PER_BLOCK_SIZE
TwoBitFile
PairingRDD
rdd
ParquetFileTraversable
util
ParquetLoad
Timers
ParquetLogger
util
PerformDuplicateMarking
Timers
PhredUtils
util
PositionOrdering
models
ProgramRecord
models
Projection
projections
pair
PairingRDD
pairWithEnds
PairingRDD
pairedFirstPrimaryMappedReads
ReadBucket
pairedFirstSecondaryMappedReads
ReadBucket
pairedInSequencing
FlagStatMetrics
pairedSecondPrimaryMappedReads
ReadBucket
pairedSecondSecondaryMappedReads
ReadBucket
parentIds
FeatureField
parse
BEDParser FeatureFile FeatureParser GTFParser IntervalListParser NarrowPeakParser
parseAttribute
AttributeUtils
parseAttributes
AttributeUtils
parseAttrs
GTFParser
partitionAndJoin
BroadcastRegionJoin RegionJoin ShuffleRegionJoin
partitionSize
GenomicRegionPartitioner ShuffleRegionJoin
passedQualityChecks
DecadentRead
paths
ParquetFileTraversable
pattern
RegExp
patternString
RegExp
pgl
SAMFileHeaderWritable
phaseQuality
GenotypeField
phaseSetId
GenotypeField
phred
QualityScore
phredToErrorProbability
PhredUtils
phredToErrorProbabilityCache
PhredUtils
phredToSuccessProbability
PhredUtils
phredToSuccessProbabilityCache
PhredUtils
phylop
DatabaseVariantAnnotationField
platform
RecordGroup
platformUnit
RecordGroup
ploidy
RichGenotype
plugins
adam
polarity
OrientedPoint
pos
ReferencePosition OrientedPoint
position
VariantContext
predicate
ADAMPlugin AccessControl EmptyAccessControl
predictedMedianInsertSize
RecordGroup
preprocessReadsForRealignment
ConsensusGenerator ConsensusGeneratorFromKnowns ConsensusGeneratorFromReads ConsensusGeneratorFromSmithWaterman
previousID
ProgramRecord
primaryAlignment
AlignmentRecordField
primaryMapped
SingleReadBucket
processingDescription
GenotypeField
projection
ADAMPlugin
projections
adam
properPair
AlignmentRecordField
properlyPaired
FlagStatMetrics