REFSEQ_TAG
SequenceRecord
ReadBucket
models
ReadBucketSerializer
models
RealignIndelsInDriver
Timers
RealignTargetGroup
Timers
RealignmentTargetFinder
realignment
RecalibrateRead
Timers
RecalibrationTable
recalibration
Recalibrator
recalibration
RecordGroup
models
RecordGroupDictionary
models
ReferenceContigMap
util
ReferenceFile
util
ReferenceOrdering
models
ReferencePartitioner
rdd
ReferencePosition
models
ReferencePositionPair
models
ReferencePositionPairSerializer
models
ReferencePositionSerializer
models
ReferenceRegion
models
ReferenceRegionSerializer
models
ReferenceUtils
models
RegExp
util
Region
Coverage
RegionJoin
rdd
RegionOrdering
models
RichAlignmentRecord
rich
RichCigar
rich
RichGenotype
rich
RichVariant
rich
rdd
adam GenomicRDD AlignedReadRDD UnalignedReadRDD
rddToADAMGenotypeRDD
ADAMContext
rddToADAMRDD
ADAMContext
rddToADAMRecordRDD
ADAMContext
rddToContigFragmentRDD
ADAMContext
rddToFragmentRDD
ADAMContext
rddToPairingRDD
PairingRDD
rddToVariantContextRDD
ADAMContext
read
ReadBucketSerializer ReferencePositionPairSerializer ReferencePositionSerializer ReferenceRegionSerializer SingleReadBucketSerializer rdd IncorrectMDTagException TargetSetSerializer ZippedTargetSetSerializer AvroSerializer TwoBitFileSerializer
read1
FlagStatMetrics
read1refPos
ReferencePositionPair
read2
FlagStatMetrics
read2refPos
ReferencePositionPair
readArray
ReadBucketSerializer SingleReadBucketSerializer
readDepth
GenotypeField VariantCallingAnnotationsField
readGroup
CovariateKey
readInFragment
AlignmentRecordField
readMapped
AlignmentRecordField
readName
AlignmentRecordField
readNameHasPairedSuffix
AlignmentRecordConverter
readNegativeStrand
AlignmentRecordField
readOffsetToReferencePosition
RichAlignmentRecord
readOffsetToReferenceSequenceContext
RichAlignmentRecord
readOptionalReferencePos
ReferencePositionPairSerializer
readPaired
AlignmentRecordField
readPositionRankSum
VariantCallingAnnotationsField
readRange
IndelRealignmentTarget
reader
AvroSerializer
reads
MDTagging
realignment
read
recalibration
read
record
BAMFilteredRecordReader RichAlignmentRecord
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 AlignedReadRDD AlignmentRecordRDD UnalignedReadRDD
recordSchema
FieldEnumeration
recordSerializer
ReadBucketSerializer SingleReadBucketSerializer
recordToRichRecord
ADAMContext RichAlignmentRecord
records
SequenceDictionary
referenceAllele
VariantField
referenceAminoAcid
DatabaseVariantAnnotationField
referenceContexts
RichAlignmentRecord
referenceFile
MDTagging
referenceIndex
SequenceRecord
referenceLength
RichAlignmentRecord
referenceLengthFromCigar
RichAlignmentRecord
referenceName
NonoverlappingRegions ReferencePosition ReferenceRegion
referencePositions
RichAlignmentRecord
referenceReadDepth
GenotypeField
refseq
SequenceRecord
region
CDS Exon Transcript UTR
regionMap
MultiContigNonoverlappingRegions
regionToWindows
Coverage
regions
Gene
regionsFor
MultiContigNonoverlappingRegions NonoverlappingRegions
registerClasses
ADAMKryoRegistrator
reportedErrorProbability
Aggregate
result
BaseQualityRecalibration ObservationAccumulator
reverseComplement
Alphabet
reverseComplementExact
Alphabet
rgs
SAMFileHeaderWritable
rich
adam
richGenotypeToGenotype
RichGenotype
richRecordToRecord
RichAlignmentRecord
richVariantToVariant
RichVariant
rmsMapQ
VariantCallingAnnotationsField
rps
ReferencePositionPairSerializer
run
ADAMPlugin
runDateEpoch
RecordGroup