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. (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)ProgramRecord
            10. (object)(case class)ReadBucket
            11. (class)ReadBucketSerializer
            12. (object)(class)RecordGroup
            13. (object)(class)RecordGroupDictionary
            14. (trait)ReferenceMapping
            15. (object)(case class)ReferencePosition
            16. (object)(case class)ReferencePositionPair
            17. (class)ReferencePositionPairSerializer
            18. (class)ReferencePositionSerializer
            19. (object)(case class)ReferencePositionWithOrientation
            20. (class)ReferencePositionWithOrientationSerializer
            21. (object)(case class)ReferenceRegion
            22. (class)ReferenceRegionSerializer
            23. (object)(case class)ReferenceRegionWithOrientation
            24. (case class)Rod
            25. (object)(class)SAMFileHeaderWritable
            26. (object)(class)SequenceDictionary
            27. (object)(class)SequenceRecord
            28. (object)(case class)SingleReadBucket
            29. (class)SingleReadBucketSerializer
            30. (object)(class)SnpTable
            31. (object)
                TagType
            32. (object)(trait)TrackedLayout
            33. (object)(class)VariantContext
            34. (case class)VCFHeaderWritable
         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. (object)
                CompressionCodecEnum
             6. (object)(case class)Footer
             7. (object)(class)GenomicRegionPartitioner
             8. (object)(class)MultiContigNonoverlappingRegions
             9. (object)(class)NonoverlappingRegions
             10. (case class)ParquetColumnChunk
             11. (case class)ParquetColumnDescriptor
             12. (object)
                 ParquetCommon
             13. (case class)ParquetRowGroup
             14. (object)
                 RegionJoin
             1. org.bdgenomics.adam.rdd.contig
                1. (object)(class)ADAMNucleotideContigFragmentContext
                2. (class)ADAMNucleotideContigFragmentRDDFunctions
             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.pileup
                1. (object)
                   ADAMPileupContext
                2. (class)ADAMPileupRDDFunctions
                3. (class)ADAMRodRDDFunctions
             5. org.bdgenomics.adam.rdd.read
                1. (object)(class)ADAMAlignmentRecordContext
                2. (class)ADAMAlignmentRecordRDDFunctions
                3. (object)(class)ADAMBAMOutputFormat
                4. (object)(class)ADAMSAMOutputFormat
                5. (object)(case class)DuplicateMetrics
                6. (object)
                   FlagStat
                7. (object)(case class)FlagStatMetrics
                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)ADAMVariationContext
                2. (object)(class)ADAMVCFOutputFormat
                3. (object)(class)ConcordanceTable
                4. (class)GenotypeRDDFunctions
                5. (object)(case class)GenotypesSummary
                6. (object)(case class)GenotypesSummaryCounts
                7. (object)
                   GenotypesSummaryFormatting
                8. (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)
                AttributeUtils
             2. (object)
                Base
             3. (class)CredentialsProperties
             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. (class)SerializableAWSCredentials
             25. (object)
                 Util
             26. (object)
                 VcfHeaderUtils
             27. (object)
                 VcfStringUtils
2. parquet
   1. parquet.avro
      1. (class)UsableAvroRecordMaterializer
   2. parquet.format
      1. parquet.format.converter
         1. (class)MyConverter