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.realignmenttarget
               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
            4. org.bdgenomics.adam.algorithms.smithwaterman
               1. (class)SmithWaterman
               2. (object)(class)SmithWatermanConstantGapScoring
               3. (class)SmithWatermanGapScoringFromFn
         2. org.bdgenomics.adam.converters
            1. (class)AlignmentRecordConverter
            2. (object)(case class)AttrKey
            3. (class)SAMRecordConverter
            4. (object)
               VariantAnnotationConverter
            5. (object)(class)VariantContextConverter
            6. (class)VCFLine
            7. (object)
               VCFLineConverter
            8. (class)VCFLineParser
         3. org.bdgenomics.adam.core
            1. org.bdgenomics.adam.core.util
               1. (object)
                  BuildInformation
         4. org.bdgenomics.adam.instrumentation
            1. (class)ADAMMetrics
            2. (class)ADAMMetricsListener
            3. (object)
               Alignment
            4. (class)ASCIITable
            5. (case class)ASCIITableHeader
            6. (object)
               DurationFormatting
            7. (class)MonitorTable
            8. (object)(class)ServoTimer
            9. (object)(class)SparkMetrics
            10. (case class)TableHeader
            11. (trait)Taggable
            12. (case class)TaskContext
            13. (class)TaskTimer
            14. (object)(trait)ValueExtractor
         5. org.bdgenomics.adam.io
            1. (trait)ByteAccess
            2. (class)ByteArrayByteAccess
            3. (class)ByteArrayLocator
            4. (object)(trait)FileLocator
            5. (class)HTTPFileLocator
            6. (class)HTTPRangedByteAccess
            7. (class)InterleavedFastqInputFormat
            8. (class)LocalFileByteAccess
            9. (class)LocalFileLocator
            10. (class)S3ByteAccess
            11. (class)S3FileLocator
         6. 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
         7. org.bdgenomics.adam.models
            1. (case class)Attribute
            2. (class)BaseFeature
            3. (class)BEDFeature
            4. (object)(case class)Consensus
            5. (object)(class)IndelTable
            6. (trait)Interval
            7. (class)NarrowPeakFeature
            8. (class)OrderedTrackedLayout
            9. (object)(case class)ReadBucket
            10. (class)ReadBucketSerializer
            11. (object)(class)RecordGroup
            12. (object)(class)RecordGroupDictionary
            13. (trait)ReferenceMapping
            14. (object)(case class)ReferencePosition
            15. (object)(case class)ReferencePositionPair
            16. (class)ReferencePositionPairSerializer
            17. (class)ReferencePositionSerializer
            18. (object)(case class)ReferencePositionWithOrientation
            19. (class)ReferencePositionWithOrientationSerializer
            20. (object)(case class)ReferenceRegion
            21. (class)ReferenceRegionSerializer
            22. (object)(case class)ReferenceRegionWithOrientation
            23. (case class)Rod
            24. (case class)SAMFileHeaderWritable
            25. (object)(class)SequenceDictionary
            26. (object)(class)SequenceRecord
            27. (object)(case class)SingleReadBucket
            28. (class)SingleReadBucketSerializer
            29. (object)(class)SnpTable
            30. (object)
                TagType
            31. (object)(trait)TrackedLayout
            32. (object)(class)VariantContext
         8. org.bdgenomics.adam.parquet_reimpl
            1. (class)AvroIndexedParquetRDD
            2. (class)AvroParquetRDD
            3. (class)ParquetAggregateType
            4. (case class)ParquetGroupType
            5. (class)ParquetLister
            6. (object)
               ParquetOriginalType
            7. (object)(class)ParquetPartition
            8. (case class)ParquetPrimitiveType
            9. (case class)ParquetSchemaType
            10. (object)(trait)ParquetType
            11. (class)PartitionPageReadStore
            12. (object)
                PrimitiveType
            13. (object)
                Repetition
            14. (object)(case class)TypePath
            1. org.bdgenomics.adam.parquet_reimpl.filters
               1. (trait)CombinedFilter
               2. (class)FilterTuple
               3. (trait)SerializableUnboundRecordFilter
            2. org.bdgenomics.adam.parquet_reimpl.index
               1. (case class)AndIndexPredicate
               2. (object)
                  AvroParquetFileMetadata
               3. (class)FlatGenotypeReferenceFolder
               4. (object)(class)IDRangeIndex
               5. (case class)IDRangeIndexEntry
               6. (class)IDRangeIndexGenerator
               7. (case class)IDRangeIndexPredicate
               8. (class)IDRangeIndexWriter
               9. (object)(trait)IndexEntryPredicate
               10. (case class)OrIndexPredicate
               11. (case class)ParquetFileMetadata
               12. (object)(class)RangeIndex
               13. (case class)RangeIndexEntry
               14. (class)RangeIndexGenerator
               15. (case class)RangeIndexPredicate
               16. (class)RangeIndexWriter
               17. (trait)ReferenceFolder
               18. (object)
                   ReferenceFoldingContext
               19. (trait)RowGroupIndex
               20. (class)RowGroupIndexEntry
               21. (trait)RowGroupIndexWriter
         9. org.bdgenomics.adam.plugins
            1. (trait)AccessControl
            2. (trait)ADAMPlugin
            3. (class)EmptyAccessControl
         10. org.bdgenomics.adam.predicates
             1. (trait)ADAMPredicate
             2. (object)
                AlignmentRecordConditions
             3. (object)
                ColumnReaderInput
             4. (object)
                GenotypeConditions
             5. (class)GenotypeRecordPASSPredicate
             6. (class)HighQualityReadPredicate
             7. (class)LocusPredicate
             8. (object)
                PredicateUtils
             9. (class)UniqueMappedReadPredicate
         11. org.bdgenomics.adam.projections
             1. (object)
                AlignmentRecordField
             2. (object)
                DatabaseVariantAnnotationField
             3. (object)
                FeatureField
             4. (class)FieldEnumeration
             5. (trait)FieldValue
             6. (object)
                Filter
             7. (object)
                FlatGenotypeField
             8. (object)
                GenotypeField
             9. (object)
                NucleotideContigFragmentField
             10. (object)
                 Projection
             11. (class)VariantCallingAnnotationsField
             12. (class)VariantField
         12. org.bdgenomics.adam.rdd
             1. (object)(class)ADAMContext
             2. (class)ADAMRDDFunctions
             3. (class)ADAMSequenceDictionaryRDDAggregator
             4. (class)ADAMSpecificRecordSequenceDictionaryRDDAggregator
             5. (class)AlignmentRecordRDDFunctions
             6. (object)
                CompressionCodecEnum
             7. (object)(case class)DuplicateMetrics
             8. (object)
                FlagStat
             9. (object)(case class)FlagStatMetrics
             10. (object)(case class)Footer
             11. (object)(class)GenomicRegionPartitioner
             12. (object)(case class)GenotypesSummary
             13. (object)(case class)GenotypesSummaryCounts
             14. (object)
                 GenotypesSummaryFormatting
             15. (object)(class)MultiContigNonoverlappingRegions
             16. (object)(class)NonoverlappingRegions
             17. (class)NucleotideContigFragmentRDDFunctions
             18. (case class)ParquetColumnChunk
             19. (case class)ParquetColumnDescriptor
             20. (object)
                 ParquetCommon
             21. (case class)ParquetRowGroup
             22. (class)PileupRDDFunctions
             23. (object)
                 RegionJoin
             24. (class)RodRDDFunctions
             1. org.bdgenomics.adam.rdd.comparisons
                1. (object)(class)ComparisonTraversalEngine
             2. org.bdgenomics.adam.rdd.features
                1. (object)(class)ADAMFeaturesContext
                2. (class)BEDParser
                3. (trait)FeatureParser
                4. (class)NarrowPeakParser
             3. org.bdgenomics.adam.rdd.normalization
                1. (object)
                   LengthNormalization
                2. (object)
                   ZScoreNormalization
             4. 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
             5. org.bdgenomics.adam.rdd.variation
                1. (object)(class)ADAMVariationContext
                2. (object)(class)ADAMVCFOutputFormat
                3. (object)(class)ConcordanceTable
                4. (class)GenotypeRDDFunctions
                5. (class)VariantContextRDDFunctions
         13. 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
         14. org.bdgenomics.adam.serialization
             1. (class)ADAMKryoRegistrator
             2. (class)AvroSerializer
             3. (case class)InputStreamWithDecoder
         15. org.bdgenomics.adam.util
             1. (object)(class)ADAMBAMOutputFormat
             2. (object)(class)ADAMSAMOutputFormat
             3. (object)
                AttributeUtils
             4. (object)
                Base
             5. (class)CredentialsProperties
             6. (case class)DeletionEvent
             7. (object)
                HadoopUtil
             8. (object)(class)Histogram
             9. (object)
                ImplicitJavaConversions
             10. (case class)InsertionEvent
             11. (class)IntervalListReader
             12. (object)
                 MapTools
             13. (case class)MatchEvent
             14. (object)(class)MdTag
             15. (object)
                 MdTagEvent
             16. (case class)MismatchEvent
             17. (object)
                 NormalizationUtils
             18. (class)ParquetFileTraversable
             19. (object)
                 ParquetLogger
             20. (object)
                 PhredUtils
             21. (class)Pileup
             22. (class)PileupEvent
             23. (object)(class)PileupTraversable
             24. (object)(class)QualityScore
             25. (object)(class)RegExp
             26. (class)SerializableAWSCredentials
             27. (object)
                 Util
             28. (object)
                 VcfHeaderUtils
             29. (object)
                 VcfStringUtils
2. parquet
   1. parquet.avro
      1. (class)UsableAvroRecordMaterializer
   2. parquet.format
      1. parquet.format.converter
         1. (class)MyConverter