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. (object)(case class)AttrKey
            2. (class)SAMRecordConverter
            3. (object)
               VariantAnnotationConverter
            4. (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. (object)
               ADAMGenotypeConditions
            2. (trait)ADAMPredicate
            3. (object)
               ADAMRecordConditions
            4. (object)
               ColumnReaderInput
            5. (class)GenotypeRecordPASSPredicate
            6. (class)HighQualityReadPredicate
            7. (class)LocusPredicate
            8. (object)
               PredicateUtils
            9. (class)UniqueMappedReadPredicate
         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)CycleCovariate
                8. (class)DinucCovariate
                9. (object)(class)Observation
                10. (object)(class)ObservationAccumulator
                11. (class)ObservationTable
                12. (object)(class)RecalibrationTable
                13. (object)(class)Recalibrator
             3. org.bdgenomics.adam.rdd.variation
                1. (class)ADAMGenotypeRDDFunctions
                2. (class)ADAMVariantContextRDDFunctions
                3. (object)(class)ADAMVariationContext
                4. (object)(class)ADAMVCFOutputFormat
                5. (object)(class)ConcordanceTable
         11. org.bdgenomics.adam.rich
             1. (object)(class)DecadentRead
             2. (class)IlluminaOptics
             3. (object)
                ReferenceMappingContext
             4. (object)(class)RichADAMGenotype
             5. (object)(class)RichADAMRecord
             6. (object)(class)RichADAMVariant
             7. (object)(class)RichCigar
         12. org.bdgenomics.adam.serialization
             1. (class)ADAMKryoRegistrator
             2. (class)AvroSerializer
             3. (case class)InputStreamWithDecoder
         13. org.bdgenomics.adam.util
             1. (object)
                AttributeUtils
             2. (object)
                Base
             3. (case class)DeletionEvent
             4. (object)
                HadoopUtil
             5. (object)(class)Histogram
             6. (object)
                ImplicitJavaConversions
             7. (case class)InsertionEvent
             8. (class)IntervalListReader
             9. (object)
                MapTools
             10. (case class)MatchEvent
             11. (object)(class)MdTag
             12. (object)
                 MdTagEvent
             13. (case class)MismatchEvent
             14. (object)
                 NormalizationUtils
             15. (class)ParquetFileTraversable
             16. (object)
                 ParquetLogger
             17. (object)
                 PhredUtils
             18. (class)Pileup
             19. (class)PileupEvent
             20. (object)(class)PileupTraversable
             21. (object)(class)QualityScore
             22. (object)(class)RegExp
             23. (object)
                 Util
             24. (object)
                 VcfHeaderUtils
             25. (object)
                 VcfStringUtils