Character
TagType
CheckingForMask
Timers
CollectingSnps
Timers
ComputeCovariates
Timers
ComputeQualityScore
Timers
ComputingCycleCovariate
Timers
ComputingDinucCovariate
Timers
ComputingOriginalScores
Timers
ConsensusGenerator
consensus
ConvertToSAM
Timers
ConvertToSAMRecord
Timers
Coverage
models
CoverageDataset
feature
CreateIndelRealignmentTargets
Timers
CreateReferencePositionPair
Timers
CreateSequenceDictionary
Timers
CreatingKnownSnpsTable
Timers
CreatingRecalibrationTable
Timers
cache
DatasetBoundGenomicDataset GenomicDataset
call
GenomicDatasetConversion
canEqual
MdTag AlignmentRecord Dbxref Feature Fragment Genotype OntologyTerm ProcessingStep Read Reference Sequence Slice TranscriptEffect Variant VariantAnnotation VariantCallingAnnotations
caseSensitive
Alphabet DNAAlphabet
cdnaLength
TranscriptEffectField TranscriptEffect
cdnaPosition
TranscriptEffectField TranscriptEffect
cdsLength
TranscriptEffectField TranscriptEffect
cdsPosition
TranscriptEffectField TranscriptEffect
checkBuffer
FastqRecordReader
cigar
DefaultHeaderLines AlignmentRecordField VariantAnnotationField AlignmentRecord VariantAnnotation
cigarX
SmithWaterman
cigarY
SmithWaterman
circular
FeatureField Feature
close
FastqRecordReader
collapse
CoverageDataset
commandLine
ProcessingStep
companion
InFormatter BEDInFormatter GFF3InFormatter GTFInFormatter NarrowPeakInFormatter InterleavedFASTQInFormatter Tab5InFormatter Tab6InFormatter BAMInFormatter FASTQInFormatter SAMInFormatter VCFInFormatter
compare
OptionalReferenceOrdering ReferenceOrdering
compareTo
ReferenceRegion
complement
Symbol
compute
ShuffleRegionJoin
computeMismatchingPositions
AlignmentRecordDataset
conf
VCFInFormatter VCFOutFormatter
consensus
algorithms
contains
ReferenceRegion
containsReferenceName
SequenceDictionary
contigMap
ReferenceContigMap
convert
AvroSchemaConverter AlignmentRecordConverter VariantContextConverter
convertFragment
AlignmentRecordConverter
convertSAMTagAndValue
AttributeUtils
convertSecondReadToTab5
AlignmentRecordConverter
convertToFastq
AlignmentRecordConverter
convertToSam
AlignmentRecordDataset
convertToTab5
AlignmentRecordConverter
convertToTab6
AlignmentRecordConverter
converter
DatasetBoundGenericGenomicDataset GenericGenomicDataset RDDBoundGenericGenomicDataset AnySAMInFormatter BAMInFormatter SAMInFormatter VCFInFormatter
converters
adam
copyVariantEndToAttribute
DatasetBoundGenotypeDataset GenotypeDataset
count
Coverage
countKmers
AlignmentRecordDataset SliceDataset
countKmersAsDataset
AlignmentRecordDataset
countOfMismatches
MdTag
coverage
CoverageDataset
coverageToAlignmentRecordsConversionFn
ADAMContext
coverageToAlignmentRecordsDatasetConversionFn
ADAMContext
coverageToCoverageConversionFn
ADAMContext
coverageToFeaturesConversionFn
ADAMContext
coverageToFeaturesDatasetConversionFn
ADAMContext
coverageToFragmentsConversionFn
ADAMContext
coverageToFragmentsDatasetConversionFn
ADAMContext
coverageToGenotypesConversionFn
ADAMContext
coverageToGenotypesDatasetConversionFn
ADAMContext
coverageToReadsConversionFn
ADAMContext
coverageToReadsDatasetConversionFn
ADAMContext
coverageToSequencesConversionFn
ADAMContext
coverageToSequencesDatasetConversionFn
ADAMContext
coverageToSlicesConversionFn
ADAMContext
coverageToSlicesDatasetConversionFn
ADAMContext
coverageToVariantContextConversionFn
ADAMContext
coverageToVariantsConversionFn
ADAMContext
coverageToVariantsDatasetConversionFn
ADAMContext
covers
ReferenceRegion
coversBy
ReferenceRegion
createMetricsListener
ADAMShell
createPredicate
ReferenceRegion
createRecordReader
InterleavedFastqInputFormat SingleFastqInputFormat
createSAMHeader
AlignmentRecordConverter
createSequenceDictionary
SequenceDataset SliceDataset
culprit
VariantCallingAnnotationsField VariantCallingAnnotations