PER_BLOCK_SIZE
TwoBitFile
PairingRDD
rdd
ParquetFileTraversable
util
ParquetLoad
Timers
ParquetLogger
util
ParsedFilter
BucketComparisons
PerformDuplicateMarking
Timers
PhredUtils
util
Pileup
util
PileupEvent
util
PileupRDDFunctions
pileup
PileupTraversable
util
PointComparisons
metrics
PredicateUtils
predicates
ProgramRecord
models
Projection
projections
pageSize
ADAMParquetArgs
pair
PairingRDD
pairWithEnds
PairingRDD
pairedFirstPrimaryMappedReads
ReadBucket
pairedFirstSecondaryMappedReads
ReadBucket
pairedInSequencing
FlagStatMetrics
pairedSecondPrimaryMappedReads
ReadBucket
pairedSecondSecondaryMappedReads
ReadBucket
parentIds
FeatureField
parse
BEDParser FeatureFile FeatureParser GTFParser NarrowPeakParser
parseAttribute
AttributeUtils
parseAttributes
AttributeUtils
parseAttrs
GTFParser
parseBlockSizes
BEDFeature
parseBlockStarts
BEDFeature
parseFilterString
BucketComparisons
parseMultiLine
FastqRecordConverter
parsePoint
BucketComparisons
partitionAndJoin
BroadcastRegionJoin ShuffleRegionJoin
partitionSize
GenomicRegionPartitioner
passedQualityChecks
DecadentRead
passedVendorQualityChecks
AlignmentRecordConditions
passesFilter
EqualityFilter InequalityFilter WrapperFilter CombinedFilter GeneratorFilter
paths
ParquetFileTraversable
pattern
RegExp
patternString
RegExp
perSampleStatistics
GenotypesSummary
pgl
SAMFileHeaderWritable
phaseQuality
GenotypeField
phaseSetId
GenotypeField
phasedCount
GenotypesSummaryCounts
phred
QualityScore
phredToErrorProbability
PhredUtils
phredToErrorProbabilityCache
PhredUtils
phredToSuccessProbability
PhredUtils
phredToSuccessProbabilityCache
PhredUtils
phylop
DatabaseVariantAnnotationField
pileup
rdd
pileups
Rod
pkn
LengthNormalization
platform
RecordGroup
platformUnit
RecordGroup
ploidy
RichGenotype
plugins
adam
pointRegex
BucketComparisons
points
BaseQualityScores DupeMismatch MapQualityScores
polarity
OrientedPoint
pos
ReferencePosition OrientedPoint
position
Rod VariantContext VariantField
precision
ConcordanceTable
predicate
ADAMPlugin AccessControl EmptyAccessControl
predicates
adam
predictedMedianInsertSize
RecordGroup
prefixSearch
DNAPrefixTrie
prefixtrie
algorithms
preprocessReadsForRealignment
ConsensusGenerator ConsensusGeneratorFromKnowns ConsensusGeneratorFromReads ConsensusGeneratorFromSmithWaterman
previousID
ProgramRecord
primaryAlignment
AlignmentRecordField
primaryMapped
SingleReadBucket
processingDescription
GenotypeField
projection
ADAMPlugin ComparisonTraversalEngine
projections
adam
properPair
AlignmentRecordField
properlyPaired
FlagStatMetrics