- AccuracyCalculator
- AccuracyCalculator.AccuracyMethod
- AccuracyStats
- AlgorithmException
- Available
- BiallelicFilter
- BiasedBinomialCaller
- BinomialCaller
- ByteMapper
- ByteToGeno
- Caller
- Case
- ClassList
- Combiner
- CombinerOption
- ComparableDistribution
- ComparableDistributionCollector
- Correlation
- CountMap
- DepthMapper
- DepthMask
- DepthMask.Method
- DepthMaskFactory
- Descent
- Distribution
- DistributionCollector
- DotsProgress
- DoubleMapper
- EM
- ExtendedXMLConfiguration
- GenoToByte
- Genotype
- GenotypeChanger
- GoldenSection
- HasDepthFilter
- ImputationOption
- Imputer
- INIException
- Input
- IntegerMapper
- KnniLDProb
- KnniLDProbOptimizedCalls
- LinkImputeR
- Log
- Log.Level
- LogBiasedBinomialCaller
- LogBinomialCaller
- MAFCalculator
- MAFFilter
- Mapper
- Matrix
- MaxDepthCombiner
- MaxDepthCombinerOptimizedCalls
- MaxDepthNoReadsChanger
- Meta
- MinDepthMissingChanger
- MultipleIntegerValue
- MultipleTest
- NotEnoughMaskableGenotypesException
- OptimizeCombiner
- OptimizeImputer
- Output
- OutputException
- ParalogHWFilter
- Pearson
- Position
- PositionChanger
- PositionFilter
- PositionMeta
- PositionMissing
- PrintStats
- ProbToCall
- ProbToCallMinDepth
- ProgrammerException
- Progress
- ProgressFactory
- ProgressFactory.ProgressType
- RenameFormatChanger
- Sample
- SampleFilter
- SampleMissing
- SilentProgress
- SingleDoubleValue
- SingleGenotypeCall
- SingleGenotypeMasked
- SingleGenotypePosition
- SingleGenotypeProbability
- SingleGenotypeReads
- SortByIndexDouble
- StandardizeCountsFormatChanger
- TextBarProgress
- TextProgress
- TopQueue
- VCF
- VCFDataException
- VCFDataLineException
- VCFException
- VCFFilter
- VCFHeaderLineException
- VCFInputException
- VCFMissingFormatException
- VCFNoDataException
- VCFUnexpectedDataException
- XMLException