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–
deprecated
org
org.apache
org.apache.parquet
org.apache.parquet.avro
(class)
AvroSchemaConverter
org.bdgenomics
org.bdgenomics.adam
org.bdgenomics.adam.algorithms
org.bdgenomics.adam.algorithms.consensus
(object)
(class)
ConsensusGenerator
org.bdgenomics.adam.algorithms.smithwaterman
(trait)
SmithWaterman
(case class)
SmithWatermanConstantGapScoring
org.bdgenomics.adam.converters
(class)
AlignmentRecordConverter
(object)
DefaultHeaderLines
(object)
(class)
VariantContextConverter
org.bdgenomics.adam.instrumentation
(object)
Timers
org.bdgenomics.adam.io
(class)
FastqInputFormat
(class)
FastqRecordReader
(class)
InterleavedFastqInputFormat
(class)
SingleFastqInputFormat
org.bdgenomics.adam.models
(object)
(trait)
Alphabet
(case class)
Attribute
(case class)
Coverage
(class)
DNAAlphabet
(object)
(case class)
MdTag
(object)
MdTagEvent
(object)
OptionalPositionOrdering
(trait)
OptionalReferenceOrdering
(object)
OptionalRegionOrdering
(object)
PositionOrdering
(object)
(case class)
ReadGroup
(object)
(case class)
ReadGroupDictionary
(trait)
ReferenceOrdering
(object)
(class)
ReferencePosition
(class)
ReferencePositionSerializer
(object)
(case class)
ReferenceRegion
(class)
ReferenceRegionSerializer
(object)
RegionOrdering
(object)
(class)
SequenceDictionary
(object)
(case class)
SequenceRecord
(object)
(class)
SnpTable
(case class)
Symbol
(object)
TagType
(object)
(class)
VariantContext
(class)
VariantContextSerializer
org.bdgenomics.adam.projections
(object)
AlignmentRecordField
(object)
DbxrefField
(object)
FeatureField
(class)
FieldEnumeration
(trait)
FieldValue
(object)
Filter
(object)
FragmentField
(object)
GenotypeField
(object)
OntologyTermField
(object)
Projection
(object)
ReadField
(object)
ReadGroupField
(object)
ReferenceField
(object)
SampleField
(object)
SequenceField
(object)
SliceField
(object)
TranscriptEffectField
(object)
VariantAnnotationField
(object)
VariantCallingAnnotationsField
(object)
VariantField
org.bdgenomics.adam.rdd
(object)
(class)
ADAMContext
(trait)
ADAMSaveAnyArgs
(class)
AvroGenomicDataset
(class)
AvroReadGroupGenomicDataset
(case class)
DatasetBoundGenericGenomicDataset
(trait)
DatasetBoundGenomicDataset
(case class)
FullOuterShuffleRegionJoin
(case class)
GenericConverter
(class)
GenericGenomicDataset
(case class)
GenomeBins
(case class)
GenomicBroadcast
(trait)
GenomicDataset
(trait)
GenomicDatasetConversion
(trait)
GenomicDatasetWithLineage
(object)
(case class)
GenomicPositionPartitioner
(object)
(case class)
GenomicRegionPartitioner
(trait)
InFormatter
(trait)
InFormatterCompanion
(case class)
InnerShuffleRegionJoin
(case class)
InnerShuffleRegionJoinAndGroupByLeft
(case class)
InnerTreeRegionJoin
(case class)
InnerTreeRegionJoinAndGroupByRight
(case class)
LeftOuterShuffleRegionJoin
(case class)
LeftOuterShuffleRegionJoinAndGroupByLeft
(class)
MultisampleAvroGenomicDataset
(trait)
MultisampleGenomicDataset
(trait)
OutFormatter
(case class)
RDDBoundGenericGenomicDataset
(case class)
ReferencePartitioner
(class)
RegionJoin
(case class)
RightOuterShuffleRegionJoinAndGroupByLeft
(case class)
RightOuterTreeRegionJoin
(case class)
RightOuterTreeRegionJoinAndGroupByRight
(class)
ShuffleRegionJoin
(trait)
SortedIntervalPartitionJoinWithVictims
(trait)
TreeRegionJoin
(trait)
VictimlessSortedIntervalPartitionJoin
org.bdgenomics.adam.rdd.feature
(object)
(case class)
BEDInFormatter
(case class)
BEDOutFormatter
(object)
(class)
CoverageDataset
(case class)
DatasetBoundCoverageDataset
(case class)
DatasetBoundFeatureDataset
(object)
(class)
FeatureDataset
(object)
(case class)
GFF3InFormatter
(case class)
GFF3OutFormatter
(object)
(case class)
GTFInFormatter
(case class)
GTFOutFormatter
(object)
(case class)
NarrowPeakInFormatter
(case class)
NarrowPeakOutFormatter
(case class)
ParquetUnboundCoverageDataset
(case class)
ParquetUnboundFeatureDataset
(case class)
RDDBoundCoverageDataset
(case class)
RDDBoundFeatureDataset
org.bdgenomics.adam.rdd.fragment
(case class)
DatasetBoundFragmentDataset
(object)
(class)
FragmentDataset
(object)
(class)
InterleavedFASTQInFormatter
(case class)
ParquetUnboundFragmentDataset
(case class)
RDDBoundFragmentDataset
(object)
(class)
Tab5InFormatter
(object)
(class)
Tab6InFormatter
org.bdgenomics.adam.rdd.read
(class)
ADAMBAMOutputFormat
(class)
ADAMBAMOutputFormatHeaderLess
(class)
ADAMCRAMOutputFormat
(class)
ADAMCRAMOutputFormatHeaderLess
(class)
ADAMSAMOutputFormat
(class)
ADAMSAMOutputFormatHeaderLess
(object)
(class)
AlignmentRecordDataset
(trait)
AnySAMInFormatter
(trait)
AnySAMInFormatterCompanion
(case class)
AnySAMOutFormatter
(object)
(case class)
BAMInFormatter
(case class)
DatasetBoundAlignmentRecordDataset
(case class)
DatasetBoundReadDataset
(object)
(class)
FASTQInFormatter
(case class)
IncorrectMDTagException
(class)
InstrumentedADAMBAMOutputFormat
(class)
InstrumentedADAMBAMOutputFormatHeaderLess
(class)
InstrumentedADAMCRAMOutputFormat
(class)
InstrumentedADAMCRAMOutputFormatHeaderLess
(class)
InstrumentedADAMSAMOutputFormat
(class)
InstrumentedADAMSAMOutputFormatHeaderLess
(case class)
ParquetUnboundAlignmentRecordDataset
(case class)
ParquetUnboundReadDataset
(object)
(case class)
QualityScoreBin
(case class)
RDDBoundAlignmentRecordDataset
(case class)
RDDBoundReadDataset
(object)
(class)
ReadDataset
(class)
ReferencePositionPairSerializer
(object)
(case class)
SAMInFormatter
(class)
SingleReadBucketSerializer
org.bdgenomics.adam.rdd.sequence
(case class)
DatasetBoundSequenceDataset
(case class)
DatasetBoundSliceDataset
(object)
(class)
FASTAInFormatter
(case class)
ParquetUnboundSequenceDataset
(case class)
ParquetUnboundSliceDataset
(case class)
RDDBoundSequenceDataset
(case class)
RDDBoundSliceDataset
(object)
(class)
SequenceDataset
(object)
(class)
SliceDataset
org.bdgenomics.adam.rdd.variant
(class)
ADAMVCFOutputFormat
(case class)
DatasetBoundGenotypeDataset
(case class)
DatasetBoundVariantContextDataset
(case class)
DatasetBoundVariantDataset
(object)
(class)
GenotypeDataset
(case class)
ParquetUnboundGenotypeDataset
(case class)
ParquetUnboundVariantDataset
(case class)
RDDBoundGenotypeDataset
(case class)
RDDBoundVariantContextDataset
(case class)
RDDBoundVariantDataset
(object)
(class)
VariantContextDataset
(object)
(class)
VariantDataset
(object)
(case class)
VCFInFormatter
(case class)
VCFOutFormatter
org.bdgenomics.adam.rich
(object)
(case class)
RichAlignmentRecord
(object)
(case class)
RichVariant
org.bdgenomics.adam.serialization
(class)
ADAMKryoRegistrator
(class)
AvroSerializer
(case class)
InputStreamWithDecoder
(class)
WritableSerializer
org.bdgenomics.adam.sql
(object)
(case class)
AlignmentRecord
(object)
(case class)
Dbxref
(object)
(case class)
Feature
(object)
(case class)
Fragment
(object)
(case class)
Genotype
(object)
(case class)
OntologyTerm
(object)
(case class)
ProcessingStep
(object)
(case class)
Read
(object)
(case class)
Reference
(object)
(case class)
Sequence
(object)
(case class)
Slice
(object)
(case class)
TranscriptEffect
(object)
(case class)
Variant
(object)
(case class)
VariantAnnotation
(object)
(case class)
VariantCallingAnnotations
(object)
(case class)
VariantContext
org.bdgenomics.adam.util
(object)
ADAMShell
(object)
AttributeUtils
(object)
FileExtensions
(object)
GenomeFileReader
(case class)
IndexedFastaFile
(class)
ParquetFileTraversable
(object)
ParquetLogger
(object)
PhredUtils
(object)
(case class)
ReferenceContigMap
(class)
ReferenceContigMapSerializer
(trait)
ReferenceFile
(object)
SequenceDictionaryReader
(object)
TextRddWriter
(class)
TwoBitFile
(class)
TwoBitFileSerializer