FASTAInFormatter
sequence
FASTA_LINE_WIDTH
SequenceDataset
FASTQInFormatter
read
FastqInputFormat
io
FastqRecordReader
io
Feature
sql
FeatureDataset
feature
FeatureField
projections
FieldEnumeration
projections
FieldValue
projections
FileExtensions
util
Filter
projections
Float
TagType
Fragment
sql
FragmentDataset
fragment
FragmentField
projections
FullOuterShuffleRegionJoin
rdd
failedVendorQualityChecks
AlignmentField Alignment
feature
rdd
featureHeaders
ADAMShell
featureId
FeatureField TranscriptEffectField Feature TranscriptEffect
featureType
FeatureField TranscriptEffectField Feature TranscriptEffect
featuresToAlignmentsConversionFn
ADAMContext
featuresToAlignmentsDatasetConversionFn
ADAMContext
featuresToCoverageConversionFn
ADAMContext
featuresToCoverageDatasetConversionFn
ADAMContext
featuresToFeaturesConversionFn
ADAMContext
featuresToFragmentsConversionFn
ADAMContext
featuresToFragmentsDatasetConversionFn
ADAMContext
featuresToGenotypesConversionFn
ADAMContext
featuresToGenotypesDatasetConversionFn
ADAMContext
featuresToReadsConversionFn
ADAMContext
featuresToReadsDatasetConversionFn
ADAMContext
featuresToSequencesConversionFn
ADAMContext
featuresToSequencesDatasetConversionFn
ADAMContext
featuresToSlicesConversionFn
ADAMContext
featuresToSlicesDatasetConversionFn
ADAMContext
featuresToVariantContextConversionFn
ADAMContext
featuresToVariantsConversionFn
ADAMContext
featuresToVariantsDatasetConversionFn
ADAMContext
filePath
IndexedFastaFile
filterByAlternateReadDepth
DatasetBoundGenotypeDataset GenotypeDataset
filterByAttribute
DatasetBoundFeatureDataset FeatureDataset
filterByMappingQuality
AlignmentDataset DatasetBoundAlignmentDataset
filterByOverlappingRegion
GenomicDataset
filterByOverlappingRegions
DatasetBoundGenomicDataset GenomicDataset
filterByQuality
DatasetBoundGenotypeDataset DatasetBoundVariantDataset GenotypeDataset VariantDataset
filterByReadDepth
DatasetBoundGenotypeDataset DatasetBoundVariantDataset GenotypeDataset VariantDataset
filterByReferenceReadDepth
DatasetBoundGenotypeDataset DatasetBoundVariantDataset GenotypeDataset VariantDataset
filterByScore
DatasetBoundFeatureDataset FeatureDataset
filterDuplicateReads
AlignmentDataset DatasetBoundAlignmentDataset
filterIndels
DatasetBoundVariantDataset VariantDataset
filterMultipleNucleotideVariants
DatasetBoundVariantDataset VariantDataset
filterNoCalls
DatasetBoundGenotypeDataset GenotypeDataset
filterSingleNucleotideVariants
DatasetBoundVariantDataset VariantDataset
filterToExon
DatasetBoundFeatureDataset FeatureDataset
filterToExons
DatasetBoundFeatureDataset FeatureDataset
filterToFeatureType
DatasetBoundFeatureDataset FeatureDataset
filterToFeatureTypes
DatasetBoundFeatureDataset FeatureDataset
filterToFiltersPassed
DatasetBoundGenotypeDataset DatasetBoundVariantDataset GenotypeDataset VariantDataset
filterToGene
DatasetBoundFeatureDataset FeatureDataset
filterToGenes
DatasetBoundFeatureDataset FeatureDataset
filterToIndels
DatasetBoundVariantDataset VariantDataset
filterToMultipleNucleotideVariants
DatasetBoundVariantDataset VariantDataset
filterToParent
DatasetBoundFeatureDataset FeatureDataset
filterToParents
DatasetBoundFeatureDataset FeatureDataset
filterToPrimaryAlignments
AlignmentDataset DatasetBoundAlignmentDataset
filterToReadGroup
AlignmentDataset DatasetBoundAlignmentDataset
filterToReadGroups
AlignmentDataset DatasetBoundAlignmentDataset
filterToReferenceName
SequenceDictionary
filterToReferenceNames
SequenceDictionary
filterToSample
AlignmentDataset DatasetBoundAlignmentDataset DatasetBoundGenotypeDataset GenotypeDataset
filterToSamples
AlignmentDataset DatasetBoundAlignmentDataset DatasetBoundGenotypeDataset GenotypeDataset
filterToSingleNucleotideVariants
DatasetBoundVariantDataset VariantDataset
filterToTranscript
DatasetBoundFeatureDataset FeatureDataset
filterToTranscripts
DatasetBoundFeatureDataset FeatureDataset
filterUnalignedReads
AlignmentDataset DatasetBoundAlignmentDataset
filterUnpairedReads
AlignmentDataset DatasetBoundAlignmentDataset
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
RichAlignment
fivePrimeReferencePosition
RichAlignment
flagStat
AlignmentDataset
flankAdjacent
SliceDataset
flatten
CoverageDataset
flattenRddByRegions
GenomicDataset
flowOrder
ReadGroup ReadGroupField
foreach
ParquetFileTraversable
formatHeaderLines
DefaultHeaderLines
formatReadDepth
DefaultHeaderLines
forwardReadDepth
DefaultHeaderLines VariantAnnotationField VariantAnnotation
fragment
rdd
fragmentsToAlignmentsConversionFn
ADAMContext
fragmentsToAlignmentsDatasetConversionFn
ADAMContext
fragmentsToCoverageConversionFn
ADAMContext
fragmentsToCoverageDatasetConversionFn
ADAMContext
fragmentsToFeaturesConversionFn
ADAMContext
fragmentsToFeaturesDatasetConversionFn
ADAMContext
fragmentsToFragmentsConversionFn
ADAMContext
fragmentsToGenotypesConversionFn
ADAMContext
fragmentsToGenotypesDatasetConversionFn
ADAMContext
fragmentsToReadsConversionFn
ADAMContext
fragmentsToReadsDatasetConversionFn
ADAMContext
fragmentsToSequencesConversionFn
ADAMContext
fragmentsToSequencesDatasetConversionFn
ADAMContext
fragmentsToSlicesConversionFn
ADAMContext
fragmentsToSlicesDatasetConversionFn
ADAMContext
fragmentsToVariantContextConversionFn
ADAMContext
fragmentsToVariantsConversionFn
ADAMContext
fragmentsToVariantsDatasetConversionFn
ADAMContext
frame
FeatureField Feature
fromADAMReference
SequenceRecord
fromAvro
ReadGroup SequenceDictionary Alignment Dbxref Feature Fragment Genotype OntologyTerm ProcessingStep Read Reference Sequence Slice TranscriptEffect Variant VariantAnnotation VariantCallingAnnotations
fromGenomicRange
ReferenceRegion
fromKnownIndels
ConsensusGenerator
fromModel
VariantContext
fromReads
ConsensusGenerator
fromReadsWithSmithWaterman
ConsensusGenerator
fromSAMHeader
ReadGroupDictionary
fromSAMSequenceDictionary
SequenceDictionary
fromSAMSequenceRecord
SequenceRecord
fromSequence
SequenceRecord
fromSlice
SequenceRecord
fromStart
ReferenceRegion
fromString
ReferenceRegion
fromVCFHeader
SequenceDictionary
fullOuterShuffleRegionJoin
GenomicDataset