1. org
   1. org.bdgenomics
      1. org.bdgenomics.adam
         1. org.bdgenomics.adam.algorithms
            1. org.bdgenomics.adam.algorithms.smithwaterman
               1. (trait)SmithWaterman
               2. (case class)SmithWatermanConstantGapScoring
         2. org.bdgenomics.adam.converters
            1. (class)AlignmentRecordConverter
         3. org.bdgenomics.adam.instrumentation
            1. (object)
               Timers
         4. org.bdgenomics.adam.io
            1. (class)InterleavedFastqInputFormat
            2. (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)RecordGroup
            12. (object)(case class)RecordGroupDictionary
            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
         6. org.bdgenomics.adam.projections
            1. (object)
               AlignmentRecordField
            2. (object)
               ContigField
            3. (object)
               DbxrefField
            4. (object)
               FeatureField
            5. (class)FieldEnumeration
            6. (trait)FieldValue
            7. (object)
               Filter
            8. (object)
               FragmentField
            9. (object)
               GenotypeField
            10. (object)
                NucleotideContigFragmentField
            11. (object)
                OntologyTermField
            12. (object)
                Projection
            13. (object)
                ReadField
            14. (object)
                RecordGroupMetadataField
            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)AvroGenomicRDD
            4. (class)AvroReadGroupGenomicRDD
            5. (object)
               FileMerger
            6. (case class)FullOuterShuffleRegionJoin
            7. (case class)GenomeBins
            8. (object)(case class)GenomicPositionPartitioner
            9. (trait)GenomicRDD
            10. (object)(case class)GenomicRegionPartitioner
            11. (trait)InFormatter
            12. (trait)InFormatterCompanion
            13. (case class)InnerShuffleRegionJoin
            14. (case class)InnerShuffleRegionJoinAndGroupByLeft
            15. (case class)InnerTreeRegionJoin
            16. (case class)InnerTreeRegionJoinAndGroupByRight
            17. (case class)LeftOuterShuffleRegionJoin
            18. (class)MultisampleAvroGenomicRDD
            19. (trait)MultisampleGenomicRDD
            20. (trait)OutFormatter
            21. (case class)ReferencePartitioner
            22. (class)RegionJoin
            23. (case class)RightOuterShuffleRegionJoin
            24. (case class)RightOuterShuffleRegionJoinAndGroupByLeft
            25. (case class)RightOuterTreeRegionJoin
            26. (case class)RightOuterTreeRegionJoinAndGroupByRight
            27. (class)ShuffleRegionJoin
            28. (trait)TreeRegionJoin
            29. (trait)Unaligned
            1. org.bdgenomics.adam.rdd.contig
               1. (case class)NucleotideContigFragmentRDD
            2. org.bdgenomics.adam.rdd.feature
               1. (case class)CoverageRDD
               2. (object)(case class)FeatureRDD
            3. org.bdgenomics.adam.rdd.fragment
               1. (case class)FragmentRDD
               2. (object)
                  InterleavedFASTQInFormatter
            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. (case class)AlignedReadRDD
               8. (trait)AlignmentRecordRDD
               9. (trait)AnySAMInFormatter
               10. (trait)AnySAMInFormatterCompanion
               11. (class)AnySAMOutFormatter
               12. (object)
                   BAMInFormatter
               13. (case class)IncorrectMDTagException
               14. (class)InstrumentedADAMBAMOutputFormat
               15. (class)InstrumentedADAMBAMOutputFormatHeaderLess
               16. (class)InstrumentedADAMCRAMOutputFormat
               17. (class)InstrumentedADAMCRAMOutputFormatHeaderLess
               18. (class)InstrumentedADAMSAMOutputFormat
               19. (class)InstrumentedADAMSAMOutputFormatHeaderLess
               20. (class)ReferencePositionPairSerializer
               21. (object)
                   SAMInFormatter
               22. (class)SingleReadBucketSerializer
               23. (object)(case class)UnalignedReadRDD
               1. org.bdgenomics.adam.rdd.read.recalibration
                  1. (object)
                     RecalibrationTable
            5. org.bdgenomics.adam.rdd.variant
               1. (class)ADAMHeaderlessVCFOutputFormat
               2. (class)ADAMVCFOutputFormat
               3. (case class)GenotypeRDD
               4. (case class)VariantAnnotationRDD
               5. (case class)VariantContextRDD
               6. (case class)VariantRDD
               7. (object)
                  VCFInFormatter
               8. (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
         10. org.bdgenomics.adam.util
             1. (object)
                AttributeUtils
             2. (object)
                Flattener
             3. (case class)IndexedFastaFile
             4. (class)ParquetFileTraversable
             5. (object)
                ParquetLogger
             6. (object)
                PhredUtils
             7. (object)(case class)ReferenceContigMap
             8. (trait)ReferenceFile
             9. (class)TwoBitFile
             10. (class)TwoBitFileSerializer