackedGraph
, vg::VG
- compact_ordered()
: vg::Transcriptome
- compact_ranks()
: vg::Paths
- compare_kmers()
: vg::Index
- COMPILER
: vg::Version
- complement
: vg::ChainIterator
, vg::ReverseGraph
- complement_components()
: vg::PhaseUnfolder
- complement_encoded_nucleotide()
: bdsg::PackedGraph
- complement_filter
: vg::ReadFilter
- CompletedTranscriptPath()
: vg::CompletedTranscriptPath
- component
: vg::SnarlSeedClusterer::Seed
- component_min_dist
: vg::MultipathMapper
- component_path_set_of_path
: vg::PathComponentIndex
- component_path_sets
: vg::PathComponentIndex
- component_to_chain_index
: vg::MinimumDistanceIndex
- component_to_chain_length
: vg::MinimumDistanceIndex
- component_to_index
: vg::SnarlSeedClusterer::TreeState
- component_topological_order()
: vg::MEMClusterer::HitGraph
- ComponentMinDistanceClusterer()
: vg::ComponentMinDistanceClusterer
- components
: vg::MEMClusterer::HitGraph
- compute_borders_and_dimensions()
: vg::Viz
- compute_chains()
: vg::SnarlManager
- compute_cluster_mapping_quality()
: vg::Mapper
- compute_group_mapping_quality()
: vg::GSSWAligner
- compute_mapping_qualities()
: vg::Mapper
- compute_mapping_quality()
: vg::GSSWAligner
- compute_mapq_caps()
: vg::MinimizerMapper
- compute_paired_mapping_quality()
: vg::GSSWAligner
- compute_path_interval()
: vg::Surjector
- compute_quality()
: vg::Packer
- compute_raw_mapping_quality_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_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
- 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_edited_transcript_paths()
: vg::Transcriptome
- construct_edited_transcript_paths_callback()
: vg::Transcriptome
- construct_graph()
: vg::Constructor
- contains()
: vg::GaplessExtension
, vg::SmallBitset
- content
: vg::BitStringTree< Item >::TreeNode
- contents
: vg::SubHandleGraph
- context_bases
: vg::GraphSynchronizer::Lock
- contig
: vg::BREAKPOINT
- control_mean
: vg::BenchmarkResult
- control_stddev
: vg::BenchmarkResult
- convert()
: vg::VcfRecordConverter
- convert_alignment()
: vg::HTSAlignmentEmitter
, vg::SplicedHTSAlignmentEmitter
- convert_multipath_alignment()
: vg::MultipathAlignmentEmitter
- convert_paired()
: vg::HTSAlignmentEmitter
- convert_unpaired()
: vg::HTSAlignmentEmitter
- coordinates
: vg::Exon
- copy()
: vg::SmallBitset
- correct
: vg::Alignment
, vg::Funnel::Item
- correctly_mapped
: vg::Alignment
- count
: bdsg::HashGraph::path_t
, vg::SmallBitset
- count_haplotypes()
: vg::GenomeState
- count_Ns()
: vg::MaximalExactMatch
- Counts()
: vg::ReadFilter::Counts
- counts
: vg::ReadFilter::Counts
- cov_bin_size
: vg::Packer
- coverage
: vg::SnarlSeedClusterer::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
- create_edge()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::MutableHandleGraph
, vg::VG
- create_gssw_graph()
: vg::GSSWAligner
- create_handle()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::MutableHandleGraph
, vg::VG
- create_hidden_handle()
: bdsg::ODGI
- 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()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::MutablePathHandleGraph
, vg::VG
- create_progress()
: vg::Progressive
- create_projector()
: vg::MultipathAlignmentGraph
- create_state()
: vg::PhaseUnfolder
- create_step()
: bdsg::ODGI
- create_variant_index()
: vg::VCFTraversalFinder
- cross_alignment()
: vg::Index
- 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
, vg::walk_t
- curr_deflxn
: vg::BandedGlobalAligner< IntType >::AltTracebackStack
- curr_sample_size()
: vg::FragmentLengthDistribution
- curr_traceback
: vg::BandedGlobalAligner< IntType >::AltTracebackStack
- current
: vg::IncrementIter
, vg::WindowedVcfBuffer
- 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::IndexedVG
, vg::StreamIndex< Message >
, vg::StreamSorter< Message >
- cut_nonref_tips()
: vg::Homogenizer
- cut_tips()
: vg::Homogenizer
- cycles_in_cactus()
: vg::IntegratedSnarlFinder::MergedAdjacencyGraph