REFSEQ_TAG
SequenceRecord
ReadBucket
models
ReadBucketSerializer
models
RealignIndelsInDriver
Timers
RealignTargetGroup
Timers
RealignmentTargetFinder
realignment
RecalibrateRead
Timers
RecalibrationTable
recalibration
Recalibrator
recalibration
RecordCondition
predicates
RecordGroup
models
RecordGroupDictionary
models
ReferenceAndAlternate
GenotypesSummaryCounts
ReferenceMapping
models
ReferenceMappingContext
rich
ReferencePosition
models
ReferencePositionPair
models
ReferencePositionPairSerializer
models
ReferencePositionSerializer
models
ReferencePositionWithOrientation
models
ReferencePositionWithOrientationSerializer
models
ReferenceRegion
models
ReferenceRegionReferenceMapping
ReferenceMappingContext
ReferenceRegionSerializer
models
ReferenceRegionWithOrientation
models
ReferenceUtils
models
RegExp
util
Region
Coverage
Residue
DecadentRead
RichAlignmentRecord
rich
RichCigar
rich
RichGenotype
rich
RichVariant
rich
Rod
models
RodRDDFunctions
pileup
rdd
adam
rddToADAMGenotypeRDD
ADAMContext
rddToADAMRDD
ADAMContext
rddToADAMRecordRDD
ADAMContext
rddToContigFragmentRDD
ADAMContext
rddToPairingRDD
PairingRDD
rddToPileupRDD
ADAMContext
rddToRodRDD
ADAMContext
rddToVariantContextRDD
ADAMContext
read
ReadBucketSerializer ReferencePositionPairSerializer ReferencePositionSerializer ReferencePositionWithOrientationSerializer ReferenceRegionSerializer SingleReadBucketSerializer rdd TargetSetSerializer ZippedTargetSetSerializer Residue AvroSerializer
read1
FlagStatMetrics
read1refPos
ReferencePositionPair
read2
FlagStatMetrics
read2refPos
ReferencePositionPair
readArray
ReadBucketSerializer SingleReadBucketSerializer
readCount
GenotypesSummaryCounts
readDepth
GenotypeField VariantCallingAnnotationsField
readGroup
CovariateKey DecadentRead
readMapped
AlignmentRecordField
readName
AlignmentRecordField DeletionEvent InsertionEvent MatchEvent MismatchEvent
readNameHasPairedSuffix
AlignmentRecordConverter
readNegativeStrand
AlignmentRecordField
readOffsetToReferencePosition
RichAlignmentRecord
readOffsetToReferenceSequenceContext
RichAlignmentRecord
readOptionalReferencePos
ReferencePositionPairSerializer
readPaired
AlignmentRecordField
readPositionRankSum
VariantCallingAnnotationsField
readRange
IndelRealignmentTarget
readRegion
RichAlignmentRecord
readToPileups
PileupTraversable
reader
AvroSerializer
realignment
read
recalibration
read
recall
ConcordanceTable
record
DecadentRead RichAlignmentRecord
recordCondition
ADAMPredicate GenotypeRecordPASSPredicate HighQualityReadPredicate UniqueMappedReadPredicate
recordFilter
RecordCondition
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
recordSchema
FieldEnumeration
recordSerializer
ReadBucketSerializer SingleReadBucketSerializer
recordToRichRecord
ADAMContext RichAlignmentRecord
records
SequenceDictionary
refPos
ReferencePositionWithOrientation
reference
ReferenceAndAlternate
referenceAllele
VariantField
referenceAminoAcid
DatabaseVariantAnnotationField
referenceBase
Pileup
referenceContexts
RichAlignmentRecord
referenceLength
RichAlignmentRecord
referenceLengthFromCigar
RichAlignmentRecord
referenceName
ReferencePosition ReferenceRegion ReferenceRegionWithOrientation NonoverlappingRegions Pileup
referencePosition
Residue Pileup
referencePositionOption
Residue
referencePositionSerializer
ReferencePositionWithOrientationSerializer
referencePositions
RichAlignmentRecord
referenceReadDepth
GenotypeField
referenceSequenceContext
Residue
refseq
SequenceRecord
region
CDS Exon ReferenceRegionWithOrientation Transcript UTR
regionMap
MultiContigNonoverlappingRegions
regionToWindows
Coverage
regions
Gene
regionsFor
MultiContigNonoverlappingRegions NonoverlappingRegions
registerClasses
ADAMKryoRegistrator
reportedErrorProbability
Aggregate
residues
DecadentRead
result
BaseQualityRecalibration ObservationAccumulator
reverseComplement
SequenceUtils
rgs
SAMFileHeaderWritable
rich
adam
richGenotypeToGenotype
RichGenotype
richRecordToRecord
RichAlignmentRecord
richVariantToVariant
RichVariant
rmsMapQ
VariantCallingAnnotationsField
rodCoverage
RodRDDFunctions
rps
ReferencePositionPairSerializer
run
ADAMPlugin
runDateEpoch
RecordGroup