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
RichAlignmentRecord
rich
RichCigar
rich
RichGenotype
rich
RichVariant
rich
Right
Alignment
Rod
models
RodRDDFunctions
rdd
RowGroupIndex
index
RowGroupIndexEntry
index
RowGroupIndexWriter
index
range
IDRangeIndexEntry
rangeGapSize
FlatGenotypeReferenceFolder
rangeSet
IDAndRangeSet
ranges
RangeIndexEntry RangeIndexGenerator
rdd
adam
rddToADAMGenotypeRDD
ADAMVariationContext
rddToADAMPileupRDD
ADAMContext
rddToADAMRDD
ADAMContext
rddToADAMRecordRDD
ADAMContext
rddToRodRDD
ADAMContext
rddToVariantContextRDD
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
FlatGenotypeField GenotypeField VariantCallingAnnotationsField
readDictionaryPage
ParquetColumnChunk
readFileMetadata
ParquetCommon
readFooter
ParquetCommon
readFully
ByteAccess
readGroup
CovariateKey DecadentRead
readInt
ParquetCommon
readMapped
AlignmentRecordField
readName
AlignmentRecordField DeletionEvent InsertionEvent MatchEvent MismatchEvent
readNegativeStrand
AlignmentRecordField
readOffsetToReferencePosition
RichAlignmentRecord
readOffsetToReferenceSequenceContext
RichAlignmentRecord
readOptionalReferencePos
ReferencePositionPairSerializer
readPageHeader
ParquetColumnChunk
readPaired
AlignmentRecordField
readPositionRankSum
VariantCallingAnnotationsField
readRange
IndelRealignmentTarget
readRegion
RichAlignmentRecord
readToPileups
PileupTraversable
reader
VCFLineParser AvroSerializer
realignmenttarget
algorithms
recalibration
rdd
recall
ConcordanceTable
record
DecadentRead RichAlignmentRecord
recordCondition
ADAMPredicate GenotypeRecordPASSPredicate HighQualityReadPredicate UniqueMappedReadPredicate
recordFilter
CombinedFilter FilterTuple
recordGroupDescription
AlignmentRecordField
recordGroupFlowOrder
AlignmentRecordField
recordGroupId
AlignmentRecordField
recordGroupKeySequence
AlignmentRecordField
recordGroupLibrary
AlignmentRecordField
recordGroupMap
RecordGroupDictionary
recordGroupName
RecordGroup AlignmentRecordField
recordGroupPlatform
AlignmentRecordField
recordGroupPlatformUnit
AlignmentRecordField
recordGroupPredictedMedianInsertSize
AlignmentRecordField
recordGroupRunDateEpoch
AlignmentRecordField
recordGroupSample
AlignmentRecordField
recordGroupSequencingCenter
AlignmentRecordField
recordGroups
RecordGroupDictionary
recordMillis
ServoTimer
recordNanos
ServoTimer
recordSchema
FieldEnumeration
recordSerializer
ReadBucketSerializer SingleReadBucketSerializer
recordStageDuration
SparkMetrics
recordToRichRecord
ADAMContext RichAlignmentRecord
records
SequenceDictionary
ref
VCFLine
refPos
ReferencePositionWithOrientation
reference
ReferenceAndAlternate
referenceAllele
FlatGenotypeField VariantField
referenceAminoAcid
DatabaseVariantAnnotationField
referenceBase
Pileup
referenceContexts
RichAlignmentRecord
referenceLength
RichAlignmentRecord
referenceLengthFromCigar
RichAlignmentRecord
referenceName
VCFLine ReferencePosition ReferenceRegion ReferenceRegionWithOrientation FlatGenotypeField NonoverlappingRegions Pileup
referencePosition
Residue Pileup
referencePositionOption
Residue
referencePositionSerializer
ReferencePositionWithOrientationSerializer
referencePositions
RichAlignmentRecord
referenceReadDepth
GenotypeField
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
RichGenotype
richRecordToRecord
RichAlignmentRecord
richVariantToVariant
RichVariant
rmsMapQ
VariantCallingAnnotationsField
rowCount
ParquetRowGroup
rowGroup
ParquetPartition
rowGroupIndex
IDRangeIndexEntry RangeIndexEntry
rowGroups
Footer
rps
ReferencePositionPairSerializer
run
ADAMPlugin
runDateEpoch
RecordGroup