ParquetFileTraversable
util
ParquetLogger
util
ParquetUnboundAlignmentRecordRDD
read
ParquetUnboundCoverageRDD
feature
ParquetUnboundFeatureRDD
feature
ParquetUnboundFragmentRDD
fragment
ParquetUnboundGenotypeRDD
variant
ParquetUnboundNucleotideContigFragmentRDD
contig
ParquetUnboundVariantRDD
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
phase
FeatureField
Feature
phaseQuality
DefaultHeaderLines
GenotypeField
Genotype
phaseSetId
DefaultHeaderLines
GenotypeField
Genotype
phased
GenotypeField
Genotype
phredLikelihoods
DefaultHeaderLines
phredToErrorProbability
PhredUtils
phredToLogProbability
PhredUtils
phredToSuccessProbability
PhredUtils
pipe
GenomicRDD
platform
RecordGroup
RecordGroupField
platformUnit
RecordGroup
RecordGroupField
pos
ReferencePosition
position
VariantContext
postProcessHits
FullOuterShuffleRegionJoin
InnerShuffleRegionJoin
InnerShuffleRegionJoinAndGroupByLeft
LeftOuterShuffleRegionJoin
LeftOuterShuffleRegionJoinAndGroupByLeft
RightOuterShuffleRegionJoinAndGroupByLeft
ShuffleRegionJoin
postProcessPruned
FullOuterShuffleRegionJoin
RightOuterShuffleRegionJoinAndGroupByLeft
SortedIntervalPartitionJoinWithVictims
predictedMedianInsertSize
RecordGroup
RecordGroupField
preprocessReadsForRealignment
ConsensusGenerator
previousId
ProcessingStep
primaryAlignment
AlignmentRecordField
AlignmentRecord
processHits
ShuffleRegionJoin
processingDescription
GenotypeField
Genotype
processingSteps
RecordGroupField
SampleField
GenomicRDDWithLineage
DatasetBoundFragmentRDD
ParquetUnboundFragmentRDD
RDDBoundFragmentRDD
DatasetBoundAlignmentRecordRDD
ParquetUnboundAlignmentRecordRDD
RDDBoundAlignmentRecordRDD
productArity
AlignmentRecord
Contig
Dbxref
Feature
Fragment
Genotype
NucleotideContigFragment
OntologyTerm
ProcessingStep
TranscriptEffect
Variant
VariantAnnotation
VariantCallingAnnotations
productElement
AlignmentRecord
Contig
Dbxref
Feature
Fragment
Genotype
NucleotideContigFragment
OntologyTerm
ProcessingStep
TranscriptEffect
Variant
VariantAnnotation
VariantCallingAnnotations
programName
ProcessingStep
projections
adam
properPair
AlignmentRecordField
AlignmentRecord
proteinHgvs
TranscriptEffectField
TranscriptEffect
proteinLength
TranscriptEffectField
TranscriptEffect
proteinPosition
TranscriptEffectField
TranscriptEffect
pruneCache
ShuffleRegionJoin
SortedIntervalPartitionJoinWithVictims
VictimlessSortedIntervalPartitionJoin