All Classes
AbstractHmlValidationRule
AbstractLattice
AbstractRangeTree
AddressType
AddressType.Country
AddressType.State
Alignments
Allele
Allele
Allele.Builder
Allele.Lesion
AlleleAssignment
AlleleException
AlleleList
AmbiguousSubstitutionMutationStrategy
Amplification
Analysis
Analysis.AnalysisAttributes
Analysis.AnalysisLinks
Analysis.AnalysisRef
Analysis.AnalysisType
Analysis.AnalysisType.SamplePhenotype
Analysis.AnalysisType.SequenceAnnotation
Analysis.AnalysisType.SequenceAssembly
Analysis.AnalysisType.SequenceVariation
Analysis.Files
Analysis.RunRef
Analysis.SampleRef
Analysis.StudyRef
AnalysisFileType
AnalysisFileType.Checklist
AnalysisSet
AttributeType
AttributeType
AttributeType
AttributeType
AttributeType
AttributeType
AttributeType
BedListener
BedReader
BedRecord
BedWriter
BiojavaPairwiseAlignment
Blastn
CenteredRangeTree
CertificationType
ClinvarPublicSetType
ClinvarPublicSetType.AcronymSet
ClinvarPublicSetType.DescrSet
ClinvarPublicSetType.SynonymSet
CompositeMutationStrategy
Concept
Concept.Builder
ConceptLattice
ConsensusSequence
ConsensusSequenceBlock
ContactType
CoverageStrategy
CredentialType
DataSourceType
DegreeType
DeletionMutationStrategy
DiploidCombination
DownsampleFastq
DownsampleInterleavedFastq
EvaluateScaffolds
Experiment
Experiment.ExperimentAttributes
Experiment.ExperimentLinks
Experiment.StudyRef
ExperimentSet
ExtractConsensus
ExtractExpectedGlstrings
ExtractExpectedHaploids
FastaToFastq
FastqDescription
FastqToFasta
FastqToSsake
FeatureParser
FeatureParserConstants
FeatureParserTokenManager
FileType
FileType
FilterConsensus
FilterInterpretableExons
FilterSamples
FilterVcf
GapPenalties
GapPenalties.Builder
GenerateBed
GeneratePairedEndReads
GeneratePairedEndReads
GenerateReads
GenerateReads
GeneSetType
Genewise
GenewiseExon
GenotypeList
Glstring
Gssp
GTRLabResearchTestType
GTRLabResearchTestType.Method
GTRLabResearchTestType.Method.TopCategory
GTRLabResearchTestType.Method.TopCategory.Category
GTRLabResearchTestType.Method.TopCategory.Category.Methodology
GTRLabResearchTestType.MethodAdd
GTRLabResearchTestType.MethodAdd.Exons
GTRLabResearchTestType.Participation
GTRLabResearchTestType.Study
GTRLabResearchTestType.StudyPerson
GTRLabTestType
GTRLabTestType.Availability
GTRLabTestType.Availability.TestExternal
GTRLabTestType.ClinicalUtility
GTRLabTestType.ClinicalUtility.Type
GTRLabTestType.Indications
GTRLabTestType.Indications.Inheritance
GTRLabTestType.Indications.Mechanism
GTRLabTestType.ManufacturerTestName
GTRLabTestType.Method
GTRLabTestType.Method.TopCategory
GTRLabTestType.Method.TopCategory.Category
GTRLabTestType.Method.TopCategory.Category.Methodology
GTRLabTestType.MethodAdd
GTRLabTestType.MethodAdd.Exons
GTRLabTestType.OtherName
GTRLabTestType.QualityControl
GTRLabTestType.Regulations
GTRLabTestType.Regulations.FDARegulatoryClearance
GTRLabTestType.Regulations.TestCertification
GTRLabTestType.Specimen
GTRLabTestType.TestAddService
GTRLabTestType.TestResults
GTRLabTestType.TestResults.ReContact
GTRLabTestType.TestResults.Research
GTRLabTestType.TestResults.VUS
GTRLabTestType.TestResults.VUS.RecruitFamily
GTRLabTestType.TestService
GTROrgType
GTROrgType.DiseaseTesting
GTROrgType.DiseaseTesting.Method
GTROrgType.DiseaseTesting.Method.TopCategory
GTROrgType.DiseaseTesting.Method.TopCategory.Category
GTROrgType.GeneTesting
GTRPublicData
GTRPublicData.GTRLabData
GTRPublicData.GTRLabData.GTRLabResearchTest
GTRPublicData.GTRLabData.GTRLabTest
GtrReader
GtrWriter
Haploid
HighScoringPair
Hml
Hmlid
HmlReader
HmlUtils
HmlValidationException
HmlValidationRule
HmlValidationRules
HmlValidator
HmlWriter
HspListener
HspReader
HspToBed
HspWriter
IdentifierType
IdentifierType
IdentifierType
IdentifierType
IdentifierType
IdentifierType
IdentifierType
IdentityMutationStrategy
IndelMutationStrategy
InsertionMutationStrategy
InstrumentModel
InterleaveFastq
IntersectBed
LabCertificationType
Lattice
LibraryDescriptorType
LibraryDescriptorType.LibraryLayout
LibraryDescriptorType.LibraryLayout.Paired
LibraryDescriptorType.LibraryLayout.Single
LibraryDescriptorType.TargetedLoci
LibraryDescriptorType.TargetedLoci.Locus
LibrarySelection
LibrarySource
LibraryStrategy
LibraryType
LiftoverBed
LinkType
LinkType
LinkType
LinkType
LinkType
LinkType
LinkType
LinkType.EntrezLink
LinkType.EntrezLink
LinkType.EntrezLink
LinkType.EntrezLink
LinkType.EntrezLink
LinkType.EntrezLink
LinkType.EntrezLink
LinkType.UrlLink
LinkType.UrlLink
LinkType.UrlLink
LinkType.UrlLink
LinkType.UrlLink
LinkType.UrlLink
LinkType.UrlLink
Locus
Locus.Util
LocusBlock
LocusException
MaskedToBed
MeanCoverageStrategy
MeasureSetType
MeasureSetType.Measure
MeasureSetType.Measure.Affects
MeasureSetType.Measure.FoundIn
MeasureSetType.Measure.FoundIn.Location
MeasureSetType.Measure.Location
MeasureTraitType
MeasureTraitType.Assertion
MeasureTraitType.ClinicalSignificance
MeasureTraitType.ClinVarAcc
MeasureTraitType.DescrSet
MeasureTraitType.ObservedIn
MeasureTraitType.Title
MergeFastq
MinimumCoverageStrategy
MiringModule
MutationStrategy
NameType
NameType
NameType
NameType
NameType
NameType
NameType
ObjectFactory
ObjectFactory
ObjectFactory
ObjectFactory
ObjectFactory
ObjectFactory
ObjectFactory
ObjectFactory
ObjectFactory
OrganizationType
OrganizationType.LabAffiliations
OrganizationType.LabContact
OrganizationType.LabServices
PairedEndAdapter
PairedEndFastqReader
PairedEndFastqReaderException
PairedEndListener
PairwiseAlignment
ParallelBiojavaPairwiseAlignment
ParseException
Partial
Partial.Order
Partial.Order.Direction
PersonnelType
PersonnelType.PublicContact
PersonType
PersonType.Certification
PersonType.Credential
PersonType.Degree
PersonType.Name
PhenotypeSetType
PipelineType
PipelineType
PipelineType
PipelineType
PipelineType
PipelineType
PipelineType
PipelineType.PipeSection
PipelineType.PipeSection
PipelineType.PipeSection
PipelineType.PipeSection
PipelineType.PipeSection
PipelineType.PipeSection
PipelineType.PipeSection
PlatformType
PlatformType
PlatformType
PlatformType
PlatformType
PlatformType
PlatformType
PlatformType.AbiSolid
PlatformType.AbiSolid
PlatformType.AbiSolid
PlatformType.AbiSolid
PlatformType.AbiSolid
PlatformType.AbiSolid
PlatformType.AbiSolid
PlatformType.Capillary
PlatformType.Capillary
PlatformType.Capillary
PlatformType.Capillary
PlatformType.Capillary
PlatformType.Capillary
PlatformType.Capillary
PlatformType.CompleteGenomics
PlatformType.CompleteGenomics
PlatformType.CompleteGenomics
PlatformType.CompleteGenomics
PlatformType.CompleteGenomics
PlatformType.CompleteGenomics
PlatformType.CompleteGenomics
PlatformType.Helicos
PlatformType.Helicos
PlatformType.Helicos
PlatformType.Helicos
PlatformType.Helicos
PlatformType.Helicos
PlatformType.Helicos
PlatformType.Illumina
PlatformType.Illumina
PlatformType.Illumina
PlatformType.Illumina
PlatformType.Illumina
PlatformType.Illumina
PlatformType.Illumina
PlatformType.IonTorrent
PlatformType.IonTorrent
PlatformType.IonTorrent
PlatformType.IonTorrent
PlatformType.IonTorrent
PlatformType.IonTorrent
PlatformType.IonTorrent
PlatformType.Ls454
PlatformType.Ls454
PlatformType.Ls454
PlatformType.Ls454
PlatformType.Ls454
PlatformType.Ls454
PlatformType.Ls454
PlatformType.PacbioSmrt
PlatformType.PacbioSmrt
PlatformType.PacbioSmrt
PlatformType.PacbioSmrt
PlatformType.PacbioSmrt
PlatformType.PacbioSmrt
PlatformType.PacbioSmrt
PoolMemberType
PoolMemberType.ReadLabel
Present
ProcessingType
ProcessingType
ProcessingType
ProcessingType
ProcessingType
ProcessingType
ProcessingType
Property
QualifiedNameType
QualifiedNameType
QualifiedNameType
QualifiedNameType
QualifiedNameType
QualifiedNameType
QualifiedNameType
QualityStrategy
RangeGeometries
RangeList
Ranges
RangeTree
RawReads
RealDistributionQualityStrategy
ReferenceAssemblyType
ReferenceAssemblyType
ReferenceAssemblyType
ReferenceAssemblyType
ReferenceAssemblyType
ReferenceAssemblyType
ReferenceAssemblyType
ReferenceAssemblyType.Custom
ReferenceAssemblyType.Custom
ReferenceAssemblyType.Custom
ReferenceAssemblyType.Custom
ReferenceAssemblyType.Custom
ReferenceAssemblyType.Custom
ReferenceAssemblyType.Custom
ReferenceAssemblyType.Custom.UrlLink
ReferenceAssemblyType.Custom.UrlLink
ReferenceAssemblyType.Custom.UrlLink
ReferenceAssemblyType.Custom.UrlLink
ReferenceAssemblyType.Custom.UrlLink
ReferenceAssemblyType.Custom.UrlLink
ReferenceAssemblyType.Custom.UrlLink
ReferenceAssemblyType.Standard
ReferenceAssemblyType.Standard
ReferenceAssemblyType.Standard
ReferenceAssemblyType.Standard
ReferenceAssemblyType.Standard
ReferenceAssemblyType.Standard
ReferenceAssemblyType.Standard
ReferenceDatabase
ReferenceDatabase.ReferenceSequence
ReferenceSequenceType
ReferenceSequenceType
ReferenceSequenceType
ReferenceSequenceType
ReferenceSequenceType
ReferenceSequenceType
ReferenceSequenceType
ReferenceSequenceType.Sequence
ReferenceSequenceType.Sequence
ReferenceSequenceType.Sequence
ReferenceSequenceType.Sequence
ReferenceSequenceType.Sequence
ReferenceSequenceType.Sequence
ReferenceSequenceType.Sequence
ReportingCenter
Run
Run.DataBlock
Run.DataBlock.Files
Run.DataBlock.Files.File
Run.ExperimentRef
Run.RunAttributes
Run.RunLinks
Run.RunType
RunSet
Sample
Sample
Sample
Sample.SampleAttributes
Sample.SampleLinks
Sample.SampleName
SampleDescriptorType
SampleDescriptorType.Pool
SampleSet
SbtNgs
SbtSanger
ScoreFunction
ScoreFunctionQualityStrategy
ScoreFunctions
SentenceCasePlugin
Sequence
SequenceQuality
SequencingDirectivesType
SequencingDirectivesType
SequencingDirectivesType
SequencingDirectivesType
SequencingDirectivesType
SequencingDirectivesType
SequencingDirectivesType
SetElementComplexType
SetElementType
SimpleCharStream
SplitFasta
SpotDescriptorType
SpotDescriptorType
SpotDescriptorType
SpotDescriptorType
SpotDescriptorType
SpotDescriptorType
SpotDescriptorType
SpotDescriptorType.SpotDecodeSpec
SpotDescriptorType.SpotDecodeSpec
SpotDescriptorType.SpotDecodeSpec
SpotDescriptorType.SpotDecodeSpec
SpotDescriptorType.SpotDecodeSpec
SpotDescriptorType.SpotDecodeSpec
SpotDescriptorType.SpotDecodeSpec
SpotDescriptorType.SpotDecodeSpec.ReadSpec
SpotDescriptorType.SpotDecodeSpec.ReadSpec
SpotDescriptorType.SpotDecodeSpec.ReadSpec
SpotDescriptorType.SpotDecodeSpec.ReadSpec
SpotDescriptorType.SpotDecodeSpec.ReadSpec
SpotDescriptorType.SpotDecodeSpec.ReadSpec
SpotDescriptorType.SpotDecodeSpec.ReadSpec
SpotDescriptorType.SpotDecodeSpec.ReadSpec.ExpectedBasecallTable
SpotDescriptorType.SpotDecodeSpec.ReadSpec.ExpectedBasecallTable
SpotDescriptorType.SpotDecodeSpec.ReadSpec.ExpectedBasecallTable
SpotDescriptorType.SpotDecodeSpec.ReadSpec.ExpectedBasecallTable
SpotDescriptorType.SpotDecodeSpec.ReadSpec.ExpectedBasecallTable
SpotDescriptorType.SpotDecodeSpec.ReadSpec.ExpectedBasecallTable
SpotDescriptorType.SpotDecodeSpec.ReadSpec.ExpectedBasecallTable
SpotDescriptorType.SpotDecodeSpec.ReadSpec.ExpectedBasecallTable.Basecall
SpotDescriptorType.SpotDecodeSpec.ReadSpec.ExpectedBasecallTable.Basecall
SpotDescriptorType.SpotDecodeSpec.ReadSpec.ExpectedBasecallTable.Basecall
SpotDescriptorType.SpotDecodeSpec.ReadSpec.ExpectedBasecallTable.Basecall
SpotDescriptorType.SpotDecodeSpec.ReadSpec.ExpectedBasecallTable.Basecall
SpotDescriptorType.SpotDecodeSpec.ReadSpec.ExpectedBasecallTable.Basecall
SpotDescriptorType.SpotDecodeSpec.ReadSpec.ExpectedBasecallTable.Basecall
SpotDescriptorType.SpotDecodeSpec.ReadSpec.RelativeOrder
SpotDescriptorType.SpotDecodeSpec.ReadSpec.RelativeOrder
SpotDescriptorType.SpotDecodeSpec.ReadSpec.RelativeOrder
SpotDescriptorType.SpotDecodeSpec.ReadSpec.RelativeOrder
SpotDescriptorType.SpotDecodeSpec.ReadSpec.RelativeOrder
SpotDescriptorType.SpotDecodeSpec.ReadSpec.RelativeOrder
SpotDescriptorType.SpotDecodeSpec.ReadSpec.RelativeOrder
SraReader
SraWriter
Sso
Ssp
StreamingVcfParser
Study
Study.Descriptor
Study.Descriptor.RelatedStudies
Study.Descriptor.RelatedStudies.RelatedStudy
Study.Descriptor.StudyType
Study.StudyAttributes
Study.StudyLinks
StudySet
StudyType
SubAmplification
Submission
Submission.Actions
Submission.Actions.Action
Submission.Actions.Action.Add
Submission.Actions.Action.Cancel
Submission.Actions.Action.Hold
Submission.Actions.Action.Modify
Submission.Actions.Action.Protect
Submission.Actions.Action.Release
Submission.Actions.Action.Suppress
Submission.Actions.Action.Validate
Submission.Contacts
Submission.Contacts.Contact
Submission.SubmissionAttributes
Submission.SubmissionLinks
SubmissionSet
SubmissionSummaryType
SubstitutionMutationStrategy
TextCitations
TextCitationsList
TextCitationsURL
TextURL
Token
TokenMgrError
TraitSetType
TraitSetType.Trait
Typing
TypingMethod
TypingTestName
TypingTestNames
URL
UrlType
UrlType
UrlType
UrlType
UrlType
UrlType
UrlType
ValidateHml
ValidateInterleavedFastq
ValidateInterpretation
Variant
VariantEffect
VcfFile
VcfFile.Filter
VcfFile.Format
VcfFile.Header
VcfFile.Info
VcfFile.Metadata
VcfFile.Metadata.Type
VcfFile.Strictness
VcfFileException
VcfGenome
VcfGenotype
VcfGenotype.Builder
VcfHeader
VcfHeader.Builder
VcfHeaderParser
VcfParseAdapter
VcfParseListener
VcfParser
VcfReader
VcfRecord
VcfRecord
VcfRecord.Builder
VcfRecordParser
VcfSample
VcfSample.Builder
VcfSampleParser
VcfStreamAdapter
VcfStreamListener
VcfWriter
XrefType
XRefType
XRefType
XRefType
XRefType
XRefType
XRefType
XRefType