1. org
   1. org.bdgenomics
      1. org.bdgenomics.adam
         1. org.bdgenomics.adam.algorithms
            1. org.bdgenomics.adam.algorithms.consensus
               1. (class)ConsensusGenerator
               2. (class)ConsensusGeneratorFromKnowns
               3. (class)ConsensusGeneratorFromReads
               4. (class)ConsensusGeneratorFromSmithWaterman
            2. org.bdgenomics.adam.algorithms.smithwaterman
               1. (class)SmithWaterman
               2. (object)(class)SmithWatermanConstantGapScoring
               3. (class)SmithWatermanGapScoringFromFn
         2. org.bdgenomics.adam.converters
            1. (object)(class)AlignmentRecordConverter
            2. (object)(case class)AttrKey
            3. (class)FastqRecordConverter
            4. (object)
               FragmentConverter
            5. (class)SAMRecordConverter
            6. (object)
               VariantAnnotationConverter
            7. (object)(class)VariantContextConverter
         3. org.bdgenomics.adam.core
            1. org.bdgenomics.adam.core.util
               1. (object)
                  BuildInformation
         4. org.bdgenomics.adam.instrumentation
            1. (object)
               Timers
         5. org.bdgenomics.adam.io
            1. (class)InterleavedFastqInputFormat
            2. (class)SingleFastqInputFormat
         6. org.bdgenomics.adam.models
            1. (object)(trait)Alphabet
            2. (case class)Attribute
            3. (object)(class)BaseFeature
            4. (object)(class)BEDFeature
            5. (class)BlockExtractable
            6. (case class)CDS
            7. (object)(case class)Consensus
            8. (class)DNAAlphabet
            9. (case class)Exon
            10. (trait)Extractable
            11. (case class)Gene
            12. (class)GTFFeature
            13. (object)(class)IndelTable
            14. (trait)Interval
            15. (class)NarrowPeakFeature
            16. (object)
                OptionalPositionOrdering
            17. (trait)OptionalReferenceOrdering
            18. (object)
                OptionalRegionOrdering
            19. (object)
                PositionOrdering
            20. (object)(case class)ProgramRecord
            21. (object)(case class)ReadBucket
            22. (class)ReadBucketSerializer
            23. (object)(class)RecordGroup
            24. (object)(class)RecordGroupDictionary
            25. (trait)ReferenceOrdering
            26. (object)(class)ReferencePosition
            27. (object)(case class)ReferencePositionPair
            28. (class)ReferencePositionPairSerializer
            29. (class)ReferencePositionSerializer
            30. (object)(case class)ReferenceRegion
            31. (class)ReferenceRegionSerializer
            32. (object)
                ReferenceUtils
            33. (object)
                RegionOrdering
            34. (object)(class)SAMFileHeaderWritable
            35. (object)(class)SequenceDictionary
            36. (object)(class)SequenceRecord
            37. (object)(case class)SingleReadBucket
            38. (class)SingleReadBucketSerializer
            39. (object)(class)SnpTable
            40. (case class)Symbol
            41. (object)
                TagType
            42. (case class)Transcript
            43. (case class)UTR
            44. (object)(class)VariantContext
            45. (case class)VCFHeaderWritable
         7. org.bdgenomics.adam.plugins
            1. (trait)AccessControl
            2. (trait)ADAMPlugin
            3. (class)EmptyAccessControl
         8. org.bdgenomics.adam.projections
            1. (object)
               AlignmentRecordField
            2. (object)
               DatabaseVariantAnnotationField
            3. (object)
               FeatureField
            4. (class)FieldEnumeration
            5. (trait)FieldValue
            6. (object)
               Filter
            7. (object)
               GenotypeField
            8. (object)
               NucleotideContigFragmentField
            9. (object)
               Projection
            10. (class)VariantCallingAnnotationsField
            11. (class)VariantField
         9. org.bdgenomics.adam.rdd
            1. (object)(class)ADAMContext
            2. (class)ADAMRDDFunctions
            3. (trait)ADAMSaveAnyArgs
            4. (class)ADAMSequenceDictionaryRDDAggregator
            5. (class)ADAMSpecificRecordSequenceDictionaryRDDAggregator
            6. (object)
               BroadcastRegionJoin
            7. (class)Coverage
            8. (case class)GenomeBins
            9. (object)(case class)GenomicPositionPartitioner
            10. (object)(case class)GenomicRegionPartitioner
            11. (class)InstrumentedADAMAvroParquetOutputFormat
            12. (object)(class)PairingRDD
            13. (case class)ReferencePartitioner
            14. (trait)RegionJoin
            15. (object)
                ShuffleRegionJoin
            1. org.bdgenomics.adam.rdd.contig
               1. (class)NucleotideContigFragmentRDDFunctions
            2. org.bdgenomics.adam.rdd.features
               1. (class)BEDParser
               2. (class)FeatureFile
               3. (trait)FeatureParser
               4. (class)GeneFeatureRDDFunctions
               5. (object)(class)GTFParser
               6. (class)IntervalListParser
               7. (class)NarrowPeakParser
            3. org.bdgenomics.adam.rdd.read
               1. (object)(class)ADAMBAMOutputFormat
               2. (object)(class)ADAMSAMOutputFormat
               3. (class)AlignmentRecordRDDFunctions
               4. (object)(case class)DuplicateMetrics
               5. (object)
                  FlagStat
               6. (object)(case class)FlagStatMetrics
               7. (class)InstrumentedADAMBAMOutputFormat
               8. (class)InstrumentedADAMSAMOutputFormat
               1. org.bdgenomics.adam.rdd.read.realignment
                  1. (object)(class)IndelRealignmentTarget
                  2. (object)(class)RealignmentTargetFinder
                  3. (object)
                     TargetOrdering
                  4. (object)(case class)TargetSet
                  5. (class)TargetSetSerializer
                  6. (object)
                     ZippedTargetOrdering
                  7. (case class)ZippedTargetSet
                  8. (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
            4. org.bdgenomics.adam.rdd.variation
               1. (object)(class)ADAMVCFOutputFormat
               2. (class)GenotypeRDDFunctions
               3. (class)VariantContextRDDFunctions
         10. org.bdgenomics.adam.rich
             1. (object)(class)DecadentRead
             2. (class)IlluminaOptics
             3. (object)(class)RichAlignmentRecord
             4. (object)(class)RichCigar
             5. (object)(class)RichGenotype
             6. (object)(class)RichVariant
         11. org.bdgenomics.adam.serialization
             1. (class)ADAMKryoRegistrator
             2. (class)AvroSerializer
             3. (case class)InputStreamWithDecoder
         12. 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. (object)
                NormalizationUtils
             9. (class)ParquetFileTraversable
             10. (object)
                 ParquetLogger
             11. (object)
                 PhredUtils
             12. (object)(class)QualityScore
             13. (trait)ReferenceFile
             14. (object)(class)RegExp
             15. (object)(class)TwoBitFile
             16. (object)(case class)TwoBitRecord
             17. (object)
                 Util
             18. (object)
                 VcfHeaderUtils
             19. (object)
                 VcfStringUtils