ParquetAggregateType
parquet_reimpl
ParquetColumnChunk
rdd
ParquetColumnDescriptor
rdd
ParquetCommon
rdd
ParquetFileMetadata
index
ParquetFileTraversable
util
ParquetGroupType
parquet_reimpl
ParquetLister
parquet_reimpl
ParquetLogger
util
ParquetOriginalType
parquet_reimpl
ParquetPartition
parquet_reimpl
ParquetPrimitiveType
parquet_reimpl
ParquetRowGroup
rdd
ParquetSchemaType
parquet_reimpl
ParquetType
parquet_reimpl
ParsedFilter
BucketComparisons
PartitionPageReadStore
parquet_reimpl
PhredUtils
util
Pileup
util
PileupEvent
util
PileupRDDFunctions
rdd
PileupTraversable
util
PointComparisons
metrics
PredicateUtils
predicates
PrimitiveType
parquet_reimpl
Projection
projections
pValue
NarrowPeakFeature FeatureField
pairedFirstPrimaryMappedReads
ReadBucket
pairedFirstSecondaryMappedReads
ReadBucket
pairedInSequencing
FlagStatMetrics
pairedSecondPrimaryMappedReads
ReadBucket
pairedSecondSecondaryMappedReads
ReadBucket
parentIds
FeatureField
parentLocator
ByteArrayLocator FileLocator HTTPFileLocator LocalFileLocator S3FileLocator
parentdbxrefs
FeatureField
parquet
root
parquetFilePath
RowGroupIndexEntry
parquet_reimpl
adam
parse
BEDParser FeatureParser NarrowPeakParser
parseAttribute
AttributeUtils
parseAttributes
AttributeUtils
parseFilterString
BucketComparisons
parseIDRangeIndexEntry
IDRangeIndex
parseMessageType
ParquetCommon
parsePoint
BucketComparisons
parseRangeIndexEntry
RangeIndex
parseRegion
IDRangeIndex RangeIndex
parseRowGroups
Footer
parseSlash
FileLocator
partition
ParquetFileMetadata
partitionAndJoin
RegionJoin
parts
CovariateKey
passedQualityChecks
DecadentRead
passedVendorQualityChecks
AlignmentRecordConditions
passesFilter
EqualityFilter InequalityFilter WrapperFilter CombinedFilter GeneratorFilter
path
IDRangeIndexEntry RangeIndexEntry ParquetColumnDescriptor
paths
ParquetAggregateType ParquetPrimitiveType ParquetSchemaType ParquetType ParquetFileTraversable
pattern
RegExp
patternString
RegExp
peak
NarrowPeakFeature FeatureField
perSampleStatistics
GenotypesSummary
phaseQuality
GenotypeField
phaseSetId
GenotypeField
phasedCount
GenotypesSummaryCounts
phred
QualityScore
phredToErrorProbability
PhredUtils
phredToErrorProbabilityCache
PhredUtils
phredToSuccessProbability
PhredUtils
phredToSuccessProbabilityCache
PhredUtils
phylop
DatabaseVariantAnnotationField
pileups
Rod
pkn
LengthNormalization
platform
RecordGroup
platformUnit
RecordGroup
ploidy
RichGenotype
plugins
adam
pointRegex
BucketComparisons
points
BaseQualityScores DupeMismatch MapQualityScores
pos
ReferencePosition
position
VCFLine Rod VariantContext FlatGenotypeField VariantField
precision
ConcordanceTable
predicate
CombinedFilter FilterTuple ADAMPlugin AccessControl EmptyAccessControl
predicates
adam
predictedMedianInsertSize
RecordGroup
prefixSearch
DNAPrefixTrie
prefixtrie
algorithms
preprocessReadsForRealignment
ConsensusGenerator ConsensusGeneratorFromKnowns ConsensusGeneratorFromReads ConsensusGeneratorFromSmithWaterman
primaryAlignment
AlignmentRecordField
primaryMapped
SingleReadBucket
primitiveType
ParquetPrimitiveType
print
ASCIITable MonitorTable SparkMetrics
processingDescription
GenotypeField
projection
ADAMPlugin ComparisonTraversalEngine
projections
adam
properPair
AlignmentRecordField
properlyPaired
FlagStatMetrics