| ►Cvg::AbstractReadSampler | |
| Cvg::NGSSimulator | |
| Cvg::Sampler | |
| Cvg::Genotyper::Affinity | |
| Cvg::AliasGraph | |
| Cvg::MinimizerMapper::aligner_stats_t | Struct to represent per-DP-method stats |
| ►Cvg::AlignerClient | |
| ►Cvg::BaseMapper | |
| Cvg::Mapper | |
| Cvg::MultipathMapper | |
| Cvg::MinimizerMapper | |
| Cvg::Surjector | |
| Cvg::Alignment | |
| Cvg::alignment_index_t | |
| Cvg::AlignmentChainModel | |
| Cvg::AlignmentChainModelVertex | |
| ►Cvg::io::AlignmentEmitter | |
| Cvg::BackTranslatingAlignmentEmitter | |
| ►Cvg::HTSAlignmentEmitter | |
| Cvg::SplicedHTSAlignmentEmitter | |
| Cvg::io::GafAlignmentEmitter | |
| Cvg::io::NullAlignmentEmitter | |
| Cvg::io::TSVAlignmentEmitter | |
| Cvg::io::VGAlignmentEmitter | |
| Cvg::SurjectingAlignmentEmitter | |
| Cvg::AlignmentValidity | |
| Cvg::BandedGlobalAligner< IntType >::AltTracebackStack | |
| Cvg::algorithms::Anchor | |
| Cvg::Annotation< T, Enabled > | |
| ►Cvg::AugmentedGraph | |
| Cvg::SupportAugmentedGraph | Augmented Graph that holds some Support annotation data specific to vg call |
| Cvg::BandedGlobalAligner< IntType >::BABuilder | |
| Cvg::BandedGlobalAligner< IntType >::BAMatrix | |
| Cvg::BandedGlobalAligner< IntType > | |
| ►Cvg::BaseAligner | |
| ►Cvg::GSSWAligner | |
| Cvg::Aligner | |
| Cvg::QualAdjAligner | |
| Cvg::BasePileup | |
| ►Cvg::subcommand::BaseValuation | |
| Cvg::subcommand::Valuation< T > | |
| Cvg::BBEdgeHash | |
| Cvg::BenchmarkResult | |
| Cvg::BitString | |
| Cvg::BitStringTree< Item > | |
| Cvg::BitStringTree< bin_t > | |
| Chandlegraph::BoolReturningWrapper< Iteratee, ReturnsBool > | |
| Chandlegraph::BoolReturningWrapper< Iteratee, false > | |
| Chandlegraph::BoolReturningWrapper< Iteratee, true > | |
| Cvg::BREAKPOINT | |
| Cvg::IndexedVG::CacheEntry | |
| Cvg::CactusSide | |
| ►Cvg::SnarlCaller::CallInfo | |
| Cvg::PoissonSupportSnarlCaller::PoissonCallInfo | |
| Cvg::NestedFlowCaller::CallRecord | Stuff we remember for each snarl call, to be used when genotyping its parent |
| Cvg::ZipCode::chain_code_t | |
| Cvg::ChainIterator | |
| CChainsConfig | |
| Cvg::ZipCodeForest::child_info_t | |
| Cvg::SnarlDistanceIndexClusterer::Cluster | Cluster information used in Giraffe |
| Cvg::SnarlDistanceIndexClusterer::ClusterHead | |
| Cvg::SnarlDistanceIndexClusterer::ClusteringProblem | |
| Cvg::Colors | |
| Cvg::Configurable | |
| Cvg::ConfigurableParser | |
| Cvg::Connection | An edge in a MultipathAlignment between Subpaths that may not be contiguous in the graph |
| Cvg::connection_t | |
| ►Cvg::ConsistencyCalculator | |
| Cvg::SimpleConsistencyCalculator | |
| Cvg::VectorView< Item >::const_iterator | Random access iterator |
| Cvg::ConstructedChunk | |
| Cvg::ContractingGraph | |
| Cvg::count_back_inserter< T > | |
| Cvg::Counts | |
| Cvg::ZipCode::decoder_t | |
| Cvg::BandedGlobalAligner< IntType >::AltTracebackStack::Deflection | |
| Cvg::DeletionAligner | |
| Cvg::DinucleotideMachine | |
| Cvg::discrete_distribution< T > | We provide a partial discrete_distribution implementation that is just the parts we need |
| Cvg::ZipCodeTree::distance_iterator | |
| ►Cvg::DistanceHeuristic | |
| Cvg::SnarlMinDistance | |
| Cvg::TipAnchoredMaxDistance | |
| ►Cvg::DozeuInterface | |
| Cvg::QualAdjXdropAligner | |
| Cvg::XdropAligner | |
| Cvg::MEMClusterer::DPScoreComparator | |
| Cvg::Edge | |
| Cvg::algorithms::Edge | |
| Cvg::EdgePileup | Keep pileup-like record for reads that span edges |
| Cvg::Edit | |
| Cvg::edit_t | |
| Cvg::endianness< IntType > | |
| Cvg::WFAExtender::ErrorModel | |
| Cvg::WFAExtender::ErrorModel::Event | |
| ►Cexception | |
| Cj2pb_error | |
| Cvg::NoAlignmentInBandException | |
| Cvg::RewindPlanException | |
| Cvg::SizeLimitExceededException | |
| Cvg::Exon | |
| ►Cvg::Explainer | |
| Cvg::DiagramExplainer | |
| Cvg::DotDumpExplainer< T > | |
| Cvg::ProblemDumpExplainer | |
| Cvg::SubgraphExplainer | |
| Cvg::TSVExplainer | |
| ►Cfalse_type | |
| Cvg::is_instantiation_of< Subject, Predicate > | |
| Cvg::IncrementalSubgraph::FCmp | |
| Cvg::FeatureSet::Feature | |
| Cvg::FeatureSet | |
| Cvg::Filter | |
| Cvg::Funnel::FilterPerformance | |
| Cvg::FlowSort | |
| Cvg::ZipCodeForest::forest_growing_state_t | This stores information about the state of the forest as we fill it in |
| Cvg::FragmentedHaplotypeVisit | |
| Cvg::FragmentLengthDistribution | |
| Cvg::FragmentLengthStatistics | |
| Cfrom_chars_result | |
| Cvg::Funnel | |
| ►Cvg::GAFOutputCaller | |
| Cvg::FlowCaller | |
| Cvg::NestedFlowCaller | |
| Cvg::VCFGenotyper | |
| Cgafkluge::GafRecord | |
| Cvg::GAFSorterFile | |
| Cvg::GAFSorterParameters | |
| Cvg::GAFSorterRecord | |
| Cgafkluge::GafStep | |
| Cvg::GaplessExtender | |
| Cvg::GaplessExtension | |
| Chaplo::gbwt_thread_t | |
| CGBWTConfig | |
| Cvg::GBWTHandler | |
| Cvg::GenomeState | |
| ►Cvg::GenomeStateCommand | |
| Cvg::AppendHaplotypeCommand | |
| Cvg::DeleteHaplotypeCommand | |
| Cvg::InsertHaplotypeCommand | |
| Cvg::ReplaceLocalHaplotypeCommand | |
| Cvg::ReplaceSnarlHaplotypeCommand | |
| Cvg::SwapHaplotypesCommand | |
| Cvg::Genotype | Describes a genotype at a particular locus |
| Cvg::GenotypeLikelihoodCalculator | |
| ►Cvg::GenotypePriorCalculator | |
| Cvg::FixedGenotypePriorCalculator | |
| Cvg::Genotyper | |
| Cvg::algorithms::GFAParser | |
| Cvg::GFFReader | |
| Cvg::GFFRecord | |
| CGiraffeMainOptions | Options struct for options for the Giraffe driver (i.e. this file) |
| Cvg::Graph | |
| Cvg::algorithms::Graph | |
| Cvg::DozeuInterface::graph_pos_s | |
| ►Cvg::GraphCaller | |
| Cvg::FlowCaller | |
| Cvg::LegacyCaller | |
| Cvg::NestedFlowCaller | |
| Cvg::VCFGenotyper | |
| CGraphHandler | |
| Cvg::GraphSynchronizer | |
| Cvg::FlowSort::Growth | |
| Chandlegraph::handle_t | Represents a traversal of a node in a graph in a particular direction |
| ►Chandlegraph::HandleGraph | |
| ►Chandlegraph::ExpandingOverlayGraph | |
| Chandlegraph::algorithms::SubHandleGraph | |
| Cvg::DagifiedGraph | |
| Cvg::DozeuPinningOverlay | |
| Cvg::IdentityOverlay | |
| Cvg::IncrementalSubgraph | |
| Cvg::NullMaskingGraph | |
| Cvg::PathSubgraph | |
| Cvg::ReverseGraph | |
| Cvg::SourceSinkOverlay | |
| Cvg::StrandSplitGraph | |
| Cvg::SubHandleGraph | |
| Cvg::SubpathOverlay | |
| Cvg::TreeSubgraph | |
| ►Chandlegraph::MutableHandleGraph | |
| ►Chandlegraph::DeletableHandleGraph | |
| ►Chandlegraph::MutablePathDeletableHandleGraph | |
| Cvg::VG | |
| ►Chandlegraph::MutablePathMutableHandleGraph | |
| Chandlegraph::MutablePathDeletableHandleGraph | |
| ►Chandlegraph::PathHandleGraph | |
| ►Chandlegraph::MutablePathHandleGraph | |
| Chandlegraph::MutablePathMutableHandleGraph | |
| ►Chandlegraph::PathPositionHandleGraph | |
| Cvg::MemoizingGraph | |
| Cxg::XG | |
| Cvg::PathSubgraphOverlay | |
| ►Chandlegraph::RankedHandleGraph | |
| ►Chandlegraph::VectorizableHandleGraph | |
| Cxg::XG | |
| Cvg::ExtraNodeGraph | |
| Cvg::IndexedVG | |
| Cvg::JoinedSpliceGraph | |
| Cvg::NetGraph | |
| Cvg::SnarlGraph | |
| ►Cvg::SubgraphOverlay | |
| Cvg::PathSubgraphOverlay | |
| Cvg::HandleGraphNodeSet | |
| Cvg::temp_file::Handler | |
| Cxg::temp_file::Handler | |
| Chaplo::haplo_DP | |
| Chaplo::haplo_DP_column | |
| Chaplo::haplo_DP_rectangle | |
| Cvg::PhasedGenome::Haplotype | |
| Cvg::PhasedGenome::HaplotypeNode | |
| Cvg::HaplotypePartitioner | |
| Cvg::Haplotypes | |
| CHaplotypesConfig | |
| Cstd::hash< const vg::Snarl > | Hash function for Snarls |
| Cstd::hash< handlegraph::edge_t > | |
| Cstd::hash< handlegraph::handle_t > | |
| Cstd::hash< handlegraph::net_handle_t > | |
| Cstd::hash< handlegraph::path_handle_t > | |
| Cstd::hash< handlegraph::step_handle_t > | |
| Cstd::hash< pair< A, B > > | |
| Cstd::hash< std::tuple< TT... > > | |
| Cstd::hash< vg::NodeSide > | |
| Cstd::hash< vg::NodeTraversal > | Hash function for NodeTraversals |
| Cstd::hash< vg::ZipCodeTree::oriented_seed_t > | Hash functor to hash oriented_seed_t with std::hash |
| Cstd::hash< vg::ZipCodeTree::seed_result_t > | Hash functor to hash seed_result_t with std::hash |
| Cvg::Genotyper::hash_ambiguous_allele_set | |
| Cvg::Genotyper::hash_node_traversal | |
| Cvg::Genotyper::hash_oriented_edge | |
| ►CHashGraph | |
| Cvg::io::ConvertedHashGraph | |
| Chaplo::hDP_gbwt_graph_accessor< GBWTType > | |
| Cvg::Haplotypes::Header | Header of the serialized file |
| ChFILE_backend | |
| Cvg::io::hFILE_cppstream | |
| Cvg::MEMClusterer::HitEdge | |
| Cvg::MEMClusterer::HitGraph | |
| Cvg::MEMClusterer::HitNode | |
| ►Cvg::HTSWriter | |
| Cvg::HTSAlignmentEmitter | |
| Cvg::MultipathAlignmentEmitter | |
| Cvg::IDScanner< Message > | |
| Cvg::IncrementIter | |
| Cvg::IndexFile | |
| Cvg::IndexingParameters | |
| Cvg::IndexingPlan | |
| Cvg::IndexRecipe | |
| Cvg::IndexRegistry | |
| Chaplo::int_itvl_t | |
| Cvg::ZipCodeForest::interval_state_t | |
| ►Cistream | |
| Cvg::io::fdistream | |
| Cvg::io::streamistream | |
| Cvg::zstd_ifstream | |
| Cvg::Funnel::Item | Represents an Item whose provenance we track |
| Cvg::ShuffledPairs::iterator | |
| Cvg::PhasedGenome::iterator | |
| Chandlegraph::PathForEachSocket::iterator | |
| Cstd::iterator_traits< vg::PhasedGenome::iterator > | |
| Cstd::iterator_traits< vg::ZipCodeTree::distance_iterator > | |
| Cstd::iterator_traits< vg::ZipCodeTree::seed_iterator > | |
| Cvg::IncrementalSubgraph::IterFCmp | |
| Cjob_type | |
| Cvg::JobSchedule | |
| Cjson_autoptr | |
| Cvg::io::JSONStreamHelper< T > | |
| Cvg::kff_recoding_t | A mapping of character values from KFF encoding to minimizer index encoding |
| Cvg::kmer_t | |
| Cvg::algorithms::kmer_t | Stores a kmer in the context of a graph |
| Cvg::KmerMatch | Used to serialize kmer matches |
| Cvg::KmerPosition | |
| Cvg::LazyRNG | |
| Chaplo::linear_haplo_structure | |
| Cvg::Recombinator::LocalHaplotype | A local haplotype sequence within a single subchain |
| Cvg::LocationSupport | Support pinned to a location, which can be either a node or an edge |
| Cvg::GraphSynchronizer::Lock | |
| Cvg::Locus | Describes a genetic locus with multiple possible alleles, a genotype, and observational support |
| Cvg::Mapping | |
| Cvg::mapping_t | |
| Cvg::MappingHash | |
| CMappingRun | |
| Cvg::NGSSimulator::MarkovDistribution< From, To > | |
| Cvg::NGSSimulator::MarkovDistribution< pair< uint8_t, bool >, pair< pair< uint8_t, bool >, pair< uint8_t, bool > > > | |
| Cvg::Masker | |
| Cvg::MatchPos | |
| Cvg::MaximalExactMatch | |
| Cvg::MCMCGenotyper | |
| Cvg::MEMAccelerator | |
| Cvg::MEMChainModel | |
| Cvg::MEMChainModelVertex | |
| ►Cvg::MEMClusterer | |
| ►Cvg::MinDistanceClusterer | |
| Cvg::ComponentMinDistanceClusterer | |
| Cvg::GreedyMinDistanceClusterer | |
| Cvg::NullClusterer | |
| Cvg::OrientedDistanceClusterer | |
| Cvg::TVSClusterer | |
| Cvg::IntegratedSnarlFinder::MergedAdjacencyGraph | |
| Cvg::io::MessageEmitter | |
| Cvg::io::MessageIterator | |
| Cvg::MinimizerMapper::Minimizer | |
| Cvg::MIPayload | |
| Cvg::multipath_alignment_t | |
| Cvg::MultipathAlignment | |
| Cvg::MultipathAlignmentGraph | |
| Cvg::MultipathProblem | |
| ►Chandlegraph::NamedNodeBackTranslation | |
| Cvg::algorithms::GFAIDMapInfo | |
| Cvg::FlatFileBackTranslation | |
| ►Cvg::NameMapper | |
| Cvg::Constructor | |
| Cvg::VariantAdder | |
| Cvg::Deconstructor::NestingInfo | |
| Chandlegraph::net_handle_t | |
| Cvg::Node | Nodes store sequence data |
| Cvg::algorithms::Node | |
| Cvg::ZipCode::node_code_t | |
| Cvg::NodePileup | |
| Cvg::NodeSide | |
| Cvg::NodeTraversal | |
| Cvg::normal_distribution< T > | |
| Chandlegraph::number_bool_packing | Define a way to pack an integer and an orientation bit into a handle_t |
| ►Cvg::OptionInterface | |
| ►Cvg::BaseOption< Value, OptionValueParser< Value > > | |
| Cvg::Option< Value, Parser > | |
| ►Cvg::BaseOption< vector< Item >, Parser > | |
| Cvg::Option< vector< Item >, Parser > | |
| Cvg::BaseOption< Value, Parser > | |
| Cvg::OptionValueParser< Value > | |
| Cvg::OptionValueParser< vector< Item > > | |
| Cvg::DozeuInterface::OrderedGraph | |
| ►Cvg::ZipCodeTree::oriented_seed_t | |
| Cvg::ZipCodeTree::seed_result_t | |
| ►Cvg::OrientedDistanceMeasurer | |
| Cvg::PathOrientedDistanceMeasurer | |
| Cvg::SnarlOrientedDistanceMeasurer | |
| ►Costream | |
| Cvg::io::fdostream | |
| Cvg::zstd_ofstream | |
| ►CPackedGraph | |
| Cvg::GFAHandleGraph | Use to load in GFAs and remember where they came from |
| Cvg::Packer | |
| Cvg::Funnel::PaintableSpace | |
| ►Cvg::PairedEndMapper | |
| Cvg::BaseMapper | |
| Cvg::ParallelKFFReader | |
| Cvg::HaplotypePartitioner::Parameters | Parameters for partition_haplotypes() |
| Cvg::Recombinator::Parameters | Parameters for generate_haplotypes() |
| Cvg::ParentGenotypeInfo | |
| Cvg::Path | |
| Chandlegraph::path_handle_t | Represents the internal id of a path entity |
| Cvg::path_mapping_t | |
| Cvg::path_t | |
| Cvg::PathBranch | |
| Cvg::PathChunker | |
| Cvg::PathComponentIndex | |
| Chandlegraph::PathForEachSocket | |
| ►CPathHandleGraphProxy | |
| Cvg::GBZGraph | |
| Cvg::PathIndex | |
| Cvg::MatchPos::PathList | |
| ►Chandlegraph::PathMetadata | |
| ►Chandlegraph::MutablePathMetadata | |
| Chandlegraph::MutablePathHandleGraph | |
| Chandlegraph::PathHandleGraph | |
| Cvg::PathNode | |
| Cvg::Paths | |
| Cvg::PhasedGenome | |
| Cvg::PhaseUnfolder | |
| Cvg::Pictographs | |
| Cvg::Pileup | Bundle up Node and Edge pileups |
| Cvg::VG::Plan | Structure for managing parallel construction of a graph |
| Cvg::Position | |
| Cvg::position_t | |
| Cvg::PositionIDScanner< Message > | |
| Cvg::subcommand::Preset | |
| Cvg::Primer | |
| Cvg::PrimerFinder | |
| Cvg::PrimerPair | |
| ►Cvg::Progressive | |
| Cvg::Constructor | |
| Cvg::HaplotypeIndexer | |
| Cvg::MSAConverter | |
| Cvg::RareVariantSimplifier | |
| Cvg::ReadFilter< Read > | |
| Cvg::SmallSnarlSimplifier | |
| Cvg::StreamSorter< Message > | |
| Cvg::VariantAdder | |
| Cvg::VG | |
| Cvg::io::ProtobufEmitter< T > | |
| Cvg::io::ProtobufIterator< T > | |
| CPruningParameters | |
| Cvg::read_alignment_index_t | Type to point to an alignment of a known read |
| Cvg::ReadMasker | |
| Cvg::RebuildJob | |
| Cvg::RebuildParameters | Parameters for rebuild_gbwt |
| Cvg::Recombinator | |
| Cvg::RecombinatorFragment | |
| Cvg::RecombinatorHaplotype | |
| CReferenceInterval | |
| Cvg::Region | |
| Cvg::RegionExpander | |
| Cvg::io::Registry | |
| Chandlegraph::return_type_of< Function > | |
| Chandlegraph::return_type_of< Returns(*)(Args...)> | |
| Chandlegraph::return_type_of< Returns(Owner::*)(Args...) const > | |
| Chandlegraph::return_type_of< Returns(Owner::*)(Args...)> | |
| Chaplo::haploMath::RRMemo | |
| ►Cruntime_error | |
| ►Cvg::algorithms::GFAFormatError | This exception will be thrown if the GFA data is not acceptable |
| Cvg::algorithms::GFADuplicatePathError | |
| Cvg::AlignmentEmbeddingError | |
| Cvg::BandMatricesTooBigException | |
| Cvg::ChainAlignmentFailedError | |
| Cvg::io::TruncatedBGZFError | Represents an error where an input blocked GZIP file has been truncated |
| Cxg::XGFormatError | |
| ►Cruntime_error | |
| Chaplo::linear_haplo_structure::linearUnrepresentable | |
| Cvg::InsufficientInputException | |
| Cvg::WFATree::ScoreProperties | |
| ►Chaplo::ScoreProvider | |
| Chaplo::GBWTScoreProvider< GBWTType > | Score haplotypes using a GBWT haplotype database (normal or dynamic) |
| Chaplo::LinearScoreProvider | Score haplotypes using a linear_haplo_structure |
| CScoringOptions | Options struct for scoring-related parameters. Defaults are in aligner.hpp |
| Cvg::SnarlDistanceIndexClusterer::Seed | Seed information used in Giraffe |
| Cvg::ZipCodeForest::seed_info_t | |
| Cvg::ZipCodeTree::seed_iterator | |
| Cvg::SnarlDistanceIndexClusterer::SeedCache | Seed information used for clustering |
| Cvg::SeqComplexity< MaxOrder > | |
| Cvg::SequenceDictionaryEntry | |
| ►Chandlegraph::Serializable | |
| ►Chandlegraph::SerializableHandleGraph | |
| Cxg::XG | |
| Chandlegraph::TriviallySerializable | |
| Cvg::ShuffledPairs | |
| Cvg::SmallBitset | |
| Cvg::Snarl | Describes a subgraph that is connected to the rest of the graph by two nodes |
| Cvg::ZipCode::snarl_code_t | |
| Cvg::NestedCachedPackedTraversalSupportFinder::snarl_less | |
| ►Cvg::SnarlCaller | |
| ►Cvg::SupportBasedSnarlCaller | |
| Cvg::PoissonSupportSnarlCaller | |
| Cvg::RatioSupportSnarlCaller | |
| ►Chandlegraph::SnarlDecomposition | |
| Chandlegraph::BuildableSnarlDecomposition | |
| Cvg::SnarlDistanceIndexClusterer | |
| ►Cvg::SnarlFinder | |
| Cvg::CactusSnarlFinder | |
| ►Cvg::HandleGraphSnarlFinder | |
| Cvg::IntegratedSnarlFinder | |
| Cvg::SnarlManager | |
| Cvg::SnarlManager::SnarlRecord | |
| Cvg::SnarlState | |
| Cvg::SnarlTraversal | |
| Cvg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild | |
| Cvg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem | |
| Chaplo::linear_haplo_structure::SNVvector | |
| Cvg::ZipCodeForest::sort_value_t | |
| ►Csparse_hash_map | |
| Cvg::hash_map< const vg::mapping_t *, pair< list< vg::mapping_t >::iterator, int64_t > > | |
| Cvg::hash_map< handlegraph::net_handle_t, size_t > | |
| Cvg::hash_map< id_t, map< int64_t, set< vg::mapping_t * > > > | |
| Cvg::hash_map< nid_t, vector< pair< nid_t, bool > > > | |
| Cvg::hash_map< nid_t, vg::Node * > | |
| Cvg::hash_map< vg::Edge *, int > | |
| Cvg::hash_map< vg::Node *, int > | |
| Cvg::pair_hash_map< pair< vg::NodeSide, vg::NodeSide >, vector< vg::Alignment * > > | |
| Cvg::pair_hash_map< pair< vg::NodeSide, vg::NodeSide >, vg::Edge * > | |
| Cvg::pair_hash_map< std::pair< gbwt::node_type, gbwt::node_type >, gbwt::node_type > | |
| Cvg::hash_map< K, V > | |
| Cvg::hash_map< K *, V > | |
| Cvg::pair_hash_map< K, V > | |
| Cvg::string_hash_map< K, V > | |
| ►Csparse_hash_set | |
| Cvg::hash_set< pair< size_t, size_t > > | |
| Cvg::hash_set< vg::id_t > | |
| Cvg::pair_hash_set< std::pair< gbwt::node_type, gbwt::node_type > > | |
| Cvg::hash_set< K > | |
| Cvg::hash_set< K * > | |
| Cvg::pair_hash_set< K > | |
| Cvg::string_hash_set< K > | |
| Cvg::SpliceRegion | |
| Cvg::SpliceStats | |
| Cvg::SSWAligner | |
| Cvg::Funnel::Stage | Represents a Stage which is a series of Items, which track their own provenance |
| Cvg::MinimizerMapper::aligner_stats_t::stat_collection_t | Collection of values you can += |
| Cvg::MinimizerMapper::aligner_stats_t::stat_set_t | Struct to represent counts of bases or seconds or invocations used by different aligners |
| Cvg::state_hash | |
| Cvg::Recombinator::Statistics | Statistics on the generated haplotypes |
| Chandlegraph::step_handle_t | A step handle is an opaque reference to a single step of an oriented node on a path in a graph |
| Cvg::str_view | |
| ►Cstreambuf | |
| Cvg::io::fdinbuf | |
| Cvg::io::fdoutbuf | |
| Cvg::io::streaminbuf | |
| Cvg::zstd_compress_buf | Zstandard compression buffer that writes to another stream buffer |
| Cvg::zstd_decompress_buf | Zstandard decompression buffer that reads from another stream buffer |
| ►Cvg::StreamIndexBase | |
| Cvg::StreamIndex< vg::algorithms::Graph > | |
| Cvg::StreamIndex< Message > | |
| Cvg::io::StreamMultiplexer | |
| Cvg::HaplotypePartitioner::Subchain | |
| Cvg::Haplotypes::Subchain | Representation of a subchain |
| Cvg::subcommand::Subcommand | |
| Cvg::Subpath | A non-branching path of a MultipathAlignment |
| Cvg::subpath_t | |
| Cvg::SummaryStatistics | |
| Cvg::Support | Aggregates information about the reads supporting an allele |
| Cvg::io::Registry::Tables | |
| Cvg::TargetValueSearch | |
| Cvg::Watchdog::thread_state_t | |
| ►Cvg::subcommand::TickChainLink | |
| Cvg::Range< T > | |
| Cvg::Range< Number > | |
| ►Cvg::subcommand::BaseArgSpec< Receiver > | |
| ►Cvg::subcommand::ArgSpec< bool, Receiver > | |
| ►Cvg::subcommand::ValueArgSpec< bool, Receiver > | |
| Cvg::subcommand::FlagArgSpec< Receiver > | |
| ►Cvg::subcommand::ArgSpec< T, Receiver > | |
| ►Cvg::subcommand::ValueArgSpec< T, Receiver, Range< T > > | |
| Cvg::subcommand::RangeArgSpec< T, Receiver > | |
| Cvg::subcommand::ValueArgSpec< T, Receiver, Holder > | |
| ►Cvg::subcommand::BaseOptionGroup | |
| Cvg::subcommand::GroupedOptionGroup | |
| Cvg::subcommand::OptionGroup< Receiver > | |
| Cvg::Haplotypes::TopLevelChain | Representation of a top-level chain |
| Cvg::algorithms::TracedScore | |
| Cvg::Transcript | |
| Cvg::Transcriptome | |
| ►Cvg::TranscriptPath | |
| Cvg::CompletedTranscriptPath | |
| Cvg::EditedTranscriptPath | |
| Cvg::Translation | |
| Cvg::Translator | |
| ►Cvg::TraversalFinder | |
| ►Cvg::ExhaustiveTraversalFinder | |
| Cvg::SupportRestrictedTraversalFinder | |
| Cvg::FlowTraversalFinder | |
| Cvg::GBWTTraversalFinder | |
| Cvg::NestedTraversalFinder | |
| Cvg::PathBasedTraversalFinder | |
| Cvg::PathRestrictedTraversalFinder | |
| Cvg::PathTraversalFinder | |
| Cvg::ReadRestrictedTraversalFinder | |
| Cvg::RepresentativeTraversalFinder | |
| Cvg::TrivialTraversalFinder | |
| Cvg::VCFTraversalFinder | |
| ►Cvg::TraversalSupportCalculator | |
| Cvg::SimpleTraversalSupportCalculator | |
| ►Cvg::TraversalSupportFinder | |
| ►Cvg::PackedTraversalSupportFinder | |
| ►Cvg::CachedPackedTraversalSupportFinder | |
| Cvg::NestedCachedPackedTraversalSupportFinder | |
| Cvg::Tree< T > | |
| Cvg::ZipCodeTree::tree_item_t | One item in the zip code tree, representing a node or edge of the tree |
| Cvg::BitStringTree< Item >::TreeNode | |
| Cvg::TreeNode< T > | |
| ►Ctrue_type | |
| Cvg::is_instantiation_of< Predicate< PredicateArgs... >, Predicate > | |
| Cvg::truncated_normal_distribution< T > | |
| Cvg::uniform_int_distribution< T > | |
| Cvg::uniform_int_distribution< size_t > | |
| Cvg::uniform_int_distribution< uint8_t > | |
| Cvg::uniform_real_distribution< T > | |
| Cvg::uniform_real_distribution< double > | |
| ►CUnionFind | |
| Cvg::SparseUnionFind | |
| Cvg::varint_vector_t | |
| Cvg::VcfBuffer | |
| ►Cvg::VCFOutputCaller | |
| Cvg::Deconstructor | |
| Cvg::FlowCaller | |
| Cvg::LegacyCaller | |
| Cvg::MCMCCaller | |
| Cvg::NestedFlowCaller | |
| Cvg::VCFGenotyper | |
| Cvg::VcfRecordConverter | |
| Cvg::VcfRecordFilter | |
| ►Cvector | |
| Cvg::Packers | |
| CVectorizer | |
| Cvg::VectorView< Item > | |
| Cvg::VectorViewInverse | |
| Cvg::Version | Class for holding vg version and build environment information |
| Cvg::VGIndexes | |
| Cvg::VGset | |
| Cvg::Visit | Describes a step of a walk through a Snarl either on a node or through a child Snarl |
| Cvg::Viz | |
| Cvg::io::VPKG | |
| Cvg::algorithms::walk_t | Record a <=k-length walk in the context of a graph |
| Cvg::wang_hash< T, ImplementationMatched > | |
| Cvg::wang_hash< handle_t > | |
| Cvg::wang_hash< handlegraph::net_handle_t > | Define wang_hash for net_handle_t's so that we can use a hash_map |
| Cvg::wang_hash< net_identifier_t > | |
| Cvg::wang_hash< NodeSide > | |
| Cvg::wang_hash< NodeTraversal > | Hash function for NodeTraversals |
| Cvg::wang_hash< path_handle_t > | |
| Cvg::wang_hash< std::pair< A, B > > | |
| Cvg::wang_hash< T * > | |
| Cvg::wang_hash< T, typename std::enable_if< std::is_integral< T >::value >::type > | |
| Cvg::Watchdog | |
| Cvg::FlowSort::WeightedGraph | |
| Cvg::WFAAlignment | |
| Cvg::WFAExtender | |
| Cvg::WFANode | |
| Cvg::WFAPoint | |
| Cvg::WFATree | |
| Cvg::WideningPRNG< PRNG, OutType > | |
| Cvg::WindowedVcfBuffer | |
| Cvg::WrappingPositionScanner< Message > | |
| Cxg::XGPath | |
| ►CZeroCopyInputStream | |
| Cvg::io::BlockedGzipInputStream | |
| ►CZeroCopyOutputStream | |
| Cvg::io::BlockedGzipOutputStream | |
| Cvg::ZipCode | |
| Cvg::ZipCodeCollection | |
| Cvg::ZipCodeForest | |
| Cvg::ZipCodeTree | |
