REFSEQ_TAG
SequenceRecord
REPEATED
Repetition
REQUIRED
Repetition
RangeIndex
index
RangeIndexEntry
index
RangeIndexGenerator
index
RangeIndexPredicate
index
RangeIndexWriter
index
ReadBucket
models
ReadBucketSerializer
models
RealignmentTargetFinder
realignmenttarget
RecalibrationTable
recalibration
Recalibrator
recalibration
RecordGroup
models
RecordGroupDictionary
models
ReferenceAndAlternate
GenotypesSummaryCounts
ReferenceFolder
index
ReferenceFoldingContext
index
ReferenceMapping
models
ReferenceMappingContext
rich
ReferencePosition
models
ReferencePositionPair
models
ReferencePositionPairSerializer
models
ReferencePositionSerializer
models
ReferencePositionWithOrientation
models
ReferencePositionWithOrientationSerializer
models
ReferenceRegion
models
ReferenceRegionReferenceMapping
ReferenceMappingContext
ReferenceRegionSerializer
models
ReferenceRegionWithOrientation
models
RegExp
util
RegionJoin
rdd
Repetition
parquet_reimpl
Residue
DecadentRead
RichADAMGenotype
rich
RichADAMRecord
rich
RichADAMVariant
rich
RichCigar
rich
Right
Alignment
RowGroupIndex
index
RowGroupIndexEntry
index
RowGroupIndexWriter
index
range
IDRangeIndexEntry
rangeGapSize
ADAMFlatGenotypeReferenceFolder
rangeSet
IDAndRangeSet
ranges
RangeIndexEntry RangeIndexGenerator
rdd
adam
rddToADAMGenotypeRDD
ADAMVariationContext
rddToADAMPileupRDD
ADAMContext
rddToADAMRDD
ADAMContext
rddToADAMRecordRDD
ADAMContext
rddToADAMRodRDD
ADAMContext
rddToADAMVariantContextRDD
ADAMVariationContext
read
TargetSetSerializer ZippedTargetSetSerializer ReadBucketSerializer ReferencePositionPairSerializer ReferencePositionSerializer ReferencePositionWithOrientationSerializer ReferenceRegionSerializer SingleReadBucketSerializer Residue AvroSerializer
read1
FlagStatMetrics
read1refPos
ReferencePositionPair
read2
FlagStatMetrics
read2refPos
ReferencePositionPair
readAllPages
ParquetColumnChunk
readArray
ReadBucketSerializer SingleReadBucketSerializer
readByteStream
ByteAccess ByteArrayByteAccess HTTPRangedByteAccess LocalFileByteAccess S3ByteAccess
readCount
GenotypesSummaryCounts
readDataPage
ParquetColumnChunk
readDepth
ADAMFlatGenotypeField VariantCallingAnnotationsField ADAMGenotypeField
readDictionaryPage
ParquetColumnChunk
readFileMetadata
ParquetCommon
readFooter
ParquetCommon
readFully
ByteAccess
readGroup
CovariateKey DecadentRead
readInt
ParquetCommon
readMapped
ADAMRecordField
readName
ADAMRecordField DeletionEvent InsertionEvent MatchEvent MismatchEvent
readNegativeStrand
ADAMRecordField
readOffsetToReferencePosition
RichADAMRecord
readOffsetToReferenceSequenceContext
RichADAMRecord
readOptionalReferencePos
ReferencePositionPairSerializer
readPageHeader
ParquetColumnChunk
readPaired
ADAMRecordField
readPositionRankSum
VariantCallingAnnotationsField
readRange
IndelRealignmentTarget
readRegion
RichADAMRecord
readToPileups
PileupTraversable
reader
VCFLineParser AvroSerializer
realignmenttarget
algorithms
recalibration
rdd
recall
ConcordanceTable
record
DecadentRead RichADAMRecord
recordCondition
ADAMPredicate GenotypeRecordPASSPredicate HighQualityReadPredicate UniqueMappedReadPredicate
recordFilter
CombinedFilter FilterTuple
recordGroupDescription
ADAMRecordField
recordGroupFlowOrder
ADAMRecordField
recordGroupId
ADAMRecordField
recordGroupKeySequence
ADAMRecordField
recordGroupLibrary
ADAMRecordField
recordGroupMap
RecordGroupDictionary
recordGroupName
RecordGroup ADAMRecordField
recordGroupPlatform
ADAMRecordField
recordGroupPlatformUnit
ADAMRecordField
recordGroupPredictedMedianInsertSize
ADAMRecordField
recordGroupRunDateEpoch
ADAMRecordField
recordGroupSample
ADAMRecordField
recordGroupSequencingCenter
ADAMRecordField
recordGroups
RecordGroupDictionary
recordMillis
ServoTimer
recordNanos
ServoTimer
recordSchema
FieldEnumeration
recordSerializer
ReadBucketSerializer SingleReadBucketSerializer
recordStageDuration
SparkMetrics
recordToRichRecord
ADAMContext RichADAMRecord
records
SequenceDictionary
ref
VCFLine
refPos
ReferencePositionWithOrientation
reference
ReferenceAndAlternate
referenceAllele
ADAMFlatGenotypeField ADAMVariantField
referenceAminoAcid
ADAMDatabaseVariantAnnotationField
referenceBase
Pileup
referenceContexts
RichADAMRecord
referenceLength
RichADAMRecord
referenceLengthFromCigar
RichADAMRecord
referenceName
VCFLine ReferencePosition ReferenceRegion ReferenceRegionWithOrientation ADAMFlatGenotypeField NonoverlappingRegions Pileup
referencePosition
Residue Pileup
referencePositionOption
Residue
referencePositionSerializer
ReferencePositionWithOrientationSerializer
referencePositions
RichADAMRecord
referenceReadDepth
ADAMGenotypeField
referenceSequenceContext
Residue
refseq
SequenceRecord
regionMap
MultiContigNonoverlappingRegions
regionsFor
MultiContigNonoverlappingRegions NonoverlappingRegions
registerClasses
ADAMKryoRegistrator
relativeLocator
ByteArrayLocator FileLocator HTTPFileLocator LocalFileLocator S3FileLocator
repetition
ParquetAggregateType ParquetPrimitiveType ParquetType
reportedErrorProbability
Aggregate
requested
ParquetFileMetadata
requestedSchema
ParquetPartition
residues
DecadentRead
result
BaseQualityRecalibration ObservationAccumulator
resultSerializationTime
ADAMSparkMetrics
rich
adam
richGenotypeToGenotype
RichADAMGenotype
richRecordToRecord
RichADAMRecord
richVariantToVariant
RichADAMVariant
rmsMapQ
VariantCallingAnnotationsField
rowCount
ParquetRowGroup
rowGroup
ParquetPartition
rowGroupIndex
IDRangeIndexEntry RangeIndexEntry
rowGroups
Footer
rps
ReferencePositionPairSerializer
run
ADAMPlugin
runDateEpoch
RecordGroup