1. org
   1. org.bdgenomics
      1. org.bdgenomics.adam
         1. org.bdgenomics.adam.algorithms
            1. org.bdgenomics.adam.algorithms.consensus
               1. (object)(trait)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. 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)(case class)RecordGroup
            11. (object)(case class)RecordGroupDictionary
            12. (object)
                ReferenceOrdering
            13. (object)(class)ReferencePosition
            14. (class)ReferencePositionSerializer
            15. (object)(case class)ReferenceRegion
            16. (class)ReferenceRegionSerializer
            17. (object)(class)SequenceDictionary
            18. (object)(case class)SequenceRecord
            19. (object)(class)SnpTable
            20. (case class)Symbol
            21. (object)
                TagType
            22. (object)(class)VariantContext
            23. (class)VariantContextSerializer
         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)(class)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)(case class)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)(case class)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)VariantContextRDD
               5. (case class)VariantRDD
               6. (object)(case class)VCFInFormatter
               7. (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. (case class)IndexedFastaFile
             3. (class)ParquetFileTraversable
             4. (object)
                ParquetLogger
             5. (object)
                PhredUtils
             6. (object)(case class)ReferenceContigMap
             7. (trait)ReferenceFile
             8. (class)TwoBitFile
             9. (class)TwoBitFileSerializer