RDDBoundAlignmentRecordRDD
read
RDDBoundCoverageRDD
feature
RDDBoundFeatureRDD
feature
RDDBoundFragmentRDD
fragment
RDDBoundGenericGenomicDataset
rdd
RDDBoundGenotypeRDD
variant
RDDBoundNucleotideContigFragmentRDD
contig
RDDBoundVariantContextRDD
variant
RDDBoundVariantRDD
variant
ReadCovariates
Timers
ReadField
projections
ReadResidues
Timers
RealignIndelsInDriver
Timers
RealignTargetGroup
Timers
RecalibrateRead
Timers
RecordGroup
models
RecordGroupDictionary
models
RecordGroupField
projections
ReferenceContigMap
util
ReferenceContigMapSerializer
util
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 DatasetBoundNucleotideContigFragmentRDD ParquetUnboundNucleotideContigFragmentRDD RDDBoundNucleotideContigFragmentRDD DatasetBoundCoverageRDD DatasetBoundFeatureRDD ParquetUnboundCoverageRDD ParquetUnboundFeatureRDD RDDBoundCoverageRDD RDDBoundFeatureRDD DatasetBoundFragmentRDD ParquetUnboundFragmentRDD RDDBoundFragmentRDD DatasetBoundAlignmentRecordRDD ParquetUnboundAlignmentRecordRDD RDDBoundAlignmentRecordRDD DatasetBoundGenotypeRDD DatasetBoundVariantContextRDD DatasetBoundVariantRDD ParquetUnboundGenotypeRDD ParquetUnboundVariantRDD RDDBoundGenotypeRDD RDDBoundVariantContextRDD RDDBoundVariantRDD
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
readInFragment
AlignmentRecordField AlignmentRecord
readMapped
AlignmentRecordField AlignmentRecord
readName
AlignmentRecordField FragmentField AlignmentRecord Fragment
readNegativeStrand
AlignmentRecordField AlignmentRecord
readPaired
AlignmentRecordField AlignmentRecord
readPositionRankSum
VariantCallingAnnotationsField VariantCallingAnnotations
reader
AvroSerializer
realignIndels
AlignmentRecordRDD
reassembleReadPairs
AlignmentRecordRDD
recalibrateBaseQualities
AlignmentRecordRDD
record
RichAlignmentRecord
recordGroupMap
RecordGroupDictionary
recordGroupName
RecordGroup AlignmentRecordField AlignmentRecord
recordGroupSample
AlignmentRecordField AlignmentRecord
recordGroups
RecordGroupDictionary AvroRecordGroupGenomicDataset DatasetBoundFragmentRDD ParquetUnboundFragmentRDD RDDBoundFragmentRDD AnySAMInFormatter BAMInFormatter DatasetBoundAlignmentRecordRDD ParquetUnboundAlignmentRecordRDD RDDBoundAlignmentRecordRDD SAMInFormatter
recordSchema
FieldEnumeration
recordSerializer
SingleReadBucketSerializer
recordToRichRecord
ADAMContext RichAlignmentRecord
records
SequenceDictionary
referenceAllele
VariantField Variant
referenceForwardReadDepth
VariantAnnotationField VariantAnnotation
referenceIndex
SequenceRecord ContigField Contig
referenceName
ReferencePosition ReferenceRegion
referenceReadDepth
GenotypeField VariantAnnotationField Genotype VariantAnnotation
referenceReverseReadDepth
VariantAnnotationField VariantAnnotation
referenceURL
ContigField Contig
refseq
SequenceRecord
regionFn
GenericConverter GenericGenomicDataset
registerClasses
ADAMKryoRegistrator
replaceHeaderLines
DatasetBoundGenotypeRDD DatasetBoundVariantContextRDD DatasetBoundVariantRDD ParquetUnboundGenotypeRDD ParquetUnboundVariantRDD RDDBoundGenotypeRDD RDDBoundVariantContextRDD RDDBoundVariantRDD VariantContextRDD
replaceProcessingSteps
GenomicDatasetWithLineage DatasetBoundFragmentRDD ParquetUnboundFragmentRDD RDDBoundFragmentRDD DatasetBoundAlignmentRecordRDD ParquetUnboundAlignmentRecordRDD RDDBoundAlignmentRecordRDD
replaceRdd
DatasetBoundGenericGenomicDataset GenomicDataset RDDBoundGenericGenomicDataset NucleotideContigFragmentRDD CoverageRDD FeatureRDD FragmentRDD AlignmentRecordRDD GenotypeRDD VariantContextRDD VariantRDD
replaceRddAndSequences
AlignmentRecordRDD
replaceRecordGroups
AvroRecordGroupGenomicDataset DatasetBoundFragmentRDD ParquetUnboundFragmentRDD RDDBoundFragmentRDD DatasetBoundAlignmentRecordRDD ParquetUnboundAlignmentRecordRDD RDDBoundAlignmentRecordRDD
replaceSamples
MultisampleGenomicDataset DatasetBoundGenotypeRDD DatasetBoundVariantContextRDD ParquetUnboundGenotypeRDD RDDBoundGenotypeRDD RDDBoundVariantContextRDD
replaceSequences
DatasetBoundGenericGenomicDataset GenomicDataset RDDBoundGenericGenomicDataset DatasetBoundNucleotideContigFragmentRDD ParquetUnboundNucleotideContigFragmentRDD RDDBoundNucleotideContigFragmentRDD DatasetBoundCoverageRDD DatasetBoundFeatureRDD ParquetUnboundCoverageRDD ParquetUnboundFeatureRDD RDDBoundCoverageRDD RDDBoundFeatureRDD DatasetBoundFragmentRDD ParquetUnboundFragmentRDD RDDBoundFragmentRDD DatasetBoundAlignmentRecordRDD ParquetUnboundAlignmentRecordRDD RDDBoundAlignmentRecordRDD DatasetBoundGenotypeRDD DatasetBoundVariantContextRDD DatasetBoundVariantRDD ParquetUnboundGenotypeRDD ParquetUnboundVariantRDD RDDBoundGenotypeRDD RDDBoundVariantContextRDD RDDBoundVariantRDD
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
RecordGroup RecordGroupField
runId
FragmentField Fragment