Character
TagType
CheckingForMask
Timers
CollectingSnps
Timers
ComputeCovariates
Timers
ComputeQualityScore
Timers
ComputingCycleCovariate
Timers
ComputingDinucCovariate
Timers
ConsensusGenerator
consensus
ContigField
projections
ConvertToSAM
Timers
ConvertToSAMRecord
Timers
Coverage
models
CoverageRDD
feature
CreateIndelRealignmentTargets
Timers
CreateReferencePositionPair
Timers
CreatingKnownSnpsTable
Timers
CreatingRecalibrationTable
Timers
canEqual
MdTag
caseSensitive
Alphabet DNAAlphabet
cdnaLength
TranscriptEffectField
cdnaPosition
TranscriptEffectField
cdsLength
TranscriptEffectField
cdsPosition
TranscriptEffectField
cigar
DefaultHeaderLines AlignmentRecordField VariantAnnotationField
cigarX
SmithWaterman
cigarY
SmithWaterman
circular
FeatureField
collapse
CoverageRDD
companion
InFormatter BEDInFormatter GFF3InFormatter GTFInFormatter NarrowPeakInFormatter InterleavedFASTQInFormatter BAMInFormatter SAMInFormatter VCFInFormatter
compare
OptionalReferenceOrdering ReferenceOrdering
compareTo
ReferenceRegion
complement
Symbol
computeMismatchingPositions
AlignmentRecordRDD
consensus
algorithms
contains
ReferenceRegion
containsRefName
SequenceDictionary
contig
NucleotideContigFragmentField rdd
contigLength
ContigField
contigMD5
ContigField
contigMap
ReferenceContigMap
contigName
Coverage AlignmentRecordField ContigField FeatureField GenotypeField VariantField
convert
AlignmentRecordConverter VariantContextConverter
convertFragment
AlignmentRecordConverter
convertSAMTagAndValue
AttributeUtils
convertToFastq
AlignmentRecordConverter
convertToSam
AlignmentRecordRDD
converter
AnySAMInFormatter BAMInFormatter SAMInFormatter VCFInFormatter
converters
adam
count
Coverage
countKmers
NucleotideContigFragmentRDD AlignmentRecordRDD
countOfMismatches
MdTag
coverage
CoverageRDD
covers
ReferenceRegion
createRecordReader
InterleavedFastqInputFormat SingleFastqInputFormat
createSAMHeader
AlignmentRecordConverter
culprit
VariantCallingAnnotationsField