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