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.instrumentation
            1. (object)
               Timers
         4. org.bdgenomics.adam.io
            1. (object)(class)BAMFilteredRecordReader
            2. (class)InterleavedFastqInputFormat
            3. (class)SingleFastqInputFormat
         5. 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)(class)MultiContigNonoverlappingRegions
            13. (object)(class)NonoverlappingRegions
            14. (object)
                OptionalPositionOrdering
            15. (trait)OptionalReferenceOrdering
            16. (object)
                OptionalRegionOrdering
            17. (object)
                PositionOrdering
            18. (object)(case class)ProgramRecord
            19. (object)(case class)ReadBucket
            20. (class)ReadBucketSerializer
            21. (object)(case class)RecordGroup
            22. (object)(case class)RecordGroupDictionary
            23. (trait)ReferenceOrdering
            24. (object)(class)ReferencePosition
            25. (object)(case class)ReferencePositionPair
            26. (class)ReferencePositionPairSerializer
            27. (class)ReferencePositionSerializer
            28. (object)(case class)ReferenceRegion
            29. (class)ReferenceRegionSerializer
            30. (object)
                ReferenceUtils
            31. (object)
                RegionOrdering
            32. (object)(class)SAMFileHeaderWritable
            33. (object)(class)SequenceDictionary
            34. (object)
                SequenceOrderingByName
            35. (object)
                SequenceOrderingByRefIdx
            36. (object)(case class)SequenceRecord
            37. (object)(case class)SingleReadBucket
            38. (class)SingleReadBucketSerializer
            39. (object)(class)SnpTable
            40. (case class)Symbol
            41. (object)
                TagType
            42. (case class)Transcript
            43. (case class)UTR
            44. (object)(class)VariantContext
            45. (case class)VCFHeaderWritable
         6. org.bdgenomics.adam.plugins
            1. (trait)AccessControl
            2. (trait)ADAMPlugin
            3. (class)EmptyAccessControl
         7. 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
         8. 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. (trait)GenomicRDD
            11. (object)(case class)GenomicRegionPartitioner
            12. (class)InstrumentedADAMAvroParquetOutputFormat
            13. (object)(class)PairingRDD
            14. (case class)ReferencePartitioner
            15. (trait)RegionJoin
            16. (case class)ShuffleRegionJoin
            17. (trait)Unaligned
            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.fragment
               1. (class)FragmentRDDFunctions
            4. org.bdgenomics.adam.rdd.read
               1. (object)(class)ADAMBAMOutputFormat
               2. (class)ADAMBAMOutputFormatHeaderLess
               3. (object)(class)ADAMSAMOutputFormat
               4. (class)ADAMSAMOutputFormatHeaderLess
               5. (case class)AlignedReadRDD
               6. (class)AlignmentRecordRDD
               7. (class)AlignmentRecordRDDFunctions
               8. (object)(case class)DuplicateMetrics
               9. (object)
                  FlagStat
               10. (object)(case class)FlagStatMetrics
               11. (case class)IncorrectMDTagException
               12. (class)InstrumentedADAMBAMOutputFormat
               13. (class)InstrumentedADAMBAMOutputFormatHeaderLess
               14. (class)InstrumentedADAMSAMOutputFormat
               15. (class)InstrumentedADAMSAMOutputFormatHeaderLess
               16. (object)(case class)MDTagging
               17. (object)(case class)UnalignedReadRDD
               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
            5. org.bdgenomics.adam.rdd.variation
               1. (object)(class)ADAMVCFOutputFormat
               2. (class)GenotypeRDDFunctions
               3. (class)VariantContextRDDFunctions
         9. org.bdgenomics.adam.rich
            1. (class)IlluminaOptics
            2. (object)(class)RichAlignmentRecord
            3. (object)(class)RichCigar
            4. (object)(class)RichGenotype
            5. (object)(class)RichVariant
         10. org.bdgenomics.adam.serialization
             1. (class)ADAMKryoRegistrator
             2. (class)AvroSerializer
             3. (case class)InputStreamWithDecoder
         11. 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. (object)(case class)ReferenceContigMap
             14. (trait)ReferenceFile
             15. (object)(class)RegExp
             16. (object)(class)TwoBitFile
             17. (class)TwoBitFileSerializer
             18. (object)
                 Util
             19. (object)
                 VcfHeaderUtils