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.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) ADAPTER_AFTER (pbcore.io.dataset.DataSetMembers.PbiFlags attribute) ADAPTER_BEFORE (pbcore.io.dataset.DataSetMembers.PbiFlags attribute) adapterDimerFraction (pbcore.io.dataset.DataSetMembers.StatsMetadata property) adapters (pbcore.io.dataset.DataSetMembers.ExternalResource property) 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) AlignmentSet (class in pbcore.io.dataset.DataSetIO) append() (pbcore.io.dataset.DataSetMembers.RecordWrapper method) assertBarcoded() (pbcore.io.dataset.DataSetIO.ReadSet method) atRowNumber() (pbcore.io.align.BamIO.IndexedBamReader method) (pbcore.io.IndexedBamReader method) attrib (pbcore.io.dataset.DataSetMembers.RecordWrapper property) Automation (class in pbcore.io.dataset.DataSetMembers) automation (pbcore.io.dataset.DataSetMembers.CollectionMetadata property) automationName (pbcore.io.dataset.DataSetMembers.PrimaryMetadata property) AutomationParameter (class in pbcore.io.dataset.DataSetMembers) automationParameter (pbcore.io.dataset.DataSetMembers.AutomationParameters property) AutomationParameters (class in pbcore.io.dataset.DataSetMembers) automationParameters (pbcore.io.dataset.DataSetMembers.Automation property) availableDists() (pbcore.io.dataset.DataSetMembers.StatsMetadata method)

B

bai (pbcore.io.dataset.DataSetMembers.ExternalResource property) bam (pbcore.io.dataset.DataSetMembers.ExternalResource property) 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 property) (pbcore.io.BamAlignment property) (pbcore.io.dataset.DataSetMembers.Kit property) BARCODE_AFTER (pbcore.io.dataset.DataSetMembers.PbiFlags attribute) BARCODE_BEFORE (pbcore.io.dataset.DataSetMembers.PbiFlags attribute) barcodeConstruction (pbcore.io.dataset.DataSetMembers.BarcodeSetMetadata property) barcodeName (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property) barcodes (pbcore.io.dataset.DataSetIO.DataSet property) (pbcore.io.dataset.DataSetMembers.ExternalResource property) BarcodeSet (class in pbcore.io.dataset.DataSetIO)

BarcodeSetMetadata (class in pbcore.io.dataset.DataSetMembers) baseFeature() (pbcore.io.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method) BinBoundaryMismatchError BindingKit (class in pbcore.io.dataset.DataSetMembers) bindingKit (pbcore.io.dataset.DataSetMembers.CollectionMetadata property) BinMismatchError BinNumberMismatchError bins (pbcore.io.dataset.DataSetMembers.ContinuousDistribution property) (pbcore.io.dataset.DataSetMembers.DiscreteDistribution property) binWidth (pbcore.io.dataset.DataSetMembers.ContinuousDistribution property) BinWidthMismatchError BioSampleMetadata (class in pbcore.io.dataset.DataSetMembers) bioSamples (pbcore.io.dataset.DataSetMembers.ReadSetMetadata property) (pbcore.io.dataset.DataSetMembers.WellSampleMetadata property) 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) cellCountInJob (pbcore.io.dataset.DataSetMembers.SecondaryMetadata property) cellIndex (pbcore.io.dataset.DataSetMembers.CollectionMetadata property) CellPac (class in pbcore.io.dataset.DataSetMembers) cellPac (pbcore.io.dataset.DataSetMembers.CollectionMetadata property) CHANNEL_DISTS (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) channelDists (pbcore.io.dataset.DataSetMembers.StatsMetadata property) checkAndResolve() (in module pbcore.io.dataset.DataSetIO) ChemistryLookupError clearCallbacks() (pbcore.io.dataset.DataSetMembers.RecordWrapper method) clippedTo() (pbcore.io.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method) close() (pbcore.io.dataset.DataSetIO.DataSet method) CollectionMetadata (class in pbcore.io.dataset.DataSetMembers) collectionNumber (pbcore.io.dataset.DataSetMembers.CollectionMetadata property) collectionPathUri (pbcore.io.dataset.DataSetMembers.OutputOptions property) collections (pbcore.io.dataset.DataSetMembers.SubreadSetMetadata property) CollectionsMetadata (class in pbcore.io.dataset.DataSetMembers) columnNames (pbcore.io.align.PacBioBamIndex.PacBioBamIndex property) comment (pbcore.io.FastaRecord property) (pbcore.io.FastqRecord property) comments (pbcore.io.dataset.DataSetMembers.WellSampleMetadata property) concentration (pbcore.io.dataset.DataSetMembers.WellSampleMetadata property) configFileName (pbcore.io.dataset.DataSetMembers.PrimaryMetadata property)

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 property) consolidate() (pbcore.io.dataset.DataSetIO.ContigSet method) (pbcore.io.dataset.DataSetIO.ReadSet method) context (pbcore.io.dataset.DataSetMembers.CollectionMetadata property) contigNames (pbcore.io.dataset.DataSetIO.ContigSet property) contigs (pbcore.io.dataset.DataSetIO.ContigSet property) 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 property) controlReadLenDist (pbcore.io.dataset.DataSetMembers.StatsMetadata property) controlReadQualDist (pbcore.io.dataset.DataSetMembers.StatsMetadata property) copy() (pbcore.io.dataset.DataSetIO.DataSet method) (pbcore.io.Gff3Record method) copyFiles (pbcore.io.dataset.DataSetMembers.OutputOptions property) 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 property) (pbcore.io.dataset.DataSetMembers.RecordWrapper property) createdBy (pbcore.io.dataset.DataSetMembers.Provenance property)

D

DataSet (class in pbcore.io.dataset.DataSetIO) DataSetMetadata (class in pbcore.io.dataset.DataSetMembers) decodeTriple() (in module pbcore.chemistry.chemistry) DeletionQV() (pbcore.io.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method) DeletionTag() (pbcore.io.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method) description (pbcore.io.dataset.DataSetIO.DataSet property) (pbcore.io.dataset.DataSetMembers.ContinuousDistribution property) (pbcore.io.dataset.DataSetMembers.DiscreteDistribution property) (pbcore.io.dataset.DataSetMembers.RecordWrapper property)

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 property)

E

enableFilters() (pbcore.io.dataset.DataSetIO.DataSet method) expirationDate (pbcore.io.dataset.DataSetMembers.Kit property) 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 property)

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 property) 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.align.BlasrIO.M4Record class method) (pbcore.io.align.BlasrIO.M5Record class method) (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 property)

G

get_contig() (pbcore.io.dataset.DataSetIO.ContigSet method) getAlignedBam() (in module pbcore.data) getBam() (in module pbcore.data.datasets) getBarcodedBam() (in module pbcore.data.datasets) getBcFofn() (in module pbcore.data) getBlasrM4() (in module pbcore.data) getBlasrM5() (in module pbcore.data) getCCSBAM() (in module pbcore.data) getDist() (pbcore.io.dataset.DataSetMembers.StatsMetadata method) getDosFormattedFasta() (in module pbcore.data) getEmptyAlignedBam() (in module pbcore.data) (in module pbcore.data.datasets) getEmptyBam() (in module pbcore.data) getEmptyBam2() (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) getLambdaFasta() (in module pbcore.data)

getMappingXml() (in module pbcore.data) getMemberV() (pbcore.io.dataset.DataSetMembers.RecordWrapper method) getMockCollectionMetadata() (in module pbcore.data.datasets) getRef() (in module pbcore.data.datasets) getStats() (in module pbcore.data.datasets) getSubreadSet() (in module pbcore.data.datasets) 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) 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) gmap (pbcore.io.dataset.DataSetMembers.ExternalResource property) GmapReferenceSet (class in pbcore.io.dataset.DataSetIO)

H

hasBarcodeInfo (pbcore.io.align.PacBioBamIndex.PacBioBamIndex property) hasCoordinateSortedInfo (pbcore.io.align.PacBioBamIndex.PacBioBamIndex property) hashfunc (pbcore.io.dataset.DataSetMembers.Property property) hasMappingInfo (pbcore.io.align.PacBioBamIndex.PacBioBamIndex property) hasPbi (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property) (pbcore.io.dataset.DataSetIO.ReadSet property)

header (pbcore.io.FastaRecord property) (pbcore.io.FastqRecord property) histogram_percentile() (in module pbcore.io.dataset.DataSetMembers) HoleNumber (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property) hqRegionSnr (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property)

I

id (pbcore.io.FastaRecord property) (pbcore.io.FastqRecord property) identity (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.align.BamIO.IndexedBamReader property) (pbcore.io.align.PacBioBamIndex.PacBioBamIndex property) (pbcore.io.BamAlignment property) (pbcore.io.IndexedBamReader property) index (pbcore.io.align.BamIO.BamReader property) (pbcore.io.align.BamIO.IndexedBamReader property) (pbcore.io.BamReader property) (pbcore.io.IndexedBamReader property) index() (pbcore.io.dataset.DataSetMembers.RecordWrapper method) IndexedBamReader (class in pbcore.io) (class in pbcore.io.align.BamIO) indices (pbcore.io.dataset.DataSetMembers.ExternalResource property) induceIndices() (pbcore.io.dataset.DataSetIO.ContigSet method) (pbcore.io.dataset.DataSetIO.DataSet method) (pbcore.io.dataset.DataSetIO.ReadSet method) inOp() (in module pbcore.io.dataset.DataSetMembers) InsertionQV() (pbcore.io.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method) insertReadLenDist (pbcore.io.dataset.DataSetMembers.StatsMetadata property) insertReadLenDists (pbcore.io.dataset.DataSetMembers.StatsMetadata property) insertReadQualDist (pbcore.io.dataset.DataSetMembers.StatsMetadata property)

insertReadQualDists (pbcore.io.dataset.DataSetMembers.StatsMetadata property) instCtrlVer (pbcore.io.dataset.DataSetMembers.CollectionMetadata property) instrumentId (pbcore.io.dataset.DataSetMembers.CollectionMetadata property) instrumentName (pbcore.io.dataset.DataSetMembers.CollectionMetadata property) intervalContour() (pbcore.io.dataset.DataSetIO.AlignmentSet method) IPD() (pbcore.io.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method) isBarcoded (pbcore.io.dataset.DataSetIO.ReadSet property) isCCS (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property) isChunk (pbcore.io.align.PacBioBamIndex.PacBioBamIndex property) isDataSet() (in module pbcore.io.dataset.DataSetIO) isFile() (in module pbcore.io.dataset.DataSetMembers) isForwardStrand (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property) isListString() (in module pbcore.io.dataset.DataSetMembers) isMapped (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property) isReverseStrand (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property) isTranscript (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property) isUnmapped (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property)

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 property) (pbcore.io.dataset.DataSetMembers.DiscreteDistribution property) leftAdaptorSequence (pbcore.io.dataset.DataSetMembers.TemplatePrepKit property) length (pbcore.io.FastaRecord property) (pbcore.io.FastqRecord property)

loadMetadata() (pbcore.io.dataset.DataSetIO.DataSet method) loadStats() (pbcore.io.dataset.DataSetIO.DataSet method) lotNumber (pbcore.io.dataset.DataSetMembers.Kit property)

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) 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.align.BamAlignment.BamAlignment property) mapQV (pbcore.io.align.BamAlignment.BamAlignment property) MapQV (pbcore.io.BamAlignment property) mapQV (pbcore.io.BamAlignment property) mapRequirement() (pbcore.io.dataset.DataSetMembers.Filters method) maxBinValue (pbcore.io.dataset.DataSetMembers.ContinuousDistribution property) maxOutlierValue (pbcore.io.dataset.DataSetMembers.ContinuousDistribution property) medianInsertDist (pbcore.io.dataset.DataSetMembers.StatsMetadata property) medianInsertDists (pbcore.io.dataset.DataSetMembers.StatsMetadata property) merge() (pbcore.io.dataset.DataSetIO.DataSet method) (pbcore.io.dataset.DataSetMembers.BioSamplesMetadata 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.ReadSetMetadata 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.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method) metadata (pbcore.io.dataset.DataSetIO.BarcodeSet property) (pbcore.io.dataset.DataSetIO.ContigSet property) (pbcore.io.dataset.DataSetIO.DataSet property) (pbcore.io.dataset.DataSetMembers.RecordWrapper property) metaname (pbcore.io.dataset.DataSetMembers.RecordWrapper property) metaType (pbcore.io.dataset.DataSetMembers.ExternalResource property) (pbcore.io.dataset.DataSetMembers.FileIndex property) (pbcore.io.dataset.DataSetMembers.ParentDataSet property) metavalue (pbcore.io.dataset.DataSetMembers.RecordWrapper property) minBinValue (pbcore.io.dataset.DataSetMembers.ContinuousDistribution property) minOutlierValue (pbcore.io.dataset.DataSetMembers.ContinuousDistribution property) MissingFileError module pbcore pbcore.chemistry pbcore.chemistry.chemistry pbcore.data pbcore.data.datasets pbcore.io.align pbcore.io.align.BamAlignment pbcore.io.align.BamIO pbcore.io.align.BlasrIO pbcore.io.align.PacBioBamIndex pbcore.io.dataset.DataSetIO pbcore.io.dataset.DataSetMembers pbcore.util.ToolRunner modulo (pbcore.io.dataset.DataSetMembers.Property property) mov2qid (pbcore.io.dataset.DataSetIO.ReadSet property) movieIds (pbcore.io.dataset.DataSetIO.ReadSet property) movieName (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property)

N

n_subreads() (in module pbcore.io.dataset.DataSetMembers) name (pbcore.io.dataset.DataSetIO.DataSet property) (pbcore.io.dataset.DataSetMembers.Property property) (pbcore.io.dataset.DataSetMembers.RecordWrapper property) (pbcore.io.dataset.DataSetMembers.RunDetailsMetadata property) (pbcore.io.FastaRecord property) (pbcore.io.FastqRecord property) namespace (pbcore.io.dataset.DataSetMembers.RecordWrapper property) 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.DataSetMetadata attribute) (pbcore.io.dataset.DataSetMembers.DNABarcode attribute) (pbcore.io.dataset.DataSetMembers.DNABarcodes 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 property) (pbcore.io.dataset.DataSetMembers.DiscreteDistribution property) numExternalResources (pbcore.io.dataset.DataSetIO.DataSet property) numPasses (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property) numRecords (pbcore.io.dataset.DataSetIO.DataSet property) (pbcore.io.dataset.DataSetMembers.DataSetMetadata property) numSequencingZmws (pbcore.io.dataset.DataSetMembers.StatsMetadata property)

O

openDataFile() (in module pbcore.io.dataset.DataSetIO) openDataSet() (in module pbcore.io.dataset.DataSetIO) operator (pbcore.io.dataset.DataSetMembers.Property property) organism (pbcore.io.dataset.DataSetMembers.ContigSetMetadata property)

OTHER_DISTS (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) otherDists (pbcore.io.dataset.DataSetMembers.StatsMetadata property) OutputOptions (class in pbcore.io.dataset.DataSetMembers) outputOptions (pbcore.io.dataset.DataSetMembers.PrimaryMetadata property)

P

PacBioBamIndex (class in pbcore.io.align.PacBioBamIndex) parameterNames (pbcore.io.dataset.DataSetMembers.AutomationParameters property) ParentDataSet (class in pbcore.io.dataset.DataSetMembers) parentDataSet (pbcore.io.dataset.DataSetMembers.Provenance property) ParentTool (class in pbcore.io.dataset.DataSetMembers) parentTool (pbcore.io.dataset.DataSetMembers.Provenance property) partNumber (pbcore.io.dataset.DataSetMembers.Kit property) 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.PacBioBamIndex module

pbcore.io.dataset.DataSetIO module pbcore.io.dataset.DataSetMembers module pbcore.util.ToolRunner module pbi (pbcore.io.dataset.DataSetMembers.ExternalResource property) 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 property) ploidy (pbcore.io.dataset.DataSetMembers.ContigSetMetadata property) pop() (pbcore.io.dataset.DataSetMembers.Filter method) (pbcore.io.dataset.DataSetMembers.RecordWrapper method) primary (pbcore.io.dataset.DataSetMembers.CollectionMetadata property) PrimaryMetadata (class in pbcore.io.dataset.DataSetMembers) processFilters() (pbcore.io.dataset.DataSetIO.DataSet method) prodDist (pbcore.io.dataset.DataSetMembers.StatsMetadata property) 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 property) pruneChildrenTo() (pbcore.io.dataset.DataSetMembers.RecordWrapper method) PulseWidth() (pbcore.io.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method)

Q

qEnd (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property) qId (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property) qid2mov (pbcore.io.dataset.DataSetIO.ReadSet property) qLen (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property) qName (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property) qname2vec() (in module pbcore.io.dataset.DataSetMembers) qnamer() (in module pbcore.io.dataset.DataSetMembers)

qnames2recarrays_by_size() (in module pbcore.io.dataset.DataSetMembers) qStart (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property) quality (pbcore.io.FastqRecord property) qualityString (pbcore.io.FastqRecord property) queryEnd (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property) queryName (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property) queryStart (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property)

R

rangeQuery() (pbcore.io.align.PacBioBamIndex.PacBioBamIndex method) read() (pbcore.io.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method) reader (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property) readGroupInfo (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property) readGroupTable (pbcore.io.dataset.DataSetIO.ReadSet property) readLenDist (pbcore.io.dataset.DataSetMembers.StatsMetadata property) readLenDists (pbcore.io.dataset.DataSetMembers.StatsMetadata property) readPositions() (pbcore.io.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method) readQualDist (pbcore.io.dataset.DataSetMembers.StatsMetadata property) readQualDists (pbcore.io.dataset.DataSetMembers.StatsMetadata property) readScore (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property) ReadSet (class in pbcore.io.dataset.DataSetIO) ReadSetMetadata (class in pbcore.io.dataset.DataSetMembers) readsInRange() (pbcore.io.align.BamIO.BamReader method) (pbcore.io.align.BamIO.IndexedBamReader method) (pbcore.io.BamReader method) (pbcore.io.dataset.DataSetIO.AlignmentSet method) (pbcore.io.IndexedBamReader method) readsInReference() (pbcore.io.dataset.DataSetIO.AlignmentSet method) readsInSubDatasets() (pbcore.io.dataset.DataSetIO.DataSet method) readType (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property) readTypeDist (pbcore.io.dataset.DataSetMembers.StatsMetadata property) reccheck() (in module pbcore.io.dataset.DataSetMembers) recordMembership() (in module pbcore.io.dataset.DataSetMembers) records (pbcore.io.dataset.DataSetIO.AlignmentSet property) (pbcore.io.dataset.DataSetIO.DataSet property) recordsByReference (pbcore.io.dataset.DataSetIO.AlignmentSet property) RecordWrapper (class in pbcore.io.dataset.DataSetMembers) reference (pbcore.io.dataset.DataSetMembers.ExternalResource property) reference() (pbcore.io.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method) referenceId (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property)

referenceInfo (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property) referenceInfo() (pbcore.io.dataset.DataSetIO.AlignmentSet method) referenceInfoTable (pbcore.io.dataset.DataSetIO.AlignmentSet property) referenceName (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property) referencePositions() (pbcore.io.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method) ReferenceSet (class in pbcore.io.dataset.DataSetIO) refIds (pbcore.io.dataset.DataSetIO.AlignmentSet property) 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 property) refNames (pbcore.io.dataset.DataSetIO.AlignmentSet property) (pbcore.io.dataset.DataSetIO.ReferenceSet property) refWindows (pbcore.io.dataset.DataSetIO.AlignmentSet property) 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 property) (pbcore.io.dataset.DataSetMembers.FileIndex property) resourceIds (pbcore.io.dataset.DataSetMembers.ExternalResources property) 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 property) resultsFolder (pbcore.io.dataset.DataSetMembers.OutputOptions property) REVERSE_PASS (pbcore.io.dataset.DataSetMembers.PbiFlags attribute) reverseComplement() (pbcore.io.FastaRecord method) (pbcore.io.FastqRecord method) rightAdaptorSequence (pbcore.io.dataset.DataSetMembers.TemplatePrepKit property) rname2tid (pbcore.io.dataset.DataSetIO.AlignmentSet property) run() (pbcore.util.ToolRunner.PBToolRunner method) runDetails (pbcore.io.dataset.DataSetMembers.CollectionMetadata property) RunDetailsMetadata (class in pbcore.io.dataset.DataSetMembers) runonce() (in module pbcore.io.dataset.DataSetMembers)

S

sample95thPct (pbcore.io.dataset.DataSetMembers.ContinuousDistribution property) sampleMean (pbcore.io.dataset.DataSetMembers.ContinuousDistribution property) sampleMed (pbcore.io.dataset.DataSetMembers.ContinuousDistribution property) sampleMedian (pbcore.io.dataset.DataSetMembers.ContinuousDistribution property) sampleMode (pbcore.io.dataset.DataSetMembers.ContinuousDistribution property) sampleN50 (pbcore.io.dataset.DataSetMembers.ContinuousDistribution property) sampleReuseEnabled (pbcore.io.dataset.DataSetMembers.WellSampleMetadata property) sampleSize (pbcore.io.dataset.DataSetMembers.ContinuousDistribution property) sampleStd (pbcore.io.dataset.DataSetMembers.ContinuousDistribution property) scraps (pbcore.io.dataset.DataSetMembers.ExternalResource property) scrapType (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property) secondary (pbcore.io.dataset.DataSetMembers.CollectionMetadata property) SecondaryMetadata (class in pbcore.io.dataset.DataSetMembers) sequence (pbcore.io.FastaRecord property) (pbcore.io.FastqRecord property) sequencingChemistry (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property) sequencingCondition (pbcore.io.dataset.DataSetMembers.PrimaryMetadata property) SequencingKitPlate (class in pbcore.io.dataset.DataSetMembers) sequencingKitPlate (pbcore.io.dataset.DataSetMembers.CollectionMetadata property) 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 property) sigProcVer (pbcore.io.dataset.DataSetMembers.CollectionMetadata property) sizeSelectionEnabled (pbcore.io.dataset.DataSetMembers.WellSampleMetadata property) 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 property) 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 property) subaccs() (in module pbcore.io.dataset.DataSetMembers) subgetter() (in module pbcore.io.dataset.DataSetMembers) submetadata (pbcore.io.dataset.DataSetMembers.RecordWrapper property) SubreadSet (class in pbcore.io.dataset.DataSetIO) SubreadSetMetadata (class in pbcore.io.dataset.DataSetMembers) subrecords (pbcore.io.dataset.DataSetMembers.RecordWrapper property) subSetNames (pbcore.io.dataset.DataSetIO.DataSet property) subsetter() (in module pbcore.io.dataset.DataSetMembers) SubstitutionQV() (pbcore.io.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method) summaryStats (pbcore.io.dataset.DataSetMembers.DataSetMetadata property)

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.DataSetMetadata attribute) (pbcore.io.dataset.DataSetMembers.DNABarcode attribute) (pbcore.io.dataset.DataSetMembers.DNABarcodes 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 property) (pbcore.io.dataset.DataSetMembers.ExternalResource property) (pbcore.io.dataset.DataSetMembers.RecordWrapper property) TemplatePrepKit (class in pbcore.io.dataset.DataSetMembers) templatePrepKit (pbcore.io.dataset.DataSetMembers.CollectionMetadata property) 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 property) tId (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property) tid2rname (pbcore.io.dataset.DataSetIO.AlignmentSet property) timeStampedName (pbcore.io.dataset.DataSetIO.DataSet property) (pbcore.io.dataset.DataSetMembers.ExternalResource property) (pbcore.io.dataset.DataSetMembers.FileIndex property) (pbcore.io.dataset.DataSetMembers.ParentDataSet property) (pbcore.io.dataset.DataSetMembers.RunDetailsMetadata property) toExternalFiles() (pbcore.io.dataset.DataSetIO.DataSet method) toFofn() (pbcore.io.dataset.DataSetIO.DataSet method) totalLength (pbcore.io.dataset.DataSetIO.DataSet property) (pbcore.io.dataset.DataSetMembers.DataSetMetadata property) transcript() (pbcore.io.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment 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 property) (pbcore.io.dataset.DataSetMembers.RecordWrapper property) UNMERGED_DISTS (pbcore.io.dataset.DataSetMembers.StatsMetadata attribute) unrolledCigar() (pbcore.io.align.BamAlignment.BamAlignment method) (pbcore.io.BamAlignment method) updateCounts() (pbcore.io.dataset.DataSetIO.ContigSet method) (pbcore.io.dataset.DataSetIO.DataSet 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 property) uuid (pbcore.io.dataset.DataSetIO.DataSet property) (pbcore.io.dataset.DataSetMembers.ConsensusReadSetRef property)

V

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

version (pbcore.io.align.PacBioBamIndex.PacBioBamIndex property) (pbcore.io.dataset.DataSetMembers.RecordWrapper property)

W

wellName (pbcore.io.dataset.DataSetMembers.WellSampleMetadata property) wellSample (pbcore.io.dataset.DataSetMembers.CollectionMetadata property) WellSampleMetadata (class in pbcore.io.dataset.DataSetMembers)

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

Z

ZeroBinWidthError zmwRanges (pbcore.io.dataset.DataSetIO.DataSet property)

zScore (pbcore.io.align.BamAlignment.BamAlignment property) (pbcore.io.BamAlignment property)