All Classes
AbstractDBAnnotationDriver
AbstractMendelianChecker
AbstractVariantContextCompatibilityChecker
AllAnnotationListTextGenerator
AlleleMatcher
AminoAcidChange
AminoAcidChangeNormalizer
AminoAcidCode
AnnotatedVariantWriter
AnnotatedVCFWriter
AnnotatePositionCommand
AnnotatePositionCommandLineParser
AnnotateVCFCommand
AnnotateVCFCommandLineParser
AnnotatingRecord
Annotation
AnnotationBuilderDispatcher
AnnotationBuilderOptions
AnnotationException
AnnotationLocation
AnnotationLocation.RankType
AnnotationLocationBuilder
AnnotationMessage
AnnotationTextGenerator
BestAnnotationListTextGenerator
BlockSubstitutionAnnotationBuilder
CannotAnnotateMendelianInheritance
CannotTranslateHGVSVariant
CDSInterval
CDSPosition
Chromosome
ChromosomeType
CommandLineParsingException
ConsumerProcessor
ConvertibleToHGVSString
CoordinateSortingChecker
DatabaseListCommand
DatabaseListCommandLineParser
DataSource
DataSourceFactory
DatasourceOptions
DBAnnotationDriver
DBAnnotationOptions
DBAnnotationOptions.MultipleMatchBehaviour
DBSNPAnnotationDriver
DBSNPGeneInfo
DBSNPInfo
DBSNPInfoFactory
DBSNPRecord
DBSNPRecordBuilder
DBSNPVariantAlleleOrigin
DBSNPVariantProperty
DBSNPVariantSuspectReasonCode
DBSNPVCFHeaderExtender
DBVariantContextAnnotator
DBVariantContextAnnotatorFactory
DeletionAnnotationBuilder
Disease
DNAUtils
DownloadCommand
DownloadCommandLineParser
DuplicationChecker
EnsemblParser
ExacAnnotationDriver
ExacPopulation
ExacRecord
ExacRecordBuilder
ExacVCFHeaderExtender
FASTAParser
FASTARecord
FeatureRecord
FeatureRecord.Strand
FeatureRecordParser
FileDownloadException
FlatBEDDataSource
FlatBEDFastaParser
FlatBEDJannovarDataFactory
FlatBEDParser
GeneWiseMendelianAnnotationProcessor
GenomeInterval
GenomePosition
GenomeRegion
GenomeRegionList
GenomeRegionListFactoryFromSAMSequenceDictionary
GenomeRegionSequenceExtractor
GenomeVariant
GenomeVariantNormalizer
GenomeVariantType
GenomicNucleotideChangeBuilder
Genotype
Genotype
GenotypeBuilder
GenotypeCalls
GenotypeCallsBuilder
GenotypeList
GenotypeListBuilder
GenotypeMatch
GFFParser
GFFParser.GFFVersion
GFFRecordParser
GTFRecordParser
HelpRequestedException
HG19RefDictBuilder
HGVSErrorStrategy
HGVSLexer
HGVSParser
HGVSParsingException
HGVSVariant
Immutable
IncompatiblePedigreeException
InfoFields
InheritanceCompatibilityChecker
InheritanceCompatibilityChecker.Builder
InheritanceCompatibilityCheckerException
InheritanceVariantContext
InheritanceVariantContextList
InsertionAnnotationBuilder
InterfaceVariantContextCompatibilityChecker
Interval
IntervalArray
IntervalEndExtractor
InvalidAttributeException
InvalidCodonException
InvalidCoordinateException
InvalidCoordinatesException
InvalidDataSourceException
InvalidGenomeVariant
Jannovar
JannovarAnnotationCommand
JannovarAnnotationCommandLineParser
JannovarCommand
JannovarData
JannovarDataFactory
JannovarDataSerializer
JannovarException
JannovarOptions
JannovarOptions.Command
JannovarVarDBException
LegacyChange
LegacyChangeParser
LegacyDeletion
LegacyIndel
LegacyInsertion
LegacyLocation
LegacyLocationType
LegacySubstitution
LegacyVariant
MendelianCheckerAD
MendelianCheckerAR
MendelianCheckerARCompoundHet
MendelianCheckerARHom
MendelianCheckerXD
MendelianCheckerXR
MendelianCheckerXRCompoundHet
MendelianCheckerXRHom
MendelianInheritanceChecker
MendelVCFHeaderExtender
ModeOfInheritance
MultiAlleleNucleotideVariant
MultiAlleleProteinVariant
MutableInterval
NucleotideChange
NucleotideChangeAllele
NucleotideChangeToGenomeVariantTranslationImplBase
NucleotideChangeToGenomeVariantTranslator
NucleotideDeletion
NucleotideDuplication
NucleotideIndel
NucleotideInsertion
NucleotideInversion
NucleotideLocationConverter
NucleotideMiscChange
NucleotideMiscChangeType
NucleotidePointLocation
NucleotidePointLocationBuilder
NucleotideRange
NucleotideSeqDescription
NucleotideShortSequenceRepeatVariability
NucleotideSubstitution
NucleotideVariant
OldVariantType
PathUtil
PedFileContents
PedFileReader
PedFileWriter
Pedigree
Pedigree.IndexedPerson
PedigreeExtractor
PedigreeQueryDecorator
PedParseException
PedPerson
Person
PositionType
ProgressBar
ProgressReporter
ProjectionException
ProteinChange
ProteinChangeAllele
ProteinDeletion
ProteinDuplication
ProteinExtension
ProteinFrameshift
ProteinIndel
ProteinInsertion
ProteinMiscChange
ProteinMiscChangeType
ProteinPointLocation
ProteinRange
ProteinSeqDescription
ProteinShortSequenceRepeatVariability
ProteinSubstitution
ProteinVariant
PutativeImpact
ReferenceDictionary
ReferenceDictionaryBuilder
ReferenceDictParser
RefSeqParser
SequenceType
SerializationException
Sex
SingleAlleleNucleotideVariant
SingleAlleleProteinVariant
SNVAnnotationBuilder
Strand
StringUtil
StructuralVariantAnnotationBuilder
TranscriptInterval
TranscriptIntervalEndExtractor
TranscriptModel
TranscriptModelBuilder
TranscriptParseException
TranscriptParser
TranscriptPosition
TranscriptProjectionDecorator
TranscriptSequenceChangeHelper
TranscriptSequenceDecorator
TranscriptSequenceOntologyDecorator
TranscriptSupportLevels
TranscriptSupportLevelsSetterFromLengths
Translator
Translator
UCSCParser
UK10KAnnotationDriver
UK10KRecord
UK10KRecordBuilder
UK10KVCFHeaderExtender
UncheckedJannovarException
VariantAnnotations
VariantAnnotationsContentDecorator
VariantAnnotationsTextGenerator
VariantAnnotator
VariantConfiguration
VariantContextAnnotator
VariantContextAnnotator.Options
VariantContextCompatibilityCheckerAutosomalDominant
VariantContextCompatibilityCheckerAutosomalRecessive
VariantContextCompatibilityCheckerAutosomalRecessiveCompoundHet
VariantContextCompatibilityCheckerAutosomalRecessiveHomozygous
VariantContextCompatibilityCheckerXDominant
VariantContextCompatibilityCheckerXRecessive
VariantContextCounter
VariantContextFilterException
VariantContextMendelianAnnotator
VariantContextProcessor
VariantContextToRecordConverter
VariantContextWriterConstructionHelper
VariantDescription
VariantDescription
VariantEffect
VariantNormalizer
VCFHeaderExtender