Character
TagType
ComputeCovariates
Timers
ComputeQualityScore
Timers
ConvertToSAM
Timers
ConvertToSAMRecord
Timers
Covariate
recalibration
CovariateKey
recalibration
CovariateSpace
recalibration
Coverage
models
CoverageRDD
features
CreateIndelRealignmentTargets
Timers
CreateKnownSnpsTable
Timers
CreateReferencePositionPair
Timers
CycleCovariate
recalibration
canEqual
MdTag
caseSensitive
Alphabet DNAAlphabet
cigar
AlignmentRecordField
cigarElement
ReferenceSequenceContext
cigarElementOffset
ReferenceSequenceContext
cigarPattern
RichAlignmentRecord
cigarToRichCigar
RichCigar
cigarX
SmithWaterman
cigarY
SmithWaterman
clinicalSignificance
DatabaseVariantAnnotationField
clinvarId
DatabaseVariantAnnotationField
clippingRankSum
VariantCallingAnnotationsField
collapse
CoverageRDD
commandLine
ProgramRecord
comments
SAMFileHeaderWritable
companion
InFormatter InterleavedFASTQInFormatter BAMInFormatter SAMInFormatter VCFInFormatter
compare
OptionalReferenceOrdering ReferenceOrdering SequenceOrderingByName SequenceOrderingByRefIdx TargetOrdering ZippedTargetOrdering QualityScore
compareTo
ReferenceRegion
complement
Symbol
compute
Covariate CycleCovariate DinucCovariate
computeExtrasDelta
RecalibrationTable
computeExtrasTables
RecalibrationTable
computeGlobalDelta
RecalibrationTable
computeQual
Recalibrator
computeQualityDelta
RecalibrationTable
computeQualityTable
RecalibrationTable
contains
ReferenceRegion SnpTable TargetOrdering
containsNone
CovariateKey
containsRefName
SequenceDictionary
contig
NucleotideContigFragmentField VariantField rdd
contigMap
ReferenceContigMap
contigName
Coverage AlignmentRecordField FeatureField GenotypeField
convert
AlignmentRecordConverter
convertFragment
AlignmentRecordConverter
convertSAMTagAndValue
AttributeUtils
convertToFastq
AlignmentRecordConverter
convertToSam
AlignmentRecordRDD
converter
AnySAMInFormatter BAMInFormatter SAMInFormatter VCFInFormatter
converters
adam
cosmicId
DatabaseVariantAnnotationField
count
Coverage
countKmers
NucleotideContigFragmentRDD AlignmentRecordRDD
countOfMismatches
MdTag
covariates
BaseQualityRecalibration RecalibrationTable
coverage
CoverageRDD
createRecordReader
InterleavedFastqInputFormat SingleFastqInputFormat
createSAMHeader
AlignmentRecordConverter
createVariantAnnotation
VariantAnnotations
crossChromosome
DuplicateMetrics
csvFieldName
Covariate CycleCovariate DinucCovariate
csvHeader
CovariateSpace ObservationTable
culprit
VariantCallingAnnotationsField
cumulativeLengths
GenomicPositionPartitioner