class icon trait icon trait icon trait icon
    1. org
        1. org.bdgenomics
            1. org.bdgenomics.adam
                1. org.bdgenomics.adam.algorithms
                    1. org.bdgenomics.adam.algorithms.consensus
                      1. (object)(class)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)FastqInputFormat
                    2. (class)FastqRecordReader
                    3. (class)InterleavedFastqInputFormat
                    4. (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)ReadGroup
                    12. (object)(case class)ReadGroupDictionary
                    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)
                      DbxrefField
                    3. (object)
                      FeatureField
                    4. (class)FieldEnumeration
                    5. (trait)FieldValue
                    6. (object)
                      Filter
                    7. (object)
                      FragmentField
                    8. (object)
                      GenotypeField
                    9. (object)
                      NucleotideContigFragmentField
                    10. (object)
                      OntologyTermField
                    11. (object)
                      Projection
                    12. (object)
                      ReadField
                    13. (object)
                      ReadGroupField
                    14. (object)
                      ReferenceField
                    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)AvroGenomicDataset
                    4. (class)AvroReadGroupGenomicDataset
                    5. (case class)DatasetBoundGenericGenomicDataset
                    6. (trait)DatasetBoundGenomicDataset
                    7. (case class)FullOuterShuffleRegionJoin
                    8. (case class)GenericConverter
                    9. (class)GenericGenomicDataset
                    10. (case class)GenomeBins
                    11. (case class)GenomicBroadcast
                    12. (trait)GenomicDataset
                    13. (trait)GenomicDatasetConversion
                    14. (trait)GenomicDatasetWithLineage
                    15. (object)(case class)GenomicPositionPartitioner
                    16. (object)(case class)GenomicRegionPartitioner
                    17. (trait)InFormatter
                    18. (trait)InFormatterCompanion
                    19. (case class)InnerShuffleRegionJoin
                    20. (case class)InnerShuffleRegionJoinAndGroupByLeft
                    21. (case class)InnerTreeRegionJoin
                    22. (case class)InnerTreeRegionJoinAndGroupByRight
                    23. (case class)LeftOuterShuffleRegionJoin
                    24. (case class)LeftOuterShuffleRegionJoinAndGroupByLeft
                    25. (class)MultisampleAvroGenomicDataset
                    26. (trait)MultisampleGenomicDataset
                    27. (trait)OutFormatter
                    28. (case class)RDDBoundGenericGenomicDataset
                    29. (case class)ReferencePartitioner
                    30. (class)RegionJoin
                    31. (case class)RightOuterShuffleRegionJoinAndGroupByLeft
                    32. (case class)RightOuterTreeRegionJoin
                    33. (case class)RightOuterTreeRegionJoinAndGroupByRight
                    34. (class)ShuffleRegionJoin
                    35. (trait)SortedIntervalPartitionJoinWithVictims
                    36. (trait)TreeRegionJoin
                    37. (trait)VictimlessSortedIntervalPartitionJoin
                    1. org.bdgenomics.adam.rdd.contig
                      1. (case class)DatasetBoundNucleotideContigFragmentDataset
                      2. (object)(class)NucleotideContigFragmentDataset
                      3. (case class)ParquetUnboundNucleotideContigFragmentDataset
                      4. (case class)RDDBoundNucleotideContigFragmentDataset
                    2. org.bdgenomics.adam.rdd.feature
                      1. (object)(case class)BEDInFormatter
                      2. (case class)BEDOutFormatter
                      3. (object)(class)CoverageDataset
                      4. (case class)DatasetBoundCoverageDataset
                      5. (case class)DatasetBoundFeatureDataset
                      6. (object)(class)FeatureDataset
                      7. (object)(case class)GFF3InFormatter
                      8. (case class)GFF3OutFormatter
                      9. (object)(case class)GTFInFormatter
                      10. (case class)GTFOutFormatter
                      11. (object)(case class)NarrowPeakInFormatter
                      12. (case class)NarrowPeakOutFormatter
                      13. (case class)ParquetUnboundCoverageDataset
                      14. (case class)ParquetUnboundFeatureDataset
                      15. (case class)RDDBoundCoverageDataset
                      16. (case class)RDDBoundFeatureDataset
                    3. org.bdgenomics.adam.rdd.fragment
                      1. (case class)DatasetBoundFragmentDataset
                      2. (object)(class)FragmentDataset
                      3. (object)(class)InterleavedFASTQInFormatter
                      4. (case class)ParquetUnboundFragmentDataset
                      5. (case class)RDDBoundFragmentDataset
                      6. (object)(class)Tab5InFormatter
                      7. (object)(class)Tab6InFormatter
                    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)(class)AlignmentRecordDataset
                      8. (trait)AnySAMInFormatter
                      9. (trait)AnySAMInFormatterCompanion
                      10. (case class)AnySAMOutFormatter
                      11. (object)(case class)BAMInFormatter
                      12. (case class)DatasetBoundAlignmentRecordDataset
                      13. (object)(class)FASTQInFormatter
                      14. (case class)IncorrectMDTagException
                      15. (class)InstrumentedADAMBAMOutputFormat
                      16. (class)InstrumentedADAMBAMOutputFormatHeaderLess
                      17. (class)InstrumentedADAMCRAMOutputFormat
                      18. (class)InstrumentedADAMCRAMOutputFormatHeaderLess
                      19. (class)InstrumentedADAMSAMOutputFormat
                      20. (class)InstrumentedADAMSAMOutputFormatHeaderLess
                      21. (case class)ParquetUnboundAlignmentRecordDataset
                      22. (object)(case class)QualityScoreBin
                      23. (case class)RDDBoundAlignmentRecordDataset
                      24. (class)ReferencePositionPairSerializer
                      25. (object)(case class)SAMInFormatter
                      26. (class)SingleReadBucketSerializer
                    5. org.bdgenomics.adam.rdd.variant
                      1. (class)ADAMVCFOutputFormat
                      2. (case class)DatasetBoundGenotypeDataset
                      3. (case class)DatasetBoundVariantContextDataset
                      4. (case class)DatasetBoundVariantDataset
                      5. (object)(class)GenotypeDataset
                      6. (case class)ParquetUnboundGenotypeDataset
                      7. (case class)ParquetUnboundVariantDataset
                      8. (case class)RDDBoundGenotypeDataset
                      9. (case class)RDDBoundVariantContextDataset
                      10. (case class)RDDBoundVariantDataset
                      11. (object)(class)VariantContextDataset
                      12. (object)(class)VariantDataset
                      13. (object)(case class)VCFInFormatter
                      14. (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.sql
                    1. (object)(case class)AlignmentRecord
                    2. (object)(case class)Dbxref
                    3. (object)(case class)Feature
                    4. (object)(case class)Fragment
                    5. (object)(case class)Genotype
                    6. (object)(case class)NucleotideContigFragment
                    7. (object)(case class)OntologyTerm
                    8. (object)(case class)ProcessingStep
                    9. (object)(case class)Reference
                    10. (object)(case class)TranscriptEffect
                    11. (object)(case class)Variant
                    12. (object)(case class)VariantAnnotation
                    13. (object)(case class)VariantCallingAnnotations
                    14. (object)(case class)VariantContext
                  10. org.bdgenomics.adam.util
                    1. (object)
                      ADAMShell
                    2. (object)
                      AttributeUtils
                    3. (object)
                      FileExtensions
                    4. (object)
                      GenomeFileReader
                    5. (case class)IndexedFastaFile
                    6. (class)ParquetFileTraversable
                    7. (object)
                      ParquetLogger
                    8. (object)
                      PhredUtils
                    9. (object)(case class)ReferenceContigMap
                    10. (class)ReferenceContigMapSerializer
                    11. (trait)ReferenceFile
                    12. (object)
                      SequenceDictionaryReader
                    13. (object)
                      TextRddWriter
                    14. (class)TwoBitFile
                    15. (class)TwoBitFileSerializer