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. (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. (class)BlockExtractable
            4. (case class)CDS
            5. (object)(case class)Coverage
            6. (class)DNAAlphabet
            7. (case class)Exon
            8. (trait)Extractable
            9. (case class)Gene
            10. (object)(class)MultiContigNonoverlappingRegions
            11. (object)(class)NonoverlappingRegions
            12. (object)
                OptionalPositionOrdering
            13. (trait)OptionalReferenceOrdering
            14. (object)
                OptionalRegionOrdering
            15. (object)
                PositionOrdering
            16. (object)(case class)ProgramRecord
            17. (object)(case class)ReadBucket
            18. (class)ReadBucketSerializer
            19. (object)(case class)RecordGroup
            20. (object)(case class)RecordGroupDictionary
            21. (trait)ReferenceOrdering
            22. (object)(class)ReferencePosition
            23. (object)(case class)ReferencePositionPair
            24. (class)ReferencePositionPairSerializer
            25. (class)ReferencePositionSerializer
            26. (object)(case class)ReferenceRegion
            27. (class)ReferenceRegionSerializer
            28. (object)
                ReferenceUtils
            29. (object)
                RegionOrdering
            30. (object)(class)SAMFileHeaderWritable
            31. (object)(class)SequenceDictionary
            32. (object)
                SequenceOrderingByName
            33. (object)
                SequenceOrderingByRefIdx
            34. (object)(case class)SequenceRecord
            35. (object)(case class)SingleReadBucket
            36. (class)SingleReadBucketSerializer
            37. (object)(class)SnpTable
            38. (case class)Symbol
            39. (object)
                TagType
            40. (case class)Transcript
            41. (case class)UTR
            42. (object)(class)VariantContext
            43. (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. (case class)GenomeBins
            6. (object)(case class)GenomicPositionPartitioner
            7. (trait)GenomicRDD
            8. (object)(case class)GenomicRegionPartitioner
            9. (class)MultisampleAvroGenomicRDD
            10. (trait)MultisampleGenomicRDD
            11. (case class)ReferencePartitioner
            12. (trait)RegionJoin
            13. (trait)Unaligned
            1. org.bdgenomics.adam.rdd.contig
               1. (object)(case class)NucleotideContigFragmentRDD
            2. org.bdgenomics.adam.rdd.features
               1. (class)BEDParser
               2. (case class)CoverageRDD
               3. (class)FeatureFile
               4. (trait)FeatureParser
               5. (object)(case class)FeatureRDD
               6. (case class)GeneRDD
               7. (object)(class)GFF3Parser
               8. (object)(class)GTFParser
               9. (class)IntervalListParser
               10. (class)NarrowPeakParser
            3. org.bdgenomics.adam.rdd.fragment
               1. (case class)FragmentRDD
            4. org.bdgenomics.adam.rdd.read
               1. (object)(class)ADAMBAMOutputFormat
               2. (class)ADAMBAMOutputFormatHeaderLess
               3. (object)(class)ADAMSAMOutputFormat
               4. (class)ADAMSAMOutputFormatHeaderLess
               5. (case class)AlignedReadRDD
               6. (trait)AlignmentRecordRDD
               7. (object)(case class)DuplicateMetrics
               8. (object)
                  FlagStat
               9. (object)(case class)FlagStatMetrics
               10. (case class)IncorrectMDTagException
               11. (class)InstrumentedADAMBAMOutputFormat
               12. (class)InstrumentedADAMBAMOutputFormatHeaderLess
               13. (class)InstrumentedADAMSAMOutputFormat
               14. (class)InstrumentedADAMSAMOutputFormatHeaderLess
               15. (object)(case class)MDTagging
               16. (object)(case class)UnalignedReadRDD
               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
            5. org.bdgenomics.adam.rdd.variation
               1. (object)(class)ADAMVCFOutputFormat
               2. (case class)DatabaseVariantAnnotationRDD
               3. (case class)GenotypeRDD
               4. (case class)VariantContextRDD
               5. (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