1. com
   1. com.typesafe
      1. com.typesafe.scalalogging
         1. (trait)AbstractLogging
         2. (trait)LazyLogging
2. htsjdk
   1. htsjdk.variant
      1. htsjdk.variant.variantcontext
         1. htsjdk.variant.variantcontext.writer
            1. (object)
               VCFHeaderWriter
      2. htsjdk.variant.vcf
         1. (object)
            VCFEncoderUtils
3. io
   1. io.projectglow
      1. (trait)DataFrameTransformer
      2. (object)
         functions
      3. (object)
         Glow
      4. (class)GlowBase
      5. (object)
         SparkShim
      6. (trait)SparkShimBase
      1. io.projectglow.bgen
         1. (object)(class)BgenFileFormat
         2. (object)(trait)BgenGenotypeReader
         3. (object)(class)BgenRecordWriter
         4. (class)BgenRowToInternalRowConverter
         5. (object)
            BgenSchemaInferrer
         6. (object)(class)BigBgenDatasource
         7. (case class)BigBgenOptions
         8. (class)ComDatabricksBgenFileFormat
         9. (class)ComDatabricksBigBgenDatasource
         10. (case class)FractionalPartIndex
         11. (case class)GenotypeCharacteristics
         12. (class)InternalRowToBgenRowConverter
         13. (case class)ProbabilityBlockSize
         14. (object)(trait)SnpBlockCompression
         15. (class)SortByDescendingFractionalPart
         16. (class)UncompressedBgenGenotypeReader
         17. (class)ZlibBgenGenotypeReader
         18. (class)ZstdBgenGenotypeReader
      2. io.projectglow.common
         1. (object)
            BgenOptions
         2. (object)
            CommonOptions
         3. (object)
            FeatureSchemas
         4. (object)(case class)GenotypeFields
         5. (trait)GlowLogging
         6. (object)
            HailUtils
         7. (trait)HasStringency
         8. (trait)Named
         9. (object)
            PlinkOptions
         10. (object)
             PythonUtils
         11. (case class)SimpleInterval
         12. (object)
             VariantSchemas
         13. (object)
             VCFOptions
         14. (object)(case class)VCFRow
         15. (object)
             WithUtils
         1. io.projectglow.common.logging
            1. (trait)HlsEventRecorder
            2. (object)
               HlsMetricDefinitions
            3. (object)
               HlsTagDefinitions
            4. (object)
               HlsTagValues
            5. (trait)HlsUsageLogging
            6. (case class)MetricDefinition
            7. (object)
               PythonHlsEventRecorder
            8. (case class)TagDefinition
      3. io.projectglow.gff
         1. (object)(class)GffDataSource
         2. (class)GffResourceRelation
      4. io.projectglow.plink
         1. (class)BedFileIterator
         2. (object)(class)PlinkFileFormat
         3. (class)PlinkRowToInternalRowConverter
      5. io.projectglow.sql
         1. (object)(class)BigFileDatasource
         2. (trait)BigFileUploader
         3. (class)Functions
         4. (object)
            GlowConf
         5. (class)GlowSQLExtensions
         6. (case class)SingleFileRelation
         7. (object)
            SingleFileWriter
         8. (object)
            SqlExtensionProvider
         1. io.projectglow.sql.dsl
            1. (class)GlowExpression
            2. (trait)ImplicitOperators
         2. io.projectglow.sql.expressions
            1. (case class)AddStructFields
            2. (trait)AggregateByIndex
            3. (case class)ArrayStatsSummary
            4. (object)(case class)ArrayToDenseVector
            5. (object)(case class)ArrayToSparseVector
            6. (case class)AssertTrueOrError
            7. (object)(case class)CallStats
            8. (case class)CallStatsStruct
            9. (case class)CallSummaryStats
            10. (object)(case class)CovariateQRContext
            11. (case class)DpSummaryStats
            12. (case class)ExpandStruct
            13. (case class)ExplodeMatrix
            14. (case class)FirthFit
            15. (case class)FirthFitState
            16. (class)FirthNewtonArgs
            17. (object)
                FirthTest
            18. (case class)GenotypeStates
            19. (case class)GqSummaryStats
            20. (object)(case class)HardCalls
            21. (object)(case class)HardyWeinberg
            22. (case class)HardyWeinbergStruct
            23. (case class)LiftOverCoordinatesExpr
            24. (object)
                LikelihoodRatioTest
            25. (object)(case class)LinearRegressionExpr
            26. (object)
                LinearRegressionGwas
            27. (object)(case class)LogisticRegressionExpr
            28. (object)
                LogisticRegressionGwas
            29. (class)LogisticRegressionState
            30. (trait)LogitTest
            31. (object)(case class)LogitTestResults
            32. (case class)LRTFitState
            33. (case class)MeanSubstitute
            34. (object)(case class)MomentAggState
            35. (class)NewtonIterationsState
            36. (case class)NewtonResult
            37. (object)(case class)NormalizeVariantExpr
            38. (case class)PerSampleSummaryStatistics
            39. (case class)RegressionStats
            40. (object)(case class)SampleCallStats
            41. (case class)SampleDpSummaryStatistics
            42. (case class)SampleGqSummaryStatistics
            43. (case class)SampleSummaryStatsState
            44. (case class)SubsetStruct
            45. (case class)UnwrappedAggregateByIndex
            46. (trait)UnwrappedAggregateFunction
            47. (object)
                VariantQcExprs
            48. (object)(trait)VariantType
            49. (object)
                VariantUtilExprs
            50. (object)(case class)VectorToArray
            51. (case class)WrappedAggregateByIndex
         3. io.projectglow.sql.optimizer
            1. (object)
               ReplaceExpressionsRule
            2. (object)
               ResolveAggregateFunctionsRule
            3. (object)
               ResolveExpandStructRule
            4. (object)
               ResolveGenotypeFields
         4. io.projectglow.sql.util
            1. (class)BGZFCodec
            2. (trait)ComDatabricksDataSource
            3. (trait)ExpectsGenotypeFields
            4. (case class)GenotypeInfo
            5. (class)HadoopLineIterator
            6. (object)(class)LeveneHaldane
            7. (trait)Rewrite
            8. (trait)RewriteAfterResolution
            9. (object)(class)RowConverter
            10. (class)SerializableConfiguration
      6. io.projectglow.transformers
         1. (object)(class)LiftOverVariantsTransformer
         1. io.projectglow.transformers.blockvariantsandsamples
            1. (object)(class)BlockVariantsAndSamplesTransformer
         2. io.projectglow.transformers.normalizevariants
            1. (object)(class)NormalizeVariantsTransformer
            2. (object)
               VariantNormalizer
         3. io.projectglow.transformers.pipe
            1. (class)CleanupPipeTransformer
            2. (class)CSVInputFormatter
            3. (class)CSVInputFormatterFactory
            4. (class)CSVOutputFormatter
            5. (class)CSVOutputFormatterFactory
            6. (trait)InputFormatter
            7. (trait)InputFormatterFactory
            8. (trait)OutputFormatter
            9. (trait)OutputFormatterFactory
            10. (class)PipeIterator
            11. (object)(class)PipeTransformer
            12. (object)
                ProcessHelper
            13. (class)UTF8TextInputFormatter
            14. (class)UTF8TextInputFormatterFactory
            15. (class)UTF8TextOutputFormatter
            16. (class)UTF8TextOutputFormatterFactory
         4. io.projectglow.transformers.splitmultiallelics
            1. (object)(class)SplitMultiallelicsTransformer
         5. io.projectglow.transformers.util
            1. (class)SnakeCaseMap
            2. (object)
               StringUtils
      7. io.projectglow.vcf
         1. (object)
            AnnotationUtils
         2. (object)(class)BigVCFDatasource
         3. (class)ComDatabricksBigVCFDatasource
         4. (class)ComDatabricksVCFFileFormat
         5. (object)
            FieldTypes
         6. (class)FilterContig
         7. (class)FilterInterval
         8. (object)
            InferSampleIds
         9. (object)(class)InternalRowToVariantContextConverter
         10. (object)(class)LineCtx
         11. (class)LineIteratorImpl
         12. (case class)ParsedFilterResult
         13. (trait)SampleIdInfo
         14. (case class)SampleIds
         15. (object)
             TabixIndexHelper
         16. (object)(class)VariantContextToInternalRowConverter
         17. (object)(class)VCFFileFormat
         18. (class)VCFFileWriter
         19. (object)
             VCFHeaderUtils
         20. (class)VCFInputFormatter
         21. (class)VCFInputFormatterFactory
         22. (class)VCFLineToInternalRowConverter
         23. (object)
             VCFMetadataLoader
         24. (class)VCFOutputFormatter
         25. (class)VCFOutputFormatterFactory
         26. (object)
             VCFRowHeaderLines
         27. (object)
             VCFSchemaInferrer
         28. (class)VCFStreamWriter
         29. (object)
             VCFWriterUtils
4. org
   1. org.apache
      1. org.apache.spark
         1. org.apache.spark.sql
            1. (object)
               SQLUtils
            1. org.apache.spark.sql.catalyst
               1. org.apache.spark.sql.catalyst.expressions
                  1. (class)QuinaryExpression
                  2. (class)SenaryExpression
            2. org.apache.spark.sql.execution
               1. org.apache.spark.sql.execution.datasources
                  1. org.apache.spark.sql.execution.datasources.csv
                     1. (object)
                        CSVDataSourceUtils
                     2. (class)MinimalFailureSafeParser
                     3. (class)SGUnivocityGenerator
                     4. (object)
                        UnivocityParserUtils
   2. org.seqdoop
      1. org.seqdoop.hadoop_bam
         1. org.seqdoop.hadoop_bam.util
            1. (object)(class)GlowBGZFOutputStream