ILLUMINA_READNAME_REGEX
RichAlignmentRecord
INT_SIZE
TwoBitFile
IlluminaOptics
rich
ImplicitJavaConversions
util
InFormatter
rdd
InFormatterCompanion
rdd
IncorrectMDTagException
read
IndelRealignmentTarget
realignment
IndelRealignmentTargetSerializer
realignment
InnerBroadcastRegionJoin
rdd
InnerShuffleRegionJoin
rdd
InnerShuffleRegionJoinAndGroupByLeft
rdd
InputStreamWithDecoder
serialization
InstrumentedADAMBAMOutputFormat
read
InstrumentedADAMBAMOutputFormatHeaderLess
read
InstrumentedADAMCRAMOutputFormat
read
InstrumentedADAMCRAMOutputFormatHeaderLess
read
InstrumentedADAMSAMOutputFormat
read
InstrumentedADAMSAMOutputFormatHeaderLess
read
Integer
TagType
InterleavedFASTQInFormatter
fragment
InterleavedFastqInputFormat
io
IntervalListReader
util
i
FlagStat
id
ProgramRecord
illuminaOptics
RichAlignmentRecord
in
AvroSerializer
inbreedingCoefficient
VariantCallingAnnotationsField
incorrectMDTags
MDTagging
indexRecordStart
TwoBitFile
input
BaseQualityRecalibration
instrumentation
adam
intListToJavaIntegerList
ImplicitJavaConversions
intersection
ReferenceRegion
invert
GenomeBins
io
adam
irts
TargetSetSerializer ZippedTargetSetSerializer
isAdjacent
ReferenceRegion
isCalled
RichGenotype
isCircular
FeatureField
isCompatibleWith
SequenceDictionary
isDeletion
RichVariant
isEmpty
SequenceDictionary IndelRealignmentTarget
isHet
RichGenotype
isHom
RichGenotype
isHomAlt
RichGenotype
isHomRef
RichGenotype
isInsertion
RichVariant
isMasked
SnpTable
isMatch
MdTag
isMismatchAtReadOffset
RichAlignmentRecord
isMismatchAtReferencePosition
RichAlignmentRecord
isMultipleNucleotideVariant
RichVariant
isNoCall
RichGenotype
isPhased
GenotypeField
isSameContig
Util
isSingleNucleotideVariant
RichVariant
isWellFormed
RichCigar