TagType
models
TargetOrdering
realignment
TargetSet
realignment
TargetSetSerializer
realignment
Timers
instrumentation
TrimCigar
Timers
TrimLowQualityInDriver
Timers
TrimMDTag
Timers
TrimRead
Timers
TrimReadsInDriver
Timers
TwoBitFile
util
TwoBitFileSerializer
util
TypeVal
TagType
TypeValue
TagType
table
QualityTable
Recalibrator
tag
Attribute
tagType
Attribute
taggedReads
MDTagging
tags
RichAlignmentRecord
target
FeatureField
text
SAMFileHeaderWritable
thousandGenomesAlleleCount
DatabaseVariantAnnotationField
thousandGenomesAlleleFrequency
DatabaseVariantAnnotationField
tile
IlluminaOptics
timerName
InstrumentedADAMBAMOutputFormat
InstrumentedADAMBAMOutputFormatHeaderLess
InstrumentedADAMCRAMOutputFormat
InstrumentedADAMCRAMOutputFormatHeaderLess
InstrumentedADAMSAMOutputFormat
InstrumentedADAMSAMOutputFormatHeaderLess
toADAMContig
SequenceRecord
toCSV
Covariate
CovariateSpace
DinucCovariate
Observation
ObservationTable
toChar
QualityScore
toCoverage
FeatureRDD
AlignmentRecordRDD
toDatabaseVariantAnnotationRDD
VariantContextRDD
toFeature
Coverage
toFeatureRDD
CoverageRDD
toFragment
SingleReadBucket
toFragments
AlignmentRecordRDD
toGenotypeRDD
VariantContextRDD
toMetadata
RecordGroup
toReads
NucleotideContigFragmentRDD
FragmentRDD
toSAMProgramRecord
ProgramRecord
toSAMReadGroupRecord
RecordGroup
toSAMSequenceDictionary
SequenceDictionary
toSAMSequenceRecord
SequenceRecord
toSamples
RecordGroupDictionary
toString
Attribute
NonoverlappingRegions
RecordGroupDictionary
SequenceDictionary
SequenceRecord
TypeVal
GenomicPositionPartitioner
IndelRealignmentTarget
CovariateKey
Observation
ObservationTable
MdTag
QualityScore
toVariantContextRDD
GenotypeRDD
toVariantRDD
VariantContextRDD
total
DuplicateMetrics
FlagStatMetrics
Observation
totalLength
GenomicPositionPartitioner
transcriptId
FeatureField
transform
GenomicRDD