| ►Ngafkluge | |
| CGafRecord | |
| CGafStep | |
| ►Ngoogle | |
| ►Nhandlegraph | |
| ►Nalgorithms | |
| CSubHandleGraph | |
| CBoolReturningWrapper | |
| CBoolReturningWrapper< Iteratee, false > | |
| CBoolReturningWrapper< Iteratee, true > | |
| CBuildableSnarlDecomposition | |
| CDeletableHandleGraph | |
| CExpandingOverlayGraph | |
| Chandle_t | Represents a traversal of a node in a graph in a particular direction |
| CHandleGraph | |
| CMutableHandleGraph | |
| CMutablePathDeletableHandleGraph | |
| CMutablePathHandleGraph | |
| CMutablePathMetadata | |
| CMutablePathMutableHandleGraph | |
| CNamedNodeBackTranslation | |
| Cnet_handle_t | |
| Cnumber_bool_packing | Define a way to pack an integer and an orientation bit into a handle_t |
| Cpath_handle_t | Represents the internal id of a path entity |
| ►CPathForEachSocket | |
| Citerator | |
| CPathHandleGraph | |
| CPathMetadata | |
| CPathPositionHandleGraph | |
| CRankedHandleGraph | |
| Creturn_type_of | |
| Creturn_type_of< Returns(*)(Args...)> | |
| Creturn_type_of< Returns(Owner::*)(Args...) const > | |
| Creturn_type_of< Returns(Owner::*)(Args...)> | |
| CSerializable | |
| CSerializableHandleGraph | |
| CSnarlDecomposition | |
| Cstep_handle_t | A step handle is an opaque reference to a single step of an oriented node on a path in a graph |
| CTriviallySerializable | |
| CVectorizableHandleGraph | |
| ►Nhaplo | |
| ►NhaploMath | |
| CRRMemo | |
| Cgbwt_thread_t | |
| CGBWTScoreProvider | Score haplotypes using a GBWT haplotype database (normal or dynamic) |
| Chaplo_DP | |
| Chaplo_DP_column | |
| Chaplo_DP_rectangle | |
| ChDP_gbwt_graph_accessor | |
| Cint_itvl_t | |
| ►Clinear_haplo_structure | |
| ClinearUnrepresentable | |
| CSNVvector | |
| CLinearScoreProvider | Score haplotypes using a linear_haplo_structure |
| CScoreProvider | |
| ►Nstd | Hash functor to hash NodeSides using std::hash |
| Chash< const vg::Snarl > | Hash function for Snarls |
| Chash< handlegraph::edge_t > | |
| Chash< handlegraph::handle_t > | |
| Chash< handlegraph::net_handle_t > | |
| Chash< handlegraph::path_handle_t > | |
| Chash< handlegraph::step_handle_t > | |
| Chash< pair< A, B > > | |
| Chash< std::tuple< TT... > > | |
| Chash< vg::NodeSide > | |
| Chash< vg::NodeTraversal > | Hash function for NodeTraversals |
| Chash< vg::ZipCodeTree::oriented_seed_t > | Hash functor to hash oriented_seed_t with std::hash |
| Chash< vg::ZipCodeTree::seed_result_t > | Hash functor to hash seed_result_t with std::hash |
| Citerator_traits< vg::PhasedGenome::iterator > | |
| Citerator_traits< vg::ZipCodeTree::distance_iterator > | |
| Citerator_traits< vg::ZipCodeTree::seed_iterator > | |
| ►Nvg | |
| ►Nalgorithms | |
| CAnchor | |
| CEdge | |
| CGFADuplicatePathError | |
| CGFAFormatError | This exception will be thrown if the GFA data is not acceptable |
| CGFAIDMapInfo | |
| CGFAParser | |
| CGraph | |
| Ckmer_t | Stores a kmer in the context of a graph |
| CNode | |
| CTracedScore | |
| Cwalk_t | Record a <=k-length walk in the context of a graph |
| ►Nio | |
| CAlignmentEmitter | |
| CBlockedGzipInputStream | |
| CBlockedGzipOutputStream | |
| CConvertedHashGraph | |
| Cfdinbuf | |
| Cfdistream | |
| Cfdostream | |
| Cfdoutbuf | |
| CGafAlignmentEmitter | |
| ChFILE_cppstream | |
| CJSONStreamHelper | |
| CMessageEmitter | |
| CMessageIterator | |
| CNullAlignmentEmitter | |
| CProtobufEmitter | |
| CProtobufIterator | |
| ►CRegistry | |
| CTables | |
| Cstreaminbuf | |
| Cstreamistream | |
| CStreamMultiplexer | |
| CTruncatedBGZFError | Represents an error where an input blocked GZIP file has been truncated |
| CTSVAlignmentEmitter | |
| CVGAlignmentEmitter | |
| CVPKG | |
| ►Nsubcommand | |
| CArgSpec | |
| CBaseArgSpec | |
| CBaseOptionGroup | |
| CBaseValuation | |
| CFlagArgSpec | |
| CGroupedOptionGroup | |
| COptionGroup | |
| CPreset | |
| CRangeArgSpec | |
| CSubcommand | |
| CTickChainLink | |
| CValuation | |
| CValueArgSpec | |
| ►Ntemp_file | |
| CHandler | |
| CAbstractReadSampler | |
| CAliasGraph | |
| CAligner | |
| CAlignerClient | |
| CAlignment | |
| Calignment_index_t | |
| CAlignmentChainModel | |
| CAlignmentChainModelVertex | |
| CAlignmentEmbeddingError | |
| CAlignmentValidity | |
| CAnnotation | |
| CAppendHaplotypeCommand | |
| CAugmentedGraph | |
| CBackTranslatingAlignmentEmitter | |
| ►CBandedGlobalAligner | |
| ►CAltTracebackStack | |
| CDeflection | |
| CBABuilder | |
| CBAMatrix | |
| CBandMatricesTooBigException | |
| CBaseAligner | |
| CBaseMapper | |
| CBaseOption | |
| CBasePileup | |
| CBBEdgeHash | |
| CBenchmarkResult | |
| CBitString | |
| ►CBitStringTree | |
| CTreeNode | |
| CBREAKPOINT | |
| CCachedPackedTraversalSupportFinder | |
| CCactusSide | |
| CCactusSnarlFinder | |
| CChainAlignmentFailedError | |
| CChainIterator | |
| CColors | |
| CCompletedTranscriptPath | |
| CComponentMinDistanceClusterer | |
| CConfigurable | |
| CConfigurableParser | |
| CConnection | An edge in a MultipathAlignment between Subpaths that may not be contiguous in the graph |
| Cconnection_t | |
| CConsistencyCalculator | |
| CConstructedChunk | |
| CConstructor | |
| CContractingGraph | |
| Ccount_back_inserter | |
| CCounts | |
| CDagifiedGraph | |
| ►CDeconstructor | |
| CNestingInfo | |
| CDeleteHaplotypeCommand | |
| CDeletionAligner | |
| CDiagramExplainer | |
| CDinucleotideMachine | |
| Cdiscrete_distribution | We provide a partial discrete_distribution implementation that is just the parts we need |
| CDistanceHeuristic | |
| CDotDumpExplainer | |
| ►CDozeuInterface | |
| Cgraph_pos_s | |
| COrderedGraph | |
| CDozeuPinningOverlay | |
| CEdge | |
| CEdgePileup | Keep pileup-like record for reads that span edges |
| CEdit | |
| Cedit_t | |
| CEditedTranscriptPath | |
| Cendianness | |
| CExhaustiveTraversalFinder | |
| CExon | |
| CExplainer | |
| CExtraNodeGraph | |
| ►CFeatureSet | |
| CFeature | |
| CFilter | |
| CFixedGenotypePriorCalculator | |
| CFlatFileBackTranslation | |
| CFlowCaller | |
| ►CFlowSort | |
| CGrowth | |
| CWeightedGraph | |
| CFlowTraversalFinder | |
| CFragmentedHaplotypeVisit | |
| CFragmentLengthDistribution | |
| CFragmentLengthStatistics | |
| ►CFunnel | |
| CFilterPerformance | |
| CItem | Represents an Item whose provenance we track |
| CPaintableSpace | |
| CStage | Represents a Stage which is a series of Items, which track their own provenance |
| CGAFOutputCaller | |
| CGAFSorterFile | |
| CGAFSorterParameters | |
| CGAFSorterRecord | |
| CGaplessExtender | |
| CGaplessExtension | |
| CGBWTHandler | |
| CGBWTTraversalFinder | |
| CGBZGraph | |
| CGenomeState | |
| CGenomeStateCommand | |
| CGenotype | Describes a genotype at a particular locus |
| CGenotypeLikelihoodCalculator | |
| CGenotypePriorCalculator | |
| ►CGenotyper | |
| CAffinity | |
| Chash_ambiguous_allele_set | |
| Chash_node_traversal | |
| Chash_oriented_edge | |
| CGFAHandleGraph | Use to load in GFAs and remember where they came from |
| CGFFReader | |
| CGFFRecord | |
| CGraph | |
| CGraphCaller | |
| ►CGraphSynchronizer | |
| CLock | |
| CGreedyMinDistanceClusterer | |
| CGSSWAligner | |
| CHandleGraphNodeSet | |
| CHandleGraphSnarlFinder | |
| CHaplotypeIndexer | |
| ►CHaplotypePartitioner | |
| CParameters | Parameters for partition_haplotypes() |
| CSubchain | |
| ►CHaplotypes | |
| CHeader | Header of the serialized file |
| CSubchain | Representation of a subchain |
| CTopLevelChain | Representation of a top-level chain |
| Chash_map | |
| Chash_map< K *, V > | |
| Chash_set | |
| Chash_set< K * > | |
| CHTSAlignmentEmitter | |
| CHTSWriter | |
| CIdentityOverlay | |
| CIDScanner | |
| ►CIncrementalSubgraph | |
| CFCmp | |
| CIterFCmp | |
| CIncrementIter | |
| ►CIndexedVG | |
| CCacheEntry | |
| CIndexFile | |
| CIndexingParameters | |
| CIndexingPlan | |
| CIndexRecipe | |
| CIndexRegistry | |
| CInsertHaplotypeCommand | |
| CInsufficientInputException | |
| ►CIntegratedSnarlFinder | |
| CMergedAdjacencyGraph | |
| Cis_instantiation_of | |
| Cis_instantiation_of< Predicate< PredicateArgs... >, Predicate > | |
| CJobSchedule | |
| CJoinedSpliceGraph | |
| Ckff_recoding_t | A mapping of character values from KFF encoding to minimizer index encoding |
| Ckmer_t | |
| CKmerMatch | Used to serialize kmer matches |
| CKmerPosition | |
| CLazyRNG | |
| CLegacyCaller | |
| CLocationSupport | Support pinned to a location, which can be either a node or an edge |
| CLocus | Describes a genetic locus with multiple possible alleles, a genotype, and observational support |
| CMapper | |
| CMapping | |
| Cmapping_t | |
| CMappingHash | |
| CMasker | |
| ►CMatchPos | |
| CPathList | |
| CMaximalExactMatch | |
| CMCMCCaller | |
| CMCMCGenotyper | |
| CMEMAccelerator | |
| CMEMChainModel | |
| CMEMChainModelVertex | |
| ►CMEMClusterer | |
| CDPScoreComparator | |
| CHitEdge | |
| CHitGraph | |
| CHitNode | |
| CMemoizingGraph | |
| CMinDistanceClusterer | |
| ►CMinimizerMapper | |
| ►Caligner_stats_t | Struct to represent per-DP-method stats |
| Cstat_collection_t | Collection of values you can += |
| Cstat_set_t | Struct to represent counts of bases or seconds or invocations used by different aligners |
| CMinimizer | |
| CMIPayload | |
| CMSAConverter | |
| Cmultipath_alignment_t | |
| CMultipathAlignment | |
| CMultipathAlignmentEmitter | |
| CMultipathAlignmentGraph | |
| CMultipathMapper | |
| CMultipathProblem | |
| CNameMapper | |
| ►CNestedCachedPackedTraversalSupportFinder | |
| Csnarl_less | |
| ►CNestedFlowCaller | |
| CCallRecord | Stuff we remember for each snarl call, to be used when genotyping its parent |
| CNestedTraversalFinder | |
| CNetGraph | |
| ►CNGSSimulator | |
| CMarkovDistribution | |
| CNoAlignmentInBandException | |
| CNode | Nodes store sequence data |
| CNodePileup | |
| CNodeSide | |
| CNodeTraversal | |
| Cnormal_distribution | |
| CNullClusterer | |
| CNullMaskingGraph | |
| COption | |
| COption< vector< Item >, Parser > | |
| COptionInterface | |
| COptionValueParser | |
| COptionValueParser< vector< Item > > | |
| COrientedDistanceClusterer | |
| COrientedDistanceMeasurer | |
| CPackedTraversalSupportFinder | |
| CPacker | |
| CPackers | |
| Cpair_hash_map | |
| Cpair_hash_set | |
| CPairedEndMapper | |
| CParallelKFFReader | |
| CParentGenotypeInfo | |
| CPath | |
| Cpath_mapping_t | |
| Cpath_t | |
| CPathBasedTraversalFinder | |
| CPathBranch | |
| CPathChunker | |
| CPathComponentIndex | |
| CPathIndex | |
| CPathNode | |
| CPathOrientedDistanceMeasurer | |
| CPathRestrictedTraversalFinder | |
| CPaths | |
| CPathSubgraph | |
| CPathSubgraphOverlay | |
| CPathTraversalFinder | |
| ►CPhasedGenome | |
| CHaplotype | |
| CHaplotypeNode | |
| Citerator | |
| CPhaseUnfolder | |
| CPictographs | |
| CPileup | Bundle up Node and Edge pileups |
| ►CPoissonSupportSnarlCaller | |
| CPoissonCallInfo | |
| CPosition | |
| Cposition_t | |
| CPositionIDScanner | |
| CPrimer | |
| CPrimerFinder | |
| CPrimerPair | |
| CProblemDumpExplainer | |
| CProgressive | |
| CQualAdjAligner | |
| CQualAdjXdropAligner | |
| CRange | |
| CRareVariantSimplifier | |
| CRatioSupportSnarlCaller | |
| Cread_alignment_index_t | Type to point to an alignment of a known read |
| CReadFilter | |
| CReadMasker | |
| CReadRestrictedTraversalFinder | |
| CRebuildJob | |
| CRebuildParameters | Parameters for rebuild_gbwt |
| ►CRecombinator | |
| CLocalHaplotype | A local haplotype sequence within a single subchain |
| CParameters | Parameters for generate_haplotypes() |
| CStatistics | Statistics on the generated haplotypes |
| CRecombinatorFragment | |
| CRecombinatorHaplotype | |
| CRegion | |
| CRegionExpander | |
| CReplaceLocalHaplotypeCommand | |
| CReplaceSnarlHaplotypeCommand | |
| CRepresentativeTraversalFinder | |
| CReverseGraph | |
| CRewindPlanException | |
| CSampler | |
| CSeqComplexity | |
| CSequenceDictionaryEntry | |
| ►CShuffledPairs | |
| Citerator | |
| CSimpleConsistencyCalculator | |
| CSimpleTraversalSupportCalculator | |
| CSizeLimitExceededException | |
| CSmallBitset | |
| CSmallSnarlSimplifier | |
| CSnarl | Describes a subgraph that is connected to the rest of the graph by two nodes |
| ►CSnarlCaller | |
| CCallInfo | |
| ►CSnarlDistanceIndexClusterer | |
| CCluster | Cluster information used in Giraffe |
| CClusterHead | |
| CClusteringProblem | |
| CSeed | Seed information used in Giraffe |
| CSeedCache | Seed information used for clustering |
| ►CSnarlTreeNodeProblem | |
| CSnarlTreeChild | |
| CSnarlFinder | |
| CSnarlGraph | |
| ►CSnarlManager | |
| CSnarlRecord | |
| CSnarlMinDistance | |
| CSnarlOrientedDistanceMeasurer | |
| CSnarlState | |
| CSnarlTraversal | |
| CSourceSinkOverlay | |
| CSparseUnionFind | |
| CSplicedHTSAlignmentEmitter | |
| CSpliceRegion | |
| CSpliceStats | |
| CSSWAligner | |
| Cstate_hash | |
| Cstr_view | |
| CStrandSplitGraph | |
| CStreamIndex | |
| CStreamIndexBase | |
| CStreamSorter | |
| Cstring_hash_map | |
| Cstring_hash_set | |
| CSubgraphExplainer | |
| CSubgraphOverlay | |
| CSubHandleGraph | |
| CSubpath | A non-branching path of a MultipathAlignment |
| Csubpath_t | |
| CSubpathOverlay | |
| CSummaryStatistics | |
| CSupport | Aggregates information about the reads supporting an allele |
| CSupportAugmentedGraph | Augmented Graph that holds some Support annotation data specific to vg call |
| CSupportBasedSnarlCaller | |
| CSupportRestrictedTraversalFinder | |
| CSurjectingAlignmentEmitter | |
| CSurjector | |
| CSwapHaplotypesCommand | |
| CTargetValueSearch | |
| CTipAnchoredMaxDistance | |
| CTranscript | |
| CTranscriptome | |
| CTranscriptPath | |
| CTranslation | |
| CTranslator | |
| CTraversalFinder | |
| CTraversalSupportCalculator | |
| CTraversalSupportFinder | |
| CTree | |
| CTreeNode | |
| CTreeSubgraph | |
| CTrivialTraversalFinder | |
| Ctruncated_normal_distribution | |
| CTSVExplainer | |
| CTVSClusterer | |
| Cuniform_int_distribution | |
| Cuniform_real_distribution | |
| CVariantAdder | |
| Cvarint_vector_t | |
| CVcfBuffer | |
| CVCFGenotyper | |
| CVCFOutputCaller | |
| CVcfRecordConverter | |
| CVcfRecordFilter | |
| CVCFTraversalFinder | |
| ►CVectorView | |
| Cconst_iterator | Random access iterator |
| CVectorViewInverse | |
| CVersion | Class for holding vg version and build environment information |
| ►CVG | |
| CPlan | Structure for managing parallel construction of a graph |
| CVGIndexes | |
| CVGset | |
| CVisit | Describes a step of a walk through a Snarl either on a node or through a child Snarl |
| CViz | |
| Cwang_hash | |
| Cwang_hash< handle_t > | |
| Cwang_hash< handlegraph::net_handle_t > | Define wang_hash for net_handle_t's so that we can use a hash_map |
| Cwang_hash< net_identifier_t > | |
| Cwang_hash< NodeSide > | |
| Cwang_hash< NodeTraversal > | Hash function for NodeTraversals |
| Cwang_hash< path_handle_t > | |
| Cwang_hash< std::pair< A, B > > | |
| Cwang_hash< T * > | |
| Cwang_hash< T, typename std::enable_if< std::is_integral< T >::value >::type > | |
| ►CWatchdog | |
| Cthread_state_t | |
| CWFAAlignment | |
| ►CWFAExtender | |
| ►CErrorModel | |
| CEvent | |
| CWFANode | |
| CWFAPoint | |
| ►CWFATree | |
| CScoreProperties | |
| CWideningPRNG | |
| CWindowedVcfBuffer | |
| CWrappingPositionScanner | |
| CXdropAligner | |
| ►CZipCode | |
| Cchain_code_t | |
| Cdecoder_t | |
| Cnode_code_t | |
| Csnarl_code_t | |
| CZipCodeCollection | |
| ►CZipCodeForest | |
| Cchild_info_t | |
| Cforest_growing_state_t | This stores information about the state of the forest as we fill it in |
| Cinterval_state_t | |
| Cseed_info_t | |
| Csort_value_t | |
| ►CZipCodeTree | |
| Cdistance_iterator | |
| Coriented_seed_t | |
| Cseed_iterator | |
| Cseed_result_t | |
| Ctree_item_t | One item in the zip code tree, representing a node or edge of the tree |
| Czstd_compress_buf | Zstandard compression buffer that writes to another stream buffer |
| Czstd_decompress_buf | Zstandard decompression buffer that reads from another stream buffer |
| Czstd_ifstream | |
| Czstd_ofstream | |
| ►Nxg | |
| ►Ntemp_file | |
| CHandler | |
| CXG | |
| CXGFormatError | |
| CXGPath | |
| CChainsConfig | |
| Cfrom_chars_result | |
| CGBWTConfig | |
| CGiraffeMainOptions | Options struct for options for the Giraffe driver (i.e. this file) |
| CGraphHandler | |
| CHaplotypesConfig | |
| ChFILE_backend | |
| Cj2pb_error | |
| Cjob_type | |
| Cjson_autoptr | |
| CMappingRun | |
| CPruningParameters | |
| CReferenceInterval | |
| CScoringOptions | Options struct for scoring-related parameters. Defaults are in aligner.hpp |
| CVectorizer | |
