Copyright | (c) 2015-2016 Brendan Hay |
---|---|
License | Mozilla Public License, v. 2.0. |
Maintainer | Brendan Hay <brendan.g.hay@gmail.com> |
Stability | auto-generated |
Portability | non-portable (GHC extensions) |
Safe Haskell | None |
Language | Haskell2010 |
- Service Configuration
- OAuth Scopes
- API Declaration
- Resources
- genomics.annotations.batchCreate
- genomics.annotations.create
- genomics.annotations.delete
- genomics.annotations.get
- genomics.annotations.search
- genomics.annotations.update
- genomics.annotationsets.create
- genomics.annotationsets.delete
- genomics.annotationsets.get
- genomics.annotationsets.search
- genomics.annotationsets.update
- genomics.callsets.create
- genomics.callsets.delete
- genomics.callsets.get
- genomics.callsets.patch
- genomics.callsets.search
- genomics.datasets.create
- genomics.datasets.delete
- genomics.datasets.get
- genomics.datasets.getIamPolicy
- genomics.datasets.list
- genomics.datasets.patch
- genomics.datasets.setIamPolicy
- genomics.datasets.testIamPermissions
- genomics.datasets.undelete
- genomics.operations.cancel
- genomics.operations.get
- genomics.operations.list
- genomics.readgroupsets.coveragebuckets.list
- genomics.readgroupsets.delete
- genomics.readgroupsets.export
- genomics.readgroupsets.get
- genomics.readgroupsets.import
- genomics.readgroupsets.patch
- genomics.readgroupsets.search
- genomics.reads.search
- genomics.references.bases.list
- genomics.references.get
- genomics.references.search
- genomics.referencesets.get
- genomics.referencesets.search
- genomics.variants.create
- genomics.variants.delete
- genomics.variants.get
- genomics.variants.import
- genomics.variants.merge
- genomics.variants.patch
- genomics.variants.search
- genomics.variantsets.create
- genomics.variantsets.delete
- genomics.variantsets.export
- genomics.variantsets.get
- genomics.variantsets.patch
- genomics.variantsets.search
- Types
- ImportVariantsRequestInfoMergeConfig
- ReadInfo
- Exon
- Status
- OperationSchema
- VariantAnnotationEffect
- Variant
- Annotation
- ListBasesResponse
- ListOperationsResponse
- GetIAMPolicyRequest
- CancelOperationRequest
- DataSet
- Read'
- OperationMetadataLabels
- VariantCall
- BatchCreateAnnotationsRequest
- MergeVariantsRequest
- ReadGroup
- Operation
- SearchReferenceSetsRequest
- Empty
- AnnotationSetType
- SearchReferencesResponse
- VariantSetMetadata
- CallSet
- CoverageBucket
- VariantAnnotation
- VariantAnnotationClinicalSignificance
- SearchReadGroupSetsRequest
- Reference
- VariantCallInfo
- ReadGroupInfo
- StatusDetailsItem
- SearchCallSetsResponse
- SetIAMPolicyRequest
- SearchReadsRequest
- OperationMetadataRequest
- MergeVariantsRequestInfoMergeConfig
- VariantInfo
- Experiment
- SearchVariantSetsRequest
- AnnotationInfo
- SearchAnnotationsResponse
- SearchAnnotationSetsRequest
- ImportReadGroupSetsRequestPartitionStrategy
- SearchVariantsResponse
- OperationMetadataRuntimeMetadata
- ClinicalCondition
- SearchCallSetsRequest
- Entry
- SearchReadsResponse
- Program
- SearchReferencesRequest
- BatchCreateAnnotationsResponse
- CodingSequence
- AnnotationType
- SearchReferenceSetsResponse
- Range
- ReadGroupSet
- Xgafv
- ExportReadGroupSetRequest
- ImportVariantsResponse
- ListCoverageBucketsResponse
- TestIAMPermissionsRequest
- ImportReadGroupSetsResponse
- LinearAlignment
- AnnotationSet
- VariantSet
- CigarUnitOperation
- VariantSetMetadataType
- TestIAMPermissionsResponse
- ListDataSetsResponse
- ImportReadGroupSetsRequest
- ImportVariantsRequest
- ExternalId
- CigarUnit
- Policy
- ExportVariantSetRequest
- VariantAnnotationType
- OperationMetadata
- ImportVariantsRequestFormat
- SearchAnnotationsRequest
- SearchVariantSetsResponse
- SearchVariantsRequest
- ExportVariantSetRequestFormat
- AnnotationSetInfo
- ComputeEngine
- SearchAnnotationSetsResponse
- CallSetInfo
- VariantSetMetadataInfo
- OperationResponse
- Transcript
- OperationEvent
- ReferenceBound
- UndeleteDataSetRequest
- Binding
- Position
- RuntimeMetadata
- SearchReadGroupSetsResponse
- ReadGroupSetInfo
- ReferenceSet
Upload, process, query, and search Genomics data in the cloud.
- genomicsService :: ServiceConfig
- genomicsScope :: Proxy '["https://www.googleapis.com/auth/genomics"]
- cloudPlatformScope :: Proxy '["https://www.googleapis.com/auth/cloud-platform"]
- genomicsReadOnlyScope :: Proxy '["https://www.googleapis.com/auth/genomics.readonly"]
- storageReadWriteScope :: Proxy '["https://www.googleapis.com/auth/devstorage.read_write"]
- bigQueryScope :: Proxy '["https://www.googleapis.com/auth/bigquery"]
- type GenomicsAPI = AnnotationsGetResource :<|> (AnnotationsCreateResource :<|> (AnnotationsBatchCreateResource :<|> (AnnotationsSearchResource :<|> (AnnotationsDeleteResource :<|> (AnnotationsUpdateResource :<|> (VariantsPatchResource :<|> (VariantsGetResource :<|> (VariantsCreateResource :<|> (VariantsImportResource :<|> (VariantsMergeResource :<|> (VariantsSearchResource :<|> (VariantsDeleteResource :<|> (ReferencesBasesListResource :<|> (ReferencesGetResource :<|> (ReferencesSearchResource :<|> (VariantSetsExportResource :<|> (VariantSetsPatchResource :<|> (VariantSetsGetResource :<|> (VariantSetsCreateResource :<|> (VariantSetsSearchResource :<|> (VariantSetsDeleteResource :<|> (AnnotationSetsGetResource :<|> (AnnotationSetsCreateResource :<|> (AnnotationSetsSearchResource :<|> (AnnotationSetsDeleteResource :<|> (AnnotationSetsUpdateResource :<|> (ReadGroupSetsCoverageBucketsListResource :<|> (ReadGroupSetsExportResource :<|> (ReadGroupSetsPatchResource :<|> (ReadGroupSetsGetResource :<|> (ReadGroupSetsImportResource :<|> (ReadGroupSetsSearchResource :<|> (ReadGroupSetsDeleteResource :<|> (ReferencesetsGetResource :<|> (ReferencesetsSearchResource :<|> (CallSetsPatchResource :<|> (CallSetsGetResource :<|> (CallSetsCreateResource :<|> (CallSetsSearchResource :<|> (CallSetsDeleteResource :<|> (OperationsListResource :<|> (OperationsGetResource :<|> (OperationsCancelResource :<|> (ReadsSearchResource :<|> (DataSetsListResource :<|> (DataSetsUndeleteResource :<|> (DataSetsGetIAMPolicyResource :<|> (DataSetsPatchResource :<|> (DataSetsGetResource :<|> (DataSetsCreateResource :<|> (DataSetsSetIAMPolicyResource :<|> (DataSetsTestIAMPermissionsResource :<|> DataSetsDeleteResource))))))))))))))))))))))))))))))))))))))))))))))))))))
- module Network.Google.Resource.Genomics.Annotations.BatchCreate
- module Network.Google.Resource.Genomics.Annotations.Create
- module Network.Google.Resource.Genomics.Annotations.Delete
- module Network.Google.Resource.Genomics.Annotations.Get
- module Network.Google.Resource.Genomics.Annotations.Search
- module Network.Google.Resource.Genomics.Annotations.Update
- module Network.Google.Resource.Genomics.AnnotationSets.Create
- module Network.Google.Resource.Genomics.AnnotationSets.Delete
- module Network.Google.Resource.Genomics.AnnotationSets.Get
- module Network.Google.Resource.Genomics.AnnotationSets.Search
- module Network.Google.Resource.Genomics.AnnotationSets.Update
- module Network.Google.Resource.Genomics.CallSets.Create
- module Network.Google.Resource.Genomics.CallSets.Delete
- module Network.Google.Resource.Genomics.CallSets.Get
- module Network.Google.Resource.Genomics.CallSets.Patch
- module Network.Google.Resource.Genomics.CallSets.Search
- module Network.Google.Resource.Genomics.DataSets.Create
- module Network.Google.Resource.Genomics.DataSets.Delete
- module Network.Google.Resource.Genomics.DataSets.Get
- module Network.Google.Resource.Genomics.DataSets.GetIAMPolicy
- module Network.Google.Resource.Genomics.DataSets.List
- module Network.Google.Resource.Genomics.DataSets.Patch
- module Network.Google.Resource.Genomics.DataSets.SetIAMPolicy
- module Network.Google.Resource.Genomics.DataSets.TestIAMPermissions
- module Network.Google.Resource.Genomics.DataSets.Undelete
- module Network.Google.Resource.Genomics.Operations.Cancel
- module Network.Google.Resource.Genomics.Operations.Get
- module Network.Google.Resource.Genomics.Operations.List
- module Network.Google.Resource.Genomics.ReadGroupSets.CoverageBuckets.List
- module Network.Google.Resource.Genomics.ReadGroupSets.Delete
- module Network.Google.Resource.Genomics.ReadGroupSets.Export
- module Network.Google.Resource.Genomics.ReadGroupSets.Get
- module Network.Google.Resource.Genomics.ReadGroupSets.Import
- module Network.Google.Resource.Genomics.ReadGroupSets.Patch
- module Network.Google.Resource.Genomics.ReadGroupSets.Search
- module Network.Google.Resource.Genomics.Reads.Search
- module Network.Google.Resource.Genomics.References.Bases.List
- module Network.Google.Resource.Genomics.References.Get
- module Network.Google.Resource.Genomics.References.Search
- module Network.Google.Resource.Genomics.Referencesets.Get
- module Network.Google.Resource.Genomics.Referencesets.Search
- module Network.Google.Resource.Genomics.Variants.Create
- module Network.Google.Resource.Genomics.Variants.Delete
- module Network.Google.Resource.Genomics.Variants.Get
- module Network.Google.Resource.Genomics.Variants.Import
- module Network.Google.Resource.Genomics.Variants.Merge
- module Network.Google.Resource.Genomics.Variants.Patch
- module Network.Google.Resource.Genomics.Variants.Search
- module Network.Google.Resource.Genomics.VariantSets.Create
- module Network.Google.Resource.Genomics.VariantSets.Delete
- module Network.Google.Resource.Genomics.VariantSets.Export
- module Network.Google.Resource.Genomics.VariantSets.Get
- module Network.Google.Resource.Genomics.VariantSets.Patch
- module Network.Google.Resource.Genomics.VariantSets.Search
- data ImportVariantsRequestInfoMergeConfig
- importVariantsRequestInfoMergeConfig :: HashMap Text Text -> ImportVariantsRequestInfoMergeConfig
- ivrimcAddtional :: Lens' ImportVariantsRequestInfoMergeConfig (HashMap Text Text)
- data ReadInfo
- readInfo :: HashMap Text [JSONValue] -> ReadInfo
- riAddtional :: Lens' ReadInfo (HashMap Text [JSONValue])
- data Exon
- exon :: Exon
- eStart :: Lens' Exon (Maybe Int64)
- eEnd :: Lens' Exon (Maybe Int64)
- eFrame :: Lens' Exon (Maybe Int32)
- data Status
- status :: Status
- sDetails :: Lens' Status [StatusDetailsItem]
- sCode :: Lens' Status (Maybe Int32)
- sMessage :: Lens' Status (Maybe Text)
- data OperationSchema
- operationSchema :: HashMap Text JSONValue -> OperationSchema
- osAddtional :: Lens' OperationSchema (HashMap Text JSONValue)
- data VariantAnnotationEffect
- data Variant
- variant :: Variant
- vVariantSetId :: Lens' Variant (Maybe Text)
- vCreated :: Lens' Variant (Maybe Int64)
- vStart :: Lens' Variant (Maybe Int64)
- vAlternateBases :: Lens' Variant [Text]
- vReferenceName :: Lens' Variant (Maybe Text)
- vNames :: Lens' Variant [Text]
- vEnd :: Lens' Variant (Maybe Int64)
- vReferenceBases :: Lens' Variant (Maybe Text)
- vId :: Lens' Variant (Maybe Text)
- vQuality :: Lens' Variant (Maybe Double)
- vFilter :: Lens' Variant [Text]
- vInfo :: Lens' Variant (Maybe VariantInfo)
- vCalls :: Lens' Variant [VariantCall]
- data Annotation
- annotation :: Annotation
- aVariant :: Lens' Annotation (Maybe VariantAnnotation)
- aAnnotationSetId :: Lens' Annotation (Maybe Text)
- aStart :: Lens' Annotation (Maybe Int64)
- aReverseStrand :: Lens' Annotation (Maybe Bool)
- aReferenceId :: Lens' Annotation (Maybe Text)
- aReferenceName :: Lens' Annotation (Maybe Text)
- aName :: Lens' Annotation (Maybe Text)
- aEnd :: Lens' Annotation (Maybe Int64)
- aId :: Lens' Annotation (Maybe Text)
- aType :: Lens' Annotation (Maybe AnnotationType)
- aTranscript :: Lens' Annotation (Maybe Transcript)
- aInfo :: Lens' Annotation (Maybe AnnotationInfo)
- data ListBasesResponse
- listBasesResponse :: ListBasesResponse
- lbrNextPageToken :: Lens' ListBasesResponse (Maybe Text)
- lbrOffSet :: Lens' ListBasesResponse (Maybe Int64)
- lbrSequence :: Lens' ListBasesResponse (Maybe Text)
- data ListOperationsResponse
- listOperationsResponse :: ListOperationsResponse
- lorNextPageToken :: Lens' ListOperationsResponse (Maybe Text)
- lorOperations :: Lens' ListOperationsResponse [Operation]
- data GetIAMPolicyRequest
- getIAMPolicyRequest :: GetIAMPolicyRequest
- data CancelOperationRequest
- cancelOperationRequest :: CancelOperationRequest
- data DataSet
- dataSet :: DataSet
- dsName :: Lens' DataSet (Maybe Text)
- dsId :: Lens' DataSet (Maybe Text)
- dsProjectId :: Lens' DataSet (Maybe Text)
- dsCreateTime :: Lens' DataSet (Maybe UTCTime)
- data Read'
- read' :: Read'
- rFragmentLength :: Lens' Read' (Maybe Int32)
- rDuplicateFragment :: Lens' Read' (Maybe Bool)
- rReadGroupSetId :: Lens' Read' (Maybe Text)
- rNextMatePosition :: Lens' Read' (Maybe Position)
- rFailedVendorQualityChecks :: Lens' Read' (Maybe Bool)
- rAlignment :: Lens' Read' (Maybe LinearAlignment)
- rFragmentName :: Lens' Read' (Maybe Text)
- rNumberReads :: Lens' Read' (Maybe Int32)
- rId :: Lens' Read' (Maybe Text)
- rSecondaryAlignment :: Lens' Read' (Maybe Bool)
- rReadGroupId :: Lens' Read' (Maybe Text)
- rSupplementaryAlignment :: Lens' Read' (Maybe Bool)
- rAlignedSequence :: Lens' Read' (Maybe Text)
- rProperPlacement :: Lens' Read' (Maybe Bool)
- rInfo :: Lens' Read' (Maybe ReadInfo)
- rReadNumber :: Lens' Read' (Maybe Int32)
- rAlignedQuality :: Lens' Read' [Int32]
- data OperationMetadataLabels
- operationMetadataLabels :: HashMap Text Text -> OperationMetadataLabels
- omlAddtional :: Lens' OperationMetadataLabels (HashMap Text Text)
- data VariantCall
- variantCall :: VariantCall
- vcGenotypeLikelihood :: Lens' VariantCall [Double]
- vcCallSetName :: Lens' VariantCall (Maybe Text)
- vcPhaseset :: Lens' VariantCall (Maybe Text)
- vcCallSetId :: Lens' VariantCall (Maybe Text)
- vcGenotype :: Lens' VariantCall [Int32]
- vcInfo :: Lens' VariantCall (Maybe VariantCallInfo)
- data BatchCreateAnnotationsRequest
- batchCreateAnnotationsRequest :: BatchCreateAnnotationsRequest
- bcarAnnotations :: Lens' BatchCreateAnnotationsRequest [Annotation]
- bcarRequestId :: Lens' BatchCreateAnnotationsRequest (Maybe Text)
- data MergeVariantsRequest
- mergeVariantsRequest :: MergeVariantsRequest
- mvrVariants :: Lens' MergeVariantsRequest [Variant]
- mvrVariantSetId :: Lens' MergeVariantsRequest (Maybe Text)
- mvrInfoMergeConfig :: Lens' MergeVariantsRequest (Maybe MergeVariantsRequestInfoMergeConfig)
- data ReadGroup
- readGroup :: ReadGroup
- reaReferenceSetId :: Lens' ReadGroup (Maybe Text)
- reaPrograms :: Lens' ReadGroup [Program]
- reaExperiment :: Lens' ReadGroup (Maybe Experiment)
- reaName :: Lens' ReadGroup (Maybe Text)
- reaDataSetId :: Lens' ReadGroup (Maybe Text)
- reaId :: Lens' ReadGroup (Maybe Text)
- reaSampleId :: Lens' ReadGroup (Maybe Text)
- reaPredictedInsertSize :: Lens' ReadGroup (Maybe Int32)
- reaDescription :: Lens' ReadGroup (Maybe Text)
- reaInfo :: Lens' ReadGroup (Maybe ReadGroupInfo)
- data Operation
- operation :: Operation
- oDone :: Lens' Operation (Maybe Bool)
- oError :: Lens' Operation (Maybe Status)
- oResponse :: Lens' Operation (Maybe OperationResponse)
- oName :: Lens' Operation (Maybe Text)
- oMetadata :: Lens' Operation (Maybe OperationSchema)
- data SearchReferenceSetsRequest
- searchReferenceSetsRequest :: SearchReferenceSetsRequest
- srsrMD5checksums :: Lens' SearchReferenceSetsRequest [Text]
- srsrAccessions :: Lens' SearchReferenceSetsRequest [Text]
- srsrPageToken :: Lens' SearchReferenceSetsRequest (Maybe Text)
- srsrAssemblyId :: Lens' SearchReferenceSetsRequest (Maybe Text)
- srsrPageSize :: Lens' SearchReferenceSetsRequest (Maybe Int32)
- data Empty
- empty :: Empty
- data AnnotationSetType
- data SearchReferencesResponse
- searchReferencesResponse :: SearchReferencesResponse
- srrNextPageToken :: Lens' SearchReferencesResponse (Maybe Text)
- srrReferences :: Lens' SearchReferencesResponse [Reference]
- data VariantSetMetadata
- variantSetMetadata :: VariantSetMetadata
- vsmValue :: Lens' VariantSetMetadata (Maybe Text)
- vsmKey :: Lens' VariantSetMetadata (Maybe Text)
- vsmId :: Lens' VariantSetMetadata (Maybe Text)
- vsmType :: Lens' VariantSetMetadata (Maybe VariantSetMetadataType)
- vsmNumber :: Lens' VariantSetMetadata (Maybe Text)
- vsmDescription :: Lens' VariantSetMetadata (Maybe Text)
- vsmInfo :: Lens' VariantSetMetadata (Maybe VariantSetMetadataInfo)
- data CallSet
- callSet :: CallSet
- csCreated :: Lens' CallSet (Maybe Int64)
- csName :: Lens' CallSet (Maybe Text)
- csId :: Lens' CallSet (Maybe Text)
- csSampleId :: Lens' CallSet (Maybe Text)
- csVariantSetIds :: Lens' CallSet [Text]
- csInfo :: Lens' CallSet (Maybe CallSetInfo)
- data CoverageBucket
- coverageBucket :: CoverageBucket
- cbRange :: Lens' CoverageBucket (Maybe Range)
- cbMeanCoverage :: Lens' CoverageBucket (Maybe Double)
- data VariantAnnotation
- variantAnnotation :: VariantAnnotation
- vaEffect :: Lens' VariantAnnotation (Maybe VariantAnnotationEffect)
- vaClinicalSignificance :: Lens' VariantAnnotation (Maybe VariantAnnotationClinicalSignificance)
- vaAlternateBases :: Lens' VariantAnnotation (Maybe Text)
- vaGeneId :: Lens' VariantAnnotation (Maybe Text)
- vaConditions :: Lens' VariantAnnotation [ClinicalCondition]
- vaType :: Lens' VariantAnnotation (Maybe VariantAnnotationType)
- vaTranscriptIds :: Lens' VariantAnnotation [Text]
- data VariantAnnotationClinicalSignificance
- data SearchReadGroupSetsRequest
- searchReadGroupSetsRequest :: SearchReadGroupSetsRequest
- srgsrDataSetIds :: Lens' SearchReadGroupSetsRequest [Text]
- srgsrName :: Lens' SearchReadGroupSetsRequest (Maybe Text)
- srgsrPageToken :: Lens' SearchReadGroupSetsRequest (Maybe Text)
- srgsrPageSize :: Lens' SearchReadGroupSetsRequest (Maybe Int32)
- data Reference
- reference :: Reference
- refLength :: Lens' Reference (Maybe Int64)
- refSourceAccessions :: Lens' Reference [Text]
- refMD5checksum :: Lens' Reference (Maybe Text)
- refName :: Lens' Reference (Maybe Text)
- refNcbiTaxonId :: Lens' Reference (Maybe Int32)
- refId :: Lens' Reference (Maybe Text)
- refSourceURI :: Lens' Reference (Maybe Text)
- data VariantCallInfo
- variantCallInfo :: HashMap Text [JSONValue] -> VariantCallInfo
- vciAddtional :: Lens' VariantCallInfo (HashMap Text [JSONValue])
- data ReadGroupInfo
- readGroupInfo :: HashMap Text [JSONValue] -> ReadGroupInfo
- rgiAddtional :: Lens' ReadGroupInfo (HashMap Text [JSONValue])
- data StatusDetailsItem
- statusDetailsItem :: HashMap Text JSONValue -> StatusDetailsItem
- sdiAddtional :: Lens' StatusDetailsItem (HashMap Text JSONValue)
- data SearchCallSetsResponse
- searchCallSetsResponse :: SearchCallSetsResponse
- scsrNextPageToken :: Lens' SearchCallSetsResponse (Maybe Text)
- scsrCallSets :: Lens' SearchCallSetsResponse [CallSet]
- data SetIAMPolicyRequest
- setIAMPolicyRequest :: SetIAMPolicyRequest
- siprPolicy :: Lens' SetIAMPolicyRequest (Maybe Policy)
- data SearchReadsRequest
- searchReadsRequest :: SearchReadsRequest
- srrStart :: Lens' SearchReadsRequest (Maybe Int64)
- srrReadGroupIds :: Lens' SearchReadsRequest [Text]
- srrReferenceName :: Lens' SearchReadsRequest (Maybe Text)
- srrEnd :: Lens' SearchReadsRequest (Maybe Int64)
- srrPageToken :: Lens' SearchReadsRequest (Maybe Text)
- srrPageSize :: Lens' SearchReadsRequest (Maybe Int32)
- srrReadGroupSetIds :: Lens' SearchReadsRequest [Text]
- data OperationMetadataRequest
- operationMetadataRequest :: HashMap Text JSONValue -> OperationMetadataRequest
- omrAddtional :: Lens' OperationMetadataRequest (HashMap Text JSONValue)
- data MergeVariantsRequestInfoMergeConfig
- mergeVariantsRequestInfoMergeConfig :: HashMap Text Text -> MergeVariantsRequestInfoMergeConfig
- mvrimcAddtional :: Lens' MergeVariantsRequestInfoMergeConfig (HashMap Text Text)
- data VariantInfo
- variantInfo :: HashMap Text [JSONValue] -> VariantInfo
- viAddtional :: Lens' VariantInfo (HashMap Text [JSONValue])
- data Experiment
- experiment :: Experiment
- eInstrumentModel :: Lens' Experiment (Maybe Text)
- ePlatformUnit :: Lens' Experiment (Maybe Text)
- eSequencingCenter :: Lens' Experiment (Maybe Text)
- eLibraryId :: Lens' Experiment (Maybe Text)
- data SearchVariantSetsRequest
- searchVariantSetsRequest :: SearchVariantSetsRequest
- svsrDataSetIds :: Lens' SearchVariantSetsRequest [Text]
- svsrPageToken :: Lens' SearchVariantSetsRequest (Maybe Text)
- svsrPageSize :: Lens' SearchVariantSetsRequest (Maybe Int32)
- data AnnotationInfo
- annotationInfo :: HashMap Text [JSONValue] -> AnnotationInfo
- aiAddtional :: Lens' AnnotationInfo (HashMap Text [JSONValue])
- data SearchAnnotationsResponse
- searchAnnotationsResponse :: SearchAnnotationsResponse
- sarAnnotations :: Lens' SearchAnnotationsResponse [Annotation]
- sarNextPageToken :: Lens' SearchAnnotationsResponse (Maybe Text)
- data SearchAnnotationSetsRequest
- searchAnnotationSetsRequest :: SearchAnnotationSetsRequest
- sasrReferenceSetId :: Lens' SearchAnnotationSetsRequest (Maybe Text)
- sasrTypes :: Lens' SearchAnnotationSetsRequest [Text]
- sasrDataSetIds :: Lens' SearchAnnotationSetsRequest [Text]
- sasrName :: Lens' SearchAnnotationSetsRequest (Maybe Text)
- sasrPageToken :: Lens' SearchAnnotationSetsRequest (Maybe Text)
- sasrPageSize :: Lens' SearchAnnotationSetsRequest (Maybe Int32)
- data ImportReadGroupSetsRequestPartitionStrategy
- data SearchVariantsResponse
- searchVariantsResponse :: SearchVariantsResponse
- svrVariants :: Lens' SearchVariantsResponse [Variant]
- svrNextPageToken :: Lens' SearchVariantsResponse (Maybe Text)
- data OperationMetadataRuntimeMetadata
- operationMetadataRuntimeMetadata :: HashMap Text JSONValue -> OperationMetadataRuntimeMetadata
- omrmAddtional :: Lens' OperationMetadataRuntimeMetadata (HashMap Text JSONValue)
- data ClinicalCondition
- clinicalCondition :: ClinicalCondition
- ccExternalIds :: Lens' ClinicalCondition [ExternalId]
- ccNames :: Lens' ClinicalCondition [Text]
- ccConceptId :: Lens' ClinicalCondition (Maybe Text)
- ccOmimId :: Lens' ClinicalCondition (Maybe Text)
- data SearchCallSetsRequest
- searchCallSetsRequest :: SearchCallSetsRequest
- scsrName :: Lens' SearchCallSetsRequest (Maybe Text)
- scsrPageToken :: Lens' SearchCallSetsRequest (Maybe Text)
- scsrVariantSetIds :: Lens' SearchCallSetsRequest [Text]
- scsrPageSize :: Lens' SearchCallSetsRequest (Maybe Int32)
- data Entry
- entry :: Entry
- eStatus :: Lens' Entry (Maybe Status)
- eAnnotation :: Lens' Entry (Maybe Annotation)
- data SearchReadsResponse
- searchReadsResponse :: SearchReadsResponse
- sNextPageToken :: Lens' SearchReadsResponse (Maybe Text)
- sAlignments :: Lens' SearchReadsResponse [Read']
- data Program
- program :: Program
- pPrevProgramId :: Lens' Program (Maybe Text)
- pName :: Lens' Program (Maybe Text)
- pVersion :: Lens' Program (Maybe Text)
- pId :: Lens' Program (Maybe Text)
- pCommandLine :: Lens' Program (Maybe Text)
- data SearchReferencesRequest
- searchReferencesRequest :: SearchReferencesRequest
- sReferenceSetId :: Lens' SearchReferencesRequest (Maybe Text)
- sMD5checksums :: Lens' SearchReferencesRequest [Text]
- sAccessions :: Lens' SearchReferencesRequest [Text]
- sPageToken :: Lens' SearchReferencesRequest (Maybe Text)
- sPageSize :: Lens' SearchReferencesRequest (Maybe Int32)
- data BatchCreateAnnotationsResponse
- batchCreateAnnotationsResponse :: BatchCreateAnnotationsResponse
- bcarEntries :: Lens' BatchCreateAnnotationsResponse [Entry]
- data CodingSequence
- codingSequence :: CodingSequence
- csStart :: Lens' CodingSequence (Maybe Int64)
- csEnd :: Lens' CodingSequence (Maybe Int64)
- data AnnotationType
- data SearchReferenceSetsResponse
- searchReferenceSetsResponse :: SearchReferenceSetsResponse
- srsrNextPageToken :: Lens' SearchReferenceSetsResponse (Maybe Text)
- srsrReferenceSets :: Lens' SearchReferenceSetsResponse [ReferenceSet]
- data Range
- range :: Range
- rStart :: Lens' Range (Maybe Int64)
- rReferenceName :: Lens' Range (Maybe Text)
- rEnd :: Lens' Range (Maybe Int64)
- data ReadGroupSet
- readGroupSet :: ReadGroupSet
- rgsReferenceSetId :: Lens' ReadGroupSet (Maybe Text)
- rgsName :: Lens' ReadGroupSet (Maybe Text)
- rgsDataSetId :: Lens' ReadGroupSet (Maybe Text)
- rgsId :: Lens' ReadGroupSet (Maybe Text)
- rgsInfo :: Lens' ReadGroupSet (Maybe ReadGroupSetInfo)
- rgsReadGroups :: Lens' ReadGroupSet [ReadGroup]
- rgsFilename :: Lens' ReadGroupSet (Maybe Text)
- data Xgafv
- data ExportReadGroupSetRequest
- exportReadGroupSetRequest :: ExportReadGroupSetRequest
- ergsrReferenceNames :: Lens' ExportReadGroupSetRequest [Text]
- ergsrExportURI :: Lens' ExportReadGroupSetRequest (Maybe Text)
- ergsrProjectId :: Lens' ExportReadGroupSetRequest (Maybe Text)
- data ImportVariantsResponse
- importVariantsResponse :: ImportVariantsResponse
- ivrCallSetIds :: Lens' ImportVariantsResponse [Text]
- data ListCoverageBucketsResponse
- listCoverageBucketsResponse :: ListCoverageBucketsResponse
- lcbrNextPageToken :: Lens' ListCoverageBucketsResponse (Maybe Text)
- lcbrBucketWidth :: Lens' ListCoverageBucketsResponse (Maybe Int64)
- lcbrCoverageBuckets :: Lens' ListCoverageBucketsResponse [CoverageBucket]
- data TestIAMPermissionsRequest
- testIAMPermissionsRequest :: TestIAMPermissionsRequest
- tiprPermissions :: Lens' TestIAMPermissionsRequest [Text]
- data ImportReadGroupSetsResponse
- importReadGroupSetsResponse :: ImportReadGroupSetsResponse
- irgsrReadGroupSetIds :: Lens' ImportReadGroupSetsResponse [Text]
- data LinearAlignment
- linearAlignment :: LinearAlignment
- laCigar :: Lens' LinearAlignment [CigarUnit]
- laMAppingQuality :: Lens' LinearAlignment (Maybe Int32)
- laPosition :: Lens' LinearAlignment (Maybe Position)
- data AnnotationSet
- annotationSet :: AnnotationSet
- asReferenceSetId :: Lens' AnnotationSet (Maybe Text)
- asName :: Lens' AnnotationSet (Maybe Text)
- asDataSetId :: Lens' AnnotationSet (Maybe Text)
- asId :: Lens' AnnotationSet (Maybe Text)
- asType :: Lens' AnnotationSet (Maybe AnnotationSetType)
- asSourceURI :: Lens' AnnotationSet (Maybe Text)
- asInfo :: Lens' AnnotationSet (Maybe AnnotationSetInfo)
- data VariantSet
- variantSet :: VariantSet
- vsReferenceSetId :: Lens' VariantSet (Maybe Text)
- vsName :: Lens' VariantSet (Maybe Text)
- vsDataSetId :: Lens' VariantSet (Maybe Text)
- vsReferenceBounds :: Lens' VariantSet [ReferenceBound]
- vsMetadata :: Lens' VariantSet [VariantSetMetadata]
- vsId :: Lens' VariantSet (Maybe Text)
- vsDescription :: Lens' VariantSet (Maybe Text)
- data CigarUnitOperation
- data VariantSetMetadataType
- data TestIAMPermissionsResponse
- testIAMPermissionsResponse :: TestIAMPermissionsResponse
- tiamprPermissions :: Lens' TestIAMPermissionsResponse [Text]
- data ListDataSetsResponse
- listDataSetsResponse :: ListDataSetsResponse
- ldsrNextPageToken :: Lens' ListDataSetsResponse (Maybe Text)
- ldsrDataSets :: Lens' ListDataSetsResponse [DataSet]
- data ImportReadGroupSetsRequest
- importReadGroupSetsRequest :: ImportReadGroupSetsRequest
- irgsrReferenceSetId :: Lens' ImportReadGroupSetsRequest (Maybe Text)
- irgsrDataSetId :: Lens' ImportReadGroupSetsRequest (Maybe Text)
- irgsrSourceURIs :: Lens' ImportReadGroupSetsRequest [Text]
- irgsrPartitionStrategy :: Lens' ImportReadGroupSetsRequest (Maybe ImportReadGroupSetsRequestPartitionStrategy)
- data ImportVariantsRequest
- importVariantsRequest :: ImportVariantsRequest
- ivrVariantSetId :: Lens' ImportVariantsRequest (Maybe Text)
- ivrFormat :: Lens' ImportVariantsRequest (Maybe ImportVariantsRequestFormat)
- ivrInfoMergeConfig :: Lens' ImportVariantsRequest (Maybe ImportVariantsRequestInfoMergeConfig)
- ivrNormalizeReferenceNames :: Lens' ImportVariantsRequest (Maybe Bool)
- ivrSourceURIs :: Lens' ImportVariantsRequest [Text]
- data ExternalId
- externalId :: ExternalId
- eiSourceName :: Lens' ExternalId (Maybe Text)
- eiId :: Lens' ExternalId (Maybe Text)
- data CigarUnit
- cigarUnit :: CigarUnit
- cuOperation :: Lens' CigarUnit (Maybe CigarUnitOperation)
- cuOperationLength :: Lens' CigarUnit (Maybe Int64)
- cuReferenceSequence :: Lens' CigarUnit (Maybe Text)
- data Policy
- policy :: Policy
- polEtag :: Lens' Policy (Maybe ByteString)
- polVersion :: Lens' Policy (Maybe Int32)
- polBindings :: Lens' Policy [Binding]
- data ExportVariantSetRequest
- exportVariantSetRequest :: ExportVariantSetRequest
- evsrBigQueryDataSet :: Lens' ExportVariantSetRequest (Maybe Text)
- evsrBigQueryTable :: Lens' ExportVariantSetRequest (Maybe Text)
- evsrFormat :: Lens' ExportVariantSetRequest (Maybe ExportVariantSetRequestFormat)
- evsrCallSetIds :: Lens' ExportVariantSetRequest [Text]
- evsrProjectId :: Lens' ExportVariantSetRequest (Maybe Text)
- data VariantAnnotationType
- data OperationMetadata
- operationMetadata :: OperationMetadata
- omClientId :: Lens' OperationMetadata (Maybe Text)
- omStartTime :: Lens' OperationMetadata (Maybe UTCTime)
- omEvents :: Lens' OperationMetadata [OperationEvent]
- omEndTime :: Lens' OperationMetadata (Maybe UTCTime)
- omLabels :: Lens' OperationMetadata (Maybe OperationMetadataLabels)
- omProjectId :: Lens' OperationMetadata (Maybe Text)
- omCreateTime :: Lens' OperationMetadata (Maybe UTCTime)
- omRuntimeMetadata :: Lens' OperationMetadata (Maybe OperationMetadataRuntimeMetadata)
- omRequest :: Lens' OperationMetadata (Maybe OperationMetadataRequest)
- data ImportVariantsRequestFormat
- data SearchAnnotationsRequest
- searchAnnotationsRequest :: SearchAnnotationsRequest
- sarStart :: Lens' SearchAnnotationsRequest (Maybe Int64)
- sarReferenceId :: Lens' SearchAnnotationsRequest (Maybe Text)
- sarReferenceName :: Lens' SearchAnnotationsRequest (Maybe Text)
- sarEnd :: Lens' SearchAnnotationsRequest (Maybe Int64)
- sarPageToken :: Lens' SearchAnnotationsRequest (Maybe Text)
- sarAnnotationSetIds :: Lens' SearchAnnotationsRequest [Text]
- sarPageSize :: Lens' SearchAnnotationsRequest (Maybe Int32)
- data SearchVariantSetsResponse
- searchVariantSetsResponse :: SearchVariantSetsResponse
- svsrNextPageToken :: Lens' SearchVariantSetsResponse (Maybe Text)
- svsrVariantSets :: Lens' SearchVariantSetsResponse [VariantSet]
- data SearchVariantsRequest
- searchVariantsRequest :: SearchVariantsRequest
- svrStart :: Lens' SearchVariantsRequest (Maybe Int64)
- svrCallSetIds :: Lens' SearchVariantsRequest [Text]
- svrReferenceName :: Lens' SearchVariantsRequest (Maybe Text)
- svrEnd :: Lens' SearchVariantsRequest (Maybe Int64)
- svrMaxCalls :: Lens' SearchVariantsRequest (Maybe Int32)
- svrPageToken :: Lens' SearchVariantsRequest (Maybe Text)
- svrVariantName :: Lens' SearchVariantsRequest (Maybe Text)
- svrVariantSetIds :: Lens' SearchVariantsRequest [Text]
- svrPageSize :: Lens' SearchVariantsRequest (Maybe Int32)
- data ExportVariantSetRequestFormat
- data AnnotationSetInfo
- annotationSetInfo :: HashMap Text [JSONValue] -> AnnotationSetInfo
- asiAddtional :: Lens' AnnotationSetInfo (HashMap Text [JSONValue])
- data ComputeEngine
- computeEngine :: ComputeEngine
- ceZone :: Lens' ComputeEngine (Maybe Text)
- ceDiskNames :: Lens' ComputeEngine [Text]
- ceMachineType :: Lens' ComputeEngine (Maybe Text)
- ceInstanceName :: Lens' ComputeEngine (Maybe Text)
- data SearchAnnotationSetsResponse
- searchAnnotationSetsResponse :: SearchAnnotationSetsResponse
- sasrNextPageToken :: Lens' SearchAnnotationSetsResponse (Maybe Text)
- sasrAnnotationSets :: Lens' SearchAnnotationSetsResponse [AnnotationSet]
- data CallSetInfo
- callSetInfo :: HashMap Text [JSONValue] -> CallSetInfo
- csiAddtional :: Lens' CallSetInfo (HashMap Text [JSONValue])
- data VariantSetMetadataInfo
- variantSetMetadataInfo :: HashMap Text [JSONValue] -> VariantSetMetadataInfo
- vsmiAddtional :: Lens' VariantSetMetadataInfo (HashMap Text [JSONValue])
- data OperationResponse
- operationResponse :: HashMap Text JSONValue -> OperationResponse
- orAddtional :: Lens' OperationResponse (HashMap Text JSONValue)
- data Transcript
- transcript :: Transcript
- tGeneId :: Lens' Transcript (Maybe Text)
- tCodingSequence :: Lens' Transcript (Maybe CodingSequence)
- tExons :: Lens' Transcript [Exon]
- data OperationEvent
- operationEvent :: OperationEvent
- oeStartTime :: Lens' OperationEvent (Maybe UTCTime)
- oeEndTime :: Lens' OperationEvent (Maybe UTCTime)
- oeDescription :: Lens' OperationEvent (Maybe Text)
- data ReferenceBound
- referenceBound :: ReferenceBound
- rbUpperBound :: Lens' ReferenceBound (Maybe Int64)
- rbReferenceName :: Lens' ReferenceBound (Maybe Text)
- data UndeleteDataSetRequest
- undeleteDataSetRequest :: UndeleteDataSetRequest
- data Binding
- binding :: Binding
- bMembers :: Lens' Binding [Text]
- bRole :: Lens' Binding (Maybe Text)
- data Position
- position :: Position
- pReverseStrand :: Lens' Position (Maybe Bool)
- pReferenceName :: Lens' Position (Maybe Text)
- pPosition :: Lens' Position (Maybe Int64)
- data RuntimeMetadata
- runtimeMetadata :: RuntimeMetadata
- rmComputeEngine :: Lens' RuntimeMetadata (Maybe ComputeEngine)
- data SearchReadGroupSetsResponse
- searchReadGroupSetsResponse :: SearchReadGroupSetsResponse
- srgsrNextPageToken :: Lens' SearchReadGroupSetsResponse (Maybe Text)
- srgsrReadGroupSets :: Lens' SearchReadGroupSetsResponse [ReadGroupSet]
- data ReadGroupSetInfo
- readGroupSetInfo :: HashMap Text [JSONValue] -> ReadGroupSetInfo
- rgsiAddtional :: Lens' ReadGroupSetInfo (HashMap Text [JSONValue])
- data ReferenceSet
- referenceSet :: ReferenceSet
- rsSourceAccessions :: Lens' ReferenceSet [Text]
- rsReferenceIds :: Lens' ReferenceSet [Text]
- rsMD5checksum :: Lens' ReferenceSet (Maybe Text)
- rsNcbiTaxonId :: Lens' ReferenceSet (Maybe Int32)
- rsId :: Lens' ReferenceSet (Maybe Text)
- rsAssemblyId :: Lens' ReferenceSet (Maybe Text)
- rsSourceURI :: Lens' ReferenceSet (Maybe Text)
- rsDescription :: Lens' ReferenceSet (Maybe Text)
Service Configuration
genomicsService :: ServiceConfig Source #
Default request referring to version v1
of the Genomics API. This contains the host and root path used as a starting point for constructing service requests.
OAuth Scopes
genomicsScope :: Proxy '["https://www.googleapis.com/auth/genomics"] Source #
View and manage Genomics data
cloudPlatformScope :: Proxy '["https://www.googleapis.com/auth/cloud-platform"] Source #
View and manage your data across Google Cloud Platform services
genomicsReadOnlyScope :: Proxy '["https://www.googleapis.com/auth/genomics.readonly"] Source #
View Genomics data
storageReadWriteScope :: Proxy '["https://www.googleapis.com/auth/devstorage.read_write"] Source #
Manage your data in Google Cloud Storage
bigQueryScope :: Proxy '["https://www.googleapis.com/auth/bigquery"] Source #
View and manage your data in Google BigQuery
API Declaration
type GenomicsAPI = AnnotationsGetResource :<|> (AnnotationsCreateResource :<|> (AnnotationsBatchCreateResource :<|> (AnnotationsSearchResource :<|> (AnnotationsDeleteResource :<|> (AnnotationsUpdateResource :<|> (VariantsPatchResource :<|> (VariantsGetResource :<|> (VariantsCreateResource :<|> (VariantsImportResource :<|> (VariantsMergeResource :<|> (VariantsSearchResource :<|> (VariantsDeleteResource :<|> (ReferencesBasesListResource :<|> (ReferencesGetResource :<|> (ReferencesSearchResource :<|> (VariantSetsExportResource :<|> (VariantSetsPatchResource :<|> (VariantSetsGetResource :<|> (VariantSetsCreateResource :<|> (VariantSetsSearchResource :<|> (VariantSetsDeleteResource :<|> (AnnotationSetsGetResource :<|> (AnnotationSetsCreateResource :<|> (AnnotationSetsSearchResource :<|> (AnnotationSetsDeleteResource :<|> (AnnotationSetsUpdateResource :<|> (ReadGroupSetsCoverageBucketsListResource :<|> (ReadGroupSetsExportResource :<|> (ReadGroupSetsPatchResource :<|> (ReadGroupSetsGetResource :<|> (ReadGroupSetsImportResource :<|> (ReadGroupSetsSearchResource :<|> (ReadGroupSetsDeleteResource :<|> (ReferencesetsGetResource :<|> (ReferencesetsSearchResource :<|> (CallSetsPatchResource :<|> (CallSetsGetResource :<|> (CallSetsCreateResource :<|> (CallSetsSearchResource :<|> (CallSetsDeleteResource :<|> (OperationsListResource :<|> (OperationsGetResource :<|> (OperationsCancelResource :<|> (ReadsSearchResource :<|> (DataSetsListResource :<|> (DataSetsUndeleteResource :<|> (DataSetsGetIAMPolicyResource :<|> (DataSetsPatchResource :<|> (DataSetsGetResource :<|> (DataSetsCreateResource :<|> (DataSetsSetIAMPolicyResource :<|> (DataSetsTestIAMPermissionsResource :<|> DataSetsDeleteResource)))))))))))))))))))))))))))))))))))))))))))))))))))) Source #
Represents the entirety of the methods and resources available for the Genomics API service.
Resources
genomics.annotations.batchCreate
genomics.annotations.create
genomics.annotations.delete
genomics.annotations.get
genomics.annotations.search
genomics.annotations.update
genomics.annotationsets.create
genomics.annotationsets.delete
genomics.annotationsets.get
genomics.annotationsets.search
genomics.annotationsets.update
genomics.callsets.create
genomics.callsets.delete
genomics.callsets.get
genomics.callsets.patch
genomics.callsets.search
genomics.datasets.create
genomics.datasets.delete
genomics.datasets.get
genomics.datasets.getIamPolicy
genomics.datasets.list
genomics.datasets.patch
genomics.datasets.setIamPolicy
genomics.datasets.testIamPermissions
genomics.datasets.undelete
genomics.operations.cancel
genomics.operations.get
genomics.operations.list
genomics.readgroupsets.coveragebuckets.list
genomics.readgroupsets.delete
genomics.readgroupsets.export
genomics.readgroupsets.get
genomics.readgroupsets.import
genomics.readgroupsets.patch
genomics.readgroupsets.search
genomics.reads.search
genomics.references.bases.list
genomics.references.get
genomics.references.search
genomics.referencesets.get
genomics.referencesets.search
genomics.variants.create
genomics.variants.delete
genomics.variants.get
genomics.variants.import
genomics.variants.merge
genomics.variants.patch
genomics.variants.search
genomics.variantsets.create
genomics.variantsets.delete
genomics.variantsets.export
genomics.variantsets.get
genomics.variantsets.patch
genomics.variantsets.search
Types
ImportVariantsRequestInfoMergeConfig
data ImportVariantsRequestInfoMergeConfig Source #
A mapping between info field keys and the InfoMergeOperations to be performed on them. This is plumbed down to the MergeVariantRequests generated by the resulting import job.
See: importVariantsRequestInfoMergeConfig
smart constructor.
importVariantsRequestInfoMergeConfig Source #
Creates a value of ImportVariantsRequestInfoMergeConfig
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
ReadInfo
A map of additional read alignment information. This must be of the form map (string key mapping to a list of string values).
See: readInfo
smart constructor.
Creates a value of ReadInfo
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
Exon
eStart :: Lens' Exon (Maybe Int64) Source #
The start position of the exon on this annotation's reference sequence, 0-based inclusive. Note that this is relative to the reference start, and **not** the containing annotation start.
eEnd :: Lens' Exon (Maybe Int64) Source #
The end position of the exon on this annotation's reference sequence, 0-based exclusive. Note that this is relative to the reference start, and *not* the containing annotation start.
eFrame :: Lens' Exon (Maybe Int32) Source #
The frame of this exon. Contains a value of 0, 1, or 2, which indicates the offset of the first coding base of the exon within the reading frame of the coding DNA sequence, if any. This field is dependent on the strandedness of this annotation (see Annotation.reverse_strand). For forward stranded annotations, this offset is relative to the exon.start. For reverse strand annotations, this offset is relative to the exon.end `- 1`. Unset if this exon does not intersect the coding sequence. Upon creation of a transcript, the frame must be populated for all or none of the coding exons.
Status
The `Status` type defines a logical error model that is suitable for different programming environments, including REST APIs and RPC APIs. It is used by gRPC. The error model is designed to be: - Simple to use and understand for most users - Flexible enough to meet unexpected needs # Overview The `Status` message contains three pieces of data: error code, error message, and error details. The error code should be an enum value of google.rpc.Code, but it may accept additional error codes if needed. The error message should be a developer-facing English message that helps developers *understand* and *resolve* the error. If a localized user-facing error message is needed, put the localized message in the error details or localize it in the client. The optional error details may contain arbitrary information about the error. There is a predefined set of error detail types in the package `google.rpc` which can be used for common error conditions. # Language mapping The `Status` message is the logical representation of the error model, but it is not necessarily the actual wire format. When the `Status` message is exposed in different client libraries and different wire protocols, it can be mapped differently. For example, it will likely be mapped to some exceptions in Java, but more likely mapped to some error codes in C. # Other uses The error model and the `Status` message can be used in a variety of environments, either with or without APIs, to provide a consistent developer experience across different environments. Example uses of this error model include: - Partial errors. If a service needs to return partial errors to the client, it may embed the `Status` in the normal response to indicate the partial errors. - Workflow errors. A typical workflow has multiple steps. Each step may have a `Status` message for error reporting purpose. - Batch operations. If a client uses batch request and batch response, the `Status` message should be used directly inside batch response, one for each error sub-response. - Asynchronous operations. If an API call embeds asynchronous operation results in its response, the status of those operations should be represented directly using the `Status` message. - Logging. If some API errors are stored in logs, the message `Status` could be used directly after any stripping needed for security/privacy reasons.
See: status
smart constructor.
sDetails :: Lens' Status [StatusDetailsItem] Source #
A list of messages that carry the error details. There will be a common set of message types for APIs to use.
sCode :: Lens' Status (Maybe Int32) Source #
The status code, which should be an enum value of google.rpc.Code.
sMessage :: Lens' Status (Maybe Text) Source #
A developer-facing error message, which should be in English. Any user-facing error message should be localized and sent in the google.rpc.Status.details field, or localized by the client.
OperationSchema
data OperationSchema Source #
An OperationMetadata object. This will always be returned with the Operation.
See: operationSchema
smart constructor.
Creates a value of OperationSchema
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
osAddtional :: Lens' OperationSchema (HashMap Text JSONValue) Source #
Properties of the object. Contains field 'type with type URL.
VariantAnnotationEffect
data VariantAnnotationEffect Source #
Effect of the variant on the coding sequence.
EffectUnspecified | EFFECT_UNSPECIFIED |
EffectOther |
|
Frameshift |
|
FramePreservingIndel |
|
SynonymousSnp |
|
NonsynonymousSnp |
|
StopGain |
|
StopLoss |
|
SpliceSiteDisruption |
|
Variant
A variant represents a change in DNA sequence relative to a reference sequence. For example, a variant could represent a SNP or an insertion. Variants belong to a variant set. For more genomics resource definitions, see Fundamentals of Google Genomics Each of the calls on a variant represent a determination of genotype with respect to that variant. For example, a call might assign probability of 0.32 to the occurrence of a SNP named rs1234 in a sample named NA12345. A call belongs to a call set, which contains related calls typically from one sample.
See: variant
smart constructor.
Creates a value of Variant
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
vVariantSetId :: Lens' Variant (Maybe Text) Source #
The ID of the variant set this variant belongs to.
vCreated :: Lens' Variant (Maybe Int64) Source #
The date this variant was created, in milliseconds from the epoch.
vStart :: Lens' Variant (Maybe Int64) Source #
The position at which this variant occurs (0-based). This corresponds to the first base of the string of reference bases.
vAlternateBases :: Lens' Variant [Text] Source #
The bases that appear instead of the reference bases.
vReferenceName :: Lens' Variant (Maybe Text) Source #
The reference on which this variant occurs. (such as `chr20` or `X`)
vEnd :: Lens' Variant (Maybe Int64) Source #
The end position (0-based) of this variant. This corresponds to the first base after the last base in the reference allele. So, the length of the reference allele is (end - start). This is useful for variants that don't explicitly give alternate bases, for example large deletions.
vReferenceBases :: Lens' Variant (Maybe Text) Source #
The reference bases for this variant. They start at the given position.
vId :: Lens' Variant (Maybe Text) Source #
The server-generated variant ID, unique across all variants.
vQuality :: Lens' Variant (Maybe Double) Source #
A measure of how likely this variant is to be real. A higher value is better.
vFilter :: Lens' Variant [Text] Source #
A list of filters (normally quality filters) this variant has failed. `PASS` indicates this variant has passed all filters.
vInfo :: Lens' Variant (Maybe VariantInfo) Source #
A map of additional variant information. This must be of the form map (string key mapping to a list of string values).
vCalls :: Lens' Variant [VariantCall] Source #
The variant calls for this particular variant. Each one represents the determination of genotype with respect to this variant.
Annotation
data Annotation Source #
An annotation describes a region of reference genome. The value of an annotation may be one of several canonical types, supplemented by arbitrary info tags. An annotation is not inherently associated with a specific sample or individual (though a client could choose to use annotations in this way). Example canonical annotation types are `GENE` and `VARIANT`.
See: annotation
smart constructor.
annotation :: Annotation Source #
Creates a value of Annotation
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
aVariant :: Lens' Annotation (Maybe VariantAnnotation) Source #
A variant annotation, which describes the effect of a variant on the genome, the coding sequence, and/or higher level consequences at the organism level e.g. pathogenicity. This field is only set for annotations of type `VARIANT`.
aAnnotationSetId :: Lens' Annotation (Maybe Text) Source #
The annotation set to which this annotation belongs.
aStart :: Lens' Annotation (Maybe Int64) Source #
The start position of the range on the reference, 0-based inclusive.
aReverseStrand :: Lens' Annotation (Maybe Bool) Source #
Whether this range refers to the reverse strand, as opposed to the forward strand. Note that regardless of this field, the start/end position of the range always refer to the forward strand.
aReferenceId :: Lens' Annotation (Maybe Text) Source #
The ID of the Google Genomics reference associated with this range.
aReferenceName :: Lens' Annotation (Maybe Text) Source #
The display name corresponding to the reference specified by `referenceId`, for example `chr1`, `1`, or `chrX`.
aEnd :: Lens' Annotation (Maybe Int64) Source #
The end position of the range on the reference, 0-based exclusive.
aId :: Lens' Annotation (Maybe Text) Source #
The server-generated annotation ID, unique across all annotations.
aType :: Lens' Annotation (Maybe AnnotationType) Source #
The data type for this annotation. Must match the containing annotation set's type.
aTranscript :: Lens' Annotation (Maybe Transcript) Source #
A transcript value represents the assertion that a particular region of the reference genome may be transcribed as RNA. An alternative splicing pattern would be represented as a separate transcript object. This field is only set for annotations of type `TRANSCRIPT`.
aInfo :: Lens' Annotation (Maybe AnnotationInfo) Source #
A map of additional read alignment information. This must be of the form map (string key mapping to a list of string values).
ListBasesResponse
data ListBasesResponse Source #
listBasesResponse :: ListBasesResponse Source #
Creates a value of ListBasesResponse
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
lbrNextPageToken :: Lens' ListBasesResponse (Maybe Text) Source #
The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there aren't any additional results.
lbrOffSet :: Lens' ListBasesResponse (Maybe Int64) Source #
The offset position (0-based) of the given `sequence` from the start of this `Reference`. This value will differ for each page in a paginated request.
lbrSequence :: Lens' ListBasesResponse (Maybe Text) Source #
A substring of the bases that make up this reference.
ListOperationsResponse
data ListOperationsResponse Source #
The response message for Operations.ListOperations.
See: listOperationsResponse
smart constructor.
listOperationsResponse :: ListOperationsResponse Source #
Creates a value of ListOperationsResponse
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
lorNextPageToken :: Lens' ListOperationsResponse (Maybe Text) Source #
The standard List next-page token.
lorOperations :: Lens' ListOperationsResponse [Operation] Source #
A list of operations that matches the specified filter in the request.
GetIAMPolicyRequest
data GetIAMPolicyRequest Source #
Request message for `GetIamPolicy` method.
See: getIAMPolicyRequest
smart constructor.
getIAMPolicyRequest :: GetIAMPolicyRequest Source #
Creates a value of GetIAMPolicyRequest
with the minimum fields required to make a request.
CancelOperationRequest
data CancelOperationRequest Source #
The request message for Operations.CancelOperation.
See: cancelOperationRequest
smart constructor.
cancelOperationRequest :: CancelOperationRequest Source #
Creates a value of CancelOperationRequest
with the minimum fields required to make a request.
DataSet
A Dataset is a collection of genomic data. For more genomics resource definitions, see Fundamentals of Google Genomics
See: dataSet
smart constructor.
Creates a value of DataSet
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
dsId :: Lens' DataSet (Maybe Text) Source #
The server-generated dataset ID, unique across all datasets.
dsProjectId :: Lens' DataSet (Maybe Text) Source #
The Google Cloud project ID that this dataset belongs to.
dsCreateTime :: Lens' DataSet (Maybe UTCTime) Source #
The time this dataset was created, in seconds from the epoch.
Read'
A read alignment describes a linear alignment of a string of DNA to a reference sequence, in addition to metadata about the fragment (the molecule of DNA sequenced) and the read (the bases which were read by the sequencer). A read is equivalent to a line in a SAM file. A read belongs to exactly one read group and exactly one read group set. For more genomics resource definitions, see Fundamentals of Google Genomics ### Reverse-stranded reads Mapped reads (reads having a non-null `alignment`) can be aligned to either the forward or the reverse strand of their associated reference. Strandedness of a mapped read is encoded by `alignment.position.reverseStrand`. If we consider the reference to be a forward-stranded coordinate space of `[0, reference.length)` with `0` as the left-most position and `reference.length` as the right-most position, reads are always aligned left to right. That is, `alignment.position.position` always refers to the left-most reference coordinate and `alignment.cigar` describes the alignment of this read to the reference from left to right. All per-base fields such as `alignedSequence` and `alignedQuality` share this same left-to-right orientation; this is true of reads which are aligned to either strand. For reverse-stranded reads, this means that `alignedSequence` is the reverse complement of the bases that were originally reported by the sequencing machine. ### Generating a reference-aligned sequence string When interacting with mapped reads, it's often useful to produce a string representing the local alignment of the read to reference. The following pseudocode demonstrates one way of doing this: out = "" offset = 0 for c in read.alignment.cigar { switch c.operation { case "ALIGNMENT_MATCH", "SEQUENCE_MATCH", "SEQUENCE_MISMATCH": out += read.alignedSequence[offset:offset+c.operationLength] offset += c.operationLength break case "CLIP_SOFT", "INSERT": offset += c.operationLength break case "PAD": out += repeat("*", c.operationLength) break case "DELETE": out += repeat("-", c.operationLength) break case "SKIP": out += repeat(" ", c.operationLength) break case "CLIP_HARD": break } } return out ### Converting to SAM's CIGAR string The following pseudocode generates a SAM CIGAR string from the `cigar` field. Note that this is a lossy conversion (`cigar.referenceSequence` is lost). cigarMap = { "ALIGNMENT_MATCH": "M", "INSERT": "I", "DELETE": "D", "SKIP": "N", "CLIP_SOFT": "S", "CLIP_HARD": "H", "PAD": "P", "SEQUENCE_MATCH": "=", "SEQUENCE_MISMATCH": "X", } cigarStr = "" for c in read.alignment.cigar { cigarStr += c.operationLength + cigarMap[c.operation] } return cigarStr
See: read'
smart constructor.
Creates a value of Read
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
rFragmentLength :: Lens' Read' (Maybe Int32) Source #
The observed length of the fragment, equivalent to TLEN in SAM.
rDuplicateFragment :: Lens' Read' (Maybe Bool) Source #
The fragment is a PCR or optical duplicate (SAM flag 0x400).
rReadGroupSetId :: Lens' Read' (Maybe Text) Source #
The ID of the read group set this read belongs to. A read belongs to exactly one read group set.
rNextMatePosition :: Lens' Read' (Maybe Position) Source #
The mapping of the primary alignment of the `(readNumber+1)%numberReads` read in the fragment. It replaces mate position and mate strand in SAM.
rFailedVendorQualityChecks :: Lens' Read' (Maybe Bool) Source #
Whether this read did not pass filters, such as platform or vendor quality controls (SAM flag 0x200).
rAlignment :: Lens' Read' (Maybe LinearAlignment) Source #
The linear alignment for this alignment record. This field is null for unmapped reads.
rFragmentName :: Lens' Read' (Maybe Text) Source #
The fragment name. Equivalent to QNAME (query template name) in SAM.
rNumberReads :: Lens' Read' (Maybe Int32) Source #
The number of reads in the fragment (extension to SAM flag 0x1).
rId :: Lens' Read' (Maybe Text) Source #
The server-generated read ID, unique across all reads. This is different from the `fragmentName`.
rSecondaryAlignment :: Lens' Read' (Maybe Bool) Source #
Whether this alignment is secondary. Equivalent to SAM flag 0x100. A secondary alignment represents an alternative to the primary alignment for this read. Aligners may return secondary alignments if a read can map ambiguously to multiple coordinates in the genome. By convention, each read has one and only one alignment where both `secondaryAlignment` and `supplementaryAlignment` are false.
rReadGroupId :: Lens' Read' (Maybe Text) Source #
The ID of the read group this read belongs to. A read belongs to exactly one read group. This is a server-generated ID which is distinct from SAM's RG tag (for that value, see ReadGroup.name).
rSupplementaryAlignment :: Lens' Read' (Maybe Bool) Source #
Whether this alignment is supplementary. Equivalent to SAM flag 0x800. Supplementary alignments are used in the representation of a chimeric alignment. In a chimeric alignment, a read is split into multiple linear alignments that map to different reference contigs. The first linear alignment in the read will be designated as the representative alignment; the remaining linear alignments will be designated as supplementary alignments. These alignments may have different mapping quality scores. In each linear alignment in a chimeric alignment, the read will be hard clipped. The `alignedSequence` and `alignedQuality` fields in the alignment record will only represent the bases for its respective linear alignment.
rAlignedSequence :: Lens' Read' (Maybe Text) Source #
The bases of the read sequence contained in this alignment record, **without CIGAR operations applied** (equivalent to SEQ in SAM). `alignedSequence` and `alignedQuality` may be shorter than the full read sequence and quality. This will occur if the alignment is part of a chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR for this read will begin/end with a hard clip operator that will indicate the length of the excised sequence.
rProperPlacement :: Lens' Read' (Maybe Bool) Source #
The orientation and the distance between reads from the fragment are consistent with the sequencing protocol (SAM flag 0x2).
rInfo :: Lens' Read' (Maybe ReadInfo) Source #
A map of additional read alignment information. This must be of the form map (string key mapping to a list of string values).
rReadNumber :: Lens' Read' (Maybe Int32) Source #
The read number in sequencing. 0-based and less than numberReads. This field replaces SAM flag 0x40 and 0x80.
rAlignedQuality :: Lens' Read' [Int32] Source #
The quality of the read sequence contained in this alignment record (equivalent to QUAL in SAM). `alignedSequence` and `alignedQuality` may be shorter than the full read sequence and quality. This will occur if the alignment is part of a chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR for this read will begin/end with a hard clip operator that will indicate the length of the excised sequence.
OperationMetadataLabels
data OperationMetadataLabels Source #
Optionally provided by the caller when submitting the request that creates the operation.
See: operationMetadataLabels
smart constructor.
operationMetadataLabels Source #
Creates a value of OperationMetadataLabels
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
VariantCall
data VariantCall Source #
A call represents the determination of genotype with respect to a particular variant. It may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named rs1234 in a call set with the name NA12345.
See: variantCall
smart constructor.
variantCall :: VariantCall Source #
Creates a value of VariantCall
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
vcGenotypeLikelihood :: Lens' VariantCall [Double] Source #
The genotype likelihoods for this variant call. Each array entry represents how likely a specific genotype is for this call. The value ordering is defined by the GL tag in the VCF spec. If Phred-scaled genotype likelihood scores (PL) are available and log10(P) genotype likelihood scores (GL) are not, PL scores are converted to GL scores. If both are available, PL scores are stored in `info`.
vcCallSetName :: Lens' VariantCall (Maybe Text) Source #
The name of the call set this variant call belongs to.
vcPhaseset :: Lens' VariantCall (Maybe Text) Source #
If this field is present, this variant call's genotype ordering implies the phase of the bases and is consistent with any other variant calls in the same reference sequence which have the same phaseset value. When importing data from VCF, if the genotype data was phased but no phase set was specified this field will be set to `*`.
vcCallSetId :: Lens' VariantCall (Maybe Text) Source #
The ID of the call set this variant call belongs to.
vcGenotype :: Lens' VariantCall [Int32] Source #
The genotype of this variant call. Each value represents either the value of the `referenceBases` field or a 1-based index into `alternateBases`. If a variant had a `referenceBases` value of `T` and an `alternateBases` value of `["A", "C"]`, and the `genotype` was `[2, 1]`, that would mean the call represented the heterozygous value `CA` for this variant. If the `genotype` was instead `[0, 1]`, the represented value would be `TA`. Ordering of the genotype values is important if the `phaseset` is present. If a genotype is not called (that is, a `.` is present in the GT string) -1 is returned.
vcInfo :: Lens' VariantCall (Maybe VariantCallInfo) Source #
A map of additional variant call information. This must be of the form map (string key mapping to a list of string values).
BatchCreateAnnotationsRequest
data BatchCreateAnnotationsRequest Source #
batchCreateAnnotationsRequest :: BatchCreateAnnotationsRequest Source #
Creates a value of BatchCreateAnnotationsRequest
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
bcarAnnotations :: Lens' BatchCreateAnnotationsRequest [Annotation] Source #
The annotations to be created. At most 4096 can be specified in a single request.
bcarRequestId :: Lens' BatchCreateAnnotationsRequest (Maybe Text) Source #
A unique request ID which enables the server to detect duplicated requests. If provided, duplicated requests will result in the same response; if not provided, duplicated requests may result in duplicated data. For a given annotation set, callers should not reuse `request_id`s when writing different batches of annotations - behavior in this case is undefined. A common approach is to use a UUID. For batch jobs where worker crashes are a possibility, consider using some unique variant of a worker or run ID.
MergeVariantsRequest
data MergeVariantsRequest Source #
mergeVariantsRequest :: MergeVariantsRequest Source #
Creates a value of MergeVariantsRequest
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
mvrVariants :: Lens' MergeVariantsRequest [Variant] Source #
The variants to be merged with existing variants.
mvrVariantSetId :: Lens' MergeVariantsRequest (Maybe Text) Source #
The destination variant set.
mvrInfoMergeConfig :: Lens' MergeVariantsRequest (Maybe MergeVariantsRequestInfoMergeConfig) Source #
A mapping between info field keys and the InfoMergeOperations to be performed on them.
ReadGroup
A read group is all the data that's processed the same way by the sequencer.
See: readGroup
smart constructor.
readGroup :: ReadGroup Source #
Creates a value of ReadGroup
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
reaReferenceSetId :: Lens' ReadGroup (Maybe Text) Source #
The reference set the reads in this read group are aligned to.
reaPrograms :: Lens' ReadGroup [Program] Source #
The programs used to generate this read group. Programs are always identical for all read groups within a read group set. For this reason, only the first read group in a returned set will have this field populated.
reaExperiment :: Lens' ReadGroup (Maybe Experiment) Source #
The experiment used to generate this read group.
reaName :: Lens' ReadGroup (Maybe Text) Source #
The read group name. This corresponds to the 'RG ID field in the SAM spec.
reaId :: Lens' ReadGroup (Maybe Text) Source #
The server-generated read group ID, unique for all read groups. Note: This is different than the 'RG ID field in the SAM spec. For that value, see name.
reaSampleId :: Lens' ReadGroup (Maybe Text) Source #
A client-supplied sample identifier for the reads in this read group.
reaPredictedInsertSize :: Lens' ReadGroup (Maybe Int32) Source #
The predicted insert size of this read group. The insert size is the length the sequenced DNA fragment from end-to-end, not including the adapters.
reaDescription :: Lens' ReadGroup (Maybe Text) Source #
A free-form text description of this read group.
reaInfo :: Lens' ReadGroup (Maybe ReadGroupInfo) Source #
A map of additional read group information. This must be of the form map (string key mapping to a list of string values).
Operation
This resource represents a long-running operation that is the result of a network API call.
See: operation
smart constructor.
oDone :: Lens' Operation (Maybe Bool) Source #
If the value is `false`, it means the operation is still in progress. If true, the operation is completed, and either `error` or `response` is available.
oError :: Lens' Operation (Maybe Status) Source #
The error result of the operation in case of failure or cancellation.
oResponse :: Lens' Operation (Maybe OperationResponse) Source #
If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If importing Variants, an ImportVariantsResponse is returned. For pipelines and exports, an empty response is returned.
oName :: Lens' Operation (Maybe Text) Source #
The server-assigned name, which is only unique within the same service that originally returns it. For example: `operations/CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw`
oMetadata :: Lens' Operation (Maybe OperationSchema) Source #
An OperationMetadata object. This will always be returned with the Operation.
SearchReferenceSetsRequest
searchReferenceSetsRequest :: SearchReferenceSetsRequest Source #
Creates a value of SearchReferenceSetsRequest
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
srsrMD5checksums :: Lens' SearchReferenceSetsRequest [Text] Source #
If present, return reference sets for which the md5checksum matches exactly.
srsrAccessions :: Lens' SearchReferenceSetsRequest [Text] Source #
If present, return reference sets for which a prefix of any of sourceAccessions match any of these strings. Accession numbers typically have a main number and a version, for example `NC_000001.11`.
srsrPageToken :: Lens' SearchReferenceSetsRequest (Maybe Text) Source #
The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of `nextPageToken` from the previous response.
srsrAssemblyId :: Lens' SearchReferenceSetsRequest (Maybe Text) Source #
If present, return reference sets for which a substring of their `assemblyId` matches this string (case insensitive).
srsrPageSize :: Lens' SearchReferenceSetsRequest (Maybe Int32) Source #
The maximum number of results to return in a single page. If unspecified, defaults to 1024. The maximum value is 4096.
Empty
A generic empty message that you can re-use to avoid defining duplicated empty messages in your APIs. A typical example is to use it as the request or the response type of an API method. For instance: service Foo { rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty); } The JSON representation for `Empty` is empty JSON object `{}`.
See: empty
smart constructor.
AnnotationSetType
data AnnotationSetType Source #
The type of annotations contained within this set.
ASTAnnotationTypeUnspecified | ANNOTATION_TYPE_UNSPECIFIED |
ASTGeneric |
|
ASTVariant |
|
ASTGene |
|
ASTTranscript |
|
SearchReferencesResponse
searchReferencesResponse :: SearchReferencesResponse Source #
Creates a value of SearchReferencesResponse
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
srrNextPageToken :: Lens' SearchReferencesResponse (Maybe Text) Source #
The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there aren't any additional results.
srrReferences :: Lens' SearchReferencesResponse [Reference] Source #
The matching references.
VariantSetMetadata
data VariantSetMetadata Source #
Metadata describes a single piece of variant call metadata. These data include a top level key and either a single value string (value) or a list of key-value pairs (info.) Value and info are mutually exclusive.
See: variantSetMetadata
smart constructor.
variantSetMetadata :: VariantSetMetadata Source #
Creates a value of VariantSetMetadata
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
vsmId :: Lens' VariantSetMetadata (Maybe Text) Source #
User-provided ID field, not enforced by this API. Two or more pieces of structured metadata with identical id and key fields are considered equivalent.
vsmType :: Lens' VariantSetMetadata (Maybe VariantSetMetadataType) Source #
The type of data. Possible types include: Integer, Float, Flag, Character, and String.
vsmNumber :: Lens' VariantSetMetadata (Maybe Text) Source #
The number of values that can be included in a field described by this metadata.
vsmDescription :: Lens' VariantSetMetadata (Maybe Text) Source #
A textual description of this metadata.
vsmInfo :: Lens' VariantSetMetadata (Maybe VariantSetMetadataInfo) Source #
Remaining structured metadata key-value pairs. This must be of the form map (string key mapping to a list of string values).
CallSet
A call set is a collection of variant calls, typically for one sample. It belongs to a variant set. For more genomics resource definitions, see Fundamentals of Google Genomics
See: callSet
smart constructor.
Creates a value of CallSet
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
csCreated :: Lens' CallSet (Maybe Int64) Source #
The date this call set was created in milliseconds from the epoch.
csId :: Lens' CallSet (Maybe Text) Source #
The server-generated call set ID, unique across all call sets.
csVariantSetIds :: Lens' CallSet [Text] Source #
The IDs of the variant sets this call set belongs to. This field must have exactly length one, as a call set belongs to a single variant set. This field is repeated for compatibility with the GA4GH 0.5.1 API.
csInfo :: Lens' CallSet (Maybe CallSetInfo) Source #
A map of additional call set information. This must be of the form map (string key mapping to a list of string values).
CoverageBucket
data CoverageBucket Source #
A bucket over which read coverage has been precomputed. A bucket corresponds to a specific range of the reference sequence.
See: coverageBucket
smart constructor.
coverageBucket :: CoverageBucket Source #
Creates a value of CoverageBucket
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
cbRange :: Lens' CoverageBucket (Maybe Range) Source #
The genomic coordinate range spanned by this bucket.
cbMeanCoverage :: Lens' CoverageBucket (Maybe Double) Source #
The average number of reads which are aligned to each individual reference base in this bucket.
VariantAnnotation
data VariantAnnotation Source #
variantAnnotation :: VariantAnnotation Source #
Creates a value of VariantAnnotation
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
vaEffect :: Lens' VariantAnnotation (Maybe VariantAnnotationEffect) Source #
Effect of the variant on the coding sequence.
vaClinicalSignificance :: Lens' VariantAnnotation (Maybe VariantAnnotationClinicalSignificance) Source #
Describes the clinical significance of a variant. It is adapted from the ClinVar controlled vocabulary for clinical significance described at: http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
vaAlternateBases :: Lens' VariantAnnotation (Maybe Text) Source #
The alternate allele for this variant. If multiple alternate alleles exist at this location, create a separate variant for each one, as they may represent distinct conditions.
vaGeneId :: Lens' VariantAnnotation (Maybe Text) Source #
Google annotation ID of the gene affected by this variant. This should be provided when the variant is created.
vaConditions :: Lens' VariantAnnotation [ClinicalCondition] Source #
The set of conditions associated with this variant. A condition describes the way a variant influences human health.
vaType :: Lens' VariantAnnotation (Maybe VariantAnnotationType) Source #
Type has been adapted from ClinVar's list of variant types.
vaTranscriptIds :: Lens' VariantAnnotation [Text] Source #
Google annotation IDs of the transcripts affected by this variant. These should be provided when the variant is created.
VariantAnnotationClinicalSignificance
data VariantAnnotationClinicalSignificance Source #
Describes the clinical significance of a variant. It is adapted from the ClinVar controlled vocabulary for clinical significance described at: http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
ClinicalSignificanceUnspecified | CLINICAL_SIGNIFICANCE_UNSPECIFIED |
ClinicalSignificanceOther |
|
Uncertain | UNCERTAIN |
Benign | BENIGN |
LikelyBenign | LIKELY_BENIGN |
LikelyPathogenic | LIKELY_PATHOGENIC |
Pathogenic | PATHOGENIC |
DrugResponse | DRUG_RESPONSE |
Histocompatibility | HISTOCOMPATIBILITY |
ConfersSensitivity | CONFERS_SENSITIVITY |
RiskFactor | RISK_FACTOR |
Association | ASSOCIATION |
Protective | PROTECTIVE |
MultipleReported |
|
SearchReadGroupSetsRequest
data SearchReadGroupSetsRequest Source #
The read group set search request.
See: searchReadGroupSetsRequest
smart constructor.
searchReadGroupSetsRequest :: SearchReadGroupSetsRequest Source #
Creates a value of SearchReadGroupSetsRequest
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
srgsrDataSetIds :: Lens' SearchReadGroupSetsRequest [Text] Source #
Restricts this query to read group sets within the given datasets. At least one ID must be provided.
srgsrName :: Lens' SearchReadGroupSetsRequest (Maybe Text) Source #
Only return read group sets for which a substring of the name matches this string.
srgsrPageToken :: Lens' SearchReadGroupSetsRequest (Maybe Text) Source #
The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of `nextPageToken` from the previous response.
srgsrPageSize :: Lens' SearchReadGroupSetsRequest (Maybe Int32) Source #
The maximum number of results to return in a single page. If unspecified, defaults to 256. The maximum value is 1024.
Reference
A reference is a canonical assembled DNA sequence, intended to act as a reference coordinate space for other genomic annotations. A single reference might represent the human chromosome 1 or mitochandrial DNA, for instance. A reference belongs to one or more reference sets. For more genomics resource definitions, see Fundamentals of Google Genomics
See: reference
smart constructor.
reference :: Reference Source #
Creates a value of Reference
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
refSourceAccessions :: Lens' Reference [Text] Source #
All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, for example `GCF_000001405.26`.
refMD5checksum :: Lens' Reference (Maybe Text) Source #
MD5 of the upper-case sequence excluding all whitespace characters (this is equivalent to SQ:M5 in SAM). This value is represented in lower case hexadecimal format.
refNcbiTaxonId :: Lens' Reference (Maybe Int32) Source #
ID from http://www.ncbi.nlm.nih.gov/taxonomy. For example, 9606 for human.
refId :: Lens' Reference (Maybe Text) Source #
The server-generated reference ID, unique across all references.
refSourceURI :: Lens' Reference (Maybe Text) Source #
The URI from which the sequence was obtained. Typically specifies a FASTA format file.
VariantCallInfo
data VariantCallInfo Source #
A map of additional variant call information. This must be of the form map (string key mapping to a list of string values).
See: variantCallInfo
smart constructor.
Creates a value of VariantCallInfo
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
ReadGroupInfo
data ReadGroupInfo Source #
A map of additional read group information. This must be of the form map (string key mapping to a list of string values).
See: readGroupInfo
smart constructor.
Creates a value of ReadGroupInfo
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
StatusDetailsItem
data StatusDetailsItem Source #
Creates a value of StatusDetailsItem
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
sdiAddtional :: Lens' StatusDetailsItem (HashMap Text JSONValue) Source #
Properties of the object. Contains field 'type with type URL.
SearchCallSetsResponse
data SearchCallSetsResponse Source #
The call set search response.
See: searchCallSetsResponse
smart constructor.
searchCallSetsResponse :: SearchCallSetsResponse Source #
Creates a value of SearchCallSetsResponse
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
scsrNextPageToken :: Lens' SearchCallSetsResponse (Maybe Text) Source #
The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there aren't any additional results.
scsrCallSets :: Lens' SearchCallSetsResponse [CallSet] Source #
The list of matching call sets.
SetIAMPolicyRequest
data SetIAMPolicyRequest Source #
Request message for `SetIamPolicy` method.
See: setIAMPolicyRequest
smart constructor.
setIAMPolicyRequest :: SetIAMPolicyRequest Source #
Creates a value of SetIAMPolicyRequest
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
siprPolicy :: Lens' SetIAMPolicyRequest (Maybe Policy) Source #
REQUIRED: The complete policy to be applied to the `resource`. The size of the policy is limited to a few 10s of KB. An empty policy is a valid policy but certain Cloud Platform services (such as Projects) might reject them.
SearchReadsRequest
data SearchReadsRequest Source #
The read search request.
See: searchReadsRequest
smart constructor.
searchReadsRequest :: SearchReadsRequest Source #
Creates a value of SearchReadsRequest
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
srrStart :: Lens' SearchReadsRequest (Maybe Int64) Source #
The start position of the range on the reference, 0-based inclusive. If specified, `referenceName` must also be specified.
srrReadGroupIds :: Lens' SearchReadsRequest [Text] Source #
The IDs of the read groups within which to search for reads. All specified read groups must belong to the same read group sets. Must specify one of `readGroupSetIds` or `readGroupIds`.
srrReferenceName :: Lens' SearchReadsRequest (Maybe Text) Source #
The reference sequence name, for example `chr1`, `1`, or `chrX`. If set to `*`, only unmapped reads are returned. If unspecified, all reads (mapped and unmapped) are returned.
srrEnd :: Lens' SearchReadsRequest (Maybe Int64) Source #
The end position of the range on the reference, 0-based exclusive. If specified, `referenceName` must also be specified.
srrPageToken :: Lens' SearchReadsRequest (Maybe Text) Source #
The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of `nextPageToken` from the previous response.
srrPageSize :: Lens' SearchReadsRequest (Maybe Int32) Source #
The maximum number of results to return in a single page. If unspecified, defaults to 256. The maximum value is 2048.
srrReadGroupSetIds :: Lens' SearchReadsRequest [Text] Source #
The IDs of the read groups sets within which to search for reads. All specified read group sets must be aligned against a common set of reference sequences; this defines the genomic coordinates for the query. Must specify one of `readGroupSetIds` or `readGroupIds`.
OperationMetadataRequest
data OperationMetadataRequest Source #
The original request that started the operation. Note that this will be in current version of the API. If the operation was started with v1beta2 API and a GetOperation is performed on v1 API, a v1 request will be returned.
See: operationMetadataRequest
smart constructor.
operationMetadataRequest Source #
Creates a value of OperationMetadataRequest
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
omrAddtional :: Lens' OperationMetadataRequest (HashMap Text JSONValue) Source #
Properties of the object. Contains field 'type with type URL.
MergeVariantsRequestInfoMergeConfig
data MergeVariantsRequestInfoMergeConfig Source #
A mapping between info field keys and the InfoMergeOperations to be performed on them.
See: mergeVariantsRequestInfoMergeConfig
smart constructor.
mergeVariantsRequestInfoMergeConfig Source #
Creates a value of MergeVariantsRequestInfoMergeConfig
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
VariantInfo
data VariantInfo Source #
A map of additional variant information. This must be of the form map (string key mapping to a list of string values).
See: variantInfo
smart constructor.
Creates a value of VariantInfo
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
viAddtional :: Lens' VariantInfo (HashMap Text [JSONValue]) Source #
Experiment
data Experiment Source #
experiment :: Experiment Source #
Creates a value of Experiment
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
eInstrumentModel :: Lens' Experiment (Maybe Text) Source #
The instrument model used as part of this experiment. This maps to sequencing technology in the SAM spec.
ePlatformUnit :: Lens' Experiment (Maybe Text) Source #
The platform unit used as part of this experiment, for example flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the 'RG PU field in the SAM spec.
eSequencingCenter :: Lens' Experiment (Maybe Text) Source #
The sequencing center used as part of this experiment.
eLibraryId :: Lens' Experiment (Maybe Text) Source #
A client-supplied library identifier; a library is a collection of DNA fragments which have been prepared for sequencing from a sample. This field is important for quality control as error or bias can be introduced during sample preparation.
SearchVariantSetsRequest
data SearchVariantSetsRequest Source #
The search variant sets request.
See: searchVariantSetsRequest
smart constructor.
searchVariantSetsRequest :: SearchVariantSetsRequest Source #
Creates a value of SearchVariantSetsRequest
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
svsrDataSetIds :: Lens' SearchVariantSetsRequest [Text] Source #
Exactly one dataset ID must be provided here. Only variant sets which belong to this dataset will be returned.
svsrPageToken :: Lens' SearchVariantSetsRequest (Maybe Text) Source #
The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of `nextPageToken` from the previous response.
svsrPageSize :: Lens' SearchVariantSetsRequest (Maybe Int32) Source #
The maximum number of results to return in a single page. If unspecified, defaults to 1024.
AnnotationInfo
data AnnotationInfo Source #
A map of additional read alignment information. This must be of the form map (string key mapping to a list of string values).
See: annotationInfo
smart constructor.
Creates a value of AnnotationInfo
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
SearchAnnotationsResponse
searchAnnotationsResponse :: SearchAnnotationsResponse Source #
Creates a value of SearchAnnotationsResponse
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
sarAnnotations :: Lens' SearchAnnotationsResponse [Annotation] Source #
The matching annotations.
sarNextPageToken :: Lens' SearchAnnotationsResponse (Maybe Text) Source #
The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there aren't any additional results.
SearchAnnotationSetsRequest
data SearchAnnotationSetsRequest Source #
searchAnnotationSetsRequest :: SearchAnnotationSetsRequest Source #
Creates a value of SearchAnnotationSetsRequest
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
sasrReferenceSetId :: Lens' SearchAnnotationSetsRequest (Maybe Text) Source #
If specified, only annotation sets associated with the given reference set are returned.
sasrTypes :: Lens' SearchAnnotationSetsRequest [Text] Source #
If specified, only annotation sets that have any of these types are returned.
sasrDataSetIds :: Lens' SearchAnnotationSetsRequest [Text] Source #
Required. The dataset IDs to search within. Caller must have `READ` access to these datasets.
sasrName :: Lens' SearchAnnotationSetsRequest (Maybe Text) Source #
Only return annotations sets for which a substring of the name matches this string (case insensitive).
sasrPageToken :: Lens' SearchAnnotationSetsRequest (Maybe Text) Source #
The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of `nextPageToken` from the previous response.
sasrPageSize :: Lens' SearchAnnotationSetsRequest (Maybe Int32) Source #
The maximum number of results to return in a single page. If unspecified, defaults to 128. The maximum value is 1024.
ImportReadGroupSetsRequestPartitionStrategy
data ImportReadGroupSetsRequestPartitionStrategy Source #
The partition strategy describes how read groups are partitioned into read group sets.
PartitionStrategyUnspecified | PARTITION_STRATEGY_UNSPECIFIED |
PerFilePerSample |
|
MergeAll |
|
SearchVariantsResponse
data SearchVariantsResponse Source #
The variant search response.
See: searchVariantsResponse
smart constructor.
searchVariantsResponse :: SearchVariantsResponse Source #
Creates a value of SearchVariantsResponse
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
svrVariants :: Lens' SearchVariantsResponse [Variant] Source #
The list of matching Variants.
svrNextPageToken :: Lens' SearchVariantsResponse (Maybe Text) Source #
The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there aren't any additional results.
OperationMetadataRuntimeMetadata
data OperationMetadataRuntimeMetadata Source #
Runtime metadata on this Operation.
See: operationMetadataRuntimeMetadata
smart constructor.
operationMetadataRuntimeMetadata Source #
Creates a value of OperationMetadataRuntimeMetadata
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
omrmAddtional :: Lens' OperationMetadataRuntimeMetadata (HashMap Text JSONValue) Source #
Properties of the object. Contains field 'type with type URL.
ClinicalCondition
data ClinicalCondition Source #
clinicalCondition :: ClinicalCondition Source #
Creates a value of ClinicalCondition
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
ccExternalIds :: Lens' ClinicalCondition [ExternalId] Source #
The set of external IDs for this condition.
ccConceptId :: Lens' ClinicalCondition (Maybe Text) Source #
The MedGen concept id associated with this gene. Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
ccOmimId :: Lens' ClinicalCondition (Maybe Text) Source #
The OMIM id for this condition. Search for these IDs at http://omim.org/
SearchCallSetsRequest
data SearchCallSetsRequest Source #
The call set search request.
See: searchCallSetsRequest
smart constructor.
searchCallSetsRequest :: SearchCallSetsRequest Source #
Creates a value of SearchCallSetsRequest
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
scsrName :: Lens' SearchCallSetsRequest (Maybe Text) Source #
Only return call sets for which a substring of the name matches this string.
scsrPageToken :: Lens' SearchCallSetsRequest (Maybe Text) Source #
The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of `nextPageToken` from the previous response.
scsrVariantSetIds :: Lens' SearchCallSetsRequest [Text] Source #
Restrict the query to call sets within the given variant sets. At least one ID must be provided.
scsrPageSize :: Lens' SearchCallSetsRequest (Maybe Int32) Source #
The maximum number of results to return in a single page. If unspecified, defaults to 1024.
Entry
Creates a value of Entry
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
eAnnotation :: Lens' Entry (Maybe Annotation) Source #
The created annotation, if creation was successful.
SearchReadsResponse
data SearchReadsResponse Source #
The read search response.
See: searchReadsResponse
smart constructor.
searchReadsResponse :: SearchReadsResponse Source #
Creates a value of SearchReadsResponse
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
sNextPageToken :: Lens' SearchReadsResponse (Maybe Text) Source #
The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there aren't any additional results.
sAlignments :: Lens' SearchReadsResponse [Read'] Source #
The list of matching alignments sorted by mapped genomic coordinate, if any, ascending in position within the same reference. Unmapped reads, which have no position, are returned contiguously and are sorted in ascending lexicographic order by fragment name.
Program
Creates a value of Program
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
pName :: Lens' Program (Maybe Text) Source #
The display name of the program. This is typically the colloquial name of the tool used, for example 'bwa' or 'picard'.
pId :: Lens' Program (Maybe Text) Source #
The user specified locally unique ID of the program. Used along with `prevProgramId` to define an ordering between programs.
SearchReferencesRequest
searchReferencesRequest :: SearchReferencesRequest Source #
Creates a value of SearchReferencesRequest
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
sReferenceSetId :: Lens' SearchReferencesRequest (Maybe Text) Source #
If present, return only references which belong to this reference set.
sMD5checksums :: Lens' SearchReferencesRequest [Text] Source #
If present, return references for which the md5checksum matches exactly.
sAccessions :: Lens' SearchReferencesRequest [Text] Source #
If present, return references for which a prefix of any of sourceAccessions match any of these strings. Accession numbers typically have a main number and a version, for example `GCF_000001405.26`.
sPageToken :: Lens' SearchReferencesRequest (Maybe Text) Source #
The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of `nextPageToken` from the previous response.
sPageSize :: Lens' SearchReferencesRequest (Maybe Int32) Source #
The maximum number of results to return in a single page. If unspecified, defaults to 1024. The maximum value is 4096.
BatchCreateAnnotationsResponse
data BatchCreateAnnotationsResponse Source #
batchCreateAnnotationsResponse :: BatchCreateAnnotationsResponse Source #
Creates a value of BatchCreateAnnotationsResponse
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
bcarEntries :: Lens' BatchCreateAnnotationsResponse [Entry] Source #
The resulting per-annotation entries, ordered consistently with the original request.
CodingSequence
data CodingSequence Source #
codingSequence :: CodingSequence Source #
Creates a value of CodingSequence
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
csStart :: Lens' CodingSequence (Maybe Int64) Source #
The start of the coding sequence on this annotation's reference sequence, 0-based inclusive. Note that this position is relative to the reference start, and *not* the containing annotation start.
csEnd :: Lens' CodingSequence (Maybe Int64) Source #
The end of the coding sequence on this annotation's reference sequence, 0-based exclusive. Note that this position is relative to the reference start, and *not* the containing annotation start.
AnnotationType
data AnnotationType Source #
The data type for this annotation. Must match the containing annotation set's type.
ATAnnotationTypeUnspecified | ANNOTATION_TYPE_UNSPECIFIED |
ATGeneric |
|
ATVariant |
|
ATGene |
|
ATTranscript |
|
SearchReferenceSetsResponse
data SearchReferenceSetsResponse Source #
searchReferenceSetsResponse :: SearchReferenceSetsResponse Source #
Creates a value of SearchReferenceSetsResponse
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
srsrNextPageToken :: Lens' SearchReferenceSetsResponse (Maybe Text) Source #
The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there aren't any additional results.
srsrReferenceSets :: Lens' SearchReferenceSetsResponse [ReferenceSet] Source #
The matching references sets.
Range
A 0-based half-open genomic coordinate range for search requests.
See: range
smart constructor.
Creates a value of Range
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
rStart :: Lens' Range (Maybe Int64) Source #
The start position of the range on the reference, 0-based inclusive.
rReferenceName :: Lens' Range (Maybe Text) Source #
The reference sequence name, for example `chr1`, `1`, or `chrX`.
rEnd :: Lens' Range (Maybe Int64) Source #
The end position of the range on the reference, 0-based exclusive.
ReadGroupSet
data ReadGroupSet Source #
A read group set is a logical collection of read groups, which are collections of reads produced by a sequencer. A read group set typically models reads corresponding to one sample, sequenced one way, and aligned one way. * A read group set belongs to one dataset. * A read group belongs to one read group set. * A read belongs to one read group. For more genomics resource definitions, see Fundamentals of Google Genomics
See: readGroupSet
smart constructor.
readGroupSet :: ReadGroupSet Source #
Creates a value of ReadGroupSet
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
rgsReferenceSetId :: Lens' ReadGroupSet (Maybe Text) Source #
The reference set to which the reads in this read group set are aligned.
rgsName :: Lens' ReadGroupSet (Maybe Text) Source #
The read group set name. By default this will be initialized to the sample name of the sequenced data contained in this set.
rgsDataSetId :: Lens' ReadGroupSet (Maybe Text) Source #
The dataset to which this read group set belongs.
rgsId :: Lens' ReadGroupSet (Maybe Text) Source #
The server-generated read group set ID, unique for all read group sets.
rgsInfo :: Lens' ReadGroupSet (Maybe ReadGroupSetInfo) Source #
A map of additional read group set information.
rgsReadGroups :: Lens' ReadGroupSet [ReadGroup] Source #
The read groups in this set. There are typically 1-10 read groups in a read group set.
rgsFilename :: Lens' ReadGroupSet (Maybe Text) Source #
The filename of the original source file for this read group set, if any.
Xgafv
V1 error format.
ExportReadGroupSetRequest
data ExportReadGroupSetRequest Source #
The read group set export request.
See: exportReadGroupSetRequest
smart constructor.
exportReadGroupSetRequest :: ExportReadGroupSetRequest Source #
Creates a value of ExportReadGroupSetRequest
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
ergsrReferenceNames :: Lens' ExportReadGroupSetRequest [Text] Source #
The reference names to export. If this is not specified, all reference sequences, including unmapped reads, are exported. Use `*` to export only unmapped reads.
ergsrExportURI :: Lens' ExportReadGroupSetRequest (Maybe Text) Source #
Required. A Google Cloud Storage URI for the exported BAM file. The currently authenticated user must have write access to the new file. An error will be returned if the URI already contains data.
ergsrProjectId :: Lens' ExportReadGroupSetRequest (Maybe Text) Source #
Required. The Google Cloud project ID that owns this export. The caller must have WRITE access to this project.
ImportVariantsResponse
data ImportVariantsResponse Source #
The variant data import response.
See: importVariantsResponse
smart constructor.
importVariantsResponse :: ImportVariantsResponse Source #
Creates a value of ImportVariantsResponse
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
ivrCallSetIds :: Lens' ImportVariantsResponse [Text] Source #
IDs of the call sets created during the import.
ListCoverageBucketsResponse
data ListCoverageBucketsResponse Source #
listCoverageBucketsResponse :: ListCoverageBucketsResponse Source #
Creates a value of ListCoverageBucketsResponse
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
lcbrNextPageToken :: Lens' ListCoverageBucketsResponse (Maybe Text) Source #
The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there aren't any additional results.
lcbrBucketWidth :: Lens' ListCoverageBucketsResponse (Maybe Int64) Source #
The length of each coverage bucket in base pairs. Note that buckets at the end of a reference sequence may be shorter. This value is omitted if the bucket width is infinity (the default behaviour, with no range or `targetBucketWidth`).
lcbrCoverageBuckets :: Lens' ListCoverageBucketsResponse [CoverageBucket] Source #
The coverage buckets. The list of buckets is sparse; a bucket with 0 overlapping reads is not returned. A bucket never crosses more than one reference sequence. Each bucket has width `bucketWidth`, unless its end is the end of the reference sequence.
TestIAMPermissionsRequest
data TestIAMPermissionsRequest Source #
Request message for `TestIamPermissions` method.
See: testIAMPermissionsRequest
smart constructor.
testIAMPermissionsRequest :: TestIAMPermissionsRequest Source #
Creates a value of TestIAMPermissionsRequest
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
tiprPermissions :: Lens' TestIAMPermissionsRequest [Text] Source #
REQUIRED: The set of permissions to check for the 'resource'. Permissions with wildcards (such as '*' or 'storage.*') are not allowed. Allowed permissions are: * `genomics.datasets.create` * `genomics.datasets.delete` * `genomics.datasets.get` * `genomics.datasets.list` * `genomics.datasets.update` * `genomics.datasets.getIamPolicy` * `genomics.datasets.setIamPolicy`
ImportReadGroupSetsResponse
data ImportReadGroupSetsResponse Source #
The read group set import response.
See: importReadGroupSetsResponse
smart constructor.
importReadGroupSetsResponse :: ImportReadGroupSetsResponse Source #
Creates a value of ImportReadGroupSetsResponse
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
irgsrReadGroupSetIds :: Lens' ImportReadGroupSetsResponse [Text] Source #
IDs of the read group sets that were created.
LinearAlignment
data LinearAlignment Source #
A linear alignment can be represented by one CIGAR string. Describes the mapped position and local alignment of the read to the reference.
See: linearAlignment
smart constructor.
linearAlignment :: LinearAlignment Source #
Creates a value of LinearAlignment
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
laCigar :: Lens' LinearAlignment [CigarUnit] Source #
Represents the local alignment of this sequence (alignment matches, indels, etc) against the reference.
laMAppingQuality :: Lens' LinearAlignment (Maybe Int32) Source #
The mapping quality of this alignment. Represents how likely the read maps to this position as opposed to other locations. Specifically, this is -10 log10 Pr(mapping position is wrong), rounded to the nearest integer.
laPosition :: Lens' LinearAlignment (Maybe Position) Source #
The position of this alignment.
AnnotationSet
data AnnotationSet Source #
An annotation set is a logical grouping of annotations that share consistent type information and provenance. Examples of annotation sets include 'all genes from refseq', and 'all variant annotations from ClinVar'.
See: annotationSet
smart constructor.
annotationSet :: AnnotationSet Source #
Creates a value of AnnotationSet
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
asReferenceSetId :: Lens' AnnotationSet (Maybe Text) Source #
The ID of the reference set that defines the coordinate space for this set's annotations.
asDataSetId :: Lens' AnnotationSet (Maybe Text) Source #
The dataset to which this annotation set belongs.
asId :: Lens' AnnotationSet (Maybe Text) Source #
The server-generated annotation set ID, unique across all annotation sets.
asType :: Lens' AnnotationSet (Maybe AnnotationSetType) Source #
The type of annotations contained within this set.
asSourceURI :: Lens' AnnotationSet (Maybe Text) Source #
The source URI describing the file from which this annotation set was generated, if any.
asInfo :: Lens' AnnotationSet (Maybe AnnotationSetInfo) Source #
A map of additional read alignment information. This must be of the form map (string key mapping to a list of string values).
VariantSet
data VariantSet Source #
A variant set is a collection of call sets and variants. It contains summary statistics of those contents. A variant set belongs to a dataset. For more genomics resource definitions, see Fundamentals of Google Genomics
See: variantSet
smart constructor.
variantSet :: VariantSet Source #
Creates a value of VariantSet
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
vsReferenceSetId :: Lens' VariantSet (Maybe Text) Source #
The reference set to which the variant set is mapped. The reference set describes the alignment provenance of the variant set, while the `referenceBounds` describe the shape of the actual variant data. The reference set's reference names are a superset of those found in the `referenceBounds`. For example, given a variant set that is mapped to the GRCh38 reference set and contains a single variant on reference 'X', `referenceBounds` would contain only an entry for 'X', while the associated reference set enumerates all possible references: '1', '2', 'X', 'Y', 'MT', etc.
vsDataSetId :: Lens' VariantSet (Maybe Text) Source #
The dataset to which this variant set belongs.
vsReferenceBounds :: Lens' VariantSet [ReferenceBound] Source #
A list of all references used by the variants in a variant set with associated coordinate upper bounds for each one.
vsMetadata :: Lens' VariantSet [VariantSetMetadata] Source #
The metadata associated with this variant set.
vsId :: Lens' VariantSet (Maybe Text) Source #
The server-generated variant set ID, unique across all variant sets.
vsDescription :: Lens' VariantSet (Maybe Text) Source #
A textual description of this variant set.
CigarUnitOperation
data CigarUnitOperation Source #
OperationUnspecified | OPERATION_UNSPECIFIED |
AlignmentMatch |
|
Insert |
|
Delete' |
|
Skip |
|
ClipSoft |
|
ClipHard |
|
Pad |
|
SequenceMatch |
|
SequenceMismatch |
|
VariantSetMetadataType
data VariantSetMetadataType Source #
The type of data. Possible types include: Integer, Float, Flag, Character, and String.
TestIAMPermissionsResponse
data TestIAMPermissionsResponse Source #
Response message for `TestIamPermissions` method.
See: testIAMPermissionsResponse
smart constructor.
testIAMPermissionsResponse :: TestIAMPermissionsResponse Source #
Creates a value of TestIAMPermissionsResponse
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
tiamprPermissions :: Lens' TestIAMPermissionsResponse [Text] Source #
A subset of `TestPermissionsRequest.permissions` that the caller is allowed.
ListDataSetsResponse
data ListDataSetsResponse Source #
The dataset list response.
See: listDataSetsResponse
smart constructor.
listDataSetsResponse :: ListDataSetsResponse Source #
Creates a value of ListDataSetsResponse
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
ldsrNextPageToken :: Lens' ListDataSetsResponse (Maybe Text) Source #
The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there aren't any additional results.
ldsrDataSets :: Lens' ListDataSetsResponse [DataSet] Source #
The list of matching Datasets.
ImportReadGroupSetsRequest
data ImportReadGroupSetsRequest Source #
The read group set import request.
See: importReadGroupSetsRequest
smart constructor.
importReadGroupSetsRequest :: ImportReadGroupSetsRequest Source #
Creates a value of ImportReadGroupSetsRequest
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
irgsrReferenceSetId :: Lens' ImportReadGroupSetsRequest (Maybe Text) Source #
The reference set to which the imported read group sets are aligned to, if any. The reference names of this reference set must be a superset of those found in the imported file headers. If no reference set id is provided, a best effort is made to associate with a matching reference set.
irgsrDataSetId :: Lens' ImportReadGroupSetsRequest (Maybe Text) Source #
Required. The ID of the dataset these read group sets will belong to. The caller must have WRITE permissions to this dataset.
irgsrSourceURIs :: Lens' ImportReadGroupSetsRequest [Text] Source #
A list of URIs pointing at BAM files in Google Cloud Storage. Those URIs can include wildcards (*), but do not add or remove matching files before import has completed. Note that Google Cloud Storage object listing is only eventually consistent: files added may be not be immediately visible to everyone. Thus, if using a wildcard it is preferable not to start the import immediately after the files are created.
irgsrPartitionStrategy :: Lens' ImportReadGroupSetsRequest (Maybe ImportReadGroupSetsRequestPartitionStrategy) Source #
The partition strategy describes how read groups are partitioned into read group sets.
ImportVariantsRequest
data ImportVariantsRequest Source #
The variant data import request.
See: importVariantsRequest
smart constructor.
importVariantsRequest :: ImportVariantsRequest Source #
Creates a value of ImportVariantsRequest
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
ivrVariantSetId :: Lens' ImportVariantsRequest (Maybe Text) Source #
Required. The variant set to which variant data should be imported.
ivrFormat :: Lens' ImportVariantsRequest (Maybe ImportVariantsRequestFormat) Source #
The format of the variant data being imported. If unspecified, defaults to to `VCF`.
ivrInfoMergeConfig :: Lens' ImportVariantsRequest (Maybe ImportVariantsRequestInfoMergeConfig) Source #
A mapping between info field keys and the InfoMergeOperations to be performed on them. This is plumbed down to the MergeVariantRequests generated by the resulting import job.
ivrNormalizeReferenceNames :: Lens' ImportVariantsRequest (Maybe Bool) Source #
Convert reference names to the canonical representation. hg19 haploytypes (those reference names containing "_hap") are not modified in any way. All other reference names are modified according to the following rules: The reference name is capitalized. The "chr" prefix is dropped for all autosomes and sex chromsomes. For example "chr17" becomes "17" and "chrX" becomes "X". All mitochondrial chromosomes ("chrM", "chrMT", etc) become "MT".
ivrSourceURIs :: Lens' ImportVariantsRequest [Text] Source #
A list of URIs referencing variant files in Google Cloud Storage. URIs can include wildcards as described here. Note that recursive wildcards ('**') are not supported.
ExternalId
data ExternalId Source #
externalId :: ExternalId Source #
Creates a value of ExternalId
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
eiSourceName :: Lens' ExternalId (Maybe Text) Source #
The name of the source of this data.
CigarUnit
A single CIGAR operation.
See: cigarUnit
smart constructor.
cigarUnit :: CigarUnit Source #
Creates a value of CigarUnit
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
cuOperationLength :: Lens' CigarUnit (Maybe Int64) Source #
The number of genomic bases that the operation runs for. Required.
cuReferenceSequence :: Lens' CigarUnit (Maybe Text) Source #
`referenceSequence` is only used at mismatches (`SEQUENCE_MISMATCH`) and deletions (`DELETE`). Filling this field replaces SAM's MD tag. If the relevant information is not available, this field is unset.
Policy
Defines an Identity and Access Management (IAM) policy. It is used to specify access control policies for Cloud Platform resources. A `Policy` consists of a list of `bindings`. A `Binding` binds a list of `members` to a `role`, where the members can be user accounts, Google groups, Google domains, and service accounts. A `role` is a named list of permissions defined by IAM. **Example** { "bindings": [ { "role": "roles/owner", "members": [ "user:mike'example.com", "group:admins'example.com", "domain:google.com", "serviceAccount:my-other-app'appspot.gserviceaccount.com", ] }, { "role": "roles/viewer", "members": ["user:sean'example.com"] } ] } For a description of IAM and its features, see the IAM developer's guide.
See: policy
smart constructor.
Creates a value of Policy
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
polEtag :: Lens' Policy (Maybe ByteString) Source #
`etag` is used for optimistic concurrency control as a way to help prevent simultaneous updates of a policy from overwriting each other. It is strongly suggested that systems make use of the `etag` in the read-modify-write cycle to perform policy updates in order to avoid race conditions: An `etag` is returned in the response to `getIamPolicy`, and systems are expected to put that etag in the request to `setIamPolicy` to ensure that their change will be applied to the same version of the policy. If no `etag` is provided in the call to `setIamPolicy`, then the existing policy is overwritten blindly.
polBindings :: Lens' Policy [Binding] Source #
Associates a list of `members` to a `role`. Multiple `bindings` must not be specified for the same `role`. `bindings` with no members will result in an error.
ExportVariantSetRequest
data ExportVariantSetRequest Source #
The variant data export request.
See: exportVariantSetRequest
smart constructor.
exportVariantSetRequest :: ExportVariantSetRequest Source #
Creates a value of ExportVariantSetRequest
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
evsrBigQueryDataSet :: Lens' ExportVariantSetRequest (Maybe Text) Source #
Required. The BigQuery dataset to export data to. This dataset must already exist. Note that this is distinct from the Genomics concept of "dataset".
evsrBigQueryTable :: Lens' ExportVariantSetRequest (Maybe Text) Source #
Required. The BigQuery table to export data to. If the table doesn't exist, it will be created. If it already exists, it will be overwritten.
evsrFormat :: Lens' ExportVariantSetRequest (Maybe ExportVariantSetRequestFormat) Source #
The format for the exported data.
evsrCallSetIds :: Lens' ExportVariantSetRequest [Text] Source #
If provided, only variant call information from the specified call sets will be exported. By default all variant calls are exported.
evsrProjectId :: Lens' ExportVariantSetRequest (Maybe Text) Source #
Required. The Google Cloud project ID that owns the destination BigQuery dataset. The caller must have WRITE access to this project. This project will also own the resulting export job.
VariantAnnotationType
data VariantAnnotationType Source #
Type has been adapted from ClinVar's list of variant types.
VATTypeUnspecified | TYPE_UNSPECIFIED |
VATTypeOther |
|
VATInsertion |
|
VATDeletion |
|
VATSubstitution |
|
VATSnp |
|
VATStructural |
|
VATCnv |
|
OperationMetadata
data OperationMetadata Source #
Metadata describing an Operation.
See: operationMetadata
smart constructor.
operationMetadata :: OperationMetadata Source #
Creates a value of OperationMetadata
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
omClientId :: Lens' OperationMetadata (Maybe Text) Source #
This field is deprecated. Use `labels` instead. Optionally provided by the caller when submitting the request that creates the operation.
omStartTime :: Lens' OperationMetadata (Maybe UTCTime) Source #
The time at which the job began to run.
omEvents :: Lens' OperationMetadata [OperationEvent] Source #
Optional event messages that were generated during the job's execution. This also contains any warnings that were generated during import or export.
omEndTime :: Lens' OperationMetadata (Maybe UTCTime) Source #
The time at which the job stopped running.
omLabels :: Lens' OperationMetadata (Maybe OperationMetadataLabels) Source #
Optionally provided by the caller when submitting the request that creates the operation.
omProjectId :: Lens' OperationMetadata (Maybe Text) Source #
The Google Cloud Project in which the job is scoped.
omCreateTime :: Lens' OperationMetadata (Maybe UTCTime) Source #
The time at which the job was submitted to the Genomics service.
omRuntimeMetadata :: Lens' OperationMetadata (Maybe OperationMetadataRuntimeMetadata) Source #
Runtime metadata on this Operation.
omRequest :: Lens' OperationMetadata (Maybe OperationMetadataRequest) Source #
The original request that started the operation. Note that this will be in current version of the API. If the operation was started with v1beta2 API and a GetOperation is performed on v1 API, a v1 request will be returned.
ImportVariantsRequestFormat
data ImportVariantsRequestFormat Source #
The format of the variant data being imported. If unspecified, defaults to to `VCF`.
FormatUnspecified | FORMAT_UNSPECIFIED |
FormatVcf |
|
FormatCompleteGenomics |
|
SearchAnnotationsRequest
searchAnnotationsRequest :: SearchAnnotationsRequest Source #
Creates a value of SearchAnnotationsRequest
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
sarStart :: Lens' SearchAnnotationsRequest (Maybe Int64) Source #
The start position of the range on the reference, 0-based inclusive. If specified, referenceId or referenceName must be specified. Defaults to 0.
sarReferenceId :: Lens' SearchAnnotationsRequest (Maybe Text) Source #
The ID of the reference to query.
sarReferenceName :: Lens' SearchAnnotationsRequest (Maybe Text) Source #
The name of the reference to query, within the reference set associated with this query.
sarEnd :: Lens' SearchAnnotationsRequest (Maybe Int64) Source #
The end position of the range on the reference, 0-based exclusive. If referenceId or referenceName must be specified, Defaults to the length of the reference.
sarPageToken :: Lens' SearchAnnotationsRequest (Maybe Text) Source #
The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of `nextPageToken` from the previous response.
sarAnnotationSetIds :: Lens' SearchAnnotationsRequest [Text] Source #
Required. The annotation sets to search within. The caller must have `READ` access to these annotation sets. All queried annotation sets must have the same type.
sarPageSize :: Lens' SearchAnnotationsRequest (Maybe Int32) Source #
The maximum number of results to return in a single page. If unspecified, defaults to 256. The maximum value is 2048.
SearchVariantSetsResponse
data SearchVariantSetsResponse Source #
The search variant sets response.
See: searchVariantSetsResponse
smart constructor.
searchVariantSetsResponse :: SearchVariantSetsResponse Source #
Creates a value of SearchVariantSetsResponse
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
svsrNextPageToken :: Lens' SearchVariantSetsResponse (Maybe Text) Source #
The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there aren't any additional results.
svsrVariantSets :: Lens' SearchVariantSetsResponse [VariantSet] Source #
The variant sets belonging to the requested dataset.
SearchVariantsRequest
data SearchVariantsRequest Source #
The variant search request.
See: searchVariantsRequest
smart constructor.
searchVariantsRequest :: SearchVariantsRequest Source #
Creates a value of SearchVariantsRequest
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
svrStart :: Lens' SearchVariantsRequest (Maybe Int64) Source #
The beginning of the window (0-based, inclusive) for which overlapping variants should be returned. If unspecified, defaults to 0.
svrCallSetIds :: Lens' SearchVariantsRequest [Text] Source #
Only return variant calls which belong to call sets with these ids. Leaving this blank returns all variant calls. If a variant has no calls belonging to any of these call sets, it won't be returned at all.
svrReferenceName :: Lens' SearchVariantsRequest (Maybe Text) Source #
Required. Only return variants in this reference sequence.
svrEnd :: Lens' SearchVariantsRequest (Maybe Int64) Source #
The end of the window, 0-based exclusive. If unspecified or 0, defaults to the length of the reference.
svrMaxCalls :: Lens' SearchVariantsRequest (Maybe Int32) Source #
The maximum number of calls to return in a single page. Note that this limit may be exceeded in the event that a matching variant contains more calls than the requested maximum. If unspecified, defaults to 5000. The maximum value is 10000.
svrPageToken :: Lens' SearchVariantsRequest (Maybe Text) Source #
The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of `nextPageToken` from the previous response.
svrVariantName :: Lens' SearchVariantsRequest (Maybe Text) Source #
Only return variants which have exactly this name.
svrVariantSetIds :: Lens' SearchVariantsRequest [Text] Source #
At most one variant set ID must be provided. Only variants from this variant set will be returned. If omitted, a call set id must be included in the request.
svrPageSize :: Lens' SearchVariantsRequest (Maybe Int32) Source #
The maximum number of variants to return in a single page. If unspecified, defaults to 5000. The maximum value is 10000.
ExportVariantSetRequestFormat
data ExportVariantSetRequestFormat Source #
The format for the exported data.
EVSRFFormatUnspecified | FORMAT_UNSPECIFIED |
EVSRFFormatBigQuery |
|
AnnotationSetInfo
data AnnotationSetInfo Source #
A map of additional read alignment information. This must be of the form map (string key mapping to a list of string values).
See: annotationSetInfo
smart constructor.
Creates a value of AnnotationSetInfo
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
ComputeEngine
data ComputeEngine Source #
Describes a Compute Engine resource that is being managed by a running pipeline.
See: computeEngine
smart constructor.
computeEngine :: ComputeEngine Source #
Creates a value of ComputeEngine
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
ceZone :: Lens' ComputeEngine (Maybe Text) Source #
The availability zone in which the instance resides.
ceDiskNames :: Lens' ComputeEngine [Text] Source #
The names of the disks that were created for this pipeline.
ceMachineType :: Lens' ComputeEngine (Maybe Text) Source #
The machine type of the instance.
ceInstanceName :: Lens' ComputeEngine (Maybe Text) Source #
The instance on which the operation is running.
SearchAnnotationSetsResponse
data SearchAnnotationSetsResponse Source #
searchAnnotationSetsResponse :: SearchAnnotationSetsResponse Source #
Creates a value of SearchAnnotationSetsResponse
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
sasrNextPageToken :: Lens' SearchAnnotationSetsResponse (Maybe Text) Source #
The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there aren't any additional results.
sasrAnnotationSets :: Lens' SearchAnnotationSetsResponse [AnnotationSet] Source #
The matching annotation sets.
CallSetInfo
data CallSetInfo Source #
A map of additional call set information. This must be of the form map (string key mapping to a list of string values).
See: callSetInfo
smart constructor.
Creates a value of CallSetInfo
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
csiAddtional :: Lens' CallSetInfo (HashMap Text [JSONValue]) Source #
VariantSetMetadataInfo
data VariantSetMetadataInfo Source #
Remaining structured metadata key-value pairs. This must be of the form map (string key mapping to a list of string values).
See: variantSetMetadataInfo
smart constructor.
variantSetMetadataInfo Source #
Creates a value of VariantSetMetadataInfo
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
OperationResponse
data OperationResponse Source #
If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If importing Variants, an ImportVariantsResponse is returned. For pipelines and exports, an empty response is returned.
See: operationResponse
smart constructor.
Creates a value of OperationResponse
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
orAddtional :: Lens' OperationResponse (HashMap Text JSONValue) Source #
Properties of the object. Contains field 'type with type URL.
Transcript
data Transcript Source #
A transcript represents the assertion that a particular region of the reference genome may be transcribed as RNA.
See: transcript
smart constructor.
transcript :: Transcript Source #
Creates a value of Transcript
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
tGeneId :: Lens' Transcript (Maybe Text) Source #
The annotation ID of the gene from which this transcript is transcribed.
tCodingSequence :: Lens' Transcript (Maybe CodingSequence) Source #
The range of the coding sequence for this transcript, if any. To determine the exact ranges of coding sequence, intersect this range with those of the exons, if any. If there are any exons, the codingSequence must start and end within them. Note that in some cases, the reference genome will not exactly match the observed mRNA transcript e.g. due to variance in the source genome from reference. In these cases, exon.frame will not necessarily match the expected reference reading frame and coding exon reference bases cannot necessarily be concatenated to produce the original transcript mRNA.
tExons :: Lens' Transcript [Exon] Source #
The exons that compose this transcript. This field should be unset for genomes where transcript splicing does not occur, for example prokaryotes. Introns are regions of the transcript that are not included in the spliced RNA product. Though not explicitly modeled here, intron ranges can be deduced; all regions of this transcript that are not exons are introns. Exonic sequences do not necessarily code for a translational product (amino acids). Only the regions of exons bounded by the codingSequence correspond to coding DNA sequence. Exons are ordered by start position and may not overlap.
OperationEvent
data OperationEvent Source #
An event that occurred during an Operation.
See: operationEvent
smart constructor.
operationEvent :: OperationEvent Source #
Creates a value of OperationEvent
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
oeStartTime :: Lens' OperationEvent (Maybe UTCTime) Source #
Optional time of when event started.
oeEndTime :: Lens' OperationEvent (Maybe UTCTime) Source #
Optional time of when event finished. An event can have a start time and no finish time. If an event has a finish time, there must be a start time.
oeDescription :: Lens' OperationEvent (Maybe Text) Source #
Required description of event.
ReferenceBound
data ReferenceBound Source #
ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
See: referenceBound
smart constructor.
referenceBound :: ReferenceBound Source #
Creates a value of ReferenceBound
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
rbUpperBound :: Lens' ReferenceBound (Maybe Int64) Source #
An upper bound (inclusive) on the starting coordinate of any variant in the reference sequence.
rbReferenceName :: Lens' ReferenceBound (Maybe Text) Source #
The name of the reference associated with this reference bound.
UndeleteDataSetRequest
undeleteDataSetRequest :: UndeleteDataSetRequest Source #
Creates a value of UndeleteDataSetRequest
with the minimum fields required to make a request.
Binding
Associates `members` with a `role`.
See: binding
smart constructor.
bMembers :: Lens' Binding [Text] Source #
Specifies the identities requesting access for a Cloud Platform resource. `members` can have the following values: * `allUsers`: A special identifier that represents anyone who is on the internet; with or without a Google account. * `allAuthenticatedUsers`: A special identifier that represents anyone who is authenticated with a Google account or a service account. * `user:{emailid}`: An email address that represents a specific Google account. For example, `alice'gmail.com` or `joe'example.com`. * `serviceAccount:{emailid}`: An email address that represents a service account. For example, `my-other-app'appspot.gserviceaccount.com`. * `group:{emailid}`: An email address that represents a Google group. For example, `admins'example.com`. * `domain:{domain}`: A Google Apps domain name that represents all the users of that domain. For example, `google.com` or `example.com`.
bRole :: Lens' Binding (Maybe Text) Source #
Role that is assigned to `members`. For example, `roles/viewer`, `roles/editor`, or `roles/owner`. Required
Position
An abstraction for referring to a genomic position, in relation to some already known reference. For now, represents a genomic position as a reference name, a base number on that reference (0-based), and a determination of forward or reverse strand.
See: position
smart constructor.
Creates a value of Position
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
pReverseStrand :: Lens' Position (Maybe Bool) Source #
Whether this position is on the reverse strand, as opposed to the forward strand.
pReferenceName :: Lens' Position (Maybe Text) Source #
The name of the reference in whatever reference set is being used.
pPosition :: Lens' Position (Maybe Int64) Source #
The 0-based offset from the start of the forward strand for that reference.
RuntimeMetadata
data RuntimeMetadata Source #
Runtime metadata that will be populated in the runtimeMetadata field of the Operation associated with a RunPipeline execution.
See: runtimeMetadata
smart constructor.
runtimeMetadata :: RuntimeMetadata Source #
Creates a value of RuntimeMetadata
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
rmComputeEngine :: Lens' RuntimeMetadata (Maybe ComputeEngine) Source #
Execution information specific to Google Compute Engine.
SearchReadGroupSetsResponse
data SearchReadGroupSetsResponse Source #
The read group set search response.
See: searchReadGroupSetsResponse
smart constructor.
searchReadGroupSetsResponse :: SearchReadGroupSetsResponse Source #
Creates a value of SearchReadGroupSetsResponse
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
srgsrNextPageToken :: Lens' SearchReadGroupSetsResponse (Maybe Text) Source #
The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there aren't any additional results.
srgsrReadGroupSets :: Lens' SearchReadGroupSetsResponse [ReadGroupSet] Source #
The list of matching read group sets.
ReadGroupSetInfo
data ReadGroupSetInfo Source #
A map of additional read group set information.
See: readGroupSetInfo
smart constructor.
Creates a value of ReadGroupSetInfo
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
ReferenceSet
data ReferenceSet Source #
A reference set is a set of references which typically comprise a reference assembly for a species, such as `GRCh38` which is representative of the human genome. A reference set defines a common coordinate space for comparing reference-aligned experimental data. A reference set contains 1 or more references. For more genomics resource definitions, see Fundamentals of Google Genomics
See: referenceSet
smart constructor.
referenceSet :: ReferenceSet Source #
Creates a value of ReferenceSet
with the minimum fields required to make a request.
Use one of the following lenses to modify other fields as desired:
rsSourceAccessions :: Lens' ReferenceSet [Text] Source #
All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, for example `NC_000001.11`.
rsReferenceIds :: Lens' ReferenceSet [Text] Source #
The IDs of the reference objects that are part of this set. `Reference.md5checksum` must be unique within this set.
rsMD5checksum :: Lens' ReferenceSet (Maybe Text) Source #
Order-independent MD5 checksum which identifies this reference set. The checksum is computed by sorting all lower case hexidecimal string `reference.md5checksum` (for all reference in this set) in ascending lexicographic order, concatenating, and taking the MD5 of that value. The resulting value is represented in lower case hexadecimal format.
rsNcbiTaxonId :: Lens' ReferenceSet (Maybe Int32) Source #
ID from http://www.ncbi.nlm.nih.gov/taxonomy (for example, 9606 for human) indicating the species which this reference set is intended to model. Note that contained references may specify a different `ncbiTaxonId`, as assemblies may contain reference sequences which do not belong to the modeled species, for example EBV in a human reference genome.
rsId :: Lens' ReferenceSet (Maybe Text) Source #
The server-generated reference set ID, unique across all reference sets.
rsAssemblyId :: Lens' ReferenceSet (Maybe Text) Source #
Public id of this reference set, such as `GRCh37`.
rsSourceURI :: Lens' ReferenceSet (Maybe Text) Source #
The URI from which the references were obtained.
rsDescription :: Lens' ReferenceSet (Maybe Text) Source #
Free text description of this reference set.