|
FlowCaller (vg) |
|
Packers (vg) |
state_hash (vg) |
FlowSort (vg) |
pair_hash_map (vg) |
step_handle_t (handlegraph) |
Genotyper::Affinity (vg) |
FlowTraversalFinder (vg) |
j2pb_error |
pair_hash_set (vg) |
StrandSplitGraph (vg) |
Aligner (vg) |
FragmentLengthDistribution (vg) |
JoinedSpliceGraph (vg) |
PairedEndMapper (vg) |
StreamIndex (vg) |
AlignerClient (vg) |
FragmentLengthStatistics (vg) |
json_autoptr |
Path (vg) |
StreamIndexBase (vg) |
Alignment (vg) |
Funnel (vg) |
JSONStreamHelper (vg::io) |
path_handle_t (handlegraph) |
StreamMultiplexer (vg::io) |
AlignmentChainModel (vg) |
|
|
path_mapping_t (vg) |
StreamSorter (vg) |
AlignmentChainModelVertex (vg) |
HashGraph::path_mapping_t (bdsg) |
string_hash_map (vg) |
AlignmentEmitter (vg::io) |
GafAlignmentEmitter (vg::io) |
keyNotFoundException (vg) |
ODGI::path_metadata_t (bdsg) |
string_hash_set (vg) |
BandedGlobalAligner::AltTracebackStack (vg) |
GAFOutputCaller (vg) |
kmer_t (vg) |
path_t (vg) |
Subcommand (vg::subcommand) |
Annotation (vg) |
GafRecord (gafkluge) |
kmer_t (vg::algorithms) |
HashGraph::path_t (bdsg) |
SubgraphOverlay (vg) |
AppendHaplotypeCommand (vg) |
GafStep (gafkluge) |
KmerMatch (vg) |
PathBasedTraversalFinder (vg) |
SubHandleGraph (vg) |
AugmentedGraph (vg) |
GaplessExtender (vg) |
KmerPosition (vg) |
PathBranch (vg) |
Subpath (vg) |
|
GaplessExtension (vg) |
|
PathChunker (vg) |
subpath_t (vg) |
gbwt_thread_t (haplo) |
PathComponentIndex (vg) |
Support (vg) |
BandedGlobalAligner::BABuilder (vg) |
GBWTScoreProvider (haplo) |
LegacyCaller (vg) |
PathForEachSocket (handlegraph) |
SupportAugmentedGraph (vg) |
BandedGlobalAligner::BAMatrix (vg) |
GBWTTraversalFinder (vg) |
linear_haplo_structure (haplo) |
PathHandleGraph (handlegraph) |
SupportBasedSnarlCaller (vg) |
BandedGlobalAligner (vg) |
GenomeState (vg) |
LinearScoreProvider (haplo) |
PathIndex (vg) |
SupportRestrictedTraversalFinder (vg) |
BaseAligner (vg) |
GenomeStateCommand (vg) |
linear_haplo_structure::linearUnrepresentable (haplo) |
PathNode (vg) |
Surjector (vg) |
BaseMapper (vg) |
Genotype (vg) |
LocationSupport (vg) |
PathOrientedDistanceMeasurer (vg) |
SwapHaplotypesCommand (vg) |
BaseOption (vg) |
GenotypeLikelihoodCalculator (vg) |
GraphSynchronizer::Lock (vg) |
PathPositionHandleGraph (handlegraph) |
|
BasePileup (vg) |
GenotypePriorCalculator (vg) |
Locus (vg) |
PathRestrictedTraversalFinder (vg) |
BenchmarkResult (vg) |
Genotyper (vg) |
|
Paths (vg) |
Registry::Tables (vg::io) |
BitString (vg) |
GFAFormatError (vg::algorithms) |
PathSubgraph (vg) |
TargetValueSearch (vg) |
BitStringTree (vg) |
GFFReader (vg) |
Mapper (vg) |
PathSubgraphOverlay (vg) |
Watchdog::thread_state_t (vg) |
BlockedGzipInputStream (vg::io) |
GFFRecord (vg) |
Mapping (vg) |
PathTraversalFinder (vg) |
TipAnchoredMaxDistance (vg) |
BlockedGzipOutputStream (vg::io) |
Graph (vg) |
mapping_t (vg) |
PhasedGenome (vg) |
Transcript (vg) |
BoolReturningWrapper (handlegraph) |
DozeuInterface::graph_pos_s (vg) |
NGSSimulator::MarkovDistribution (vg) |
PhaseUnfolder (vg) |
Transcriptome (vg) |
BoolReturningWrapper< Iteratee, Iterated, bool > (handlegraph) |
GraphCaller (vg) |
MaximalExactMatch (vg) |
Pictographs (vg) |
TranscriptPath (vg) |
BoolReturningWrapper< Iteratee, Iterated, void > (handlegraph) |
GraphSynchronizer (vg) |
MCMCCaller (vg) |
Pileup (vg) |
Translation (vg) |
BREAKPOINT (vg) |
GreedyMinDistanceClusterer (vg) |
MCMCGenotyper (vg) |
VG::Plan (vg) |
Translator (vg) |
|
FlowSort::Growth (vg) |
MEMChainModel (vg) |
PoissonSupportSnarlCaller::PoissonCallInfo (vg) |
TraversalFinder (vg) |
GSSWAligner (vg) |
MEMChainModelVertex (vg) |
PoissonSupportSnarlCaller (vg) |
TraversalSupportCalculator (vg) |
CachedPackedTraversalSupportFinder (vg) |
|
MEMClusterer (vg) |
Position (vg) |
TraversalSupportFinder (vg) |
IndexedVG::CacheEntry (vg) |
MemoizingGraph (vg) |
position_t (vg) |
Tree (vg) |
CactusSide (vg) |
handle_t (handlegraph) |
IntegratedSnarlFinder::MergedAdjacencyGraph (vg) |
PositionIDScanner (vg) |
BitStringTree::TreeNode (vg) |
CactusSnarlFinder (vg) |
HandleGraph (handlegraph) |
MessageEmitter (vg::io) |
Progressive (vg) |
TreeNode (vg) |
SnarlCaller::CallInfo (vg) |
HandleGraphSnarlFinder (vg) |
MessageIterator (vg::io) |
ProtobufEmitter (vg::io) |
SnarlSeedClusterer::TreeState (vg) |
MinimumDistanceIndex::ChainIndex (vg) |
Handler (vg::temp_file) |
MinDistanceClusterer (vg) |
ProtobufIterator (vg::io) |
TreeSubgraph (vg) |
ChainIterator (vg) |
Handler (xg::temp_file) |
MinimizerMapper::Minimizer (vg) |
PruningParameters |
TrivialTraversalFinder (vg) |
SnarlSeedClusterer::Cluster (vg) |
haplo_DP (haplo) |
MinimizerMapper (vg) |
|
TSVAlignmentEmitter (vg::io) |
Colors (vg) |
haplo_DP_column (haplo) |
MinimumDistanceIndex (vg) |
TVSClusterer (vg) |
CompletedTranscriptPath (vg) |
haplo_DP_rectangle (haplo) |
MIPayload (vg) |
QualAdjAligner (vg) |
|
ComponentMinDistanceClusterer (vg) |
PhasedGenome::Haplotype (vg) |
MSAConverter (vg) |
QualAdjXdropAligner (vg) |
Configurable (vg) |
HaplotypeIndexer (vg) |
multipath_alignment_t (vg) |
|
uniform_int_distribution (vg) |
ConfigurableParser (vg) |
PhasedGenome::HaplotypeNode (vg) |
MultipathAlignment (vg) |
uniform_real_distribution (vg) |
Connection (vg) |
hash< const vg::Snarl > (std) |
MultipathAlignmentEmitter (vg) |
Range (vg) |
|
connection_t (vg) |
hash< handlegraph::handle_t > (std) |
MultipathAlignmentGraph (vg) |
RankedHandleGraph (handlegraph) |
ConsistencyCalculator (vg) |
hash< handlegraph::path_handle_t > (std) |
MultipathMapper (vg) |
RareVariantSimplifier (vg) |
VariantAdder (vg) |
ConstructedChunk (vg) |
hash< handlegraph::step_handle_t > (std) |
MultipathProblem (vg) |
RatioSupportSnarlCaller (vg) |
VcfBuffer (vg) |
Constructor (vg) |
hash< pair< A, B > > (std) |
MutableHandleGraph (handlegraph) |
ReadFilter (vg) |
VCFGenotyper (vg) |
ReadFilter::Counts (vg) |
hash< std::tuple< TT... > > (std) |
MutablePathDeletableHandleGraph (handlegraph) |
ReadRestrictedTraversalFinder (vg) |
VCFOutputCaller (vg) |
|
hash< vg::NodeSide > (std) |
MutablePathHandleGraph (handlegraph) |
Region (vg) |
VcfRecordConverter (vg) |
hash< vg::NodeTraversal > (std) |
MutablePathMutableHandleGraph (handlegraph) |
RegionExpander (vg) |
VcfRecordFilter (vg) |
DagifiedGraph (vg) |
Genotyper::hash_ambiguous_allele_set (vg) |
|
Registry (vg::io) |
VCFTraversalFinder (vg) |
Deconstructor (vg) |
hash_map (vg) |
ReplaceLocalHaplotypeCommand (vg) |
VectorizableHandleGraph (handlegraph) |
BandedGlobalAligner::AltTracebackStack::Deflection (vg) |
hash_map< K *, V > (vg) |
NameMapper (vg) |
ReplaceSnarlHaplotypeCommand (vg) |
Vectorizer |
DeletableHandleGraph (handlegraph) |
Genotyper::hash_node_traversal (vg) |
NestedTraversalFinder (vg) |
RepresentativeTraversalFinder (vg) |
Version (vg) |
DeleteHaplotypeCommand (vg) |
Genotyper::hash_oriented_edge (vg) |
NetGraph (vg) |
ReverseGraph (vg) |
VG (vg) |
DepthMap (vg) |
hash_set (vg) |
SnarlSeedClusterer::NetgraphNode (vg) |
RRMemo (haplo::haploMath) |
VGAlignmentEmitter (vg::io) |
DinucleotideMachine (vg) |
hash_set< K * > (vg) |
NGSSimulator (vg) |
|
VGset (vg) |
discrete_distribution (vg) |
HashGraph (bdsg) |
NoAlignmentInBandException (vg) |
Visit (vg) |
DistanceHeuristic (vg) |
hDP_gbwt_graph_accessor (haplo) |
Node (vg) |
Sampler (vg) |
Viz (vg) |
DozeuInterface (vg) |
hFILE_backend |
HashGraph::node_t (bdsg) |
ScoreProvider (haplo) |
VPKG (vg::io) |
DozeuPinningOverlay (vg) |
hFILE_cppstream (vg::io) |
SnarlSeedClusterer::NodeClusters (vg) |
SnarlSeedClusterer::Seed (vg) |
|
MEMClusterer::DPScoreComparator (vg) |
MEMClusterer::HitEdge (vg) |
NodePileup (vg) |
SerializableHandleGraph (handlegraph) |
|
MEMClusterer::HitGraph (vg) |
NodeSide (vg) |
ShuffledPairs (vg) |
walk_t (vg::algorithms) |
MEMClusterer::HitNode (vg) |
NodeTraversal (vg) |
SimpleConsistencyCalculator (vg) |
walk_t (vg) |
Edge (vg) |
Homogenizer (vg) |
normal_distribution (vg) |
SimpleTraversalSupportCalculator (vg) |
wang_hash (vg) |
ODGI::edge_helper (bdsg) |
HTSAlignmentEmitter (vg) |
NullAlignmentEmitter (vg::io) |
SmallBitset (vg) |
wang_hash< handle_t > (vg) |
EdgePileup (vg) |
|
NullClusterer (vg) |
SmallSnarlSimplifier (vg) |
wang_hash< NodeSide > (vg) |
Edit (vg) |
NullMaskingGraph (vg) |
Snarl (vg) |
wang_hash< NodeTraversal > (vg) |
edit_t (vg) |
IdentityOverlay (vg) |
number_bool_packing (handlegraph) |
SnarlCaller (vg) |
wang_hash< path_handle_t > (vg) |
EditedTranscriptPath (vg) |
IDScanner (vg) |
|
SnarlFinder (vg) |
wang_hash< std::pair< A, B > > (vg) |
endianness (vg) |
IncrementalSubgraph (vg) |
MinimumDistanceIndex::SnarlIndex (vg) |
wang_hash< T * > (vg) |
ExhaustiveTraversalFinder (vg) |
IncrementIter (vg) |
ODGI (bdsg) |
SnarlManager (vg) |
wang_hash< T, typename std::enable_if< std::is_integral< T >::value >::type > (vg) |
Exon (vg) |
Index (vg) |
Option (vg) |
SnarlMinDistance (vg) |
Watchdog (vg) |
ExpandingOverlayGraph (handlegraph) |
IndexedVG (vg) |
Option< vector< Item >, Parser > (vg) |
SnarlOrientedDistanceMeasurer (vg) |
FlowSort::WeightedGraph (vg) |
ExtraNodeGraph (vg) |
IndexManager (vg) |
OptionInterface (vg) |
SnarlManager::SnarlRecord (vg) |
WideningPRNG (vg) |
|
indexOpenException (vg) |
OptionValueParser (vg) |
SnarlSeedClusterer (vg) |
WindowedVcfBuffer (vg) |
InsertHaplotypeCommand (vg) |
OptionValueParser< vector< Item > > (vg) |
SnarlState (vg) |
WrappingPositionScanner (vg) |
fdinbuf (vg::io) |
int_itvl_t (haplo) |
DozeuInterface::OrderedGraph (vg) |
SnarlTraversal (vg) |
|
fdistream (vg::io) |
IntegratedSnarlFinder (vg) |
OrientedDistanceClusterer (vg) |
linear_haplo_structure::SNVvector (haplo) |
fdostream (vg::io) |
is_instantiation_of (vg) |
OrientedDistanceMeasurer (vg) |
SourceSinkOverlay (vg) |
XdropAligner (vg) |
fdoutbuf (vg::io) |
is_instantiation_of< Predicate< PredicateArgs... >, Predicate > (vg) |
|
SplicedHTSAlignmentEmitter (vg) |
XG (xg) |
FeatureSet::Feature (vg) |
Funnel::Item (vg) |
SpliceMotifs (vg) |
XGFormatError (xg) |
FeatureSet (vg) |
PhasedGenome::iterator (vg) |
PackedGraph (bdsg) |
SpliceRegion (vg) |
XGPath (xg) |
Filter (vg) |
ShuffledPairs::iterator (vg) |
PackedGraph::PackedPath (bdsg) |
SRPE (vg) |
|
Funnel::FilterPerformance (vg) |
PathForEachSocket::iterator (handlegraph) |
PackedTraversalSupportFinder (vg) |
SSWAligner (vg) |
|
FixedGenotypePriorCalculator (vg) |
iterator_traits< vg::PhasedGenome::iterator > (std) |
Packer (vg) |
Funnel::Stage (vg) |
|
| | | | |