FASTQInFormatter
read
FastqInputFormat
io
Feature
sql
FeatureField
projections
FeatureRDD
feature
FieldEnumeration
projections
FieldValue
projections
FileExtensions
util
Filter
projections
FinalizingRealignments
Timers
FindTargets
Timers
Float
TagType
Fragment
sql
FragmentField
projections
FragmentRDD
fragment
FullOuterShuffleJoin
Timers
FullOuterShuffleRegionJoin
rdd
failedVendorQualityChecks
AlignmentRecordField AlignmentRecord
feature
rdd
featureId
FeatureField TranscriptEffectField Feature TranscriptEffect
featureType
FeatureField TranscriptEffectField Feature TranscriptEffect
featuresToAlignmentRecordsConversionFn
ADAMContext
featuresToAlignmentRecordsDatasetConversionFn
ADAMContext
featuresToContigsConversionFn
ADAMContext
featuresToContigsDatasetConversionFn
ADAMContext
featuresToCoverageConversionFn
ADAMContext
featuresToCoverageDatasetConversionFn
ADAMContext
featuresToFeaturesConversionFn
ADAMContext
featuresToFragmentsConversionFn
ADAMContext
featuresToFragmentsDatasetConversionFn
ADAMContext
featuresToGenotypesConversionFn
ADAMContext
featuresToGenotypesDatasetConversionFn
ADAMContext
featuresToVariantContextConversionFn
ADAMContext
featuresToVariantsConversionFn
ADAMContext
featuresToVariantsDatasetConversionFn
ADAMContext
filePath
IndexedFastaFile
filterByOverlappingRegion
GenomicDataset
filterByOverlappingRegions
DatasetBoundGenomicDataset GenomicDataset
filtersApplied
VariantCallingAnnotationsField VariantField Variant VariantCallingAnnotations
filtersFailed
VariantCallingAnnotationsField VariantField Variant VariantCallingAnnotations
filtersPassed
VariantCallingAnnotationsField VariantField Variant VariantCallingAnnotations
finalizeHits
ShuffleRegionJoin SortedIntervalPartitionJoinWithVictims VictimlessSortedIntervalPartitionJoin
findConsensus
ConsensusGenerator
fisherStrand
DefaultHeaderLines
fisherStrandBiasPValue
VariantCallingAnnotationsField VariantCallingAnnotations
fivePrimePosition
RichAlignmentRecord
fivePrimeReferencePosition
RichAlignmentRecord
flagStat
AlignmentRecordRDD
flankAdjacentFragments
NucleotideContigFragmentRDD
flatten
CoverageRDD
flattenRddByRegions
GenomicDataset
flowOrder
RecordGroup RecordGroupField
foreach
ParquetFileTraversable
formatHeaderLines
DefaultHeaderLines
formatReadDepth
DefaultHeaderLines
forwardReadDepth
DefaultHeaderLines VariantAnnotationField VariantAnnotation
fragment
rdd
fragmentSize
FragmentField Fragment
fragments
NucleotideContigFragmentField NucleotideContigFragment
fragmentsToAlignmentRecordsConversionFn
ADAMContext
fragmentsToAlignmentRecordsDatasetConversionFn
ADAMContext
fragmentsToContigsConversionFn
ADAMContext
fragmentsToContigsDatasetConversionFn
ADAMContext
fragmentsToCoverageConversionFn
ADAMContext
fragmentsToCoverageDatasetConversionFn
ADAMContext
fragmentsToFeaturesConversionFn
ADAMContext
fragmentsToFeaturesDatasetConversionFn
ADAMContext
fragmentsToFragmentsConversionFn
ADAMContext
fragmentsToGenotypesConversionFn
ADAMContext
fragmentsToGenotypesDatasetConversionFn
ADAMContext
fragmentsToVariantContextConversionFn
ADAMContext
fragmentsToVariantsConversionFn
ADAMContext
fragmentsToVariantsDatasetConversionFn
ADAMContext
frame
FeatureField Feature
fromADAMContig
SequenceRecord
fromADAMContigFragment
SequenceRecord
fromAvro
RecordGroup SequenceDictionary AlignmentRecord Contig Dbxref Feature Fragment Genotype NucleotideContigFragment OntologyTerm ProcessingStep TranscriptEffect Variant VariantAnnotation VariantCallingAnnotations
fromGenomicRange
ReferenceRegion
fromKnownIndels
ConsensusGenerator
fromModel
VariantContext
fromReads
ConsensusGenerator
fromReadsWithSmithWaterman
ConsensusGenerator
fromSAMHeader
RecordGroupDictionary
fromSAMSequenceDictionary
SequenceDictionary
fromSAMSequenceRecord
SequenceRecord
fromStart
ReferenceRegion
fromString
ReferenceRegion
fromVCFHeader
SequenceDictionary
fullOuterShuffleRegionJoin
GenomicDataset