Character
TagType
CheckingForMask
Timers
CollectingSnps
Timers
ComputeCovariates
Timers
ComputeQualityScore
Timers
ComputingCycleCovariate
Timers
ComputingDinucCovariate
Timers
ComputingOriginalScores
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