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)FastqInputFormat
            2. (class)InterleavedFastqInputFormat
            3. (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
            25. (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)
                RecordGroupField
            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)AvroRecordGroupGenomicRDD
            5. (case class)FullOuterShuffleRegionJoin
            6. (case class)GenericGenomicRDD
            7. (case class)GenomeBins
            8. (trait)GenomicDataset
            9. (trait)GenomicDatasetConversion
            10. (object)(case class)GenomicPositionPartitioner
            11. (trait)GenomicRDD
            12. (trait)GenomicRDDWithLineage
            13. (object)(case class)GenomicRegionPartitioner
            14. (trait)InFormatter
            15. (trait)InFormatterCompanion
            16. (case class)InnerShuffleRegionJoin
            17. (case class)InnerShuffleRegionJoinAndGroupByLeft
            18. (case class)InnerTreeRegionJoin
            19. (case class)InnerTreeRegionJoinAndGroupByRight
            20. (case class)LeftOuterShuffleRegionJoin
            21. (case class)LeftOuterShuffleRegionJoinAndGroupByLeft
            22. (class)MultisampleAvroGenomicRDD
            23. (trait)MultisampleGenomicRDD
            24. (trait)OutFormatter
            25. (case class)ReferencePartitioner
            26. (class)RegionJoin
            27. (case class)RightOuterShuffleRegionJoinAndGroupByLeft
            28. (case class)RightOuterTreeRegionJoin
            29. (case class)RightOuterTreeRegionJoinAndGroupByRight
            30. (class)ShuffleRegionJoin
            31. (trait)SortedIntervalPartitionJoinWithVictims
            32. (trait)TreeRegionJoin
            33. (trait)VictimlessSortedIntervalPartitionJoin
            1. org.bdgenomics.adam.rdd.contig
               1. (case class)DatasetBoundNucleotideContigFragmentRDD
               2. (object)(class)NucleotideContigFragmentRDD
               3. (case class)ParquetUnboundNucleotideContigFragmentRDD
               4. (case class)RDDBoundNucleotideContigFragmentRDD
            2. org.bdgenomics.adam.rdd.feature
               1. (object)(case class)BEDInFormatter
               2. (case class)BEDOutFormatter
               3. (class)CoverageRDD
               4. (case class)DatasetBoundCoverageRDD
               5. (case class)DatasetBoundFeatureRDD
               6. (object)(class)FeatureRDD
               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)ParquetUnboundCoverageRDD
               14. (case class)ParquetUnboundFeatureRDD
               15. (case class)RDDBoundCoverageRDD
               16. (case class)RDDBoundFeatureRDD
            3. org.bdgenomics.adam.rdd.fragment
               1. (case class)DatasetBoundFragmentRDD
               2. (object)(class)FragmentRDD
               3. (object)(class)InterleavedFASTQInFormatter
               4. (case class)ParquetUnboundFragmentRDD
               5. (case class)RDDBoundFragmentRDD
               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)AlignmentRecordRDD
               8. (trait)AnySAMInFormatter
               9. (trait)AnySAMInFormatterCompanion
               10. (case class)AnySAMOutFormatter
               11. (object)(case class)BAMInFormatter
               12. (case class)DatasetBoundAlignmentRecordRDD
               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)ParquetUnboundAlignmentRecordRDD
               22. (object)(case class)QualityScoreBin
               23. (case class)RDDBoundAlignmentRecordRDD
               24. (class)ReferencePositionPairSerializer
               25. (object)(case class)SAMInFormatter
               26. (class)SingleReadBucketSerializer
            5. org.bdgenomics.adam.rdd.variant
               1. (class)ADAMVCFOutputFormat
               2. (case class)DatasetBoundGenotypeRDD
               3. (case class)DatasetBoundVariantRDD
               4. (object)(class)GenotypeRDD
               5. (case class)ParquetUnboundGenotypeRDD
               6. (case class)ParquetUnboundVariantRDD
               7. (case class)RDDBoundGenotypeRDD
               8. (case class)RDDBoundVariantRDD
               9. (object)(case class)VariantContextRDD
               10. (object)(class)VariantRDD
               11. (object)(case class)VCFInFormatter
               12. (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)(class)AlignmentRecord
             2. (object)(class)Contig
             3. (object)(class)Dbxref
             4. (object)(class)Feature
             5. (object)(class)Fragment
             6. (object)(class)Genotype
             7. (object)(class)NucleotideContigFragment
             8. (object)(class)OntologyTerm
             9. (object)(class)ProcessingStep
             10. (object)(class)TranscriptEffect
             11. (object)(class)Variant
             12. (object)(class)VariantAnnotation
             13. (object)(class)VariantCallingAnnotations
         11. org.bdgenomics.adam.util
             1. (object)
                AttributeUtils
             2. (object)
                GenomeFileReader
             3. (case class)IndexedFastaFile
             4. (class)ParquetFileTraversable
             5. (object)
                ParquetLogger
             6. (object)
                PhredUtils
             7. (object)(case class)ReferenceContigMap
             8. (class)ReferenceContigMapSerializer
             9. (trait)ReferenceFile
             10. (object)
                 SequenceDictionaryReader
             11. (object)
                 TextRddWriter
             12. (class)TwoBitFile
             13. (class)TwoBitFileSerializer