ParquetFileTraversable
util
ParquetLogger
util
ParquetUnboundAlignmentRecordDataset
read
ParquetUnboundCoverageDataset
feature
ParquetUnboundFeatureDataset
feature
ParquetUnboundFragmentDataset
fragment
ParquetUnboundGenotypeDataset
variant
ParquetUnboundNucleotideContigFragmentDataset
contig
ParquetUnboundVariantDataset
variant
PerformDuplicateMarking
Timers
PhredUtils
util
PositionOrdering
models
ProcessingStep
sql
Projection
projections
pad
ReferenceRegion
parentIds
FeatureField Feature
parseAttribute
AttributeUtils
parseAttributes
AttributeUtils
partitionAndJoin
InnerTreeRegionJoin InnerTreeRegionJoinAndGroupByRight RegionJoin RightOuterTreeRegionJoin RightOuterTreeRegionJoinAndGroupByRight ShuffleRegionJoin
partitionSize
GenomicRegionPartitioner
persist
DatasetBoundGenomicDataset GenomicDataset
phase
FeatureField Feature
phaseQuality
DefaultHeaderLines GenotypeField Genotype
phaseSetId
DefaultHeaderLines GenotypeField Genotype
phased
GenotypeField Genotype
phredLikelihoods
DefaultHeaderLines
phredToErrorProbability
PhredUtils
phredToLogProbability
PhredUtils
phredToSuccessProbability
PhredUtils
pipe
GenomicDataset
platform
ReadGroup ReadGroupField
platformModel
ReadGroupField
platformUnit
ReadGroup ReadGroupField
pos
ReferencePosition
position
VariantContext
positionAtFirstRecord
FastqRecordReader
postProcessHits
FullOuterShuffleRegionJoin InnerShuffleRegionJoin InnerShuffleRegionJoinAndGroupByLeft LeftOuterShuffleRegionJoin LeftOuterShuffleRegionJoinAndGroupByLeft RightOuterShuffleRegionJoinAndGroupByLeft ShuffleRegionJoin
postProcessPruned
FullOuterShuffleRegionJoin RightOuterShuffleRegionJoinAndGroupByLeft SortedIntervalPartitionJoinWithVictims
predictedMedianInsertSize
ReadGroup ReadGroupField
preprocessReadsForRealignment
ConsensusGenerator
previousId
ProcessingStep
primaryAlignment
AlignmentRecordField AlignmentRecord
printAlignmentAttributes
ADAMShell
printFeatureAttributes
ADAMShell
printFormatFields
ADAMShell
printGenotypeFilters
ADAMShell
printInfoFields
ADAMShell
printMetrics
ADAMShell
printSampleAttributes
ADAMShell
printVariantFilters
ADAMShell
processHits
ShuffleRegionJoin
processingDescription
GenotypeField Genotype
processingSteps
ReadGroupField SampleField GenomicDatasetWithLineage DatasetBoundFragmentDataset ParquetUnboundFragmentDataset RDDBoundFragmentDataset DatasetBoundAlignmentRecordDataset ParquetUnboundAlignmentRecordDataset RDDBoundAlignmentRecordDataset
productArity
AlignmentRecord Dbxref Feature Fragment Genotype NucleotideContigFragment OntologyTerm ProcessingStep Reference TranscriptEffect Variant VariantAnnotation VariantCallingAnnotations
productElement
AlignmentRecord Dbxref Feature Fragment Genotype NucleotideContigFragment OntologyTerm ProcessingStep Reference TranscriptEffect Variant VariantAnnotation VariantCallingAnnotations
productFn
GenericConverter GenericGenomicDataset GenomicDataset NucleotideContigFragmentDataset CoverageDataset FeatureDataset FragmentDataset AlignmentRecordDataset GenotypeDataset VariantContextDataset VariantDataset
programName
ProcessingStep
projections
adam
properPair
AlignmentRecordField AlignmentRecord
proteinHgvs
TranscriptEffectField TranscriptEffect
proteinLength
TranscriptEffectField TranscriptEffect
proteinPosition
TranscriptEffectField TranscriptEffect
pruneCache
ShuffleRegionJoin SortedIntervalPartitionJoinWithVictims VictimlessSortedIntervalPartitionJoin