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
            2. (class)SAMRecordConverter
            3. (object)
               VariantAnnotations
         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. (object)(case class)Coverage
            4. (class)DNAAlphabet
            5. (object)(class)MultiContigNonoverlappingRegions
            6. (object)(class)NonoverlappingRegions
            7. (object)
               OptionalPositionOrdering
            8. (trait)OptionalReferenceOrdering
            9. (object)
               OptionalRegionOrdering
            10. (object)
                PositionOrdering
            11. (object)(case class)ProgramRecord
            12. (object)(case class)ReadBucket
            13. (class)ReadBucketSerializer
            14. (object)(case class)RecordGroup
            15. (object)(case class)RecordGroupDictionary
            16. (trait)ReferenceOrdering
            17. (object)(class)ReferencePosition
            18. (object)(case class)ReferencePositionPair
            19. (class)ReferencePositionPairSerializer
            20. (class)ReferencePositionSerializer
            21. (object)(case class)ReferenceRegion
            22. (class)ReferenceRegionSerializer
            23. (object)
                RegionOrdering
            24. (object)(class)SAMFileHeaderWritable
            25. (object)(class)SequenceDictionary
            26. (object)
                SequenceOrderingByName
            27. (object)
                SequenceOrderingByRefIdx
            28. (object)(case class)SequenceRecord
            29. (object)(case class)SingleReadBucket
            30. (class)SingleReadBucketSerializer
            31. (object)(class)SnpTable
            32. (case class)Symbol
            33. (object)
                TagType
            34. (object)(class)VariantContext
            35. (case class)VCFHeaderWritable
         6. org.bdgenomics.adam.projections
            1. (object)
               AlignmentRecordField
            2. (object)
               DatabaseVariantAnnotationField
            3. (object)
               DbxrefField
            4. (object)
               FeatureField
            5. (class)FieldEnumeration
            6. (trait)FieldValue
            7. (object)
               Filter
            8. (object)
               GenotypeField
            9. (object)
               NucleotideContigFragmentField
            10. (object)
                OntologyTermField
            11. (object)
                Projection
            12. (object)
                VariantCallingAnnotationsField
            13. (object)
                VariantField
         7. org.bdgenomics.adam.rdd
            1. (object)(class)ADAMContext
            2. (trait)ADAMSaveAnyArgs
            3. (class)AvroGenomicRDD
            4. (class)AvroReadGroupGenomicRDD
            5. (trait)BroadcastRegionJoin
            6. (object)
               FileMerger
            7. (case class)FullOuterShuffleRegionJoin
            8. (case class)GenomeBins
            9. (object)(case class)GenomicPositionPartitioner
            10. (trait)GenomicRDD
            11. (object)(case class)GenomicRegionPartitioner
            12. (case class)InnerBroadcastRegionJoin
            13. (case class)InnerShuffleRegionJoin
            14. (case class)InnerShuffleRegionJoinAndGroupByLeft
            15. (case class)LeftOuterShuffleRegionJoin
            16. (class)MultisampleAvroGenomicRDD
            17. (trait)MultisampleGenomicRDD
            18. (case class)ReferencePartitioner
            19. (trait)RegionJoin
            20. (case class)RightOuterBroadcastRegionJoin
            21. (case class)RightOuterShuffleRegionJoin
            22. (case class)RightOuterShuffleRegionJoinAndGroupByLeft
            23. (trait)ShuffleRegionJoin
            24. (trait)Unaligned
            1. org.bdgenomics.adam.rdd.contig
               1. (object)(case class)NucleotideContigFragmentRDD
            2. org.bdgenomics.adam.rdd.features
               1. (case class)CoverageRDD
               2. (object)(case class)FeatureRDD
            3. org.bdgenomics.adam.rdd.fragment
               1. (case class)FragmentRDD
            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. (object)(case class)DuplicateMetrics
               10. (object)
                   FlagStat
               11. (object)(case class)FlagStatMetrics
               12. (case class)IncorrectMDTagException
               13. (class)InstrumentedADAMBAMOutputFormat
               14. (class)InstrumentedADAMBAMOutputFormatHeaderLess
               15. (class)InstrumentedADAMCRAMOutputFormat
               16. (class)InstrumentedADAMCRAMOutputFormatHeaderLess
               17. (class)InstrumentedADAMSAMOutputFormat
               18. (class)InstrumentedADAMSAMOutputFormatHeaderLess
               19. (object)(case class)MDTagging
               20. (object)(case class)UnalignedReadRDD
               1. org.bdgenomics.adam.rdd.read.realignment
                  1. (object)(class)IndelRealignmentTarget
                  2. (class)IndelRealignmentTargetSerializer
                  3. (object)(class)RealignmentTargetFinder
                  4. (object)
                     TargetOrdering
                  5. (object)(case class)TargetSet
                  6. (class)TargetSetSerializer
                  7. (object)
                     ZippedTargetOrdering
                  8. (case class)ZippedTargetSet
                  9. (class)ZippedTargetSetSerializer
               2. org.bdgenomics.adam.rdd.read.recalibration
                  1. (class)AbstractCovariate
                  2. (object)(class)Aggregate
                  3. (object)(class)BaseQualityRecalibration
                  4. (trait)Covariate
                  5. (class)CovariateKey
                  6. (object)(class)CovariateSpace
                  7. (class)CycleCovariate
                  8. (class)DinucCovariate
                  9. (class)ExtrasTables
                  10. (object)(class)Observation
                  11. (object)(class)ObservationAccumulator
                  12. (class)ObservationTable
                  13. (class)QualityTable
                  14. (object)(class)RecalibrationTable
                  15. (object)(class)Recalibrator
            5. org.bdgenomics.adam.rdd.variation
               1. (class)ADAMHeaderlessVCFOutputFormat
               2. (class)ADAMVCFOutputFormat
               3. (case class)DatabaseVariantAnnotationRDD
               4. (case class)GenotypeRDD
               5. (case class)VariantContextRDD
               6. (case class)VariantRDD
         8. org.bdgenomics.adam.rich
            1. (class)IlluminaOptics
            2. (case class)ReferenceSequenceContext
            3. (object)(class)RichAlignmentRecord
            4. (object)(class)RichCigar
            5. (object)(class)RichGenotype
            6. (object)(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. (object)
                ImplicitJavaConversions
             4. (class)IntervalListReader
             5. (object)
                MapTools
             6. (object)(class)MdTag
             7. (object)
                MdTagEvent
             8. (class)ParquetFileTraversable
             9. (object)
                ParquetLogger
             10. (object)
                 PhredUtils
             11. (object)(class)QualityScore
             12. (object)(case class)ReferenceContigMap
             13. (trait)ReferenceFile
             14. (object)(class)RegExp
             15. (object)(class)TwoBitFile
             16. (class)TwoBitFileSerializer
             17. (object)
                 Util