1. org
   1. org.bdgenomics
      1. org.bdgenomics.adam
         1. org.bdgenomics.adam.algorithms
            1. org.bdgenomics.adam.algorithms.realignmenttarget
               1. (class)GenericRange
               2. (object)(case class)IndelRange
               3. (class)IndelRangeSerializer
               4. (object)(class)IndelRealignmentTarget
               5. (class)RangeAccumulator
               6. (object)(class)RealignmentTargetFinder
               7. (object)(case class)SNPRange
               8. (class)SNPRangeSerializer
               9. (object)
                  TargetOrdering
               10. (class)TreeSetSerializer
               11. (object)
                   ZippedTargetOrdering
            2. org.bdgenomics.adam.algorithms.smithwaterman
               1. (class)SmithWaterman
               2. (object)(class)SmithWatermanConstantGapScoring
               3. (class)SmithWatermanGapScoringFromFn
         2. org.bdgenomics.adam.converters
            1. (class)ADAMRecordConverter
            2. (object)(case class)AttrKey
            3. (class)SAMRecordConverter
            4. (object)
               VariantAnnotationConverter
            5. (object)(class)VariantContextConverter
            6. (class)VCFLine
            7. (object)
               VCFLineConverter
            8. (class)VCFLineParser
         3. org.bdgenomics.adam.core
            1. org.bdgenomics.adam.core.util
               1. (object)
                  BuildInformation
         4. org.bdgenomics.adam.io
            1. (class)InterleavedFastqInputFormat
         5. org.bdgenomics.adam.metrics
            1. (object)
               BaseQualityScores
            2. (class)BooleanComparisons
            3. (object)(trait)BucketComparisons
            4. (object)(class)Collection
            5. (class)CombinedComparisons
            6. (object)
               DefaultComparisons
            7. (object)
               DupeMismatch
            8. (class)LongComparisons
            9. (object)
               MappedPosition
            10. (object)
                MapQualityScores
            11. (object)
                OverMatched
            12. (class)PointComparisons
            1. org.bdgenomics.adam.metrics.aggregators
               1. (trait)Aggregated
               2. (object)(class)AggregatedCollection
               3. (trait)Aggregator
               4. (class)CombinedAggregator
               5. (class)HistogramAggregator
               6. (class)UniqueAggregator
               7. (class)UniqueWritable
               8. (trait)Writable
            2. org.bdgenomics.adam.metrics.filters
               1. (class)CombinedFilter
               2. (class)ComparisonsFilter
               3. (trait)GeneratorFilter
         6. org.bdgenomics.adam.models
            1. (case class)ADAMRod
            2. (object)(class)ADAMVariantContext
            3. (case class)Attribute
            4. (object)(case class)Consensus
            5. (object)(case class)ReadBucket
            6. (class)ReadBucketSerializer
            7. (object)(class)RecordGroupDictionary
            8. (trait)ReferenceMapping
            9. (object)(case class)ReferencePosition
            10. (object)(case class)ReferencePositionPair
            11. (class)ReferencePositionPairSerializer
            12. (class)ReferencePositionSerializer
            13. (object)(case class)ReferencePositionWithOrientation
            14. (class)ReferencePositionWithOrientationSerializer
            15. (object)(case class)ReferenceRegion
            16. (class)ReferenceRegionSerializer
            17. (case class)SAMFileHeaderWritable
            18. (object)(class)SequenceDictionary
            19. (object)(class)SequenceRecord
            20. (object)(case class)SingleReadBucket
            21. (class)SingleReadBucketSerializer
            22. (object)(class)SnpTable
            23. (object)
                TagType
         7. org.bdgenomics.adam.plugins
            1. (trait)AccessControl
            2. (trait)ADAMPlugin
            3. (class)EmptyAccessControl
         8. org.bdgenomics.adam.predicates
            1. (object)
               ADAMGenotypeConditions
            2. (trait)ADAMPredicate
            3. (object)
               ADAMRecordConditions
            4. (object)
               ColumnReaderInput
            5. (class)GenotypeRecordPASSPredicate
            6. (class)HighQualityReadPredicate
            7. (class)LocusPredicate
            8. (object)
               PredicateUtils
            9. (class)UniqueMappedReadPredicate
         9. org.bdgenomics.adam.projections
            1. (object)
               ADAMDatabaseVariantAnnotationField
            2. (object)
               ADAMFlatGenotypeField
            3. (object)
               ADAMNucleotideContigFragmentField
            4. (object)
               ADAMRecordField
            5. (class)ADAMVariantField
            6. (class)FieldEnumeration
            7. (trait)FieldValue
            8. (object)
               Filter
            9. (object)
               Projection
            10. (class)VariantCallingAnnotationsField
            1. org.bdgenomics.adam.projections.variation
               1. (object)
                  ADAMGenotypeField
         10. org.bdgenomics.adam.rdd
             1. (object)(class)ADAMContext
             2. (class)ADAMNucleotideContigFragmentRDDFunctions
             3. (class)ADAMPileupRDDFunctions
             4. (class)ADAMRDDFunctions
             5. (class)ADAMRecordRDDFunctions
             6. (class)ADAMRodRDDFunctions
             7. (class)ADAMSequenceDictionaryRDDAggregator
             8. (class)ADAMSpecificRecordSequenceDictionaryRDDAggregator
             9. (object)(case class)DuplicateMetrics
             10. (object)
                 FlagStat
             11. (object)(case class)FlagStatMetrics
             12. (object)(class)GenomicRegionPartitioner
             13. (object)(case class)GenotypesSummary
             14. (object)(case class)GenotypesSummaryCounts
             15. (object)
                 GenotypesSummaryFormatting
             16. (object)(class)MultiContigNonoverlappingRegions
             17. (object)(class)NonoverlappingRegions
             18. (object)
                 RegionJoin
             1. org.bdgenomics.adam.rdd.comparisons
                1. (object)(class)ComparisonTraversalEngine
             2. org.bdgenomics.adam.rdd.recalibration
                1. (class)AbstractCovariate
                2. (object)(class)Aggregate
                3. (object)(class)BaseQualityRecalibration
                4. (trait)Covariate
                5. (class)CovariateKey
                6. (object)(class)CovariateSpace
                7. (class)CycleCovariate
                8. (class)DinucCovariate
                9. (object)(class)Observation
                10. (object)(class)ObservationAccumulator
                11. (class)ObservationTable
                12. (object)(class)RecalibrationTable
                13. (object)(class)Recalibrator
             3. org.bdgenomics.adam.rdd.variation
                1. (class)ADAMGenotypeRDDFunctions
                2. (class)ADAMVariantContextRDDFunctions
                3. (object)(class)ADAMVariationContext
                4. (object)(class)ADAMVCFOutputFormat
                5. (object)(class)ConcordanceTable
         11. org.bdgenomics.adam.rich
             1. (object)(class)DecadentRead
             2. (class)IlluminaOptics
             3. (object)
                ReferenceMappingContext
             4. (object)(class)RichADAMGenotype
             5. (object)(class)RichADAMRecord
             6. (object)(class)RichADAMVariant
             7. (object)(class)RichCigar
         12. org.bdgenomics.adam.serialization
             1. (class)ADAMKryoRegistrator
             2. (class)AvroSerializer
             3. (case class)InputStreamWithDecoder
         13. org.bdgenomics.adam.util
             1. (object)(class)ADAMBAMOutputFormat
             2. (object)(class)ADAMSAMOutputFormat
             3. (object)
                AttributeUtils
             4. (object)
                Base
             5. (trait)ByteAccess
             6. (class)ByteArrayByteAccess
             7. (class)ByteArrayLocator
             8. (class)CredentialsProperties
             9. (case class)DeletionEvent
             10. (object)(trait)FileLocator
             11. (object)
                 HadoopUtil
             12. (object)(class)Histogram
             13. (object)
                 ImplicitJavaConversions
             14. (case class)InsertionEvent
             15. (class)IntervalListReader
             16. (class)LocalFileByteAccess
             17. (class)LocalFileLocator
             18. (object)
                 MapTools
             19. (case class)MatchEvent
             20. (object)(class)MdTag
             21. (object)
                 MdTagEvent
             22. (case class)MismatchEvent
             23. (object)
                 NormalizationUtils
             24. (class)ParquetFileTraversable
             25. (object)
                 ParquetLogger
             26. (object)
                 PhredUtils
             27. (class)Pileup
             28. (class)PileupEvent
             29. (object)(class)PileupTraversable
             30. (object)(class)QualityScore
             31. (object)(class)RegExp
             32. (class)S3ByteAccess
             33. (class)S3FileLocator
             34. (class)SerializableAWSCredentials
             35. (object)
                 Util
             36. (object)
                 VcfHeaderUtils
             37. (object)
                 VcfStringUtils