Cvg::Genotyper::Affinity | |
►Cvg::AlignerClient | |
►Cvg::BaseMapper | |
Cvg::Mapper | |
Cvg::MultipathMapper | |
Cvg::MinimizerMapper | |
Cvg::Surjector | |
Cvg::Alignment | |
Cvg::AlignmentChainModel | |
Cvg::AlignmentChainModelVertex | |
►Cvg::io::AlignmentEmitter | |
►Cvg::HTSAlignmentEmitter | |
Cvg::SplicedHTSAlignmentEmitter | |
Cvg::io::GafAlignmentEmitter | |
Cvg::io::NullAlignmentEmitter | |
Cvg::io::TSVAlignmentEmitter | |
Cvg::io::VGAlignmentEmitter | |
Cvg::BandedGlobalAligner< IntType >::AltTracebackStack | |
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::BenchmarkResult | |
Cvg::BitString | |
Cvg::BitStringTree< Item > | |
Cvg::BitStringTree< bin_t > | |
Chandlegraph::BoolReturningWrapper< Iteratee, Iterated, IterateeReturnType > | |
Chandlegraph::BoolReturningWrapper< Iteratee, Iterated, bool > | This specialization handles wrapping bool-returning callables |
Chandlegraph::BoolReturningWrapper< Iteratee, Iterated, void > | This specialization handles wrapping void-returning callables |
Cvg::BREAKPOINT | |
Cvg::IndexedVG::CacheEntry | |
Cvg::CactusSide | |
►Cvg::SnarlCaller::CallInfo | |
Cvg::PoissonSupportSnarlCaller::PoissonCallInfo | |
Cvg::MinimumDistanceIndex::ChainIndex | |
Cvg::ChainIterator | |
Cvg::SnarlSeedClusterer::Cluster | Cluster information used in Giraffe |
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::ConstructedChunk | |
Cvg::ReadFilter::Counts | |
Cvg::Deconstructor | |
Cvg::BandedGlobalAligner< IntType >::AltTracebackStack::Deflection | |
Cvg::DepthMap | |
Cvg::DinucleotideMachine | |
Cvg::discrete_distribution< T > | We provide a partial discrete_distribution implementation that is just the parts we need |
►Cvg::DistanceHeuristic | |
Cvg::SnarlMinDistance | |
Cvg::TipAnchoredMaxDistance | |
►Cvg::DozeuInterface | |
Cvg::QualAdjXdropAligner | |
Cvg::XdropAligner | |
Cvg::MEMClusterer::DPScoreComparator | |
Cvg::Edge | |
Cbdsg::ODGI::edge_helper | |
Cvg::EdgePileup | Keep pileup-like record for reads that span edges |
Cvg::Edit | |
Cvg::edit_t | |
Cvg::endianness< IntType > | |
►Cexception | |
Cj2pb_error | |
Cvg::indexOpenException | |
Cvg::keyNotFoundException | |
Cvg::NoAlignmentInBandException | |
Cvg::Exon | |
►Cfalse_type | |
Cvg::is_instantiation_of< Subject, Predicate > | |
Cvg::FeatureSet::Feature | |
Cvg::FeatureSet | |
Cvg::Filter | |
Cvg::Funnel::FilterPerformance | |
Cvg::FlowSort | |
Cvg::FragmentLengthDistribution | |
Cvg::FragmentLengthStatistics | |
Cvg::Funnel | |
►Cvg::GAFOutputCaller | |
Cvg::FlowCaller | |
Cvg::VCFGenotyper | |
Cgafkluge::GafRecord | |
Cgafkluge::GafStep | |
Cvg::GaplessExtender | |
Cvg::GaplessExtension | |
Chaplo::gbwt_thread_t | |
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::GFFReader | |
Cvg::GFFRecord | |
Cvg::Graph | |
Cvg::DozeuInterface::graph_pos_s | |
►Cvg::GraphCaller | |
Cvg::FlowCaller | |
Cvg::LegacyCaller | |
Cvg::VCFGenotyper | |
Cvg::GraphSynchronizer | |
Cvg::FlowSort::Growth | |
Chandlegraph::handle_t | Represents the internal id of a node traversal |
►Chandlegraph::HandleGraph | |
►Chandlegraph::ExpandingOverlayGraph | |
Cvg::DagifiedGraph | |
Cvg::DozeuPinningOverlay | |
Cvg::IdentityOverlay | |
Cvg::IncrementalSubgraph | |
Cvg::NullMaskingGraph | |
Cvg::PathSubgraph | |
Cvg::ReverseGraph | |
Cvg::StrandSplitGraph | |
Cvg::SubHandleGraph | |
Cvg::TreeSubgraph | |
►Chandlegraph::MutableHandleGraph | |
►Chandlegraph::DeletableHandleGraph | |
►Chandlegraph::MutablePathDeletableHandleGraph | |
Cbdsg::HashGraph | |
Cbdsg::ODGI | |
Cbdsg::PackedGraph | |
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::SourceSinkOverlay | |
►Cvg::SubgraphOverlay | |
Cvg::PathSubgraphOverlay | |
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 | |
Cstd::hash< const vg::Snarl > | Hash function for Snarls |
Cstd::hash< handlegraph::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 |
Cvg::Genotyper::hash_ambiguous_allele_set | |
Cvg::Genotyper::hash_node_traversal | |
Cvg::Genotyper::hash_oriented_edge | |
Chaplo::hDP_gbwt_graph_accessor< GBWTType > | |
ChFILE_backend | |
Cvg::io::hFILE_cppstream | |
Cvg::MEMClusterer::HitEdge | |
Cvg::MEMClusterer::HitGraph | |
Cvg::MEMClusterer::HitNode | |
Cvg::Homogenizer | |
Cvg::IDScanner< Message > | |
Cvg::IncrementIter | |
Cvg::Index | |
Chaplo::int_itvl_t | |
►Cistream | |
Cvg::io::fdistream | |
Cvg::Funnel::Item | Represents an Item whose provenance we track |
Cvg::PhasedGenome::iterator | |
Cvg::ShuffledPairs::iterator | |
Chandlegraph::PathForEachSocket::iterator | |
Cstd::iterator_traits< vg::PhasedGenome::iterator > | |
Cjson_autoptr | |
Cvg::io::JSONStreamHelper< T > | |
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 | |
Chaplo::linear_haplo_structure | |
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::NGSSimulator::MarkovDistribution< From, To > | |
Cvg::NGSSimulator::MarkovDistribution< pair< uint8_t, bool >, pair< pair< uint8_t, bool >, pair< uint8_t, bool > > > | |
Cvg::MaximalExactMatch | |
Cvg::MCMCGenotyper | |
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::MinimumDistanceIndex | |
Cvg::MIPayload | |
Cvg::multipath_alignment_t | |
Cvg::MultipathAlignment | |
Cvg::MultipathAlignmentEmitter | |
Cvg::MultipathAlignmentGraph | |
Cvg::MultipathProblem | |
►Cvg::NameMapper | |
Cvg::Constructor | |
Cvg::VariantAdder | |
Cvg::SnarlSeedClusterer::NetgraphNode | |
Cvg::NGSSimulator | |
Cvg::Node | Nodes store sequence data |
Cbdsg::HashGraph::node_t | |
Cvg::SnarlSeedClusterer::NodeClusters | |
Cvg::NodePileup | |
Cvg::NodeSide | |
Cvg::NodeTraversal | |
Cvg::normal_distribution< T > | |
Cvg::normal_distribution< double > | |
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::OrientedDistanceMeasurer | |
Cvg::PathOrientedDistanceMeasurer | |
Cvg::SnarlOrientedDistanceMeasurer | |
►Costream | |
Cvg::io::fdostream | |
Cbdsg::PackedGraph::PackedPath | |
Cvg::Packer | |
►Cvg::PairedEndMapper | |
Cvg::BaseMapper | |
Cvg::Path | |
Chandlegraph::path_handle_t | Represents the internal id of a path entity |
Cvg::path_mapping_t | |
Cbdsg::HashGraph::path_mapping_t | |
Cbdsg::ODGI::path_metadata_t | |
Cvg::path_t | |
Cbdsg::HashGraph::path_t | |
Cvg::PathBranch | |
Cvg::PathChunker | |
Cvg::PathComponentIndex | |
Chandlegraph::PathForEachSocket | |
Cvg::PathIndex | |
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::Progressive | |
Cvg::Constructor | |
Cvg::HaplotypeIndexer | |
Cvg::IndexManager | |
Cvg::MSAConverter | |
Cvg::RareVariantSimplifier | |
Cvg::SmallSnarlSimplifier | |
Cvg::StreamSorter< Message > | |
Cvg::VariantAdder | |
Cvg::VG | |
Cvg::io::ProtobufEmitter< T > | |
Cvg::io::ProtobufIterator< T > | |
CPruningParameters | |
Cvg::Range< Number > | This defines a range of values to test, from start to <=end, going up by step |
Cvg::ReadFilter | |
Cvg::Region | |
Cvg::RegionExpander | |
Cvg::io::Registry | |
Chaplo::haploMath::RRMemo | |
►Cruntime_error | |
Chaplo::linear_haplo_structure::linearUnrepresentable | |
Cvg::algorithms::GFAFormatError | This exception will be thrown if the GFA data is not acceptable |
Cxg::XGFormatError | |
Cvg::Sampler | |
►Chaplo::ScoreProvider | |
Chaplo::GBWTScoreProvider< GBWTType > | Score haplotypes using a GBWT haplotype database (normal or dynamic) |
Chaplo::LinearScoreProvider | Score haplotypes using a linear_haplo_structure |
Cvg::SnarlSeedClusterer::Seed | Seed information used in Giraffe |
►Chandlegraph::SerializableHandleGraph | |
Cbdsg::HashGraph | |
Cbdsg::ODGI | |
Cbdsg::PackedGraph | |
Cxg::XG | |
Cvg::ShuffledPairs | |
Cvg::SmallBitset | |
Cvg::Snarl | Describes a subgraph that is connected to the rest of the graph by two nodes |
►Cvg::SnarlCaller | |
►Cvg::SupportBasedSnarlCaller | |
Cvg::PoissonSupportSnarlCaller | |
Cvg::RatioSupportSnarlCaller | |
►Cvg::SnarlFinder | |
Cvg::CactusSnarlFinder | |
►Cvg::HandleGraphSnarlFinder | |
Cvg::IntegratedSnarlFinder | |
Cvg::MinimumDistanceIndex::SnarlIndex | |
Cvg::SnarlManager | |
Cvg::SnarlManager::SnarlRecord | |
Cvg::SnarlSeedClusterer | |
Cvg::SnarlState | |
Cvg::SnarlTraversal | |
Chaplo::linear_haplo_structure::SNVvector | |
►Csparse_hash_map | |
Cvg::hash_map< const vg::mapping_t *, pair< list< vg::mapping_t >::iterator, int64_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< size_t, size_t > | |
Cvg::hash_map< size_t, vector< pair< vg::SnarlSeedClusterer::NetgraphNode, vg::SnarlSeedClusterer::NodeClusters > > > | |
Cvg::hash_map< size_t, vg::hash_map< size_t, pair< size_t, vg::SnarlSeedClusterer::NodeClusters > > > | |
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::SpliceMotifs | |
Cvg::SpliceRegion | |
Cvg::SRPE | |
Cvg::SSWAligner | |
Cvg::Funnel::Stage | Represents a Stage which is a series of Items, which track their own provenance |
Cvg::state_hash | |
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 |
►Cstreambuf | |
Cvg::io::fdinbuf | |
Cvg::io::fdoutbuf | |
►Cvg::StreamIndexBase | |
Cvg::StreamIndex< vg::Graph > | |
Cvg::StreamIndex< Message > | |
Cvg::io::StreamMultiplexer | |
Cvg::subcommand::Subcommand | |
Cvg::Subpath | A non-branching path of a MultipathAlignment |
Cvg::subpath_t | |
Cvg::Support | Aggregates information about the reads supporting an allele |
Cvg::io::Registry::Tables | |
Cvg::TargetValueSearch | |
Cvg::Watchdog::thread_state_t | |
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::Tree< T > | |
Cvg::BitStringTree< Item >::TreeNode | |
Cvg::TreeNode< T > | |
Cvg::SnarlSeedClusterer::TreeState | |
►Ctrue_type | |
Cvg::is_instantiation_of< Predicate< PredicateArgs... >, Predicate > | |
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 > | |
Cvg::VcfBuffer | |
►Cvg::VCFOutputCaller | |
Cvg::FlowCaller | |
Cvg::LegacyCaller | |
Cvg::MCMCCaller | |
Cvg::VCFGenotyper | |
Cvg::VcfRecordConverter | |
Cvg::VcfRecordFilter | |
►Cvector | |
Cvg::Packers | |
CVectorizer | |
Cvg::Version | Class for holding vg version and build environment information |
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 | Stores a walk in the context of a graph |
Cvg::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< 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::WideningPRNG< PRNG, OutType > | |
Cvg::WindowedVcfBuffer | |
Cvg::WrappingPositionScanner< Message > | |
Cxg::XGPath | |
►CZeroCopyInputStream | |
Cvg::io::BlockedGzipInputStream | |
►CZeroCopyOutputStream | |
Cvg::io::BlockedGzipOutputStream | |