TagType
models
TargetOrdering
realignment
TargetSet
realignment
TargetSetSerializer
realignment
Timers
instrumentation
Transcript
models
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
targetsToAdd
ConsensusGenerator
ConsensusGeneratorFromKnowns
ConsensusGeneratorFromReads
text
SAMFileHeaderWritable
thousandGenomesAlleleCount
DatabaseVariantAnnotationField
thousandGenomesAlleleFrequency
DatabaseVariantAnnotationField
tile
IlluminaOptics
timerName
InstrumentedADAMAvroParquetOutputFormat
InstrumentedADAMBAMOutputFormat
InstrumentedADAMSAMOutputFormat
toADAMContig
SequenceRecord
toCSV
Covariate
CovariateSpace
DinucCovariate
Observation
ObservationTable
toChar
QualityScore
toFragment
SingleReadBucket
toFragments
AlignmentRecordRDDFunctions
toReads
NucleotideContigFragmentRDDFunctions
FragmentRDDFunctions
toSAMProgramRecord
ProgramRecord
toSAMReadGroupRecord
RecordGroup
toSAMSequenceDictionary
SequenceDictionary
toSAMSequenceRecord
SequenceRecord
toString
Attribute
Consensus
NonoverlappingRegions
SequenceDictionary
SequenceRecord
TypeVal
GenomicPositionPartitioner
IndelRealignmentTarget
CovariateKey
Observation
ObservationTable
MdTag
QualityScore
toVariantContext
GenotypeRDDFunctions
total
DuplicateMetrics
FlagStatMetrics
Observation
totalLength
GenomicPositionPartitioner
transcriptId
CDS
Exon
UTR
transcripts
Gene