vg
tools for working with variation graphs
Loading...
Searching...
No Matches
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
A
AbstractReadSampler (vg)
Genotyper::Affinity (vg)
AliasGraph (vg)
Aligner (vg)
AlignerClient (vg)
Alignment (vg)
alignment_index_t (vg)
AlignmentChainModel (vg)
AlignmentChainModelVertex (vg)
AlignmentEmitter (vg::io)
AlignmentValidity (vg)
BandedGlobalAligner::AltTracebackStack (vg)
Anchor (vg::algorithms)
Annotation (vg)
AppendHaplotypeCommand (vg)
ArgSpec (vg::subcommand)
AugmentedGraph (vg)
B
BandedGlobalAligner::BABuilder (vg)
BackTranslatingAlignmentEmitter (vg)
BandedGlobalAligner::BAMatrix (vg)
BandedGlobalAligner (vg)
BaseAligner (vg)
BaseArgSpec (vg::subcommand)
BaseMapper (vg)
BaseOption (vg)
BaseOptionGroup (vg::subcommand)
BasePileup (vg)
BaseValuation (vg::subcommand)
BBEdgeHash (vg)
BenchmarkResult (vg)
BitString (vg)
BitStringTree (vg)
BlockedGzipInputStream (vg::io)
BlockedGzipOutputStream (vg::io)
BoolReturningWrapper (handlegraph)
BoolReturningWrapper< Iteratee, false > (handlegraph)
BoolReturningWrapper< Iteratee, true > (handlegraph)
BREAKPOINT (vg)
BuildableSnarlDecomposition (handlegraph)
C
CachedPackedTraversalSupportFinder (vg)
IndexedVG::CacheEntry (vg)
CactusSide (vg)
CactusSnarlFinder (vg)
SnarlCaller::CallInfo (vg)
NestedFlowCaller::CallRecord (vg)
ChainIterator (vg)
SnarlDistanceIndexClusterer::Cluster (vg)
SnarlDistanceIndexClusterer::ClusterHead (vg)
SnarlDistanceIndexClusterer::ClusteringProblem (vg)
Colors (vg)
compare_gaf
CompletedTranscriptPath (vg)
ComponentMinDistanceClusterer (vg)
Configurable (vg)
ConfigurableParser (vg)
Connection (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)
Deconstructor (vg)
BandedGlobalAligner::AltTracebackStack::Deflection (vg)
DeletableHandleGraph (handlegraph)
DeleteHaplotypeCommand (vg)
DeletionAligner (vg)
DiagramExplainer (vg)
DinucleotideMachine (vg)
discrete_distribution (vg)
DistanceHeuristic (vg)
DotDumpExplainer (vg)
DozeuInterface (vg)
DozeuPinningOverlay (vg)
MEMClusterer::DPScoreComparator (vg)
E
Edge (vg::algorithms)
Edge (vg)
EdgePileup (vg)
Edit (vg)
edit_t (vg)
EditedTranscriptPath (vg)
endianness (vg)
WFAExtender::ErrorModel (vg)
WFAExtender::ErrorModel::Event (vg)
ExhaustiveTraversalFinder (vg)
Exon (vg)
ExpandingOverlayGraph (handlegraph)
Explainer (vg)
ExtraNodeGraph (vg)
F
IncrementalSubgraph::FCmp (vg)
fdinbuf (vg::io)
fdistream (vg::io)
fdostream (vg::io)
fdoutbuf (vg::io)
FeatureSet::Feature (vg)
FeatureSet (vg)
Filter (vg)
Funnel::FilterPerformance (vg)
FixedGenotypePriorCalculator (vg)
FlagArgSpec (vg::subcommand)
FlatFileBackTranslation (vg)
FlowCaller (vg)
FlowSort (vg)
FlowTraversalFinder (vg)
FragmentLengthDistribution (vg)
FragmentLengthStatistics (vg)
Funnel (vg)
G
GafAlignmentEmitter (vg::io)
GafFile
GAFOutputCaller (vg)
GafRecord (gafkluge)
GafStep (gafkluge)
GaplessExtender (vg)
GaplessExtension (vg)
gbwt_thread_t (haplo)
GBWTConfig
GBWTHandler (vg)
GBWTScoreProvider (haplo)
GBWTTraversalFinder (vg)
GBZGraph (vg)
GenomeState (vg)
GenomeStateCommand (vg)
Genotype (vg)
GenotypeLikelihoodCalculator (vg)
GenotypePriorCalculator (vg)
Genotyper (vg)
GFADuplicatePathError (vg::algorithms)
GFAFormatError (vg::algorithms)
GFAHandleGraph (vg)
GFAIDMapInfo (vg::algorithms)
GFAParser (vg::algorithms)
GFFReader (vg)
GFFRecord (vg)
GiraffeMainOptions
Graph (vg::algorithms)
Graph (vg)
DozeuInterface::graph_pos_s (vg)
GraphCaller (vg)
GraphHandler
GraphSynchronizer (vg)
greater_gaffile
GreedyMinDistanceClusterer (vg)
GroupedOptionGroup (vg::subcommand)
FlowSort::Growth (vg)
GSSWAligner (vg)
H
handle_t (handlegraph)
HandleGraph (handlegraph)
HandleGraphNodeSet (vg)
HandleGraphSnarlFinder (vg)
Handler (vg::temp_file)
Handler (xg::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< handlegraph::edge_t > (std)
hash< handlegraph::handle_t > (std)
hash< handlegraph::net_handle_t > (std)
hash< handlegraph::path_handle_t > (std)
hash< handlegraph::step_handle_t > (std)
hash< pair< A, B > > (std)
hash< std::tuple< TT... > > (std)
hash< vg::NodeSide > (std)
hash< vg::NodeTraversal > (std)
Genotyper::hash_ambiguous_allele_set (vg)
hash_map (vg)
hash_map< K *, V > (vg)
Genotyper::hash_node_traversal (vg)
Genotyper::hash_oriented_edge (vg)
hash_set (vg)
hash_set< K * > (vg)
hDP_gbwt_graph_accessor (haplo)
Haplotypes::Header (vg)
hFILE_backend
hFILE_cppstream (vg::io)
MEMClusterer::HitEdge (vg)
MEMClusterer::HitGraph (vg)
MEMClusterer::HitNode (vg)
HTSAlignmentEmitter (vg)
HTSWriter (vg)
I
IdentityOverlay (vg)
IDScanner (vg)
IncrementalSubgraph (vg)
IncrementIter (vg)
IndexedVG (vg)
IndexFile (vg)
IndexingParameters (vg)
IndexingPlan (vg)
IndexRecipe (vg)
IndexRegistry (vg)
InsertHaplotypeCommand (vg)
InsufficientInputException (vg)
int_itvl_t (haplo)
IntegratedSnarlFinder (vg)
is_instantiation_of (vg)
is_instantiation_of< Predicate< PredicateArgs... >, Predicate > (vg)
Funnel::Item (vg)
PathForEachSocket::iterator (handlegraph)
PhasedGenome::iterator (vg)
ShuffledPairs::iterator (vg)
iterator_traits< vg::PhasedGenome::iterator > (std)
IncrementalSubgraph::IterFCmp (vg)
J
j2pb_error
job_type
JobSchedule (vg)
JoinedSpliceGraph (vg)
json_autoptr
JSONStreamHelper (vg::io)
K
kff_recoding_t (vg)
kmer_t (vg::algorithms)
kmer_t (vg)
KmerMatch (vg)
KmerPosition (vg)
L
LazyRNG (vg)
LegacyCaller (vg)
linear_haplo_structure (haplo)
LinearScoreProvider (haplo)
linear_haplo_structure::linearUnrepresentable (haplo)
Recombinator::LocalHaplotype (vg)
LocationSupport (vg)
GraphSynchronizer::Lock (vg)
Locus (vg)
M
Mapper (vg)
Mapping (vg)
mapping_t (vg)
MappingHash (vg)
MappingRun
NGSSimulator::MarkovDistribution (vg)
MatchPos (vg)
MaximalExactMatch (vg)
MCMCCaller (vg)
MCMCGenotyper (vg)
MEMAccelerator (vg)
MEMChainModel (vg)
MEMChainModelVertex (vg)
MEMClusterer (vg)
MemoizingGraph (vg)
IntegratedSnarlFinder::MergedAdjacencyGraph (vg)
MessageEmitter (vg::io)
MessageIterator (vg::io)
MinDistanceClusterer (vg)
MinimizerMapper::Minimizer (vg)
MinimizerMapper (vg)
MIPayload (vg)
MIPayloadValues (vg)
MSAConverter (vg)
multipath_alignment_t (vg)
MultipathAlignment (vg)
MultipathAlignmentEmitter (vg)
MultipathAlignmentGraph (vg)
MultipathMapper (vg)
MultipathProblem (vg)
MutableHandleGraph (handlegraph)
MutablePathDeletableHandleGraph (handlegraph)
MutablePathHandleGraph (handlegraph)
MutablePathMetadata (handlegraph)
MutablePathMutableHandleGraph (handlegraph)
N
NamedNodeBackTranslation (handlegraph)
NameMapper (vg)
NestedCachedPackedTraversalSupportFinder (vg)
NestedFlowCaller (vg)
NestedTraversalFinder (vg)
Deconstructor::NestingInfo (vg)
net_handle_t (handlegraph)
NetGraph (vg)
NGSSimulator (vg)
NoAlignmentInBandException (vg)
Node (vg::algorithms)
Node (vg)
NodePileup (vg)
NodeSide (vg)
NodeTraversal (vg)
normal_distribution (vg)
NullAlignmentEmitter (vg::io)
NullClusterer (vg)
NullMaskingGraph (vg)
number_bool_packing (handlegraph)
O
Option (vg)
Option< vector< Item >, Parser > (vg)
OptionGroup (vg::subcommand)
OptionInterface (vg)
OptionValueParser (vg)
OptionValueParser< vector< Item > > (vg)
DozeuInterface::OrderedGraph (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 (vg)
path_handle_t (handlegraph)
path_mapping_t (vg)
path_t (vg)
PathBasedTraversalFinder (vg)
PathBranch (vg)
PathChunker (vg)
PathComponentIndex (vg)
PathForEachSocket (handlegraph)
PathHandleGraph (handlegraph)
PathIndex (vg)
MatchPos::PathList (vg)
PathMetadata (handlegraph)
PathNode (vg)
PathOrientedDistanceMeasurer (vg)
PathPositionHandleGraph (handlegraph)
PathRestrictedTraversalFinder (vg)
Paths (vg)
PathSubgraph (vg)
PathSubgraphOverlay (vg)
PathTraversalFinder (vg)
PhasedGenome (vg)
PhaseUnfolder (vg)
Pictographs (vg)
Pileup (vg)
VG::Plan (vg)
PoissonSupportSnarlCaller::PoissonCallInfo (vg)
PoissonSupportSnarlCaller (vg)
Position (vg)
position_t (vg)
PositionIDScanner (vg)
Preset (vg::subcommand)
ProblemDumpExplainer (vg)
Progressive (vg)
ProtobufEmitter (vg::io)
ProtobufIterator (vg::io)
PruningParameters
Q
QualAdjAligner (vg)
QualAdjXdropAligner (vg)
R
Range (vg)
RangeArgSpec (vg::subcommand)
RankedHandleGraph (handlegraph)
RareVariantSimplifier (vg)
RatioSupportSnarlCaller (vg)
read_alignment_index_t (vg)
ReadFilter (vg)
ReadMasker (vg)
ReadRestrictedTraversalFinder (vg)
RebuildJob (vg)
RebuildParameters (vg)
Recombinator (vg)
RecombinatorHaplotype (vg)
ReferenceInterval
Region (vg)
RegionExpander (vg)
Registry (vg::io)
ReplaceLocalHaplotypeCommand (vg)
ReplaceSnarlHaplotypeCommand (vg)
RepresentativeTraversalFinder (vg)
return_type_of (handlegraph)
return_type_of< Returns(*)(Args...)> (handlegraph)
return_type_of< Returns(Owner::*)(Args...) const > (handlegraph)
return_type_of< Returns(Owner::*)(Args...)> (handlegraph)
ReverseGraph (vg)
RewindPlanException (vg)
RRMemo (haplo::haploMath)
S
Sampler (vg)
WFATree::ScoreProperties (vg)
ScoreProvider (haplo)
ScoringOptions
SnarlDistanceIndexClusterer::Seed (vg)
SnarlDistanceIndexClusterer::SeedCache (vg)
SeqComplexity (vg)
Serializable (handlegraph)
SerializableHandleGraph (handlegraph)
ShuffledPairs (vg)
SimpleConsistencyCalculator (vg)
SimpleTraversalSupportCalculator (vg)
SizeLimitExceededException (vg)
SmallBitset (vg)
SmallSnarlSimplifier (vg)
Snarl (vg)
NestedCachedPackedTraversalSupportFinder::snarl_less (vg)
SnarlCaller (vg)
SnarlDecomposition (handlegraph)
SnarlDistanceIndexClusterer (vg)
SnarlFinder (vg)
SnarlGraph (vg)
SnarlManager (vg)
SnarlMinDistance (vg)
SnarlOrientedDistanceMeasurer (vg)
SnarlManager::SnarlRecord (vg)
SnarlState (vg)
SnarlTraversal (vg)
SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild (vg)
SnarlDistanceIndexClusterer::SnarlTreeNodeProblem (vg)
linear_haplo_structure::SNVvector (haplo)
SourceSinkOverlay (vg)
SparseUnionFind (vg)
SplicedHTSAlignmentEmitter (vg)
SpliceRegion (vg)
SpliceStats (vg)
SSWAligner (vg)
Funnel::Stage (vg)
state_hash (vg)
Recombinator::Statistics (vg)
step_handle_t (handlegraph)
StrandSplitGraph (vg)
streaminbuf (vg::io)
StreamIndex (vg)
StreamIndexBase (vg)
streamistream (vg::io)
StreamMultiplexer (vg::io)
StreamSorter (vg)
string_hash_map (vg)
string_hash_set (vg)
HaplotypePartitioner::Subchain (vg)
Haplotypes::Subchain (vg)
Subcommand (vg::subcommand)
SubgraphOverlay (vg)
SubHandleGraph (handlegraph::algorithms)
SubHandleGraph (vg)
Subpath (vg)
subpath_t (vg)
SubpathOverlay (vg)
SummaryStatistics (vg)
Support (vg)
SupportAugmentedGraph (vg)
SupportBasedSnarlCaller (vg)
SupportRestrictedTraversalFinder (vg)
SurjectingAlignmentEmitter (vg)
Surjector (vg)
SwapHaplotypesCommand (vg)
T
Registry::Tables (vg::io)
TargetValueSearch (vg)
Watchdog::thread_state_t (vg)
TickChainLink (vg::subcommand)
TipAnchoredMaxDistance (vg)
Haplotypes::TopLevelChain (vg)
TracedScore (vg::algorithms)
Transcript (vg)
Transcriptome (vg)
TranscriptPath (vg)
Translation (vg)
Translator (vg)
TraversalFinder (vg)
TraversalSupportCalculator (vg)
TraversalSupportFinder (vg)
Tree (vg)
BitStringTree::TreeNode (vg)
TreeNode (vg)
TreeSubgraph (vg)
TriviallySerializable (handlegraph)
TrivialTraversalFinder (vg)
truncated_normal_distribution (vg)
TSVAlignmentEmitter (vg::io)
TVSClusterer (vg)
U
uniform_int_distribution (vg)
uniform_real_distribution (vg)
V
Valuation (vg::subcommand)
ValueArgSpec (vg::subcommand)
VariantAdder (vg)
VcfBuffer (vg)
VCFGenotyper (vg)
VCFOutputCaller (vg)
VcfRecordConverter (vg)
VcfRecordFilter (vg)
VCFTraversalFinder (vg)
VectorizableHandleGraph (handlegraph)
Vectorizer
VectorView (vg)
VectorViewInverse (vg)
Version (vg)
VG (vg)
VGAlignmentEmitter (vg::io)
VGIndexes (vg)
VGset (vg)
Visit (vg)
Viz (vg)
VPKG (vg::io)
W
walk_t (vg::algorithms)
wang_hash (vg)
wang_hash< handle_t > (vg)
wang_hash< handlegraph::net_handle_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)
XG (xg)
XGFormatError (xg)
XGPath (xg)