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)ADAMRecordConverter
            2. (object)(case class)AttrKey
            3. (class)SAMRecordConverter
            4. (object)
               VariantAnnotationConverter
            5. (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. (case class)SAMFileHeaderWritable
            18. (object)(class)SequenceDictionary
            19. (object)(class)SequenceRecord
            20. (object)(case class)SingleReadBucket
            21. (class)SingleReadBucketSerializer
            22. (object)(class)SnpTable
            23. (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)(class)ADAMBAMOutputFormat
             2. (object)(class)ADAMSAMOutputFormat
             3. (object)
                AttributeUtils
             4. (object)
                Base
             5. (case class)DeletionEvent
             6. (object)
                HadoopUtil
             7. (object)(class)Histogram
             8. (object)
                ImplicitJavaConversions
             9. (case class)InsertionEvent
             10. (class)IntervalListReader
             11. (object)
                 MapTools
             12. (case class)MatchEvent
             13. (object)(class)MdTag
             14. (object)
                 MdTagEvent
             15. (case class)MismatchEvent
             16. (object)
                 NormalizationUtils
             17. (class)ParquetFileTraversable
             18. (object)
                 ParquetLogger
             19. (object)
                 PhredUtils
             20. (class)Pileup
             21. (class)PileupEvent
             22. (object)(class)PileupTraversable
             23. (object)(class)QualityScore
             24. (object)(class)RegExp
             25. (object)
                 Util
             26. (object)
                 VcfHeaderUtils
             27. (object)
                 VcfStringUtils