1. au
   1. au.csiro
      1. au.csiro.pbdava
         1. au.csiro.pbdava.ssparkle
            1. au.csiro.pbdava.ssparkle.common
               1. au.csiro.pbdava.ssparkle.common.arg4j
                  1. (object)(trait)AppRunner
                  2. (trait)AppRunner2
                  3. (trait)TestArgs
               2. au.csiro.pbdava.ssparkle.common.utils
                  1. (object)
                     CSVUtils
                  2. (object)
                     FastUtilConversions
                  3. (object)
                     LoanUtils
                  4. (trait)Logging
                  5. (class)Long2DoubleOpenHashMap2Map
                  6. (object)
                     MiscUtils
                  7. (trait)Prof
                  8. (object)(class)ReusablePrintStream
                  9. (object)
                     SerialUtils
                  10. (object)
                      Timed
                  11. (case class)TimedResult
                  12. (case class)Timer
            2. au.csiro.pbdava.ssparkle.spark
               1. (trait)SparkApp
               2. (object)
                  SparkUtils
      2. au.csiro.sparkle
         1. au.csiro.sparkle.cmd
            1. (class)CmdApp
            2. (class)DefaultObjectFactory
            3. (class)MultiCmdApp
         2. au.csiro.sparkle.common
            1. (class)LoanUtils
            2. (trait)ObjectFactory
            3. (class)ObjectProvider
            4. (class)ScalaUtils
            5. (class)ThrowingConsumer
            6. (class)ThrowingFunction
            1. au.csiro.sparkle.common.args4j
               1. (class)ArgsApp
               2. (class)ArgsObjectFactory
               3. (class)DateOptionHandler
               4. (trait)HasUsage
               5. (class)IntListOptionHandler
               6. (class)ObjectOptionHandler
               7. (class)RegisterHandlers
         3. au.csiro.sparkle.spark
            1. (class)AppContext
            2. (class)Counter
            3. (class)Long2LongAccumulableParam
            4. (class)SparkleJavaApp
            5. (trait)SparkTask
            6. (class)SparkUtils
      3. au.csiro.variantspark
         1. au.csiro.variantspark.algo
            1. (trait)AggregablePairwiseOperation
            2. (class)ArrayOps
            3. (trait)BatchTreeModel
            4. (trait)CanSplit
            5. (class)CanSplitArrayByte
            6. (class)CanSplitVector
            7. (trait)ClassificationSplitter
            8. (object)(class)DecisionTree
            9. (object)(class)DecisionTreeModel
            10. (class)DecisionTreeNode
            11. (case class)DecisionTreeParams
            12. (case class)DeterministicMerger
            13. (class)FastGini
            14. (object)
                IdentityVarImportanceNormalizer
            15. (class)JClassificationSplitter
            16. (class)JConfusionClassificationSplitter
            17. (class)JMaskedClassificationSplitter
            18. (object)(case class)LeafNode
            19. (class)LowerTriangMatrix
            20. (trait)Merger
            21. (case class)PairWiseAggregator
            22. (object)(trait)PairwiseOperation
            23. (trait)PredictiveModel
            24. (trait)PredictiveModelWithImportance
            25. (object)(class)RandomForest
            26. (trait)RandomForestCallback
            27. (case class)RandomForestMember
            28. (case class)RandomForestModel
            29. (case class)RandomForestParams
            30. (case class)RandomizingMerger
            31. (case class)SplitInfo
            32. (object)(case class)SplitNode
            33. (class)StandardImportanceNormalizer
            34. (case class)SubsetInfo
            35. (object)
                To100ImportanceNormalizer
            36. (object)
                ToOneImportanceNormalizer
            37. (case class)VariableSplitter
            38. (trait)VarImportanceNormalizer
            39. (object)(case class)VarSplitInfo
            40. (case class)VotingAggregator
            41. (object)(class)WideKMeans
            1. au.csiro.variantspark.algo.metrics
               1. (object)
                  AtLeastOneSharedAltAlleleCount
               2. (object)
                  BitwiseAndPairwiseRevMetric
               3. (object)
                  EuclideanPairwiseMetric
               4. (object)
                  ManhattanPairwiseMetric
               5. (object)
                  MultiPairwiseRevMetric
               6. (object)
                  SharedAltAlleleCount
         2. au.csiro.variantspark.api
            1. (class)AnalyticsFunctions
            2. (object)
               CommonPairwiseOperation
            3. (object)(class)ImportanceAnalysis
            4. (trait)SqlContextHolder
            5. (object)(class)VSContext
         3. au.csiro.variantspark.cli
            1. (object)(class)AnalyzeRFCmd
            2. (object)(class)BuildVarIndexCmd
            3. (object)(class)CochranArmanCmd
            4. (object)(class)ConvertCmd
            5. (object)(class)FilterCmd
            6. (object)(class)GenerateFamilyCmd
            7. (object)(class)GenerateFeaturesCmd
            8. (object)(class)GenerateLabelsCmd
            9. (object)(class)GenerateLabelsNoiseCmd
            10. (object)
                GeneratePoplulationCmd
            11. (class)GeneratePopulationCmd
            12. (object)(class)ImportanceCmd
            13. (object)
                IndexAccumulator
            14. (object)(class)PairWiseDistanceCmd
            15. (object)(class)TestCmd
            16. (object)(class)VariantSparkApp
            17. (object)(class)VcfToLabels
            1. au.csiro.variantspark.cli.args
               1. (trait)FeatureSourceArgs
               2. (trait)HailArgs
               3. (trait)LabelSourceArgs
               4. (trait)SparkArgs
         4. au.csiro.variantspark.cmd
            1. (trait)Echoable
            2. (object)
               EchoUtils
         5. au.csiro.variantspark.data
            1. (case class)BoundedOrdinal
            2. (case class)Factor
            3. (object)
               UnboundedOrdinal
            4. (trait)VariableType
         6. au.csiro.variantspark.genomics
            1. (object)(case class)ContigSet
            2. (object)(case class)ContigSpec
            3. (object)
               Defaults
            4. (case class)GenomicCoord
            5. (object)(case class)GenotypeSpec
            6. (object)
               ReferenceContigSet
            1. au.csiro.variantspark.genomics.family
               1. (trait)FamilyMember
               2. (object)(case class)FamilySpec
               3. (object)(case class)FamilyTrio
               4. (case class)Founder
               5. (object)
                  Gender
               6. (trait)Individual
               7. (object)
                  IndividualID
               8. (case class)Offspring
               9. (object)
                  ParentalRole
               10. (object)(case class)PedigreeTree
            2. au.csiro.variantspark.genomics.impl
               1. (class)BamMutationFactory
               2. (object)(case class)ContigRecombinationDistribution
               3. (object)(case class)HapMapMeiosisSpecFactory
               4. (object)(case class)RecombinationDistribution
               5. (trait)ReferenceSequence
               6. (case class)SimpleMeiosisSpecFactory
            3. au.csiro.variantspark.genomics.reprod
               1. (case class)ContigRecombinationMap
               2. (case class)GameteSpec
               3. (case class)GameteSpecFactory
               4. (case class)MeiosisSpec
               5. (trait)MeiosisSpecFactory
               6. (trait)MutableVariant
               7. (object)(case class)Mutation
               8. (object)(case class)MutationSet
               9. (trait)MutationSetFactory
               10. (object)(case class)OffspringSpec
               11. (object)(case class)RecombinationMap
         7. au.csiro.variantspark.hail
            1. (class)VSGenericDatasetFunctions
            2. (class)VSHailContextFunctions
            3. (class)VSHailFunctions
            1. au.csiro.variantspark.hail.adapter
               1. (object)(class)HailContextAdapter
               2. (object)(class)HailFeatureSource
               3. (object)(class)HailLabelSource
            2. au.csiro.variantspark.hail.family
               1. (object)(class)DatasetMutationFactory
               2. (class)FamilyVariantBuilder
               3. (object)(class)GenerateFamily
               4. (class)HailMutableVariantAdapter
            3. au.csiro.variantspark.hail.methods
               1. (object)
                  PairwiseComputation
               2. (object)(class)RfImportanceAnalysis
            4. au.csiro.variantspark.hail.variant
               1. (class)PhasedGenotype
               1. au.csiro.variantspark.hail.variant.io
                  1. (object)
                     ExportVCFEx
               2. au.csiro.variantspark.hail.variant.phased
                  1. (object)(class)BiCall
                  2. (class)PhasedGenericRecordReader
         8. au.csiro.variantspark.input
            1. (case class)CsvFeatureSource
            2. (class)CsvLabelSource
            3. (object)(class)DefaultCSVFormatSpec
            4. (case class)DefVariantToFeatureConverter
            5. (class)DelegatingLineIterator
            6. (class)ExtendedVCFCodec
            7. (case class)Feature
            8. (trait)FeatureSource
            9. (class)HashingLabelSource
            10. (case class)HeaderAndVersion
            11. (trait)LabelSource
            12. (case class)ParquetFeatureSource
            13. (trait)VariantToFeatureConverter
            14. (object)(class)VCFFeatureSource
            15. (object)(class)VCFSource
            16. (case class)VectorFeature
            1. au.csiro.variantspark.input.generate
               1. (object)(class)EffectLabelGenerator
               2. (object)(class)NoisyEffectLabelGenerator
               3. (case class)OrdinalFeatureGenerator
         9. au.csiro.variantspark.metrics
            1. (object)
               Gini
            2. (object)
               Metrics
         10. au.csiro.variantspark.output
             1. (case class)CSVFeatureSink
             2. (case class)CSVFeatureSink2
             3. (trait)FeatureSink
             4. (class)ParquetFeatureSink
         11. au.csiro.variantspark.stats
             1. (class)CochranArmitageTest
             2. (object)(class)CochranArmitageTestCalculator
             3. (class)CochranArmitageTestScorer
         12. au.csiro.variantspark.tests
             1. (object)
                TestWideDecisionTree
             2. (object)
                TestWideKMeans
         13. au.csiro.variantspark.utils
             1. (trait)CanSize
             2. (object)
                CV
             3. (object)(case class)FactorVariable
             4. (object)(class)HdfsPath
             5. (object)(class)IndexedRDDFunction
             6. (class)IndexedVectorRDDFunction
             7. (object)(class)Projector
             8. (object)
                RDDProjections
             9. (object)(class)Sample
             10. (object)
                 Sampling
             11. (object)(class)VectorRDDFunction
         14. au.csiro.variantspark.work
             1. (object)
                AnyValTest
             2. (object)
                Appl
             3. (object)
                BreezeTest
             4. (object)
                CaseTest
             5. (object)
                DataSetTest
             6. (class)ImplicitTest
             7. (class)IntTest1
             8. (case class)IntTest2
             9. (object)
                ObjectTest
             10. (object)
                 RegexTest
             11. (object)(class)Sampler
             12. (object)
                 StreamTest
             13. (object)
                 VcfReaderTest
             1. au.csiro.variantspark.work.hail
                1. (object)
                   HailApp
                2. (object)
                   HailHipsterApp
                3. (object)
                   HailTestApp
2. breeze
   1. breeze.stats
3. is
   1. is.hail
      1. is.hail.expr
      2. is.hail.utils