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