ILLUMINA_READNAME_REGEX
RichAlignmentRecord
INFO_KEYS
VariantAnnotationConverter
INT_SIZE
TwoBitFile
IlluminaOptics
rich
ImplicitJavaConversions
util
IncorrectMDTagException
read
IndelRealignmentTarget
realignment
IndelTable
models
IndexedBamInputFormat
samtools
InputStreamWithDecoder
serialization
InstrumentedADAMAvroParquetOutputFormat
rdd
InstrumentedADAMBAMOutputFormat
read
InstrumentedADAMBAMOutputFormatHeaderLess
read
InstrumentedADAMSAMOutputFormat
read
InstrumentedADAMSAMOutputFormatHeaderLess
read
Integer
TagType
InterleavedFastqInputFormat
io
Interval
models
IntervalListParser
features
IntervalListReader
util
i
FlagStat
id
Gene ProgramRecord Transcript
illuminaOptics
RichAlignmentRecord
in
AvroSerializer
inbreedingCoefficient
VariantCallingAnnotationsField
incorrectMDTags
MDTagging
indelTable
ConsensusGeneratorFromKnowns
index
Consensus
indexRecordStart
TwoBitFile
infoHeaderLines
VariantAnnotationConverter
initialize
BAMFilteredRecordReader
input
BaseQualityRecalibration
insertIntoReference
Consensus
instrumentation
adam
intListToJavaIntegerList
ADAMContext ImplicitJavaConversions
intersection
ReferenceRegion
invert
GenomeBins
io
adam
isAdjacent
ReferenceRegion
isCalled
RichGenotype
isCompatibleWith
SequenceDictionary
isDeletion
RichVariant
isEmpty
IndelRealignmentTarget
isHet
RichGenotype
isHom
RichGenotype
isHomAlt
RichGenotype
isHomRef
RichGenotype
isInitialized
BAMFilteredRecordReader
isInsertion
RichVariant
isMasked
SnpTable
isMatch
MdTag
isMismatchAtReadOffset
RichAlignmentRecord
isMismatchAtReferencePosition
RichAlignmentRecord
isMultipleNucleotideVariant
RichVariant
isNoCall
RichGenotype
isPhased
GenotypeField
isSameContig
Util
isSingleNucleotideVariant
RichVariant
isWellFormed
RichCigar
iterableToJavaCollection
ADAMContext