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. (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. (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. (trait)InFormatter
            13. (trait)InFormatterCompanion
            14. (case class)InnerBroadcastRegionJoin
            15. (case class)InnerShuffleRegionJoin
            16. (case class)InnerShuffleRegionJoinAndGroupByLeft
            17. (case class)LeftOuterShuffleRegionJoin
            18. (class)MultisampleAvroGenomicRDD
            19. (trait)MultisampleGenomicRDD
            20. (trait)OutFormatter
            21. (case class)ReferencePartitioner
            22. (trait)RegionJoin
            23. (case class)RightOuterBroadcastRegionJoin
            24. (case class)RightOuterShuffleRegionJoin
            25. (case class)RightOuterShuffleRegionJoinAndGroupByLeft
            26. (trait)ShuffleRegionJoin
            27. (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
               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. (object)(case class)DuplicateMetrics
               14. (object)
                   FlagStat
               15. (object)(case class)FlagStatMetrics
               16. (case class)IncorrectMDTagException
               17. (class)InstrumentedADAMBAMOutputFormat
               18. (class)InstrumentedADAMBAMOutputFormatHeaderLess
               19. (class)InstrumentedADAMCRAMOutputFormat
               20. (class)InstrumentedADAMCRAMOutputFormatHeaderLess
               21. (class)InstrumentedADAMSAMOutputFormat
               22. (class)InstrumentedADAMSAMOutputFormatHeaderLess
               23. (object)(case class)MDTagging
               24. (object)(case class)SAMInFormatter
               25. (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
               7. (object)(case class)VCFInFormatter
               8. (case class)VCFOutFormatter
         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