All Classes

  • 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