Character
TagType
CheckingForMask
Timers
CollectingSnps
Timers
ComputeCovariates
Timers
ComputeQualityScore
Timers
ComputingCycleCovariate
Timers
ComputingDinucCovariate
Timers
ComputingOriginalScores
Timers
ConsensusGenerator
consensus
Contig
sql
ContigField
projections
ConvertToSAM
Timers
ConvertToSAMRecord
Timers
Coverage
models
CoverageRDD
feature
CreateIndelRealignmentTargets
Timers
CreateReferencePositionPair
Timers
CreatingKnownSnpsTable
Timers
CreatingRecalibrationTable
Timers
call
GenomicDatasetConversion
canEqual
MdTag AlignmentRecord Contig Dbxref Feature Fragment Genotype NucleotideContigFragment OntologyTerm ProcessingStep TranscriptEffect Variant VariantAnnotation VariantCallingAnnotations
caseSensitive
Alphabet DNAAlphabet
cdnaLength
TranscriptEffectField TranscriptEffect
cdnaPosition
TranscriptEffectField TranscriptEffect
cdsLength
TranscriptEffectField TranscriptEffect
cdsPosition
TranscriptEffectField TranscriptEffect
cigar
DefaultHeaderLines AlignmentRecordField VariantAnnotationField AlignmentRecord VariantAnnotation
cigarX
SmithWaterman
cigarY
SmithWaterman
circular
FeatureField Feature
collapse
CoverageRDD
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
AlignmentRecordRDD
conf
VCFInFormatter VCFOutFormatter
consensus
algorithms
contains
ReferenceRegion
containsRefName
SequenceDictionary
contig
rdd
contigLength
ContigField NucleotideContigFragmentField Contig NucleotideContigFragment
contigMD5
ContigField Contig
contigMap
ReferenceContigMap
contigName
Coverage AlignmentRecordField ContigField FeatureField GenotypeField NucleotideContigFragmentField VariantField AlignmentRecord Contig Feature Genotype NucleotideContigFragment Variant
contigsToAlignmentRecordsConversionFn
ADAMContext
contigsToAlignmentRecordsDatasetConversionFn
ADAMContext
contigsToCoverageConversionFn
ADAMContext
contigsToCoverageDatasetConversionFn
ADAMContext
contigsToFeaturesConversionFn
ADAMContext
contigsToFeaturesDatasetConversionFn
ADAMContext
contigsToFragmentsConversionFn
ADAMContext
contigsToFragmentsDatasetConversionFn
ADAMContext
contigsToGenotypesConversionFn
ADAMContext
contigsToGenotypesDatasetConversionFn
ADAMContext
contigsToVariantContextConversionFn
ADAMContext
contigsToVariantsConversionFn
ADAMContext
contigsToVariantsDatasetConversionFn
ADAMContext
convert
AlignmentRecordConverter VariantContextConverter
convertFragment
AlignmentRecordConverter
convertSAMTagAndValue
AttributeUtils
convertSecondReadToTab5
AlignmentRecordConverter
convertToFastq
AlignmentRecordConverter
convertToSam
AlignmentRecordRDD
convertToTab5
AlignmentRecordConverter
convertToTab6
AlignmentRecordConverter
converter
AnySAMInFormatter BAMInFormatter SAMInFormatter VCFInFormatter
converters
adam
count
Coverage
countKmers
NucleotideContigFragmentRDD AlignmentRecordRDD
countKmersAsDataset
AlignmentRecordRDD
countOfMismatches
MdTag
coverage
CoverageRDD
coverageToAlignmentRecordsConversionFn
ADAMContext
coverageToAlignmentRecordsDatasetConversionFn
ADAMContext
coverageToContigsConversionFn
ADAMContext
coverageToContigsDatasetConversionFn
ADAMContext
coverageToFeaturesConversionFn
ADAMContext
coverageToFeaturesDatasetConversionFn
ADAMContext
coverageToFragmentsConversionFn
ADAMContext
coverageToFragmentsDatasetConversionFn
ADAMContext
coverageToGenotypesConversionFn
ADAMContext
coverageToGenotypesDatasetConversionFn
ADAMContext
coverageToVariantContextConversionFn
ADAMContext
coverageToVariantsConversionFn
ADAMContext
coverageToVariantsDatasetConversionFn
ADAMContext
covers
ReferenceRegion
coversBy
ReferenceRegion
createPredicate
ReferenceRegion
createRecordReader
InterleavedFastqInputFormat SingleFastqInputFormat
createSAMHeader
AlignmentRecordConverter
culprit
VariantCallingAnnotationsField VariantCallingAnnotations