ILLUMINA_READNAME_REGEX
RichADAMRecord
INFO_KEYS
VariantAnnotationConverter
IlluminaOptics
rich
ImplicitJavaConversions
util
IndelRange
realignmenttarget
IndelRangeSerializer
realignmenttarget
IndelRealignmentTarget
realignmenttarget
InequalityFilter
BucketComparisons
InputStreamWithDecoder
serialization
InsertionEvent
util
Integer
TagType
InterleavedFastqInputFormat
io
IntervalListReader
util
id
VCFLine
illuminaOptics
RichADAMRecord
in
AvroSerializer
inbreedingCoefficient
VariantCallingAnnotationsField
indelRange
IndelRange
indelSet
IndelRealignmentTarget
index
Consensus
info
VCFLine
infoHeaderLines
VariantAnnotationConverter
initialValue
Aggregator
CombinedAggregator
HistogramAggregator
UniqueAggregator
input
BaseQualityRecalibration
insertIntoReference
Consensus
insertedSequence
InsertionEvent
insertionCount
GenotypesSummaryCounts
insertions
Pileup
intListToJavaIntegerList
ADAMContext
ImplicitJavaConversions
io
adam
isAdjacent
ReferenceRegion
isAligned
DecadentRead
isCanonicalRecord
DecadentRead
isCompatibleWith
SequenceDictionary
isDeletion
RichADAMVariant
isDirectory
HadoopUtil
isDuplicate
DecadentRead
isEmpty
IndelRealignmentTarget
isFalse
PredicateUtils
isFirstOfPair
DecadentRead
isHighQuality
ADAMRecordConditions
isInsertion
Residue
RichADAMVariant
isMapped
ADAMRecordConditions
isMasked
SnpTable
isMatch
MdTag
isMismatch
Residue
isMismatchAtReadOffset
RichADAMRecord
isMismatchAtReferencePosition
RichADAMRecord
isMultipleNucleotideVariant
RichADAMVariant
isNegativeRead
DecadentRead
isPaired
DecadentRead
isPassing
ADAMGenotypeConditions
isPhased
ADAMGenotypeField
isPrimaryAlignment
ADAMRecordConditions
DecadentRead
isRegularBase
Residue
isReverseStrand
MatchEvent
MismatchEvent
isSNP
Residue
isSameContig
Util
isSecondOfPair
DecadentRead
isSingleNucleotideVariant
RichADAMVariant
isSingleSample
ADAMRod
isSplitable
InterleavedFastqInputFormat
isTrue
PredicateUtils
isUnique
ADAMRecordConditions
isWellFormed
RichCigar
iterableToJavaCollection
ADAMContext