- AbstractMendelianChecker
- Alignment
- AllAnnotationListTextGenerator
- AltGeneIDType
- AminoAcidChange
- AminoAcidChangeNormalizer
- Anchor
- Anchors
- Annotation
- AnnotationBuilderDispatcher
- AnnotationBuilderOptions
- AnnotationException
- AnnotationLocation
- AnnotationLocation.RankType
- AnnotationLocationBuilder
- AnnotationMessage
- BestAnnotationListTextGenerator
- BlockSubstitutionAnnotationBuilder
- CDSInterval
- CDSPosition
- Chromosome
- ChromosomeType
- DataSource
- DataSourceFactory
- DatasourceOptions
- DeletionAnnotationBuilder
- Disease
- DNAUtils
- DuplicationChecker
- EnsemblParser
- FASTAParser
- FASTARecord
- FeatureRecord
- FeatureRecord.Strand
- FeatureRecordParser
- FileDownloadException
- FlatBEDDataSource
- FlatBEDFastaParser
- FlatBEDJannovarDataFactory
- FlatBEDParser
- GenomeInterval
- GenomePosition
- GenomeVariant
- GenomeVariantNormalizer
- GenomeVariantType
- GenomicNucleotideChangeBuilder
- Genotype
- Genotype
- GenotypeBuilder
- GenotypeCalls
- GenotypeCallsBuilder
- GenotypeList
- GenotypeListBuilder
- GFFParser
- GFFParser.GFFVersion
- GFFRecordParser
- GTFRecordParser
- HG19RefDictBuilder
- HGNCParser
- HGNCRecord
- Immutable
- IncompatiblePedigreeException
- IndexedFASTAReader
- InheritanceCheckerMT
- InsertionAnnotationBuilder
- Interval
- IntervalArray
- IntervalEndExtractor
- InvalidAttributeException
- InvalidCodonException
- InvalidCoordinateException
- InvalidDataSourceException
- InvalidGenomeVariant
- JannovarData
- JannovarDataFactory
- JannovarDataSerializer
- JannovarException
- MendelianCheckerAD
- MendelianCheckerAR
- MendelianCheckerARCompoundHet
- MendelianCheckerARHom
- MendelianCheckerXD
- MendelianCheckerXR
- MendelianCheckerXRCompoundHet
- MendelianCheckerXRHom
- MendelianInheritanceChecker
- ModeOfInheritance
- MutableInterval
- NucleotidePointLocationBuilder
- OldVariantType
- PathUtil
- PedFileContents
- PedFileReader
- PedFileWriter
- Pedigree
- Pedigree.IndexedPerson
- PedigreeExtractor
- PedigreeQueryDecorator
- PedParseException
- PedPerson
- Person
- PositionType
- ProgressBar
- ProjectionException
- PutativeImpact
- ReferenceDictionary
- ReferenceDictionaryBuilder
- ReferenceDictParser
- RefSeqFastaRecordIdFormat
- RefSeqParser
- SerializationException
- Sex
- SNVAnnotationBuilder
- Strand
- StringUtil
- StructuralVariantAnnotationBuilder
- SubModeOfInheritance
- SVAnnotation
- SVAnnotationBuilderDispatcher
- SVAnnotations
- SVAnnotator
- SVBreakend
- SVBreakend.Side
- SVBreakendAnnotationBuilder
- SVCopyNumberVariant
- SVCopyNumberVariantAnnotationBuilder
- SVDeletion
- SVDeletionAnnotationBuilder
- SVDescription
- SVDescription.Type
- SVDuplication
- SVDuplicationAnnotationBuilder
- SVGenomeVariant
- SVInsertion
- SVInsertionAnnotationBuilder
- SVInversion
- SVInversionAnnotationBuilder
- SVMobileElementDeletion
- SVMobileElementDeletionAnnotationBuilder
- SVMobileElementInsertion
- SVMobileElementInsertionAnnotationBuilder
- SVTandemDuplication
- SVTandemDuplicationAnnotationBuilder
- SVUnknown
- TranscriptInterval
- TranscriptIntervalEndExtractor
- TranscriptModel
- TranscriptModelBuilder
- TranscriptModelBuilder.AlignmentPart
- TranscriptModelBuilderHGNCExtender
- TranscriptParseException
- TranscriptParser
- TranscriptPosition
- TranscriptProjectionDecorator
- TranscriptSequenceChangeHelper
- TranscriptSequenceDecorator
- TranscriptSequenceOntologyDecorator
- TranscriptSupportLevels
- TranscriptSupportLevelsSetterFromLengths
- Translator
- UCSCParser
- UncheckedJannovarException
- VariantAnnotations
- VariantAnnotationsContentDecorator
- VariantAnnotationsTextGenerator
- VariantAnnotator
- VariantDescription
- VariantEffect
- VersionComparator
- VersionTokenizer