Character
TagType
ComputeCovariates
Timers
ComputeQualityScore
Timers
ContigField
projections
ConvertToSAM
Timers
ConvertToSAMRecord
Timers
Coverage
models
CoverageRDD
feature
CreateIndelRealignmentTargets
Timers
CreateKnownSnpsTable
Timers
CreateReferencePositionPair
Timers
canEqual
MdTag
caseSensitive
Alphabet
DNAAlphabet
cdnaLength
TranscriptEffectField
cdnaPosition
TranscriptEffectField
cdsLength
TranscriptEffectField
cdsPosition
TranscriptEffectField
cigar
AlignmentRecordField
VariantAnnotationField
cigarX
SmithWaterman
cigarY
SmithWaterman
circular
FeatureField
collapse
CoverageRDD
companion
InFormatter
compare
OptionalReferenceOrdering
ReferenceOrdering
compareTo
ReferenceRegion
complement
Symbol
computeExtrasTables
RecalibrationTable
computeMismatchingPositions
AlignmentRecordRDD
computeQualityTable
RecalibrationTable
contains
ReferenceRegion
SnpTable
containsRefName
SequenceDictionary
contig
NucleotideContigFragmentField
rdd
contigLength
ContigField
contigLengths
SequenceDictionary
contigMD5
ContigField
contigMap
ReferenceContigMap
contigName
Coverage
AlignmentRecordField
ContigField
FeatureField
GenotypeField
VariantField
convert
AlignmentRecordConverter
convertFragment
AlignmentRecordConverter
convertSAMTagAndValue
AttributeUtils
convertToFastq
AlignmentRecordConverter
convertToSam
AlignmentRecordRDD
converter
AnySAMInFormatter
converters
adam
count
Coverage
countKmers
NucleotideContigFragmentRDD
AlignmentRecordRDD
countOfMismatches
MdTag
coverage
CoverageRDD
createRecordReader
InterleavedFastqInputFormat
SingleFastqInputFormat
createSAMHeader
AlignmentRecordConverter
culprit
VariantCallingAnnotationsField