C
Base
CALLED
ConcordanceTable
CDS
models
CIGAR_CODEC
RichAlignmentRecord PileupTraversable
CLINVAR_KEYS
VariantAnnotationConverter
COSMIC_KEYS
VariantAnnotationConverter
Character
TagType
ColumnReaderInput
predicates ColumnReaderInput
ColumnReaderInputBoolean
ColumnReaderInput
ColumnReaderInputDouble
ColumnReaderInput
ColumnReaderInputFloat
ColumnReaderInput
ColumnReaderInputInt
ColumnReaderInput
ColumnReaderInputLong
ColumnReaderInput
ColumnReaderInputString
ColumnReaderInput
CombinedComparisons
metrics
CombinedFilter
filters
ComparisonTraversalEngine
comparisons
ComparisonsFilter
filters
ComputeCovariates
Timers
ComputeQualityScore
Timers
ConcordanceTable
variation
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
cds
Transcript
chrom
OrientedPoint
cigar
AlignmentRecordField
cigarPattern
RichAlignmentRecord
cigarToRichCigar
RichCigar
cigarX
SmithWaterman
cigarY
SmithWaterman
clean
VcfStringUtils
clearHeader
ADAMBAMOutputFormat ADAMSAMOutputFormat
clinicalSignificance
DatabaseVariantAnnotationField
clinvarId
DatabaseVariantAnnotationField
clippingRankSum
VariantCallingAnnotationsField
cloy
DecadentRead
collapseAdjacent
Coverage
columnFilter
FieldCondition
combine
ComparisonTraversalEngine GenotypesSummaryCounts
commandLine
ProgramRecord
comments
SAMFileHeaderWritable
compare
ReferencePosition ReferencePositionWithOrientation ReferenceRegion ReferenceRegionWithOrientation OrientedPoint TargetOrdering ZippedTargetOrdering QualityScore
comparison
CombinedFilter ComparisonsFilter GeneratorFilter
comparisons
DefaultComparisons read
complement
SequenceUtils
compressionCodec
ADAMParquetArgs
compute
Covariate CycleCovariate DinucCovariate
computeExtrasDelta
RecalibrationTable
computeGlobalDelta
RecalibrationTable
computeQual
Recalibrator
computeQualityDelta
RecalibrationTable
concordance
ConcordanceTable
concordanceWith
GenotypeRDDFunctions
consensus
algorithms Consensus
constantGapFn
SmithWatermanConstantGapScoring
contains
DNAPrefixTrie ReferenceRegion ReferenceRegionWithOrientation SnpTable TargetOrdering
containsNone
CovariateKey
containsRefName
SequenceDictionary
contig
AlignmentRecordField FeatureField NucleotideContigFragmentField VariantField rdd
convert
AlignmentRecordConverter SAMRecordConverter VariantAnnotationConverter VariantContextConverter ColumnReaderInput ColumnReaderInputBoolean ColumnReaderInputDouble ColumnReaderInputFloat ColumnReaderInputInt ColumnReaderInputLong ColumnReaderInputString
convertBaseFeatureRDDToGeneFeatureRDD
ADAMContext
convertPair
FastqRecordConverter
convertRdd
FragmentConverter
convertRead
FastqRecordConverter
convertSAMTagAndValue
AttributeUtils
convertToAnnotation
VariantContextConverter
convertToFastq
AlignmentRecordConverter
converters
adam
core
adam
cosmicId
DatabaseVariantAnnotationField
countOfMismatches
MdTag
covariates
BaseQualityRecalibration RecalibrationTable
createFilter
BooleanComparisons BucketComparisons CombinedComparisons LongComparisons PointComparisons
createRecordReader
InterleavedFastqInputFormat SingleFastqInputFormat
createSAMHeader
AlignmentRecordConverter
crossChromosome
DuplicateMetrics
csvFieldName
Covariate CycleCovariate DinucCovariate
csvHeader
CovariateSpace ObservationTable
culprit
VariantCallingAnnotationsField
cumulativeLengths
GenomicPositionPartitioner