Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

Nhaplo
NhaploMath
CRRMemo
Cint_itvl_t
Cgbwt_thread_t
ChDP_gbwt_graph_accessor
Chaplo_DP_rectangle
Chaplo_DP_column
Chaplo_DP
CScoreProvider
CGBWTScoreProvider	Score haplotypes using a GBWT haplotype database (normal or dynamic)
Nstd	Hash functor to hash NodeSides using std::hash
Chash< const vg::Snarl >	Hash function for Snarls
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
CChainScoringScheme
CChainsResult
CChainWithRec
CEdge
CGFADuplicatePathError
CGFAFormatError	This exception will be thrown if the GFA data is not acceptable
CGFAIDMapInfo
CGFAParser
CGFATextParser
CGFAzParser
CPendingRGFAVisit
CGraph
Ckmer_t	Stores a kmer in the context of a graph
CNode
CTracedScore
Ctransition_info	Represents a possible transition between anchors
Cwalk_t	Record a <=k-length walk in the context of a graph
Nio
CConvertedHashGraph
CJSONStreamHelper
Nsubcommand
CArgSpec
CBaseArgSpec
CBaseOptionGroup
CBaseValuation
CFlagArgSpec
CGroupedOptionGroup
CNegationFlagArgSpec
COptionGroup
CPreset
CRangeArgSpec
CSubcommand
CTickChainLink
CValuation
CValueArgSpec
Ntemp_file
CHandler
CAbstractReadSampler
CAliasGraph
CAligner
CAlignerClient
CAlignmentChainModel
CAlignmentChainModelVertex
CAlignmentEmbeddingError
CAlignmentEmitter
CAlignmentScorer
CAlignmentValidity
CAnnotation
CAugmentedGraph
CBackTranslatingAlignmentEmitter
CBandedGlobalAligner
CBAMatrix
CAltTracebackStack
CDeflection
CBABuilder
CBandMatricesTooBigException
CBaseAligner
CBaseMapper
CBaseOption
CBBEdgeHash
CBenchmarkResult
CBitString
CBitStringTree
CTreeNode
CCachedPackedTraversalSupportFinder
CCactusSide
CCactusSnarlFinder
CcerrWrapper
CChainAlignmentFailedError
CChainIterator
CColors
CCompletedTranscriptPath
CComponentMinDistanceClusterer
CConfigurable
CConfigurableParser
Cconnection_t
CConsistencyCalculator
CConstructedChunk
CConstructor
CContractingGraph
Ccount_back_inserter
CCounts
CDagifiedGraph
CDeconstructor
CChildContext
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
Cedit_t
CEditAlignmentScorer
CEditedTranscriptPath
CExhaustiveTraversalFinder
CExon
CExpandingOverlayGraph
CExplainer
CFeatureSet
CFeature
CFixedGenotypePriorCalculator
CFlatFileBackTranslation
CFlowCaller
CFlowSort
CWeightedGraph
CGrowth
CFlowTraversalFinder
CFragmentedHaplotypeVisit
CFragmentLengthDistribution
CFragmentLengthStatistics
CFunnel
CFilterPerformance
CPaintableSpace
CItem	Represents an Item whose provenance we track
CStage	Represents a Stage which is a series of Items, which track their own provenance
CGAFOutputCaller
CGAFSorterFile
CGAFSorterParameters
CGAFSorterRecord
CGaplessExtender
CGaplessExtension
CGBWTHandler
CGBWTTraversalFinder
CGBZGraph
CGenotypeLikelihoodCalculator
CGenotypePriorCalculator
CGenotyper
CAffinity
CGFAHandleGraph	Use to load in GFAs and remember where they came from
CGFFReader
CGFFRecord
CGraph
CGraphCaller
CGraphSynchronizer
CLock
CGreedyMinDistanceClusterer
CGrefCover
CTopLevelSnarlStats
CGSSWAligner
CHandleGraphNodeSet
CHandleGraphSnarlFinder
CHaplotypeIndexer
CHaplotypePartitioner
CSubchain
CParameters	Parameters for partition_haplotypes()
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
CIndexFile
CIndexingParameters
CIndexingPlan
CIndexRecipe
CIndexRegistry
CIndirectVectorView
CInsufficientInputException
CIntegratedSnarlFinder
CMergedAdjacencyGraph
CIntervalUnion
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
CKmerPosition
CLazyRNG
CLegacyCaller
CLoggedGapAlignmentScorer
CLogger
CMapper
Cmapping_t
CMappingHash
CMappingQualityCalculator
CMasker
CMatchPos
CPathList
CMatrixAlignmentScorer
CMaximalExactMatch
CMCMCCaller
CMCMCGenotyper
CMEMAccelerator
CMEMChainModel
CMEMChainModelVertex
CMEMClusterer
CHitEdge
CHitNode
CHitGraph
CDPScoreComparator
CMemoizingGraph
CMinDistanceClusterer
CMinimizerIndexParameters	Minimizer index construction parameters
CMinimizerMapper
CMinimizer
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
Cread_alignment_index_t	Type to point to an alignment of a known read
Calignment_index_t
CMIPayload
CMSAConverter
Cmultipath_alignment_t
CMultipathAlignmentEmitter
CMultipathAlignmentGraph
CMultipathMapper
CMultipathProblem
CNameMapper
CNestedCachedPackedTraversalSupportFinder
Csnarl_less
CNestedFlowCaller
CCallRecord	Stuff we remember for each snarl call, to be used when genotyping its parent
CNetGraph
CNGSSimulator
CMarkovDistribution
CNoAlignmentInBandException
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_mapping_t
Cpath_t
CPathBasedTraversalFinder
CPathBranch
CPathChunker
CPathComponentIndex
CPathIndex
CPathNode
CPathOrientedDistanceMeasurer
CPathPiece	A maximal piece of a path whose nodes and edges all exist in a GBWT index
CPathRestrictedTraversalFinder
CPaths
CPathSubgraph
CPathSubgraphOverlay
CPathTraversalFinder
CPhasedGenome
CHaplotypeNode
CHaplotype
Citerator
CPhaseUnfolder
CPictographs
CPoissonSupportSnarlCaller
CPoissonCallInfo
Cposition_t
CPositionIDScanner
CPrimer
CPrimerFinder
CPrimerPair
CProblemDumpExplainer
CProgressive
CQualAdjAligner
CQualAdjAlignmentScorer
CQualAdjXdropAligner
CRange
CRareVariantSimplifier
CRatioSupportSnarlCaller
CReadFilter
CReadMasker
CReadRestrictedTraversalFinder
CRebuildJob
CRebuildParameters	Parameters for rebuild_gbwt
CRecombinator
CStatistics	Statistics on the generated haplotypes
CParameters	Parameters for generate_haplotypes()
CLocalHaplotype	A local haplotype sequence within a single subchain
CRecombinatorFragment
CRecombinatorHaplotype
CRegion
CRegionExpander
CRepresentativeTraversalFinder
CReverseGraph
CRewindPlanException
CSampler
CSeqComplexity
CSequenceDictionaryEntry
CShuffledPairs
Citerator
CSimpleConsistencyCalculator
CSimpleTraversalSupportCalculator
CSizeLimitExceededException
CSmallBitset
CSmallSnarlSimplifier
CSnarlCaller
CCallInfo
CSnarlDistanceIndexClusterer
CSeed	Seed information used in Giraffe
CSeedCache	Seed information used for clustering
CCluster	Cluster information used in Giraffe
CSnarlTreeNodeProblem
CSnarlTreeChild
CClusterHead
CClusteringProblem
CSnarlFinder
CSnarlGraph
CSnarlManager
CSnarlRecord
CSnarlMinDistance
CSnarlOrientedDistanceMeasurer
CSourceSinkOverlay
CSparseUnionFind
CSplicedHTSAlignmentEmitter
CSpliceRegion
CSpliceStats
CSSWAligner
Cstate_hash
CStrandSplitGraph
CStreamIndex
CStreamIndexBase
CStreamSorter
Cstring_hash_map
Cstring_hash_set
CSubgraphExplainer
CSubgraphOverlay
CSubHandleGraph
Csubpath_t
CSubpathOverlay
CSummaryStatistics
CSupportAugmentedGraph	Augmented Graph that holds some Support annotation data specific to vg call
CSupportBasedSnarlCaller
CSupportRestrictedTraversalFinder
CSurjectingAlignmentEmitter
CSurjector
CTargetValueSearch
CTipAnchoredMaxDistance
CTranscript
CTranscriptome
CTranscriptPath
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
CSuppressedRef
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
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
Cdecoder_t
Cnode_code_t
Cchain_code_t
Csnarl_code_t
CZipCodeCollection
CZipCodeForest
Cforest_growing_state_t	This stores information about the state of the forest as we fill it in
Cseed_info_t
Cchild_info_t
Cinterval_state_t
Csort_value_t
CZipCodeTree
Ctree_item_t	One item in the zip code tree, representing a node or edge of the tree
Coriented_seed_t
Cseed_result_t
Cseed_iterator
Cdistance_iterator
Citeration_position
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
CChainsConfig
CGBWTConfig
CGiraffeMainOptions	Options struct for options for the Giraffe driver (i.e. this file)
CGraphHandler
CHaplotypesConfig
Cjob_type
CMappingRun
CMinimizerConfig
CPruningParameters
CReferenceInterval
CScoringOptions	Options struct for scoring-related parameters. Defaults are in aligner.hpp
CVectorizer