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. (object)(class)VariantContextConverter
         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)(case 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. (case class)FullOuterShuffleRegionJoin
            6. (case class)GenomeBins
            7. (object)(case class)GenomicPositionPartitioner
            8. (trait)GenomicRDD
            9. (object)(case class)GenomicRegionPartitioner
            10. (trait)InFormatter
            11. (trait)InFormatterCompanion
            12. (case class)InnerShuffleRegionJoin
            13. (case class)InnerShuffleRegionJoinAndGroupByLeft
            14. (case class)InnerTreeRegionJoin
            15. (case class)InnerTreeRegionJoinAndGroupByRight
            16. (case class)LeftOuterShuffleRegionJoin
            17. (class)MultisampleAvroGenomicRDD
            18. (trait)MultisampleGenomicRDD
            19. (trait)OutFormatter
            20. (case class)ReferencePartitioner
            21. (class)RegionJoin
            22. (case class)RightOuterShuffleRegionJoin
            23. (case class)RightOuterShuffleRegionJoinAndGroupByLeft
            24. (case class)RightOuterTreeRegionJoin
            25. (case class)RightOuterTreeRegionJoinAndGroupByRight
            26. (class)ShuffleRegionJoin
            27. (trait)TreeRegionJoin
            28. (trait)Unaligned
            1. org.bdgenomics.adam.rdd.contig
               1. (case class)NucleotideContigFragmentRDD
            2. org.bdgenomics.adam.rdd.feature
               1. (object)(case class)BEDInFormatter
               2. (case class)BEDOutFormatter
               3. (case class)CoverageRDD
               4. (object)(case class)FeatureRDD
               5. (object)(case class)GFF3InFormatter
               6. (case class)GFF3OutFormatter
               7. (object)(case class)GTFInFormatter
               8. (case class)GTFOutFormatter
               9. (object)(case class)NarrowPeakInFormatter
               10. (case class)NarrowPeakOutFormatter
            3. org.bdgenomics.adam.rdd.fragment
               1. (object)(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. (object)(case class)AlignmentRecordRDD
               8. (trait)AnySAMInFormatter
               9. (trait)AnySAMInFormatterCompanion
               10. (class)AnySAMOutFormatter
               11. (object)(case class)BAMInFormatter
               12. (case class)IncorrectMDTagException
               13. (class)InstrumentedADAMBAMOutputFormat
               14. (class)InstrumentedADAMBAMOutputFormatHeaderLess
               15. (class)InstrumentedADAMCRAMOutputFormat
               16. (class)InstrumentedADAMCRAMOutputFormatHeaderLess
               17. (class)InstrumentedADAMSAMOutputFormat
               18. (class)InstrumentedADAMSAMOutputFormatHeaderLess
               19. (class)ReferencePositionPairSerializer
               20. (object)(case class)SAMInFormatter
               21. (class)SingleReadBucketSerializer
            5. org.bdgenomics.adam.rdd.variant
               1. (class)ADAMHeaderlessVCFOutputFormat
               2. (object)(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
            4. (class)WritableSerializer
         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. (class)ReferenceContigMapSerializer
             8. (trait)ReferenceFile
             9. (object)(class)TwoBitFile
             10. (class)TwoBitFileSerializer