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
RichAlignmentRecord
target
FeatureField Feature
targetsToAdd
ConsensusGenerator
thousandGenomes
DefaultHeaderLines VariantAnnotationField VariantAnnotation
timerName
InstrumentedADAMBAMOutputFormat InstrumentedADAMBAMOutputFormatHeaderLess InstrumentedADAMCRAMOutputFormat InstrumentedADAMCRAMOutputFormatHeaderLess InstrumentedADAMSAMOutputFormat InstrumentedADAMSAMOutputFormatHeaderLess
toADAMContig
SequenceRecord
toAvro
AlignmentRecord Contig Dbxref Feature Fragment Genotype NucleotideContigFragment OntologyTerm ProcessingStep TranscriptEffect Variant VariantAnnotation VariantCallingAnnotations
toCoverage
DatasetBoundFeatureRDD FeatureRDD ParquetUnboundFeatureRDD RDDBoundFeatureRDD AlignmentRecordRDD RDDBoundAlignmentRecordRDD
toDF
GenomicDataset
toEnd
ReferenceRegion
toFeature
Coverage
toFeatures
CoverageRDD DatasetBoundCoverageRDD ParquetUnboundCoverageRDD RDDBoundCoverageRDD
toFragments
AlignmentRecordRDD
toGenotypes
VariantContextRDD
toMetadata
RecordGroup
toModel
VariantContext
toPredicate
ReferenceRegion
toReads
NucleotideContigFragmentRDD FragmentRDD
toSAMReadGroupRecord
RecordGroup
toSAMSequenceDictionary
SequenceDictionary
toSAMSequenceRecord
SequenceRecord
toSamples
RecordGroupDictionary
toSqlFeature
Coverage
toString
Attribute MdTag RecordGroupDictionary SequenceDictionary SequenceRecord TypeVal AvroRecordGroupGenomicDataset GenomicDataset GenomicPositionPartitioner MultisampleGenomicDataset ReferenceContigMap
toVariantContexts
GenotypeRDD VariantRDD
toVariants
GenotypeRDD VariantContextRDD
total
TranscriptEffectField TranscriptEffect
totalLength
SliceField
transcriptEffects
DefaultHeaderLines VariantAnnotationField VariantAnnotation
transcriptHgvs
TranscriptEffectField TranscriptEffect
transcriptId
FeatureField Feature
transform
GenomicDataset
transformDataFrame
GenomicDataset
transformDataset
DatasetBoundGenericGenomicDataset GenomicDataset RDDBoundGenericGenomicDataset NucleotideContigFragmentRDD CoverageRDD DatasetBoundFeatureRDD FeatureRDD DatasetBoundFragmentRDD FragmentRDD AlignmentRecordRDD DatasetBoundAlignmentRecordRDD DatasetBoundGenotypeRDD DatasetBoundVariantContextRDD DatasetBoundVariantRDD GenotypeRDD VariantContextRDD VariantRDD
transmute
GenomicDataset
transmuteDataFrame
GenomicDataset
transmuteDataset
GenomicDataset