{-# LANGUAGE DataKinds #-} {-# LANGUAGE NoImplicitPrelude #-} {-# LANGUAGE TypeOperators #-} {-# OPTIONS_GHC -fno-warn-unused-imports #-} {-# OPTIONS_GHC -fno-warn-duplicate-exports #-} -- | -- Module : Network.Google.Genomics -- Copyright : (c) 2015-2016 Brendan Hay -- License : Mozilla Public License, v. 2.0. -- Maintainer : Brendan Hay -- Stability : auto-generated -- Portability : non-portable (GHC extensions) -- -- Upload, process, query, and search Genomics data in the cloud. -- -- /See:/ module Network.Google.Genomics ( -- * Service Configuration genomicsService -- * OAuth Scopes , genomicsScope , cloudPlatformScope , genomicsReadOnlyScope , storageReadWriteScope , bigQueryScope -- * API Declaration , GenomicsAPI -- * Resources -- ** genomics.annotations.batchCreate , module Network.Google.Resource.Genomics.Annotations.BatchCreate -- ** genomics.annotations.create , module Network.Google.Resource.Genomics.Annotations.Create -- ** genomics.annotations.delete , module Network.Google.Resource.Genomics.Annotations.Delete -- ** genomics.annotations.get , module Network.Google.Resource.Genomics.Annotations.Get -- ** genomics.annotations.search , module Network.Google.Resource.Genomics.Annotations.Search -- ** genomics.annotations.update , module Network.Google.Resource.Genomics.Annotations.Update -- ** genomics.annotationsets.create , module Network.Google.Resource.Genomics.AnnotationSets.Create -- ** genomics.annotationsets.delete , module Network.Google.Resource.Genomics.AnnotationSets.Delete -- ** genomics.annotationsets.get , module Network.Google.Resource.Genomics.AnnotationSets.Get -- ** genomics.annotationsets.search , module Network.Google.Resource.Genomics.AnnotationSets.Search -- ** genomics.annotationsets.update , module Network.Google.Resource.Genomics.AnnotationSets.Update -- ** genomics.callsets.create , module Network.Google.Resource.Genomics.CallSets.Create -- ** genomics.callsets.delete , module Network.Google.Resource.Genomics.CallSets.Delete -- ** genomics.callsets.get , module Network.Google.Resource.Genomics.CallSets.Get -- ** genomics.callsets.patch , module Network.Google.Resource.Genomics.CallSets.Patch -- ** genomics.callsets.search , module Network.Google.Resource.Genomics.CallSets.Search -- ** genomics.datasets.create , module Network.Google.Resource.Genomics.DataSets.Create -- ** genomics.datasets.delete , module Network.Google.Resource.Genomics.DataSets.Delete -- ** genomics.datasets.get , module Network.Google.Resource.Genomics.DataSets.Get -- ** genomics.datasets.getIamPolicy , module Network.Google.Resource.Genomics.DataSets.GetIAMPolicy -- ** genomics.datasets.list , module Network.Google.Resource.Genomics.DataSets.List -- ** genomics.datasets.patch , module Network.Google.Resource.Genomics.DataSets.Patch -- ** genomics.datasets.setIamPolicy , module Network.Google.Resource.Genomics.DataSets.SetIAMPolicy -- ** genomics.datasets.testIamPermissions , module Network.Google.Resource.Genomics.DataSets.TestIAMPermissions -- ** genomics.datasets.undelete , module Network.Google.Resource.Genomics.DataSets.Undelete -- ** genomics.operations.cancel , module Network.Google.Resource.Genomics.Operations.Cancel -- ** genomics.operations.get , module Network.Google.Resource.Genomics.Operations.Get -- ** genomics.operations.list , module Network.Google.Resource.Genomics.Operations.List -- ** genomics.readgroupsets.coveragebuckets.list , module Network.Google.Resource.Genomics.ReadGroupSets.CoverageBuckets.List -- ** genomics.readgroupsets.delete , module Network.Google.Resource.Genomics.ReadGroupSets.Delete -- ** genomics.readgroupsets.export , module Network.Google.Resource.Genomics.ReadGroupSets.Export -- ** genomics.readgroupsets.get , module Network.Google.Resource.Genomics.ReadGroupSets.Get -- ** genomics.readgroupsets.import , module Network.Google.Resource.Genomics.ReadGroupSets.Import -- ** genomics.readgroupsets.patch , module Network.Google.Resource.Genomics.ReadGroupSets.Patch -- ** genomics.readgroupsets.search , module Network.Google.Resource.Genomics.ReadGroupSets.Search -- ** genomics.reads.search , module Network.Google.Resource.Genomics.Reads.Search -- ** genomics.references.bases.list , module Network.Google.Resource.Genomics.References.Bases.List -- ** genomics.references.get , module Network.Google.Resource.Genomics.References.Get -- ** genomics.references.search , module Network.Google.Resource.Genomics.References.Search -- ** genomics.referencesets.get , module Network.Google.Resource.Genomics.Referencesets.Get -- ** genomics.referencesets.search , module Network.Google.Resource.Genomics.Referencesets.Search -- ** genomics.variants.create , module Network.Google.Resource.Genomics.Variants.Create -- ** genomics.variants.delete , module Network.Google.Resource.Genomics.Variants.Delete -- ** genomics.variants.get , module Network.Google.Resource.Genomics.Variants.Get -- ** genomics.variants.import , module Network.Google.Resource.Genomics.Variants.Import -- ** genomics.variants.merge , module Network.Google.Resource.Genomics.Variants.Merge -- ** genomics.variants.patch , module Network.Google.Resource.Genomics.Variants.Patch -- ** genomics.variants.search , module Network.Google.Resource.Genomics.Variants.Search -- ** genomics.variantsets.create , module Network.Google.Resource.Genomics.VariantSets.Create -- ** genomics.variantsets.delete , module Network.Google.Resource.Genomics.VariantSets.Delete -- ** genomics.variantsets.export , module Network.Google.Resource.Genomics.VariantSets.Export -- ** genomics.variantsets.get , module Network.Google.Resource.Genomics.VariantSets.Get -- ** genomics.variantsets.patch , module Network.Google.Resource.Genomics.VariantSets.Patch -- ** genomics.variantsets.search , module Network.Google.Resource.Genomics.VariantSets.Search -- * Types -- ** ImportVariantsRequestInfoMergeConfig , ImportVariantsRequestInfoMergeConfig , importVariantsRequestInfoMergeConfig , ivrimcAddtional -- ** ReadInfo , ReadInfo , readInfo , riAddtional -- ** Exon , Exon , exon , eStart , eEnd , eFrame -- ** Status , Status , status , sDetails , sCode , sMessage -- ** OperationSchema , OperationSchema , operationSchema , osAddtional -- ** VariantAnnotationEffect , VariantAnnotationEffect (..) -- ** Variant , Variant , variant , vVariantSetId , vCreated , vStart , vAlternateBases , vReferenceName , vNames , vEnd , vReferenceBases , vId , vQuality , vFilter , vInfo , vCalls -- ** Annotation , Annotation , annotation , aVariant , aAnnotationSetId , aStart , aReverseStrand , aReferenceId , aReferenceName , aName , aEnd , aId , aType , aTranscript , aInfo -- ** ListBasesResponse , ListBasesResponse , listBasesResponse , lbrNextPageToken , lbrOffSet , lbrSequence -- ** ListOperationsResponse , ListOperationsResponse , listOperationsResponse , lorNextPageToken , lorOperations -- ** GetIAMPolicyRequest , GetIAMPolicyRequest , getIAMPolicyRequest -- ** CancelOperationRequest , CancelOperationRequest , cancelOperationRequest -- ** DataSet , DataSet , dataSet , dsName , dsId , dsProjectId , dsCreateTime -- ** Read' , Read' , read' , rFragmentLength , rDuplicateFragment , rReadGroupSetId , rNextMatePosition , rFailedVendorQualityChecks , rAlignment , rFragmentName , rNumberReads , rId , rSecondaryAlignment , rReadGroupId , rSupplementaryAlignment , rAlignedSequence , rProperPlacement , rInfo , rReadNumber , rAlignedQuality -- ** OperationMetadataLabels , OperationMetadataLabels , operationMetadataLabels , omlAddtional -- ** VariantCall , VariantCall , variantCall , vcGenotypeLikelihood , vcCallSetName , vcPhaseset , vcCallSetId , vcGenotype , vcInfo -- ** BatchCreateAnnotationsRequest , BatchCreateAnnotationsRequest , batchCreateAnnotationsRequest , bcarAnnotations , bcarRequestId -- ** MergeVariantsRequest , MergeVariantsRequest , mergeVariantsRequest , mvrVariants , mvrVariantSetId , mvrInfoMergeConfig -- ** ReadGroup , ReadGroup , readGroup , reaReferenceSetId , reaPrograms , reaExperiment , reaName , reaDataSetId , reaId , reaSampleId , reaPredictedInsertSize , reaDescription , reaInfo -- ** Operation , Operation , operation , oDone , oError , oResponse , oName , oMetadata -- ** SearchReferenceSetsRequest , SearchReferenceSetsRequest , searchReferenceSetsRequest , srsrMD5checksums , srsrAccessions , srsrPageToken , srsrAssemblyId , srsrPageSize -- ** Empty , Empty , empty -- ** AnnotationSetType , AnnotationSetType (..) -- ** SearchReferencesResponse , SearchReferencesResponse , searchReferencesResponse , srrNextPageToken , srrReferences -- ** VariantSetMetadata , VariantSetMetadata , variantSetMetadata , vsmValue , vsmKey , vsmId , vsmType , vsmNumber , vsmDescription , vsmInfo -- ** CallSet , CallSet , callSet , csCreated , csName , csId , csSampleId , csVariantSetIds , csInfo -- ** CoverageBucket , CoverageBucket , coverageBucket , cbRange , cbMeanCoverage -- ** VariantAnnotation , VariantAnnotation , variantAnnotation , vaEffect , vaClinicalSignificance , vaAlternateBases , vaGeneId , vaConditions , vaType , vaTranscriptIds -- ** VariantAnnotationClinicalSignificance , VariantAnnotationClinicalSignificance (..) -- ** SearchReadGroupSetsRequest , SearchReadGroupSetsRequest , searchReadGroupSetsRequest , srgsrDataSetIds , srgsrName , srgsrPageToken , srgsrPageSize -- ** Reference , Reference , reference , refLength , refSourceAccessions , refMD5checksum , refName , refNcbiTaxonId , refId , refSourceURI -- ** VariantCallInfo , VariantCallInfo , variantCallInfo , vciAddtional -- ** ReadGroupInfo , ReadGroupInfo , readGroupInfo , rgiAddtional -- ** StatusDetailsItem , StatusDetailsItem , statusDetailsItem , sdiAddtional -- ** SearchCallSetsResponse , SearchCallSetsResponse , searchCallSetsResponse , scsrNextPageToken , scsrCallSets -- ** SetIAMPolicyRequest , SetIAMPolicyRequest , setIAMPolicyRequest , siprPolicy -- ** SearchReadsRequest , SearchReadsRequest , searchReadsRequest , srrStart , srrReadGroupIds , srrReferenceName , srrEnd , srrPageToken , srrPageSize , srrReadGroupSetIds -- ** OperationMetadataRequest , OperationMetadataRequest , operationMetadataRequest , omrAddtional -- ** MergeVariantsRequestInfoMergeConfig , MergeVariantsRequestInfoMergeConfig , mergeVariantsRequestInfoMergeConfig , mvrimcAddtional -- ** VariantInfo , VariantInfo , variantInfo , viAddtional -- ** Experiment , Experiment , experiment , eInstrumentModel , ePlatformUnit , eSequencingCenter , eLibraryId -- ** SearchVariantSetsRequest , SearchVariantSetsRequest , searchVariantSetsRequest , svsrDataSetIds , svsrPageToken , svsrPageSize -- ** AnnotationInfo , AnnotationInfo , annotationInfo , aiAddtional -- ** SearchAnnotationsResponse , SearchAnnotationsResponse , searchAnnotationsResponse , sarAnnotations , sarNextPageToken -- ** SearchAnnotationSetsRequest , SearchAnnotationSetsRequest , searchAnnotationSetsRequest , sasrReferenceSetId , sasrTypes , sasrDataSetIds , sasrName , sasrPageToken , sasrPageSize -- ** ImportReadGroupSetsRequestPartitionStrategy , ImportReadGroupSetsRequestPartitionStrategy (..) -- ** SearchVariantsResponse , SearchVariantsResponse , searchVariantsResponse , svrVariants , svrNextPageToken -- ** OperationMetadataRuntimeMetadata , OperationMetadataRuntimeMetadata , operationMetadataRuntimeMetadata , omrmAddtional -- ** ClinicalCondition , ClinicalCondition , clinicalCondition , ccExternalIds , ccNames , ccConceptId , ccOmimId -- ** SearchCallSetsRequest , SearchCallSetsRequest , searchCallSetsRequest , scsrName , scsrPageToken , scsrVariantSetIds , scsrPageSize -- ** Entry , Entry , entry , eStatus , eAnnotation -- ** SearchReadsResponse , SearchReadsResponse , searchReadsResponse , sNextPageToken , sAlignments -- ** Program , Program , program , pPrevProgramId , pName , pVersion , pId , pCommandLine -- ** SearchReferencesRequest , SearchReferencesRequest , searchReferencesRequest , sReferenceSetId , sMD5checksums , sAccessions , sPageToken , sPageSize -- ** BatchCreateAnnotationsResponse , BatchCreateAnnotationsResponse , batchCreateAnnotationsResponse , bcarEntries -- ** CodingSequence , CodingSequence , codingSequence , csStart , csEnd -- ** AnnotationType , AnnotationType (..) -- ** SearchReferenceSetsResponse , SearchReferenceSetsResponse , searchReferenceSetsResponse , srsrNextPageToken , srsrReferenceSets -- ** Range , Range , range , rStart , rReferenceName , rEnd -- ** ReadGroupSet , ReadGroupSet , readGroupSet , rgsReferenceSetId , rgsName , rgsDataSetId , rgsId , rgsInfo , rgsReadGroups , rgsFilename -- ** Xgafv , Xgafv (..) -- ** ExportReadGroupSetRequest , ExportReadGroupSetRequest , exportReadGroupSetRequest , ergsrReferenceNames , ergsrExportURI , ergsrProjectId -- ** ImportVariantsResponse , ImportVariantsResponse , importVariantsResponse , ivrCallSetIds -- ** ListCoverageBucketsResponse , ListCoverageBucketsResponse , listCoverageBucketsResponse , lcbrNextPageToken , lcbrBucketWidth , lcbrCoverageBuckets -- ** TestIAMPermissionsRequest , TestIAMPermissionsRequest , testIAMPermissionsRequest , tiprPermissions -- ** ImportReadGroupSetsResponse , ImportReadGroupSetsResponse , importReadGroupSetsResponse , irgsrReadGroupSetIds -- ** LinearAlignment , LinearAlignment , linearAlignment , laCigar , laMAppingQuality , laPosition -- ** AnnotationSet , AnnotationSet , annotationSet , asReferenceSetId , asName , asDataSetId , asId , asType , asSourceURI , asInfo -- ** VariantSet , VariantSet , variantSet , vsReferenceSetId , vsName , vsDataSetId , vsReferenceBounds , vsMetadata , vsId , vsDescription -- ** CigarUnitOperation , CigarUnitOperation (..) -- ** VariantSetMetadataType , VariantSetMetadataType (..) -- ** TestIAMPermissionsResponse , TestIAMPermissionsResponse , testIAMPermissionsResponse , tiamprPermissions -- ** ListDataSetsResponse , ListDataSetsResponse , listDataSetsResponse , ldsrNextPageToken , ldsrDataSets -- ** ImportReadGroupSetsRequest , ImportReadGroupSetsRequest , importReadGroupSetsRequest , irgsrReferenceSetId , irgsrDataSetId , irgsrSourceURIs , irgsrPartitionStrategy -- ** ImportVariantsRequest , ImportVariantsRequest , importVariantsRequest , ivrVariantSetId , ivrFormat , ivrInfoMergeConfig , ivrNormalizeReferenceNames , ivrSourceURIs -- ** ExternalId , ExternalId , externalId , eiSourceName , eiId -- ** CigarUnit , CigarUnit , cigarUnit , cuOperation , cuOperationLength , cuReferenceSequence -- ** Policy , Policy , policy , polEtag , polVersion , polBindings -- ** ExportVariantSetRequest , ExportVariantSetRequest , exportVariantSetRequest , evsrBigQueryDataSet , evsrBigQueryTable , evsrFormat , evsrCallSetIds , evsrProjectId -- ** VariantAnnotationType , VariantAnnotationType (..) -- ** OperationMetadata , OperationMetadata , operationMetadata , omClientId , omStartTime , omEvents , omEndTime , omLabels , omProjectId , omCreateTime , omRuntimeMetadata , omRequest -- ** ImportVariantsRequestFormat , ImportVariantsRequestFormat (..) -- ** SearchAnnotationsRequest , SearchAnnotationsRequest , searchAnnotationsRequest , sarStart , sarReferenceId , sarReferenceName , sarEnd , sarPageToken , sarAnnotationSetIds , sarPageSize -- ** SearchVariantSetsResponse , SearchVariantSetsResponse , searchVariantSetsResponse , svsrNextPageToken , svsrVariantSets -- ** SearchVariantsRequest , SearchVariantsRequest , searchVariantsRequest , svrStart , svrCallSetIds , svrReferenceName , svrEnd , svrMaxCalls , svrPageToken , svrVariantName , svrVariantSetIds , svrPageSize -- ** ExportVariantSetRequestFormat , ExportVariantSetRequestFormat (..) -- ** AnnotationSetInfo , AnnotationSetInfo , annotationSetInfo , asiAddtional -- ** ComputeEngine , ComputeEngine , computeEngine , ceZone , ceDiskNames , ceMachineType , ceInstanceName -- ** SearchAnnotationSetsResponse , SearchAnnotationSetsResponse , searchAnnotationSetsResponse , sasrNextPageToken , sasrAnnotationSets -- ** CallSetInfo , CallSetInfo , callSetInfo , csiAddtional -- ** VariantSetMetadataInfo , VariantSetMetadataInfo , variantSetMetadataInfo , vsmiAddtional -- ** OperationResponse , OperationResponse , operationResponse , orAddtional -- ** Transcript , Transcript , transcript , tGeneId , tCodingSequence , tExons -- ** OperationEvent , OperationEvent , operationEvent , oeStartTime , oeEndTime , oeDescription -- ** ReferenceBound , ReferenceBound , referenceBound , rbUpperBound , rbReferenceName -- ** UndeleteDataSetRequest , UndeleteDataSetRequest , undeleteDataSetRequest -- ** Binding , Binding , binding , bMembers , bRole -- ** Position , Position , position , pReverseStrand , pReferenceName , pPosition -- ** RuntimeMetadata , RuntimeMetadata , runtimeMetadata , rmComputeEngine -- ** SearchReadGroupSetsResponse , SearchReadGroupSetsResponse , searchReadGroupSetsResponse , srgsrNextPageToken , srgsrReadGroupSets -- ** ReadGroupSetInfo , ReadGroupSetInfo , readGroupSetInfo , rgsiAddtional -- ** ReferenceSet , ReferenceSet , referenceSet , rsSourceAccessions , rsReferenceIds , rsMD5checksum , rsNcbiTaxonId , rsId , rsAssemblyId , rsSourceURI , rsDescription ) where import Network.Google.Genomics.Types import Network.Google.Prelude import Network.Google.Resource.Genomics.Annotations.BatchCreate import Network.Google.Resource.Genomics.Annotations.Create import Network.Google.Resource.Genomics.Annotations.Delete import Network.Google.Resource.Genomics.Annotations.Get import Network.Google.Resource.Genomics.Annotations.Search import Network.Google.Resource.Genomics.Annotations.Update import Network.Google.Resource.Genomics.AnnotationSets.Create import Network.Google.Resource.Genomics.AnnotationSets.Delete import Network.Google.Resource.Genomics.AnnotationSets.Get import Network.Google.Resource.Genomics.AnnotationSets.Search import Network.Google.Resource.Genomics.AnnotationSets.Update import Network.Google.Resource.Genomics.CallSets.Create import Network.Google.Resource.Genomics.CallSets.Delete import Network.Google.Resource.Genomics.CallSets.Get import Network.Google.Resource.Genomics.CallSets.Patch import Network.Google.Resource.Genomics.CallSets.Search import Network.Google.Resource.Genomics.DataSets.Create import Network.Google.Resource.Genomics.DataSets.Delete import Network.Google.Resource.Genomics.DataSets.Get import Network.Google.Resource.Genomics.DataSets.GetIAMPolicy import Network.Google.Resource.Genomics.DataSets.List import Network.Google.Resource.Genomics.DataSets.Patch import Network.Google.Resource.Genomics.DataSets.SetIAMPolicy import Network.Google.Resource.Genomics.DataSets.TestIAMPermissions import Network.Google.Resource.Genomics.DataSets.Undelete import Network.Google.Resource.Genomics.Operations.Cancel import Network.Google.Resource.Genomics.Operations.Get import Network.Google.Resource.Genomics.Operations.List import Network.Google.Resource.Genomics.ReadGroupSets.CoverageBuckets.List import Network.Google.Resource.Genomics.ReadGroupSets.Delete import Network.Google.Resource.Genomics.ReadGroupSets.Export import Network.Google.Resource.Genomics.ReadGroupSets.Get import Network.Google.Resource.Genomics.ReadGroupSets.Import import Network.Google.Resource.Genomics.ReadGroupSets.Patch import Network.Google.Resource.Genomics.ReadGroupSets.Search import Network.Google.Resource.Genomics.Reads.Search import Network.Google.Resource.Genomics.References.Bases.List import Network.Google.Resource.Genomics.References.Get import Network.Google.Resource.Genomics.References.Search import Network.Google.Resource.Genomics.Referencesets.Get import Network.Google.Resource.Genomics.Referencesets.Search import Network.Google.Resource.Genomics.Variants.Create import Network.Google.Resource.Genomics.Variants.Delete import Network.Google.Resource.Genomics.Variants.Get import Network.Google.Resource.Genomics.Variants.Import import Network.Google.Resource.Genomics.Variants.Merge import Network.Google.Resource.Genomics.Variants.Patch import Network.Google.Resource.Genomics.Variants.Search import Network.Google.Resource.Genomics.VariantSets.Create import Network.Google.Resource.Genomics.VariantSets.Delete import Network.Google.Resource.Genomics.VariantSets.Export import Network.Google.Resource.Genomics.VariantSets.Get import Network.Google.Resource.Genomics.VariantSets.Patch import Network.Google.Resource.Genomics.VariantSets.Search {- $resources TODO -} -- | Represents the entirety of the methods and resources available for the Genomics API service. 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