C
Base
CALLED
ConcordanceTable
CIGAR_CODEC
RichAlignmentRecord
PileupTraversable
CLINVAR_KEYS
VariantAnnotationConverter
COSMIC_KEYS
VariantAnnotationConverter
Center
Alignment
Character
TagType
Collection
metrics
ColumnReaderInput
predicates
ColumnReaderInput
ColumnReaderInputBoolean
ColumnReaderInput
ColumnReaderInputDouble
ColumnReaderInput
ColumnReaderInputFloat
ColumnReaderInput
ColumnReaderInputInt
ColumnReaderInput
ColumnReaderInputString
ColumnReaderInput
CombinedAggregator
aggregators
CombinedComparisons
metrics
CombinedFilter
filters
filters
ComparisonTraversalEngine
comparisons
ComparisonsFilter
filters
CompressionCodec
CompressionCodecEnum
CompressionCodecEnum
rdd
ConcordanceTable
variation
Consensus
models
ConsensusGenerator
consensus
ConsensusGeneratorFromKnowns
consensus
ConsensusGeneratorFromReads
consensus
ConsensusGeneratorFromSmithWaterman
consensus
CountTag
ServoTimer
Covariate
recalibration
CovariateKey
recalibration
CovariateSpace
recalibration
CredentialsProperties
util
CycleCovariate
recalibration
canCombine
FlatGenotypeReferenceFolder
canEqual
MdTag
cartesianFilter
RegionJoin
charSequenceToList
ADAMContext
ImplicitJavaConversions
charSequenceToString
ADAMContext
ImplicitJavaConversions
cigar
AlignmentRecordField
cigarPattern
RichAlignmentRecord
cigarToRichCigar
RichCigar
cigarX
SmithWaterman
cigarY
SmithWaterman
clean
VcfStringUtils
clearHeader
ADAMBAMOutputFormat
ADAMSAMOutputFormat
clinicalSignificance
DatabaseVariantAnnotationField
clinvarId
DatabaseVariantAnnotationField
clippingRankSum
VariantCallingAnnotationsField
close
VCFLineParser
IDRangeIndexWriter
RangeIndexWriter
RowGroupIndexWriter
cloy
DecadentRead
columnChunks
ParquetRowGroup
columnDescriptor
ParquetColumnChunk
ParquetColumnDescriptor
combine
Aggregator
CombinedAggregator
HistogramAggregator
UniqueAggregator
FlatGenotypeReferenceFolder
GenotypesSummaryCounts
ComparisonTraversalEngine
compare
TargetOrdering
ZippedTargetOrdering
ReferencePosition
ReferencePositionWithOrientation
ReferenceRegion
ReferenceRegionWithOrientation
QualityScore
comparison
CombinedFilter
ComparisonsFilter
GeneratorFilter
comparisons
DefaultComparisons
rdd
compressedSize
ParquetColumnChunk
compressionCodec
ParquetColumnChunk
compute
AvroIndexedParquetRDD
AvroParquetRDD
Covariate
CycleCovariate
DinucCovariate
computeExtrasDelta
RecalibrationTable
computeGlobalDelta
RecalibrationTable
computeQual
Recalibrator
computeQualityDelta
RecalibrationTable
concordance
ConcordanceTable
concordanceWith
GenotypeRDDFunctions
configuration
CredentialsProperties
configuredValue
CredentialsProperties
consensus
algorithms
Consensus
constantGapFn
SmithWatermanConstantGapScoring
contains
DNAPrefixTrie
TargetOrdering
ReferenceRegion
ReferenceRegionWithOrientation
SnpTable
containsNone
CovariateKey
containsRefName
SequenceDictionary
contig
BaseFeature
AlignmentRecordField
FeatureField
NucleotideContigFragmentField
VariantField
convert
AlignmentRecordConverter
SAMRecordConverter
VCFLineConverter
VariantAnnotationConverter
VariantContextConverter
ColumnReaderInput
ColumnReaderInputBoolean
ColumnReaderInputDouble
ColumnReaderInputFloat
ColumnReaderInputInt
ColumnReaderInputString
MyConverter
convertAvroSchema
AvroParquetRDD
AvroParquetFileMetadata
IDRangeIndexGenerator
RangeIndexGenerator
convertFromType
ParquetType
convertSAMTagAndValue
AttributeUtils
convertToAnnotation
VariantContextConverter
convertToParquet
ParquetGroupType
ParquetPrimitiveType
ParquetSchemaType
ParquetType
converter
ParquetCommon
format
converters
adam
core
adam
cosmicId
DatabaseVariantAnnotationField
count
Aggregated
AggregatedCollection
UniqueWritable
FlatGenotypeReferenceFolder
Histogram
countIdentical
Aggregated
AggregatedCollection
UniqueWritable
Histogram
countOfMismatches
MdTag
countSubset
Histogram
covariates
BaseQualityRecalibration
RecalibrationTable
createFilter
BooleanComparisons
BucketComparisons
CombinedComparisons
LongComparisons
PointComparisons
createRecordReader
InterleavedFastqInputFormat
createSAMHeader
AlignmentRecordConverter
createSparkContext
ADAMContext
credentials
S3FileLocator
crossChromosome
DuplicateMetrics
csvFieldName
Covariate
CycleCovariate
DinucCovariate
csvHeader
CovariateSpace
ObservationTable
culprit
VariantCallingAnnotationsField
cumulativeLengths
GenomicRegionPartitioner