ILLUMINA_READNAME_REGEX
RichADAMRecord
IlluminaOptics
rich
ImplicitJavaConversions
util
IndelRange
realignmenttarget
IndelRangeSerializer
realignmenttarget
IndelRealignmentTarget
realignmenttarget
InequalityFilter
BucketComparisons
InputStreamWithDecoder
serialization
InsertionEvent
util
Integer
TagType
InterleavedFastqInputFormat
io
IntervalListReader
util
id
SequenceRecord
ids
GenomicRegionPartitioner
illuminaOptics
RichADAMRecord
in
AvroSerializer
inbreedingCoefficient
VariantCallingAnnotationsField
indelRange
IndelRange
indelSet
IndelRealignmentTarget
index
Consensus
infoHeaderLines
VariantAnnotationConverter
initialValue
Aggregator
CombinedAggregator
HistogramAggregator
UniqueAggregator
insertIntoReference
Consensus
insertedSequence
InsertionEvent
insertionCount
GenotypesSummaryCounts
insertions
Pileup
intListToJavaIntegerList
ADAMContext
ImplicitJavaConversions
io
adam
isAdjacent
ReferenceRegion
isAligned
DecadentRead
isCanonicalRecord
DecadentRead
isCompatibleWith
SequenceDictionary
isDeletion
RichADAMVariant
isDuplicate
DecadentRead
isEmpty
IndelRealignmentTarget
isInsertion
Residue
RichADAMVariant
isMasked
SnpTable
isMatch
MdTag
isMismatch
Residue
isMismatchAtReadOffset
RichADAMRecord
isMismatchAtReferencePosition
RichADAMRecord
isMultipleNucleotideVariant
RichADAMVariant
isNegativeRead
DecadentRead
isPhased
ADAMGenotypeField
isPrimaryAlignment
DecadentRead
isRegularBase
Residue
isReverseStrand
MatchEvent
MismatchEvent
isSNP
Residue
isSingleNucleotideVariant
RichADAMVariant
isSingleSample
ADAMRod
isSplitable
InterleavedFastqInputFormat
isWellFormed
RichCigar
iterableToJavaCollection
ADAMContext