ILLUMINA_READNAME_REGEX
RichAlignmentRecord
INFO_KEYS
VariantAnnotationConverter
INT_SIZE
TwoBitFile
IlluminaOptics
rich
ImplicitJavaConversions
util
IndelRealignmentTarget
realignment
IndelTable
models
InequalityFilter
BucketComparisons
InputStreamWithDecoder
serialization
InsertionEvent
util
InstrumentedADAMAvroParquetOutputFormat
rdd
InstrumentedADAMBAMOutputFormat
read
InstrumentedADAMSAMOutputFormat
read
Integer
TagType
InterleavedFastqInputFormat
io
Interval
models
IntervalListReader
util
id
Gene
ProgramRecord
Transcript
illuminaOptics
RichAlignmentRecord
in
AvroSerializer
inbreedingCoefficient
VariantCallingAnnotationsField
indelTable
ConsensusGeneratorFromKnowns
index
Consensus
indexRecordStart
TwoBitFile
infoHeaderLines
VariantAnnotationConverter
input
BaseQualityRecalibration
insertIntoReference
Consensus
insertedSequence
InsertionEvent
insertionCount
GenotypesSummaryCounts
insertions
Pileup
instrumentation
adam
intListToJavaIntegerList
ADAMContext
ImplicitJavaConversions
intersection
ReferenceRegion
invert
GenomeBins
io
adam
isAdjacent
ReferenceRegion
isAligned
DecadentRead
isCanonicalRecord
DecadentRead
isCompatibleWith
SequenceDictionary
isDeletion
RichVariant
isDirectory
HadoopUtil
isDuplicate
DecadentRead
isEmpty
IndelRealignmentTarget
isFirstOfPair
DecadentRead
isHighQuality
AlignmentRecordConditions
isInsertion
Residue
RichVariant
isMapped
AlignmentRecordConditions
isMasked
SnpTable
isMatch
MdTag
isMismatch
Residue
isMismatchAtReadOffset
RichAlignmentRecord
isMismatchAtReferencePosition
RichAlignmentRecord
isMultipleNucleotideVariant
RichVariant
isNegativeRead
DecadentRead
isPaired
DecadentRead
isPassing
GenotypeConditions
isPhased
GenotypeField
isPrimaryAlignment
AlignmentRecordConditions
DecadentRead
isRegularBase
Residue
isReverseStrand
MatchEvent
MismatchEvent
isSNP
Residue
isSameContig
Util
isSecondOfPair
DecadentRead
isSingleNucleotideVariant
RichVariant
isSingleSample
Rod
isUnique
AlignmentRecordConditions
isWellFormed
RichCigar
iterableToJavaCollection
ADAMContext