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
ReferenceSequenceContext
rich
RegExp
util
RegionJoin
rdd
RegionOrdering
models
RichAlignmentRecord
rich
RichCigar
rich
RichGenotype
rich
RichVariant
rich
RightOuterBroadcastRegionJoin
rdd
RightOuterShuffleRegionJoin
rdd
RightOuterShuffleRegionJoinAndGroupByLeft
rdd
rdd
adam GenomicRDD NucleotideContigFragmentRDD CoverageRDD FeatureRDD FragmentRDD AlignedReadRDD UnalignedReadRDD DatabaseVariantAnnotationRDD GenotypeRDD VariantContextRDD VariantRDD
rddToADAMRDD
ADAMContext
read
ReadBucketSerializer ReferencePositionPairSerializer ReferencePositionSerializer ReferenceRegionSerializer SingleReadBucketSerializer OutFormatter rdd AnySAMOutFormatter IncorrectMDTagException IndelRealignmentTargetSerializer TargetSetSerializer ZippedTargetSetSerializer VCFOutFormatter AvroSerializer TwoBitFileSerializer
read1
FlagStatMetrics
read1refPos
ReferencePositionPair
read2
FlagStatMetrics
read2refPos
ReferencePositionPair
readArray
ReadBucketSerializer SingleReadBucketSerializer
readDepth
GenotypeField VariantCallingAnnotationsField
readGroup
CovariateKey
readInFragment
AlignmentRecordField
readMapped
AlignmentRecordField
readName
AlignmentRecordField
readNegativeStrand
AlignmentRecordField
readOffsetToReferencePosition
RichAlignmentRecord
readOffsetToReferenceSequenceContext
RichAlignmentRecord
readOptionalReferencePos
ReferencePositionPairSerializer
readPaired
AlignmentRecordField
readPositionRankSum
VariantCallingAnnotationsField
readRange
IndelRealignmentTarget
reader
AvroSerializer
reads
MDTagging
readsToVCConversionFn
ADAMContext
realignIndels
AlignmentRecordRDD
realignment
read
reassembleReadPairs
AlignmentRecordRDD
recalibateBaseQualities
AlignmentRecordRDD
recalibration
read
record
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 AvroReadGroupGenomicRDD FragmentRDD AlignedReadRDD AnySAMInFormatter BAMInFormatter SAMInFormatter UnalignedReadRDD
recordSchema
FieldEnumeration
recordSerializer
ReadBucketSerializer SingleReadBucketSerializer
recordToRichRecord
ADAMContext RichAlignmentRecord
records
SequenceDictionary
referenceAllele
VariantField
referenceAminoAcid
DatabaseVariantAnnotationField
referenceBase
ReferenceSequenceContext
referenceContexts
RichAlignmentRecord
referenceFile
MDTagging
referenceIndex
SequenceRecord
referenceLength
RichAlignmentRecord
referenceLengthFromCigar
RichAlignmentRecord
referenceName
NonoverlappingRegions ReferencePosition ReferenceRegion
referencePositions
RichAlignmentRecord
referenceReadDepth
GenotypeField
refseq
SequenceRecord
regionMap
MultiContigNonoverlappingRegions
regionsFor
MultiContigNonoverlappingRegions NonoverlappingRegions BroadcastRegionJoin InnerBroadcastRegionJoin RightOuterBroadcastRegionJoin
registerClasses
ADAMKryoRegistrator
replaceRdd
GenomicRDD NucleotideContigFragmentRDD CoverageRDD FeatureRDD FragmentRDD AlignedReadRDD UnalignedReadRDD DatabaseVariantAnnotationRDD GenotypeRDD VariantContextRDD VariantRDD
replaceRddAndSequences
AlignedReadRDD AlignmentRecordRDD UnalignedReadRDD
reportedErrorProbability
Aggregate
result
BaseQualityRecalibration ObservationAccumulator
reverseComplement
Alphabet
reverseComplementExact
Alphabet
rgs
SAMFileHeaderWritable
rich
adam
richGenotypeToGenotype
RichGenotype
richRecordToRecord
RichAlignmentRecord
richVariantToVariant
RichVariant
rightOuterBroadcastRegionJoin
GenomicRDD
rightOuterShuffleRegionJoin
GenomicRDD
rightOuterShuffleRegionJoinAndGroupByLeft
GenomicRDD
rmsMapQ
VariantCallingAnnotationsField
rps
ReferencePositionPairSerializer
runDateEpoch
RecordGroup