FILE_INDEX_OFFSET
TwoBitFile
FORMAT_KEYS
VariantAnnotationConverter
FastqRecordConverter
converters
FeatureField
projections
FeatureFile
features
FeatureParser
features
FeatureReferenceMapping
ReferenceMappingContext
FieldCondition
predicates
FieldEnumeration
projections
FieldValue
projections
Filter
projections
FindTargets
Timers
FlagStat
read
FlagStatMetrics
read
Float
TagType
FragmentConverter
converters
failedQuality
FlagStatMetrics
failedVendorQualityChecks
AlignmentRecordField
feature
BEDFeature BaseFeature GTFFeature NarrowPeakFeature
featureId
FeatureField
featureType
FeatureField
features
rdd
fieldName
FieldCondition
filter
ParsedFilter FieldCondition RecordCondition MultiContigNonoverlappingRegions
filterByOverlappingRegion
AlignmentRecordRDDFunctions GenotypeRDDFunctions
filterStringRegex
BucketComparisons
filters
metrics CombinedFilter
find
ComparisonTraversalEngine RegExp
findComparison
DefaultComparisons
findConsensus
ConsensusGenerator ConsensusGeneratorFromKnowns ConsensusGeneratorFromReads
findCoverageRegions
Coverage
findFiles
ADAMContext
findOverlappingRegions
NonoverlappingRegions
findTargets
RealignmentTargetFinder
firstOfPair
AlignmentRecordField
fivePrime
ReferencePosition ReferencePositionWithOrientation
fivePrimePosition
RichAlignmentRecord
flowOrder
RecordGroup
foreach
IntervalListReader ParquetFileTraversable PileupTraversable
formatHeaderLines
VariantAnnotationConverter
format_csv
GenotypesSummaryFormatting
format_human_readable
GenotypesSummaryFormatting
fragmentNumber
NucleotideContigFragmentField
fragmentSequence
NucleotideContigFragmentField
fragmentStartPosition
NucleotideContigFragmentField
frameChar
BaseFeature
fromADAMContig
SequenceRecord
fromADAMContigFragment
SequenceRecord
fromADAMRecord
SequenceRecord
fromErrorProbability
QualityScore
fromSAMHeader
RecordGroupDictionary SequenceDictionary
fromSAMReader
RecordGroupDictionary SequenceDictionary
fromSAMSequenceDictionary
SequenceDictionary
fromSAMSequenceRecord
SequenceRecord
fromSpecificRecord
SequenceRecord