class icon trait icon trait icon trait icon
    1. org
        1. org.apache
            1. org.apache.parquet
                1. org.apache.parquet.avro
                  1. (class)AvroSchemaConverter
            2. 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