Tab5InFormatter
fragment
Tab6InFormatter
fragment
TagType
models
TextRddWriter
util
Timers
instrumentation
TranscriptEffect
sql
TranscriptEffectField
projections
TreeJoin
Timers
TreeRegionJoin
rdd
TrimCigar
Timers
TrimLowQualityInDriver
Timers
TrimMDTag
Timers
TrimRead
Timers
TrimReadsInDriver
Timers
TwoBitFile
util
TwoBitFileSerializer
util
TypeVal
TagType
tTag
DatasetBoundGenericGenomicDataset
RDDBoundGenericGenomicDataset
tag
Attribute
tagHolder
DatasetBoundGenericGenomicDataset
RDDBoundGenericGenomicDataset
tagType
Attribute
tags
RichAlignment
target
FeatureField
Feature
targetsToAdd
ConsensusGenerator
thousandGenomes
DefaultHeaderLines
VariantAnnotationField
VariantAnnotation
timerName
InstrumentedADAMBAMOutputFormat
InstrumentedADAMBAMOutputFormatHeaderLess
InstrumentedADAMCRAMOutputFormat
InstrumentedADAMCRAMOutputFormatHeaderLess
InstrumentedADAMSAMOutputFormat
InstrumentedADAMSAMOutputFormatHeaderLess
toADAMReference
SequenceRecord
toAlignments
DatasetBoundFragmentDataset
FragmentDataset
ReadDataset
toAvro
Alignment
Dbxref
Feature
Fragment
Genotype
OntologyTerm
ProcessingStep
Read
Reference
Sequence
Slice
TranscriptEffect
Variant
VariantAnnotation
VariantCallingAnnotations
toCoverage
DatasetBoundFeatureDataset
FeatureDataset
ParquetUnboundFeatureDataset
RDDBoundFeatureDataset
AlignmentDataset
RDDBoundAlignmentDataset
toDF
GenomicDataset
toEnd
ReferenceRegion
toFeature
Coverage
toFeatures
CoverageDataset
DatasetBoundCoverageDataset
ParquetUnboundCoverageDataset
RDDBoundCoverageDataset
toFragments
AlignmentDataset
toGenotypes
VariantContextDataset
toMetadata
ReadGroup
toModel
VariantContext
toPredicate
ReferenceRegion
toReads
AlignmentDataset
SequenceDataset
SliceDataset
toSAMReadGroupRecord
ReadGroup
toSAMSequenceDictionary
SequenceDictionary
toSAMSequenceRecord
SequenceRecord
toSamples
ReadGroupDictionary
toSequences
ReadDataset
SliceDataset
toSlices
ReadDataset
SequenceDataset
toSqlFeature
Coverage
toString
Attribute
MdTag
ReadGroupDictionary
SequenceDictionary
SequenceRecord
TypeVal
AvroReadGroupGenomicDataset
GenomicDataset
GenomicPositionPartitioner
MultisampleGenomicDataset
ReferenceContigMap
toVariantContexts
GenotypeDataset
VariantDataset
toVariants
GenotypeDataset
VariantContextDataset
total
TranscriptEffectField
TranscriptEffect
totalLength
SliceField
Slice
transcriptEffects
DefaultHeaderLines
VariantAnnotationField
VariantAnnotation
transcriptHgvs
TranscriptEffectField
TranscriptEffect
transcriptId
FeatureField
Feature
transform
GenomicDataset
transformDataFrame
GenomicDataset
transformDataset
DatasetBoundGenericGenomicDataset
GenomicDataset
RDDBoundGenericGenomicDataset
CoverageDataset
DatasetBoundFeatureDataset
FeatureDataset
DatasetBoundFragmentDataset
FragmentDataset
AlignmentDataset
DatasetBoundAlignmentDataset
DatasetBoundReadDataset
ReadDataset
DatasetBoundSequenceDataset
DatasetBoundSliceDataset
SequenceDataset
SliceDataset
DatasetBoundGenotypeDataset
DatasetBoundVariantContextDataset
DatasetBoundVariantDataset
GenotypeDataset
VariantContextDataset
VariantDataset
transmute
GenomicDataset
transmuteDataFrame
GenomicDataset
transmuteDataset
GenomicDataset