Index

_

__add__() (pbcore.io.dataset.DataSetIO.DataSet method) __call__() (pbcore.io.dataset.DataSetIO.MetaDataSet method) __deepcopy__() (pbcore.io.dataset.DataSetIO.DataSet method) __eq__() (pbcore.io.dataset.DataSetIO.DataSet method) __getitem__() (pbcore.io.dataset.DataSetMembers.BioSamplesMetadata method) (pbcore.io.dataset.DataSetMembers.CollectionsMetadata method) (pbcore.io.dataset.DataSetMembers.ContigsMetadata 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.Parameters method) (pbcore.io.dataset.DataSetMembers.RecordWrapper method)

__init__() (pbcore.io.dataset.DataSetIO.DataSet method) __iter__() (pbcore.io.dataset.DataSetMembers.BioSamplesMetadata method) (pbcore.io.dataset.DataSetMembers.CollectionsMetadata method) (pbcore.io.dataset.DataSetMembers.ContigsMetadata 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.Parameters method) (pbcore.io.dataset.DataSetMembers.RecordWrapper method) __metaclass__ (pbcore.io.dataset.DataSetIO.DataSet attribute) __repr__() (pbcore.io.dataset.DataSetIO.DataSet method) (pbcore.io.dataset.DataSetMembers.RecordWrapper method)

A

accuracy (pbcore.io.align.CmpH5IO.CmpH5Alignment attribute) (pbcore.io.CmpH5Alignment attribute) adapterDimerFraction (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) adapterRegions (pbcore.io.BasH5IO.Zmw attribute) (pbcore.io.BasH5Reader.Zmw attribute) adapterRegionsNoQC (pbcore.io.BasH5IO.Zmw attribute) (pbcore.io.BasH5Reader.Zmw attribute) adapters (pbcore.io.BasH5IO.Zmw attribute) (pbcore.io.BasH5Reader.Zmw attribute) adaptersNoQC (pbcore.io.BasH5IO.Zmw attribute) (pbcore.io.BasH5Reader.Zmw attribute) addDatasets() (pbcore.io.dataset.DataSetIO.DataSet method) addExternalResources() (pbcore.io.dataset.DataSetIO.DataSet 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.DataSetIO.ReferenceSet method) (pbcore.io.dataset.DataSetMembers.RecordWrapper method) addParameter() (pbcore.io.dataset.DataSetMembers.AutomationParameters method) addRequirement() (pbcore.io.dataset.DataSetMembers.Filter method) (pbcore.io.dataset.DataSetMembers.Filters method) addResources() (pbcore.io.dataset.DataSetMembers.ExternalResources method) aEnd (pbcore.io.align.CmpH5IO.CmpH5Alignment attribute) (pbcore.io.CmpH5Alignment attribute)

alignmentArray() (pbcore.io.align.CmpH5IO.CmpH5Alignment method) (pbcore.io.CmpH5Alignment method) alignmentIndex (pbcore.io.align.CmpH5IO.CmpH5Reader attribute) (pbcore.io.CmpH5Reader attribute) AlignmentSet (class in pbcore.io.dataset.DataSetIO) allSequencingZmws (pbcore.io.BasH5Reader attribute) append() (pbcore.io.dataset.DataSetMembers.RecordWrapper method) aStart (pbcore.io.align.CmpH5IO.CmpH5Alignment attribute) (pbcore.io.CmpH5Alignment attribute) atRowNumber() (pbcore.io.align.BamIO.IndexedBamReader method) (pbcore.io.IndexedBamReader method) 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)

B

backticks() (in module pbcore.util.Process) BamAlignment (class in pbcore.io) (class in pbcore.io.align.BamAlignment) BamReader (class in pbcore.io) (class in pbcore.io.align.BamIO) barcode (pbcore.io.align.BamAlignment.BamAlignment attribute) (pbcore.io.BamAlignment attribute) (pbcore.io.CmpH5Alignment attribute) (pbcore.io.CmpH5Reader attribute) (pbcore.io.align.CmpH5IO.CmpH5Alignment attribute) (pbcore.io.align.CmpH5IO.CmpH5Reader attribute) barcodeConstruction (pbcore.io.dataset.DataSetMembers.BarcodeSetMetadata attribute) barcodeName (pbcore.io.align.BamAlignment.BamAlignment attribute) (pbcore.io.BamAlignment attribute) (pbcore.io.CmpH5Alignment attribute) (pbcore.io.CmpH5Reader attribute) (pbcore.io.align.CmpH5IO.CmpH5Alignment attribute) (pbcore.io.align.CmpH5IO.CmpH5Reader attribute) barcodes (pbcore.io.align.CmpH5IO.CmpH5Reader attribute) (pbcore.io.CmpH5Reader 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) 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 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) bioSamplePointers (pbcore.io.dataset.DataSetMembers.WellSampleMetadata attribute) BioSamplePointersMetadata (class in pbcore.io.dataset.DataSetMembers) bioSamples (pbcore.io.dataset.DataSetMembers.SubreadSetMetadata attribute) BioSamplesMetadata (class in pbcore.io.dataset.DataSetMembers)

C

ccsRead (pbcore.io.BasH5IO.Zmw attribute) (pbcore.io.BasH5Reader.Zmw attribute) ccsReads() (pbcore.io.BasH5Reader method) cellIndex (pbcore.io.dataset.DataSetMembers.CollectionMetadata attribute) cellPac (pbcore.io.dataset.DataSetMembers.CollectionMetadata attribute) chemistryBarcodeTriple (pbcore.io.BasH5Reader attribute) ChemistryLookupError clippedTo() (pbcore.io.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method) (pbcore.io.CmpH5Alignment method) (pbcore.io.align.CmpH5IO.CmpH5Alignment method) close() (pbcore.io.align.CmpH5IO.CmpH5Reader method) (pbcore.io.BasH5Reader method) (pbcore.io.CmpH5Reader method) (pbcore.io.dataset.DataSetIO.DataSet method) cmpH5 (pbcore.io.align.CmpH5IO.CmpH5Alignment attribute) (pbcore.io.CmpH5Alignment attribute) CmpH5Alignment (class in pbcore.io) (class in pbcore.io.align.CmpH5IO) CmpH5Reader (class in pbcore.io) (class in pbcore.io.align.CmpH5IO) CollectionMetadata (class in pbcore.io.dataset.DataSetMembers) collectionNumber (pbcore.io.dataset.DataSetMembers.CollectionMetadata attribute) collectionPathUri (pbcore.io.dataset.DataSetMembers.PrimaryMetadata attribute) collections (pbcore.io.dataset.DataSetMembers.SubreadSetMetadata attribute) CollectionsMetadata (class in pbcore.io.dataset.DataSetMembers) columnNames (pbcore.io.align.PacBioBamIndex.PacBioBamIndex attribute) 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) ConsensusReadSet (class in pbcore.io.dataset.DataSetIO) context (pbcore.io.dataset.DataSetMembers.CollectionMetadata attribute) ContigMetadata (class in pbcore.io.dataset.DataSetMembers) contigs (pbcore.io.dataset.DataSetIO.ReferenceSet attribute) (pbcore.io.dataset.DataSetMembers.ContigSetMetadata attribute) (pbcore.io.dataset.DataSetMembers.ReferenceSetMetadata attribute) ContigSet (class in pbcore.io.dataset.DataSetIO) ContigSetMetadata (class in pbcore.io.dataset.DataSetMembers) ContigsMetadata (class in pbcore.io.dataset.DataSetMembers) ContinuousDistribution (class in pbcore.io.dataset.DataSetMembers) 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.PrimaryMetadata attribute) CopyFilesMetadata (class in pbcore.io.dataset.DataSetMembers) countRecords() (pbcore.io.dataset.DataSetIO.DataSet method) createdAt (pbcore.io.dataset.DataSetMembers.BioSampleMetadata attribute) createdBy (pbcore.io.dataset.DataSetMembers.Provenance attribute)

D

DataSet (class in pbcore.io.dataset.DataSetIO) DataSetMetadata (class in pbcore.io.dataset.DataSetMembers) DataSetMetaTypes (class in pbcore.io.dataset.DataSetIO) decodeTriple() (in module pbcore.chemistry.chemistry) DeletionQV() (pbcore.io.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method) (pbcore.io.BasH5IO.ZmwRead method) (pbcore.io.BasH5Reader.ZmwRead method) (pbcore.io.CmpH5Alignment method) (pbcore.io.align.CmpH5IO.CmpH5Alignment method)

DeletionTag() (pbcore.io.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method) (pbcore.io.BasH5IO.ZmwRead method) (pbcore.io.BasH5Reader.ZmwRead method) (pbcore.io.CmpH5Alignment method) (pbcore.io.align.CmpH5IO.CmpH5Alignment method) description (pbcore.io.dataset.DataSetMembers.ContinuousDistribution attribute) (pbcore.io.dataset.DataSetMembers.DiscreteDistribution attribute) (pbcore.io.dataset.DataSetMembers.RecordWrapper attribute) digest (pbcore.io.dataset.DataSetMembers.ContigMetadata attribute) disableFilters() (pbcore.io.dataset.DataSetIO.DataSet method) DiscreteDistribution (class in pbcore.io.dataset.DataSetMembers)

E

EmptyCmpH5Error enableFilters() (pbcore.io.dataset.DataSetIO.DataSet method) extend() (pbcore.io.dataset.DataSetMembers.RecordWrapper method)

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

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) Filters (class in pbcore.io.dataset.DataSetMembers) filters (pbcore.io.dataset.DataSetIO.DataSet attribute) findChildren() (pbcore.io.dataset.DataSetMembers.RecordWrapper method) fromString() (pbcore.io.align.BlasrIO.M4Record class method) (pbcore.io.FastaRecord class method) (pbcore.io.FastqRecord class method) (pbcore.io.Gff3Record class method) (pbcore.io.align.BlasrIO.M5Record class method) fullRefNames (pbcore.io.dataset.DataSetIO.DataSet attribute)

G

get_contig() (pbcore.io.dataset.DataSetIO.ReferenceSet method) getBam() (in module pbcore.data.datasets) 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)

getDosFormattedFasta() (in module pbcore.data) getFasta() (in module pbcore.data) getFofn() (in module pbcore.data.datasets) getFofns() (in module pbcore.data) getGff3() (in module pbcore.data) getHdfSubreadSet() (in module pbcore.data.datasets) getLambdaFasta() (in module pbcore.data) getMemberV() (pbcore.io.dataset.DataSetMembers.RecordWrapper method) getRef() (in module pbcore.data.datasets) getStats() (in module pbcore.data.datasets) getSubreadSet() (in module pbcore.data.datasets) getTinyFasta() (in module pbcore.data) getUnalignedBam() (in module pbcore.data) getV() (pbcore.io.dataset.DataSetMembers.RecordWrapper method) getVersion() (pbcore.util.ToolRunner.PBToolRunner method) getXml() (in module pbcore.data.datasets) getXmlWithStats() (in module pbcore.data.datasets) Gff3Record (class in pbcore.io) GffReader (class in pbcore.io) GffWriter (class in pbcore.io)

H

hasConsensusBasecalls (pbcore.io.BasH5Reader attribute) hasPbi (pbcore.io.dataset.DataSetIO.DataSet attribute) hasPulseFeature() (pbcore.io.align.CmpH5IO.CmpH5Reader method) (pbcore.io.CmpH5Reader method) hasRawBasecalls (pbcore.io.BasH5Reader attribute) header (pbcore.io.FastaRecord attribute) (pbcore.io.FastqRecord attribute) HoleNumber (pbcore.io.align.BamAlignment.BamAlignment attribute)

holeNumber (pbcore.io.align.CmpH5IO.CmpH5Alignment attribute) (pbcore.io.align.CmpH5IO.CmpH5Reader attribute) 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) hqRegion (pbcore.io.BasH5IO.Zmw attribute) (pbcore.io.BasH5Reader.Zmw attribute) hqRegionSnr (pbcore.io.BasH5IO.Zmw attribute) (pbcore.io.BasH5Reader.Zmw attribute)

I

id (pbcore.io.FastaRecord attribute) (pbcore.io.FastqRecord attribute) identity (pbcore.io.align.BamAlignment.BamAlignment attribute) (pbcore.io.BamAlignment attribute) (pbcore.io.CmpH5Alignment attribute) (pbcore.io.align.CmpH5IO.CmpH5Alignment attribute) index (pbcore.io.align.BamIO.BamReader attribute) (pbcore.io.BamReader attribute) (pbcore.io.BasH5IO.Zmw attribute) (pbcore.io.BasH5Reader.Zmw attribute) (pbcore.io.CmpH5Reader attribute) (pbcore.io.IndexedBamReader attribute) (pbcore.io.align.BamIO.IndexedBamReader attribute) (pbcore.io.align.CmpH5IO.CmpH5Reader attribute) index() (pbcore.io.dataset.DataSetMembers.RecordWrapper method) IndexedBamReader (class in pbcore.io) (class in pbcore.io.align.BamIO) indexRecords (pbcore.io.dataset.DataSetIO.DataSet attribute) indices (pbcore.io.dataset.DataSetMembers.ExternalResource attribute) InsertionQV() (pbcore.io.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method) (pbcore.io.BasH5IO.ZmwRead method) (pbcore.io.BasH5Reader.ZmwRead method) (pbcore.io.CmpH5Alignment method) (pbcore.io.align.CmpH5IO.CmpH5Alignment method) insertReadLenDist (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) insertReadQualDist (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) insertRegions (pbcore.io.BasH5IO.Zmw attribute) (pbcore.io.BasH5Reader.Zmw attribute) insertRegionsNoQC (pbcore.io.BasH5IO.Zmw attribute) (pbcore.io.BasH5Reader.Zmw attribute) instCtrlVer (pbcore.io.dataset.DataSetMembers.CollectionMetadata attribute)

instrumentId (pbcore.io.dataset.DataSetMembers.CollectionMetadata attribute) instrumentName (pbcore.io.dataset.DataSetMembers.CollectionMetadata attribute) IPD() (pbcore.io.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method) (pbcore.io.BasH5IO.ZmwRead method) (pbcore.io.BasH5Reader.ZmwRead method) (pbcore.io.CmpH5Alignment method) (pbcore.io.align.CmpH5IO.CmpH5Alignment method) isBarcoded (pbcore.io.align.CmpH5IO.CmpH5Reader attribute) (pbcore.io.CmpH5Reader attribute) isCCS (pbcore.io.align.BamAlignment.BamAlignment attribute) (pbcore.io.BamAlignment attribute) isCmpH5 (pbcore.io.dataset.DataSetIO.DataSet attribute) isEmpty (pbcore.io.align.CmpH5IO.CmpH5Reader attribute) (pbcore.io.CmpH5Reader attribute) isForwardStrand (pbcore.io.align.BamAlignment.BamAlignment attribute) (pbcore.io.BamAlignment attribute) (pbcore.io.CmpH5Alignment attribute) (pbcore.io.align.CmpH5IO.CmpH5Alignment attribute) isMapped (pbcore.io.align.BamAlignment.BamAlignment attribute) (pbcore.io.BamAlignment attribute) isReverseStrand (pbcore.io.align.BamAlignment.BamAlignment attribute) (pbcore.io.BamAlignment attribute) (pbcore.io.CmpH5Alignment attribute) (pbcore.io.align.CmpH5IO.CmpH5Alignment attribute) isSorted (pbcore.io.align.CmpH5IO.CmpH5Reader attribute) (pbcore.io.CmpH5Reader attribute) isUnmapped (pbcore.io.align.BamAlignment.BamAlignment attribute) (pbcore.io.BamAlignment attribute)

L

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

listZmwMetrics() (pbcore.io.BasH5IO.Zmw method) (pbcore.io.BasH5Reader.Zmw method) loadStats() (pbcore.io.dataset.DataSetIO.DataSet method)

M

M4Reader (class in pbcore.io.align.BlasrIO) M4Record (class in pbcore.io.align.BlasrIO) M5Reader (class in pbcore.io.align.BlasrIO) M5Record (class in pbcore.io.align.BlasrIO) makePathsAbsolute() (pbcore.io.dataset.DataSetIO.DataSet method) makePathsRelative() (pbcore.io.dataset.DataSetIO.DataSet method) MapQV (pbcore.io.align.BamAlignment.BamAlignment attribute) mapQV (pbcore.io.align.BamAlignment.BamAlignment attribute) (pbcore.io.align.CmpH5IO.CmpH5Alignment attribute) (pbcore.io.align.CmpH5IO.CmpH5Reader attribute) MapQV (pbcore.io.BamAlignment attribute) mapQV (pbcore.io.BamAlignment attribute) (pbcore.io.CmpH5Alignment attribute) (pbcore.io.CmpH5Reader attribute) 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.DataSetMembers.BioSamplesMetadata method) (pbcore.io.dataset.DataSetMembers.CollectionsMetadata method) (pbcore.io.dataset.DataSetMembers.ContigSetMetadata method) (pbcore.io.dataset.DataSetMembers.ContigsMetadata 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.Filter method) (pbcore.io.dataset.DataSetMembers.Filters method) (pbcore.io.dataset.DataSetMembers.Parameters method) (pbcore.io.dataset.DataSetMembers.RecordWrapper method) (pbcore.io.dataset.DataSetMembers.ReferenceSetMetadata method) (pbcore.io.dataset.DataSetMembers.StatsMetadata method) (pbcore.io.dataset.DataSetMembers.SubreadSetMetadata method) MergeQV() (pbcore.io.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method) (pbcore.io.BasH5IO.ZmwRead method) (pbcore.io.BasH5Reader.ZmwRead method) (pbcore.io.CmpH5Alignment method) (pbcore.io.align.CmpH5IO.CmpH5Alignment method) metadata (pbcore.io.dataset.DataSetIO.DataSet attribute) (pbcore.io.dataset.DataSetMembers.RecordWrapper attribute) MetaDataSet (class in pbcore.io.dataset.DataSetIO) metaname (pbcore.io.dataset.DataSetMembers.RecordWrapper attribute) metaType (pbcore.io.dataset.DataSetMembers.ExternalResource attribute) (pbcore.io.dataset.DataSetMembers.FileIndex attribute) metavalue (pbcore.io.dataset.DataSetMembers.RecordWrapper attribute) minBinValue (pbcore.io.dataset.DataSetMembers.ContinuousDistribution attribute) minOutlierValue (pbcore.io.dataset.DataSetMembers.ContinuousDistribution attribute) movieInfo (pbcore.io.align.CmpH5IO.CmpH5Alignment attribute) (pbcore.io.CmpH5Alignment attribute) movieInfo() (pbcore.io.align.CmpH5IO.CmpH5Reader method) (pbcore.io.CmpH5Reader method) movieInfoTable (pbcore.io.align.CmpH5IO.CmpH5Reader attribute) (pbcore.io.CmpH5Reader attribute) movieName (pbcore.io.align.BamAlignment.BamAlignment attribute) (pbcore.io.BamAlignment attribute) (pbcore.io.BasH5Reader attribute) (pbcore.io.CmpH5Alignment attribute) (pbcore.io.align.CmpH5IO.CmpH5Alignment attribute) movieNames (pbcore.io.align.CmpH5IO.CmpH5Reader attribute) (pbcore.io.CmpH5Reader attribute)

N

name (pbcore.io.dataset.DataSetIO.DataSet attribute) (pbcore.io.FastaRecord attribute) (pbcore.io.FastqRecord attribute) (pbcore.io.dataset.DataSetMembers.Parameter attribute) (pbcore.io.dataset.DataSetMembers.RecordWrapper attribute) (pbcore.io.dataset.DataSetMembers.RunDetailsMetadata attribute) newUuid() (pbcore.io.dataset.DataSetIO.DataSet method) numBins (pbcore.io.dataset.DataSetMembers.ContinuousDistribution attribute) (pbcore.io.dataset.DataSetMembers.DiscreteDistribution attribute) numExternalResources (pbcore.io.dataset.DataSetIO.DataSet attribute)

numPasses (pbcore.io.align.BamAlignment.BamAlignment attribute) (pbcore.io.BamAlignment attribute) (pbcore.io.BasH5IO.Zmw attribute) (pbcore.io.BasH5Reader.Zmw attribute) (pbcore.io.CmpH5Alignment attribute) (pbcore.io.align.CmpH5IO.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) openDataSet() (in module pbcore.io.dataset.DataSetIO)

openIndexedAlignmentFile() (in module pbcore.io) operator (pbcore.io.dataset.DataSetMembers.Parameter attribute) opMap() (pbcore.io.dataset.DataSetMembers.Filters method) organism (pbcore.io.dataset.DataSetMembers.ReferenceSetMetadata attribute)

P

PacBioBamIndex (class in pbcore.io.align.PacBioBamIndex) Parameter (class in pbcore.io.dataset.DataSetMembers) Parameters (class in pbcore.io.dataset.DataSetMembers) ParentTool (class in pbcore.io.dataset.DataSetMembers) parentTool (pbcore.io.dataset.DataSetMembers.Provenance attribute) parts (pbcore.io.BasH5Reader attribute) pbcore (module) pbcore.chemistry (module) pbcore.chemistry.chemistry (module) pbcore.data (module) pbcore.data.datasets (module) pbcore.io.align (module) pbcore.io.align.BamAlignment (module) pbcore.io.align.BamIO (module) pbcore.io.align.BlasrIO (module) pbcore.io.align.CmpH5IO (module) pbcore.io.align.PacBioBamIndex (module) pbcore.io.dataset.DataSetIO (module) pbcore.io.dataset.DataSetMembers (module) pbcore.util.Process (module)

pbcore.util.ToolRunner (module) PBMultiToolRunner (class in pbcore.util.ToolRunner) PBToolRunner (class in pbcore.util.ToolRunner) plateId (pbcore.io.dataset.DataSetMembers.WellSampleMetadata attribute) plist (pbcore.io.dataset.DataSetMembers.Filter attribute) ploidy (pbcore.io.dataset.DataSetMembers.ReferenceSetMetadata 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) Provenance (class in pbcore.io.dataset.DataSetMembers) provenance (pbcore.io.dataset.DataSetMembers.DataSetMetadata attribute) pruneChildrenTo() (pbcore.io.dataset.DataSetMembers.RecordWrapper method) pulseFeature() (pbcore.io.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method) (pbcore.io.CmpH5Alignment method) (pbcore.io.align.CmpH5IO.CmpH5Alignment method) pulseFeaturesAvailable() (pbcore.io.align.CmpH5IO.CmpH5Reader method) (pbcore.io.CmpH5Reader method) PulseWidth() (pbcore.io.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method) (pbcore.io.BasH5IO.ZmwRead method) (pbcore.io.BasH5Reader.ZmwRead method) (pbcore.io.CmpH5Alignment method) (pbcore.io.align.CmpH5IO.CmpH5Alignment method)

Q

qEnd (pbcore.io.align.BamAlignment.BamAlignment attribute) (pbcore.io.BamAlignment attribute) qId (pbcore.io.align.BamAlignment.BamAlignment attribute) (pbcore.io.BamAlignment attribute) (pbcore.io.CmpH5Alignment attribute) (pbcore.io.CmpH5Reader attribute) (pbcore.io.align.CmpH5IO.CmpH5Alignment attribute) (pbcore.io.align.CmpH5IO.CmpH5Reader attribute) qLen (pbcore.io.align.BamAlignment.BamAlignment attribute) (pbcore.io.BamAlignment attribute) qName (pbcore.io.align.BamAlignment.BamAlignment attribute) (pbcore.io.BamAlignment attribute) qStart (pbcore.io.align.BamAlignment.BamAlignment attribute) (pbcore.io.BamAlignment attribute) quality (pbcore.io.FastqRecord attribute)

qualityString (pbcore.io.FastqRecord attribute) QualityValue() (pbcore.io.align.CmpH5IO.CmpH5Alignment method) (pbcore.io.BasH5IO.ZmwRead method) (pbcore.io.BasH5Reader.ZmwRead method) (pbcore.io.CmpH5Alignment method) queryEnd (pbcore.io.align.BamAlignment.BamAlignment attribute) (pbcore.io.BamAlignment attribute) queryName (pbcore.io.align.BamAlignment.BamAlignment attribute) (pbcore.io.BamAlignment attribute) queryStart (pbcore.io.align.BamAlignment.BamAlignment attribute) (pbcore.io.BamAlignment attribute) qv() (pbcore.io.BasH5IO.ZmwRead method) (pbcore.io.BasH5Reader.ZmwRead method)

R

rangeQuery() (pbcore.io.align.PacBioBamIndex.PacBioBamIndex method) read() (pbcore.io.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method) (pbcore.io.BasH5IO.Zmw method) (pbcore.io.BasH5Reader.Zmw method) (pbcore.io.CmpH5Alignment method) (pbcore.io.align.CmpH5IO.CmpH5Alignment method) readEnd (pbcore.io.BasH5IO.ZmwRead attribute) (pbcore.io.BasH5Reader.ZmwRead attribute) reader (pbcore.io.align.BamAlignment.BamAlignment attribute) (pbcore.io.BamAlignment attribute) (pbcore.io.CmpH5Alignment attribute) (pbcore.io.align.CmpH5IO.CmpH5Alignment attribute) ReadGroupID (pbcore.io.align.CmpH5IO.CmpH5Alignment attribute) (pbcore.io.CmpH5Alignment attribute) (pbcore.io.CmpH5Reader attribute) (pbcore.io.align.CmpH5IO.CmpH5Reader attribute) readGroupInfo (pbcore.io.align.BamAlignment.BamAlignment attribute) (pbcore.io.BamAlignment attribute) (pbcore.io.CmpH5Alignment attribute) (pbcore.io.align.CmpH5IO.CmpH5Alignment attribute) readGroupInfo() (pbcore.io.align.CmpH5IO.CmpH5Reader method) (pbcore.io.CmpH5Reader method) readGroupTable (pbcore.io.align.CmpH5IO.CmpH5Reader attribute) (pbcore.io.CmpH5Reader attribute) (pbcore.io.dataset.DataSetIO.DataSet 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.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method) (pbcore.io.CmpH5Alignment method) (pbcore.io.align.CmpH5IO.CmpH5Alignment method) readQualDist (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) readQualDists (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) reads() (pbcore.io.BasH5Reader method) readScore (pbcore.io.BasH5IO.Zmw attribute) (pbcore.io.BasH5Reader.Zmw attribute) ReadSet (class in pbcore.io.dataset.DataSetIO) readsInRange() (pbcore.io.align.BamIO.BamReader method) (pbcore.io.BamReader method) (pbcore.io.CmpH5Reader method) (pbcore.io.IndexedBamReader method) (pbcore.io.align.BamIO.IndexedBamReader method) (pbcore.io.align.CmpH5IO.CmpH5Reader method) (pbcore.io.dataset.DataSetIO.DataSet method) readsInReference() (pbcore.io.dataset.DataSetIO.DataSet method) readsInSubDatasets() (pbcore.io.dataset.DataSetIO.DataSet method) readStart (pbcore.io.BasH5IO.ZmwRead attribute) (pbcore.io.BasH5Reader.ZmwRead attribute) readType (pbcore.io.align.BamAlignment.BamAlignment attribute) (pbcore.io.BamAlignment attribute) (pbcore.io.CmpH5Alignment attribute) (pbcore.io.CmpH5Reader attribute) (pbcore.io.align.CmpH5IO.CmpH5Alignment attribute) (pbcore.io.align.CmpH5IO.CmpH5Reader attribute) readTypeDist (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) records (pbcore.io.dataset.DataSetIO.AlignmentSet attribute) (pbcore.io.dataset.DataSetIO.DataSet attribute) RecordWrapper (class in pbcore.io.dataset.DataSetMembers) reference() (pbcore.io.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method) (pbcore.io.CmpH5Alignment method) (pbcore.io.align.CmpH5IO.CmpH5Alignment method) referenceId (pbcore.io.align.BamAlignment.BamAlignment attribute) (pbcore.io.BamAlignment attribute) (pbcore.io.CmpH5Alignment attribute) (pbcore.io.align.CmpH5IO.CmpH5Alignment attribute)

referenceInfo (pbcore.io.align.BamAlignment.BamAlignment attribute) (pbcore.io.BamAlignment attribute) (pbcore.io.CmpH5Alignment attribute) (pbcore.io.align.CmpH5IO.CmpH5Alignment attribute) referenceInfo() (pbcore.io.align.CmpH5IO.CmpH5Reader method) (pbcore.io.CmpH5Reader method) (pbcore.io.dataset.DataSetIO.DataSet method) referenceInfoTable (pbcore.io.align.CmpH5IO.CmpH5Reader attribute) (pbcore.io.CmpH5Reader attribute) (pbcore.io.dataset.DataSetIO.DataSet attribute) referenceName (pbcore.io.align.BamAlignment.BamAlignment attribute) (pbcore.io.BamAlignment attribute) (pbcore.io.CmpH5Alignment attribute) (pbcore.io.align.CmpH5IO.CmpH5Alignment attribute) referencePositions() (pbcore.io.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method) (pbcore.io.CmpH5Alignment method) (pbcore.io.align.CmpH5IO.CmpH5Alignment method) ReferenceSet (class in pbcore.io.dataset.DataSetIO) ReferenceSetMetadata (class in pbcore.io.dataset.DataSetMembers) reFilter() (pbcore.io.dataset.DataSetIO.DataSet method) refInfo() (pbcore.io.dataset.DataSetIO.DataSet method) refLength() (pbcore.io.dataset.DataSetIO.DataSet method) refLengths (pbcore.io.dataset.DataSetIO.DataSet attribute) refNames (pbcore.io.dataset.DataSetIO.DataSet attribute) (pbcore.io.dataset.DataSetIO.ReferenceSet attribute) refWindows (pbcore.io.dataset.DataSetIO.DataSet attribute) regionTable (pbcore.io.BasH5IO.Zmw attribute) (pbcore.io.BasH5Reader.Zmw attribute) registerCallback() (pbcore.io.dataset.DataSetMembers.Filters method) removeChildren() (pbcore.io.dataset.DataSetMembers.RecordWrapper 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.DataSet method) (pbcore.io.dataset.DataSetIO.ReferenceSet method) resources (pbcore.io.dataset.DataSetMembers.ExternalResources attribute) resultsFolder (pbcore.io.dataset.DataSetMembers.PrimaryMetadata attribute) reverseComplement() (pbcore.io.FastaRecord method) (pbcore.io.FastqRecord method) rowNumber (pbcore.io.align.CmpH5IO.CmpH5Alignment attribute) (pbcore.io.CmpH5Alignment attribute) run() (pbcore.util.ToolRunner.PBToolRunner method) runDetails (pbcore.io.dataset.DataSetMembers.CollectionMetadata attribute) RunDetailsMetadata (class in pbcore.io.dataset.DataSetMembers) runId (pbcore.io.dataset.DataSetMembers.RunDetailsMetadata attribute)

S

sample95thPct (pbcore.io.dataset.DataSetMembers.ContinuousDistribution attribute) sampleMean (pbcore.io.dataset.DataSetMembers.ContinuousDistribution attribute) sampleMed (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) sequence (pbcore.io.FastaRecord attribute) (pbcore.io.FastqRecord attribute) sequencingChemistry (pbcore.io.align.BamAlignment.BamAlignment attribute) (pbcore.io.BamAlignment attribute) (pbcore.io.BasH5Reader attribute) (pbcore.io.CmpH5Alignment attribute) (pbcore.io.CmpH5Reader attribute) (pbcore.io.align.CmpH5IO.CmpH5Alignment attribute) (pbcore.io.align.CmpH5IO.CmpH5Reader attribute) sequencingCondition (pbcore.io.dataset.DataSetMembers.PrimaryMetadata attribute) sequencingZmws (pbcore.io.BasH5Reader attribute) setMemberV() (pbcore.io.dataset.DataSetMembers.RecordWrapper method) setV() (pbcore.io.dataset.DataSetMembers.RecordWrapper method) shortInsertFraction (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) sigProcVer (pbcore.io.dataset.DataSetMembers.CollectionMetadata attribute) similarity (pbcore.io.align.CmpH5IO.CmpH5Alignment attribute) (pbcore.io.CmpH5Alignment attribute) sizeSelectionEnabled (pbcore.io.dataset.DataSetMembers.WellSampleMetadata attribute) softwareVersion() (pbcore.io.align.CmpH5IO.CmpH5Reader method) (pbcore.io.CmpH5Reader method)

sort() (pbcore.io.dataset.DataSetMembers.ExternalResources method) split() (pbcore.io.dataset.DataSetIO.DataSet method) stageHotstartEnabled (pbcore.io.dataset.DataSetMembers.WellSampleMetadata attribute) start() (pbcore.util.ToolRunner.PBToolRunner method) StatsMetadata (class in pbcore.io.dataset.DataSetMembers) submetadata (pbcore.io.dataset.DataSetMembers.RecordWrapper attribute) subreads (pbcore.io.BasH5IO.Zmw attribute) (pbcore.io.BasH5Reader.Zmw attribute) subreads() (pbcore.io.BasH5Reader method) SubreadSet (class in pbcore.io.dataset.DataSetIO) SubreadSetMetadata (class in pbcore.io.dataset.DataSetMembers) subreadsNoQC (pbcore.io.BasH5IO.Zmw attribute) (pbcore.io.BasH5Reader.Zmw attribute) subrecords (pbcore.io.dataset.DataSetMembers.RecordWrapper attribute) subSetNames (pbcore.io.dataset.DataSetIO.DataSet attribute) SubstitutionQV() (pbcore.io.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method) (pbcore.io.BasH5IO.ZmwRead method) (pbcore.io.BasH5Reader.ZmwRead method) (pbcore.io.CmpH5Alignment method) (pbcore.io.align.CmpH5IO.CmpH5Alignment method) SubstitutionTag() (pbcore.io.BasH5IO.ZmwRead method) (pbcore.io.BasH5Reader.ZmwRead method) summaryStats (pbcore.io.dataset.DataSetMembers.DataSetMetadata attribute)

T

tags (pbcore.io.dataset.DataSetMembers.ExternalResource attribute) (pbcore.io.dataset.DataSetMembers.RecordWrapper attribute) testCompatibility() (pbcore.io.dataset.DataSetMembers.Filters method) testParam() (pbcore.io.dataset.DataSetMembers.Filters method) tests() (pbcore.io.dataset.DataSetMembers.Filters method) tId (pbcore.io.align.BamAlignment.BamAlignment attribute) (pbcore.io.BamAlignment 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.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method) (pbcore.io.CmpH5Alignment method) (pbcore.io.align.CmpH5IO.CmpH5Alignment method) tripleFromMetadataXML() (in module pbcore.chemistry.chemistry)

U

uniqueId (pbcore.io.dataset.DataSetMembers.BioSampleMetadata attribute) (pbcore.io.dataset.DataSetMembers.WellSampleMetadata attribute) unrolledCigar() (pbcore.io.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method)

useCount (pbcore.io.dataset.DataSetMembers.WellSampleMetadata attribute) uuid (pbcore.io.dataset.DataSetIO.DataSet attribute)

V

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

version (pbcore.io.align.CmpH5IO.CmpH5Reader attribute) (pbcore.io.CmpH5Reader attribute) (pbcore.io.align.PacBioBamIndex.PacBioBamIndex attribute) (pbcore.io.dataset.DataSetMembers.RecordWrapper attribute) versionAtLeast() (pbcore.io.align.CmpH5IO.CmpH5Reader method) (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

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) ZmwRead (class in pbcore.io.BasH5IO) zScore (pbcore.io.align.BamAlignment.BamAlignment attribute) (pbcore.io.BamAlignment attribute) (pbcore.io.CmpH5Alignment attribute) (pbcore.io.align.CmpH5IO.CmpH5Alignment attribute)