CDS
models
CLINVAR_KEYS
VariantAnnotationConverter
COSMIC_KEYS
VariantAnnotationConverter
Character
TagType
ComputeCovariates
Timers
ComputeQualityScore
Timers
Consensus
models
ConsensusGenerator
consensus
ConsensusGeneratorFromKnowns
consensus
ConsensusGeneratorFromReads
consensus
ConsensusGeneratorFromSmithWaterman
consensus
ConvertToSAM
Timers
ConvertToSAMRecord
Timers
Covariate
recalibration
CovariateKey
recalibration
CovariateSpace
recalibration
Coverage
rdd
CreateIndelRealignmentTargets
Timers
CreateKnownSnpsTable
Timers
CreateReferencePositionPair
Timers
CycleCovariate
recalibration
calculateCoverageRegions
Coverage
canEqual
MdTag
cartesianFilter
BroadcastRegionJoin
caseSensitive
Alphabet
DNAAlphabet
cds
Transcript
chrom
OrientedPoint
cigar
AlignmentRecordField
cigarPattern
RichAlignmentRecord
cigarToRichCigar
RichCigar
cigarX
SmithWaterman
cigarY
SmithWaterman
clean
VcfStringUtils
clearHeader
ADAMBAMOutputFormat
ADAMSAMOutputFormat
ADAMVCFOutputFormat
clinicalSignificance
DatabaseVariantAnnotationField
clinvarId
DatabaseVariantAnnotationField
clippingRankSum
VariantCallingAnnotationsField
close
BAMFilteredRecordReader
codec
BAMFilteredRecordReader
collapseAdjacent
Coverage
commandLine
ProgramRecord
comments
SAMFileHeaderWritable
compare
OptionalReferenceOrdering
ReferenceOrdering
SequenceOrderingByName
SequenceOrderingByRefIdx
OrientedPoint
TargetOrdering
ZippedTargetOrdering
QualityScore
compareTo
ReferenceRegion
complement
Symbol
compute
Covariate
CycleCovariate
DinucCovariate
computeExtrasDelta
RecalibrationTable
computeExtrasTables
RecalibrationTable
computeGlobalDelta
RecalibrationTable
computeQual
Recalibrator
computeQualityDelta
RecalibrationTable
computeQualityTable
RecalibrationTable
consensus
algorithms
Consensus
constantGapFn
SmithWatermanConstantGapScoring
contains
ReferenceRegion
SnpTable
TargetOrdering
containsNone
CovariateKey
containsRefName
SequenceDictionary
contig
AlignmentRecordField
FeatureField
NucleotideContigFragmentField
VariantField
rdd
contigMap
ReferenceContigMap
convert
AlignmentRecordConverter
SAMRecordConverter
VariantAnnotationConverter
VariantContextConverter
convertBaseFeatureRDDToFeatureRDD
ADAMContext
convertFragment
AlignmentRecordConverter
FastqRecordConverter
convertPair
FastqRecordConverter
convertRdd
FragmentConverter
convertRead
FastqRecordConverter
convertSAMTagAndValue
AttributeUtils
convertToAnnotation
VariantContextConverter
convertToFastq
AlignmentRecordConverter
converters
adam
core
adam
cosmicId
DatabaseVariantAnnotationField
countKmers
NucleotideContigFragmentRDDFunctions
countOfMismatches
MdTag
covariates
BaseQualityRecalibration
RecalibrationTable
createRecordReader
IndexedBamInputFormat
InterleavedFastqInputFormat
SingleFastqInputFormat
createSAMHeader
AlignmentRecordConverter
crossChromosome
DuplicateMetrics
csvFieldName
Covariate
CycleCovariate
DinucCovariate
csvHeader
CovariateSpace
ObservationTable
culprit
VariantCallingAnnotationsField
cumulativeLengths
GenomicPositionPartitioner