C
Base
CALLED
ConcordanceTable
CIGAR_CODEC
RichADAMRecord
PileupTraversable
CLINVAR_KEYS
VariantAnnotationConverter
COSMIC_KEYS
VariantAnnotationConverter
Character
TagType
Collection
metrics
ColumnReaderInput
predicates
ColumnReaderInput
ColumnReaderInputBoolean
ColumnReaderInput
ColumnReaderInputDouble
ColumnReaderInput
ColumnReaderInputFloat
ColumnReaderInput
ColumnReaderInputInt
ColumnReaderInput
ColumnReaderInputString
ColumnReaderInput
CombinedAggregator
aggregators
CombinedComparisons
metrics
CombinedFilter
filters
ComparisonTraversalEngine
comparisons
ComparisonsFilter
filters
ConcordanceTable
variation
Consensus
models
Covariate
recalibration
CovariateKey
recalibration
CovariateSpace
recalibration
CycleCovariate
recalibration
cartesianFilter
RegionJoin
charSequenceToList
ADAMContext
ImplicitJavaConversions
charSequenceToString
ADAMContext
ImplicitJavaConversions
cigar
ADAMRecordField
cigarToRichCigar
RichCigar
cigarX
SmithWaterman
cigarY
SmithWaterman
clean
VcfStringUtils
clinicalSignificance
ADAMDatabaseVariantAnnotationField
clinvarId
ADAMDatabaseVariantAnnotationField
clippingRankSum
VariantCallingAnnotationsField
cloy
DecadentRead
combine
Aggregator
CombinedAggregator
HistogramAggregator
UniqueAggregator
GenotypesSummaryCounts
ComparisonTraversalEngine
compare
IndelRange
SNPRange
TargetOrdering
ZippedTargetOrdering
ReferencePosition
ReferencePositionWithOrientation
ReferenceRegion
QualityScore
compareRange
GenericRange
IndelRange
SNPRange
compareReadRange
GenericRange
comparison
CombinedFilter
ComparisonsFilter
GeneratorFilter
comparisons
DefaultComparisons
rdd
compute
Covariate
CycleCovariate
DinucCovariate
computeExtrasDelta
RecalibrationTable
computeGlobalDelta
RecalibrationTable
computeQual
Recalibrator
computeQualityDelta
RecalibrationTable
concordance
ConcordanceTable
concordanceWith
ADAMGenotypeRDDFunctions
consensus
Consensus
constantGapFn
SmithWatermanConstantGapScoring
contains
TargetOrdering
ReferenceRegion
SnpTable
containsNone
CovariateKey
containsRefName
SequenceDictionary
contig
ADAMNucleotideContigFragmentField
ADAMRecordField
ADAMVariantField
convert
SAMRecordConverter
VariantAnnotationConverter
VariantContextConverter
ColumnReaderInput
ColumnReaderInputBoolean
ColumnReaderInputDouble
ColumnReaderInputFloat
ColumnReaderInputInt
ColumnReaderInputString
convertSAMTagAndValue
AttributeUtils
convertToAnnotation
VariantContextConverter
converters
adam
core
adam
cosmicId
ADAMDatabaseVariantAnnotationField
count
Aggregated
AggregatedCollection
UniqueWritable
Histogram
countIdentical
Aggregated
AggregatedCollection
UniqueWritable
Histogram
countSubset
Histogram
covariates
BaseQualityRecalibration
RecalibrationTable
createFilter
BooleanComparisons
BucketComparisons
CombinedComparisons
LongComparisons
PointComparisons
createRecordReader
InterleavedFastqInputFormat
createSparkContext
ADAMContext
crossChromosome
DuplicateMetrics
csvFieldName
Covariate
CycleCovariate
DinucCovariate
csvHeader
CovariateSpace
ObservationTable
culprit
VariantCallingAnnotationsField
cumulativeLengths
GenomicRegionPartitioner