1. htsjdk
   1. htsjdk.samtools
      1. (object)(class)IndexedBamInputFormat
2. 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.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. (object)
               FragmentConverter
            5. (class)SAMRecordConverter
            6. (object)
               VariantAnnotationConverter
            7. (object)(class)VariantContextConverter
         3. org.bdgenomics.adam.core
            1. org.bdgenomics.adam.core.util
               1. (object)
                  BuildInformation
         4. org.bdgenomics.adam.instrumentation
            1. (object)
               Timers
         5. org.bdgenomics.adam.io
            1. (object)(class)BAMFilteredRecordReader
            2. (class)InterleavedFastqInputFormat
            3. (class)SingleFastqInputFormat
         6. org.bdgenomics.adam.models
            1. (object)(trait)Alphabet
            2. (case class)Attribute
            3. (class)BlockExtractable
            4. (case class)CDS
            5. (object)(case class)Consensus
            6. (class)DNAAlphabet
            7. (case class)Exon
            8. (trait)Extractable
            9. (case class)Gene
            10. (object)(class)IndelTable
            11. (trait)Interval
            12. (object)
                OptionalPositionOrdering
            13. (trait)OptionalReferenceOrdering
            14. (object)
                OptionalRegionOrdering
            15. (object)
                PositionOrdering
            16. (object)(case class)ProgramRecord
            17. (object)(case class)ReadBucket
            18. (class)ReadBucketSerializer
            19. (object)(class)RecordGroup
            20. (object)(class)RecordGroupDictionary
            21. (trait)ReferenceOrdering
            22. (object)(class)ReferencePosition
            23. (object)(case class)ReferencePositionPair
            24. (class)ReferencePositionPairSerializer
            25. (class)ReferencePositionSerializer
            26. (object)(case class)ReferenceRegion
            27. (class)ReferenceRegionSerializer
            28. (object)
                ReferenceUtils
            29. (object)
                RegionOrdering
            30. (object)(class)SAMFileHeaderWritable
            31. (object)(class)SequenceDictionary
            32. (object)
                SequenceOrdering
            33. (object)(class)SequenceRecord
            34. (object)(case class)SingleReadBucket
            35. (class)SingleReadBucketSerializer
            36. (object)(class)SnpTable
            37. (case class)Symbol
            38. (object)
                TagType
            39. (case class)Transcript
            40. (case class)UTR
            41. (object)(class)VariantContext
            42. (case class)VCFHeaderWritable
         7. org.bdgenomics.adam.plugins
            1. (trait)AccessControl
            2. (trait)ADAMPlugin
            3. (class)EmptyAccessControl
         8. org.bdgenomics.adam.projections
            1. (object)
               AlignmentRecordField
            2. (object)
               DatabaseVariantAnnotationField
            3. (object)
               FeatureField
            4. (class)FieldEnumeration
            5. (trait)FieldValue
            6. (object)
               Filter
            7. (object)
               GenotypeField
            8. (object)
               NucleotideContigFragmentField
            9. (object)
               Projection
            10. (object)
                VariantCallingAnnotationsField
            11. (object)
                VariantField
         9. org.bdgenomics.adam.rdd
            1. (object)(class)ADAMContext
            2. (class)ADAMRDDFunctions
            3. (trait)ADAMSaveAnyArgs
            4. (class)ADAMSequenceDictionaryRDDAggregator
            5. (class)ADAMSpecificRecordSequenceDictionaryRDDAggregator
            6. (object)
               BroadcastRegionJoin
            7. (class)Coverage
            8. (case class)GenomeBins
            9. (object)(case class)GenomicPositionPartitioner
            10. (object)(case class)GenomicRegionPartitioner
            11. (class)InstrumentedADAMAvroParquetOutputFormat
            12. (object)(class)PairingRDD
            13. (case class)ReferencePartitioner
            14. (trait)RegionJoin
            15. (case class)ShuffleRegionJoin
            1. org.bdgenomics.adam.rdd.contig
               1. (class)NucleotideContigFragmentRDDFunctions
            2. org.bdgenomics.adam.rdd.features
               1. (class)BEDParser
               2. (class)FeatureFile
               3. (trait)FeatureParser
               4. (class)FeatureRDDFunctions
               5. (object)(class)GTFParser
               6. (class)IntervalListParser
               7. (class)NarrowPeakParser
            3. org.bdgenomics.adam.rdd.read
               1. (object)(class)ADAMBAMOutputFormat
               2. (object)(class)ADAMSAMOutputFormat
               3. (class)AlignmentRecordRDDFunctions
               4. (object)(case class)DuplicateMetrics
               5. (object)
                  FlagStat
               6. (object)(case class)FlagStatMetrics
               7. (class)InstrumentedADAMBAMOutputFormat
               8. (class)InstrumentedADAMSAMOutputFormat
               1. 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
               2. 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. (class)ExtrasTables
                  10. (object)(class)Observation
                  11. (object)(class)ObservationAccumulator
                  12. (class)ObservationTable
                  13. (class)QualityTable
                  14. (object)(class)RecalibrationTable
                  15. (object)(class)Recalibrator
            4. org.bdgenomics.adam.rdd.variation
               1. (object)(class)ADAMVCFOutputFormat
               2. (class)GenotypeRDDFunctions
               3. (class)VariantContextRDDFunctions
         10. org.bdgenomics.adam.rich
             1. (object)(class)DecadentRead
             2. (class)IlluminaOptics
             3. (object)(class)RichAlignmentRecord
             4. (object)(class)RichCigar
             5. (object)(class)RichGenotype
             6. (object)(class)RichVariant
         11. org.bdgenomics.adam.serialization
             1. (class)ADAMKryoRegistrator
             2. (class)AvroSerializer
             3. (case class)InputStreamWithDecoder
         12. org.bdgenomics.adam.util
             1. (object)
                AttributeUtils
             2. (object)
                Flattener
             3. (object)
                ImplicitJavaConversions
             4. (class)IntervalListReader
             5. (object)
                MapTools
             6. (object)(class)MdTag
             7. (object)
                MdTagEvent
             8. (object)
                NormalizationUtils
             9. (class)ParquetFileTraversable
             10. (object)
                 ParquetLogger
             11. (object)
                 PhredUtils
             12. (object)(class)QualityScore
             13. (trait)ReferenceFile
             14. (object)(class)RegExp
             15. (object)(class)TwoBitFile
             16. (object)(case class)TwoBitRecord
             17. (object)
                 Util
             18. (object)
                 VcfHeaderUtils
             19. (object)
                 VcfStringUtils