Class Index

A

B

C

D

E

F

G

H

I

J

K

L

M

N

O

P

Q

R

S

T

U

V

W

X

Z

A

AbstractReadSampler (vg)

Genotyper::Affinity (vg)

AliasGraph (vg)

Aligner (vg)

MinimizerMapper::aligner_stats_t (vg)

AlignerClient (vg)

MinimizerMapper::alignment_index_t (vg)

AlignmentChainModel (vg)

AlignmentChainModelVertex (vg)

AlignmentEmbeddingError (vg)

AlignmentEmitter (vg)

AlignmentScorer (vg)

AlignmentValidity (vg)

BandedGlobalAligner::AltTracebackStack (vg)

Anchor (vg::algorithms)

Annotation (vg)

ArgSpec (vg::subcommand)

AugmentedGraph (vg)

B

BandedGlobalAligner::BABuilder (vg)

BackTranslatingAlignmentEmitter (vg)

BandedGlobalAligner::BAMatrix (vg)

BandedGlobalAligner (vg)

BandMatricesTooBigException (vg)

BaseAligner (vg)

BaseArgSpec (vg::subcommand)

BaseMapper (vg)

BaseOption (vg)

BaseOptionGroup (vg::subcommand)

BaseValuation (vg::subcommand)

BBEdgeHash (vg)

BenchmarkResult (vg)

BitString (vg)

BitStringTree (vg)

C

CachedPackedTraversalSupportFinder (vg)

CactusSide (vg)

CactusSnarlFinder (vg)

SnarlCaller::CallInfo (vg)

NestedFlowCaller::CallRecord (vg)

cerrWrapper (vg)

ZipCode::chain_code_t (vg)

ChainAlignmentFailedError (vg)

ChainIterator (vg)

ChainsConfig

ChainScoringScheme (vg::algorithms)

ChainsResult (vg::algorithms)

ChainWithRec (vg::algorithms)

ZipCodeForest::child_info_t (vg)

Deconstructor::ChildContext (vg)

SnarlDistanceIndexClusterer::Cluster (vg)

SnarlDistanceIndexClusterer::ClusterHead (vg)

SnarlDistanceIndexClusterer::ClusteringProblem (vg)

Colors (vg)

CompletedTranscriptPath (vg)

ComponentMinDistanceClusterer (vg)

Configurable (vg)

ConfigurableParser (vg)

connection_t (vg)

ConsistencyCalculator (vg)

VectorView::const_iterator (vg)

ConstructedChunk (vg)

Constructor (vg)

ContractingGraph (vg)

ConvertedHashGraph (vg::io)

count_back_inserter (vg)

Counts (vg)

D

DagifiedGraph (vg)

ZipCode::decoder_t (vg)

Deconstructor (vg)

BandedGlobalAligner::AltTracebackStack::Deflection (vg)

DeletionAligner (vg)

DiagramExplainer (vg)

DinucleotideMachine (vg)

discrete_distribution (vg)

ZipCodeTree::distance_iterator (vg)

DistanceHeuristic (vg)

DotDumpExplainer (vg)

DozeuInterface (vg)

DozeuPinningOverlay (vg)

MEMClusterer::DPScoreComparator (vg)

E

Edge (vg::algorithms)

edit_t (vg)

EditAlignmentScorer (vg)

EditedTranscriptPath (vg)

WFAExtender::ErrorModel (vg)

WFAExtender::ErrorModel::Event (vg)

ExhaustiveTraversalFinder (vg)

Exon (vg)

ExpandingOverlayGraph (vg)

Explainer (vg)

F

IncrementalSubgraph::FCmp (vg)

FeatureSet::Feature (vg)

FeatureSet (vg)

Funnel::FilterPerformance (vg)

FixedGenotypePriorCalculator (vg)

FlagArgSpec (vg::subcommand)

FlatFileBackTranslation (vg)

FlowCaller (vg)

FlowSort (vg)

FlowTraversalFinder (vg)

ZipCodeForest::forest_growing_state_t (vg)

FragmentedHaplotypeVisit (vg)

FragmentLengthDistribution (vg)

FragmentLengthStatistics (vg)

Funnel (vg)

G

GAFOutputCaller (vg)

GAFSorterFile (vg)

GAFSorterParameters (vg)

GAFSorterRecord (vg)

GaplessExtender (vg)

GaplessExtension (vg)

gbwt_thread_t (haplo)

GBWTConfig

GBWTHandler (vg)

GBWTScoreProvider (haplo)

GBWTTraversalFinder (vg)

GBZGraph (vg)

GenotypeLikelihoodCalculator (vg)

GenotypePriorCalculator (vg)

Genotyper (vg)

GFADuplicatePathError (vg::algorithms)

GFAFormatError (vg::algorithms)

GFAHandleGraph (vg)

GFAIDMapInfo (vg::algorithms)

GFAParser (vg::algorithms)

GFATextParser (vg::algorithms)

GFAzParser (vg::algorithms)

GFFReader (vg)

GFFRecord (vg)

GiraffeMainOptions

Graph (vg::algorithms)

Graph (vg)

DozeuInterface::graph_pos_s (vg)

GraphCaller (vg)

GraphHandler

GraphSynchronizer (vg)

GreedyMinDistanceClusterer (vg)

GrefCover (vg)

GroupedOptionGroup (vg::subcommand)

FlowSort::Growth (vg)

GSSWAligner (vg)

H

HandleGraphNodeSet (vg)

HandleGraphSnarlFinder (vg)

Handler (vg::temp_file)

haplo_DP (haplo)

haplo_DP_column (haplo)

haplo_DP_rectangle (haplo)

PhasedGenome::Haplotype (vg)

HaplotypeIndexer (vg)

PhasedGenome::HaplotypeNode (vg)

HaplotypePartitioner (vg)

Haplotypes (vg)

HaplotypesConfig

hash< const vg::Snarl > (std)

hash< pair< A, B > > (std)

hash< std::tuple< TT... > > (std)

hash< vg::NodeSide > (std)

hash< vg::NodeTraversal > (std)

hash< vg::ZipCodeTree::oriented_seed_t > (std)

hash< vg::ZipCodeTree::seed_result_t > (std)

hash_map (vg)

hash_map< K *, V > (vg)

hash_set (vg)

hash_set< K * > (vg)

hDP_gbwt_graph_accessor (haplo)

Haplotypes::Header (vg)

MEMClusterer::HitEdge (vg)

MEMClusterer::HitGraph (vg)

MEMClusterer::HitNode (vg)

HTSAlignmentEmitter (vg)

HTSWriter (vg)

I

IdentityOverlay (vg)

IDScanner (vg)

IncrementalSubgraph (vg)

IncrementIter (vg)

IndexFile (vg)

IndexingParameters (vg)

IndexingPlan (vg)

IndexRecipe (vg)

IndexRegistry (vg)

IndirectVectorView (vg)

InsufficientInputException (vg)

int_itvl_t (haplo)

IntegratedSnarlFinder (vg)

ZipCodeForest::interval_state_t (vg)

IntervalUnion (vg)

is_instantiation_of (vg)

is_instantiation_of< Predicate< PredicateArgs... >, Predicate > (vg)

Funnel::Item (vg)

ZipCodeTree::distance_iterator::iteration_position (vg)

PhasedGenome::iterator (vg)

ShuffledPairs::iterator (vg)

iterator_traits< vg::PhasedGenome::iterator > (std)

iterator_traits< vg::ZipCodeTree::distance_iterator > (std)

iterator_traits< vg::ZipCodeTree::seed_iterator > (std)

IncrementalSubgraph::IterFCmp (vg)

J

job_type

JobSchedule (vg)

JoinedSpliceGraph (vg)

JSONStreamHelper (vg::io)

K

kff_recoding_t (vg)

kmer_t (vg::algorithms)

kmer_t (vg)

KmerPosition (vg)

L

LazyRNG (vg)

LegacyCaller (vg)

Recombinator::LocalHaplotype (vg)

GraphSynchronizer::Lock (vg)

LoggedGapAlignmentScorer (vg)

Logger (vg)

M

Mapper (vg)

mapping_t (vg)

MappingHash (vg)

MappingQualityCalculator (vg)

MappingRun

NGSSimulator::MarkovDistribution (vg)

Masker (vg)

MatchPos (vg)

MatrixAlignmentScorer (vg)

MaximalExactMatch (vg)

MCMCCaller (vg)

MCMCGenotyper (vg)

MEMAccelerator (vg)

MEMChainModel (vg)

MEMChainModelVertex (vg)

MEMClusterer (vg)

MemoizingGraph (vg)

IntegratedSnarlFinder::MergedAdjacencyGraph (vg)

MinDistanceClusterer (vg)

MinimizerMapper::Minimizer (vg)

MinimizerConfig

MinimizerIndexParameters (vg)

MinimizerMapper (vg)

MIPayload (vg)

MSAConverter (vg)

multipath_alignment_t (vg)

MultipathAlignmentEmitter (vg)

MultipathAlignmentGraph (vg)

MultipathMapper (vg)

MultipathProblem (vg)

N

NameMapper (vg)

NegationFlagArgSpec (vg::subcommand)

NestedCachedPackedTraversalSupportFinder (vg)

NestedFlowCaller (vg)

NetGraph (vg)

NGSSimulator (vg)

NoAlignmentInBandException (vg)

Node (vg::algorithms)

ZipCode::node_code_t (vg)

NodeSide (vg)

NodeTraversal (vg)

normal_distribution (vg)

NullClusterer (vg)

NullMaskingGraph (vg)

O

Option (vg)

Option< vector< Item >, Parser > (vg)

OptionGroup (vg::subcommand)

OptionInterface (vg)

OptionValueParser (vg)

OptionValueParser< vector< Item > > (vg)

DozeuInterface::OrderedGraph (vg)

ZipCodeTree::oriented_seed_t (vg)

OrientedDistanceClusterer (vg)

OrientedDistanceMeasurer (vg)

P

PackedTraversalSupportFinder (vg)

Packer (vg)

Packers (vg)

Funnel::PaintableSpace (vg)

pair_hash_map (vg)

pair_hash_set (vg)

PairedEndMapper (vg)

ParallelKFFReader (vg)

HaplotypePartitioner::Parameters (vg)

Recombinator::Parameters (vg)

ParentGenotypeInfo (vg)

path_mapping_t (vg)

path_t (vg)

PathBasedTraversalFinder (vg)

PathBranch (vg)

PathChunker (vg)

PathComponentIndex (vg)

PathIndex (vg)

MatchPos::PathList (vg)

PathNode (vg)

PathOrientedDistanceMeasurer (vg)

PathPiece (vg)

PathRestrictedTraversalFinder (vg)

Paths (vg)

PathSubgraph (vg)

PathSubgraphOverlay (vg)

PathTraversalFinder (vg)

GFAzParser::PendingRGFAVisit (vg::algorithms)

PhasedGenome (vg)

PhaseUnfolder (vg)

Pictographs (vg)

VG::Plan (vg)

PoissonSupportSnarlCaller::PoissonCallInfo (vg)

PoissonSupportSnarlCaller (vg)

position_t (vg)

PositionIDScanner (vg)

Preset (vg::subcommand)

Primer (vg)

PrimerFinder (vg)

PrimerPair (vg)

ProblemDumpExplainer (vg)

Progressive (vg)

PruningParameters

Q

QualAdjAligner (vg)

QualAdjAlignmentScorer (vg)

QualAdjXdropAligner (vg)

R

Range (vg)

RangeArgSpec (vg::subcommand)

RareVariantSimplifier (vg)

RatioSupportSnarlCaller (vg)

MinimizerMapper::read_alignment_index_t (vg)

ReadFilter (vg)

ReadMasker (vg)

ReadRestrictedTraversalFinder (vg)

RebuildJob (vg)

RebuildParameters (vg)

Recombinator (vg)

RecombinatorFragment (vg)

RecombinatorHaplotype (vg)

ReferenceInterval

Region (vg)

RegionExpander (vg)

RepresentativeTraversalFinder (vg)

ReverseGraph (vg)

RewindPlanException (vg)

RRMemo (haplo::haploMath)

S

Sampler (vg)

WFATree::ScoreProperties (vg)

ScoreProvider (haplo)

ScoringOptions

SnarlDistanceIndexClusterer::Seed (vg)

ZipCodeForest::seed_info_t (vg)

ZipCodeTree::seed_iterator (vg)

ZipCodeTree::seed_result_t (vg)

SnarlDistanceIndexClusterer::SeedCache (vg)

SeqComplexity (vg)

SequenceDictionaryEntry (vg)

ShuffledPairs (vg)

SimpleConsistencyCalculator (vg)

SimpleTraversalSupportCalculator (vg)

SizeLimitExceededException (vg)

SmallBitset (vg)

SmallSnarlSimplifier (vg)

ZipCode::snarl_code_t (vg)

NestedCachedPackedTraversalSupportFinder::snarl_less (vg)

SnarlCaller (vg)

SnarlDistanceIndexClusterer (vg)

SnarlFinder (vg)

SnarlGraph (vg)

SnarlManager (vg)

SnarlMinDistance (vg)

SnarlOrientedDistanceMeasurer (vg)

SnarlManager::SnarlRecord (vg)

SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild (vg)

SnarlDistanceIndexClusterer::SnarlTreeNodeProblem (vg)

ZipCodeForest::sort_value_t (vg)

SourceSinkOverlay (vg)

SparseUnionFind (vg)

SplicedHTSAlignmentEmitter (vg)

SpliceRegion (vg)

SpliceStats (vg)

SSWAligner (vg)

Funnel::Stage (vg)

MinimizerMapper::aligner_stats_t::stat_collection_t (vg)

MinimizerMapper::aligner_stats_t::stat_set_t (vg)

state_hash (vg)

Recombinator::Statistics (vg)

StrandSplitGraph (vg)

StreamIndex (vg)

StreamIndexBase (vg)

StreamSorter (vg)

string_hash_map (vg)

string_hash_set (vg)

HaplotypePartitioner::Subchain (vg)

Haplotypes::Subchain (vg)

Subcommand (vg::subcommand)

SubgraphExplainer (vg)

SubgraphOverlay (vg)

SubHandleGraph (vg)

subpath_t (vg)

SubpathOverlay (vg)

SummaryStatistics (vg)

SupportAugmentedGraph (vg)

SupportBasedSnarlCaller (vg)

SupportRestrictedTraversalFinder (vg)

VCFOutputCaller::SuppressedRef (vg)

SurjectingAlignmentEmitter (vg)

Surjector (vg)

T

TargetValueSearch (vg)

Watchdog::thread_state_t (vg)

TickChainLink (vg::subcommand)

TipAnchoredMaxDistance (vg)

Haplotypes::TopLevelChain (vg)

GrefCover::TopLevelSnarlStats (vg)

TracedScore (vg::algorithms)

Transcript (vg)

Transcriptome (vg)

TranscriptPath (vg)

transition_info (vg::algorithms)

Translator (vg)

TraversalFinder (vg)

TraversalSupportCalculator (vg)

TraversalSupportFinder (vg)

Tree (vg)

ZipCodeTree::tree_item_t (vg)

BitStringTree::TreeNode (vg)

TreeNode (vg)

TreeSubgraph (vg)

TrivialTraversalFinder (vg)

truncated_normal_distribution (vg)

TSVExplainer (vg)

TVSClusterer (vg)

U

uniform_int_distribution (vg)

uniform_real_distribution (vg)

V

Valuation (vg::subcommand)

ValueArgSpec (vg::subcommand)

VariantAdder (vg)

varint_vector_t (vg)

VcfBuffer (vg)

VCFGenotyper (vg)

VCFOutputCaller (vg)

VcfRecordConverter (vg)

VcfRecordFilter (vg)

VCFTraversalFinder (vg)

Vectorizer

VectorView (vg)

VectorViewInverse (vg)

Version (vg)

VG (vg)

VGIndexes (vg)

VGset (vg)

Viz (vg)

W

walk_t (vg::algorithms)

wang_hash (vg)

wang_hash< handle_t > (vg)

wang_hash< handlegraph::net_handle_t > (vg)

wang_hash< net_identifier_t > (vg)

wang_hash< NodeSide > (vg)

wang_hash< NodeTraversal > (vg)

wang_hash< path_handle_t > (vg)

wang_hash< std::pair< A, B > > (vg)

wang_hash< T * > (vg)

wang_hash< T, typename std::enable_if< std::is_integral< T >::value >::type > (vg)

Watchdog (vg)

FlowSort::WeightedGraph (vg)

WFAAlignment (vg)

WFAExtender (vg)

WFANode (vg)

WFAPoint (vg)

WFATree (vg)

WideningPRNG (vg)

WindowedVcfBuffer (vg)

WrappingPositionScanner (vg)

X

XdropAligner (vg)

Z

ZipCode (vg)

ZipCodeCollection (vg)

ZipCodeForest (vg)

ZipCodeTree (vg)

zstd_compress_buf (vg)

zstd_decompress_buf (vg)

zstd_ifstream (vg)

zstd_ofstream (vg)