1. org
        1. org.bdgenomics
            1. org.bdgenomics.adam
                1. org.bdgenomics.adam.algorithms
                    1. org.bdgenomics.adam.algorithms.consensus
                      1. (object)(trait)ConsensusGenerator
                    2. org.bdgenomics.adam.algorithms.smithwaterman
                      1. (trait)SmithWaterman
                      2. (case class)SmithWatermanConstantGapScoring
                  1. org.bdgenomics.adam.converters
                    1. (class)AlignmentRecordConverter
                    2. (object)
                      DefaultHeaderLines
                    3. (object)(class)VariantContextConverter
                  2. org.bdgenomics.adam.instrumentation
                    1. (object)
                      Timers
                  3. org.bdgenomics.adam.io
                    1. (class)InterleavedFastqInputFormat
                    2. (class)SingleFastqInputFormat
                  4. org.bdgenomics.adam.models
                    1. (object)(trait)Alphabet
                    2. (case class)Attribute
                    3. (case class)Coverage
                    4. (class)DNAAlphabet
                    5. (object)(case class)MdTag
                    6. (object)
                      MdTagEvent
                    7. (object)
                      OptionalPositionOrdering
                    8. (trait)OptionalReferenceOrdering
                    9. (object)
                      OptionalRegionOrdering
                    10. (object)
                      PositionOrdering
                    11. (object)(case class)RecordGroup
                    12. (object)(case class)RecordGroupDictionary
                    13. (trait)ReferenceOrdering
                    14. (object)(class)ReferencePosition
                    15. (class)ReferencePositionSerializer
                    16. (object)(case class)ReferenceRegion
                    17. (class)ReferenceRegionSerializer
                    18. (object)
                      RegionOrdering
                    19. (object)(class)SequenceDictionary
                    20. (object)(case class)SequenceRecord
                    21. (object)(class)SnpTable
                    22. (case class)Symbol
                    23. (object)
                      TagType
                    24. (object)(class)VariantContext
                    25. (class)VariantContextSerializer
                  5. org.bdgenomics.adam.projections
                    1. (object)
                      AlignmentRecordField
                    2. (object)
                      ContigField
                    3. (object)
                      DbxrefField
                    4. (object)
                      FeatureField
                    5. (class)FieldEnumeration
                    6. (trait)FieldValue
                    7. (object)
                      Filter
                    8. (object)
                      FragmentField
                    9. (object)
                      GenotypeField
                    10. (object)
                      NucleotideContigFragmentField
                    11. (object)
                      OntologyTermField
                    12. (object)
                      Projection
                    13. (object)
                      ReadField
                    14. (object)
                      RecordGroupMetadataField
                    15. (object)
                      SampleField
                    16. (object)
                      SequenceField
                    17. (object)
                      SliceField
                    18. (object)
                      TranscriptEffectField
                    19. (object)
                      VariantAnnotationField
                    20. (object)
                      VariantCallingAnnotationsField
                    21. (object)
                      VariantField
                  6. org.bdgenomics.adam.rdd
                    1. (object)(class)ADAMContext
                    2. (trait)ADAMSaveAnyArgs
                    3. (class)AvroGenomicRDD
                    4. (class)AvroReadGroupGenomicRDD
                    5. (case class)FullOuterShuffleRegionJoin
                    6. (case class)GenomeBins
                    7. (object)(case class)GenomicPositionPartitioner
                    8. (trait)GenomicRDD
                    9. (object)(case class)GenomicRegionPartitioner
                    10. (trait)InFormatter
                    11. (trait)InFormatterCompanion
                    12. (case class)InnerShuffleRegionJoin
                    13. (case class)InnerShuffleRegionJoinAndGroupByLeft
                    14. (case class)InnerTreeRegionJoin
                    15. (case class)InnerTreeRegionJoinAndGroupByRight
                    16. (case class)LeftOuterShuffleRegionJoin
                    17. (class)MultisampleAvroGenomicRDD
                    18. (trait)MultisampleGenomicRDD
                    19. (trait)OutFormatter
                    20. (case class)ReferencePartitioner
                    21. (class)RegionJoin
                    22. (case class)RightOuterShuffleRegionJoin
                    23. (case class)RightOuterShuffleRegionJoinAndGroupByLeft
                    24. (case class)RightOuterTreeRegionJoin
                    25. (case class)RightOuterTreeRegionJoinAndGroupByRight
                    26. (class)ShuffleRegionJoin
                    27. (trait)TreeRegionJoin
                    28. (trait)Unaligned
                    1. org.bdgenomics.adam.rdd.contig
                      1. (case class)NucleotideContigFragmentRDD
                    2. org.bdgenomics.adam.rdd.feature
                      1. (object)(case class)BEDInFormatter
                      2. (case class)BEDOutFormatter
                      3. (case class)CoverageRDD
                      4. (object)(case class)FeatureRDD
                      5. (object)(case class)GFF3InFormatter
                      6. (case class)GFF3OutFormatter
                      7. (object)(case class)GTFInFormatter
                      8. (case class)GTFOutFormatter
                      9. (object)(case class)NarrowPeakInFormatter
                      10. (case class)NarrowPeakOutFormatter
                    3. org.bdgenomics.adam.rdd.fragment
                      1. (object)(case class)FragmentRDD
                      2. (object)(class)InterleavedFASTQInFormatter
                    4. org.bdgenomics.adam.rdd.read
                      1. (class)ADAMBAMOutputFormat
                      2. (class)ADAMBAMOutputFormatHeaderLess
                      3. (class)ADAMCRAMOutputFormat
                      4. (class)ADAMCRAMOutputFormatHeaderLess
                      5. (class)ADAMSAMOutputFormat
                      6. (class)ADAMSAMOutputFormatHeaderLess
                      7. (object)(case class)AlignmentRecordRDD
                      8. (trait)AnySAMInFormatter
                      9. (trait)AnySAMInFormatterCompanion
                      10. (class)AnySAMOutFormatter
                      11. (object)(case class)BAMInFormatter
                      12. (case class)IncorrectMDTagException
                      13. (class)InstrumentedADAMBAMOutputFormat
                      14. (class)InstrumentedADAMBAMOutputFormatHeaderLess
                      15. (class)InstrumentedADAMCRAMOutputFormat
                      16. (class)InstrumentedADAMCRAMOutputFormatHeaderLess
                      17. (class)InstrumentedADAMSAMOutputFormat
                      18. (class)InstrumentedADAMSAMOutputFormatHeaderLess
                      19. (class)ReferencePositionPairSerializer
                      20. (object)(case class)SAMInFormatter
                      21. (class)SingleReadBucketSerializer
                    5. org.bdgenomics.adam.rdd.variant
                      1. (class)ADAMHeaderlessVCFOutputFormat
                      2. (class)ADAMVCFOutputFormat
                      3. (case class)GenotypeRDD
                      4. (case class)VariantContextRDD
                      5. (case class)VariantRDD
                      6. (object)(case class)VCFInFormatter
                      7. (case class)VCFOutFormatter
                  7. org.bdgenomics.adam.rich
                    1. (object)(case class)RichAlignmentRecord
                    2. (object)(case class)RichVariant
                  8. org.bdgenomics.adam.serialization
                    1. (class)ADAMKryoRegistrator
                    2. (class)AvroSerializer
                    3. (case class)InputStreamWithDecoder
                    4. (class)WritableSerializer
                  9. org.bdgenomics.adam.util
                    1. (object)
                      AttributeUtils
                    2. (case class)IndexedFastaFile
                    3. (class)ParquetFileTraversable
                    4. (object)
                      ParquetLogger
                    5. (object)
                      PhredUtils
                    6. (object)(case class)ReferenceContigMap
                    7. (trait)ReferenceFile
                    8. (class)TwoBitFile
                    9. (class)TwoBitFileSerializer