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. (object)(class)AlignmentRecordConverter
            2. (object)(case class)AttrKey
            3. (class)FastqRecordConverter
            4. (class)SAMRecordConverter
            5. (object)
               VariantAnnotationConverter
            6. (object)(class)VariantContextConverter
            7. (class)VCFLine
            8. (object)
               VCFLineConverter
            9. (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
            12. (class)SingleFastqInputFormat
         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. (object)(class)BaseFeature
            3. (object)(class)BEDFeature
            4. (class)BlockExtractable
            5. (case class)CDS
            6. (object)(case class)Consensus
            7. (case class)Exon
            8. (trait)Extractable
            9. (case class)Gene
            10. (object)(class)GeneContext
            11. (class)GTFFeature
            12. (object)(class)IndelTable
            13. (trait)Interval
            14. (class)NarrowPeakFeature
            15. (class)OrderedTrackedLayout
            16. (object)(case class)ProgramRecord
            17. (object)(case class)ReadBucket
            18. (class)ReadBucketSerializer
            19. (object)(class)RecordGroup
            20. (object)(class)RecordGroupDictionary
            21. (trait)ReferenceMapping
            22. (object)(case class)ReferencePosition
            23. (object)(case class)ReferencePositionPair
            24. (class)ReferencePositionPairSerializer
            25. (class)ReferencePositionSerializer
            26. (object)(case class)ReferencePositionWithOrientation
            27. (class)ReferencePositionWithOrientationSerializer
            28. (object)(case class)ReferenceRegion
            29. (class)ReferenceRegionSerializer
            30. (object)(case class)ReferenceRegionWithOrientation
            31. (object)
                ReferenceUtils
            32. (case class)Rod
            33. (object)(class)SAMFileHeaderWritable
            34. (object)(class)SequenceDictionary
            35. (object)(class)SequenceRecord
            36. (object)(case class)SingleReadBucket
            37. (class)SingleReadBucketSerializer
            38. (object)(class)SnpTable
            39. (object)
                TagType
            40. (object)(trait)TrackedLayout
            41. (case class)Transcript
            42. (case class)UTR
            43. (object)(class)VariantContext
            44. (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)(case class)FieldCondition
             5. (object)
                GenotypeConditions
             6. (class)GenotypeRecordPASSPredicate
             7. (class)HighQualityReadPredicate
             8. (class)LocusPredicate
             9. (object)
                PredicateUtils
             10. (object)(class)RecordCondition
             11. (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. (trait)ADAMParquetArgs
             3. (class)ADAMRDDFunctions
             4. (trait)ADAMSaveAnyArgs
             5. (trait)ADAMSaveArgs
             6. (class)ADAMSequenceDictionaryRDDAggregator
             7. (class)ADAMSpecificRecordSequenceDictionaryRDDAggregator
             8. (object)
                CompressionCodecEnum
             9. (object)(case class)Footer
             10. (object)(case class)GenomicRegionPartitioner
             11. (object)(class)MultiContigNonoverlappingRegions
             12. (object)(class)NonoverlappingRegions
             13. (case class)ParquetColumnChunk
             14. (case class)ParquetColumnDescriptor
             15. (object)
                 ParquetCommon
             16. (case class)ParquetRowGroup
             17. (object)
                 RegionJoin
             1. org.bdgenomics.adam.rdd.contig
                1. (object)(class)NucleotideContigFragmentContext
                2. (class)NucleotideContigFragmentRDDFunctions
             2. org.bdgenomics.adam.rdd.features
                1. (class)BEDParser
                2. (class)FeatureFile
                3. (trait)FeatureParser
                4. (object)(class)FeaturesContext
                5. (object)(class)GeneFeatureRDD
                6. (object)(class)GTFParser
                7. (class)NarrowPeakParser
             3. org.bdgenomics.adam.rdd.normalization
                1. (object)
                   LengthNormalization
                2. (object)
                   ZScoreNormalization
             4. org.bdgenomics.adam.rdd.pileup
                1. (object)
                   PileupContext
                2. (class)PileupRDDFunctions
                3. (class)RodRDDFunctions
             5. org.bdgenomics.adam.rdd.read
                1. (object)(class)ADAMBAMOutputFormat
                2. (object)(class)ADAMSAMOutputFormat
                3. (object)(class)AlignmentRecordContext
                4. (class)AlignmentRecordRDDFunctions
                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)ADAMVCFOutputFormat
                2. (object)(class)ConcordanceTable
                3. (class)GenotypeRDDFunctions
                4. (object)(case class)GenotypesSummary
                5. (object)(case class)GenotypesSummaryCounts
                6. (object)
                   GenotypesSummaryFormatting
                7. (class)VariantContextRDDFunctions
                8. (object)(class)VariationContext
         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. (object)
                 SequenceUtils
             25. (class)SerializableAWSCredentials
             26. (object)
                 Util
             27. (object)
                 VcfHeaderUtils
             28. (object)
                 VcfStringUtils
2. parquet
   1. parquet.avro
      1. (class)UsableAvroRecordMaterializer
   2. parquet.format
      1. parquet.format.converter
         1. (class)MyConverter