RangeAccumulator
realignmenttarget
ReadBucket
models
ReadBucketSerializer
models
RealignmentTargetFinder
realignmenttarget
RecalibrationTable
recalibration
Recalibrator
recalibration
RecordGroupDictionary
models
ReferenceAndAlternate
GenotypesSummaryCounts
ReferenceLocation
rich
ReferenceMapping
models
ReferenceMappingContext
rich
ReferencePosition
models
ReferencePositionPair
models
ReferencePositionPairSerializer
models
ReferencePositionSerializer
models
ReferencePositionWithOrientation
models
ReferencePositionWithOrientationSerializer
models
ReferenceRegion
models
ReferenceRegionReferenceMapping
ReferenceMappingContext
ReferenceRegionSerializer
models
RegExp
util
RegionJoin
rdd
Residue
DecadentRead
RichADAMGenotype
rich
RichADAMRecord
rich
RichADAMVariant
rich
RichCigar
rich
RichRDDReferenceRecords
rich
rdd
adam
rddToADAMGenotypeRDD
ADAMVariationContext
rddToADAMPileupRDD
ADAMContext
rddToADAMRDD
ADAMContext
rddToADAMRecordRDD
ADAMContext
rddToADAMRodRDD
ADAMContext
rddToADAMVariantContextRDD
ADAMVariationContext
read
IndelRangeSerializer SNPRangeSerializer TreeSetSerializer ReadBucketSerializer ReferencePositionPairSerializer ReferencePositionSerializer ReferencePositionWithOrientationSerializer ReferenceRegionSerializer SingleReadBucketSerializer Residue AvroSerializer
read1
FlagStatMetrics
read1refPos
ReferencePositionPair
read2
FlagStatMetrics
read2refPos
ReferencePositionPair
readArray
ReadBucketSerializer SingleReadBucketSerializer
readCount
GenotypesSummaryCounts
readDepth
VariantCallingAnnotationsField ADAMGenotypeField
readGroup
CovariateKey DecadentRead
readGroups
RecordGroupDictionary
readMapped
ADAMRecordField
readName
ADAMRecordField DeletionEvent InsertionEvent MatchEvent MismatchEvent
readNegativeStrand
ADAMRecordField
readOffsetToReferencePosition
RichADAMRecord
readOptionalReferencePos
ReferencePositionPairSerializer
readPaired
ADAMRecordField
readPositionRankSum
VariantCallingAnnotationsField
readRange
GenericRange IndelRange IndelRealignmentTarget SNPRange
readToPileups
PileupTraversable
reader
AvroSerializer
reads
BaseQualityRecalibration
realignmenttarget
algorithms
recalibration
rdd
recall
ConcordanceTable
record
DecadentRead RichADAMRecord
recordGroupDescription
ADAMRecordField
recordGroupFlowOrder
ADAMRecordField
recordGroupId
ADAMRecordField
recordGroupKeySequence
ADAMRecordField
recordGroupLibrary
ADAMRecordField
recordGroupName
ADAMRecordField
recordGroupPlatform
ADAMRecordField
recordGroupPlatformUnit
ADAMRecordField
recordGroupPredictedMedianInsertSize
ADAMRecordField
recordGroupRunDateEpoch
ADAMRecordField
recordGroupSample
ADAMRecordField
recordGroupSequencingCenter
ADAMRecordField
recordSchema
FieldEnumeration
recordSerializer
ReadBucketSerializer SingleReadBucketSerializer
recordToRichRecord
ADAMContext RichADAMRecord
records
SequenceDictionary
recordsIn
SequenceDictionary
refId
ReferencePosition ReferenceRegion
refPos
ReferencePositionWithOrientation
reference
ReferenceAndAlternate
referenceAllele
ADAMVariantField
referenceAminoAcid
ADAMDatabaseVariantAnnotationField
referenceBase
Pileup
referenceId
ADAMRecordField NonoverlappingRegions Pileup
referenceLength
ADAMRecordField NonoverlappingRegions
referenceLocation
Residue
referenceLocationOption
Residue
referenceName
ADAMRecordField Pileup
referencePosition
Pileup
referencePositionSerializer
ReferencePositionWithOrientationSerializer
referencePositions
RichADAMRecord
referenceReadDepth
ADAMGenotypeField
referenceRegionToReferenceMapped
ReferenceMappingContext
referenceUrl
ADAMRecordField
regex
HeaderReader
regionMap
MultiContigNonoverlappingRegions
regionsFor
MultiContigNonoverlappingRegions NonoverlappingRegions
registerClasses
ADAMKryoRegistrator
remap
SequenceDictionary
remapReferenceId
ReferenceMapping ADAMRecordReferenceMapping ReferenceRegionReferenceMapping RichRDDReferenceRecords
reportedErrorProbability
Aggregate
result
BaseQualityRecalibration ObservationAccumulator
rich
adam
richGenotypeToGenotype
RichADAMGenotype
richRecordToRecord
RichADAMRecord
richVariantToVariant
RichADAMVariant
rmsMapQ
VariantCallingAnnotationsField
rps
ReferencePositionPairSerializer
run
ADAMPlugin