1. org
   1. org.bdgenomics
      1. org.bdgenomics.adam
         1. org.bdgenomics.adam.algorithms
            1. org.bdgenomics.adam.algorithms.realignmenttarget
               1. (class)GenericRange
               2. (object)(case class)IndelRange
               3. (class)IndelRangeSerializer
               4. (object)(class)IndelRealignmentTarget
               5. (class)RangeAccumulator
               6. (object)(class)RealignmentTargetFinder
               7. (object)(case class)SNPRange
               8. (class)SNPRangeSerializer
               9. (object)
                  TargetOrdering
               10. (class)TreeSetSerializer
               11. (object)
                   ZippedTargetOrdering
            2. org.bdgenomics.adam.algorithms.smithwaterman
               1. (class)SmithWaterman
               2. (object)(class)SmithWatermanConstantGapScoring
               3. (class)SmithWatermanGapScoringFromFn
         2. org.bdgenomics.adam.converters
            1. (class)SAMRecordConverter
            2. (object)
               VariantAnnotationConverter
            3. (object)(class)VariantContextConverter
         3. org.bdgenomics.adam.core
            1. org.bdgenomics.adam.core.util
               1. (object)
                  BuildInformation
         4. org.bdgenomics.adam.io
            1. (class)InterleavedFastqInputFormat
         5. org.bdgenomics.adam.metrics
            1. (object)
               BaseQualityScores
            2. (class)BooleanComparisons
            3. (object)(trait)BucketComparisons
            4. (object)(class)Collection
            5. (class)CombinedComparisons
            6. (object)
               DefaultComparisons
            7. (object)
               DupeMismatch
            8. (class)LongComparisons
            9. (object)
               MappedPosition
            10. (object)
                MapQualityScores
            11. (object)
                OverMatched
            12. (class)PointComparisons
            1. org.bdgenomics.adam.metrics.aggregators
               1. (trait)Aggregated
               2. (object)(class)AggregatedCollection
               3. (trait)Aggregator
               4. (class)CombinedAggregator
               5. (class)HistogramAggregator
               6. (class)UniqueAggregator
               7. (class)UniqueWritable
               8. (trait)Writable
            2. org.bdgenomics.adam.metrics.filters
               1. (class)CombinedFilter
               2. (class)ComparisonsFilter
               3. (trait)GeneratorFilter
         6. org.bdgenomics.adam.models
            1. (case class)ADAMRod
            2. (object)(class)ADAMVariantContext
            3. (case class)Attribute
            4. (object)(case class)Consensus
            5. (object)(case class)ReadBucket
            6. (class)ReadBucketSerializer
            7. (object)(class)RecordGroupDictionary
            8. (trait)ReferenceMapping
            9. (object)(case class)ReferencePosition
            10. (object)(case class)ReferencePositionPair
            11. (class)ReferencePositionPairSerializer
            12. (class)ReferencePositionSerializer
            13. (object)(case class)ReferencePositionWithOrientation
            14. (class)ReferencePositionWithOrientationSerializer
            15. (object)(case class)ReferenceRegion
            16. (class)ReferenceRegionSerializer
            17. (object)(class)SequenceDictionary
            18. (object)(class)SequenceRecord
            19. (object)(case class)SingleReadBucket
            20. (class)SingleReadBucketSerializer
            21. (object)(class)SnpTable
            22. (object)
                TagType
         7. org.bdgenomics.adam.plugins
            1. (trait)AccessControl
            2. (trait)ADAMPlugin
            3. (class)EmptyAccessControl
         8. org.bdgenomics.adam.predicates
            1. (class)GenotypeVarFilterPASSPredicate
            2. (class)LocusPredicate
         9. org.bdgenomics.adam.projections
            1. (object)
               ADAMDatabaseVariantAnnotationField
            2. (object)
               ADAMNucleotideContigFragmentField
            3. (object)
               ADAMRecordField
            4. (class)ADAMVariantField
            5. (class)FieldEnumeration
            6. (trait)FieldValue
            7. (object)
               Filter
            8. (object)
               Projection
            9. (class)VariantCallingAnnotationsField
            1. org.bdgenomics.adam.projections.variation
               1. (object)
                  ADAMGenotypeField
         10. org.bdgenomics.adam.rdd
             1. (object)(class)ADAMContext
             2. (class)ADAMNucleotideContigFragmentRDDFunctions
             3. (class)ADAMPileupRDDFunctions
             4. (class)ADAMRDDFunctions
             5. (class)ADAMRecordRDDFunctions
             6. (class)ADAMRodRDDFunctions
             7. (class)ADAMSequenceDictionaryRDDAggregator
             8. (class)ADAMSpecificRecordSequenceDictionaryRDDAggregator
             9. (object)(case class)DuplicateMetrics
             10. (object)
                 FlagStat
             11. (object)(case class)FlagStatMetrics
             12. (object)(class)GenomicRegionPartitioner
             13. (object)(case class)GenotypesSummary
             14. (object)(case class)GenotypesSummaryCounts
             15. (object)
                 GenotypesSummaryFormatting
             16. (object)(class)MultiContigNonoverlappingRegions
             17. (object)(class)NonoverlappingRegions
             18. (object)
                 RegionJoin
             1. org.bdgenomics.adam.rdd.comparisons
                1. (object)(class)ComparisonTraversalEngine
             2. org.bdgenomics.adam.rdd.recalibration
                1. (class)AbstractCovariate
                2. (object)(class)Aggregate
                3. (object)(class)BaseQualityRecalibration
                4. (trait)Covariate
                5. (class)CovariateKey
                6. (object)(class)CovariateSpace
                7. (class)DinucCovariate
                8. (object)(class)Observation
                9. (object)(class)ObservationAccumulator
                10. (class)ObservationTable
                11. (object)(class)RecalibrationTable
                12. (object)(class)Recalibrator
             3. org.bdgenomics.adam.rdd.variation
                1. (class)ADAMGenotypeRDDFunctions
                2. (class)ADAMVariantContextRDDFunctions
                3. (object)(class)ADAMVariationContext
                4. (object)(class)ConcordanceTable
         11. org.bdgenomics.adam.rich
             1. (object)(class)DecadentRead
             2. (class)IlluminaOptics
             3. (class)ReferenceLocation
             4. (object)
                ReferenceMappingContext
             5. (object)(class)RichADAMGenotype
             6. (object)(class)RichADAMRecord
             7. (object)(class)RichADAMVariant
             8. (object)(class)RichCigar
             9. (object)(class)RichRDDReferenceRecords
         12. org.bdgenomics.adam.serialization
             1. (object)
                ADAMKryoProperties
             2. (class)ADAMKryoRegistrator
             3. (class)AvroSerializer
             4. (case class)InputStreamWithDecoder
         13. org.bdgenomics.adam.util
             1. (object)(class)ADAMVCFOutputFormat
             2. (object)
                AttributeUtils
             3. (object)
                Base
             4. (case class)DeletionEvent
             5. (object)
                HadoopUtil
             6. (object)(class)Histogram
             7. (object)
                ImplicitJavaConversions
             8. (case class)InsertionEvent
             9. (class)IntervalListReader
             10. (object)
                 MapTools
             11. (case class)MatchEvent
             12. (object)(class)MdTag
             13. (object)
                 MdTagEvent
             14. (case class)MismatchEvent
             15. (object)
                 NormalizationUtils
             16. (class)ParquetFileTraversable
             17. (object)
                 ParquetLogger
             18. (object)
                 PhredUtils
             19. (class)Pileup
             20. (class)PileupEvent
             21. (object)(class)PileupTraversable
             22. (object)(class)QualityScore
             23. (object)(class)RegExp
             24. (object)
                 Util
             25. (object)
                 VcfHeaderUtils
             26. (object)
                 VcfStringUtils