vg
tools for working with variation graphs
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
FlatFileBackTranslation
(
vg
)
iterator_traits< vg::ZipCodeTree::reverse_iterator >
(
std
)
PathForEachSocket
(
handlegraph
)
StreamMultiplexer
(
vg::io
)
FlowCaller
(
vg
)
IncrementalSubgraph::IterFCmp
(
vg
)
PathHandleGraph
(
handlegraph
)
StreamSorter
(
vg
)
AbstractReadSampler
(
vg
)
FlowSort
(
vg
)
j
PathIndex
(
vg
)
string_hash_map
(
vg
)
Genotyper::Affinity
(
vg
)
FlowTraversalFinder
(
vg
)
MatchPos::PathList
(
vg
)
string_hash_set
(
vg
)
AliasGraph
(
vg
)
ZipCodeForest::forest_growing_state_t
(
vg
)
j2pb_error
PathMetadata
(
handlegraph
)
Haplotypes::Subchain
(
vg
)
Aligner
(
vg
)
FragmentedHaplotypeVisit
(
vg
)
job_type
PathNode
(
vg
)
HaplotypePartitioner::Subchain
(
vg
)
MinimizerMapper::aligner_stats_t
(
vg
)
FragmentLengthDistribution
(
vg
)
JobSchedule
(
vg
)
PathOrientedDistanceMeasurer
(
vg
)
Subcommand
(
vg::subcommand
)
AlignerClient
(
vg
)
FragmentLengthStatistics
(
vg
)
JoinedSpliceGraph
(
vg
)
PathPositionHandleGraph
(
handlegraph
)
SubgraphExplainer
(
vg
)
Alignment
(
vg
)
Funnel
(
vg
)
json_autoptr
PathRestrictedTraversalFinder
(
vg
)
SubgraphOverlay
(
vg
)
alignment_index_t
(
vg
)
g
JSONStreamHelper
(
vg::io
)
Paths
(
vg
)
SubHandleGraph
(
handlegraph::algorithms
)
AlignmentChainModel
(
vg
)
k
PathSubgraph
(
vg
)
SubHandleGraph
(
vg
)
AlignmentChainModelVertex
(
vg
)
GafAlignmentEmitter
(
vg::io
)
PathSubgraphOverlay
(
vg
)
Subpath
(
vg
)
AlignmentEmitter
(
vg::io
)
GAFOutputCaller
(
vg
)
kff_recoding_t
(
vg
)
PathTraversalFinder
(
vg
)
subpath_t
(
vg
)
AlignmentValidity
(
vg
)
GafRecord
(
gafkluge
)
kmer_t
(
vg
)
PhasedGenome
(
vg
)
SubpathOverlay
(
vg
)
BandedGlobalAligner::AltTracebackStack
(
vg
)
GAFSorterFile
(
vg
)
kmer_t
(
vg::algorithms
)
PhaseUnfolder
(
vg
)
SummaryStatistics
(
vg
)
Anchor
(
vg::algorithms
)
GAFSorterParameters
(
vg
)
KmerMatch
(
vg
)
Pictographs
(
vg
)
Support
(
vg
)
Annotation
(
vg
)
GAFSorterRecord
(
vg
)
KmerPosition
(
vg
)
Pileup
(
vg
)
SupportAugmentedGraph
(
vg
)
AppendHaplotypeCommand
(
vg
)
GafStep
(
gafkluge
)
l
VG::Plan
(
vg
)
SupportBasedSnarlCaller
(
vg
)
ArgSpec
(
vg::subcommand
)
GaplessExtender
(
vg
)
PoissonSupportSnarlCaller::PoissonCallInfo
(
vg
)
SupportRestrictedTraversalFinder
(
vg
)
AugmentedGraph
(
vg
)
GaplessExtension
(
vg
)
LazyRNG
(
vg
)
PoissonSupportSnarlCaller
(
vg
)
SurjectingAlignmentEmitter
(
vg
)
b
gbwt_thread_t
(
haplo
)
LegacyCaller
(
vg
)
Position
(
vg
)
Surjector
(
vg
)
GBWTConfig
linear_haplo_structure
(
haplo
)
position_t
(
vg
)
SwapHaplotypesCommand
(
vg
)
BandedGlobalAligner::BABuilder
(
vg
)
GBWTHandler
(
vg
)
LinearScoreProvider
(
haplo
)
PositionIDScanner
(
vg
)
t
BackTranslatingAlignmentEmitter
(
vg
)
GBWTScoreProvider
(
haplo
)
linear_haplo_structure::linearUnrepresentable
(
haplo
)
Preset
(
vg::subcommand
)
BandedGlobalAligner::BAMatrix
(
vg
)
GBWTTraversalFinder
(
vg
)
Recombinator::LocalHaplotype
(
vg
)
Primer
(
vg
)
Registry::Tables
(
vg::io
)
BandedGlobalAligner
(
vg
)
GBZGraph
(
vg
)
LocationSupport
(
vg
)
PrimerFinder
(
vg
)
TargetValueSearch
(
vg
)
BandMatricesTooBigException
(
vg
)
GenomeState
(
vg
)
GraphSynchronizer::Lock
(
vg
)
PrimerPair
(
vg
)
Watchdog::thread_state_t
(
vg
)
BaseAligner
(
vg
)
GenomeStateCommand
(
vg
)
Locus
(
vg
)
ProblemDumpExplainer
(
vg
)
TickChainLink
(
vg::subcommand
)
BaseArgSpec
(
vg::subcommand
)
Genotype
(
vg
)
m
Progressive
(
vg
)
TipAnchoredMaxDistance
(
vg
)
BaseMapper
(
vg
)
GenotypeLikelihoodCalculator
(
vg
)
ProtobufEmitter
(
vg::io
)
Haplotypes::TopLevelChain
(
vg
)
BaseOption
(
vg
)
GenotypePriorCalculator
(
vg
)
Mapper
(
vg
)
ProtobufIterator
(
vg::io
)
TracedScore
(
vg::algorithms
)
BaseOptionGroup
(
vg::subcommand
)
Genotyper
(
vg
)
Mapping
(
vg
)
PruningParameters
Transcript
(
vg
)
BasePileup
(
vg
)
GFADuplicatePathError
(
vg::algorithms
)
mapping_t
(
vg
)
q
Transcriptome
(
vg
)
BaseValuation
(
vg::subcommand
)
GFAFormatError
(
vg::algorithms
)
MappingHash
(
vg
)
TranscriptPath
(
vg
)
BBEdgeHash
(
vg
)
GFAHandleGraph
(
vg
)
MappingRun
QualAdjAligner
(
vg
)
Translation
(
vg
)
BenchmarkResult
(
vg
)
GFAIDMapInfo
(
vg::algorithms
)
NGSSimulator::MarkovDistribution
(
vg
)
QualAdjXdropAligner
(
vg
)
Translator
(
vg
)
BitString
(
vg
)
GFAParser
(
vg::algorithms
)
Masker
(
vg
)
r
TraversalFinder
(
vg
)
BitStringTree
(
vg
)
GFFReader
(
vg
)
MatchPos
(
vg
)
TraversalSupportCalculator
(
vg
)
BlockedGzipInputStream
(
vg::io
)
GFFRecord
(
vg
)
MaximalExactMatch
(
vg
)
Range
(
vg
)
TraversalSupportFinder
(
vg
)
BlockedGzipOutputStream
(
vg::io
)
GiraffeMainOptions
MCMCCaller
(
vg
)
RangeArgSpec
(
vg::subcommand
)
Tree
(
vg
)
BoolReturningWrapper
(
handlegraph
)
Graph
(
vg
)
MCMCGenotyper
(
vg
)
RankedHandleGraph
(
handlegraph
)
ZipCodeTree::tree_item_t
(
vg
)
BoolReturningWrapper< Iteratee, false >
(
handlegraph
)
Graph
(
vg::algorithms
)
MEMAccelerator
(
vg
)
RareVariantSimplifier
(
vg
)
TreeNode
(
vg
)
BoolReturningWrapper< Iteratee, true >
(
handlegraph
)
DozeuInterface::graph_pos_s
(
vg
)
MEMChainModel
(
vg
)
RatioSupportSnarlCaller
(
vg
)
BitStringTree::TreeNode
(
vg
)
BREAKPOINT
(
vg
)
GraphCaller
(
vg
)
MEMChainModelVertex
(
vg
)
read_alignment_index_t
(
vg
)
TreeSubgraph
(
vg
)
BuildableSnarlDecomposition
(
handlegraph
)
GraphHandler
MEMClusterer
(
vg
)
ReadFilter
(
vg
)
TriviallySerializable
(
handlegraph
)
c
GraphSynchronizer
(
vg
)
MemoizingGraph
(
vg
)
ReadMasker
(
vg
)
TrivialTraversalFinder
(
vg
)
GreedyMinDistanceClusterer
(
vg
)
IntegratedSnarlFinder::MergedAdjacencyGraph
(
vg
)
ReadRestrictedTraversalFinder
(
vg
)
truncated_normal_distribution
(
vg
)
CachedPackedTraversalSupportFinder
(
vg
)
GroupedOptionGroup
(
vg::subcommand
)
MessageEmitter
(
vg::io
)
RebuildJob
(
vg
)
TruncatedBGZFError
(
vg::io
)
IndexedVG::CacheEntry
(
vg
)
FlowSort::Growth
(
vg
)
MessageIterator
(
vg::io
)
RebuildParameters
(
vg
)
TSVAlignmentEmitter
(
vg::io
)
CactusSide
(
vg
)
GSSWAligner
(
vg
)
MinDistanceClusterer
(
vg
)
Recombinator
(
vg
)
TSVExplainer
(
vg
)
CactusSnarlFinder
(
vg
)
h
MinimizerMapper::Minimizer
(
vg
)
RecombinatorFragment
(
vg
)
TVSClusterer
(
vg
)
SnarlCaller::CallInfo
(
vg
)
MinimizerMapper
(
vg
)
RecombinatorHaplotype
(
vg
)
u
NestedFlowCaller::CallRecord
(
vg
)
handle_t
(
handlegraph
)
MIPayload
(
vg
)
ReferenceInterval
ZipCode::chain_code_t
(
vg
)
HandleGraph
(
handlegraph
)
MSAConverter
(
vg
)
Region
(
vg
)
uniform_int_distribution
(
vg
)
ChainAlignmentFailedError
(
vg
)
HandleGraphNodeSet
(
vg
)
multipath_alignment_t
(
vg
)
RegionExpander
(
vg
)
uniform_real_distribution
(
vg
)
ChainIterator
(
vg
)
HandleGraphSnarlFinder
(
vg
)
MultipathAlignment
(
vg
)
Registry
(
vg::io
)
v
ZipCodeForest::child_info_t
(
vg
)
Handler
(
vg::temp_file
)
MultipathAlignmentEmitter
(
vg
)
ReplaceLocalHaplotypeCommand
(
vg
)
SnarlDistanceIndexClusterer::Cluster
(
vg
)
Handler
(
xg::temp_file
)
MultipathAlignmentGraph
(
vg
)
ReplaceSnarlHaplotypeCommand
(
vg
)
Valuation
(
vg::subcommand
)
SnarlDistanceIndexClusterer::ClusterHead
(
vg
)
haplo_DP
(
haplo
)
MultipathMapper
(
vg
)
RepresentativeTraversalFinder
(
vg
)
ValueArgSpec
(
vg::subcommand
)
SnarlDistanceIndexClusterer::ClusteringProblem
(
vg
)
haplo_DP_column
(
haplo
)
MultipathProblem
(
vg
)
return_type_of
(
handlegraph
)
VariantAdder
(
vg
)
Colors
(
vg
)
haplo_DP_rectangle
(
haplo
)
MutableHandleGraph
(
handlegraph
)
return_type_of< Returns(*)(Args...)>
(
handlegraph
)
varint_vector_t
(
vg
)
CompletedTranscriptPath
(
vg
)
PhasedGenome::Haplotype
(
vg
)
MutablePathDeletableHandleGraph
(
handlegraph
)
return_type_of< Returns(Owner::*)(Args...) const >
(
handlegraph
)
VcfBuffer
(
vg
)
ComponentMinDistanceClusterer
(
vg
)
HaplotypeIndexer
(
vg
)
MutablePathHandleGraph
(
handlegraph
)
return_type_of< Returns(Owner::*)(Args...)>
(
handlegraph
)
VCFGenotyper
(
vg
)
Configurable
(
vg
)
PhasedGenome::HaplotypeNode
(
vg
)
MutablePathMetadata
(
handlegraph
)
ZipCodeTree::reverse_iterator
(
vg
)
VCFOutputCaller
(
vg
)
ConfigurableParser
(
vg
)
HaplotypePartitioner
(
vg
)
MutablePathMutableHandleGraph
(
handlegraph
)
ReverseGraph
(
vg
)
VcfRecordConverter
(
vg
)
Connection
(
vg
)
Haplotypes
(
vg
)
n
RewindPlanException
(
vg
)
VcfRecordFilter
(
vg
)
connection_t
(
vg
)
HaplotypesConfig
RRMemo
(
haplo::haploMath
)
VCFTraversalFinder
(
vg
)
ConsistencyCalculator
(
vg
)
hash< const vg::Snarl >
(
std
)
NamedNodeBackTranslation
(
handlegraph
)
s
VectorizableHandleGraph
(
handlegraph
)
VectorView::const_iterator
(
vg
)
hash< handlegraph::edge_t >
(
std
)
NameMapper
(
vg
)
Vectorizer
ConstructedChunk
(
vg
)
hash< handlegraph::handle_t >
(
std
)
NestedCachedPackedTraversalSupportFinder
(
vg
)
Sampler
(
vg
)
VectorView
(
vg
)
Constructor
(
vg
)
hash< handlegraph::net_handle_t >
(
std
)
NestedFlowCaller
(
vg
)
WFATree::ScoreProperties
(
vg
)
VectorViewInverse
(
vg
)
ContractingGraph
(
vg
)
hash< handlegraph::path_handle_t >
(
std
)
NestedTraversalFinder
(
vg
)
ScoreProvider
(
haplo
)
Version
(
vg
)
ConvertedHashGraph
(
vg::io
)
hash< handlegraph::step_handle_t >
(
std
)
Deconstructor::NestingInfo
(
vg
)
ScoringOptions
VG
(
vg
)
count_back_inserter
(
vg
)
hash< pair< A, B > >
(
std
)
net_handle_t
(
handlegraph
)
SnarlDistanceIndexClusterer::Seed
(
vg
)
VGAlignmentEmitter
(
vg::io
)
Counts
(
vg
)
hash< std::tuple< TT... > >
(
std
)
NetGraph
(
vg
)
ZipCodeTree::seed_result_t
(
vg
)
VGIndexes
(
vg
)
d
hash< vg::NodeSide >
(
std
)
NGSSimulator
(
vg
)
SnarlDistanceIndexClusterer::SeedCache
(
vg
)
VGset
(
vg
)
hash< vg::NodeTraversal >
(
std
)
NoAlignmentInBandException
(
vg
)
SeqComplexity
(
vg
)
Visit
(
vg
)
DagifiedGraph
(
vg
)
hash< vg::ZipCodeTree::oriented_seed_t >
(
std
)
Node
(
vg
)
Serializable
(
handlegraph
)
Viz
(
vg
)
ZipCode::decoder_t
(
vg
)
hash< vg::ZipCodeTree::seed_result_t >
(
std
)
Node
(
vg::algorithms
)
SerializableHandleGraph
(
handlegraph
)
VPKG
(
vg::io
)
Deconstructor
(
vg
)
Genotyper::hash_ambiguous_allele_set
(
vg
)
ZipCode::node_code_t
(
vg
)
ShuffledPairs
(
vg
)
w
BandedGlobalAligner::AltTracebackStack::Deflection
(
vg
)
hash_map
(
vg
)
NodePileup
(
vg
)
SimpleConsistencyCalculator
(
vg
)
DeletableHandleGraph
(
handlegraph
)
hash_map< K *, V >
(
vg
)
NodeSide
(
vg
)
SimpleTraversalSupportCalculator
(
vg
)
walk_t
(
vg::algorithms
)
DeleteHaplotypeCommand
(
vg
)
Genotyper::hash_node_traversal
(
vg
)
NodeTraversal
(
vg
)
SizeLimitExceededException
(
vg
)
wang_hash
(
vg
)
DeletionAligner
(
vg
)
Genotyper::hash_oriented_edge
(
vg
)
normal_distribution
(
vg
)
SmallBitset
(
vg
)
wang_hash< handle_t >
(
vg
)
DiagramExplainer
(
vg
)
hash_set
(
vg
)
NullAlignmentEmitter
(
vg::io
)
SmallSnarlSimplifier
(
vg
)
wang_hash< handlegraph::net_handle_t >
(
vg
)
DinucleotideMachine
(
vg
)
hash_set< K * >
(
vg
)
NullClusterer
(
vg
)
Snarl
(
vg
)
wang_hash< net_identifier_t >
(
vg
)
discrete_distribution
(
vg
)
hDP_gbwt_graph_accessor
(
haplo
)
NullMaskingGraph
(
vg
)
ZipCode::snarl_code_t
(
vg
)
wang_hash< NodeSide >
(
vg
)
DistanceHeuristic
(
vg
)
Haplotypes::Header
(
vg
)
number_bool_packing
(
handlegraph
)
NestedCachedPackedTraversalSupportFinder::snarl_less
(
vg
)
wang_hash< NodeTraversal >
(
vg
)
DotDumpExplainer
(
vg
)
hFILE_backend
o
SnarlCaller
(
vg
)
wang_hash< path_handle_t >
(
vg
)
DozeuInterface
(
vg
)
hFILE_cppstream
(
vg::io
)
SnarlDecomposition
(
handlegraph
)
wang_hash< std::pair< A, B > >
(
vg
)
DozeuPinningOverlay
(
vg
)
MEMClusterer::HitEdge
(
vg
)
Option
(
vg
)
SnarlDistanceIndexClusterer
(
vg
)
wang_hash< T * >
(
vg
)
MEMClusterer::DPScoreComparator
(
vg
)
MEMClusterer::HitGraph
(
vg
)
Option< vector< Item >, Parser >
(
vg
)
SnarlFinder
(
vg
)
wang_hash< T, typename std::enable_if< std::is_integral< T >::value >::type >
(
vg
)
e
MEMClusterer::HitNode
(
vg
)
OptionGroup
(
vg::subcommand
)
SnarlGraph
(
vg
)
Watchdog
(
vg
)
HTSAlignmentEmitter
(
vg
)
OptionInterface
(
vg
)
SnarlManager
(
vg
)
FlowSort::WeightedGraph
(
vg
)
Edge
(
vg
)
HTSWriter
(
vg
)
OptionValueParser
(
vg
)
SnarlMinDistance
(
vg
)
WFAAlignment
(
vg
)
Edge
(
vg::algorithms
)
i
OptionValueParser< vector< Item > >
(
vg
)
SnarlOrientedDistanceMeasurer
(
vg
)
WFAExtender
(
vg
)
EdgePileup
(
vg
)
DozeuInterface::OrderedGraph
(
vg
)
SnarlManager::SnarlRecord
(
vg
)
WFANode
(
vg
)
Edit
(
vg
)
IdentityOverlay
(
vg
)
ZipCodeTree::oriented_seed_t
(
vg
)
SnarlState
(
vg
)
WFAPoint
(
vg
)
edit_t
(
vg
)
IDScanner
(
vg
)
OrientedDistanceClusterer
(
vg
)
SnarlTraversal
(
vg
)
WFATree
(
vg
)
EditedTranscriptPath
(
vg
)
IncrementalSubgraph
(
vg
)
OrientedDistanceMeasurer
(
vg
)
SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild
(
vg
)
WideningPRNG
(
vg
)
endianness
(
vg
)
IncrementIter
(
vg
)
p
SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
(
vg
)
WindowedVcfBuffer
(
vg
)
WFAExtender::ErrorModel
(
vg
)
IndexedVG
(
vg
)
linear_haplo_structure::SNVvector
(
haplo
)
WrappingPositionScanner
(
vg
)
WFAExtender::ErrorModel::Event
(
vg
)
IndexFile
(
vg
)
PackedTraversalSupportFinder
(
vg
)
ZipCodeForest::sort_value_t
(
vg
)
x
ExhaustiveTraversalFinder
(
vg
)
IndexingParameters
(
vg
)
Packer
(
vg
)
SourceSinkOverlay
(
vg
)
Exon
(
vg
)
IndexingPlan
(
vg
)
Packers
(
vg
)
SparseUnionFind
(
vg
)
XdropAligner
(
vg
)
ExpandingOverlayGraph
(
handlegraph
)
IndexRecipe
(
vg
)
Funnel::PaintableSpace
(
vg
)
SplicedHTSAlignmentEmitter
(
vg
)
XG
(
xg
)
Explainer
(
vg
)
IndexRegistry
(
vg
)
pair_hash_map
(
vg
)
SpliceRegion
(
vg
)
XGFormatError
(
xg
)
ExtraNodeGraph
(
vg
)
InsertHaplotypeCommand
(
vg
)
pair_hash_set
(
vg
)
SpliceStats
(
vg
)
XGPath
(
xg
)
f
InsufficientInputException
(
vg
)
PairedEndMapper
(
vg
)
SSWAligner
(
vg
)
z
int_itvl_t
(
haplo
)
ParallelKFFReader
(
vg
)
Funnel::Stage
(
vg
)
IncrementalSubgraph::FCmp
(
vg
)
IntegratedSnarlFinder
(
vg
)
HaplotypePartitioner::Parameters
(
vg
)
MinimizerMapper::aligner_stats_t::stat_collection_t
(
vg
)
ZipCode
(
vg
)
fdinbuf
(
vg::io
)
ZipCodeForest::interval_state_t
(
vg
)
Recombinator::Parameters
(
vg
)
MinimizerMapper::aligner_stats_t::stat_set_t
(
vg
)
ZipCodeCollection
(
vg
)
fdistream
(
vg::io
)
is_instantiation_of
(
vg
)
ParentGenotypeInfo
(
vg
)
state_hash
(
vg
)
ZipCodeForest
(
vg
)
fdostream
(
vg::io
)
is_instantiation_of< Predicate< PredicateArgs... >, Predicate >
(
vg
)
Path
(
vg
)
Recombinator::Statistics
(
vg
)
ZipCodeTree
(
vg
)
fdoutbuf
(
vg::io
)
Funnel::Item
(
vg
)
path_handle_t
(
handlegraph
)
step_handle_t
(
handlegraph
)
zstd_compress_buf
(
vg
)
FeatureSet::Feature
(
vg
)
PhasedGenome::iterator
(
vg
)
path_mapping_t
(
vg
)
str_view
(
vg
)
zstd_decompress_buf
(
vg
)
FeatureSet
(
vg
)
ShuffledPairs::iterator
(
vg
)
path_t
(
vg
)
StrandSplitGraph
(
vg
)
zstd_ifstream
(
vg
)
Filter
(
vg
)
ZipCodeTree::iterator
(
vg
)
PathBasedTraversalFinder
(
vg
)
streaminbuf
(
vg::io
)
zstd_ofstream
(
vg
)
Funnel::FilterPerformance
(
vg
)
PathForEachSocket::iterator
(
handlegraph
)
PathBranch
(
vg
)
StreamIndex
(
vg
)
FixedGenotypePriorCalculator
(
vg
)
iterator_traits< vg::PhasedGenome::iterator >
(
std
)
PathChunker
(
vg
)
StreamIndexBase
(
vg
)
FlagArgSpec
(
vg::subcommand
)
iterator_traits< vg::ZipCodeTree::iterator >
(
std
)
PathComponentIndex
(
vg
)
streamistream
(
vg::io
)
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