RDDBoundAlignmentDataset
read
RDDBoundCoverageDataset
feature
RDDBoundFeatureDataset
feature
RDDBoundFragmentDataset
fragment
RDDBoundGenericGenomicDataset
rdd
RDDBoundGenotypeDataset
variant
RDDBoundReadDataset
read
RDDBoundSequenceDataset
sequence
RDDBoundSliceDataset
sequence
RDDBoundVariantContextDataset
variant
RDDBoundVariantDataset
variant
Read
sql
ReadCovariates
Timers
ReadDataset
read
ReadField
projections
ReadGroup
models
ReadGroupDictionary
models
ReadGroupField
projections
ReadResidues
Timers
RealignIndelsInDriver
Timers
RealignTargetGroup
Timers
RecalibrateRead
Timers
Reference
sql
ReferenceContigMap
util
ReferenceContigMapSerializer
util
ReferenceField
projections
ReferenceFile
util
ReferenceOrdering
models
ReferencePartitioner
rdd
ReferencePosition
models
ReferencePositionPairSerializer
read
ReferencePositionSerializer
models
ReferenceRegion
models
ReferenceRegionSerializer
models
RegionJoin
rdd
RegionOrdering
models
RichAlignment
rich
RichVariant
rich
RightOuterBroadcastJoin
Timers
RightOuterBroadcastJoinAndGroupByRight
Timers
RightOuterShuffleJoin
Timers
RightOuterShuffleJoinAndGroupByLeft
Timers
RightOuterShuffleRegionJoinAndGroupByLeft
rdd
RightOuterTreeRegionJoin
rdd
RightOuterTreeRegionJoinAndGroupByRight
rdd
RunningMapSideJoin
Timers
rank
TranscriptEffectField TranscriptEffect
rdd
adam DatasetBoundGenericGenomicDataset GenomicDataset RDDBoundGenericGenomicDataset DatasetBoundCoverageDataset DatasetBoundFeatureDataset ParquetUnboundCoverageDataset ParquetUnboundFeatureDataset RDDBoundCoverageDataset RDDBoundFeatureDataset DatasetBoundFragmentDataset ParquetUnboundFragmentDataset RDDBoundFragmentDataset DatasetBoundAlignmentDataset DatasetBoundReadDataset ParquetUnboundAlignmentDataset ParquetUnboundReadDataset RDDBoundAlignmentDataset RDDBoundReadDataset DatasetBoundSequenceDataset DatasetBoundSliceDataset ParquetUnboundSequenceDataset ParquetUnboundSliceDataset RDDBoundSequenceDataset RDDBoundSliceDataset DatasetBoundGenotypeDataset DatasetBoundVariantContextDataset DatasetBoundVariantDataset ParquetUnboundGenotypeDataset ParquetUnboundVariantDataset RDDBoundGenotypeDataset RDDBoundVariantContextDataset RDDBoundVariantDataset
read
ReferencePositionSerializer ReferenceRegionSerializer VariantContextSerializer OutFormatter BEDOutFormatter GFF3OutFormatter GTFOutFormatter NarrowPeakOutFormatter rdd AnySAMOutFormatter IncorrectMDTagException ReferencePositionPairSerializer SingleReadBucketSerializer VCFOutFormatter AvroSerializer WritableSerializer ReferenceContigMapSerializer TwoBitFileSerializer
readArray
SingleReadBucketSerializer
readDepth
DefaultHeaderLines GenotypeField VariantAnnotationField Genotype VariantAnnotation
readGroupId
AlignmentField FragmentField Alignment Fragment
readGroupMap
ReadGroupDictionary
readGroupSampleId
AlignmentField Alignment
readGroups
ReadGroupDictionary AvroReadGroupGenomicDataset DatasetBoundFragmentDataset ParquetUnboundFragmentDataset RDDBoundFragmentDataset AnySAMInFormatter BAMInFormatter DatasetBoundAlignmentDataset ParquetUnboundAlignmentDataset RDDBoundAlignmentDataset SAMInFormatter
readHeaders
ADAMShell
readInFragment
AlignmentField Alignment
readMapped
AlignmentField Alignment
readName
AlignmentField Alignment
readNegativeStrand
AlignmentField Alignment
readPaired
AlignmentField Alignment
readPositionRankSum
VariantCallingAnnotationsField VariantCallingAnnotations
reader
AvroSerializer
readsToAlignmentsConversionFn
ADAMContext
readsToAlignmentsDatasetConversionFn
ADAMContext
readsToCoverageConversionFn
ADAMContext
readsToCoverageDatasetConversionFn
ADAMContext
readsToFeaturesConversionFn
ADAMContext
readsToFeaturesDatasetConversionFn
ADAMContext
readsToFragmentsConversionFn
ADAMContext
readsToFragmentsDatasetConversionFn
ADAMContext
readsToGenotypesConversionFn
ADAMContext
readsToGenotypesDatasetConversionFn
ADAMContext
readsToReadsConversionFn
ADAMContext
readsToSequencesConversionFn
ADAMContext
readsToSequencesDatasetConversionFn
ADAMContext
readsToSlicesConversionFn
ADAMContext
readsToSlicesDatasetConversionFn
ADAMContext
readsToVariantContextsConversionFn
ADAMContext
readsToVariantsConversionFn
ADAMContext
readsToVariantsDatasetConversionFn
ADAMContext
realignIndels
AlignmentDataset
reassembleReadPairs
AlignmentDataset
recalibrateBaseQualities
AlignmentDataset
record
RichAlignment
recordSchema
FieldEnumeration
recordSerializer
SingleReadBucketSerializer
recordToRichRecord
ADAMContext RichAlignment
records
SequenceDictionary
referenceAllele
VariantField Variant
referenceForwardReadDepth
VariantAnnotationField VariantAnnotation
referenceName
Coverage ReferencePosition ReferenceRegion AlignmentField FeatureField GenotypeField VariantField Alignment Feature Genotype Variant VariantContext
referenceReadDepth
GenotypeField VariantAnnotationField Genotype VariantAnnotation
referenceReverseReadDepth
VariantAnnotationField VariantAnnotation
refseq
SequenceRecord
regionFn
GenericConverter GenericGenomicDataset
registerClasses
ADAMKryoRegistrator
replaceHeaderLines
DatasetBoundGenotypeDataset DatasetBoundVariantContextDataset DatasetBoundVariantDataset ParquetUnboundGenotypeDataset ParquetUnboundVariantDataset RDDBoundGenotypeDataset RDDBoundVariantContextDataset RDDBoundVariantDataset VariantContextDataset
replaceProcessingSteps
GenomicDatasetWithLineage DatasetBoundFragmentDataset ParquetUnboundFragmentDataset RDDBoundFragmentDataset DatasetBoundAlignmentDataset ParquetUnboundAlignmentDataset RDDBoundAlignmentDataset
replaceRdd
DatasetBoundGenericGenomicDataset GenomicDataset RDDBoundGenericGenomicDataset CoverageDataset FeatureDataset FragmentDataset AlignmentDataset ReadDataset SequenceDataset SliceDataset GenotypeDataset VariantContextDataset VariantDataset
replaceRddAndSequences
AlignmentDataset
replaceReadGroups
AvroReadGroupGenomicDataset DatasetBoundFragmentDataset ParquetUnboundFragmentDataset RDDBoundFragmentDataset DatasetBoundAlignmentDataset ParquetUnboundAlignmentDataset RDDBoundAlignmentDataset
replaceSamples
MultisampleGenomicDataset DatasetBoundCoverageDataset DatasetBoundFeatureDataset ParquetUnboundCoverageDataset ParquetUnboundFeatureDataset RDDBoundCoverageDataset RDDBoundFeatureDataset DatasetBoundGenotypeDataset DatasetBoundVariantContextDataset ParquetUnboundGenotypeDataset RDDBoundGenotypeDataset RDDBoundVariantContextDataset
replaceSequences
DatasetBoundGenericGenomicDataset GenomicDataset RDDBoundGenericGenomicDataset DatasetBoundCoverageDataset DatasetBoundFeatureDataset ParquetUnboundCoverageDataset ParquetUnboundFeatureDataset RDDBoundCoverageDataset RDDBoundFeatureDataset DatasetBoundFragmentDataset ParquetUnboundFragmentDataset RDDBoundFragmentDataset DatasetBoundAlignmentDataset DatasetBoundReadDataset ParquetUnboundAlignmentDataset ParquetUnboundReadDataset RDDBoundAlignmentDataset RDDBoundReadDataset DatasetBoundSequenceDataset DatasetBoundSliceDataset ParquetUnboundSequenceDataset ParquetUnboundSliceDataset RDDBoundSequenceDataset RDDBoundSliceDataset DatasetBoundGenotypeDataset DatasetBoundVariantContextDataset DatasetBoundVariantDataset ParquetUnboundGenotypeDataset ParquetUnboundVariantDataset RDDBoundGenotypeDataset RDDBoundVariantContextDataset RDDBoundVariantDataset
reverseComplement
Alphabet
reverseComplementExact
Alphabet
reverseReadDepth
DefaultHeaderLines VariantAnnotationField VariantAnnotation
rich
adam
richRecordToRecord
RichAlignment
rightOuterBroadcastRegionJoin
GenomicDataset
rightOuterBroadcastRegionJoinAgainst
GenomicDataset
rightOuterBroadcastRegionJoinAgainstAndGroupByRight
GenomicDataset
rightOuterBroadcastRegionJoinAndGroupByRight
GenomicDataset
rightOuterShuffleRegionJoin
GenomicDataset
rightOuterShuffleRegionJoinAndGroupByLeft
GenomicDataset
rightRdd
FullOuterShuffleRegionJoin InnerShuffleRegionJoin InnerShuffleRegionJoinAndGroupByLeft LeftOuterShuffleRegionJoin LeftOuterShuffleRegionJoinAndGroupByLeft RightOuterShuffleRegionJoinAndGroupByLeft ShuffleRegionJoin
rmsMapQ
VariantCallingAnnotationsField VariantCallingAnnotations
rmsMapq
DefaultHeaderLines
rpSerializer
VariantContextSerializer
rps
ReferencePositionPairSerializer
runDateEpoch
ReadGroup ReadGroupField