RDDBoundAlignmentRecordDataset
read
RDDBoundCoverageDataset
feature
RDDBoundFeatureDataset
feature
RDDBoundFragmentDataset
fragment
RDDBoundGenericGenomicDataset
rdd
RDDBoundGenotypeDataset
variant
RDDBoundNucleotideContigFragmentDataset
contig
RDDBoundVariantContextDataset
variant
RDDBoundVariantDataset
variant
ReadCovariates
Timers
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
RichAlignmentRecord
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 DatasetBoundNucleotideContigFragmentDataset ParquetUnboundNucleotideContigFragmentDataset RDDBoundNucleotideContigFragmentDataset DatasetBoundCoverageDataset DatasetBoundFeatureDataset ParquetUnboundCoverageDataset ParquetUnboundFeatureDataset RDDBoundCoverageDataset RDDBoundFeatureDataset DatasetBoundFragmentDataset ParquetUnboundFragmentDataset RDDBoundFragmentDataset DatasetBoundAlignmentRecordDataset ParquetUnboundAlignmentRecordDataset RDDBoundAlignmentRecordDataset 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
AlignmentRecordField FragmentField AlignmentRecord Fragment
readGroupMap
ReadGroupDictionary
readGroupSampleId
AlignmentRecordField AlignmentRecord
readGroups
ReadGroupDictionary AvroReadGroupGenomicDataset DatasetBoundFragmentDataset ParquetUnboundFragmentDataset RDDBoundFragmentDataset AnySAMInFormatter BAMInFormatter DatasetBoundAlignmentRecordDataset ParquetUnboundAlignmentRecordDataset RDDBoundAlignmentRecordDataset SAMInFormatter
readInFragment
AlignmentRecordField AlignmentRecord
readMapped
AlignmentRecordField AlignmentRecord
readName
AlignmentRecordField AlignmentRecord
readNegativeStrand
AlignmentRecordField AlignmentRecord
readPaired
AlignmentRecordField AlignmentRecord
readPositionRankSum
VariantCallingAnnotationsField VariantCallingAnnotations
reader
AvroSerializer
realignIndels
AlignmentRecordDataset
reassembleReadPairs
AlignmentRecordDataset
recalibrateBaseQualities
AlignmentRecordDataset
record
RichAlignmentRecord
recordSchema
FieldEnumeration
recordSerializer
SingleReadBucketSerializer
recordToRichRecord
ADAMContext RichAlignmentRecord
records
SequenceDictionary
referenceAllele
VariantField Variant
referenceForwardReadDepth
VariantAnnotationField VariantAnnotation
referenceName
Coverage ReferencePosition ReferenceRegion AlignmentRecordField FeatureField GenotypeField VariantField AlignmentRecord 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 DatasetBoundAlignmentRecordDataset ParquetUnboundAlignmentRecordDataset RDDBoundAlignmentRecordDataset
replaceRdd
DatasetBoundGenericGenomicDataset GenomicDataset RDDBoundGenericGenomicDataset NucleotideContigFragmentDataset CoverageDataset FeatureDataset FragmentDataset AlignmentRecordDataset GenotypeDataset VariantContextDataset VariantDataset
replaceRddAndSequences
AlignmentRecordDataset
replaceReadGroups
AvroReadGroupGenomicDataset DatasetBoundFragmentDataset ParquetUnboundFragmentDataset RDDBoundFragmentDataset DatasetBoundAlignmentRecordDataset ParquetUnboundAlignmentRecordDataset RDDBoundAlignmentRecordDataset
replaceSamples
MultisampleGenomicDataset DatasetBoundCoverageDataset DatasetBoundFeatureDataset ParquetUnboundCoverageDataset ParquetUnboundFeatureDataset RDDBoundCoverageDataset RDDBoundFeatureDataset DatasetBoundGenotypeDataset DatasetBoundVariantContextDataset ParquetUnboundGenotypeDataset RDDBoundGenotypeDataset RDDBoundVariantContextDataset
replaceSequences
DatasetBoundGenericGenomicDataset GenomicDataset RDDBoundGenericGenomicDataset DatasetBoundNucleotideContigFragmentDataset ParquetUnboundNucleotideContigFragmentDataset RDDBoundNucleotideContigFragmentDataset DatasetBoundCoverageDataset DatasetBoundFeatureDataset ParquetUnboundCoverageDataset ParquetUnboundFeatureDataset RDDBoundCoverageDataset RDDBoundFeatureDataset DatasetBoundFragmentDataset ParquetUnboundFragmentDataset RDDBoundFragmentDataset DatasetBoundAlignmentRecordDataset ParquetUnboundAlignmentRecordDataset RDDBoundAlignmentRecordDataset DatasetBoundGenotypeDataset DatasetBoundVariantContextDataset DatasetBoundVariantDataset ParquetUnboundGenotypeDataset ParquetUnboundVariantDataset RDDBoundGenotypeDataset RDDBoundVariantContextDataset RDDBoundVariantDataset
reverseComplement
Alphabet
reverseComplementExact
Alphabet
reverseReadDepth
DefaultHeaderLines VariantAnnotationField VariantAnnotation
rich
adam
richRecordToRecord
RichAlignmentRecord
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