ReadCovariates
Timers
ReadField
projections
ReadResidues
Timers
RealignIndelsInDriver
Timers
RealignTargetGroup
Timers
RecalibrateRead
Timers
RecordGroup
models
RecordGroupDictionary
models
RecordGroupMetadataField
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
RightOuterShuffleRegionJoin
rdd
RightOuterShuffleRegionJoinAndGroupByLeft
rdd
RightOuterTreeRegionJoin
rdd
RightOuterTreeRegionJoinAndGroupByRight
rdd
RunningMapSideJoin
Timers
rank
TranscriptEffectField
rdd
adam GenomicRDD NucleotideContigFragmentRDD CoverageRDD FeatureRDD FragmentRDD AlignmentRecordRDD GenotypeRDD VariantContextRDD VariantRDD
rddToADAMRDD
ADAMContext
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
readInFragment
AlignmentRecordField
readMapped
AlignmentRecordField
readName
AlignmentRecordField FragmentField
readNegativeStrand
AlignmentRecordField
readPaired
AlignmentRecordField
readPositionRankSum
VariantCallingAnnotationsField
reader
AvroSerializer
readsToVCConversionFn
ADAMContext
realignIndels
AlignmentRecordRDD
reassembleReadPairs
AlignmentRecordRDD
recalibrateBaseQualities
AlignmentRecordRDD
record
RichAlignmentRecord
recordGroupMap
RecordGroupDictionary
recordGroupName
RecordGroup AlignmentRecordField
recordGroupSample
AlignmentRecordField
recordGroups
RecordGroupDictionary AvroReadGroupGenomicRDD FragmentRDD AlignmentRecordRDD AnySAMInFormatter BAMInFormatter SAMInFormatter
recordSchema
FieldEnumeration
recordSerializer
SingleReadBucketSerializer
recordToRichRecord
ADAMContext RichAlignmentRecord
records
SequenceDictionary
referenceAllele
VariantField
referenceForwardReadDepth
VariantAnnotationField
referenceIndex
SequenceRecord ContigField
referenceName
ReferencePosition ReferenceRegion
referenceReadDepth
GenotypeField VariantAnnotationField
referenceReverseReadDepth
VariantAnnotationField
referenceURL
ContigField
refseq
SequenceRecord
registerClasses
ADAMKryoRegistrator
replaceRdd
GenomicRDD NucleotideContigFragmentRDD CoverageRDD FeatureRDD FragmentRDD AlignmentRecordRDD GenotypeRDD VariantContextRDD VariantRDD
replaceRddAndSequences
AlignmentRecordRDD
reverseComplement
Alphabet
reverseComplementExact
Alphabet
reverseReadDepth
DefaultHeaderLines VariantAnnotationField
rich
adam
richRecordToRecord
RichAlignmentRecord
rightOuterBroadcastRegionJoin
GenomicRDD
rightOuterBroadcastRegionJoinAndGroupByRight
GenomicRDD
rightOuterShuffleRegionJoin
GenomicRDD
rightOuterShuffleRegionJoinAndGroupByLeft
GenomicRDD
rmsMapQ
VariantCallingAnnotationsField
rmsMapq
DefaultHeaderLines
rpSerializer
VariantContextSerializer
rps
ReferencePositionPairSerializer
runDateEpoch
RecordGroup RecordGroupMetadataField
runId
FragmentField