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.prefixtrie
               1. (object)(trait)DNAPrefixTrie
            3. 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.metrics
            1. (object)
               BaseQualityScores
            2. (class)BooleanComparisons
            3. (object)(trait)BucketComparisons
            4. (class)CombinedComparisons
            5. (object)
               DefaultComparisons
            6. (object)
               DupeMismatch
            7. (class)LongComparisons
            8. (object)
               MappedPosition
            9. (object)
               MapQualityScores
            10. (object)
                OverMatched
            11. (class)PointComparisons
            1. org.bdgenomics.adam.metrics.filters
               1. (class)CombinedFilter
               2. (class)ComparisonsFilter
               3. (trait)GeneratorFilter
         7. org.bdgenomics.adam.models
            1. (case class)Attribute
            2. (object)(class)BaseFeature
            3. (object)(class)BEDFeature
            4. (class)BlockExtractable
            5. (case class)CDS
            6. (object)(case class)Consensus
            7. (case class)Exon
            8. (trait)Extractable
            9. (case class)Gene
            10. (class)GTFFeature
            11. (object)(class)IndelTable
            12. (trait)Interval
            13. (class)NarrowPeakFeature
            14. (class)OrderedTrackedLayout
            15. (object)(case class)ProgramRecord
            16. (object)(case class)ReadBucket
            17. (class)ReadBucketSerializer
            18. (object)(class)RecordGroup
            19. (object)(class)RecordGroupDictionary
            20. (trait)ReferenceMapping
            21. (object)(case class)ReferencePosition
            22. (object)(case class)ReferencePositionPair
            23. (class)ReferencePositionPairSerializer
            24. (class)ReferencePositionSerializer
            25. (object)(case class)ReferencePositionWithOrientation
            26. (class)ReferencePositionWithOrientationSerializer
            27. (object)(case class)ReferenceRegion
            28. (class)ReferenceRegionSerializer
            29. (object)(case class)ReferenceRegionWithOrientation
            30. (object)
                ReferenceUtils
            31. (case class)Rod
            32. (object)(class)SAMFileHeaderWritable
            33. (object)(class)SequenceDictionary
            34. (object)(class)SequenceRecord
            35. (object)(case class)SingleReadBucket
            36. (class)SingleReadBucketSerializer
            37. (object)(class)SnpTable
            38. (object)
                TagType
            39. (object)(trait)TrackedLayout
            40. (case class)Transcript
            41. (case class)UTR
            42. (object)(class)VariantContext
            43. (case class)VCFHeaderWritable
         8. org.bdgenomics.adam.plugins
            1. (trait)AccessControl
            2. (trait)ADAMPlugin
            3. (class)EmptyAccessControl
         9. org.bdgenomics.adam.predicates
            1. (trait)ADAMPredicate
            2. (object)
               AlignmentRecordConditions
            3. (object)
               ColumnReaderInput
            4. (object)(case class)FieldCondition
            5. (object)
               GenotypeConditions
            6. (class)GenotypeRecordPASSPredicate
            7. (class)HighQualityReadPredicate
            8. (class)LocusPredicate
            9. (object)
               PredicateUtils
            10. (object)(class)RecordCondition
            11. (class)UniqueMappedReadPredicate
         10. 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
         11. org.bdgenomics.adam.rdd
             1. (object)(class)ADAMContext
             2. (trait)ADAMParquetArgs
             3. (class)ADAMRDDFunctions
             4. (trait)ADAMSaveAnyArgs
             5. (trait)ADAMSaveArgs
             6. (class)ADAMSequenceDictionaryRDDAggregator
             7. (class)ADAMSpecificRecordSequenceDictionaryRDDAggregator
             8. (object)
                BroadcastRegionJoin
             9. (class)Coverage
             10. (case class)GenomeBins
             11. (object)(case class)GenomicPositionPartitioner
             12. (object)(case class)GenomicRegionPartitioner
             13. (class)InstrumentedADAMAvroParquetOutputFormat
             14. (object)(class)MultiContigNonoverlappingRegions
             15. (object)(class)NonoverlappingRegions
             16. (object)(class)PairingRDD
             17. (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)NarrowPeakParser
             3. org.bdgenomics.adam.rdd.normalization
                1. (object)
                   LengthNormalization
                2. (object)
                   ZScoreNormalization
             4. org.bdgenomics.adam.rdd.pileup
                1. (class)PileupRDDFunctions
                2. (class)RodRDDFunctions
             5. 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.comparisons
                   1. (object)(class)ComparisonTraversalEngine
                2. 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
                3. 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. (object)(class)Observation
                   10. (object)(class)ObservationAccumulator
                   11. (class)ObservationTable
                   12. (object)(class)RecalibrationTable
                   13. (object)(class)Recalibrator
             6. org.bdgenomics.adam.rdd.variation
                1. (object)(class)ADAMVCFOutputFormat
                2. (object)(class)ConcordanceTable
                3. (class)GenotypeRDDFunctions
                4. (object)(case class)GenotypesSummary
                5. (object)(case class)GenotypesSummaryCounts
                6. (object)
                   GenotypesSummaryFormatting
                7. (class)VariantContextRDDFunctions
         12. org.bdgenomics.adam.rich
             1. (object)(class)DecadentRead
             2. (class)IlluminaOptics
             3. (object)
                ReferenceMappingContext
             4. (object)(class)RichAlignmentRecord
             5. (object)(class)RichCigar
             6. (object)(class)RichGenotype
             7. (object)(class)RichVariant
         13. org.bdgenomics.adam.serialization
             1. (class)ADAMKryoRegistrator
             2. (class)AvroSerializer
             3. (case class)InputStreamWithDecoder
         14. org.bdgenomics.adam.util
             1. (object)
                AttributeUtils
             2. (object)
                Base
             3. (case class)DeletionEvent
             4. (object)
                HadoopUtil
             5. (object)
                ImplicitJavaConversions
             6. (case class)InsertionEvent
             7. (class)IntervalListReader
             8. (object)
                MapTools
             9. (case class)MatchEvent
             10. (object)(class)MdTag
             11. (object)
                 MdTagEvent
             12. (case class)MismatchEvent
             13. (object)
                 NormalizationUtils
             14. (class)ParquetFileTraversable
             15. (object)
                 ParquetLogger
             16. (object)
                 PhredUtils
             17. (class)Pileup
             18. (class)PileupEvent
             19. (object)(class)PileupTraversable
             20. (object)(class)QualityScore
             21. (object)(class)RegExp
             22. (object)
                 SequenceUtils
             23. (object)(class)TwoBitFile
             24. (object)(case class)TwoBitRecord
             25. (object)
                 Util
             26. (object)
                 VcfHeaderUtils
             27. (object)
                 VcfStringUtils