C
Base
CALLED
ConcordanceTable
CDS
models
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
ColumnReaderInputLong
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
cds
Transcript
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
columnFilter
FieldCondition
combine
Aggregator CombinedAggregator HistogramAggregator UniqueAggregator FlatGenotypeReferenceFolder ComparisonTraversalEngine GenotypesSummaryCounts
commandLine
ProgramRecord
comments
SAMFileHeaderWritable
compare
ReferencePosition ReferencePositionWithOrientation ReferenceRegion ReferenceRegionWithOrientation TargetOrdering ZippedTargetOrdering QualityScore
comparison
CombinedFilter ComparisonsFilter GeneratorFilter
comparisons
DefaultComparisons read
complement
SequenceUtils
compressedSize
ParquetColumnChunk
compressionCodec
ADAMParquetArgs 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 ReferenceRegion ReferenceRegionWithOrientation SnpTable TargetOrdering
containsNone
CovariateKey
containsRefName
SequenceDictionary
contig
AlignmentRecordField FeatureField NucleotideContigFragmentField VariantField rdd
convert
AlignmentRecordConverter SAMRecordConverter VCFLineConverter VariantAnnotationConverter VariantContextConverter ColumnReaderInput ColumnReaderInputBoolean ColumnReaderInputDouble ColumnReaderInputFloat ColumnReaderInputInt ColumnReaderInputLong ColumnReaderInputString MyConverter
convertAvroSchema
AvroParquetRDD AvroParquetFileMetadata IDRangeIndexGenerator RangeIndexGenerator
convertBaseFeatureRDDToGeneFeatureRDD
GeneFeatureRDD
convertFromType
ParquetType
convertPair
FastqRecordConverter
convertRead
FastqRecordConverter
convertSAMTagAndValue
AttributeUtils
convertToAnnotation
VariantContextConverter
convertToFastq
AlignmentRecordConverter
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 SingleFastqInputFormat
createSAMHeader
AlignmentRecordConverter
credentials
S3FileLocator
crossChromosome
DuplicateMetrics
csvFieldName
Covariate CycleCovariate DinucCovariate
csvHeader
CovariateSpace ObservationTable
culprit
VariantCallingAnnotationsField
cumulativeLengths
GenomicRegionPartitioner