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
                  1. 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
                  2. org.bdgenomics.adam.core
                      1. org.bdgenomics.adam.core.util
                        1. (object)
                          BuildInformation
                    1. org.bdgenomics.adam.instrumentation
                      1. (object)
                        Timers
                    2. org.bdgenomics.adam.io
                      1. (class)InterleavedFastqInputFormat
                      2. (class)SingleFastqInputFormat
                    3. 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
                    4. org.bdgenomics.adam.plugins
                      1. (trait)AccessControl
                      2. (trait)ADAMPlugin
                      3. (class)EmptyAccessControl
                    5. 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
                    6. 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
                    7. 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
                    8. org.bdgenomics.adam.serialization
                      1. (class)ADAMKryoRegistrator
                      2. (class)AvroSerializer
                      3. (case class)InputStreamWithDecoder
                    9. 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