1. org
   1. org.bdgenomics
      1. org.bdgenomics.adam
         1. org.bdgenomics.adam.algorithms
            1. org.bdgenomics.adam.algorithms.consensus
               1. (object)(class)ConsensusGenerator
            2. org.bdgenomics.adam.algorithms.smithwaterman
               1. (trait)SmithWaterman
               2. (case class)SmithWatermanConstantGapScoring
         2. org.bdgenomics.adam.converters
            1. (class)AlignmentRecordConverter
            2. (object)
               DefaultHeaderLines
            3. (object)(class)VariantContextConverter
         3. org.bdgenomics.adam.instrumentation
            1. (object)
               Timers
         4. org.bdgenomics.adam.io
            1. (class)FastqInputFormat
            2. (class)FastqRecordReader
            3. (class)InterleavedFastqInputFormat
            4. (class)SingleFastqInputFormat
         5. org.bdgenomics.adam.models
            1. (object)(trait)Alphabet
            2. (case class)Attribute
            3. (case class)Coverage
            4. (class)DNAAlphabet
            5. (object)(case class)MdTag
            6. (object)
               MdTagEvent
            7. (object)
               OptionalPositionOrdering
            8. (trait)OptionalReferenceOrdering
            9. (object)
               OptionalRegionOrdering
            10. (object)
                PositionOrdering
            11. (object)(case class)ReadGroup
            12. (object)(case class)ReadGroupDictionary
            13. (trait)ReferenceOrdering
            14. (object)(class)ReferencePosition
            15. (class)ReferencePositionSerializer
            16. (object)(case class)ReferenceRegion
            17. (class)ReferenceRegionSerializer
            18. (object)
                RegionOrdering
            19. (object)(class)SequenceDictionary
            20. (object)(case class)SequenceRecord
            21. (object)(class)SnpTable
            22. (case class)Symbol
            23. (object)
                TagType
            24. (object)(class)VariantContext
            25. (class)VariantContextSerializer
         6. org.bdgenomics.adam.projections
            1. (object)
               AlignmentRecordField
            2. (object)
               DbxrefField
            3. (object)
               FeatureField
            4. (class)FieldEnumeration
            5. (trait)FieldValue
            6. (object)
               Filter
            7. (object)
               FragmentField
            8. (object)
               GenotypeField
            9. (object)
               NucleotideContigFragmentField
            10. (object)
                OntologyTermField
            11. (object)
                Projection
            12. (object)
                ReadField
            13. (object)
                ReadGroupField
            14. (object)
                ReferenceField
            15. (object)
                SampleField
            16. (object)
                SequenceField
            17. (object)
                SliceField
            18. (object)
                TranscriptEffectField
            19. (object)
                VariantAnnotationField
            20. (object)
                VariantCallingAnnotationsField
            21. (object)
                VariantField
         7. org.bdgenomics.adam.rdd
            1. (object)(class)ADAMContext
            2. (trait)ADAMSaveAnyArgs
            3. (class)AvroGenomicDataset
            4. (class)AvroReadGroupGenomicDataset
            5. (case class)DatasetBoundGenericGenomicDataset
            6. (trait)DatasetBoundGenomicDataset
            7. (case class)FullOuterShuffleRegionJoin
            8. (case class)GenericConverter
            9. (class)GenericGenomicDataset
            10. (case class)GenomeBins
            11. (case class)GenomicBroadcast
            12. (trait)GenomicDataset
            13. (trait)GenomicDatasetConversion
            14. (trait)GenomicDatasetWithLineage
            15. (object)(case class)GenomicPositionPartitioner
            16. (object)(case class)GenomicRegionPartitioner
            17. (trait)InFormatter
            18. (trait)InFormatterCompanion
            19. (case class)InnerShuffleRegionJoin
            20. (case class)InnerShuffleRegionJoinAndGroupByLeft
            21. (case class)InnerTreeRegionJoin
            22. (case class)InnerTreeRegionJoinAndGroupByRight
            23. (case class)LeftOuterShuffleRegionJoin
            24. (case class)LeftOuterShuffleRegionJoinAndGroupByLeft
            25. (class)MultisampleAvroGenomicDataset
            26. (trait)MultisampleGenomicDataset
            27. (trait)OutFormatter
            28. (case class)RDDBoundGenericGenomicDataset
            29. (case class)ReferencePartitioner
            30. (class)RegionJoin
            31. (case class)RightOuterShuffleRegionJoinAndGroupByLeft
            32. (case class)RightOuterTreeRegionJoin
            33. (case class)RightOuterTreeRegionJoinAndGroupByRight
            34. (class)ShuffleRegionJoin
            35. (trait)SortedIntervalPartitionJoinWithVictims
            36. (trait)TreeRegionJoin
            37. (trait)VictimlessSortedIntervalPartitionJoin
            1. org.bdgenomics.adam.rdd.contig
               1. (case class)DatasetBoundNucleotideContigFragmentDataset
               2. (object)(class)NucleotideContigFragmentDataset
               3. (case class)ParquetUnboundNucleotideContigFragmentDataset
               4. (case class)RDDBoundNucleotideContigFragmentDataset
            2. org.bdgenomics.adam.rdd.feature
               1. (object)(case class)BEDInFormatter
               2. (case class)BEDOutFormatter
               3. (object)(class)CoverageDataset
               4. (case class)DatasetBoundCoverageDataset
               5. (case class)DatasetBoundFeatureDataset
               6. (object)(class)FeatureDataset
               7. (object)(case class)GFF3InFormatter
               8. (case class)GFF3OutFormatter
               9. (object)(case class)GTFInFormatter
               10. (case class)GTFOutFormatter
               11. (object)(case class)NarrowPeakInFormatter
               12. (case class)NarrowPeakOutFormatter
               13. (case class)ParquetUnboundCoverageDataset
               14. (case class)ParquetUnboundFeatureDataset
               15. (case class)RDDBoundCoverageDataset
               16. (case class)RDDBoundFeatureDataset
            3. org.bdgenomics.adam.rdd.fragment
               1. (case class)DatasetBoundFragmentDataset
               2. (object)(class)FragmentDataset
               3. (object)(class)InterleavedFASTQInFormatter
               4. (case class)ParquetUnboundFragmentDataset
               5. (case class)RDDBoundFragmentDataset
               6. (object)(class)Tab5InFormatter
               7. (object)(class)Tab6InFormatter
            4. org.bdgenomics.adam.rdd.read
               1. (class)ADAMBAMOutputFormat
               2. (class)ADAMBAMOutputFormatHeaderLess
               3. (class)ADAMCRAMOutputFormat
               4. (class)ADAMCRAMOutputFormatHeaderLess
               5. (class)ADAMSAMOutputFormat
               6. (class)ADAMSAMOutputFormatHeaderLess
               7. (object)(class)AlignmentRecordDataset
               8. (trait)AnySAMInFormatter
               9. (trait)AnySAMInFormatterCompanion
               10. (case class)AnySAMOutFormatter
               11. (object)(case class)BAMInFormatter
               12. (case class)DatasetBoundAlignmentRecordDataset
               13. (object)(class)FASTQInFormatter
               14. (case class)IncorrectMDTagException
               15. (class)InstrumentedADAMBAMOutputFormat
               16. (class)InstrumentedADAMBAMOutputFormatHeaderLess
               17. (class)InstrumentedADAMCRAMOutputFormat
               18. (class)InstrumentedADAMCRAMOutputFormatHeaderLess
               19. (class)InstrumentedADAMSAMOutputFormat
               20. (class)InstrumentedADAMSAMOutputFormatHeaderLess
               21. (case class)ParquetUnboundAlignmentRecordDataset
               22. (object)(case class)QualityScoreBin
               23. (case class)RDDBoundAlignmentRecordDataset
               24. (class)ReferencePositionPairSerializer
               25. (object)(case class)SAMInFormatter
               26. (class)SingleReadBucketSerializer
            5. org.bdgenomics.adam.rdd.variant
               1. (class)ADAMVCFOutputFormat
               2. (case class)DatasetBoundGenotypeDataset
               3. (case class)DatasetBoundVariantContextDataset
               4. (case class)DatasetBoundVariantDataset
               5. (object)(class)GenotypeDataset
               6. (case class)ParquetUnboundGenotypeDataset
               7. (case class)ParquetUnboundVariantDataset
               8. (case class)RDDBoundGenotypeDataset
               9. (case class)RDDBoundVariantContextDataset
               10. (case class)RDDBoundVariantDataset
               11. (object)(class)VariantContextDataset
               12. (object)(class)VariantDataset
               13. (object)(case class)VCFInFormatter
               14. (case class)VCFOutFormatter
         8. org.bdgenomics.adam.rich
            1. (object)(case class)RichAlignmentRecord
            2. (object)(case class)RichVariant
         9. org.bdgenomics.adam.serialization
            1. (class)ADAMKryoRegistrator
            2. (class)AvroSerializer
            3. (case class)InputStreamWithDecoder
            4. (class)WritableSerializer
         10. org.bdgenomics.adam.sql
             1. (object)(case class)AlignmentRecord
             2. (object)(case class)Dbxref
             3. (object)(case class)Feature
             4. (object)(case class)Fragment
             5. (object)(case class)Genotype
             6. (object)(case class)NucleotideContigFragment
             7. (object)(case class)OntologyTerm
             8. (object)(case class)ProcessingStep
             9. (object)(case class)Reference
             10. (object)(case class)TranscriptEffect
             11. (object)(case class)Variant
             12. (object)(case class)VariantAnnotation
             13. (object)(case class)VariantCallingAnnotations
             14. (object)(case class)VariantContext
         11. org.bdgenomics.adam.util
             1. (object)
                ADAMShell
             2. (object)
                AttributeUtils
             3. (object)
                FileExtensions
             4. (object)
                GenomeFileReader
             5. (case class)IndexedFastaFile
             6. (class)ParquetFileTraversable
             7. (object)
                ParquetLogger
             8. (object)
                PhredUtils
             9. (object)(case class)ReferenceContigMap
             10. (class)ReferenceContigMapSerializer
             11. (trait)ReferenceFile
             12. (object)
                 SequenceDictionaryReader
             13. (object)
                 TextRddWriter
             14. (class)TwoBitFile
             15. (class)TwoBitFileSerializer