Index

_

__add__() (pbcore.io.dataset.DataSetIO.DataSet method) __deepcopy__() (pbcore.io.dataset.DataSetIO.DataSet method) __eq__() (pbcore.io.dataset.DataSetIO.DataSet method) __getitem__() (pbcore.io.dataset.DataSetMembers.AutomationParameters method) (pbcore.io.dataset.DataSetMembers.BioSamplesMetadata method) (pbcore.io.dataset.DataSetMembers.CollectionsMetadata method) (pbcore.io.dataset.DataSetMembers.DNABarcodes method) (pbcore.io.dataset.DataSetMembers.ExternalResources method) (pbcore.io.dataset.DataSetMembers.FileIndices method) (pbcore.io.dataset.DataSetMembers.Filter method) (pbcore.io.dataset.DataSetMembers.Filters method) (pbcore.io.dataset.DataSetMembers.Properties method) (pbcore.io.dataset.DataSetMembers.RecordWrapper method) (pbcore.io.dataset.DataSetMembers.StatsMetadata method) __init__() (pbcore.io.dataset.DataSetIO.AlignmentSet method) (pbcore.io.dataset.DataSetIO.BarcodeSet method) (pbcore.io.dataset.DataSetIO.ContigSet method) (pbcore.io.dataset.DataSetIO.DataSet method) (pbcore.io.dataset.DataSetIO.GmapReferenceSet method) (pbcore.io.dataset.DataSetIO.HdfSubreadSet method) (pbcore.io.dataset.DataSetIO.ReadSet method) (pbcore.io.dataset.DataSetIO.ReferenceSet method) (pbcore.io.dataset.DataSetIO.SubreadSet method)

__iter__() (pbcore.io.dataset.DataSetMembers.BioSamplesMetadata method) (pbcore.io.dataset.DataSetMembers.CollectionsMetadata method) (pbcore.io.dataset.DataSetMembers.DNABarcodes method) (pbcore.io.dataset.DataSetMembers.ExternalResources method) (pbcore.io.dataset.DataSetMembers.FileIndices method) (pbcore.io.dataset.DataSetMembers.Filter method) (pbcore.io.dataset.DataSetMembers.Filters method) (pbcore.io.dataset.DataSetMembers.Properties method) (pbcore.io.dataset.DataSetMembers.RecordWrapper method) __repr__() (pbcore.io.dataset.DataSetIO.DataSet method) (pbcore.io.dataset.DataSetMembers.RecordWrapper method)

A

accs() (in module pbcore.io.dataset.DataSetMembers) accuracy (pbcore.io.CmpH5Alignment attribute) ADAPTER_AFTER (pbcore.io.dataset.DataSetMembers.PbiFlags attribute) ADAPTER_BEFORE (pbcore.io.dataset.DataSetMembers.PbiFlags attribute) adapterDimerFraction (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) adapters (pbcore.io.dataset.DataSetMembers.ExternalResource attribute) addBarcode() (pbcore.io.dataset.DataSetMembers.DNABarcodes method) addDatasets() (pbcore.io.dataset.DataSetIO.DataSet method) addExternalResources() (pbcore.io.dataset.DataSetIO.DataSet method) addFilter() (pbcore.io.dataset.DataSetMembers.Filters method) addFilterList() (pbcore.io.dataset.DataSetMembers.Filters method) addFilters() (pbcore.io.dataset.DataSetIO.DataSet method) addIndices() (pbcore.io.dataset.DataSetMembers.ExternalResource method) addMetadata() (pbcore.io.dataset.DataSetIO.BarcodeSet method) (pbcore.io.dataset.DataSetIO.ContigSet method) (pbcore.io.dataset.DataSetIO.DataSet method) (pbcore.io.dataset.DataSetIO.ReadSet method) (pbcore.io.dataset.DataSetMembers.RecordWrapper method) addParameter() (pbcore.io.dataset.DataSetMembers.AutomationParameters method) addParentDataSet() (pbcore.io.dataset.DataSetMembers.DataSetMetadata method) (pbcore.io.dataset.DataSetMembers.Provenance method)

addRequirement() (pbcore.io.dataset.DataSetMembers.Filter method) (pbcore.io.dataset.DataSetMembers.Filters method) addResources() (pbcore.io.dataset.DataSetMembers.ExternalResources method) addSample() (pbcore.io.dataset.DataSetMembers.BioSamplesMetadata method) aEnd (pbcore.io.CmpH5Alignment attribute) alignmentArray() (pbcore.io.CmpH5Alignment method) alignmentIndex (pbcore.io.CmpH5Reader attribute) AlignmentSet (class in pbcore.io.dataset.DataSetIO) allSequencingZmws (pbcore.io.BasH5Reader attribute) append() (pbcore.io.dataset.DataSetMembers.RecordWrapper method) assertBarcoded() (pbcore.io.dataset.DataSetIO.ReadSet method) aStart (pbcore.io.CmpH5Alignment attribute) atRowNumber() (pbcore.io.IndexedBamReader method) attrib (pbcore.io.dataset.DataSetMembers.RecordWrapper attribute) Automation (class in pbcore.io.dataset.DataSetMembers) automation (pbcore.io.dataset.DataSetMembers.CollectionMetadata attribute) automationName (pbcore.io.dataset.DataSetMembers.PrimaryMetadata attribute) AutomationParameter (class in pbcore.io.dataset.DataSetMembers) automationParameter (pbcore.io.dataset.DataSetMembers.AutomationParameters attribute) AutomationParameters (class in pbcore.io.dataset.DataSetMembers) automationParameters (pbcore.io.dataset.DataSetMembers.Automation attribute) availableDists() (pbcore.io.dataset.DataSetMembers.StatsMetadata method)

B

backticks() (in module pbcore.util.Process) bai (pbcore.io.dataset.DataSetMembers.ExternalResource attribute) bam (pbcore.io.dataset.DataSetMembers.ExternalResource attribute) BamAlignment (class in pbcore.io) BamReader (class in pbcore.io) barcode (pbcore.io.BamAlignment attribute) (pbcore.io.CmpH5Alignment attribute) (pbcore.io.CmpH5Reader attribute) (pbcore.io.dataset.DataSetMembers.Kit attribute) BARCODE_AFTER (pbcore.io.dataset.DataSetMembers.PbiFlags attribute) BARCODE_BEFORE (pbcore.io.dataset.DataSetMembers.PbiFlags attribute) barcodeConstruction (pbcore.io.dataset.DataSetMembers.BarcodeSetMetadata attribute) barcodeName (pbcore.io.BamAlignment attribute) (pbcore.io.CmpH5Alignment attribute) (pbcore.io.CmpH5Reader attribute) barcodes (pbcore.io.CmpH5Reader attribute) (pbcore.io.dataset.DataSetIO.DataSet attribute) (pbcore.io.dataset.DataSetMembers.ExternalResource attribute) BarcodeSet (class in pbcore.io.dataset.DataSetIO) BarcodeSetMetadata (class in pbcore.io.dataset.DataSetMembers) basecalls() (pbcore.io.BasH5IO.ZmwRead method) (pbcore.io.BasH5Reader.ZmwRead method) baseFeature() (pbcore.io.BamAlignment method) (pbcore.io.CmpH5Alignment method)

baseFeaturesAvailable() (pbcore.io.CmpH5Reader method) BasH5Reader (class in pbcore.io) BasH5Reader.CCSZmwRead (class in pbcore.io) BasH5Reader.Zmw (class in pbcore.io) BasH5Reader.ZmwRead (class in pbcore.io) baxH5 (pbcore.io.BasH5IO.Zmw attribute) (pbcore.io.BasH5IO.ZmwRead attribute) (pbcore.io.BasH5Reader.Zmw attribute) (pbcore.io.BasH5Reader.ZmwRead attribute) BinBoundaryMismatchError BindingKit (class in pbcore.io.dataset.DataSetMembers) bindingKit (pbcore.io.dataset.DataSetMembers.CollectionMetadata attribute) BinMismatchError BinNumberMismatchError bins (pbcore.io.dataset.DataSetMembers.ContinuousDistribution attribute) (pbcore.io.dataset.DataSetMembers.DiscreteDistribution attribute) binWidth (pbcore.io.dataset.DataSetMembers.ContinuousDistribution attribute) BinWidthMismatchError BioSampleMetadata (class in pbcore.io.dataset.DataSetMembers) bioSamples (pbcore.io.dataset.DataSetMembers.WellSampleMetadata attribute) BioSamplesMetadata (class in pbcore.io.dataset.DataSetMembers) breakqname() (in module pbcore.io.dataset.DataSetMembers) broadcastFilters() (pbcore.io.dataset.DataSetMembers.Filters method)

C

castableTypes() (pbcore.io.dataset.DataSetIO.DataSet class method) ccsRead (pbcore.io.BasH5IO.Zmw attribute) (pbcore.io.BasH5Reader.Zmw attribute) ccsReads() (pbcore.io.BasH5Reader method) cellCountInJob (pbcore.io.dataset.DataSetMembers.SecondaryMetadata attribute) cellIndex (pbcore.io.dataset.DataSetMembers.CollectionMetadata attribute) CellPac (class in pbcore.io.dataset.DataSetMembers) cellPac (pbcore.io.dataset.DataSetMembers.CollectionMetadata attribute) CHANNEL_DISTS (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) channelDists (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) checkAndResolve() (in module pbcore.io.dataset.DataSetIO) chemistryBarcodeTriple (pbcore.io.BasH5Reader attribute) ChemistryLookupError clearCallbacks() (pbcore.io.dataset.DataSetMembers.RecordWrapper method) clippedTo() (pbcore.io.BamAlignment method) (pbcore.io.CmpH5Alignment method) close() (pbcore.io.BasH5Reader method) (pbcore.io.CmpH5Reader method) (pbcore.io.dataset.DataSetIO.DataSet method) cmpH5 (pbcore.io.CmpH5Alignment attribute) CmpH5Alignment (class in pbcore.io) CmpH5Reader (class in pbcore.io) CollectionMetadata (class in pbcore.io.dataset.DataSetMembers) collectionNumber (pbcore.io.dataset.DataSetMembers.CollectionMetadata attribute) collectionPathUri (pbcore.io.dataset.DataSetMembers.OutputOptions attribute) collections (pbcore.io.dataset.DataSetMembers.SubreadSetMetadata attribute) CollectionsMetadata (class in pbcore.io.dataset.DataSetMembers) comment (pbcore.io.FastaRecord attribute) (pbcore.io.FastqRecord attribute)

comments (pbcore.io.dataset.DataSetMembers.WellSampleMetadata attribute) concentration (pbcore.io.dataset.DataSetMembers.WellSampleMetadata attribute) configFileName (pbcore.io.dataset.DataSetMembers.PrimaryMetadata attribute) ConsensusAlignmentSet (class in pbcore.io.dataset.DataSetIO) ConsensusReadSet (class in pbcore.io.dataset.DataSetIO) ConsensusReadSetRef (class in pbcore.io.dataset.DataSetMembers) consensusReadSetRef (pbcore.io.dataset.DataSetMembers.CollectionMetadata attribute) consolidate() (pbcore.io.dataset.DataSetIO.AlignmentSet method) (pbcore.io.dataset.DataSetIO.ContigSet method) (pbcore.io.dataset.DataSetIO.HdfSubreadSet method) (pbcore.io.dataset.DataSetIO.ReadSet method) context (pbcore.io.dataset.DataSetMembers.CollectionMetadata attribute) contigNames (pbcore.io.dataset.DataSetIO.ContigSet attribute) contigs (pbcore.io.dataset.DataSetIO.ContigSet attribute) ContigSet (class in pbcore.io.dataset.DataSetIO) ContigSetMetadata (class in pbcore.io.dataset.DataSetMembers) ContinuousDistribution (class in pbcore.io.dataset.DataSetMembers) control (pbcore.io.dataset.DataSetMembers.ExternalResource attribute) controlReadLenDist (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) controlReadQualDist (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) copy() (pbcore.io.dataset.DataSetIO.DataSet method) (pbcore.io.Gff3Record method) copyFiles (pbcore.io.dataset.DataSetMembers.OutputOptions attribute) copyFiles() (pbcore.io.dataset.DataSetIO.DataSet method) CopyFilesMetadata (class in pbcore.io.dataset.DataSetMembers) copyTo() (pbcore.io.dataset.DataSetIO.DataSet method) countRecords() (pbcore.io.dataset.DataSetIO.AlignmentSet method) createdAt (pbcore.io.dataset.DataSetIO.DataSet attribute) (pbcore.io.dataset.DataSetMembers.RecordWrapper attribute) createdBy (pbcore.io.dataset.DataSetMembers.Provenance attribute)

D

DataSet (class in pbcore.io.dataset.DataSetIO) DataSetMetadata (class in pbcore.io.dataset.DataSetMembers) decodeTriple() (in module pbcore.chemistry.chemistry) DeletionQV() (pbcore.io.BamAlignment method) (pbcore.io.BasH5IO.ZmwRead method) (pbcore.io.BasH5Reader.ZmwRead method) (pbcore.io.CmpH5Alignment method) DeletionTag() (pbcore.io.BamAlignment method) (pbcore.io.BasH5IO.ZmwRead method) (pbcore.io.BasH5Reader.ZmwRead method) (pbcore.io.CmpH5Alignment method)

description (pbcore.io.dataset.DataSetIO.DataSet attribute) (pbcore.io.dataset.DataSetMembers.ContinuousDistribution attribute) (pbcore.io.dataset.DataSetMembers.DiscreteDistribution attribute) (pbcore.io.dataset.DataSetMembers.RecordWrapper attribute) disableFilters() (pbcore.io.dataset.DataSetIO.DataSet method) DiscreteDistribution (class in pbcore.io.dataset.DataSetMembers) divideKeys() (in module pbcore.io.dataset.DataSetIO) DNABarcode (class in pbcore.io.dataset.DataSetMembers) DNABarcodes (class in pbcore.io.dataset.DataSetMembers) (pbcore.io.dataset.DataSetMembers.BioSampleMetadata attribute)

E

enableFilters() (pbcore.io.dataset.DataSetIO.DataSet method) expirationDate (pbcore.io.dataset.DataSetMembers.Kit attribute) extend() (pbcore.io.dataset.DataSetMembers.RecordWrapper method)

ExternalResource (class in pbcore.io.dataset.DataSetMembers) ExternalResources (class in pbcore.io.dataset.DataSetMembers) externalResources (pbcore.io.dataset.DataSetMembers.ExternalResource attribute)

F

FastaReader (class in pbcore.io) FastaRecord (class in pbcore.io) FastaTable (in module pbcore.io) FastaWriter (class in pbcore.io) FastqReader (class in pbcore.io) FastqRecord (class in pbcore.io) FastqWriter (class in pbcore.io) FileIndex (class in pbcore.io.dataset.DataSetMembers) FileIndices (class in pbcore.io.dataset.DataSetMembers) Filter (class in pbcore.io.dataset.DataSetMembers) filter_read() (in module pbcore.io.dataset.DataSetMembers) filtered() (in module pbcore.io.dataset.DataSetIO)

filterIndexRecords() (pbcore.io.dataset.DataSetMembers.Filters method) Filters (class in pbcore.io.dataset.DataSetMembers) filters (pbcore.io.dataset.DataSetIO.DataSet attribute) findChildren() (pbcore.io.dataset.DataSetMembers.RecordWrapper method) flagMap() (pbcore.io.dataset.DataSetMembers.PbiFlags class method) FORWARD_PASS (pbcore.io.dataset.DataSetMembers.PbiFlags attribute) fromFile() (in module pbcore.io.dataset.DataSetMembers) fromString() (pbcore.io.dataset.DataSetMembers.Filters method) (pbcore.io.FastaRecord class method) (pbcore.io.FastqRecord class method) (pbcore.io.Gff3Record class method) fullRefNames (pbcore.io.dataset.DataSetIO.AlignmentSet attribute)

G

get_contig() (pbcore.io.dataset.DataSetIO.ContigSet method) getBamAndCmpH5() (in module pbcore.data) getBasH5_v20() (in module pbcore.data) getBasH5_v21() (in module pbcore.data) getBasH5_v23() (in module pbcore.data) getBasH5s() (in module pbcore.data) getBaxForBam() (in module pbcore.data) getBaxH5_v20() (in module pbcore.data) getBaxH5_v21() (in module pbcore.data) getBaxH5_v23() (in module pbcore.data) getBcFofn() (in module pbcore.data) getBcH5s() (in module pbcore.data) getBlasrM4() (in module pbcore.data) getBlasrM5() (in module pbcore.data) getCCSBAM() (in module pbcore.data) getCCSH5() (in module pbcore.data) getCmpH5() (in module pbcore.data) getCmpH5AndBas() (in module pbcore.data) getCmpH5s() (in module pbcore.data) getDist() (pbcore.io.dataset.DataSetMembers.StatsMetadata method) getDosFormattedFasta() (in module pbcore.data)

getEmptyAlignedBam() (in module pbcore.data) getEmptyBam() (in module pbcore.data) getFasta() (in module pbcore.data) getFofns() (in module pbcore.data) getGff3() (in module pbcore.data) getLambdaFasta() (in module pbcore.data) getMappingXml() (in module pbcore.data) getMemberV() (pbcore.io.dataset.DataSetMembers.RecordWrapper method) getMovieSampleNames() (pbcore.io.dataset.DataSetIO.SubreadSet method) (pbcore.io.dataset.DataSetMembers.SubreadSetMetadata method) getter() (in module pbcore.io.dataset.DataSetMembers) getTinyFasta() (in module pbcore.data) getUnalignedBam() (in module pbcore.data) getV() (pbcore.io.dataset.DataSetMembers.RecordWrapper method) getVersion() (pbcore.util.ToolRunner.PBToolRunner method) getWeird() (in module pbcore.data) Gff3Record (class in pbcore.io) GffReader (class in pbcore.io) GffWriter (class in pbcore.io) gmap (pbcore.io.dataset.DataSetMembers.ExternalResource attribute) GmapReferenceSet (class in pbcore.io.dataset.DataSetIO)

H

hasBaseFeature() (pbcore.io.CmpH5Reader method) hasConsensusBasecalls (pbcore.io.BasH5Reader attribute) hashfunc (pbcore.io.dataset.DataSetMembers.Property attribute) hasPbi (pbcore.io.BamAlignment attribute) (pbcore.io.dataset.DataSetIO.ReadSet attribute) hasRawBasecalls (pbcore.io.BasH5Reader attribute) HdfSubreadSet (class in pbcore.io.dataset.DataSetIO) header (pbcore.io.FastaRecord attribute) (pbcore.io.FastqRecord attribute) histogram_percentile() (in module pbcore.io.dataset.DataSetMembers)

HoleNumber (pbcore.io.BamAlignment attribute) holeNumber (pbcore.io.BasH5IO.Zmw attribute) (pbcore.io.BasH5IO.ZmwRead attribute) (pbcore.io.BasH5Reader.Zmw attribute) (pbcore.io.BasH5Reader.ZmwRead attribute) (pbcore.io.CmpH5Alignment attribute) (pbcore.io.CmpH5Reader attribute) hqRegionSnr (pbcore.io.BamAlignment attribute) (pbcore.io.BasH5IO.Zmw attribute) (pbcore.io.BasH5Reader.Zmw attribute) (pbcore.io.CmpH5Alignment attribute)

I

id (pbcore.io.FastaRecord attribute) (pbcore.io.FastqRecord attribute) identity (pbcore.io.BamAlignment attribute) (pbcore.io.CmpH5Alignment attribute) (pbcore.io.IndexedBamReader attribute) index (pbcore.io.BamReader attribute) (pbcore.io.BasH5IO.Zmw attribute) (pbcore.io.BasH5Reader.Zmw attribute) (pbcore.io.CmpH5Reader attribute) (pbcore.io.IndexedBamReader attribute) index() (pbcore.io.dataset.DataSetMembers.RecordWrapper method) IndexedBamReader (class in pbcore.io) indices (pbcore.io.dataset.DataSetMembers.ExternalResource attribute) induceIndices() (pbcore.io.dataset.DataSetIO.AlignmentSet method) (pbcore.io.dataset.DataSetIO.ContigSet method) (pbcore.io.dataset.DataSetIO.DataSet method) (pbcore.io.dataset.DataSetIO.HdfSubreadSet method) (pbcore.io.dataset.DataSetIO.ReadSet method) inNd() (in module pbcore.io.dataset.DataSetMembers) InsertionQV() (pbcore.io.BamAlignment method) (pbcore.io.BasH5IO.ZmwRead method) (pbcore.io.BasH5Reader.ZmwRead method) (pbcore.io.CmpH5Alignment method) insertReadLenDist (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) insertReadLenDists (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute)

insertReadQualDist (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) insertReadQualDists (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) instCtrlVer (pbcore.io.dataset.DataSetMembers.CollectionMetadata attribute) instrumentId (pbcore.io.dataset.DataSetMembers.CollectionMetadata attribute) instrumentName (pbcore.io.dataset.DataSetMembers.CollectionMetadata attribute) intervalContour() (pbcore.io.dataset.DataSetIO.AlignmentSet method) IPD() (pbcore.io.BamAlignment method) (pbcore.io.BasH5IO.ZmwRead method) (pbcore.io.BasH5Reader.ZmwRead method) (pbcore.io.CmpH5Alignment method) isBarcoded (pbcore.io.CmpH5Reader attribute) (pbcore.io.dataset.DataSetIO.ReadSet attribute) isCCS (pbcore.io.BamAlignment attribute) isCmpH5 (pbcore.io.dataset.DataSetIO.ReadSet attribute) isDataSet() (in module pbcore.io.dataset.DataSetIO) isEmpty (pbcore.io.CmpH5Reader attribute) isFile() (in module pbcore.io.dataset.DataSetMembers) isForwardStrand (pbcore.io.BamAlignment attribute) (pbcore.io.CmpH5Alignment attribute) isListString() (in module pbcore.io.dataset.DataSetMembers) isMapped (pbcore.io.BamAlignment attribute) isReverseStrand (pbcore.io.BamAlignment attribute) (pbcore.io.CmpH5Alignment attribute) isSorted (pbcore.io.CmpH5Reader attribute) isTranscript (pbcore.io.BamAlignment attribute) isUnmapped (pbcore.io.BamAlignment attribute)

K

KEEP_WITH_PARENT (pbcore.io.dataset.DataSetMembers.FileIndex attribute) (pbcore.io.dataset.DataSetMembers.RecordWrapper attribute)

Kit (class in pbcore.io.dataset.DataSetMembers)

L

labels (pbcore.io.dataset.DataSetMembers.ContinuousDistribution attribute) (pbcore.io.dataset.DataSetMembers.DiscreteDistribution attribute) leftAdaptorSequence (pbcore.io.dataset.DataSetMembers.TemplatePrepKit attribute) length (pbcore.io.FastaRecord attribute) (pbcore.io.FastqRecord attribute)

listZmwMetrics() (pbcore.io.BasH5IO.Zmw method) (pbcore.io.BasH5Reader.Zmw method) loadMetadata() (pbcore.io.dataset.DataSetIO.DataSet method) loadStats() (pbcore.io.dataset.DataSetIO.DataSet method) lotNumber (pbcore.io.dataset.DataSetMembers.Kit attribute)

M

make_mod_hash_acc() (in module pbcore.io.dataset.DataSetMembers) makePathsAbsolute() (pbcore.io.dataset.DataSetIO.DataSet method) makePathsRelative() (pbcore.io.dataset.DataSetIO.DataSet method) map_val_or_vec() (in module pbcore.io.dataset.DataSetMembers) mapOp() (in module pbcore.io.dataset.DataSetMembers) MapQV (pbcore.io.BamAlignment attribute) mapQV (pbcore.io.BamAlignment attribute) (pbcore.io.CmpH5Alignment attribute) (pbcore.io.CmpH5Reader attribute) mapRequirement() (pbcore.io.dataset.DataSetMembers.Filters method) maxBinValue (pbcore.io.dataset.DataSetMembers.ContinuousDistribution attribute) maxOutlierValue (pbcore.io.dataset.DataSetMembers.ContinuousDistribution attribute) medianInsertDist (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) medianInsertDists (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) merge() (pbcore.io.dataset.DataSetIO.DataSet method) (pbcore.io.dataset.DataSetMembers.CollectionsMetadata method) (pbcore.io.dataset.DataSetMembers.ContinuousDistribution method) (pbcore.io.dataset.DataSetMembers.DataSetMetadata method) (pbcore.io.dataset.DataSetMembers.DiscreteDistribution method) (pbcore.io.dataset.DataSetMembers.ExternalResource method) (pbcore.io.dataset.DataSetMembers.ExternalResources method) (pbcore.io.dataset.DataSetMembers.Filter method) (pbcore.io.dataset.DataSetMembers.Filters method) (pbcore.io.dataset.DataSetMembers.Properties method) (pbcore.io.dataset.DataSetMembers.RecordWrapper method) (pbcore.io.dataset.DataSetMembers.StatsMetadata method) (pbcore.io.dataset.DataSetMembers.SubreadSetMetadata method)

MERGED_DISTS (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) MergeQV() (pbcore.io.BamAlignment method) (pbcore.io.BasH5IO.ZmwRead method) (pbcore.io.BasH5Reader.ZmwRead method) (pbcore.io.CmpH5Alignment method) metadata (pbcore.io.dataset.DataSetIO.DataSet attribute) (pbcore.io.dataset.DataSetMembers.RecordWrapper attribute) metaname (pbcore.io.dataset.DataSetMembers.RecordWrapper attribute) metaType (pbcore.io.dataset.DataSetMembers.ExternalResource attribute) (pbcore.io.dataset.DataSetMembers.FileIndex attribute) (pbcore.io.dataset.DataSetMembers.ParentDataSet attribute) metavalue (pbcore.io.dataset.DataSetMembers.RecordWrapper attribute) minBinValue (pbcore.io.dataset.DataSetMembers.ContinuousDistribution attribute) minOutlierValue (pbcore.io.dataset.DataSetMembers.ContinuousDistribution attribute) modulo (pbcore.io.dataset.DataSetMembers.Property attribute) mov2qid (pbcore.io.dataset.DataSetIO.ReadSet attribute) movieIds (pbcore.io.dataset.DataSetIO.ReadSet attribute) movieInfo (pbcore.io.CmpH5Alignment attribute) movieInfo() (pbcore.io.CmpH5Reader method) movieInfoTable (pbcore.io.CmpH5Reader attribute) movieName (pbcore.io.BamAlignment attribute) (pbcore.io.BasH5Reader attribute) (pbcore.io.CmpH5Alignment attribute) movieNames (pbcore.io.CmpH5Reader attribute)

N

n_subreads() (in module pbcore.io.dataset.DataSetMembers) name (pbcore.io.dataset.DataSetIO.DataSet attribute) (pbcore.io.FastaRecord attribute) (pbcore.io.FastqRecord attribute) (pbcore.io.dataset.DataSetMembers.Property attribute) (pbcore.io.dataset.DataSetMembers.RecordWrapper attribute) (pbcore.io.dataset.DataSetMembers.RunDetailsMetadata attribute) namespace (pbcore.io.dataset.DataSetMembers.RecordWrapper attribute) newRandomUuid() (pbcore.io.dataset.DataSetIO.DataSet method) newUuid() (in module pbcore.io.dataset.DataSetMembers) (pbcore.io.dataset.DataSetIO.DataSet method) NO_LOCAL_CONTEXT (pbcore.io.dataset.DataSetMembers.PbiFlags attribute) NS (pbcore.io.dataset.DataSetMembers.Automation attribute) (pbcore.io.dataset.DataSetMembers.AutomationParameter attribute) (pbcore.io.dataset.DataSetMembers.AutomationParameters attribute) (pbcore.io.dataset.DataSetMembers.BioSampleMetadata attribute) (pbcore.io.dataset.DataSetMembers.BioSamplesMetadata attribute) (pbcore.io.dataset.DataSetMembers.CellPac attribute) (pbcore.io.dataset.DataSetMembers.CollectionMetadata attribute) (pbcore.io.dataset.DataSetMembers.CollectionsMetadata attribute) (pbcore.io.dataset.DataSetMembers.DNABarcode attribute) (pbcore.io.dataset.DataSetMembers.DNABarcodes attribute) (pbcore.io.dataset.DataSetMembers.DataSetMetadata attribute) (pbcore.io.dataset.DataSetMembers.ExternalResource attribute) (pbcore.io.dataset.DataSetMembers.ExternalResources attribute) (pbcore.io.dataset.DataSetMembers.FileIndex attribute) (pbcore.io.dataset.DataSetMembers.FileIndices attribute) (pbcore.io.dataset.DataSetMembers.Filter attribute) (pbcore.io.dataset.DataSetMembers.Filters attribute) (pbcore.io.dataset.DataSetMembers.OutputOptions attribute) (pbcore.io.dataset.DataSetMembers.ParentDataSet attribute) (pbcore.io.dataset.DataSetMembers.ParentTool attribute) (pbcore.io.dataset.DataSetMembers.PrimaryMetadata attribute) (pbcore.io.dataset.DataSetMembers.Properties attribute) (pbcore.io.dataset.DataSetMembers.Property attribute) (pbcore.io.dataset.DataSetMembers.Provenance attribute) (pbcore.io.dataset.DataSetMembers.RecordWrapper attribute) (pbcore.io.dataset.DataSetMembers.RunDetailsMetadata attribute) (pbcore.io.dataset.DataSetMembers.WellSampleMetadata attribute)

numBins (pbcore.io.dataset.DataSetMembers.ContinuousDistribution attribute) (pbcore.io.dataset.DataSetMembers.DiscreteDistribution attribute) numEvents (pbcore.io.BasH5IO.Zmw attribute) (pbcore.io.BasH5Reader.Zmw attribute) numExternalResources (pbcore.io.dataset.DataSetIO.DataSet attribute) numPasses (pbcore.io.BamAlignment attribute) (pbcore.io.BasH5IO.Zmw attribute) (pbcore.io.BasH5Reader.Zmw attribute) (pbcore.io.CmpH5Alignment attribute) numRecords (pbcore.io.dataset.DataSetIO.DataSet attribute) (pbcore.io.dataset.DataSetMembers.DataSetMetadata attribute) numSequencingZmws (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute)

O

offsetBegin (pbcore.io.BasH5IO.ZmwRead attribute) (pbcore.io.BasH5Reader.ZmwRead attribute) offsetEnd (pbcore.io.BasH5IO.ZmwRead attribute) (pbcore.io.BasH5Reader.ZmwRead attribute) openAlignmentFile() (in module pbcore.io) openDataFile() (in module pbcore.io.dataset.DataSetIO) openDataSet() (in module pbcore.io.dataset.DataSetIO)

openIndexedAlignmentFile() (in module pbcore.io) operator (pbcore.io.dataset.DataSetMembers.Property attribute) organism (pbcore.io.dataset.DataSetMembers.ContigSetMetadata attribute) OTHER_DISTS (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) otherDists (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) OutputOptions (class in pbcore.io.dataset.DataSetMembers) outputOptions (pbcore.io.dataset.DataSetMembers.PrimaryMetadata attribute)

P

parameterNames (pbcore.io.dataset.DataSetMembers.AutomationParameters attribute) ParentDataSet (class in pbcore.io.dataset.DataSetMembers) parentDataSet (pbcore.io.dataset.DataSetMembers.Provenance attribute) ParentTool (class in pbcore.io.dataset.DataSetMembers) parentTool (pbcore.io.dataset.DataSetMembers.Provenance attribute) partNumber (pbcore.io.dataset.DataSetMembers.Kit attribute) parts (pbcore.io.BasH5Reader attribute) pbcore (module) pbcore.chemistry (module) pbcore.chemistry.chemistry (module) pbcore.data (module) pbcore.io.dataset.DataSetIO (module) pbcore.io.dataset.DataSetMembers (module) pbcore.util.Process (module) pbcore.util.ToolRunner (module) pbi (pbcore.io.dataset.DataSetMembers.ExternalResource attribute) PbiFlags (class in pbcore.io.dataset.DataSetMembers) PBMultiToolRunner (class in pbcore.util.ToolRunner) PBToolRunner (class in pbcore.util.ToolRunner) plist (pbcore.io.dataset.DataSetMembers.Filter attribute) ploidy (pbcore.io.dataset.DataSetMembers.ContigSetMetadata attribute)

pop() (pbcore.io.dataset.DataSetMembers.Filter method) (pbcore.io.dataset.DataSetMembers.RecordWrapper method) PreBaseFrames() (pbcore.io.BasH5IO.ZmwRead method) (pbcore.io.BasH5Reader.ZmwRead method) primary (pbcore.io.dataset.DataSetMembers.CollectionMetadata attribute) PrimaryMetadata (class in pbcore.io.dataset.DataSetMembers) processFilters() (pbcore.io.dataset.DataSetIO.DataSet method) prodDist (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) productivity (pbcore.io.BasH5IO.Zmw attribute) (pbcore.io.BasH5Reader.Zmw attribute) Properties (class in pbcore.io.dataset.DataSetMembers) Property (class in pbcore.io.dataset.DataSetMembers) Provenance (class in pbcore.io.dataset.DataSetMembers) provenance (pbcore.io.dataset.DataSetMembers.DataSetMetadata attribute) pruneChildrenTo() (pbcore.io.dataset.DataSetMembers.RecordWrapper method) PulseIndex() (pbcore.io.BasH5IO.ZmwRead method) (pbcore.io.BasH5Reader.ZmwRead method) PulseWidth() (pbcore.io.BamAlignment method) (pbcore.io.BasH5IO.ZmwRead method) (pbcore.io.BasH5Reader.ZmwRead method) (pbcore.io.CmpH5Alignment method)

Q

qEnd (pbcore.io.BamAlignment attribute) qId (pbcore.io.BamAlignment attribute) (pbcore.io.CmpH5Alignment attribute) (pbcore.io.CmpH5Reader attribute) qid2mov (pbcore.io.dataset.DataSetIO.ReadSet attribute) qLen (pbcore.io.BamAlignment attribute) qName (pbcore.io.BamAlignment attribute) qname2vec() (in module pbcore.io.dataset.DataSetMembers) qnamer() (in module pbcore.io.dataset.DataSetMembers) qStart (pbcore.io.BamAlignment attribute)

quality (pbcore.io.FastqRecord attribute) qualityString (pbcore.io.FastqRecord attribute) QualityValue() (pbcore.io.BasH5IO.ZmwRead method) (pbcore.io.BasH5Reader.ZmwRead method) (pbcore.io.CmpH5Alignment method) queryEnd (pbcore.io.BamAlignment attribute) queryName (pbcore.io.BamAlignment attribute) queryStart (pbcore.io.BamAlignment attribute) qv() (pbcore.io.BasH5IO.ZmwRead method) (pbcore.io.BasH5Reader.ZmwRead method)

R

read() (pbcore.io.BamAlignment method) (pbcore.io.BasH5IO.Zmw method) (pbcore.io.BasH5Reader.Zmw method) (pbcore.io.CmpH5Alignment method) readEnd (pbcore.io.BasH5IO.ZmwRead attribute) (pbcore.io.BasH5Reader.ZmwRead attribute) reader (pbcore.io.BamAlignment attribute) (pbcore.io.CmpH5Alignment attribute) ReadGroupID (pbcore.io.CmpH5Alignment attribute) (pbcore.io.CmpH5Reader attribute) readGroupInfo (pbcore.io.BamAlignment attribute) (pbcore.io.CmpH5Alignment attribute) readGroupInfo() (pbcore.io.CmpH5Reader method) readGroupTable (pbcore.io.CmpH5Reader attribute) (pbcore.io.dataset.DataSetIO.ReadSet attribute) readLenDist (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) readLenDists (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) readName (pbcore.io.BasH5IO.ZmwRead attribute) (pbcore.io.BasH5Reader.CCSZmwRead attribute) (pbcore.io.BasH5Reader.ZmwRead attribute) readNoQC() (pbcore.io.BasH5IO.Zmw method) (pbcore.io.BasH5Reader.Zmw method) readPositions() (pbcore.io.BamAlignment method) (pbcore.io.CmpH5Alignment method) readQualDist (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) readQualDists (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) reads() (pbcore.io.BasH5Reader method) readScore (pbcore.io.BamAlignment attribute) (pbcore.io.BasH5IO.Zmw attribute) (pbcore.io.BasH5Reader.Zmw attribute) ReadSet (class in pbcore.io.dataset.DataSetIO) readsInRange() (pbcore.io.BamReader method) (pbcore.io.CmpH5Reader method) (pbcore.io.IndexedBamReader method) (pbcore.io.dataset.DataSetIO.AlignmentSet method) readsInReference() (pbcore.io.dataset.DataSetIO.AlignmentSet method) readsInSubDatasets() (pbcore.io.dataset.DataSetIO.DataSet method) readStart (pbcore.io.BasH5IO.ZmwRead attribute) (pbcore.io.BasH5Reader.ZmwRead attribute) readType (pbcore.io.BamAlignment attribute) (pbcore.io.CmpH5Alignment attribute) (pbcore.io.CmpH5Reader attribute) readTypeDist (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) records (pbcore.io.dataset.DataSetIO.AlignmentSet attribute) (pbcore.io.dataset.DataSetIO.DataSet attribute) recordsByReference (pbcore.io.dataset.DataSetIO.AlignmentSet attribute) RecordWrapper (class in pbcore.io.dataset.DataSetMembers) reference (pbcore.io.dataset.DataSetMembers.ExternalResource attribute)

reference() (pbcore.io.BamAlignment method) (pbcore.io.CmpH5Alignment method) referenceId (pbcore.io.BamAlignment attribute) (pbcore.io.CmpH5Alignment attribute) referenceInfo (pbcore.io.BamAlignment attribute) (pbcore.io.CmpH5Alignment attribute) referenceInfo() (pbcore.io.CmpH5Reader method) (pbcore.io.dataset.DataSetIO.AlignmentSet method) referenceInfoTable (pbcore.io.CmpH5Reader attribute) (pbcore.io.dataset.DataSetIO.AlignmentSet attribute) referenceName (pbcore.io.BamAlignment attribute) (pbcore.io.CmpH5Alignment attribute) referencePositions() (pbcore.io.BamAlignment method) (pbcore.io.CmpH5Alignment method) ReferenceSet (class in pbcore.io.dataset.DataSetIO) refIds (pbcore.io.dataset.DataSetIO.AlignmentSet attribute) reFilter() (pbcore.io.dataset.DataSetIO.DataSet method) refInfo() (pbcore.io.dataset.DataSetIO.AlignmentSet method) refLength() (pbcore.io.dataset.DataSetIO.AlignmentSet method) refLengths (pbcore.io.dataset.DataSetIO.AlignmentSet attribute) refNames (pbcore.io.dataset.DataSetIO.AlignmentSet attribute) (pbcore.io.dataset.DataSetIO.ReferenceSet attribute) refWindows (pbcore.io.dataset.DataSetIO.AlignmentSet attribute) regionTable (pbcore.io.BasH5IO.Zmw attribute) (pbcore.io.BasH5Reader.Zmw attribute) registerCallback() (pbcore.io.dataset.DataSetMembers.RecordWrapper method) removeChildren() (pbcore.io.dataset.DataSetMembers.RecordWrapper method) removeFilter() (pbcore.io.dataset.DataSetMembers.Filters method) removeRequirement() (pbcore.io.dataset.DataSetMembers.Filter method) (pbcore.io.dataset.DataSetMembers.Filters method) resourceId (pbcore.io.dataset.DataSetMembers.ExternalResource attribute) (pbcore.io.dataset.DataSetMembers.FileIndex attribute) resourceIds (pbcore.io.dataset.DataSetMembers.ExternalResources attribute) resourceReaders() (pbcore.io.dataset.DataSetIO.AlignmentSet method) (pbcore.io.dataset.DataSetIO.ContigSet method) (pbcore.io.dataset.DataSetIO.DataSet method) (pbcore.io.dataset.DataSetIO.ReadSet method) resources (pbcore.io.dataset.DataSetMembers.ExternalResources attribute) resultsFolder (pbcore.io.dataset.DataSetMembers.OutputOptions attribute) REVERSE_PASS (pbcore.io.dataset.DataSetMembers.PbiFlags attribute) reverseComplement() (pbcore.io.FastaRecord method) (pbcore.io.FastqRecord method) rightAdaptorSequence (pbcore.io.dataset.DataSetMembers.TemplatePrepKit attribute) rname2tid (pbcore.io.dataset.DataSetIO.AlignmentSet attribute) rowNumber (pbcore.io.CmpH5Alignment attribute) run() (pbcore.util.ToolRunner.PBToolRunner method) runDetails (pbcore.io.dataset.DataSetMembers.CollectionMetadata attribute) RunDetailsMetadata (class in pbcore.io.dataset.DataSetMembers) runonce() (in module pbcore.io.dataset.DataSetMembers)

S

sample95thPct (pbcore.io.dataset.DataSetMembers.ContinuousDistribution attribute) sampleMean (pbcore.io.dataset.DataSetMembers.ContinuousDistribution attribute) sampleMed (pbcore.io.dataset.DataSetMembers.ContinuousDistribution attribute) sampleMedian (pbcore.io.dataset.DataSetMembers.ContinuousDistribution attribute) sampleMode (pbcore.io.dataset.DataSetMembers.ContinuousDistribution attribute) sampleReuseEnabled (pbcore.io.dataset.DataSetMembers.WellSampleMetadata attribute) sampleSize (pbcore.io.dataset.DataSetMembers.ContinuousDistribution attribute) sampleStd (pbcore.io.dataset.DataSetMembers.ContinuousDistribution attribute) scraps (pbcore.io.dataset.DataSetMembers.ExternalResource attribute) scrapType (pbcore.io.BamAlignment attribute) secondary (pbcore.io.dataset.DataSetMembers.CollectionMetadata attribute) SecondaryMetadata (class in pbcore.io.dataset.DataSetMembers) sequence (pbcore.io.FastaRecord attribute) (pbcore.io.FastqRecord attribute) sequencingChemistry (pbcore.io.BamAlignment attribute) (pbcore.io.BasH5Reader attribute) (pbcore.io.CmpH5Alignment attribute) (pbcore.io.CmpH5Reader attribute) sequencingCondition (pbcore.io.dataset.DataSetMembers.PrimaryMetadata attribute) SequencingKitPlate (class in pbcore.io.dataset.DataSetMembers) sequencingKitPlate (pbcore.io.dataset.DataSetMembers.CollectionMetadata attribute) sequencingZmws (pbcore.io.BasH5Reader attribute) setify() (in module pbcore.io.dataset.DataSetMembers) setMemberV() (pbcore.io.dataset.DataSetMembers.RecordWrapper method) setter() (in module pbcore.io.dataset.DataSetMembers) setV() (pbcore.io.dataset.DataSetMembers.RecordWrapper method) shortInsertFraction (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) sigProcVer (pbcore.io.dataset.DataSetMembers.CollectionMetadata attribute) similarity (pbcore.io.CmpH5Alignment attribute)

sizeSelectionEnabled (pbcore.io.dataset.DataSetMembers.WellSampleMetadata attribute) softwareVersion() (pbcore.io.CmpH5Reader method) sort() (pbcore.io.dataset.DataSetMembers.ExternalResources method) split() (pbcore.io.dataset.DataSetIO.ContigSet method) (pbcore.io.dataset.DataSetIO.DataSet method) split_movies() (pbcore.io.dataset.DataSetIO.ReadSet method) split_references() (pbcore.io.dataset.DataSetIO.AlignmentSet method) splitContour() (pbcore.io.dataset.DataSetIO.AlignmentSet method) splitKeys() (in module pbcore.io.dataset.DataSetIO) stageHotstartEnabled (pbcore.io.dataset.DataSetMembers.WellSampleMetadata attribute) start() (pbcore.util.ToolRunner.PBToolRunner method) StatsMetadata (class in pbcore.io.dataset.DataSetMembers) str2list() (in module pbcore.io.dataset.DataSetMembers) sts (pbcore.io.dataset.DataSetMembers.ExternalResource attribute) subaccs() (in module pbcore.io.dataset.DataSetMembers) subgetter() (in module pbcore.io.dataset.DataSetMembers) submetadata (pbcore.io.dataset.DataSetMembers.RecordWrapper attribute) subreads() (pbcore.io.BasH5Reader method) SubreadSet (class in pbcore.io.dataset.DataSetIO) SubreadSetMetadata (class in pbcore.io.dataset.DataSetMembers) subrecords (pbcore.io.dataset.DataSetMembers.RecordWrapper attribute) subSetNames (pbcore.io.dataset.DataSetIO.DataSet attribute) subsetter() (in module pbcore.io.dataset.DataSetMembers) SubstitutionQV() (pbcore.io.BamAlignment method) (pbcore.io.BasH5IO.ZmwRead method) (pbcore.io.BasH5Reader.ZmwRead method) (pbcore.io.CmpH5Alignment method) SubstitutionTag() (pbcore.io.BasH5IO.ZmwRead method) (pbcore.io.BasH5Reader.ZmwRead method) summaryStats (pbcore.io.dataset.DataSetMembers.DataSetMetadata attribute)

T

TAG (pbcore.io.dataset.DataSetMembers.BarcodeSetMetadata attribute) (pbcore.io.dataset.DataSetMembers.BioSampleMetadata attribute) (pbcore.io.dataset.DataSetMembers.BioSamplesMetadata attribute) (pbcore.io.dataset.DataSetMembers.CollectionMetadata attribute) (pbcore.io.dataset.DataSetMembers.CollectionsMetadata attribute) (pbcore.io.dataset.DataSetMembers.ContigSetMetadata attribute) (pbcore.io.dataset.DataSetMembers.CopyFilesMetadata attribute) (pbcore.io.dataset.DataSetMembers.DNABarcode attribute) (pbcore.io.dataset.DataSetMembers.DNABarcodes attribute) (pbcore.io.dataset.DataSetMembers.DataSetMetadata attribute) (pbcore.io.dataset.DataSetMembers.PrimaryMetadata attribute) (pbcore.io.dataset.DataSetMembers.RunDetailsMetadata attribute) (pbcore.io.dataset.DataSetMembers.SecondaryMetadata attribute) (pbcore.io.dataset.DataSetMembers.SubreadSetMetadata attribute) (pbcore.io.dataset.DataSetMembers.WellSampleMetadata attribute) tags (pbcore.io.dataset.DataSetIO.DataSet attribute) (pbcore.io.dataset.DataSetMembers.ExternalResource attribute) (pbcore.io.dataset.DataSetMembers.RecordWrapper attribute) TemplatePrepKit (class in pbcore.io.dataset.DataSetMembers) templatePrepKit (pbcore.io.dataset.DataSetMembers.CollectionMetadata attribute)

testCompatibility() (pbcore.io.dataset.DataSetMembers.Filters method) testField() (pbcore.io.dataset.DataSetMembers.Filters method) testParam() (pbcore.io.dataset.DataSetMembers.Filters method) tests() (pbcore.io.dataset.DataSetMembers.Filters method) text (pbcore.io.dataset.DataSetMembers.RecordWrapper attribute) tId (pbcore.io.BamAlignment attribute) tid2rname (pbcore.io.dataset.DataSetIO.AlignmentSet attribute) timeStampedName (pbcore.io.dataset.DataSetIO.DataSet attribute) (pbcore.io.dataset.DataSetMembers.ExternalResource attribute) (pbcore.io.dataset.DataSetMembers.FileIndex attribute) (pbcore.io.dataset.DataSetMembers.ParentDataSet attribute) (pbcore.io.dataset.DataSetMembers.RunDetailsMetadata attribute) toExternalFiles() (pbcore.io.dataset.DataSetIO.DataSet method) toFofn() (pbcore.io.dataset.DataSetIO.DataSet method) totalLength (pbcore.io.dataset.DataSetIO.DataSet attribute) (pbcore.io.dataset.DataSetMembers.DataSetMetadata attribute) transcript() (pbcore.io.BamAlignment method) (pbcore.io.CmpH5Alignment method) TranscriptAlignmentSet (class in pbcore.io.dataset.DataSetIO) TranscriptSet (class in pbcore.io.dataset.DataSetIO) tripleFromMetadataXML() (in module pbcore.chemistry.chemistry)

U

uniqueId (pbcore.io.dataset.DataSetIO.DataSet attribute) (pbcore.io.dataset.DataSetMembers.RecordWrapper attribute) UNMERGED_DISTS (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) unrolledCigar() (pbcore.io.BamAlignment method) updateCounts() (pbcore.io.dataset.DataSetIO.ContigSet method) (pbcore.io.dataset.DataSetIO.DataSet method) (pbcore.io.dataset.DataSetIO.HdfSubreadSet method) (pbcore.io.dataset.DataSetIO.ReadSet method)

updateNamespace() (in module pbcore.io.dataset.DataSetMembers) updateTag() (in module pbcore.io.dataset.DataSetMembers) uri2fn() (in module pbcore.io.dataset.DataSetMembers) uri2scheme() (in module pbcore.io.dataset.DataSetMembers) useCount (pbcore.io.dataset.DataSetMembers.WellSampleMetadata attribute) uuid (pbcore.io.dataset.DataSetIO.DataSet attribute) (pbcore.io.dataset.DataSetMembers.ConsensusReadSetRef attribute)

V

validateArgs() (pbcore.util.ToolRunner.PBToolRunner method) value (pbcore.io.dataset.DataSetMembers.AutomationParameter attribute) (pbcore.io.dataset.DataSetMembers.Property attribute) (pbcore.io.dataset.DataSetMembers.RecordWrapper attribute)

version (pbcore.io.CmpH5Reader attribute) (pbcore.io.dataset.DataSetMembers.RecordWrapper attribute) versionAtLeast() (pbcore.io.CmpH5Reader method)

W

wellName (pbcore.io.dataset.DataSetMembers.WellSampleMetadata attribute) wellSample (pbcore.io.dataset.DataSetMembers.CollectionMetadata attribute) WellSampleMetadata (class in pbcore.io.dataset.DataSetMembers) WidthInFrames() (pbcore.io.BasH5IO.ZmwRead method) (pbcore.io.BasH5Reader.ZmwRead method)

write() (pbcore.io.dataset.DataSetIO.DataSet method) writeRecord() (pbcore.io.FastaWriter method) (pbcore.io.FastqWriter method)

Z

ZeroBinWidthError Zmw (class in pbcore.io.BasH5IO) zmw (pbcore.io.BasH5IO.ZmwRead attribute) (pbcore.io.BasH5Reader.ZmwRead attribute) zmwMetric() (pbcore.io.BasH5IO.Zmw method) (pbcore.io.BasH5Reader.Zmw method)

zmwName (pbcore.io.BasH5IO.Zmw attribute) (pbcore.io.BasH5Reader.Zmw attribute) zmwRanges (pbcore.io.dataset.DataSetIO.DataSet attribute) ZmwRead (class in pbcore.io.BasH5IO) zScore (pbcore.io.BamAlignment attribute) (pbcore.io.CmpH5Alignment attribute)