ILLUMINA_READNAME_REGEX
RichAlignmentRecord
INFO_KEYS
VariantAnnotationConverter
INT_SIZE
TwoBitFile
IlluminaOptics
rich
ImplicitJavaConversions
util
IndelRealignmentTarget
realignment
IndelTable
models
IndexedBamInputFormat
samtools
InputStreamWithDecoder
serialization
InstrumentedADAMAvroParquetOutputFormat
rdd
InstrumentedADAMBAMOutputFormat
read
InstrumentedADAMSAMOutputFormat
read
Integer
TagType
InterleavedFastqInputFormat
io
Interval
models
IntervalListParser
features
IntervalListReader
util
id
Gene ProgramRecord Transcript
illuminaOptics
RichAlignmentRecord
in
AvroSerializer
inbreedingCoefficient
VariantCallingAnnotationsField
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
isAligned
DecadentRead
isCanonicalRecord
DecadentRead
isCompatibleWith
SequenceDictionary
isDeletion
RichVariant
isDuplicate
DecadentRead
isEmpty
IndelRealignmentTarget
isFirstOfPair
DecadentRead
isInitialized
BAMFilteredRecordReader
isInsertion
Residue RichVariant
isMasked
SnpTable
isMatch
MdTag
isMismatch
Residue
isMismatchAtReadOffset
RichAlignmentRecord
isMismatchAtReferencePosition
RichAlignmentRecord
isMultipleNucleotideVariant
RichVariant
isNegativeRead
DecadentRead
isPaired
DecadentRead
isPhased
GenotypeField
isPrimaryAlignment
DecadentRead
isRegularBase
Residue
isSNP
Residue
isSameContig
Util
isSecondOfPair
DecadentRead
isSingleNucleotideVariant
RichVariant
isWellFormed
RichCigar
iterableToJavaCollection
ADAMContext