| Index: generated/googleapis/lib/genomics/v1.dart
|
| diff --git a/generated/googleapis/lib/genomics/v1.dart b/generated/googleapis/lib/genomics/v1.dart
|
| index 20900ef9b01cbbc3e6a445ca79c5bd5a0d22a8b1..771db62e562aa2c661463f4be7f5a20dd5010cbc 100644
|
| --- a/generated/googleapis/lib/genomics/v1.dart
|
| +++ b/generated/googleapis/lib/genomics/v1.dart
|
| @@ -9,83 +9,90 @@ import 'dart:convert' as convert;
|
| import 'package:_discoveryapis_commons/_discoveryapis_commons.dart' as commons;
|
| import 'package:http/http.dart' as http;
|
|
|
| -export 'package:_discoveryapis_commons/_discoveryapis_commons.dart' show
|
| - ApiRequestError, DetailedApiRequestError;
|
| +export 'package:_discoveryapis_commons/_discoveryapis_commons.dart'
|
| + show ApiRequestError, DetailedApiRequestError;
|
|
|
| const core.String USER_AGENT = 'dart-api-client genomics/v1';
|
|
|
| -/** Upload, process, query, and search Genomics data in the cloud. */
|
| +/// Upload, process, query, and search Genomics data in the cloud.
|
| class GenomicsApi {
|
| - /** View and manage your data in Google BigQuery */
|
| + /// View and manage your data in Google BigQuery
|
| static const BigqueryScope = "https://www.googleapis.com/auth/bigquery";
|
|
|
| - /** View and manage your data across Google Cloud Platform services */
|
| - static const CloudPlatformScope = "https://www.googleapis.com/auth/cloud-platform";
|
| + /// View and manage your data across Google Cloud Platform services
|
| + static const CloudPlatformScope =
|
| + "https://www.googleapis.com/auth/cloud-platform";
|
|
|
| - /** Manage your data in Google Cloud Storage */
|
| - static const DevstorageReadWriteScope = "https://www.googleapis.com/auth/devstorage.read_write";
|
| + /// Manage your data in Google Cloud Storage
|
| + static const DevstorageReadWriteScope =
|
| + "https://www.googleapis.com/auth/devstorage.read_write";
|
|
|
| - /** View and manage Genomics data */
|
| + /// View and manage Genomics data
|
| static const GenomicsScope = "https://www.googleapis.com/auth/genomics";
|
|
|
| - /** View Genomics data */
|
| - static const GenomicsReadonlyScope = "https://www.googleapis.com/auth/genomics.readonly";
|
| -
|
| + /// View Genomics data
|
| + static const GenomicsReadonlyScope =
|
| + "https://www.googleapis.com/auth/genomics.readonly";
|
|
|
| final commons.ApiRequester _requester;
|
|
|
| - AnnotationsResourceApi get annotations => new AnnotationsResourceApi(_requester);
|
| - AnnotationsetsResourceApi get annotationsets => new AnnotationsetsResourceApi(_requester);
|
| + AnnotationsResourceApi get annotations =>
|
| + new AnnotationsResourceApi(_requester);
|
| + AnnotationsetsResourceApi get annotationsets =>
|
| + new AnnotationsetsResourceApi(_requester);
|
| CallsetsResourceApi get callsets => new CallsetsResourceApi(_requester);
|
| DatasetsResourceApi get datasets => new DatasetsResourceApi(_requester);
|
| OperationsResourceApi get operations => new OperationsResourceApi(_requester);
|
| - ReadgroupsetsResourceApi get readgroupsets => new ReadgroupsetsResourceApi(_requester);
|
| + ReadgroupsetsResourceApi get readgroupsets =>
|
| + new ReadgroupsetsResourceApi(_requester);
|
| ReadsResourceApi get reads => new ReadsResourceApi(_requester);
|
| ReferencesResourceApi get references => new ReferencesResourceApi(_requester);
|
| - ReferencesetsResourceApi get referencesets => new ReferencesetsResourceApi(_requester);
|
| + ReferencesetsResourceApi get referencesets =>
|
| + new ReferencesetsResourceApi(_requester);
|
| VariantsResourceApi get variants => new VariantsResourceApi(_requester);
|
| - VariantsetsResourceApi get variantsets => new VariantsetsResourceApi(_requester);
|
| -
|
| - GenomicsApi(http.Client client, {core.String rootUrl: "https://genomics.googleapis.com/", core.String servicePath: ""}) :
|
| - _requester = new commons.ApiRequester(client, rootUrl, servicePath, USER_AGENT);
|
| + VariantsetsResourceApi get variantsets =>
|
| + new VariantsetsResourceApi(_requester);
|
| +
|
| + GenomicsApi(http.Client client,
|
| + {core.String rootUrl: "https://genomics.googleapis.com/",
|
| + core.String servicePath: ""})
|
| + : _requester =
|
| + new commons.ApiRequester(client, rootUrl, servicePath, USER_AGENT);
|
| }
|
|
|
| -
|
| class AnnotationsResourceApi {
|
| final commons.ApiRequester _requester;
|
|
|
| - AnnotationsResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Creates one or more new annotations atomically. All annotations must
|
| - * belong to the same annotation set. Caller must have WRITE
|
| - * permission for this annotation set. For optimal performance, batch
|
| - * positionally adjacent annotations together.
|
| - *
|
| - * If the request has a systemic issue, such as an attempt to write to
|
| - * an inaccessible annotation set, the entire RPC will fail accordingly. For
|
| - * lesser data issues, when possible an error will be isolated to the
|
| - * corresponding batch entry in the response; the remaining well formed
|
| - * annotations will be created normally.
|
| - *
|
| - * For details on the requirements for each individual annotation resource,
|
| - * see
|
| - * CreateAnnotation.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [BatchCreateAnnotationsResponse].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<BatchCreateAnnotationsResponse> batchCreate(BatchCreateAnnotationsRequest request) {
|
| + AnnotationsResourceApi(commons.ApiRequester client) : _requester = client;
|
| +
|
| + /// Creates one or more new annotations atomically. All annotations must
|
| + /// belong to the same annotation set. Caller must have WRITE
|
| + /// permission for this annotation set. For optimal performance, batch
|
| + /// positionally adjacent annotations together.
|
| + ///
|
| + /// If the request has a systemic issue, such as an attempt to write to
|
| + /// an inaccessible annotation set, the entire RPC will fail accordingly. For
|
| + /// lesser data issues, when possible an error will be isolated to the
|
| + /// corresponding batch entry in the response; the remaining well formed
|
| + /// annotations will be created normally.
|
| + ///
|
| + /// For details on the requirements for each individual annotation resource,
|
| + /// see
|
| + /// CreateAnnotation.
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// Completes with a [BatchCreateAnnotationsResponse].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| + async.Future<BatchCreateAnnotationsResponse> batchCreate(
|
| + BatchCreateAnnotationsRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -99,52 +106,50 @@ class AnnotationsResourceApi {
|
|
|
| _url = 'v1/annotations:batchCreate';
|
|
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new BatchCreateAnnotationsResponse.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Creates a new annotation. Caller must have WRITE permission
|
| - * for the associated annotation set.
|
| - *
|
| - * The following fields are required:
|
| - *
|
| - * * annotationSetId
|
| - * * referenceName or
|
| - * referenceId
|
| - *
|
| - * ### Transcripts
|
| - *
|
| - * For annotations of type TRANSCRIPT, the following fields of
|
| - * transcript must be provided:
|
| - *
|
| - * * exons.start
|
| - * * exons.end
|
| - *
|
| - * All other fields may be optionally specified, unless documented as being
|
| - * server-generated (for example, the `id` field). The annotated
|
| - * range must be no longer than 100Mbp (mega base pairs). See the
|
| - * Annotation resource
|
| - * for additional restrictions on each field.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [Annotation].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + var _response = _requester.request(_url, "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| + return _response
|
| + .then((data) => new BatchCreateAnnotationsResponse.fromJson(data));
|
| + }
|
| +
|
| + /// Creates a new annotation. Caller must have WRITE permission
|
| + /// for the associated annotation set.
|
| + ///
|
| + /// The following fields are required:
|
| + ///
|
| + /// * annotationSetId
|
| + /// * referenceName or
|
| + /// referenceId
|
| + ///
|
| + /// ### Transcripts
|
| + ///
|
| + /// For annotations of type TRANSCRIPT, the following fields of
|
| + /// transcript must be provided:
|
| + ///
|
| + /// * exons.start
|
| + /// * exons.end
|
| + ///
|
| + /// All other fields may be optionally specified, unless documented as being
|
| + /// server-generated (for example, the `id` field). The annotated
|
| + /// range must be no longer than 100Mbp (mega base pairs). See the
|
| + /// Annotation resource
|
| + /// for additional restrictions on each field.
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// Completes with a [Annotation].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<Annotation> create(Annotation request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -159,32 +164,29 @@ class AnnotationsResourceApi {
|
|
|
| _url = 'v1/annotations';
|
|
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new Annotation.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Deletes an annotation. Caller must have WRITE permission for
|
| - * the associated annotation set.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [annotationId] - The ID of the annotation to be deleted.
|
| - *
|
| - * Completes with a [Empty].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + /// Deletes an annotation. Caller must have WRITE permission for
|
| + /// the associated annotation set.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [annotationId] - The ID of the annotation to be deleted.
|
| + ///
|
| + /// Completes with a [Empty].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<Empty> delete(core.String annotationId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -199,32 +201,29 @@ class AnnotationsResourceApi {
|
|
|
| _url = 'v1/annotations/' + commons.Escaper.ecapeVariable('$annotationId');
|
|
|
| - var _response = _requester.request(_url,
|
| - "DELETE",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "DELETE",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new Empty.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Gets an annotation. Caller must have READ permission
|
| - * for the associated annotation set.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [annotationId] - The ID of the annotation to be retrieved.
|
| - *
|
| - * Completes with a [Annotation].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + /// Gets an annotation. Caller must have READ permission
|
| + /// for the associated annotation set.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [annotationId] - The ID of the annotation to be retrieved.
|
| + ///
|
| + /// Completes with a [Annotation].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<Annotation> get(core.String annotationId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -239,38 +238,38 @@ class AnnotationsResourceApi {
|
|
|
| _url = 'v1/annotations/' + commons.Escaper.ecapeVariable('$annotationId');
|
|
|
| - var _response = _requester.request(_url,
|
| - "GET",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "GET",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new Annotation.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Searches for annotations that match the given criteria. Results are
|
| - * ordered by genomic coordinate (by reference sequence, then position).
|
| - * Annotations with equivalent genomic coordinates are returned in an
|
| - * unspecified order. This order is consistent, such that two queries for the
|
| - * same content (regardless of page size) yield annotations in the same order
|
| - * across their respective streams of paginated responses. Caller must have
|
| - * READ permission for the queried annotation sets.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [SearchAnnotationsResponse].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<SearchAnnotationsResponse> search(SearchAnnotationsRequest request) {
|
| + /// Searches for annotations that match the given criteria. Results are
|
| + /// ordered by genomic coordinate (by reference sequence, then position).
|
| + /// Annotations with equivalent genomic coordinates are returned in an
|
| + /// unspecified order. This order is consistent, such that two queries for
|
| + /// the
|
| + /// same content (regardless of page size) yield annotations in the same
|
| + /// order
|
| + /// across their respective streams of paginated responses. Caller must have
|
| + /// READ permission for the queried annotation sets.
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// Completes with a [SearchAnnotationsResponse].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| + async.Future<SearchAnnotationsResponse> search(
|
| + SearchAnnotationsRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -284,43 +283,42 @@ class AnnotationsResourceApi {
|
|
|
| _url = 'v1/annotations/search';
|
|
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new SearchAnnotationsResponse.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Updates an annotation. Caller must have
|
| - * WRITE permission for the associated dataset.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [annotationId] - The ID of the annotation to be updated.
|
| - *
|
| - * [updateMask] - An optional mask specifying which fields to update. Mutable
|
| - * fields are
|
| - * name,
|
| - * variant,
|
| - * transcript, and
|
| - * info. If unspecified, all mutable
|
| - * fields will be updated.
|
| - *
|
| - * Completes with a [Annotation].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<Annotation> update(Annotation request, core.String annotationId, {core.String updateMask}) {
|
| + var _response = _requester.request(_url, "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| + return _response
|
| + .then((data) => new SearchAnnotationsResponse.fromJson(data));
|
| + }
|
| +
|
| + /// Updates an annotation. Caller must have
|
| + /// WRITE permission for the associated dataset.
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [annotationId] - The ID of the annotation to be updated.
|
| + ///
|
| + /// [updateMask] - An optional mask specifying which fields to update.
|
| + /// Mutable fields are
|
| + /// name,
|
| + /// variant,
|
| + /// transcript, and
|
| + /// info. If unspecified, all mutable
|
| + /// fields will be updated.
|
| + ///
|
| + /// Completes with a [Annotation].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| + async.Future<Annotation> update(Annotation request, core.String annotationId,
|
| + {core.String updateMask}) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -340,49 +338,43 @@ class AnnotationsResourceApi {
|
|
|
| _url = 'v1/annotations/' + commons.Escaper.ecapeVariable('$annotationId');
|
|
|
| - var _response = _requester.request(_url,
|
| - "PUT",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "PUT",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new Annotation.fromJson(data));
|
| }
|
| -
|
| }
|
|
|
| -
|
| class AnnotationsetsResourceApi {
|
| final commons.ApiRequester _requester;
|
|
|
| - AnnotationsetsResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Creates a new annotation set. Caller must have WRITE permission for the
|
| - * associated dataset.
|
| - *
|
| - * The following fields are required:
|
| - *
|
| - * * datasetId
|
| - * * referenceSetId
|
| - *
|
| - * All other fields may be optionally specified, unless documented as being
|
| - * server-generated (for example, the `id` field).
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [AnnotationSet].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + AnnotationsetsResourceApi(commons.ApiRequester client) : _requester = client;
|
| +
|
| + /// Creates a new annotation set. Caller must have WRITE permission for the
|
| + /// associated dataset.
|
| + ///
|
| + /// The following fields are required:
|
| + ///
|
| + /// * datasetId
|
| + /// * referenceSetId
|
| + ///
|
| + /// All other fields may be optionally specified, unless documented as being
|
| + /// server-generated (for example, the `id` field).
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// Completes with a [AnnotationSet].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<AnnotationSet> create(AnnotationSet request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -397,32 +389,29 @@ class AnnotationsetsResourceApi {
|
|
|
| _url = 'v1/annotationsets';
|
|
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new AnnotationSet.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Deletes an annotation set. Caller must have WRITE permission
|
| - * for the associated annotation set.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [annotationSetId] - The ID of the annotation set to be deleted.
|
| - *
|
| - * Completes with a [Empty].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + /// Deletes an annotation set. Caller must have WRITE permission
|
| + /// for the associated annotation set.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [annotationSetId] - The ID of the annotation set to be deleted.
|
| + ///
|
| + /// Completes with a [Empty].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<Empty> delete(core.String annotationSetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -435,34 +424,32 @@ class AnnotationsetsResourceApi {
|
| throw new core.ArgumentError("Parameter annotationSetId is required.");
|
| }
|
|
|
| - _url = 'v1/annotationsets/' + commons.Escaper.ecapeVariable('$annotationSetId');
|
| + _url = 'v1/annotationsets/' +
|
| + commons.Escaper.ecapeVariable('$annotationSetId');
|
|
|
| - var _response = _requester.request(_url,
|
| - "DELETE",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "DELETE",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new Empty.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Gets an annotation set. Caller must have READ permission for
|
| - * the associated dataset.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [annotationSetId] - The ID of the annotation set to be retrieved.
|
| - *
|
| - * Completes with a [AnnotationSet].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + /// Gets an annotation set. Caller must have READ permission for
|
| + /// the associated dataset.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [annotationSetId] - The ID of the annotation set to be retrieved.
|
| + ///
|
| + /// Completes with a [AnnotationSet].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<AnnotationSet> get(core.String annotationSetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -475,38 +462,39 @@ class AnnotationsetsResourceApi {
|
| throw new core.ArgumentError("Parameter annotationSetId is required.");
|
| }
|
|
|
| - _url = 'v1/annotationsets/' + commons.Escaper.ecapeVariable('$annotationSetId');
|
| + _url = 'v1/annotationsets/' +
|
| + commons.Escaper.ecapeVariable('$annotationSetId');
|
|
|
| - var _response = _requester.request(_url,
|
| - "GET",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "GET",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new AnnotationSet.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Searches for annotation sets that match the given criteria. Annotation sets
|
| - * are returned in an unspecified order. This order is consistent, such that
|
| - * two queries for the same content (regardless of page size) yield annotation
|
| - * sets in the same order across their respective streams of paginated
|
| - * responses. Caller must have READ permission for the queried datasets.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [SearchAnnotationSetsResponse].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<SearchAnnotationSetsResponse> search(SearchAnnotationSetsRequest request) {
|
| + /// Searches for annotation sets that match the given criteria. Annotation
|
| + /// sets
|
| + /// are returned in an unspecified order. This order is consistent, such that
|
| + /// two queries for the same content (regardless of page size) yield
|
| + /// annotation
|
| + /// sets in the same order across their respective streams of paginated
|
| + /// responses. Caller must have READ permission for the queried datasets.
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// Completes with a [SearchAnnotationSetsResponse].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| + async.Future<SearchAnnotationSetsResponse> search(
|
| + SearchAnnotationSetsRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -520,43 +508,44 @@ class AnnotationsetsResourceApi {
|
|
|
| _url = 'v1/annotationsets/search';
|
|
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new SearchAnnotationSetsResponse.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Updates an annotation set. The update must respect all mutability
|
| - * restrictions and other invariants described on the annotation set resource.
|
| - * Caller must have WRITE permission for the associated dataset.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [annotationSetId] - The ID of the annotation set to be updated.
|
| - *
|
| - * [updateMask] - An optional mask specifying which fields to update. Mutable
|
| - * fields are
|
| - * name,
|
| - * source_uri, and
|
| - * info. If unspecified, all
|
| - * mutable fields will be updated.
|
| - *
|
| - * Completes with a [AnnotationSet].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<AnnotationSet> update(AnnotationSet request, core.String annotationSetId, {core.String updateMask}) {
|
| + var _response = _requester.request(_url, "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| + return _response
|
| + .then((data) => new SearchAnnotationSetsResponse.fromJson(data));
|
| + }
|
| +
|
| + /// Updates an annotation set. The update must respect all mutability
|
| + /// restrictions and other invariants described on the annotation set
|
| + /// resource.
|
| + /// Caller must have WRITE permission for the associated dataset.
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [annotationSetId] - The ID of the annotation set to be updated.
|
| + ///
|
| + /// [updateMask] - An optional mask specifying which fields to update.
|
| + /// Mutable fields are
|
| + /// name,
|
| + /// source_uri, and
|
| + /// info. If unspecified, all
|
| + /// mutable fields will be updated.
|
| + ///
|
| + /// Completes with a [AnnotationSet].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| + async.Future<AnnotationSet> update(
|
| + AnnotationSet request, core.String annotationSetId,
|
| + {core.String updateMask}) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -574,46 +563,41 @@ class AnnotationsetsResourceApi {
|
| _queryParams["updateMask"] = [updateMask];
|
| }
|
|
|
| - _url = 'v1/annotationsets/' + commons.Escaper.ecapeVariable('$annotationSetId');
|
| + _url = 'v1/annotationsets/' +
|
| + commons.Escaper.ecapeVariable('$annotationSetId');
|
|
|
| - var _response = _requester.request(_url,
|
| - "PUT",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "PUT",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new AnnotationSet.fromJson(data));
|
| }
|
| -
|
| }
|
|
|
| -
|
| class CallsetsResourceApi {
|
| final commons.ApiRequester _requester;
|
|
|
| - CallsetsResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Creates a new call set.
|
| - *
|
| - * For the definitions of call sets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [CallSet].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + CallsetsResourceApi(commons.ApiRequester client) : _requester = client;
|
| +
|
| + /// Creates a new call set.
|
| + ///
|
| + /// For the definitions of call sets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// Completes with a [CallSet].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<CallSet> create(CallSet request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -628,35 +612,32 @@ class CallsetsResourceApi {
|
|
|
| _url = 'v1/callsets';
|
|
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new CallSet.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Deletes a call set.
|
| - *
|
| - * For the definitions of call sets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [callSetId] - The ID of the call set to be deleted.
|
| - *
|
| - * Completes with a [Empty].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + /// Deletes a call set.
|
| + ///
|
| + /// For the definitions of call sets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [callSetId] - The ID of the call set to be deleted.
|
| + ///
|
| + /// Completes with a [Empty].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<Empty> delete(core.String callSetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -671,35 +652,32 @@ class CallsetsResourceApi {
|
|
|
| _url = 'v1/callsets/' + commons.Escaper.ecapeVariable('$callSetId');
|
|
|
| - var _response = _requester.request(_url,
|
| - "DELETE",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "DELETE",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new Empty.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Gets a call set by ID.
|
| - *
|
| - * For the definitions of call sets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [callSetId] - The ID of the call set.
|
| - *
|
| - * Completes with a [CallSet].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + /// Gets a call set by ID.
|
| + ///
|
| + /// For the definitions of call sets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [callSetId] - The ID of the call set.
|
| + ///
|
| + /// Completes with a [CallSet].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<CallSet> get(core.String callSetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -714,46 +692,44 @@ class CallsetsResourceApi {
|
|
|
| _url = 'v1/callsets/' + commons.Escaper.ecapeVariable('$callSetId');
|
|
|
| - var _response = _requester.request(_url,
|
| - "GET",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "GET",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new CallSet.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Updates a call set.
|
| - *
|
| - * For the definitions of call sets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * This method supports patch semantics.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [callSetId] - The ID of the call set to be updated.
|
| - *
|
| - * [updateMask] - An optional mask specifying which fields to update. At this
|
| - * time, the only
|
| - * mutable field is name. The only
|
| - * acceptable value is "name". If unspecified, all mutable fields will be
|
| - * updated.
|
| - *
|
| - * Completes with a [CallSet].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<CallSet> patch(CallSet request, core.String callSetId, {core.String updateMask}) {
|
| + /// Updates a call set.
|
| + ///
|
| + /// For the definitions of call sets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// This method supports patch semantics.
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [callSetId] - The ID of the call set to be updated.
|
| + ///
|
| + /// [updateMask] - An optional mask specifying which fields to update. At
|
| + /// this time, the only
|
| + /// mutable field is name. The only
|
| + /// acceptable value is "name". If unspecified, all mutable fields will be
|
| + /// updated.
|
| + ///
|
| + /// Completes with a [CallSet].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| + async.Future<CallSet> patch(CallSet request, core.String callSetId,
|
| + {core.String updateMask}) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -773,38 +749,35 @@ class CallsetsResourceApi {
|
|
|
| _url = 'v1/callsets/' + commons.Escaper.ecapeVariable('$callSetId');
|
|
|
| - var _response = _requester.request(_url,
|
| - "PATCH",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "PATCH",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new CallSet.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Gets a list of call sets matching the criteria.
|
| - *
|
| - * For the definitions of call sets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * Implements
|
| - * [GlobalAllianceApi.searchCallSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L178).
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [SearchCallSetsResponse].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + /// Gets a list of call sets matching the criteria.
|
| + ///
|
| + /// For the definitions of call sets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// Implements
|
| + /// [GlobalAllianceApi.searchCallSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L178).
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// Completes with a [SearchCallSetsResponse].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<SearchCallSetsResponse> search(SearchCallSetsRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -819,44 +792,38 @@ class CallsetsResourceApi {
|
|
|
| _url = 'v1/callsets/search';
|
|
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new SearchCallSetsResponse.fromJson(data));
|
| }
|
| -
|
| }
|
|
|
| -
|
| class DatasetsResourceApi {
|
| final commons.ApiRequester _requester;
|
|
|
| - DatasetsResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Creates a new dataset.
|
| - *
|
| - * For the definitions of datasets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [Dataset].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + DatasetsResourceApi(commons.ApiRequester client) : _requester = client;
|
| +
|
| + /// Creates a new dataset.
|
| + ///
|
| + /// For the definitions of datasets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// Completes with a [Dataset].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<Dataset> create(Dataset request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -871,40 +838,37 @@ class DatasetsResourceApi {
|
|
|
| _url = 'v1/datasets';
|
|
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new Dataset.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Deletes a dataset and all of its contents (all read group sets,
|
| - * reference sets, variant sets, call sets, annotation sets, etc.)
|
| - * This is reversible (up to one week after the deletion) via
|
| - * the
|
| - * datasets.undelete
|
| - * operation.
|
| - *
|
| - * For the definitions of datasets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [datasetId] - The ID of the dataset to be deleted.
|
| - *
|
| - * Completes with a [Empty].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + /// Deletes a dataset and all of its contents (all read group sets,
|
| + /// reference sets, variant sets, call sets, annotation sets, etc.)
|
| + /// This is reversible (up to one week after the deletion) via
|
| + /// the
|
| + /// datasets.undelete
|
| + /// operation.
|
| + ///
|
| + /// For the definitions of datasets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [datasetId] - The ID of the dataset to be deleted.
|
| + ///
|
| + /// Completes with a [Empty].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<Empty> delete(core.String datasetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -919,35 +883,32 @@ class DatasetsResourceApi {
|
|
|
| _url = 'v1/datasets/' + commons.Escaper.ecapeVariable('$datasetId');
|
|
|
| - var _response = _requester.request(_url,
|
| - "DELETE",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "DELETE",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new Empty.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Gets a dataset by ID.
|
| - *
|
| - * For the definitions of datasets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [datasetId] - The ID of the dataset.
|
| - *
|
| - * Completes with a [Dataset].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + /// Gets a dataset by ID.
|
| + ///
|
| + /// For the definitions of datasets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [datasetId] - The ID of the dataset.
|
| + ///
|
| + /// Completes with a [Dataset].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<Dataset> get(core.String datasetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -962,45 +923,43 @@ class DatasetsResourceApi {
|
|
|
| _url = 'v1/datasets/' + commons.Escaper.ecapeVariable('$datasetId');
|
|
|
| - var _response = _requester.request(_url,
|
| - "GET",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "GET",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new Dataset.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Gets the access control policy for the dataset. This is empty if the
|
| - * policy or resource does not exist.
|
| - *
|
| - * See <a href="/iam/docs/managing-policies#getting_a_policy">Getting a
|
| - * Policy</a> for more information.
|
| - *
|
| - * For the definitions of datasets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [resource] - REQUIRED: The resource for which policy is being specified.
|
| - * Format is
|
| - * `datasets/<dataset ID>`.
|
| - * Value must have pattern "^datasets/[^/]+$".
|
| - *
|
| - * Completes with a [Policy].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<Policy> getIamPolicy(GetIamPolicyRequest request, core.String resource) {
|
| + /// Gets the access control policy for the dataset. This is empty if the
|
| + /// policy or resource does not exist.
|
| + ///
|
| + /// See <a href="/iam/docs/managing-policies#getting_a_policy">Getting a
|
| + /// Policy</a> for more information.
|
| + ///
|
| + /// For the definitions of datasets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [resource] - REQUIRED: The resource for which policy is being specified.
|
| + /// Format is
|
| + /// `datasets/<dataset ID>`.
|
| + /// Value must have pattern "^datasets/[^/]+$".
|
| + ///
|
| + /// Completes with a [Policy].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| + async.Future<Policy> getIamPolicy(
|
| + GetIamPolicyRequest request, core.String resource) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1015,47 +974,47 @@ class DatasetsResourceApi {
|
| throw new core.ArgumentError("Parameter resource is required.");
|
| }
|
|
|
| - _url = 'v1/' + commons.Escaper.ecapeVariableReserved('$resource') + ':getIamPolicy';
|
| + _url = 'v1/' +
|
| + commons.Escaper.ecapeVariableReserved('$resource') +
|
| + ':getIamPolicy';
|
|
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new Policy.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Lists datasets within a project.
|
| - *
|
| - * For the definitions of datasets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [projectId] - Required. The Google Cloud project ID to list datasets for.
|
| - *
|
| - * [pageToken] - 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.
|
| - *
|
| - * [pageSize] - The maximum number of results to return in a single page. If
|
| - * unspecified,
|
| - * defaults to 50. The maximum value is 1024.
|
| - *
|
| - * Completes with a [ListDatasetsResponse].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<ListDatasetsResponse> list({core.String projectId, core.String pageToken, core.int pageSize}) {
|
| + /// Lists datasets within a project.
|
| + ///
|
| + /// For the definitions of datasets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [pageToken] - 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.
|
| + ///
|
| + /// [pageSize] - The maximum number of results to return in a single page. If
|
| + /// unspecified,
|
| + /// defaults to 50. The maximum value is 1024.
|
| + ///
|
| + /// [projectId] - Required. The Google Cloud project ID to list datasets for.
|
| + ///
|
| + /// Completes with a [ListDatasetsResponse].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| + async.Future<ListDatasetsResponse> list(
|
| + {core.String pageToken, core.int pageSize, core.String projectId}) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1063,58 +1022,56 @@ class DatasetsResourceApi {
|
| var _downloadOptions = commons.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (projectId != null) {
|
| - _queryParams["projectId"] = [projectId];
|
| - }
|
| if (pageToken != null) {
|
| _queryParams["pageToken"] = [pageToken];
|
| }
|
| if (pageSize != null) {
|
| _queryParams["pageSize"] = ["${pageSize}"];
|
| }
|
| + if (projectId != null) {
|
| + _queryParams["projectId"] = [projectId];
|
| + }
|
|
|
| _url = 'v1/datasets';
|
|
|
| - var _response = _requester.request(_url,
|
| - "GET",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "GET",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new ListDatasetsResponse.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Updates a dataset.
|
| - *
|
| - * For the definitions of datasets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * This method supports patch semantics.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [datasetId] - The ID of the dataset to be updated.
|
| - *
|
| - * [updateMask] - An optional mask specifying which fields to update. At this
|
| - * time, the only
|
| - * mutable field is name. The only
|
| - * acceptable value is "name". If unspecified, all mutable fields will be
|
| - * updated.
|
| - *
|
| - * Completes with a [Dataset].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<Dataset> patch(Dataset request, core.String datasetId, {core.String updateMask}) {
|
| + /// Updates a dataset.
|
| + ///
|
| + /// For the definitions of datasets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// This method supports patch semantics.
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [datasetId] - The ID of the dataset to be updated.
|
| + ///
|
| + /// [updateMask] - An optional mask specifying which fields to update. At
|
| + /// this time, the only
|
| + /// mutable field is name. The only
|
| + /// acceptable value is "name". If unspecified, all mutable fields will be
|
| + /// updated.
|
| + ///
|
| + /// Completes with a [Dataset].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| + async.Future<Dataset> patch(Dataset request, core.String datasetId,
|
| + {core.String updateMask}) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1134,45 +1091,43 @@ class DatasetsResourceApi {
|
|
|
| _url = 'v1/datasets/' + commons.Escaper.ecapeVariable('$datasetId');
|
|
|
| - var _response = _requester.request(_url,
|
| - "PATCH",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "PATCH",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new Dataset.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Sets the access control policy on the specified dataset. Replaces any
|
| - * existing policy.
|
| - *
|
| - * For the definitions of datasets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * See <a href="/iam/docs/managing-policies#setting_a_policy">Setting a
|
| - * Policy</a> for more information.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [resource] - REQUIRED: The resource for which policy is being specified.
|
| - * Format is
|
| - * `datasets/<dataset ID>`.
|
| - * Value must have pattern "^datasets/[^/]+$".
|
| - *
|
| - * Completes with a [Policy].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<Policy> setIamPolicy(SetIamPolicyRequest request, core.String resource) {
|
| + /// Sets the access control policy on the specified dataset. Replaces any
|
| + /// existing policy.
|
| + ///
|
| + /// For the definitions of datasets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// See <a href="/iam/docs/managing-policies#setting_a_policy">Setting a
|
| + /// Policy</a> for more information.
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [resource] - REQUIRED: The resource for which policy is being specified.
|
| + /// Format is
|
| + /// `datasets/<dataset ID>`.
|
| + /// Value must have pattern "^datasets/[^/]+$".
|
| + ///
|
| + /// Completes with a [Policy].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| + async.Future<Policy> setIamPolicy(
|
| + SetIamPolicyRequest request, core.String resource) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1187,45 +1142,45 @@ class DatasetsResourceApi {
|
| throw new core.ArgumentError("Parameter resource is required.");
|
| }
|
|
|
| - _url = 'v1/' + commons.Escaper.ecapeVariableReserved('$resource') + ':setIamPolicy';
|
| + _url = 'v1/' +
|
| + commons.Escaper.ecapeVariableReserved('$resource') +
|
| + ':setIamPolicy';
|
|
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new Policy.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Returns permissions that a caller has on the specified resource.
|
| - * See <a href="/iam/docs/managing-policies#testing_permissions">Testing
|
| - * Permissions</a> for more information.
|
| - *
|
| - * For the definitions of datasets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [resource] - REQUIRED: The resource for which policy is being specified.
|
| - * Format is
|
| - * `datasets/<dataset ID>`.
|
| - * Value must have pattern "^datasets/[^/]+$".
|
| - *
|
| - * Completes with a [TestIamPermissionsResponse].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<TestIamPermissionsResponse> testIamPermissions(TestIamPermissionsRequest request, core.String resource) {
|
| + /// Returns permissions that a caller has on the specified resource.
|
| + /// See <a href="/iam/docs/managing-policies#testing_permissions">Testing
|
| + /// Permissions</a> for more information.
|
| + ///
|
| + /// For the definitions of datasets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [resource] - REQUIRED: The resource for which policy is being specified.
|
| + /// Format is
|
| + /// `datasets/<dataset ID>`.
|
| + /// Value must have pattern "^datasets/[^/]+$".
|
| + ///
|
| + /// Completes with a [TestIamPermissionsResponse].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| + async.Future<TestIamPermissionsResponse> testIamPermissions(
|
| + TestIamPermissionsRequest request, core.String resource) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1240,42 +1195,44 @@ class DatasetsResourceApi {
|
| throw new core.ArgumentError("Parameter resource is required.");
|
| }
|
|
|
| - _url = 'v1/' + commons.Escaper.ecapeVariableReserved('$resource') + ':testIamPermissions';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new TestIamPermissionsResponse.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Undeletes a dataset by restoring a dataset which was deleted via this API.
|
| - *
|
| - * For the definitions of datasets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * This operation is only possible for a week after the deletion occurred.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [datasetId] - The ID of the dataset to be undeleted.
|
| - *
|
| - * Completes with a [Dataset].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<Dataset> undelete(UndeleteDatasetRequest request, core.String datasetId) {
|
| + _url = 'v1/' +
|
| + commons.Escaper.ecapeVariableReserved('$resource') +
|
| + ':testIamPermissions';
|
| +
|
| + var _response = _requester.request(_url, "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| + return _response
|
| + .then((data) => new TestIamPermissionsResponse.fromJson(data));
|
| + }
|
| +
|
| + /// Undeletes a dataset by restoring a dataset which was deleted via this
|
| + /// API.
|
| + ///
|
| + /// For the definitions of datasets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// This operation is only possible for a week after the deletion occurred.
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [datasetId] - The ID of the dataset to be undeleted.
|
| + ///
|
| + /// Completes with a [Dataset].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| + async.Future<Dataset> undelete(
|
| + UndeleteDatasetRequest request, core.String datasetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1290,49 +1247,45 @@ class DatasetsResourceApi {
|
| throw new core.ArgumentError("Parameter datasetId is required.");
|
| }
|
|
|
| - _url = 'v1/datasets/' + commons.Escaper.ecapeVariable('$datasetId') + ':undelete';
|
| + _url = 'v1/datasets/' +
|
| + commons.Escaper.ecapeVariable('$datasetId') +
|
| + ':undelete';
|
|
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new Dataset.fromJson(data));
|
| }
|
| -
|
| }
|
|
|
| -
|
| class OperationsResourceApi {
|
| final commons.ApiRequester _requester;
|
|
|
| - OperationsResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Starts asynchronous cancellation on a long-running operation. The server
|
| - * makes a best effort to cancel the operation, but success is not guaranteed.
|
| - * Clients may use Operations.GetOperation or Operations.ListOperations to
|
| - * check whether the cancellation succeeded or the operation completed despite
|
| - * cancellation.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [name] - The name of the operation resource to be cancelled.
|
| - * Value must have pattern "^operations/.+$".
|
| - *
|
| - * Completes with a [Empty].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + OperationsResourceApi(commons.ApiRequester client) : _requester = client;
|
| +
|
| + /// Starts asynchronous cancellation on a long-running operation. The server
|
| + /// makes a best effort to cancel the operation, but success is not
|
| + /// guaranteed. Clients may use Operations.GetOperation or
|
| + /// Operations.ListOperations to check whether the cancellation succeeded or
|
| + /// the operation completed despite cancellation.
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [name] - The name of the operation resource to be cancelled.
|
| + /// Value must have pattern "^operations/.+$".
|
| + ///
|
| + /// Completes with a [Empty].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<Empty> cancel(CancelOperationRequest request, core.String name) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -1350,34 +1303,32 @@ class OperationsResourceApi {
|
|
|
| _url = 'v1/' + commons.Escaper.ecapeVariableReserved('$name') + ':cancel';
|
|
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new Empty.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Gets the latest state of a long-running operation. Clients can use this
|
| - * method to poll the operation result at intervals as recommended by the API
|
| - * service.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [name] - The name of the operation resource.
|
| - * Value must have pattern "^operations/.+$".
|
| - *
|
| - * Completes with a [Operation].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + /// Gets the latest state of a long-running operation. Clients can use this
|
| + /// method to poll the operation result at intervals as recommended by the
|
| + /// API
|
| + /// service.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [name] - The name of the operation resource.
|
| + /// Value must have pattern "^operations/.+$".
|
| + ///
|
| + /// Completes with a [Operation].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<Operation> get(core.String name) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -1392,59 +1343,57 @@ class OperationsResourceApi {
|
|
|
| _url = 'v1/' + commons.Escaper.ecapeVariableReserved('$name');
|
|
|
| - var _response = _requester.request(_url,
|
| - "GET",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "GET",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new Operation.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Lists operations that match the specified filter in the request.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [name] - The name of the operation's parent resource.
|
| - * Value must have pattern "^operations$".
|
| - *
|
| - * [pageToken] - The standard list page token.
|
| - *
|
| - * [pageSize] - The maximum number of results to return. If unspecified,
|
| - * defaults to
|
| - * 256. The maximum value is 2048.
|
| - *
|
| - * [filter] - A string for filtering Operations.
|
| - * The following filter fields are supported:
|
| - *
|
| - * * projectId: Required. Corresponds to
|
| - * OperationMetadata.projectId.
|
| - * * createTime: The time this job was created, in seconds from the
|
| - * [epoch](http://en.wikipedia.org/wiki/Unix_time). Can use `>=` and/or `<=`
|
| - * operators.
|
| - * * status: Can be `RUNNING`, `SUCCESS`, `FAILURE`, or `CANCELED`. Only
|
| - * one status may be specified.
|
| - * * labels.key where key is a label key.
|
| - *
|
| - * Examples:
|
| - *
|
| - * * `projectId = my-project AND createTime >= 1432140000`
|
| - * * `projectId = my-project AND createTime >= 1432140000 AND createTime <=
|
| - * 1432150000 AND status = RUNNING`
|
| - * * `projectId = my-project AND labels.color = *`
|
| - * * `projectId = my-project AND labels.color = red`
|
| - *
|
| - * Completes with a [ListOperationsResponse].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<ListOperationsResponse> list(core.String name, {core.String pageToken, core.int pageSize, core.String filter}) {
|
| + /// Lists operations that match the specified filter in the request.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [name] - The name of the operation's parent resource.
|
| + /// Value must have pattern "^operations$".
|
| + ///
|
| + /// [pageToken] - The standard list page token.
|
| + ///
|
| + /// [pageSize] - The maximum number of results to return. If unspecified,
|
| + /// defaults to
|
| + /// 256. The maximum value is 2048.
|
| + ///
|
| + /// [filter] - A string for filtering Operations.
|
| + /// The following filter fields are supported:
|
| + ///
|
| + /// * projectId: Required. Corresponds to
|
| + /// OperationMetadata.projectId.
|
| + /// * createTime: The time this job was created, in seconds from the
|
| + /// [epoch](http://en.wikipedia.org/wiki/Unix_time). Can use `>=` and/or `<=`
|
| + /// operators.
|
| + /// * status: Can be `RUNNING`, `SUCCESS`, `FAILURE`, or `CANCELED`. Only
|
| + /// one status may be specified.
|
| + /// * labels.key where key is a label key.
|
| + ///
|
| + /// Examples:
|
| + ///
|
| + /// * `projectId = my-project AND createTime >= 1432140000`
|
| + /// * `projectId = my-project AND createTime >= 1432140000 AND createTime <=
|
| + /// 1432150000 AND status = RUNNING`
|
| + /// * `projectId = my-project AND labels.color = *`
|
| + /// * `projectId = my-project AND labels.color = red`
|
| + ///
|
| + /// Completes with a [ListOperationsResponse].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| + async.Future<ListOperationsResponse> list(core.String name,
|
| + {core.String pageToken, core.int pageSize, core.String filter}) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1467,48 +1416,43 @@ class OperationsResourceApi {
|
|
|
| _url = 'v1/' + commons.Escaper.ecapeVariableReserved('$name');
|
|
|
| - var _response = _requester.request(_url,
|
| - "GET",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "GET",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new ListOperationsResponse.fromJson(data));
|
| }
|
| -
|
| }
|
|
|
| -
|
| class ReadgroupsetsResourceApi {
|
| final commons.ApiRequester _requester;
|
|
|
| - ReadgroupsetsCoveragebucketsResourceApi get coveragebuckets => new ReadgroupsetsCoveragebucketsResourceApi(_requester);
|
| -
|
| - ReadgroupsetsResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Deletes a read group set.
|
| - *
|
| - * For the definitions of read group sets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [readGroupSetId] - The ID of the read group set to be deleted. The caller
|
| - * must have WRITE
|
| - * permissions to the dataset associated with this read group set.
|
| - *
|
| - * Completes with a [Empty].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + ReadgroupsetsCoveragebucketsResourceApi get coveragebuckets =>
|
| + new ReadgroupsetsCoveragebucketsResourceApi(_requester);
|
| +
|
| + ReadgroupsetsResourceApi(commons.ApiRequester client) : _requester = client;
|
| +
|
| + /// Deletes a read group set.
|
| + ///
|
| + /// For the definitions of read group sets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [readGroupSetId] - The ID of the read group set to be deleted. The caller
|
| + /// must have WRITE
|
| + /// permissions to the dataset associated with this read group set.
|
| + ///
|
| + /// Completes with a [Empty].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<Empty> delete(core.String readGroupSetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -1521,47 +1465,46 @@ class ReadgroupsetsResourceApi {
|
| throw new core.ArgumentError("Parameter readGroupSetId is required.");
|
| }
|
|
|
| - _url = 'v1/readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId');
|
| + _url =
|
| + 'v1/readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId');
|
|
|
| - var _response = _requester.request(_url,
|
| - "DELETE",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "DELETE",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new Empty.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Exports a read group set to a BAM file in Google Cloud Storage.
|
| - *
|
| - * For the definitions of read group sets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * Note that currently there may be some differences between exported BAM
|
| - * files and the original BAM file at the time of import. See
|
| - * ImportReadGroupSets
|
| - * for caveats.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [readGroupSetId] - Required. The ID of the read group set to export. The
|
| - * caller must have
|
| - * READ access to this read group set.
|
| - *
|
| - * Completes with a [Operation].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<Operation> export(ExportReadGroupSetRequest request, core.String readGroupSetId) {
|
| + /// Exports a read group set to a BAM file in Google Cloud Storage.
|
| + ///
|
| + /// For the definitions of read group sets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// Note that currently there may be some differences between exported BAM
|
| + /// files and the original BAM file at the time of import. See
|
| + /// ImportReadGroupSets
|
| + /// for caveats.
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [readGroupSetId] - Required. The ID of the read group set to export. The
|
| + /// caller must have
|
| + /// READ access to this read group set.
|
| + ///
|
| + /// Completes with a [Operation].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| + async.Future<Operation> export(
|
| + ExportReadGroupSetRequest request, core.String readGroupSetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1576,37 +1519,36 @@ class ReadgroupsetsResourceApi {
|
| throw new core.ArgumentError("Parameter readGroupSetId is required.");
|
| }
|
|
|
| - _url = 'v1/readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId') + ':export';
|
| + _url = 'v1/readgroupsets/' +
|
| + commons.Escaper.ecapeVariable('$readGroupSetId') +
|
| + ':export';
|
|
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new Operation.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Gets a read group set by ID.
|
| - *
|
| - * For the definitions of read group sets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [readGroupSetId] - The ID of the read group set.
|
| - *
|
| - * Completes with a [ReadGroupSet].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + /// Gets a read group set by ID.
|
| + ///
|
| + /// For the definitions of read group sets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [readGroupSetId] - The ID of the read group set.
|
| + ///
|
| + /// Completes with a [ReadGroupSet].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<ReadGroupSet> get(core.String readGroupSetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -1619,50 +1561,49 @@ class ReadgroupsetsResourceApi {
|
| throw new core.ArgumentError("Parameter readGroupSetId is required.");
|
| }
|
|
|
| - _url = 'v1/readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId');
|
| + _url =
|
| + 'v1/readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId');
|
|
|
| - var _response = _requester.request(_url,
|
| - "GET",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "GET",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new ReadGroupSet.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Creates read group sets by asynchronously importing the provided
|
| - * information.
|
| - *
|
| - * For the definitions of read group sets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * The caller must have WRITE permissions to the dataset.
|
| - *
|
| - * ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import
|
| - *
|
| - * - Tags will be converted to strings - tag types are not preserved
|
| - * - Comments (`@CO`) in the input file header will not be preserved
|
| - * - Original header order of references (`@SQ`) will not be preserved
|
| - * - Any reverse stranded unmapped reads will be reverse complemented, and
|
| - * their qualities (also the "BQ" and "OQ" tags, if any) will be reversed
|
| - * - Unmapped reads will be stripped of positional information (reference name
|
| - * and position)
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [Operation].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + /// Creates read group sets by asynchronously importing the provided
|
| + /// information.
|
| + ///
|
| + /// For the definitions of read group sets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// The caller must have WRITE permissions to the dataset.
|
| + ///
|
| + /// ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import
|
| + ///
|
| + /// - Tags will be converted to strings - tag types are not preserved
|
| + /// - Comments (`@CO`) in the input file header will not be preserved
|
| + /// - Original header order of references (`@SQ`) will not be preserved
|
| + /// - Any reverse stranded unmapped reads will be reverse complemented, and
|
| + /// their qualities (also the "BQ" and "OQ" tags, if any) will be reversed
|
| + /// - Unmapped reads will be stripped of positional information (reference
|
| + /// name
|
| + /// and position)
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// Completes with a [Operation].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<Operation> import(ImportReadGroupSetsRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -1677,51 +1618,50 @@ class ReadgroupsetsResourceApi {
|
|
|
| _url = 'v1/readgroupsets:import';
|
|
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new Operation.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Updates a read group set.
|
| - *
|
| - * For the definitions of read group sets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * This method supports patch semantics.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [readGroupSetId] - The ID of the read group set to be updated. The caller
|
| - * must have WRITE
|
| - * permissions to the dataset associated with this read group set.
|
| - *
|
| - * [updateMask] - An optional mask specifying which fields to update.
|
| - * Supported fields:
|
| - *
|
| - * * name.
|
| - * * referenceSetId.
|
| - *
|
| - * Leaving `updateMask` unset is equivalent to specifying all mutable
|
| - * fields.
|
| - *
|
| - * Completes with a [ReadGroupSet].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<ReadGroupSet> patch(ReadGroupSet request, core.String readGroupSetId, {core.String updateMask}) {
|
| + /// Updates a read group set.
|
| + ///
|
| + /// For the definitions of read group sets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// This method supports patch semantics.
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [readGroupSetId] - The ID of the read group set to be updated. The caller
|
| + /// must have WRITE
|
| + /// permissions to the dataset associated with this read group set.
|
| + ///
|
| + /// [updateMask] - An optional mask specifying which fields to update.
|
| + /// Supported fields:
|
| + ///
|
| + /// * name.
|
| + /// * referenceSetId.
|
| + ///
|
| + /// Leaving `updateMask` unset is equivalent to specifying all mutable
|
| + /// fields.
|
| + ///
|
| + /// Completes with a [ReadGroupSet].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| + async.Future<ReadGroupSet> patch(
|
| + ReadGroupSet request, core.String readGroupSetId,
|
| + {core.String updateMask}) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1739,41 +1679,40 @@ class ReadgroupsetsResourceApi {
|
| _queryParams["updateMask"] = [updateMask];
|
| }
|
|
|
| - _url = 'v1/readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId');
|
| + _url =
|
| + 'v1/readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId');
|
|
|
| - var _response = _requester.request(_url,
|
| - "PATCH",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "PATCH",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new ReadGroupSet.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Searches for read group sets matching the criteria.
|
| - *
|
| - * For the definitions of read group sets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * Implements
|
| - * [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135).
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [SearchReadGroupSetsResponse].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<SearchReadGroupSetsResponse> search(SearchReadGroupSetsRequest request) {
|
| + /// Searches for read group sets matching the criteria.
|
| + ///
|
| + /// For the definitions of read group sets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// Implements
|
| + /// [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135).
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// Completes with a [SearchReadGroupSetsResponse].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| + async.Future<SearchReadGroupSetsResponse> search(
|
| + SearchReadGroupSetsRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1787,85 +1726,89 @@ class ReadgroupsetsResourceApi {
|
|
|
| _url = 'v1/readgroupsets/search';
|
|
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new SearchReadGroupSetsResponse.fromJson(data));
|
| + var _response = _requester.request(_url, "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| + return _response
|
| + .then((data) => new SearchReadGroupSetsResponse.fromJson(data));
|
| }
|
| -
|
| }
|
|
|
| -
|
| class ReadgroupsetsCoveragebucketsResourceApi {
|
| final commons.ApiRequester _requester;
|
|
|
| - ReadgroupsetsCoveragebucketsResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Lists fixed width coverage buckets for a read group set, each of which
|
| - * correspond to a range of a reference sequence. Each bucket summarizes
|
| - * coverage information across its corresponding genomic range.
|
| - *
|
| - * For the definitions of read group sets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * Coverage is defined as the number of reads which are aligned to a given
|
| - * base in the reference sequence. Coverage buckets are available at several
|
| - * precomputed bucket widths, enabling retrieval of various coverage 'zoom
|
| - * levels'. The caller must have READ permissions for the target read group
|
| - * set.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [readGroupSetId] - Required. The ID of the read group set over which
|
| - * coverage is requested.
|
| - *
|
| - * [end] - The end position of the range on the reference, 0-based exclusive.
|
| - * If
|
| - * specified, `referenceName` must also be specified. If unset or 0, defaults
|
| - * to the length of the reference.
|
| - *
|
| - * [pageToken] - 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.
|
| - *
|
| - * [pageSize] - The maximum number of results to return in a single page. If
|
| - * unspecified,
|
| - * defaults to 1024. The maximum value is 2048.
|
| - *
|
| - * [start] - The start position of the range on the reference, 0-based
|
| - * inclusive. If
|
| - * specified, `referenceName` must also be specified. Defaults to 0.
|
| - *
|
| - * [targetBucketWidth] - The desired width of each reported coverage bucket in
|
| - * base pairs. This
|
| - * will be rounded down to the nearest precomputed bucket width; the value
|
| - * of which is returned as `bucketWidth` in the response. Defaults
|
| - * to infinity (each bucket spans an entire reference sequence) or the length
|
| - * of the target range, if specified. The smallest precomputed
|
| - * `bucketWidth` is currently 2048 base pairs; this is subject to
|
| - * change.
|
| - *
|
| - * [referenceName] - The name of the reference to query, within the reference
|
| - * set associated
|
| - * with this query. Optional.
|
| - *
|
| - * Completes with a [ListCoverageBucketsResponse].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<ListCoverageBucketsResponse> list(core.String readGroupSetId, {core.String end, core.String pageToken, core.int pageSize, core.String start, core.String targetBucketWidth, core.String referenceName}) {
|
| + ReadgroupsetsCoveragebucketsResourceApi(commons.ApiRequester client)
|
| + : _requester = client;
|
| +
|
| + /// Lists fixed width coverage buckets for a read group set, each of which
|
| + /// correspond to a range of a reference sequence. Each bucket summarizes
|
| + /// coverage information across its corresponding genomic range.
|
| + ///
|
| + /// For the definitions of read group sets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// Coverage is defined as the number of reads which are aligned to a given
|
| + /// base in the reference sequence. Coverage buckets are available at several
|
| + /// precomputed bucket widths, enabling retrieval of various coverage 'zoom
|
| + /// levels'. The caller must have READ permissions for the target read group
|
| + /// set.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [readGroupSetId] - Required. The ID of the read group set over which
|
| + /// coverage is requested.
|
| + ///
|
| + /// [start] - The start position of the range on the reference, 0-based
|
| + /// inclusive. If
|
| + /// specified, `referenceName` must also be specified. Defaults to 0.
|
| + ///
|
| + /// [targetBucketWidth] - The desired width of each reported coverage bucket
|
| + /// in base pairs. This
|
| + /// will be rounded down to the nearest precomputed bucket width; the value
|
| + /// of which is returned as `bucketWidth` in the response. Defaults
|
| + /// to infinity (each bucket spans an entire reference sequence) or the
|
| + /// length
|
| + /// of the target range, if specified. The smallest precomputed
|
| + /// `bucketWidth` is currently 2048 base pairs; this is subject to
|
| + /// change.
|
| + ///
|
| + /// [referenceName] - The name of the reference to query, within the
|
| + /// reference set associated
|
| + /// with this query. Optional.
|
| + ///
|
| + /// [end] - The end position of the range on the reference, 0-based
|
| + /// exclusive. If
|
| + /// specified, `referenceName` must also be specified. If unset or 0,
|
| + /// defaults
|
| + /// to the length of the reference.
|
| + ///
|
| + /// [pageToken] - 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.
|
| + ///
|
| + /// [pageSize] - The maximum number of results to return in a single page. If
|
| + /// unspecified,
|
| + /// defaults to 1024. The maximum value is 2048.
|
| + ///
|
| + /// Completes with a [ListCoverageBucketsResponse].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| + async.Future<ListCoverageBucketsResponse> list(core.String readGroupSetId,
|
| + {core.String start,
|
| + core.String targetBucketWidth,
|
| + core.String referenceName,
|
| + core.String end,
|
| + core.String pageToken,
|
| + core.int pageSize}) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1876,15 +1819,6 @@ class ReadgroupsetsCoveragebucketsResourceApi {
|
| if (readGroupSetId == null) {
|
| throw new core.ArgumentError("Parameter readGroupSetId is required.");
|
| }
|
| - if (end != null) {
|
| - _queryParams["end"] = [end];
|
| - }
|
| - if (pageToken != null) {
|
| - _queryParams["pageToken"] = [pageToken];
|
| - }
|
| - if (pageSize != null) {
|
| - _queryParams["pageSize"] = ["${pageSize}"];
|
| - }
|
| if (start != null) {
|
| _queryParams["start"] = [start];
|
| }
|
| @@ -1894,66 +1828,75 @@ class ReadgroupsetsCoveragebucketsResourceApi {
|
| if (referenceName != null) {
|
| _queryParams["referenceName"] = [referenceName];
|
| }
|
| + if (end != null) {
|
| + _queryParams["end"] = [end];
|
| + }
|
| + if (pageToken != null) {
|
| + _queryParams["pageToken"] = [pageToken];
|
| + }
|
| + if (pageSize != null) {
|
| + _queryParams["pageSize"] = ["${pageSize}"];
|
| + }
|
|
|
| - _url = 'v1/readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId') + '/coveragebuckets';
|
| + _url = 'v1/readgroupsets/' +
|
| + commons.Escaper.ecapeVariable('$readGroupSetId') +
|
| + '/coveragebuckets';
|
|
|
| - var _response = _requester.request(_url,
|
| - "GET",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ListCoverageBucketsResponse.fromJson(data));
|
| + var _response = _requester.request(_url, "GET",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| + return _response
|
| + .then((data) => new ListCoverageBucketsResponse.fromJson(data));
|
| }
|
| -
|
| }
|
|
|
| -
|
| class ReadsResourceApi {
|
| final commons.ApiRequester _requester;
|
|
|
| - ReadsResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Gets a list of reads for one or more read group sets.
|
| - *
|
| - * For the definitions of read group sets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * Reads search operates over a genomic coordinate space of reference sequence
|
| - * & position defined over the reference sequences to which the requested
|
| - * read group sets are aligned.
|
| - *
|
| - * If a target positional range is specified, search returns all reads whose
|
| - * alignment to the reference genome overlap the range. A query which
|
| - * specifies only read group set IDs yields all reads in those read group
|
| - * sets, including unmapped reads.
|
| - *
|
| - * All reads returned (including reads on subsequent pages) are ordered by
|
| - * genomic coordinate (by reference sequence, then position). Reads with
|
| - * equivalent genomic coordinates are returned in an unspecified order. This
|
| - * order is consistent, such that two queries for the same content (regardless
|
| - * of page size) yield reads in the same order across their respective streams
|
| - * of paginated responses.
|
| - *
|
| - * Implements
|
| - * [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L85).
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [SearchReadsResponse].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + ReadsResourceApi(commons.ApiRequester client) : _requester = client;
|
| +
|
| + /// Gets a list of reads for one or more read group sets.
|
| + ///
|
| + /// For the definitions of read group sets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// Reads search operates over a genomic coordinate space of reference
|
| + /// sequence
|
| + /// & position defined over the reference sequences to which the requested
|
| + /// read group sets are aligned.
|
| + ///
|
| + /// If a target positional range is specified, search returns all reads whose
|
| + /// alignment to the reference genome overlap the range. A query which
|
| + /// specifies only read group set IDs yields all reads in those read group
|
| + /// sets, including unmapped reads.
|
| + ///
|
| + /// All reads returned (including reads on subsequent pages) are ordered by
|
| + /// genomic coordinate (by reference sequence, then position). Reads with
|
| + /// equivalent genomic coordinates are returned in an unspecified order. This
|
| + /// order is consistent, such that two queries for the same content
|
| + /// (regardless
|
| + /// of page size) yield reads in the same order across their respective
|
| + /// streams
|
| + /// of paginated responses.
|
| + ///
|
| + /// Implements
|
| + /// [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L85).
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// Completes with a [SearchReadsResponse].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<SearchReadsResponse> search(SearchReadsRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -1968,49 +1911,44 @@ class ReadsResourceApi {
|
|
|
| _url = 'v1/reads/search';
|
|
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new SearchReadsResponse.fromJson(data));
|
| }
|
| -
|
| }
|
|
|
| -
|
| class ReferencesResourceApi {
|
| final commons.ApiRequester _requester;
|
|
|
| - ReferencesBasesResourceApi get bases => new ReferencesBasesResourceApi(_requester);
|
| -
|
| - ReferencesResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Gets a reference.
|
| - *
|
| - * For the definitions of references and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * Implements
|
| - * [GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L158).
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [referenceId] - The ID of the reference.
|
| - *
|
| - * Completes with a [Reference].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + ReferencesBasesResourceApi get bases =>
|
| + new ReferencesBasesResourceApi(_requester);
|
| +
|
| + ReferencesResourceApi(commons.ApiRequester client) : _requester = client;
|
| +
|
| + /// Gets a reference.
|
| + ///
|
| + /// For the definitions of references and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// Implements
|
| + /// [GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L158).
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [referenceId] - The ID of the reference.
|
| + ///
|
| + /// Completes with a [Reference].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<Reference> get(core.String referenceId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -2025,39 +1963,37 @@ class ReferencesResourceApi {
|
|
|
| _url = 'v1/references/' + commons.Escaper.ecapeVariable('$referenceId');
|
|
|
| - var _response = _requester.request(_url,
|
| - "GET",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "GET",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new Reference.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Searches for references which match the given criteria.
|
| - *
|
| - * For the definitions of references and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * Implements
|
| - * [GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L146).
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [SearchReferencesResponse].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<SearchReferencesResponse> search(SearchReferencesRequest request) {
|
| + /// Searches for references which match the given criteria.
|
| + ///
|
| + /// For the definitions of references and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// Implements
|
| + /// [GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L146).
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// Completes with a [SearchReferencesResponse].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| + async.Future<SearchReferencesResponse> search(
|
| + SearchReferencesRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -2071,64 +2007,64 @@ class ReferencesResourceApi {
|
|
|
| _url = 'v1/references/search';
|
|
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new SearchReferencesResponse.fromJson(data));
|
| + var _response = _requester.request(_url, "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| + return _response
|
| + .then((data) => new SearchReferencesResponse.fromJson(data));
|
| }
|
| -
|
| }
|
|
|
| -
|
| class ReferencesBasesResourceApi {
|
| final commons.ApiRequester _requester;
|
|
|
| - ReferencesBasesResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Lists the bases in a reference, optionally restricted to a range.
|
| - *
|
| - * For the definitions of references and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * Implements
|
| - * [GlobalAllianceApi.getReferenceBases](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L221).
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [referenceId] - The ID of the reference.
|
| - *
|
| - * [pageSize] - The maximum number of bases to return in a single page. If
|
| - * unspecified,
|
| - * defaults to 200Kbp (kilo base pairs). The maximum value is 10Mbp (mega base
|
| - * pairs).
|
| - *
|
| - * [start] - The start position (0-based) of this query. Defaults to 0.
|
| - *
|
| - * [end] - The end position (0-based, exclusive) of this query. Defaults to
|
| - * the length
|
| - * of this reference.
|
| - *
|
| - * [pageToken] - 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.
|
| - *
|
| - * Completes with a [ListBasesResponse].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<ListBasesResponse> list(core.String referenceId, {core.int pageSize, core.String start, core.String end, core.String pageToken}) {
|
| + ReferencesBasesResourceApi(commons.ApiRequester client) : _requester = client;
|
| +
|
| + /// Lists the bases in a reference, optionally restricted to a range.
|
| + ///
|
| + /// For the definitions of references and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// Implements
|
| + /// [GlobalAllianceApi.getReferenceBases](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L221).
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [referenceId] - The ID of the reference.
|
| + ///
|
| + /// [start] - The start position (0-based) of this query. Defaults to 0.
|
| + ///
|
| + /// [end] - The end position (0-based, exclusive) of this query. Defaults to
|
| + /// the length
|
| + /// of this reference.
|
| + ///
|
| + /// [pageToken] - 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.
|
| + ///
|
| + /// [pageSize] - The maximum number of bases to return in a single page. If
|
| + /// unspecified,
|
| + /// defaults to 200Kbp (kilo base pairs). The maximum value is 10Mbp (mega
|
| + /// base
|
| + /// pairs).
|
| + ///
|
| + /// Completes with a [ListBasesResponse].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| + async.Future<ListBasesResponse> list(core.String referenceId,
|
| + {core.String start,
|
| + core.String end,
|
| + core.String pageToken,
|
| + core.int pageSize}) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -2139,9 +2075,6 @@ class ReferencesBasesResourceApi {
|
| if (referenceId == null) {
|
| throw new core.ArgumentError("Parameter referenceId is required.");
|
| }
|
| - if (pageSize != null) {
|
| - _queryParams["pageSize"] = ["${pageSize}"];
|
| - }
|
| if (start != null) {
|
| _queryParams["start"] = [start];
|
| }
|
| @@ -2151,50 +2084,49 @@ class ReferencesBasesResourceApi {
|
| if (pageToken != null) {
|
| _queryParams["pageToken"] = [pageToken];
|
| }
|
| + if (pageSize != null) {
|
| + _queryParams["pageSize"] = ["${pageSize}"];
|
| + }
|
|
|
| - _url = 'v1/references/' + commons.Escaper.ecapeVariable('$referenceId') + '/bases';
|
| + _url = 'v1/references/' +
|
| + commons.Escaper.ecapeVariable('$referenceId') +
|
| + '/bases';
|
|
|
| - var _response = _requester.request(_url,
|
| - "GET",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "GET",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new ListBasesResponse.fromJson(data));
|
| }
|
| -
|
| }
|
|
|
| -
|
| class ReferencesetsResourceApi {
|
| final commons.ApiRequester _requester;
|
|
|
| - ReferencesetsResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Gets a reference set.
|
| - *
|
| - * For the definitions of references and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * Implements
|
| - * [GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L83).
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [referenceSetId] - The ID of the reference set.
|
| - *
|
| - * Completes with a [ReferenceSet].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + ReferencesetsResourceApi(commons.ApiRequester client) : _requester = client;
|
| +
|
| + /// Gets a reference set.
|
| + ///
|
| + /// For the definitions of references and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// Implements
|
| + /// [GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L83).
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [referenceSetId] - The ID of the reference set.
|
| + ///
|
| + /// Completes with a [ReferenceSet].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<ReferenceSet> get(core.String referenceSetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -2207,41 +2139,40 @@ class ReferencesetsResourceApi {
|
| throw new core.ArgumentError("Parameter referenceSetId is required.");
|
| }
|
|
|
| - _url = 'v1/referencesets/' + commons.Escaper.ecapeVariable('$referenceSetId');
|
| + _url =
|
| + 'v1/referencesets/' + commons.Escaper.ecapeVariable('$referenceSetId');
|
|
|
| - var _response = _requester.request(_url,
|
| - "GET",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "GET",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new ReferenceSet.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Searches for reference sets which match the given criteria.
|
| - *
|
| - * For the definitions of references and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * Implements
|
| - * [GlobalAllianceApi.searchReferenceSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L71)
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [SearchReferenceSetsResponse].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<SearchReferenceSetsResponse> search(SearchReferenceSetsRequest request) {
|
| + /// Searches for reference sets which match the given criteria.
|
| + ///
|
| + /// For the definitions of references and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// Implements
|
| + /// [GlobalAllianceApi.searchReferenceSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L71)
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// Completes with a [SearchReferenceSetsResponse].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| + async.Future<SearchReferenceSetsResponse> search(
|
| + SearchReferenceSetsRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -2255,44 +2186,39 @@ class ReferencesetsResourceApi {
|
|
|
| _url = 'v1/referencesets/search';
|
|
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new SearchReferenceSetsResponse.fromJson(data));
|
| + var _response = _requester.request(_url, "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| + return _response
|
| + .then((data) => new SearchReferenceSetsResponse.fromJson(data));
|
| }
|
| -
|
| }
|
|
|
| -
|
| class VariantsResourceApi {
|
| final commons.ApiRequester _requester;
|
|
|
| - VariantsResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Creates a new variant.
|
| - *
|
| - * For the definitions of variants and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [Variant].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + VariantsResourceApi(commons.ApiRequester client) : _requester = client;
|
| +
|
| + /// Creates a new variant.
|
| + ///
|
| + /// For the definitions of variants and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// Completes with a [Variant].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<Variant> create(Variant request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -2307,35 +2233,32 @@ class VariantsResourceApi {
|
|
|
| _url = 'v1/variants';
|
|
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new Variant.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Deletes a variant.
|
| - *
|
| - * For the definitions of variants and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantId] - The ID of the variant to be deleted.
|
| - *
|
| - * Completes with a [Empty].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + /// Deletes a variant.
|
| + ///
|
| + /// For the definitions of variants and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [variantId] - The ID of the variant to be deleted.
|
| + ///
|
| + /// Completes with a [Empty].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<Empty> delete(core.String variantId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -2350,35 +2273,32 @@ class VariantsResourceApi {
|
|
|
| _url = 'v1/variants/' + commons.Escaper.ecapeVariable('$variantId');
|
|
|
| - var _response = _requester.request(_url,
|
| - "DELETE",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "DELETE",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new Empty.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Gets a variant by ID.
|
| - *
|
| - * For the definitions of variants and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantId] - The ID of the variant.
|
| - *
|
| - * Completes with a [Variant].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + /// Gets a variant by ID.
|
| + ///
|
| + /// For the definitions of variants and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [variantId] - The ID of the variant.
|
| + ///
|
| + /// Completes with a [Variant].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<Variant> get(core.String variantId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -2393,48 +2313,48 @@ class VariantsResourceApi {
|
|
|
| _url = 'v1/variants/' + commons.Escaper.ecapeVariable('$variantId');
|
|
|
| - var _response = _requester.request(_url,
|
| - "GET",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "GET",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new Variant.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Creates variant data by asynchronously importing the provided information.
|
| - *
|
| - * For the definitions of variant sets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * The variants for import will be merged with any existing variant that
|
| - * matches its reference sequence, start, end, reference bases, and
|
| - * alternative bases. If no such variant exists, a new one will be created.
|
| - *
|
| - * When variants are merged, the call information from the new variant
|
| - * is added to the existing variant, and Variant info fields are merged
|
| - * as specified in
|
| - * infoMergeConfig.
|
| - * As a special case, for single-sample VCF files, QUAL and FILTER fields will
|
| - * be moved to the call level; these are sometimes interpreted in a
|
| - * call-specific context.
|
| - * Imported VCF headers are appended to the metadata already in a variant set.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [Operation].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + /// Creates variant data by asynchronously importing the provided
|
| + /// information.
|
| + ///
|
| + /// For the definitions of variant sets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// The variants for import will be merged with any existing variant that
|
| + /// matches its reference sequence, start, end, reference bases, and
|
| + /// alternative bases. If no such variant exists, a new one will be created.
|
| + ///
|
| + /// When variants are merged, the call information from the new variant
|
| + /// is added to the existing variant, and Variant info fields are merged
|
| + /// as specified in
|
| + /// infoMergeConfig.
|
| + /// As a special case, for single-sample VCF files, QUAL and FILTER fields
|
| + /// will
|
| + /// be moved to the call level; these are sometimes interpreted in a
|
| + /// call-specific context.
|
| + /// Imported VCF headers are appended to the metadata already in a variant
|
| + /// set.
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// Completes with a [Operation].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<Operation> import(ImportVariantsRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -2449,121 +2369,119 @@ class VariantsResourceApi {
|
|
|
| _url = 'v1/variants:import';
|
|
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new Operation.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Merges the given variants with existing variants.
|
| - *
|
| - * For the definitions of variants and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * Each variant will be
|
| - * merged with an existing variant that matches its reference sequence,
|
| - * start, end, reference bases, and alternative bases. If no such variant
|
| - * exists, a new one will be created.
|
| - *
|
| - * When variants are merged, the call information from the new variant
|
| - * is added to the existing variant. Variant info fields are merged as
|
| - * specified in the
|
| - * infoMergeConfig
|
| - * field of the MergeVariantsRequest.
|
| - *
|
| - * Please exercise caution when using this method! It is easy to introduce
|
| - * mistakes in existing variants and difficult to back out of them. For
|
| - * example,
|
| - * suppose you were trying to merge a new variant with an existing one and
|
| - * both
|
| - * variants contain calls that belong to callsets with the same callset ID.
|
| - *
|
| - * // Existing variant - irrelevant fields trimmed for clarity
|
| - * {
|
| - * "variantSetId": "10473108253681171589",
|
| - * "referenceName": "1",
|
| - * "start": "10582",
|
| - * "referenceBases": "G",
|
| - * "alternateBases": [
|
| - * "A"
|
| - * ],
|
| - * "calls": [
|
| - * {
|
| - * "callSetId": "10473108253681171589-0",
|
| - * "callSetName": "CALLSET0",
|
| - * "genotype": [
|
| - * 0,
|
| - * 1
|
| - * ],
|
| - * }
|
| - * ]
|
| - * }
|
| - *
|
| - * // New variant with conflicting call information
|
| - * {
|
| - * "variantSetId": "10473108253681171589",
|
| - * "referenceName": "1",
|
| - * "start": "10582",
|
| - * "referenceBases": "G",
|
| - * "alternateBases": [
|
| - * "A"
|
| - * ],
|
| - * "calls": [
|
| - * {
|
| - * "callSetId": "10473108253681171589-0",
|
| - * "callSetName": "CALLSET0",
|
| - * "genotype": [
|
| - * 1,
|
| - * 1
|
| - * ],
|
| - * }
|
| - * ]
|
| - * }
|
| - *
|
| - * The resulting merged variant would overwrite the existing calls with those
|
| - * from the new variant:
|
| - *
|
| - * {
|
| - * "variantSetId": "10473108253681171589",
|
| - * "referenceName": "1",
|
| - * "start": "10582",
|
| - * "referenceBases": "G",
|
| - * "alternateBases": [
|
| - * "A"
|
| - * ],
|
| - * "calls": [
|
| - * {
|
| - * "callSetId": "10473108253681171589-0",
|
| - * "callSetName": "CALLSET0",
|
| - * "genotype": [
|
| - * 1,
|
| - * 1
|
| - * ],
|
| - * }
|
| - * ]
|
| - * }
|
| - *
|
| - * This may be the desired outcome, but it is up to the user to determine if
|
| - * if that is indeed the case.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [Empty].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + /// Merges the given variants with existing variants.
|
| + ///
|
| + /// For the definitions of variants and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// Each variant will be
|
| + /// merged with an existing variant that matches its reference sequence,
|
| + /// start, end, reference bases, and alternative bases. If no such variant
|
| + /// exists, a new one will be created.
|
| + ///
|
| + /// When variants are merged, the call information from the new variant
|
| + /// is added to the existing variant. Variant info fields are merged as
|
| + /// specified in the
|
| + /// infoMergeConfig
|
| + /// field of the MergeVariantsRequest.
|
| + ///
|
| + /// Please exercise caution when using this method! It is easy to introduce
|
| + /// mistakes in existing variants and difficult to back out of them. For
|
| + /// example,
|
| + /// suppose you were trying to merge a new variant with an existing one and
|
| + /// both
|
| + /// variants contain calls that belong to callsets with the same callset ID.
|
| + ///
|
| + /// // Existing variant - irrelevant fields trimmed for clarity
|
| + /// {
|
| + /// "variantSetId": "10473108253681171589",
|
| + /// "referenceName": "1",
|
| + /// "start": "10582",
|
| + /// "referenceBases": "G",
|
| + /// "alternateBases": [
|
| + /// "A"
|
| + /// ],
|
| + /// "calls": [
|
| + /// {
|
| + /// "callSetId": "10473108253681171589-0",
|
| + /// "callSetName": "CALLSET0",
|
| + /// "genotype": [
|
| + /// 0,
|
| + /// 1
|
| + /// ],
|
| + /// }
|
| + /// ]
|
| + /// }
|
| + ///
|
| + /// // New variant with conflicting call information
|
| + /// {
|
| + /// "variantSetId": "10473108253681171589",
|
| + /// "referenceName": "1",
|
| + /// "start": "10582",
|
| + /// "referenceBases": "G",
|
| + /// "alternateBases": [
|
| + /// "A"
|
| + /// ],
|
| + /// "calls": [
|
| + /// {
|
| + /// "callSetId": "10473108253681171589-0",
|
| + /// "callSetName": "CALLSET0",
|
| + /// "genotype": [
|
| + /// 1,
|
| + /// 1
|
| + /// ],
|
| + /// }
|
| + /// ]
|
| + /// }
|
| + ///
|
| + /// The resulting merged variant would overwrite the existing calls with
|
| + /// those
|
| + /// from the new variant:
|
| + ///
|
| + /// {
|
| + /// "variantSetId": "10473108253681171589",
|
| + /// "referenceName": "1",
|
| + /// "start": "10582",
|
| + /// "referenceBases": "G",
|
| + /// "alternateBases": [
|
| + /// "A"
|
| + /// ],
|
| + /// "calls": [
|
| + /// {
|
| + /// "callSetId": "10473108253681171589-0",
|
| + /// "callSetName": "CALLSET0",
|
| + /// "genotype": [
|
| + /// 1,
|
| + /// 1
|
| + /// ],
|
| + /// }
|
| + /// ]
|
| + /// }
|
| + ///
|
| + /// This may be the desired outcome, but it is up to the user to determine if
|
| + /// if that is indeed the case.
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// Completes with a [Empty].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<Empty> merge(MergeVariantsRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -2578,47 +2496,46 @@ class VariantsResourceApi {
|
|
|
| _url = 'v1/variants:merge';
|
|
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new Empty.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Updates a variant.
|
| - *
|
| - * For the definitions of variants and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * This method supports patch semantics. Returns the modified variant without
|
| - * its calls.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantId] - The ID of the variant to be updated.
|
| - *
|
| - * [updateMask] - An optional mask specifying which fields to update. At this
|
| - * time, mutable
|
| - * fields are names and
|
| - * info. Acceptable values are "names" and
|
| - * "info". If unspecified, all mutable fields will be updated.
|
| - *
|
| - * Completes with a [Variant].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<Variant> patch(Variant request, core.String variantId, {core.String updateMask}) {
|
| + /// Updates a variant.
|
| + ///
|
| + /// For the definitions of variants and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// This method supports patch semantics. Returns the modified variant
|
| + /// without
|
| + /// its calls.
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [variantId] - The ID of the variant to be updated.
|
| + ///
|
| + /// [updateMask] - An optional mask specifying which fields to update. At
|
| + /// this time, mutable
|
| + /// fields are names and
|
| + /// info. Acceptable values are "names" and
|
| + /// "info". If unspecified, all mutable fields will be updated.
|
| + ///
|
| + /// Completes with a [Variant].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| + async.Future<Variant> patch(Variant request, core.String variantId,
|
| + {core.String updateMask}) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -2638,38 +2555,35 @@ class VariantsResourceApi {
|
|
|
| _url = 'v1/variants/' + commons.Escaper.ecapeVariable('$variantId');
|
|
|
| - var _response = _requester.request(_url,
|
| - "PATCH",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "PATCH",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new Variant.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Gets a list of variants matching the criteria.
|
| - *
|
| - * For the definitions of variants and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * Implements
|
| - * [GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L126).
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [SearchVariantsResponse].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + /// Gets a list of variants matching the criteria.
|
| + ///
|
| + /// For the definitions of variants and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// Implements
|
| + /// [GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L126).
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// Completes with a [SearchVariantsResponse].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<SearchVariantsResponse> search(SearchVariantsRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -2684,48 +2598,42 @@ class VariantsResourceApi {
|
|
|
| _url = 'v1/variants/search';
|
|
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new SearchVariantsResponse.fromJson(data));
|
| }
|
| -
|
| }
|
|
|
| -
|
| class VariantsetsResourceApi {
|
| final commons.ApiRequester _requester;
|
|
|
| - VariantsetsResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Creates a new variant set.
|
| - *
|
| - * For the definitions of variant sets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * The provided variant set must have a valid `datasetId` set - all other
|
| - * fields are optional. Note that the `id` field will be ignored, as this is
|
| - * assigned by the server.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [VariantSet].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + VariantsetsResourceApi(commons.ApiRequester client) : _requester = client;
|
| +
|
| + /// Creates a new variant set.
|
| + ///
|
| + /// For the definitions of variant sets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// The provided variant set must have a valid `datasetId` set - all other
|
| + /// fields are optional. Note that the `id` field will be ignored, as this is
|
| + /// assigned by the server.
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// Completes with a [VariantSet].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<VariantSet> create(VariantSet request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -2740,36 +2648,34 @@ class VariantsetsResourceApi {
|
|
|
| _url = 'v1/variantsets';
|
|
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new VariantSet.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Deletes a variant set including all variants, call sets, and calls within.
|
| - * This is not reversible.
|
| - *
|
| - * For the definitions of variant sets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantSetId] - The ID of the variant set to be deleted.
|
| - *
|
| - * Completes with a [Empty].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + /// Deletes a variant set including all variants, call sets, and calls
|
| + /// within.
|
| + /// This is not reversible.
|
| + ///
|
| + /// For the definitions of variant sets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [variantSetId] - The ID of the variant set to be deleted.
|
| + ///
|
| + /// Completes with a [Empty].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<Empty> delete(core.String variantSetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -2784,40 +2690,38 @@ class VariantsetsResourceApi {
|
|
|
| _url = 'v1/variantsets/' + commons.Escaper.ecapeVariable('$variantSetId');
|
|
|
| - var _response = _requester.request(_url,
|
| - "DELETE",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "DELETE",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new Empty.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Exports variant set data to an external destination.
|
| - *
|
| - * For the definitions of variant sets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantSetId] - Required. The ID of the variant set that contains variant
|
| - * data which
|
| - * should be exported. The caller must have READ access to this variant set.
|
| - *
|
| - * Completes with a [Operation].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<Operation> export(ExportVariantSetRequest request, core.String variantSetId) {
|
| + /// Exports variant set data to an external destination.
|
| + ///
|
| + /// For the definitions of variant sets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [variantSetId] - Required. The ID of the variant set that contains
|
| + /// variant data which
|
| + /// should be exported. The caller must have READ access to this variant set.
|
| + ///
|
| + /// Completes with a [Operation].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| + async.Future<Operation> export(
|
| + ExportVariantSetRequest request, core.String variantSetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -2832,37 +2736,36 @@ class VariantsetsResourceApi {
|
| throw new core.ArgumentError("Parameter variantSetId is required.");
|
| }
|
|
|
| - _url = 'v1/variantsets/' + commons.Escaper.ecapeVariable('$variantSetId') + ':export';
|
| + _url = 'v1/variantsets/' +
|
| + commons.Escaper.ecapeVariable('$variantSetId') +
|
| + ':export';
|
|
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new Operation.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Gets a variant set by ID.
|
| - *
|
| - * For the definitions of variant sets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantSetId] - Required. The ID of the variant set.
|
| - *
|
| - * Completes with a [VariantSet].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| + /// Gets a variant set by ID.
|
| + ///
|
| + /// For the definitions of variant sets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [variantSetId] - Required. The ID of the variant set.
|
| + ///
|
| + /// Completes with a [VariantSet].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| async.Future<VariantSet> get(core.String variantSetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| @@ -2877,48 +2780,47 @@ class VariantsetsResourceApi {
|
|
|
| _url = 'v1/variantsets/' + commons.Escaper.ecapeVariable('$variantSetId');
|
|
|
| - var _response = _requester.request(_url,
|
| - "GET",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "GET",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new VariantSet.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Updates a variant set using patch semantics.
|
| - *
|
| - * For the definitions of variant sets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantSetId] - The ID of the variant to be updated (must already exist).
|
| - *
|
| - * [updateMask] - An optional mask specifying which fields to update.
|
| - * Supported fields:
|
| - *
|
| - * * metadata.
|
| - * * name.
|
| - * * description.
|
| - *
|
| - * Leaving `updateMask` unset is equivalent to specifying all mutable
|
| - * fields.
|
| - *
|
| - * Completes with a [VariantSet].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<VariantSet> patch(VariantSet request, core.String variantSetId, {core.String updateMask}) {
|
| + /// Updates a variant set using patch semantics.
|
| + ///
|
| + /// For the definitions of variant sets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// [variantSetId] - The ID of the variant to be updated (must already
|
| + /// exist).
|
| + ///
|
| + /// [updateMask] - An optional mask specifying which fields to update.
|
| + /// Supported fields:
|
| + ///
|
| + /// * metadata.
|
| + /// * name.
|
| + /// * description.
|
| + ///
|
| + /// Leaving `updateMask` unset is equivalent to specifying all mutable
|
| + /// fields.
|
| + ///
|
| + /// Completes with a [VariantSet].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| + async.Future<VariantSet> patch(VariantSet request, core.String variantSetId,
|
| + {core.String updateMask}) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -2938,39 +2840,37 @@ class VariantsetsResourceApi {
|
|
|
| _url = 'v1/variantsets/' + commons.Escaper.ecapeVariable('$variantSetId');
|
|
|
| - var _response = _requester.request(_url,
|
| - "PATCH",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| + var _response = _requester.request(_url, "PATCH",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| return _response.then((data) => new VariantSet.fromJson(data));
|
| }
|
|
|
| - /**
|
| - * Returns a list of all variant sets matching search criteria.
|
| - *
|
| - * For the definitions of variant sets and other genomics resources, see
|
| - * [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - *
|
| - * Implements
|
| - * [GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L49).
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [SearchVariantSetsResponse].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<SearchVariantSetsResponse> search(SearchVariantSetsRequest request) {
|
| + /// Returns a list of all variant sets matching search criteria.
|
| + ///
|
| + /// For the definitions of variant sets and other genomics resources, see
|
| + /// [Fundamentals of Google
|
| + /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| + ///
|
| + /// Implements
|
| + /// [GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L49).
|
| + ///
|
| + /// [request] - The metadata request object.
|
| + ///
|
| + /// Request parameters:
|
| + ///
|
| + /// Completes with a [SearchVariantSetsResponse].
|
| + ///
|
| + /// Completes with a [commons.ApiRequestError] if the API endpoint returned
|
| + /// an error.
|
| + ///
|
| + /// If the used [http.Client] completes with an error when making a REST
|
| + /// call, this method will complete with the same error.
|
| + async.Future<SearchVariantSetsResponse> search(
|
| + SearchVariantSetsRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -2984,93 +2884,88 @@ class VariantsetsResourceApi {
|
|
|
| _url = 'v1/variantsets/search';
|
|
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new SearchVariantSetsResponse.fromJson(data));
|
| + var _response = _requester.request(_url, "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| + return _response
|
| + .then((data) => new SearchVariantSetsResponse.fromJson(data));
|
| }
|
| -
|
| }
|
|
|
| -
|
| -
|
| -/**
|
| - * 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`.
|
| - */
|
| +/// 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`.
|
| class Annotation {
|
| - /** The annotation set to which this annotation belongs. */
|
| + /// The annotation set to which this annotation belongs.
|
| core.String annotationSetId;
|
| - /** The end position of the range on the reference, 0-based exclusive. */
|
| +
|
| + /// The end position of the range on the reference, 0-based exclusive.
|
| core.String end;
|
| - /** The server-generated annotation ID, unique across all annotations. */
|
| +
|
| + /// The server-generated annotation ID, unique across all annotations.
|
| core.String id;
|
| - /**
|
| - * A map of additional read alignment information. This must be of the form
|
| - * map<string, string[]> (string key mapping to a list of string values).
|
| - *
|
| - * The values for Object must be JSON objects. It can consist of `num`,
|
| - * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| - */
|
| +
|
| + /// A map of additional read alignment information. This must be of the form
|
| + /// map<string, string[]> (string key mapping to a list of string values).
|
| + ///
|
| + /// The values for Object must be JSON objects. It can consist of `num`,
|
| + /// `String`, `bool` and `null` as well as `Map` and `List` values.
|
| core.Map<core.String, core.List<core.Object>> info;
|
| - /** The display name of this annotation. */
|
| +
|
| + /// The display name of this annotation.
|
| core.String name;
|
| - /** The ID of the Google Genomics reference associated with this range. */
|
| +
|
| + /// The ID of the Google Genomics reference associated with this range.
|
| core.String referenceId;
|
| - /**
|
| - * The display name corresponding to the reference specified by
|
| - * `referenceId`, for example `chr1`, `1`, or `chrX`.
|
| - */
|
| +
|
| + /// The display name corresponding to the reference specified by
|
| + /// `referenceId`, for example `chr1`, `1`, or `chrX`.
|
| core.String referenceName;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.bool reverseStrand;
|
| - /** The start position of the range on the reference, 0-based inclusive. */
|
| +
|
| + /// The start position of the range on the reference, 0-based inclusive.
|
| core.String start;
|
| - /**
|
| - * 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`.
|
| - */
|
| +
|
| + /// 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`.
|
| Transcript transcript;
|
| - /**
|
| - * The data type for this annotation. Must match the containing annotation
|
| - * set's type.
|
| - * Possible string values are:
|
| - * - "ANNOTATION_TYPE_UNSPECIFIED"
|
| - * - "GENERIC" : A `GENERIC` annotation type should be used when no other
|
| - * annotation
|
| - * type will suffice. This represents an untyped annotation of the reference
|
| - * genome.
|
| - * - "VARIANT" : A `VARIANT` annotation type.
|
| - * - "GENE" : A `GENE` annotation type represents the existence of a gene at
|
| - * the
|
| - * associated reference coordinates. The start coordinate is typically the
|
| - * gene's transcription start site and the end is typically the end of the
|
| - * gene's last exon.
|
| - * - "TRANSCRIPT" : A `TRANSCRIPT` annotation type represents the assertion
|
| - * that a
|
| - * particular region of the reference genome may be transcribed as RNA.
|
| - */
|
| +
|
| + /// The data type for this annotation. Must match the containing annotation
|
| + /// set's type.
|
| + /// Possible string values are:
|
| + /// - "ANNOTATION_TYPE_UNSPECIFIED"
|
| + /// - "GENERIC" : A `GENERIC` annotation type should be used when no other
|
| + /// annotation
|
| + /// type will suffice. This represents an untyped annotation of the reference
|
| + /// genome.
|
| + /// - "VARIANT" : A `VARIANT` annotation type.
|
| + /// - "GENE" : A `GENE` annotation type represents the existence of a gene at
|
| + /// the
|
| + /// associated reference coordinates. The start coordinate is typically the
|
| + /// gene's transcription start site and the end is typically the end of the
|
| + /// gene's last exon.
|
| + /// - "TRANSCRIPT" : A `TRANSCRIPT` annotation type represents the assertion
|
| + /// that a
|
| + /// particular region of the reference genome may be transcribed as RNA.
|
| core.String type;
|
| - /**
|
| - * 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`.
|
| - */
|
| +
|
| + /// 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`.
|
| VariantAnnotation variant;
|
|
|
| Annotation();
|
| @@ -3115,7 +3010,8 @@ class Annotation {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (annotationSetId != null) {
|
| _json["annotationSetId"] = annotationSetId;
|
| }
|
| @@ -3156,56 +3052,52 @@ class Annotation {
|
| }
|
| }
|
|
|
| -/**
|
| - * 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'.
|
| - */
|
| +/// 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'.
|
| class AnnotationSet {
|
| - /** The dataset to which this annotation set belongs. */
|
| + /// The dataset to which this annotation set belongs.
|
| core.String datasetId;
|
| - /**
|
| - * The server-generated annotation set ID, unique across all annotation sets.
|
| - */
|
| +
|
| + /// The server-generated annotation set ID, unique across all annotation
|
| + /// sets.
|
| core.String id;
|
| - /**
|
| - * A map of additional read alignment information. This must be of the form
|
| - * map<string, string[]> (string key mapping to a list of string values).
|
| - *
|
| - * The values for Object must be JSON objects. It can consist of `num`,
|
| - * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| - */
|
| +
|
| + /// A map of additional read alignment information. This must be of the form
|
| + /// map<string, string[]> (string key mapping to a list of string values).
|
| + ///
|
| + /// The values for Object must be JSON objects. It can consist of `num`,
|
| + /// `String`, `bool` and `null` as well as `Map` and `List` values.
|
| core.Map<core.String, core.List<core.Object>> info;
|
| - /** The display name for this annotation set. */
|
| +
|
| + /// The display name for this annotation set.
|
| core.String name;
|
| - /**
|
| - * The ID of the reference set that defines the coordinate space for this
|
| - * set's annotations.
|
| - */
|
| +
|
| + /// The ID of the reference set that defines the coordinate space for this
|
| + /// set's annotations.
|
| core.String referenceSetId;
|
| - /**
|
| - * The source URI describing the file from which this annotation set was
|
| - * generated, if any.
|
| - */
|
| +
|
| + /// The source URI describing the file from which this annotation set was
|
| + /// generated, if any.
|
| core.String sourceUri;
|
| - /**
|
| - * The type of annotations contained within this set.
|
| - * Possible string values are:
|
| - * - "ANNOTATION_TYPE_UNSPECIFIED"
|
| - * - "GENERIC" : A `GENERIC` annotation type should be used when no other
|
| - * annotation
|
| - * type will suffice. This represents an untyped annotation of the reference
|
| - * genome.
|
| - * - "VARIANT" : A `VARIANT` annotation type.
|
| - * - "GENE" : A `GENE` annotation type represents the existence of a gene at
|
| - * the
|
| - * associated reference coordinates. The start coordinate is typically the
|
| - * gene's transcription start site and the end is typically the end of the
|
| - * gene's last exon.
|
| - * - "TRANSCRIPT" : A `TRANSCRIPT` annotation type represents the assertion
|
| - * that a
|
| - * particular region of the reference genome may be transcribed as RNA.
|
| - */
|
| +
|
| + /// The type of annotations contained within this set.
|
| + /// Possible string values are:
|
| + /// - "ANNOTATION_TYPE_UNSPECIFIED"
|
| + /// - "GENERIC" : A `GENERIC` annotation type should be used when no other
|
| + /// annotation
|
| + /// type will suffice. This represents an untyped annotation of the reference
|
| + /// genome.
|
| + /// - "VARIANT" : A `VARIANT` annotation type.
|
| + /// - "GENE" : A `GENE` annotation type represents the existence of a gene at
|
| + /// the
|
| + /// associated reference coordinates. The start coordinate is typically the
|
| + /// gene's transcription start site and the end is typically the end of the
|
| + /// gene's last exon.
|
| + /// - "TRANSCRIPT" : A `TRANSCRIPT` annotation type represents the assertion
|
| + /// that a
|
| + /// particular region of the reference genome may be transcribed as RNA.
|
| core.String type;
|
|
|
| AnnotationSet();
|
| @@ -3235,7 +3127,8 @@ class AnnotationSet {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (datasetId != null) {
|
| _json["datasetId"] = datasetId;
|
| }
|
| @@ -3262,27 +3155,28 @@ class AnnotationSet {
|
| }
|
|
|
| class BatchCreateAnnotationsRequest {
|
| - /**
|
| - * The annotations to be created. At most 4096 can be specified in a single
|
| - * request.
|
| - */
|
| + /// The annotations to be created. At most 4096 can be specified in a single
|
| + /// request.
|
| core.List<Annotation> annotations;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String requestId;
|
|
|
| BatchCreateAnnotationsRequest();
|
|
|
| BatchCreateAnnotationsRequest.fromJson(core.Map _json) {
|
| if (_json.containsKey("annotations")) {
|
| - annotations = _json["annotations"].map((value) => new Annotation.fromJson(value)).toList();
|
| + annotations = _json["annotations"]
|
| + .map((value) => new Annotation.fromJson(value))
|
| + .toList();
|
| }
|
| if (_json.containsKey("requestId")) {
|
| requestId = _json["requestId"];
|
| @@ -3290,9 +3184,11 @@ class BatchCreateAnnotationsRequest {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (annotations != null) {
|
| - _json["annotations"] = annotations.map((value) => (value).toJson()).toList();
|
| + _json["annotations"] =
|
| + annotations.map((value) => (value).toJson()).toList();
|
| }
|
| if (requestId != null) {
|
| _json["requestId"] = requestId;
|
| @@ -3302,22 +3198,22 @@ class BatchCreateAnnotationsRequest {
|
| }
|
|
|
| class BatchCreateAnnotationsResponse {
|
| - /**
|
| - * The resulting per-annotation entries, ordered consistently with the
|
| - * original request.
|
| - */
|
| + /// The resulting per-annotation entries, ordered consistently with the
|
| + /// original request.
|
| core.List<Entry> entries;
|
|
|
| BatchCreateAnnotationsResponse();
|
|
|
| BatchCreateAnnotationsResponse.fromJson(core.Map _json) {
|
| if (_json.containsKey("entries")) {
|
| - entries = _json["entries"].map((value) => new Entry.fromJson(value)).toList();
|
| + entries =
|
| + _json["entries"].map((value) => new Entry.fromJson(value)).toList();
|
| }
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (entries != null) {
|
| _json["entries"] = entries.map((value) => (value).toJson()).toList();
|
| }
|
| @@ -3325,38 +3221,35 @@ class BatchCreateAnnotationsResponse {
|
| }
|
| }
|
|
|
| -/** Associates `members` with a `role`. */
|
| +/// Associates `members` with a `role`.
|
| class Binding {
|
| - /**
|
| - * 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`.
|
| - */
|
| + /// 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`.
|
| core.List<core.String> members;
|
| - /**
|
| - * Role that is assigned to `members`.
|
| - * For example, `roles/viewer`, `roles/editor`, or `roles/owner`.
|
| - * Required
|
| - */
|
| +
|
| + /// Role that is assigned to `members`.
|
| + /// For example, `roles/viewer`, `roles/editor`, or `roles/owner`.
|
| + /// Required
|
| core.String role;
|
|
|
| Binding();
|
| @@ -3371,7 +3264,8 @@ class Binding {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (members != null) {
|
| _json["members"] = members;
|
| }
|
| @@ -3382,37 +3276,36 @@ class Binding {
|
| }
|
| }
|
|
|
| -/**
|
| - * 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](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - */
|
| +/// 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](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| class CallSet {
|
| - /** The date this call set was created in milliseconds from the epoch. */
|
| + /// The date this call set was created in milliseconds from the epoch.
|
| core.String created;
|
| - /** The server-generated call set ID, unique across all call sets. */
|
| +
|
| + /// The server-generated call set ID, unique across all call sets.
|
| core.String id;
|
| - /**
|
| - * A map of additional call set information. This must be of the form
|
| - * map<string, string[]> (string key mapping to a list of string values).
|
| - *
|
| - * The values for Object must be JSON objects. It can consist of `num`,
|
| - * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| - */
|
| +
|
| + /// A map of additional call set information. This must be of the form
|
| + /// map<string, string[]> (string key mapping to a list of string values).
|
| + ///
|
| + /// The values for Object must be JSON objects. It can consist of `num`,
|
| + /// `String`, `bool` and `null` as well as `Map` and `List` values.
|
| core.Map<core.String, core.List<core.Object>> info;
|
| - /** The call set name. */
|
| +
|
| + /// The call set name.
|
| core.String name;
|
| - /** The sample ID this call set corresponds to. */
|
| +
|
| + /// The sample ID this call set corresponds to.
|
| core.String sampleId;
|
| - /**
|
| - * 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](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variants.avdl#L76).
|
| - */
|
| +
|
| + /// 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](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variants.avdl#L76).
|
| core.List<core.String> variantSetIds;
|
|
|
| CallSet();
|
| @@ -3439,7 +3332,8 @@ class CallSet {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (created != null) {
|
| _json["created"] = created;
|
| }
|
| @@ -3462,80 +3356,77 @@ class CallSet {
|
| }
|
| }
|
|
|
| -/** The request message for Operations.CancelOperation. */
|
| +/// The request message for Operations.CancelOperation.
|
| class CancelOperationRequest {
|
| -
|
| CancelOperationRequest();
|
|
|
| - CancelOperationRequest.fromJson(core.Map _json) {
|
| - }
|
| + CancelOperationRequest.fromJson(core.Map _json) {}
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| return _json;
|
| }
|
| }
|
|
|
| -/** A single CIGAR operation. */
|
| +/// A single CIGAR operation.
|
| class CigarUnit {
|
| - /**
|
| - *
|
| - * Possible string values are:
|
| - * - "OPERATION_UNSPECIFIED"
|
| - * - "ALIGNMENT_MATCH" : An alignment match indicates that a sequence can be
|
| - * aligned to the
|
| - * reference without evidence of an INDEL. Unlike the
|
| - * `SEQUENCE_MATCH` and `SEQUENCE_MISMATCH` operators,
|
| - * the `ALIGNMENT_MATCH` operator does not indicate whether the
|
| - * reference and read sequences are an exact match. This operator is
|
| - * equivalent to SAM's `M`.
|
| - * - "INSERT" : The insert operator indicates that the read contains evidence
|
| - * of bases
|
| - * being inserted into the reference. This operator is equivalent to SAM's
|
| - * `I`.
|
| - * - "DELETE" : The delete operator indicates that the read contains evidence
|
| - * of bases
|
| - * being deleted from the reference. This operator is equivalent to SAM's
|
| - * `D`.
|
| - * - "SKIP" : The skip operator indicates that this read skips a long segment
|
| - * of the
|
| - * reference, but the bases have not been deleted. This operator is commonly
|
| - * used when working with RNA-seq data, where reads may skip long segments
|
| - * of the reference between exons. This operator is equivalent to SAM's
|
| - * `N`.
|
| - * - "CLIP_SOFT" : The soft clip operator indicates that bases at the
|
| - * start/end of a read
|
| - * have not been considered during alignment. This may occur if the majority
|
| - * of a read maps, except for low quality bases at the start/end of a read.
|
| - * This operator is equivalent to SAM's `S`. Bases that are soft
|
| - * clipped will still be stored in the read.
|
| - * - "CLIP_HARD" : The hard clip operator indicates that bases at the
|
| - * start/end of a read
|
| - * have been omitted from this alignment. This may occur if this linear
|
| - * alignment is part of a chimeric alignment, or if the read has been
|
| - * trimmed (for example, during error correction or to trim poly-A tails for
|
| - * RNA-seq). This operator is equivalent to SAM's `H`.
|
| - * - "PAD" : The pad operator indicates that there is padding in an alignment.
|
| - * This
|
| - * operator is equivalent to SAM's `P`.
|
| - * - "SEQUENCE_MATCH" : This operator indicates that this portion of the
|
| - * aligned sequence exactly
|
| - * matches the reference. This operator is equivalent to SAM's `=`.
|
| - * - "SEQUENCE_MISMATCH" : This operator indicates that this portion of the
|
| - * aligned sequence is an
|
| - * alignment match to the reference, but a sequence mismatch. This can
|
| - * indicate a SNP or a read error. This operator is equivalent to SAM's
|
| - * `X`.
|
| - */
|
| + ///
|
| + /// Possible string values are:
|
| + /// - "OPERATION_UNSPECIFIED"
|
| + /// - "ALIGNMENT_MATCH" : An alignment match indicates that a sequence can be
|
| + /// aligned to the
|
| + /// reference without evidence of an INDEL. Unlike the
|
| + /// `SEQUENCE_MATCH` and `SEQUENCE_MISMATCH` operators,
|
| + /// the `ALIGNMENT_MATCH` operator does not indicate whether the
|
| + /// reference and read sequences are an exact match. This operator is
|
| + /// equivalent to SAM's `M`.
|
| + /// - "INSERT" : The insert operator indicates that the read contains
|
| + /// evidence of bases
|
| + /// being inserted into the reference. This operator is equivalent to SAM's
|
| + /// `I`.
|
| + /// - "DELETE" : The delete operator indicates that the read contains
|
| + /// evidence of bases
|
| + /// being deleted from the reference. This operator is equivalent to SAM's
|
| + /// `D`.
|
| + /// - "SKIP" : The skip operator indicates that this read skips a long
|
| + /// segment of the
|
| + /// reference, but the bases have not been deleted. This operator is commonly
|
| + /// used when working with RNA-seq data, where reads may skip long segments
|
| + /// of the reference between exons. This operator is equivalent to SAM's
|
| + /// `N`.
|
| + /// - "CLIP_SOFT" : The soft clip operator indicates that bases at the
|
| + /// start/end of a read
|
| + /// have not been considered during alignment. This may occur if the majority
|
| + /// of a read maps, except for low quality bases at the start/end of a read.
|
| + /// This operator is equivalent to SAM's `S`. Bases that are soft
|
| + /// clipped will still be stored in the read.
|
| + /// - "CLIP_HARD" : The hard clip operator indicates that bases at the
|
| + /// start/end of a read
|
| + /// have been omitted from this alignment. This may occur if this linear
|
| + /// alignment is part of a chimeric alignment, or if the read has been
|
| + /// trimmed (for example, during error correction or to trim poly-A tails for
|
| + /// RNA-seq). This operator is equivalent to SAM's `H`.
|
| + /// - "PAD" : The pad operator indicates that there is padding in an
|
| + /// alignment. This
|
| + /// operator is equivalent to SAM's `P`.
|
| + /// - "SEQUENCE_MATCH" : This operator indicates that this portion of the
|
| + /// aligned sequence exactly
|
| + /// matches the reference. This operator is equivalent to SAM's `=`.
|
| + /// - "SEQUENCE_MISMATCH" : This operator indicates that this portion of the
|
| + /// aligned sequence is an
|
| + /// alignment match to the reference, but a sequence mismatch. This can
|
| + /// indicate a SNP or a read error. This operator is equivalent to SAM's
|
| + /// `X`.
|
| core.String operation;
|
| - /** The number of genomic bases that the operation runs for. Required. */
|
| +
|
| + /// The number of genomic bases that the operation runs for. Required.
|
| core.String operationLength;
|
| - /**
|
| - * `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.
|
| - */
|
| +
|
| + /// `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.
|
| core.String referenceSequence;
|
|
|
| CigarUnit();
|
| @@ -3553,7 +3444,8 @@ class CigarUnit {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (operation != null) {
|
| _json["operation"] = operation;
|
| }
|
| @@ -3568,19 +3460,18 @@ class CigarUnit {
|
| }
|
|
|
| class ClinicalCondition {
|
| - /**
|
| - * The MedGen concept id associated with this gene.
|
| - * Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
|
| - */
|
| + /// The MedGen concept id associated with this gene.
|
| + /// Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
|
| core.String conceptId;
|
| - /** The set of external IDs for this condition. */
|
| +
|
| + /// The set of external IDs for this condition.
|
| core.List<ExternalId> externalIds;
|
| - /** A set of names for the condition. */
|
| +
|
| + /// A set of names for the condition.
|
| core.List<core.String> names;
|
| - /**
|
| - * The OMIM id for this condition.
|
| - * Search for these IDs at http://omim.org/
|
| - */
|
| +
|
| + /// The OMIM id for this condition.
|
| + /// Search for these IDs at http://omim.org/
|
| core.String omimId;
|
|
|
| ClinicalCondition();
|
| @@ -3590,7 +3481,9 @@ class ClinicalCondition {
|
| conceptId = _json["conceptId"];
|
| }
|
| if (_json.containsKey("externalIds")) {
|
| - externalIds = _json["externalIds"].map((value) => new ExternalId.fromJson(value)).toList();
|
| + externalIds = _json["externalIds"]
|
| + .map((value) => new ExternalId.fromJson(value))
|
| + .toList();
|
| }
|
| if (_json.containsKey("names")) {
|
| names = _json["names"];
|
| @@ -3601,12 +3494,14 @@ class ClinicalCondition {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (conceptId != null) {
|
| _json["conceptId"] = conceptId;
|
| }
|
| if (externalIds != null) {
|
| - _json["externalIds"] = externalIds.map((value) => (value).toJson()).toList();
|
| + _json["externalIds"] =
|
| + externalIds.map((value) => (value).toJson()).toList();
|
| }
|
| if (names != null) {
|
| _json["names"] = names;
|
| @@ -3619,17 +3514,14 @@ class ClinicalCondition {
|
| }
|
|
|
| class CodingSequence {
|
| - /**
|
| - * 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.
|
| - */
|
| + /// 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.
|
| core.String end;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String start;
|
|
|
| CodingSequence();
|
| @@ -3644,7 +3536,8 @@ class CodingSequence {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (end != null) {
|
| _json["end"] = end;
|
| }
|
| @@ -3655,18 +3548,19 @@ class CodingSequence {
|
| }
|
| }
|
|
|
| -/**
|
| - * Describes a Compute Engine resource that is being managed by a running
|
| - * pipeline.
|
| - */
|
| +/// Describes a Compute Engine resource that is being managed by a running
|
| +/// pipeline.
|
| class ComputeEngine {
|
| - /** The names of the disks that were created for this pipeline. */
|
| + /// The names of the disks that were created for this pipeline.
|
| core.List<core.String> diskNames;
|
| - /** The instance on which the operation is running. */
|
| +
|
| + /// The instance on which the operation is running.
|
| core.String instanceName;
|
| - /** The machine type of the instance. */
|
| +
|
| + /// The machine type of the instance.
|
| core.String machineType;
|
| - /** The availability zone in which the instance resides. */
|
| +
|
| + /// The availability zone in which the instance resides.
|
| core.String zone;
|
|
|
| ComputeEngine();
|
| @@ -3687,7 +3581,8 @@ class ComputeEngine {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (diskNames != null) {
|
| _json["diskNames"] = diskNames;
|
| }
|
| @@ -3704,17 +3599,15 @@ class ComputeEngine {
|
| }
|
| }
|
|
|
| -/**
|
| - * A bucket over which read coverage has been precomputed. A bucket corresponds
|
| - * to a specific range of the reference sequence.
|
| - */
|
| +/// A bucket over which read coverage has been precomputed. A bucket
|
| +/// corresponds
|
| +/// to a specific range of the reference sequence.
|
| class CoverageBucket {
|
| - /**
|
| - * The average number of reads which are aligned to each individual
|
| - * reference base in this bucket.
|
| - */
|
| + /// The average number of reads which are aligned to each individual
|
| + /// reference base in this bucket.
|
| core.double meanCoverage;
|
| - /** The genomic coordinate range spanned by this bucket. */
|
| +
|
| + /// The genomic coordinate range spanned by this bucket.
|
| Range range;
|
|
|
| CoverageBucket();
|
| @@ -3729,7 +3622,8 @@ class CoverageBucket {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (meanCoverage != null) {
|
| _json["meanCoverage"] = meanCoverage;
|
| }
|
| @@ -3740,20 +3634,21 @@ class CoverageBucket {
|
| }
|
| }
|
|
|
| -/**
|
| - * A Dataset is a collection of genomic data.
|
| - *
|
| - * For more genomics resource definitions, see [Fundamentals of Google
|
| - * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - */
|
| +/// A Dataset is a collection of genomic data.
|
| +///
|
| +/// For more genomics resource definitions, see [Fundamentals of Google
|
| +/// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| class Dataset {
|
| - /** The time this dataset was created, in seconds from the epoch. */
|
| + /// The time this dataset was created, in seconds from the epoch.
|
| core.String createTime;
|
| - /** The server-generated dataset ID, unique across all datasets. */
|
| +
|
| + /// The server-generated dataset ID, unique across all datasets.
|
| core.String id;
|
| - /** The dataset name. */
|
| +
|
| + /// The dataset name.
|
| core.String name;
|
| - /** The Google Cloud project ID that this dataset belongs to. */
|
| +
|
| + /// The Google Cloud project ID that this dataset belongs to.
|
| core.String projectId;
|
|
|
| Dataset();
|
| @@ -3774,7 +3669,8 @@ class Dataset {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (createTime != null) {
|
| _json["createTime"] = createTime;
|
| }
|
| @@ -3791,34 +3687,32 @@ class Dataset {
|
| }
|
| }
|
|
|
| -/**
|
| - * 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 `{}`.
|
| - */
|
| +/// 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 `{}`.
|
| class Empty {
|
| -
|
| Empty();
|
|
|
| - Empty.fromJson(core.Map _json) {
|
| - }
|
| + Empty.fromJson(core.Map _json) {}
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| return _json;
|
| }
|
| }
|
|
|
| class Entry {
|
| - /** The created annotation, if creation was successful. */
|
| + /// The created annotation, if creation was successful.
|
| Annotation annotation;
|
| - /** The creation status. */
|
| +
|
| + /// The creation status.
|
| Status status;
|
|
|
| Entry();
|
| @@ -3833,7 +3727,8 @@ class Entry {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (annotation != null) {
|
| _json["annotation"] = (annotation).toJson();
|
| }
|
| @@ -3845,33 +3740,29 @@ class Entry {
|
| }
|
|
|
| class Exon {
|
| - /**
|
| - * 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.
|
| - */
|
| + /// 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.
|
| core.String end;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.int frame;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String start;
|
|
|
| Exon();
|
| @@ -3889,7 +3780,8 @@ class Exon {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (end != null) {
|
| _json["end"] = end;
|
| }
|
| @@ -3904,25 +3796,22 @@ class Exon {
|
| }
|
|
|
| class Experiment {
|
| - /**
|
| - * The instrument model used as part of this experiment. This maps to
|
| - * sequencing technology in the SAM spec.
|
| - */
|
| + /// The instrument model used as part of this experiment. This maps to
|
| + /// sequencing technology in the SAM spec.
|
| core.String instrumentModel;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String libraryId;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String platformUnit;
|
| - /** The sequencing center used as part of this experiment. */
|
| +
|
| + /// The sequencing center used as part of this experiment.
|
| core.String sequencingCenter;
|
|
|
| Experiment();
|
| @@ -3943,7 +3832,8 @@ class Experiment {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (instrumentModel != null) {
|
| _json["instrumentModel"] = instrumentModel;
|
| }
|
| @@ -3960,24 +3850,20 @@ class Experiment {
|
| }
|
| }
|
|
|
| -/** The read group set export request. */
|
| +/// The read group set export request.
|
| class ExportReadGroupSetRequest {
|
| - /**
|
| - * 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.
|
| - */
|
| + /// 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.
|
| core.String exportUri;
|
| - /**
|
| - * Required. The Google Cloud project ID that owns this
|
| - * export. The caller must have WRITE access to this project.
|
| - */
|
| +
|
| + /// Required. The Google Cloud project ID that owns this
|
| + /// export. The caller must have WRITE access to this project.
|
| core.String projectId;
|
| - /**
|
| - * The reference names to export. If this is not specified, all reference
|
| - * sequences, including unmapped reads, are exported.
|
| - * Use `*` to export only unmapped reads.
|
| - */
|
| +
|
| + /// The reference names to export. If this is not specified, all reference
|
| + /// sequences, including unmapped reads, are exported.
|
| + /// Use `*` to export only unmapped reads.
|
| core.List<core.String> referenceNames;
|
|
|
| ExportReadGroupSetRequest();
|
| @@ -3995,7 +3881,8 @@ class ExportReadGroupSetRequest {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (exportUri != null) {
|
| _json["exportUri"] = exportUri;
|
| }
|
| @@ -4009,36 +3896,32 @@ class ExportReadGroupSetRequest {
|
| }
|
| }
|
|
|
| -/** The variant data export request. */
|
| +/// The variant data export request.
|
| class ExportVariantSetRequest {
|
| - /**
|
| - * Required. The BigQuery dataset to export data to. This dataset must already
|
| - * exist. Note that this is distinct from the Genomics concept of "dataset".
|
| - */
|
| + /// Required. The BigQuery dataset to export data to. This dataset must
|
| + /// already
|
| + /// exist. Note that this is distinct from the Genomics concept of "dataset".
|
| core.String bigqueryDataset;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String bigqueryTable;
|
| - /**
|
| - * If provided, only variant call information from the specified call sets
|
| - * will be exported. By default all variant calls are exported.
|
| - */
|
| +
|
| + /// If provided, only variant call information from the specified call sets
|
| + /// will be exported. By default all variant calls are exported.
|
| core.List<core.String> callSetIds;
|
| - /**
|
| - * The format for the exported data.
|
| - * Possible string values are:
|
| - * - "FORMAT_UNSPECIFIED"
|
| - * - "FORMAT_BIGQUERY" : Export the data to Google BigQuery.
|
| - */
|
| +
|
| + /// The format for the exported data.
|
| + /// Possible string values are:
|
| + /// - "FORMAT_UNSPECIFIED"
|
| + /// - "FORMAT_BIGQUERY" : Export the data to Google BigQuery.
|
| core.String format;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String projectId;
|
|
|
| ExportVariantSetRequest();
|
| @@ -4062,7 +3945,8 @@ class ExportVariantSetRequest {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (bigqueryDataset != null) {
|
| _json["bigqueryDataset"] = bigqueryDataset;
|
| }
|
| @@ -4083,9 +3967,10 @@ class ExportVariantSetRequest {
|
| }
|
|
|
| class ExternalId {
|
| - /** The id used by the source of this data. */
|
| + /// The id used by the source of this data.
|
| core.String id;
|
| - /** The name of the source of this data. */
|
| +
|
| + /// The name of the source of this data.
|
| core.String sourceName;
|
|
|
| ExternalId();
|
| @@ -4100,7 +3985,8 @@ class ExternalId {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (id != null) {
|
| _json["id"] = id;
|
| }
|
| @@ -4111,66 +3997,63 @@ class ExternalId {
|
| }
|
| }
|
|
|
| -/** Request message for `GetIamPolicy` method. */
|
| +/// Request message for `GetIamPolicy` method.
|
| class GetIamPolicyRequest {
|
| -
|
| GetIamPolicyRequest();
|
|
|
| - GetIamPolicyRequest.fromJson(core.Map _json) {
|
| - }
|
| + GetIamPolicyRequest.fromJson(core.Map _json) {}
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| return _json;
|
| }
|
| }
|
|
|
| -/** The read group set import request. */
|
| +/// The read group set import request.
|
| class ImportReadGroupSetsRequest {
|
| - /**
|
| - * Required. The ID of the dataset these read group sets will belong to. The
|
| - * caller must have WRITE permissions to this dataset.
|
| - */
|
| + /// Required. The ID of the dataset these read group sets will belong to. The
|
| + /// caller must have WRITE permissions to this dataset.
|
| core.String datasetId;
|
| - /**
|
| - * The partition strategy describes how read groups are partitioned into read
|
| - * group sets.
|
| - * Possible string values are:
|
| - * - "PARTITION_STRATEGY_UNSPECIFIED"
|
| - * - "PER_FILE_PER_SAMPLE" : In most cases, this strategy yields one read
|
| - * group set per file. This is
|
| - * the default behavior.
|
| - *
|
| - * Allocate one read group set per file per sample. For BAM files, read
|
| - * groups are considered to share a sample if they have identical sample
|
| - * names. Furthermore, all reads for each file which do not belong to a read
|
| - * group, if any, will be grouped into a single read group set per-file.
|
| - * - "MERGE_ALL" : Includes all read groups in all imported files into a
|
| - * single read group
|
| - * set. Requires that the headers for all imported files are equivalent. All
|
| - * reads which do not belong to a read group, if any, will be grouped into a
|
| - * separate read group set.
|
| - */
|
| +
|
| + /// The partition strategy describes how read groups are partitioned into
|
| + /// read
|
| + /// group sets.
|
| + /// Possible string values are:
|
| + /// - "PARTITION_STRATEGY_UNSPECIFIED"
|
| + /// - "PER_FILE_PER_SAMPLE" : In most cases, this strategy yields one read
|
| + /// group set per file. This is
|
| + /// the default behavior.
|
| + ///
|
| + /// Allocate one read group set per file per sample. For BAM files, read
|
| + /// groups are considered to share a sample if they have identical sample
|
| + /// names. Furthermore, all reads for each file which do not belong to a read
|
| + /// group, if any, will be grouped into a single read group set per-file.
|
| + /// - "MERGE_ALL" : Includes all read groups in all imported files into a
|
| + /// single read group
|
| + /// set. Requires that the headers for all imported files are equivalent. All
|
| + /// reads which do not belong to a read group, if any, will be grouped into a
|
| + /// separate read group set.
|
| core.String partitionStrategy;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String referenceSetId;
|
| - /**
|
| - * A list of URIs pointing at [BAM
|
| - * files](https://samtools.github.io/hts-specs/SAMv1.pdf)
|
| - * 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.
|
| - */
|
| +
|
| + /// A list of URIs pointing at [BAM
|
| + /// files](https://samtools.github.io/hts-specs/SAMv1.pdf)
|
| + /// 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.
|
| core.List<core.String> sourceUris;
|
|
|
| ImportReadGroupSetsRequest();
|
| @@ -4191,7 +4074,8 @@ class ImportReadGroupSetsRequest {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (datasetId != null) {
|
| _json["datasetId"] = datasetId;
|
| }
|
| @@ -4208,9 +4092,9 @@ class ImportReadGroupSetsRequest {
|
| }
|
| }
|
|
|
| -/** The read group set import response. */
|
| +/// The read group set import response.
|
| class ImportReadGroupSetsResponse {
|
| - /** IDs of the read group sets that were created. */
|
| + /// IDs of the read group sets that were created.
|
| core.List<core.String> readGroupSetIds;
|
|
|
| ImportReadGroupSetsResponse();
|
| @@ -4222,7 +4106,8 @@ class ImportReadGroupSetsResponse {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (readGroupSetIds != null) {
|
| _json["readGroupSetIds"] = readGroupSetIds;
|
| }
|
| @@ -4230,49 +4115,47 @@ class ImportReadGroupSetsResponse {
|
| }
|
| }
|
|
|
| -/** The variant data import request. */
|
| +/// The variant data import request.
|
| class ImportVariantsRequest {
|
| - /**
|
| - * The format of the variant data being imported. If unspecified, defaults to
|
| - * to `VCF`.
|
| - * Possible string values are:
|
| - * - "FORMAT_UNSPECIFIED"
|
| - * - "FORMAT_VCF" : VCF (Variant Call Format). The VCF files may be gzip
|
| - * compressed. gVCF is
|
| - * also supported. Disclaimer: gzip VCF imports are currently much slower
|
| - * than equivalent uncompressed VCF imports. For this reason, uncompressed
|
| - * VCF is currently recommended for imports with more than 1GB combined
|
| - * uncompressed size, or for time sensitive imports.
|
| - * - "FORMAT_COMPLETE_GENOMICS" : Complete Genomics masterVarBeta format. The
|
| - * masterVarBeta files may
|
| - * be bzip2 compressed.
|
| - */
|
| + /// The format of the variant data being imported. If unspecified, defaults
|
| + /// to
|
| + /// to `VCF`.
|
| + /// Possible string values are:
|
| + /// - "FORMAT_UNSPECIFIED"
|
| + /// - "FORMAT_VCF" : VCF (Variant Call Format). The VCF files may be gzip
|
| + /// compressed. gVCF is
|
| + /// also supported. Disclaimer: gzip VCF imports are currently much slower
|
| + /// than equivalent uncompressed VCF imports. For this reason, uncompressed
|
| + /// VCF is currently recommended for imports with more than 1GB combined
|
| + /// uncompressed size, or for time sensitive imports.
|
| + /// - "FORMAT_COMPLETE_GENOMICS" : Complete Genomics masterVarBeta format.
|
| + /// The masterVarBeta files may
|
| + /// be bzip2 compressed.
|
| core.String format;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.Map<core.String, core.String> infoMergeConfig;
|
| - /**
|
| - * 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".
|
| - */
|
| +
|
| + /// 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".
|
| core.bool normalizeReferenceNames;
|
| - /**
|
| - * A list of URIs referencing variant files in Google Cloud Storage. URIs can
|
| - * include wildcards [as described
|
| - * here](https://cloud.google.com/storage/docs/gsutil/addlhelp/WildcardNames).
|
| - * Note that recursive wildcards ('**') are not supported.
|
| - */
|
| +
|
| + /// A list of URIs referencing variant files in Google Cloud Storage. URIs
|
| + /// can
|
| + /// include wildcards [as described
|
| + /// here](https://cloud.google.com/storage/docs/gsutil/addlhelp/WildcardNames).
|
| + /// Note that recursive wildcards ('**') are not supported.
|
| core.List<core.String> sourceUris;
|
| - /** Required. The variant set to which variant data should be imported. */
|
| +
|
| + /// Required. The variant set to which variant data should be imported.
|
| core.String variantSetId;
|
|
|
| ImportVariantsRequest();
|
| @@ -4296,7 +4179,8 @@ class ImportVariantsRequest {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (format != null) {
|
| _json["format"] = format;
|
| }
|
| @@ -4316,9 +4200,9 @@ class ImportVariantsRequest {
|
| }
|
| }
|
|
|
| -/** The variant data import response. */
|
| +/// The variant data import response.
|
| class ImportVariantsResponse {
|
| - /** IDs of the call sets created during the import. */
|
| + /// IDs of the call sets created during the import.
|
| core.List<core.String> callSetIds;
|
|
|
| ImportVariantsResponse();
|
| @@ -4330,7 +4214,8 @@ class ImportVariantsResponse {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (callSetIds != null) {
|
| _json["callSetIds"] = callSetIds;
|
| }
|
| @@ -4338,32 +4223,30 @@ class ImportVariantsResponse {
|
| }
|
| }
|
|
|
| -/**
|
| - * A linear alignment can be represented by one CIGAR string. Describes the
|
| - * mapped position and local alignment of the read to the reference.
|
| - */
|
| +/// A linear alignment can be represented by one CIGAR string. Describes the
|
| +/// mapped position and local alignment of the read to the reference.
|
| class LinearAlignment {
|
| - /**
|
| - * Represents the local alignment of this sequence (alignment matches, indels,
|
| - * etc) against the reference.
|
| - */
|
| + /// Represents the local alignment of this sequence (alignment matches,
|
| + /// indels,
|
| + /// etc) against the reference.
|
| core.List<CigarUnit> cigar;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.int mappingQuality;
|
| - /** The position of this alignment. */
|
| +
|
| + /// The position of this alignment.
|
| Position position;
|
|
|
| LinearAlignment();
|
|
|
| LinearAlignment.fromJson(core.Map _json) {
|
| if (_json.containsKey("cigar")) {
|
| - cigar = _json["cigar"].map((value) => new CigarUnit.fromJson(value)).toList();
|
| + cigar =
|
| + _json["cigar"].map((value) => new CigarUnit.fromJson(value)).toList();
|
| }
|
| if (_json.containsKey("mappingQuality")) {
|
| mappingQuality = _json["mappingQuality"];
|
| @@ -4374,7 +4257,8 @@ class LinearAlignment {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (cigar != null) {
|
| _json["cigar"] = cigar.map((value) => (value).toJson()).toList();
|
| }
|
| @@ -4389,19 +4273,17 @@ class LinearAlignment {
|
| }
|
|
|
| class ListBasesResponse {
|
| - /**
|
| - * 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.
|
| - */
|
| + /// 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.
|
| core.String nextPageToken;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String offset;
|
| - /** A substring of the bases that make up this reference. */
|
| +
|
| + /// A substring of the bases that make up this reference.
|
| core.String sequence;
|
|
|
| ListBasesResponse();
|
| @@ -4419,7 +4301,8 @@ class ListBasesResponse {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (nextPageToken != null) {
|
| _json["nextPageToken"] = nextPageToken;
|
| }
|
| @@ -4434,25 +4317,22 @@ class ListBasesResponse {
|
| }
|
|
|
| class ListCoverageBucketsResponse {
|
| - /**
|
| - * 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`).
|
| - */
|
| + /// 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`).
|
| core.String bucketWidth;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.List<CoverageBucket> coverageBuckets;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String nextPageToken;
|
|
|
| ListCoverageBucketsResponse();
|
| @@ -4462,7 +4342,9 @@ class ListCoverageBucketsResponse {
|
| bucketWidth = _json["bucketWidth"];
|
| }
|
| if (_json.containsKey("coverageBuckets")) {
|
| - coverageBuckets = _json["coverageBuckets"].map((value) => new CoverageBucket.fromJson(value)).toList();
|
| + coverageBuckets = _json["coverageBuckets"]
|
| + .map((value) => new CoverageBucket.fromJson(value))
|
| + .toList();
|
| }
|
| if (_json.containsKey("nextPageToken")) {
|
| nextPageToken = _json["nextPageToken"];
|
| @@ -4470,12 +4352,14 @@ class ListCoverageBucketsResponse {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (bucketWidth != null) {
|
| _json["bucketWidth"] = bucketWidth;
|
| }
|
| if (coverageBuckets != null) {
|
| - _json["coverageBuckets"] = coverageBuckets.map((value) => (value).toJson()).toList();
|
| + _json["coverageBuckets"] =
|
| + coverageBuckets.map((value) => (value).toJson()).toList();
|
| }
|
| if (nextPageToken != null) {
|
| _json["nextPageToken"] = nextPageToken;
|
| @@ -4484,22 +4368,23 @@ class ListCoverageBucketsResponse {
|
| }
|
| }
|
|
|
| -/** The dataset list response. */
|
| +/// The dataset list response.
|
| class ListDatasetsResponse {
|
| - /** The list of matching Datasets. */
|
| + /// The list of matching Datasets.
|
| core.List<Dataset> datasets;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String nextPageToken;
|
|
|
| ListDatasetsResponse();
|
|
|
| ListDatasetsResponse.fromJson(core.Map _json) {
|
| if (_json.containsKey("datasets")) {
|
| - datasets = _json["datasets"].map((value) => new Dataset.fromJson(value)).toList();
|
| + datasets = _json["datasets"]
|
| + .map((value) => new Dataset.fromJson(value))
|
| + .toList();
|
| }
|
| if (_json.containsKey("nextPageToken")) {
|
| nextPageToken = _json["nextPageToken"];
|
| @@ -4507,7 +4392,8 @@ class ListDatasetsResponse {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (datasets != null) {
|
| _json["datasets"] = datasets.map((value) => (value).toJson()).toList();
|
| }
|
| @@ -4518,11 +4404,12 @@ class ListDatasetsResponse {
|
| }
|
| }
|
|
|
| -/** The response message for Operations.ListOperations. */
|
| +/// The response message for Operations.ListOperations.
|
| class ListOperationsResponse {
|
| - /** The standard List next-page token. */
|
| + /// The standard List next-page token.
|
| core.String nextPageToken;
|
| - /** A list of operations that matches the specified filter in the request. */
|
| +
|
| + /// A list of operations that matches the specified filter in the request.
|
| core.List<Operation> operations;
|
|
|
| ListOperationsResponse();
|
| @@ -4532,31 +4419,35 @@ class ListOperationsResponse {
|
| nextPageToken = _json["nextPageToken"];
|
| }
|
| if (_json.containsKey("operations")) {
|
| - operations = _json["operations"].map((value) => new Operation.fromJson(value)).toList();
|
| + operations = _json["operations"]
|
| + .map((value) => new Operation.fromJson(value))
|
| + .toList();
|
| }
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (nextPageToken != null) {
|
| _json["nextPageToken"] = nextPageToken;
|
| }
|
| if (operations != null) {
|
| - _json["operations"] = operations.map((value) => (value).toJson()).toList();
|
| + _json["operations"] =
|
| + operations.map((value) => (value).toJson()).toList();
|
| }
|
| return _json;
|
| }
|
| }
|
|
|
| class MergeVariantsRequest {
|
| - /**
|
| - * A mapping between info field keys and the InfoMergeOperations to
|
| - * be performed on them.
|
| - */
|
| + /// A mapping between info field keys and the InfoMergeOperations to
|
| + /// be performed on them.
|
| core.Map<core.String, core.String> infoMergeConfig;
|
| - /** The destination variant set. */
|
| +
|
| + /// The destination variant set.
|
| core.String variantSetId;
|
| - /** The variants to be merged with existing variants. */
|
| +
|
| + /// The variants to be merged with existing variants.
|
| core.List<Variant> variants;
|
|
|
| MergeVariantsRequest();
|
| @@ -4569,12 +4460,15 @@ class MergeVariantsRequest {
|
| variantSetId = _json["variantSetId"];
|
| }
|
| if (_json.containsKey("variants")) {
|
| - variants = _json["variants"].map((value) => new Variant.fromJson(value)).toList();
|
| + variants = _json["variants"]
|
| + .map((value) => new Variant.fromJson(value))
|
| + .toList();
|
| }
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (infoMergeConfig != null) {
|
| _json["infoMergeConfig"] = infoMergeConfig;
|
| }
|
| @@ -4588,41 +4482,36 @@ class MergeVariantsRequest {
|
| }
|
| }
|
|
|
| -/**
|
| - * This resource represents a long-running operation that is the result of a
|
| - * network API call.
|
| - */
|
| +/// This resource represents a long-running operation that is the result of a
|
| +/// network API call.
|
| class Operation {
|
| - /**
|
| - * 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.
|
| - */
|
| + /// 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.
|
| core.bool done;
|
| - /** The error result of the operation in case of failure or cancellation. */
|
| +
|
| + /// The error result of the operation in case of failure or cancellation.
|
| Status error;
|
| - /**
|
| - * An OperationMetadata object. This will always be returned with the
|
| - * Operation.
|
| - *
|
| - * The values for Object must be JSON objects. It can consist of `num`,
|
| - * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| - */
|
| +
|
| + /// An OperationMetadata object. This will always be returned with the
|
| + /// Operation.
|
| + ///
|
| + /// The values for Object must be JSON objects. It can consist of `num`,
|
| + /// `String`, `bool` and `null` as well as `Map` and `List` values.
|
| core.Map<core.String, core.Object> metadata;
|
| - /**
|
| - * The server-assigned name, which is only unique within the same service that
|
| - * originally returns it. For example:
|
| - * `operations/CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw`
|
| - */
|
| +
|
| + /// The server-assigned name, which is only unique within the same service
|
| + /// that originally returns it. For example:
|
| + /// `operations/CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw`
|
| core.String name;
|
| - /**
|
| - * If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If
|
| - * importing Variants, an ImportVariantsResponse is returned. For pipelines
|
| - * and exports, an empty response is returned.
|
| - *
|
| - * The values for Object must be JSON objects. It can consist of `num`,
|
| - * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| - */
|
| +
|
| + /// If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned.
|
| + /// If importing Variants, an ImportVariantsResponse is returned. For
|
| + /// pipelines and exports, an empty response is returned.
|
| + ///
|
| + /// The values for Object must be JSON objects. It can consist of `num`,
|
| + /// `String`, `bool` and `null` as well as `Map` and `List` values.
|
| core.Map<core.String, core.Object> response;
|
|
|
| Operation();
|
| @@ -4646,7 +4535,8 @@ class Operation {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (done != null) {
|
| _json["done"] = done;
|
| }
|
| @@ -4666,16 +4556,17 @@ class Operation {
|
| }
|
| }
|
|
|
| -/** An event that occurred during an Operation. */
|
| +/// An event that occurred during an Operation.
|
| class OperationEvent {
|
| - /** Required description of event. */
|
| + /// Required description of event.
|
| core.String description;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String endTime;
|
| - /** Optional time of when event started. */
|
| +
|
| + /// Optional time of when event started.
|
| core.String startTime;
|
|
|
| OperationEvent();
|
| @@ -4693,7 +4584,8 @@ class OperationEvent {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (description != null) {
|
| _json["description"] = description;
|
| }
|
| @@ -4707,47 +4599,48 @@ class OperationEvent {
|
| }
|
| }
|
|
|
| -/** Metadata describing an Operation. */
|
| +/// Metadata describing an Operation.
|
| class OperationMetadata {
|
| - /**
|
| - * This field is deprecated. Use `labels` instead. Optionally provided by the
|
| - * caller when submitting the request that creates the operation.
|
| - */
|
| + /// This field is deprecated. Use `labels` instead. Optionally provided by
|
| + /// the
|
| + /// caller when submitting the request that creates the operation.
|
| core.String clientId;
|
| - /** The time at which the job was submitted to the Genomics service. */
|
| +
|
| + /// The time at which the job was submitted to the Genomics service.
|
| core.String createTime;
|
| - /** The time at which the job stopped running. */
|
| +
|
| + /// The time at which the job stopped running.
|
| core.String endTime;
|
| - /**
|
| - * Optional event messages that were generated during the job's execution.
|
| - * This also contains any warnings that were generated during import
|
| - * or export.
|
| - */
|
| +
|
| + /// Optional event messages that were generated during the job's execution.
|
| + /// This also contains any warnings that were generated during import
|
| + /// or export.
|
| core.List<OperationEvent> events;
|
| - /**
|
| - * Optionally provided by the caller when submitting the request that creates
|
| - * the operation.
|
| - */
|
| +
|
| + /// Optionally provided by the caller when submitting the request that
|
| + /// creates
|
| + /// the operation.
|
| core.Map<core.String, core.String> labels;
|
| - /** The Google Cloud Project in which the job is scoped. */
|
| +
|
| + /// The Google Cloud Project in which the job is scoped.
|
| core.String projectId;
|
| - /**
|
| - * 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.
|
| - *
|
| - * The values for Object must be JSON objects. It can consist of `num`,
|
| - * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| - */
|
| +
|
| + /// 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.
|
| + ///
|
| + /// The values for Object must be JSON objects. It can consist of `num`,
|
| + /// `String`, `bool` and `null` as well as `Map` and `List` values.
|
| core.Map<core.String, core.Object> request;
|
| - /**
|
| - * Runtime metadata on this Operation.
|
| - *
|
| - * The values for Object must be JSON objects. It can consist of `num`,
|
| - * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| - */
|
| +
|
| + /// Runtime metadata on this Operation.
|
| + ///
|
| + /// The values for Object must be JSON objects. It can consist of `num`,
|
| + /// `String`, `bool` and `null` as well as `Map` and `List` values.
|
| core.Map<core.String, core.Object> runtimeMetadata;
|
| - /** The time at which the job began to run. */
|
| +
|
| + /// The time at which the job began to run.
|
| core.String startTime;
|
|
|
| OperationMetadata();
|
| @@ -4763,7 +4656,9 @@ class OperationMetadata {
|
| endTime = _json["endTime"];
|
| }
|
| if (_json.containsKey("events")) {
|
| - events = _json["events"].map((value) => new OperationEvent.fromJson(value)).toList();
|
| + events = _json["events"]
|
| + .map((value) => new OperationEvent.fromJson(value))
|
| + .toList();
|
| }
|
| if (_json.containsKey("labels")) {
|
| labels = _json["labels"];
|
| @@ -4783,7 +4678,8 @@ class OperationMetadata {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (clientId != null) {
|
| _json["clientId"] = clientId;
|
| }
|
| @@ -4815,73 +4711,75 @@ class OperationMetadata {
|
| }
|
| }
|
|
|
| -/**
|
| - * 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](https://cloud.google.com/iam).
|
| - */
|
| +/// 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](https://cloud.google.com/iam).
|
| class Policy {
|
| - /**
|
| - * Associates a list of `members` to a `role`.
|
| - * `bindings` with no members will result in an error.
|
| - */
|
| + /// Associates a list of `members` to a `role`.
|
| + /// `bindings` with no members will result in an error.
|
| core.List<Binding> bindings;
|
| - /**
|
| - * `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.
|
| - */
|
| +
|
| + /// `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.
|
| core.String etag;
|
| core.List<core.int> get etagAsBytes {
|
| return convert.BASE64.decode(etag);
|
| }
|
|
|
| void set etagAsBytes(core.List<core.int> _bytes) {
|
| - etag = convert.BASE64.encode(_bytes).replaceAll("/", "_").replaceAll("+", "-");
|
| + etag =
|
| + convert.BASE64.encode(_bytes).replaceAll("/", "_").replaceAll("+", "-");
|
| }
|
| - /** Version of the `Policy`. The default version is 0. */
|
| +
|
| + /// Version of the `Policy`. The default version is 0.
|
| core.int version;
|
|
|
| Policy();
|
|
|
| Policy.fromJson(core.Map _json) {
|
| if (_json.containsKey("bindings")) {
|
| - bindings = _json["bindings"].map((value) => new Binding.fromJson(value)).toList();
|
| + bindings = _json["bindings"]
|
| + .map((value) => new Binding.fromJson(value))
|
| + .toList();
|
| }
|
| if (_json.containsKey("etag")) {
|
| etag = _json["etag"];
|
| @@ -4892,7 +4790,8 @@ class Policy {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (bindings != null) {
|
| _json["bindings"] = bindings.map((value) => (value).toJson()).toList();
|
| }
|
| @@ -4906,23 +4805,20 @@ class Policy {
|
| }
|
| }
|
|
|
| -/**
|
| - * 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.
|
| - */
|
| +/// 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.
|
| class Position {
|
| - /**
|
| - * The 0-based offset from the start of the forward strand for that reference.
|
| - */
|
| + /// The 0-based offset from the start of the forward strand for that
|
| + /// reference.
|
| core.String position;
|
| - /** The name of the reference in whatever reference set is being used. */
|
| +
|
| + /// The name of the reference in whatever reference set is being used.
|
| core.String referenceName;
|
| - /**
|
| - * Whether this position is on the reverse strand, as opposed to the forward
|
| - * strand.
|
| - */
|
| +
|
| + /// Whether this position is on the reverse strand, as opposed to the forward
|
| + /// strand.
|
| core.bool reverseStrand;
|
|
|
| Position();
|
| @@ -4940,7 +4836,8 @@ class Position {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (position != null) {
|
| _json["position"] = position;
|
| }
|
| @@ -4955,21 +4852,21 @@ class Position {
|
| }
|
|
|
| class Program {
|
| - /** The command line used to run this program. */
|
| + /// The command line used to run this program.
|
| core.String commandLine;
|
| - /**
|
| - * The user specified locally unique ID of the program. Used along with
|
| - * `prevProgramId` to define an ordering between programs.
|
| - */
|
| +
|
| + /// The user specified locally unique ID of the program. Used along with
|
| + /// `prevProgramId` to define an ordering between programs.
|
| core.String id;
|
| - /**
|
| - * The display name of the program. This is typically the colloquial name of
|
| - * the tool used, for example 'bwa' or 'picard'.
|
| - */
|
| +
|
| + /// The display name of the program. This is typically the colloquial name of
|
| + /// the tool used, for example 'bwa' or 'picard'.
|
| core.String name;
|
| - /** The ID of the program run before this one. */
|
| +
|
| + /// The ID of the program run before this one.
|
| core.String prevProgramId;
|
| - /** The version of the program run. */
|
| +
|
| + /// The version of the program run.
|
| core.String version;
|
|
|
| Program();
|
| @@ -4993,7 +4890,8 @@ class Program {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (commandLine != null) {
|
| _json["commandLine"] = commandLine;
|
| }
|
| @@ -5013,16 +4911,16 @@ class Program {
|
| }
|
| }
|
|
|
| -/** A 0-based half-open genomic coordinate range for search requests. */
|
| +/// A 0-based half-open genomic coordinate range for search requests.
|
| class Range {
|
| - /** The end position of the range on the reference, 0-based exclusive. */
|
| + /// The end position of the range on the reference, 0-based exclusive.
|
| core.String end;
|
| - /**
|
| - * The reference sequence name, for example `chr1`,
|
| - * `1`, or `chrX`.
|
| - */
|
| +
|
| + /// The reference sequence name, for example `chr1`,
|
| + /// `1`, or `chrX`.
|
| core.String referenceName;
|
| - /** The start position of the range on the reference, 0-based inclusive. */
|
| +
|
| + /// The start position of the range on the reference, 0-based inclusive.
|
| core.String start;
|
|
|
| Range();
|
| @@ -5040,7 +4938,8 @@ class Range {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (end != null) {
|
| _json["end"] = end;
|
| }
|
| @@ -5054,192 +4953,190 @@ class Range {
|
| }
|
| }
|
|
|
| -/**
|
| - * 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](https://cloud.google.com/genomics/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
|
| - */
|
| +/// 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](https://cloud.google.com/genomics/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
|
| class Read {
|
| - /**
|
| - * 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.
|
| - */
|
| + /// 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.
|
| core.List<core.int> alignedQuality;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String alignedSequence;
|
| - /**
|
| - * The linear alignment for this alignment record. This field is null for
|
| - * unmapped reads.
|
| - */
|
| +
|
| + /// The linear alignment for this alignment record. This field is null for
|
| + /// unmapped reads.
|
| LinearAlignment alignment;
|
| - /** The fragment is a PCR or optical duplicate (SAM flag 0x400). */
|
| +
|
| + /// The fragment is a PCR or optical duplicate (SAM flag 0x400).
|
| core.bool duplicateFragment;
|
| - /**
|
| - * Whether this read did not pass filters, such as platform or vendor quality
|
| - * controls (SAM flag 0x200).
|
| - */
|
| +
|
| + /// Whether this read did not pass filters, such as platform or vendor
|
| + /// quality
|
| + /// controls (SAM flag 0x200).
|
| core.bool failedVendorQualityChecks;
|
| - /** The observed length of the fragment, equivalent to TLEN in SAM. */
|
| +
|
| + /// The observed length of the fragment, equivalent to TLEN in SAM.
|
| core.int fragmentLength;
|
| - /** The fragment name. Equivalent to QNAME (query template name) in SAM. */
|
| +
|
| + /// The fragment name. Equivalent to QNAME (query template name) in SAM.
|
| core.String fragmentName;
|
| - /**
|
| - * The server-generated read ID, unique across all reads. This is different
|
| - * from the `fragmentName`.
|
| - */
|
| +
|
| + /// The server-generated read ID, unique across all reads. This is different
|
| + /// from the `fragmentName`.
|
| core.String id;
|
| - /**
|
| - * A map of additional read alignment information. This must be of the form
|
| - * map<string, string[]> (string key mapping to a list of string values).
|
| - *
|
| - * The values for Object must be JSON objects. It can consist of `num`,
|
| - * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| - */
|
| +
|
| + /// A map of additional read alignment information. This must be of the form
|
| + /// map<string, string[]> (string key mapping to a list of string values).
|
| + ///
|
| + /// The values for Object must be JSON objects. It can consist of `num`,
|
| + /// `String`, `bool` and `null` as well as `Map` and `List` values.
|
| core.Map<core.String, core.List<core.Object>> info;
|
| - /**
|
| - * The mapping of the primary alignment of the
|
| - * `(readNumber+1)%numberReads` read in the fragment. It replaces
|
| - * mate position and mate strand in SAM.
|
| - */
|
| +
|
| + /// The mapping of the primary alignment of the
|
| + /// `(readNumber+1)%numberReads` read in the fragment. It replaces
|
| + /// mate position and mate strand in SAM.
|
| Position nextMatePosition;
|
| - /** The number of reads in the fragment (extension to SAM flag 0x1). */
|
| +
|
| + /// The number of reads in the fragment (extension to SAM flag 0x1).
|
| core.int numberReads;
|
| - /**
|
| - * The orientation and the distance between reads from the fragment are
|
| - * consistent with the sequencing protocol (SAM flag 0x2).
|
| - */
|
| +
|
| + /// The orientation and the distance between reads from the fragment are
|
| + /// consistent with the sequencing protocol (SAM flag 0x2).
|
| core.bool properPlacement;
|
| - /**
|
| - * 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).
|
| - */
|
| +
|
| + /// 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).
|
| core.String readGroupId;
|
| - /**
|
| - * The ID of the read group set this read belongs to. A read belongs to
|
| - * exactly one read group set.
|
| - */
|
| +
|
| + /// The ID of the read group set this read belongs to. A read belongs to
|
| + /// exactly one read group set.
|
| core.String readGroupSetId;
|
| - /**
|
| - * The read number in sequencing. 0-based and less than numberReads. This
|
| - * field replaces SAM flag 0x40 and 0x80.
|
| - */
|
| +
|
| + /// The read number in sequencing. 0-based and less than numberReads. This
|
| + /// field replaces SAM flag 0x40 and 0x80.
|
| core.int readNumber;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.bool secondaryAlignment;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.bool supplementaryAlignment;
|
|
|
| Read();
|
| @@ -5299,7 +5196,8 @@ class Read {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (alignedQuality != null) {
|
| _json["alignedQuality"] = alignedQuality;
|
| }
|
| @@ -5355,49 +5253,49 @@ class Read {
|
| }
|
| }
|
|
|
| -/**
|
| - * A read group is all the data that's processed the same way by the sequencer.
|
| - */
|
| +/// A read group is all the data that's processed the same way by the
|
| +/// sequencer.
|
| class ReadGroup {
|
| - /** The dataset to which this read group belongs. */
|
| + /// The dataset to which this read group belongs.
|
| core.String datasetId;
|
| - /** A free-form text description of this read group. */
|
| +
|
| + /// A free-form text description of this read group.
|
| core.String description;
|
| - /** The experiment used to generate this read group. */
|
| +
|
| + /// The experiment used to generate this read group.
|
| Experiment experiment;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String id;
|
| - /**
|
| - * A map of additional read group information. This must be of the form
|
| - * map<string, string[]> (string key mapping to a list of string values).
|
| - *
|
| - * The values for Object must be JSON objects. It can consist of `num`,
|
| - * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| - */
|
| +
|
| + /// A map of additional read group information. This must be of the form
|
| + /// map<string, string[]> (string key mapping to a list of string values).
|
| + ///
|
| + /// The values for Object must be JSON objects. It can consist of `num`,
|
| + /// `String`, `bool` and `null` as well as `Map` and `List` values.
|
| core.Map<core.String, core.List<core.Object>> info;
|
| - /**
|
| - * The read group name. This corresponds to the @RG ID field in the SAM spec.
|
| - */
|
| +
|
| + /// The read group name. This corresponds to the @RG ID field in the SAM
|
| + /// spec.
|
| core.String name;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.int predictedInsertSize;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.List<Program> programs;
|
| - /** The reference set the reads in this read group are aligned to. */
|
| +
|
| + /// The reference set the reads in this read group are aligned to.
|
| core.String referenceSetId;
|
| - /** A client-supplied sample identifier for the reads in this read group. */
|
| +
|
| + /// A client-supplied sample identifier for the reads in this read group.
|
| core.String sampleId;
|
|
|
| ReadGroup();
|
| @@ -5425,7 +5323,9 @@ class ReadGroup {
|
| predictedInsertSize = _json["predictedInsertSize"];
|
| }
|
| if (_json.containsKey("programs")) {
|
| - programs = _json["programs"].map((value) => new Program.fromJson(value)).toList();
|
| + programs = _json["programs"]
|
| + .map((value) => new Program.fromJson(value))
|
| + .toList();
|
| }
|
| if (_json.containsKey("referenceSetId")) {
|
| referenceSetId = _json["referenceSetId"];
|
| @@ -5436,7 +5336,8 @@ class ReadGroup {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (datasetId != null) {
|
| _json["datasetId"] = datasetId;
|
| }
|
| @@ -5471,50 +5372,45 @@ class ReadGroup {
|
| }
|
| }
|
|
|
| -/**
|
| - * 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](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - */
|
| +/// 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](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| class ReadGroupSet {
|
| - /** The dataset to which this read group set belongs. */
|
| + /// The dataset to which this read group set belongs.
|
| core.String datasetId;
|
| - /**
|
| - * The filename of the original source file for this read group set, if any.
|
| - */
|
| +
|
| + /// The filename of the original source file for this read group set, if any.
|
| core.String filename;
|
| - /**
|
| - * The server-generated read group set ID, unique for all read group sets.
|
| - */
|
| +
|
| + /// The server-generated read group set ID, unique for all read group sets.
|
| core.String id;
|
| - /**
|
| - * A map of additional read group set information.
|
| - *
|
| - * The values for Object must be JSON objects. It can consist of `num`,
|
| - * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| - */
|
| +
|
| + /// A map of additional read group set information.
|
| + ///
|
| + /// The values for Object must be JSON objects. It can consist of `num`,
|
| + /// `String`, `bool` and `null` as well as `Map` and `List` values.
|
| core.Map<core.String, core.List<core.Object>> info;
|
| - /**
|
| - * The read group set name. By default this will be initialized to the sample
|
| - * name of the sequenced data contained in this set.
|
| - */
|
| +
|
| + /// The read group set name. By default this will be initialized to the
|
| + /// sample
|
| + /// name of the sequenced data contained in this set.
|
| core.String name;
|
| - /**
|
| - * The read groups in this set. There are typically 1-10 read groups in a read
|
| - * group set.
|
| - */
|
| +
|
| + /// The read groups in this set. There are typically 1-10 read groups in a
|
| + /// read
|
| + /// group set.
|
| core.List<ReadGroup> readGroups;
|
| - /**
|
| - * The reference set to which the reads in this read group set are aligned.
|
| - */
|
| +
|
| + /// The reference set to which the reads in this read group set are aligned.
|
| core.String referenceSetId;
|
|
|
| ReadGroupSet();
|
| @@ -5536,7 +5432,9 @@ class ReadGroupSet {
|
| name = _json["name"];
|
| }
|
| if (_json.containsKey("readGroups")) {
|
| - readGroups = _json["readGroups"].map((value) => new ReadGroup.fromJson(value)).toList();
|
| + readGroups = _json["readGroups"]
|
| + .map((value) => new ReadGroup.fromJson(value))
|
| + .toList();
|
| }
|
| if (_json.containsKey("referenceSetId")) {
|
| referenceSetId = _json["referenceSetId"];
|
| @@ -5544,7 +5442,8 @@ class ReadGroupSet {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (datasetId != null) {
|
| _json["datasetId"] = datasetId;
|
| }
|
| @@ -5561,7 +5460,8 @@ class ReadGroupSet {
|
| _json["name"] = name;
|
| }
|
| if (readGroups != null) {
|
| - _json["readGroups"] = readGroups.map((value) => (value).toJson()).toList();
|
| + _json["readGroups"] =
|
| + readGroups.map((value) => (value).toJson()).toList();
|
| }
|
| if (referenceSetId != null) {
|
| _json["referenceSetId"] = referenceSetId;
|
| @@ -5570,41 +5470,40 @@ class ReadGroupSet {
|
| }
|
| }
|
|
|
| -/**
|
| - * 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](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - */
|
| +/// 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](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| class Reference {
|
| - /** The server-generated reference ID, unique across all references. */
|
| + /// The server-generated reference ID, unique across all references.
|
| core.String id;
|
| - /** The length of this reference's sequence. */
|
| +
|
| + /// The length of this reference's sequence.
|
| core.String length;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String md5checksum;
|
| - /** The name of this reference, for example `22`. */
|
| +
|
| + /// The name of this reference, for example `22`.
|
| core.String name;
|
| - /**
|
| - * ID from http://www.ncbi.nlm.nih.gov/taxonomy. For example, 9606 for human.
|
| - */
|
| +
|
| + /// ID from http://www.ncbi.nlm.nih.gov/taxonomy. For example, 9606 for
|
| + /// human.
|
| core.int ncbiTaxonId;
|
| - /**
|
| - * All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
|
| - * with a version number, for example `GCF_000001405.26`.
|
| - */
|
| +
|
| + /// All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
|
| + /// with a version number, for example `GCF_000001405.26`.
|
| core.List<core.String> sourceAccessions;
|
| - /**
|
| - * The URI from which the sequence was obtained. Typically specifies a FASTA
|
| - * format file.
|
| - */
|
| +
|
| + /// The URI from which the sequence was obtained. Typically specifies a FASTA
|
| + /// format file.
|
| core.String sourceUri;
|
|
|
| Reference();
|
| @@ -5634,7 +5533,8 @@ class Reference {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (id != null) {
|
| _json["id"] = id;
|
| }
|
| @@ -5660,17 +5560,14 @@ class Reference {
|
| }
|
| }
|
|
|
| -/**
|
| - * ReferenceBound records an upper bound for the starting coordinate of
|
| - * variants in a particular reference.
|
| - */
|
| +/// ReferenceBound records an upper bound for the starting coordinate of
|
| +/// variants in a particular reference.
|
| class ReferenceBound {
|
| - /** The name of the reference associated with this reference bound. */
|
| + /// The name of the reference associated with this reference bound.
|
| core.String referenceName;
|
| - /**
|
| - * An upper bound (inclusive) on the starting coordinate of any
|
| - * variant in the reference sequence.
|
| - */
|
| +
|
| + /// An upper bound (inclusive) on the starting coordinate of any
|
| + /// variant in the reference sequence.
|
| core.String upperBound;
|
|
|
| ReferenceBound();
|
| @@ -5685,7 +5582,8 @@ class ReferenceBound {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (referenceName != null) {
|
| _json["referenceName"] = referenceName;
|
| }
|
| @@ -5696,52 +5594,51 @@ class ReferenceBound {
|
| }
|
| }
|
|
|
| -/**
|
| - * 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](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - */
|
| +/// 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](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| class ReferenceSet {
|
| - /** Public id of this reference set, such as `GRCh37`. */
|
| + /// Public id of this reference set, such as `GRCh37`.
|
| core.String assemblyId;
|
| - /** Free text description of this reference set. */
|
| +
|
| + /// Free text description of this reference set.
|
| core.String description;
|
| - /**
|
| - * The server-generated reference set ID, unique across all reference sets.
|
| - */
|
| +
|
| + /// The server-generated reference set ID, unique across all reference sets.
|
| core.String id;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String md5checksum;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.int ncbiTaxonId;
|
| - /**
|
| - * The IDs of the reference objects that are part of this set.
|
| - * `Reference.md5checksum` must be unique within this set.
|
| - */
|
| +
|
| + /// The IDs of the reference objects that are part of this set.
|
| + /// `Reference.md5checksum` must be unique within this set.
|
| core.List<core.String> referenceIds;
|
| - /**
|
| - * All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
|
| - * with a version number, for example `NC_000001.11`.
|
| - */
|
| +
|
| + /// All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
|
| + /// with a version number, for example `NC_000001.11`.
|
| core.List<core.String> sourceAccessions;
|
| - /** The URI from which the references were obtained. */
|
| +
|
| + /// The URI from which the references were obtained.
|
| core.String sourceUri;
|
|
|
| ReferenceSet();
|
| @@ -5774,7 +5671,8 @@ class ReferenceSet {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (assemblyId != null) {
|
| _json["assemblyId"] = assemblyId;
|
| }
|
| @@ -5803,13 +5701,11 @@ class ReferenceSet {
|
| }
|
| }
|
|
|
| -/**
|
| - * Runtime metadata that will be populated in the
|
| - * runtimeMetadata
|
| - * field of the Operation associated with a RunPipeline execution.
|
| - */
|
| +/// Runtime metadata that will be populated in the
|
| +/// runtimeMetadata
|
| +/// field of the Operation associated with a RunPipeline execution.
|
| class RuntimeMetadata {
|
| - /** Execution information specific to Google Compute Engine. */
|
| + /// Execution information specific to Google Compute Engine.
|
| ComputeEngine computeEngine;
|
|
|
| RuntimeMetadata();
|
| @@ -5821,7 +5717,8 @@ class RuntimeMetadata {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (computeEngine != null) {
|
| _json["computeEngine"] = (computeEngine).toJson();
|
| }
|
| @@ -5830,36 +5727,32 @@ class RuntimeMetadata {
|
| }
|
|
|
| class SearchAnnotationSetsRequest {
|
| - /**
|
| - * Required. The dataset IDs to search within. Caller must have `READ` access
|
| - * to these datasets.
|
| - */
|
| + /// Required. The dataset IDs to search within. Caller must have `READ`
|
| + /// access
|
| + /// to these datasets.
|
| core.List<core.String> datasetIds;
|
| - /**
|
| - * Only return annotations sets for which a substring of the name matches this
|
| - * string (case insensitive).
|
| - */
|
| +
|
| + /// Only return annotations sets for which a substring of the name matches
|
| + /// this
|
| + /// string (case insensitive).
|
| core.String name;
|
| - /**
|
| - * The maximum number of results to return in a single page. If unspecified,
|
| - * defaults to 128. The maximum value is 1024.
|
| - */
|
| +
|
| + /// The maximum number of results to return in a single page. If unspecified,
|
| + /// defaults to 128. The maximum value is 1024.
|
| core.int pageSize;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String pageToken;
|
| - /**
|
| - * If specified, only annotation sets associated with the given reference set
|
| - * are returned.
|
| - */
|
| +
|
| + /// If specified, only annotation sets associated with the given reference
|
| + /// set
|
| + /// are returned.
|
| core.String referenceSetId;
|
| - /**
|
| - * If specified, only annotation sets that have any of these types are
|
| - * returned.
|
| - */
|
| +
|
| + /// If specified, only annotation sets that have any of these types are
|
| + /// returned.
|
| core.List<core.String> types;
|
|
|
| SearchAnnotationSetsRequest();
|
| @@ -5886,7 +5779,8 @@ class SearchAnnotationSetsRequest {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (datasetIds != null) {
|
| _json["datasetIds"] = datasetIds;
|
| }
|
| @@ -5910,20 +5804,21 @@ class SearchAnnotationSetsRequest {
|
| }
|
|
|
| class SearchAnnotationSetsResponse {
|
| - /** The matching annotation sets. */
|
| + /// The matching annotation sets.
|
| core.List<AnnotationSet> annotationSets;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String nextPageToken;
|
|
|
| SearchAnnotationSetsResponse();
|
|
|
| SearchAnnotationSetsResponse.fromJson(core.Map _json) {
|
| if (_json.containsKey("annotationSets")) {
|
| - annotationSets = _json["annotationSets"].map((value) => new AnnotationSet.fromJson(value)).toList();
|
| + annotationSets = _json["annotationSets"]
|
| + .map((value) => new AnnotationSet.fromJson(value))
|
| + .toList();
|
| }
|
| if (_json.containsKey("nextPageToken")) {
|
| nextPageToken = _json["nextPageToken"];
|
| @@ -5931,9 +5826,11 @@ class SearchAnnotationSetsResponse {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (annotationSets != null) {
|
| - _json["annotationSets"] = annotationSets.map((value) => (value).toJson()).toList();
|
| + _json["annotationSets"] =
|
| + annotationSets.map((value) => (value).toJson()).toList();
|
| }
|
| if (nextPageToken != null) {
|
| _json["nextPageToken"] = nextPageToken;
|
| @@ -5943,44 +5840,38 @@ class SearchAnnotationSetsResponse {
|
| }
|
|
|
| class SearchAnnotationsRequest {
|
| - /**
|
| - * 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.
|
| - */
|
| + /// 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.
|
| core.List<core.String> annotationSetIds;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String end;
|
| - /**
|
| - * The maximum number of results to return in a single page. If unspecified,
|
| - * defaults to 256. The maximum value is 2048.
|
| - */
|
| +
|
| + /// The maximum number of results to return in a single page. If unspecified,
|
| + /// defaults to 256. The maximum value is 2048.
|
| core.int pageSize;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String pageToken;
|
| - /** The ID of the reference to query. */
|
| +
|
| + /// The ID of the reference to query.
|
| core.String referenceId;
|
| - /**
|
| - * The name of the reference to query, within the reference set associated
|
| - * with this query.
|
| - */
|
| +
|
| + /// The name of the reference to query, within the reference set associated
|
| + /// with this query.
|
| core.String referenceName;
|
| - /**
|
| - * The start position of the range on the reference, 0-based inclusive. If
|
| - * specified,
|
| - * referenceId or
|
| - * referenceName
|
| - * must be specified. Defaults to 0.
|
| - */
|
| +
|
| + /// The start position of the range on the reference, 0-based inclusive. If
|
| + /// specified,
|
| + /// referenceId or
|
| + /// referenceName
|
| + /// must be specified. Defaults to 0.
|
| core.String start;
|
|
|
| SearchAnnotationsRequest();
|
| @@ -6010,7 +5901,8 @@ class SearchAnnotationsRequest {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (annotationSetIds != null) {
|
| _json["annotationSetIds"] = annotationSetIds;
|
| }
|
| @@ -6037,20 +5929,21 @@ class SearchAnnotationsRequest {
|
| }
|
|
|
| class SearchAnnotationsResponse {
|
| - /** The matching annotations. */
|
| + /// The matching annotations.
|
| core.List<Annotation> annotations;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String nextPageToken;
|
|
|
| SearchAnnotationsResponse();
|
|
|
| SearchAnnotationsResponse.fromJson(core.Map _json) {
|
| if (_json.containsKey("annotations")) {
|
| - annotations = _json["annotations"].map((value) => new Annotation.fromJson(value)).toList();
|
| + annotations = _json["annotations"]
|
| + .map((value) => new Annotation.fromJson(value))
|
| + .toList();
|
| }
|
| if (_json.containsKey("nextPageToken")) {
|
| nextPageToken = _json["nextPageToken"];
|
| @@ -6058,9 +5951,11 @@ class SearchAnnotationsResponse {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (annotations != null) {
|
| - _json["annotations"] = annotations.map((value) => (value).toJson()).toList();
|
| + _json["annotations"] =
|
| + annotations.map((value) => (value).toJson()).toList();
|
| }
|
| if (nextPageToken != null) {
|
| _json["nextPageToken"] = nextPageToken;
|
| @@ -6069,28 +5964,24 @@ class SearchAnnotationsResponse {
|
| }
|
| }
|
|
|
| -/** The call set search request. */
|
| +/// The call set search request.
|
| class SearchCallSetsRequest {
|
| - /**
|
| - * Only return call sets for which a substring of the name matches this
|
| - * string.
|
| - */
|
| + /// Only return call sets for which a substring of the name matches this
|
| + /// string.
|
| core.String name;
|
| - /**
|
| - * The maximum number of results to return in a single page. If unspecified,
|
| - * defaults to 1024.
|
| - */
|
| +
|
| + /// The maximum number of results to return in a single page. If unspecified,
|
| + /// defaults to 1024.
|
| core.int pageSize;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String pageToken;
|
| - /**
|
| - * Restrict the query to call sets within the given variant sets. At least one
|
| - * ID must be provided.
|
| - */
|
| +
|
| + /// Restrict the query to call sets within the given variant sets. At least
|
| + /// one
|
| + /// ID must be provided.
|
| core.List<core.String> variantSetIds;
|
|
|
| SearchCallSetsRequest();
|
| @@ -6111,7 +6002,8 @@ class SearchCallSetsRequest {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (name != null) {
|
| _json["name"] = name;
|
| }
|
| @@ -6128,22 +6020,23 @@ class SearchCallSetsRequest {
|
| }
|
| }
|
|
|
| -/** The call set search response. */
|
| +/// The call set search response.
|
| class SearchCallSetsResponse {
|
| - /** The list of matching call sets. */
|
| + /// The list of matching call sets.
|
| core.List<CallSet> callSets;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String nextPageToken;
|
|
|
| SearchCallSetsResponse();
|
|
|
| SearchCallSetsResponse.fromJson(core.Map _json) {
|
| if (_json.containsKey("callSets")) {
|
| - callSets = _json["callSets"].map((value) => new CallSet.fromJson(value)).toList();
|
| + callSets = _json["callSets"]
|
| + .map((value) => new CallSet.fromJson(value))
|
| + .toList();
|
| }
|
| if (_json.containsKey("nextPageToken")) {
|
| nextPageToken = _json["nextPageToken"];
|
| @@ -6151,7 +6044,8 @@ class SearchCallSetsResponse {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (callSets != null) {
|
| _json["callSets"] = callSets.map((value) => (value).toJson()).toList();
|
| }
|
| @@ -6162,28 +6056,25 @@ class SearchCallSetsResponse {
|
| }
|
| }
|
|
|
| -/** The read group set search request. */
|
| +/// The read group set search request.
|
| class SearchReadGroupSetsRequest {
|
| - /**
|
| - * Restricts this query to read group sets within the given datasets. At least
|
| - * one ID must be provided.
|
| - */
|
| + /// Restricts this query to read group sets within the given datasets. At
|
| + /// least
|
| + /// one ID must be provided.
|
| core.List<core.String> datasetIds;
|
| - /**
|
| - * Only return read group sets for which a substring of the name matches this
|
| - * string.
|
| - */
|
| +
|
| + /// Only return read group sets for which a substring of the name matches
|
| + /// this
|
| + /// string.
|
| core.String name;
|
| - /**
|
| - * The maximum number of results to return in a single page. If unspecified,
|
| - * defaults to 256. The maximum value is 1024.
|
| - */
|
| +
|
| + /// The maximum number of results to return in a single page. If unspecified,
|
| + /// defaults to 256. The maximum value is 1024.
|
| core.int pageSize;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String pageToken;
|
|
|
| SearchReadGroupSetsRequest();
|
| @@ -6204,7 +6095,8 @@ class SearchReadGroupSetsRequest {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (datasetIds != null) {
|
| _json["datasetIds"] = datasetIds;
|
| }
|
| @@ -6221,15 +6113,14 @@ class SearchReadGroupSetsRequest {
|
| }
|
| }
|
|
|
| -/** The read group set search response. */
|
| +/// The read group set search response.
|
| class SearchReadGroupSetsResponse {
|
| - /**
|
| - * 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.
|
| - */
|
| + /// 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.
|
| core.String nextPageToken;
|
| - /** The list of matching read group sets. */
|
| +
|
| + /// The list of matching read group sets.
|
| core.List<ReadGroupSet> readGroupSets;
|
|
|
| SearchReadGroupSetsResponse();
|
| @@ -6239,63 +6130,63 @@ class SearchReadGroupSetsResponse {
|
| nextPageToken = _json["nextPageToken"];
|
| }
|
| if (_json.containsKey("readGroupSets")) {
|
| - readGroupSets = _json["readGroupSets"].map((value) => new ReadGroupSet.fromJson(value)).toList();
|
| + readGroupSets = _json["readGroupSets"]
|
| + .map((value) => new ReadGroupSet.fromJson(value))
|
| + .toList();
|
| }
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (nextPageToken != null) {
|
| _json["nextPageToken"] = nextPageToken;
|
| }
|
| if (readGroupSets != null) {
|
| - _json["readGroupSets"] = readGroupSets.map((value) => (value).toJson()).toList();
|
| + _json["readGroupSets"] =
|
| + readGroupSets.map((value) => (value).toJson()).toList();
|
| }
|
| return _json;
|
| }
|
| }
|
|
|
| -/** The read search request. */
|
| +/// The read search request.
|
| class SearchReadsRequest {
|
| - /**
|
| - * The end position of the range on the reference, 0-based exclusive. If
|
| - * specified, `referenceName` must also be specified.
|
| - */
|
| + /// The end position of the range on the reference, 0-based exclusive. If
|
| + /// specified, `referenceName` must also be specified.
|
| core.String end;
|
| - /**
|
| - * The maximum number of results to return in a single page. If unspecified,
|
| - * defaults to 256. The maximum value is 2048.
|
| - */
|
| +
|
| + /// The maximum number of results to return in a single page. If unspecified,
|
| + /// defaults to 256. The maximum value is 2048.
|
| core.int pageSize;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String pageToken;
|
| - /**
|
| - * 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`.
|
| - */
|
| +
|
| + /// 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`.
|
| core.List<core.String> readGroupIds;
|
| - /**
|
| - * 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`.
|
| - */
|
| +
|
| + /// 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`.
|
| core.List<core.String> readGroupSetIds;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String referenceName;
|
| - /**
|
| - * The start position of the range on the reference, 0-based inclusive. If
|
| - * specified, `referenceName` must also be specified.
|
| - */
|
| +
|
| + /// The start position of the range on the reference, 0-based inclusive. If
|
| + /// specified, `referenceName` must also be specified.
|
| core.String start;
|
|
|
| SearchReadsRequest();
|
| @@ -6325,7 +6216,8 @@ class SearchReadsRequest {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (end != null) {
|
| _json["end"] = end;
|
| }
|
| @@ -6351,27 +6243,25 @@ class SearchReadsRequest {
|
| }
|
| }
|
|
|
| -/** The read search response. */
|
| +/// The read search response.
|
| class SearchReadsResponse {
|
| - /**
|
| - * 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.
|
| - */
|
| + /// 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.
|
| core.List<Read> alignments;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String nextPageToken;
|
|
|
| SearchReadsResponse();
|
|
|
| SearchReadsResponse.fromJson(core.Map _json) {
|
| if (_json.containsKey("alignments")) {
|
| - alignments = _json["alignments"].map((value) => new Read.fromJson(value)).toList();
|
| + alignments =
|
| + _json["alignments"].map((value) => new Read.fromJson(value)).toList();
|
| }
|
| if (_json.containsKey("nextPageToken")) {
|
| nextPageToken = _json["nextPageToken"];
|
| @@ -6379,9 +6269,11 @@ class SearchReadsResponse {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (alignments != null) {
|
| - _json["alignments"] = alignments.map((value) => (value).toJson()).toList();
|
| + _json["alignments"] =
|
| + alignments.map((value) => (value).toJson()).toList();
|
| }
|
| if (nextPageToken != null) {
|
| _json["nextPageToken"] = nextPageToken;
|
| @@ -6391,33 +6283,28 @@ class SearchReadsResponse {
|
| }
|
|
|
| class SearchReferenceSetsRequest {
|
| - /**
|
| - * 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`.
|
| - */
|
| + /// 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`.
|
| core.List<core.String> accessions;
|
| - /**
|
| - * If present, return reference sets for which a substring of their
|
| - * `assemblyId` matches this string (case insensitive).
|
| - */
|
| +
|
| + /// If present, return reference sets for which a substring of their
|
| + /// `assemblyId` matches this string (case insensitive).
|
| core.String assemblyId;
|
| - /**
|
| - * If present, return reference sets for which the
|
| - * md5checksum matches exactly.
|
| - */
|
| +
|
| + /// If present, return reference sets for which the
|
| + /// md5checksum matches exactly.
|
| core.List<core.String> md5checksums;
|
| - /**
|
| - * The maximum number of results to return in a single page. If unspecified,
|
| - * defaults to 1024. The maximum value is 4096.
|
| - */
|
| +
|
| + /// The maximum number of results to return in a single page. If unspecified,
|
| + /// defaults to 1024. The maximum value is 4096.
|
| core.int pageSize;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String pageToken;
|
|
|
| SearchReferenceSetsRequest();
|
| @@ -6441,7 +6328,8 @@ class SearchReferenceSetsRequest {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (accessions != null) {
|
| _json["accessions"] = accessions;
|
| }
|
| @@ -6462,13 +6350,12 @@ class SearchReferenceSetsRequest {
|
| }
|
|
|
| class SearchReferenceSetsResponse {
|
| - /**
|
| - * 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.
|
| - */
|
| + /// 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.
|
| core.String nextPageToken;
|
| - /** The matching references sets. */
|
| +
|
| + /// The matching references sets.
|
| core.List<ReferenceSet> referenceSets;
|
|
|
| SearchReferenceSetsResponse();
|
| @@ -6478,47 +6365,48 @@ class SearchReferenceSetsResponse {
|
| nextPageToken = _json["nextPageToken"];
|
| }
|
| if (_json.containsKey("referenceSets")) {
|
| - referenceSets = _json["referenceSets"].map((value) => new ReferenceSet.fromJson(value)).toList();
|
| + referenceSets = _json["referenceSets"]
|
| + .map((value) => new ReferenceSet.fromJson(value))
|
| + .toList();
|
| }
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (nextPageToken != null) {
|
| _json["nextPageToken"] = nextPageToken;
|
| }
|
| if (referenceSets != null) {
|
| - _json["referenceSets"] = referenceSets.map((value) => (value).toJson()).toList();
|
| + _json["referenceSets"] =
|
| + referenceSets.map((value) => (value).toJson()).toList();
|
| }
|
| return _json;
|
| }
|
| }
|
|
|
| class SearchReferencesRequest {
|
| - /**
|
| - * 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`.
|
| - */
|
| + /// 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`.
|
| core.List<core.String> accessions;
|
| - /**
|
| - * If present, return references for which the
|
| - * md5checksum matches exactly.
|
| - */
|
| +
|
| + /// If present, return references for which the
|
| + /// md5checksum matches exactly.
|
| core.List<core.String> md5checksums;
|
| - /**
|
| - * The maximum number of results to return in a single page. If unspecified,
|
| - * defaults to 1024. The maximum value is 4096.
|
| - */
|
| +
|
| + /// The maximum number of results to return in a single page. If unspecified,
|
| + /// defaults to 1024. The maximum value is 4096.
|
| core.int pageSize;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String pageToken;
|
| - /** If present, return only references which belong to this reference set. */
|
| +
|
| + /// If present, return only references which belong to this reference set.
|
| core.String referenceSetId;
|
|
|
| SearchReferencesRequest();
|
| @@ -6542,7 +6430,8 @@ class SearchReferencesRequest {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (accessions != null) {
|
| _json["accessions"] = accessions;
|
| }
|
| @@ -6563,13 +6452,12 @@ class SearchReferencesRequest {
|
| }
|
|
|
| class SearchReferencesResponse {
|
| - /**
|
| - * 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.
|
| - */
|
| + /// 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.
|
| core.String nextPageToken;
|
| - /** The matching references. */
|
| +
|
| + /// The matching references.
|
| core.List<Reference> references;
|
|
|
| SearchReferencesResponse();
|
| @@ -6579,39 +6467,39 @@ class SearchReferencesResponse {
|
| nextPageToken = _json["nextPageToken"];
|
| }
|
| if (_json.containsKey("references")) {
|
| - references = _json["references"].map((value) => new Reference.fromJson(value)).toList();
|
| + references = _json["references"]
|
| + .map((value) => new Reference.fromJson(value))
|
| + .toList();
|
| }
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (nextPageToken != null) {
|
| _json["nextPageToken"] = nextPageToken;
|
| }
|
| if (references != null) {
|
| - _json["references"] = references.map((value) => (value).toJson()).toList();
|
| + _json["references"] =
|
| + references.map((value) => (value).toJson()).toList();
|
| }
|
| return _json;
|
| }
|
| }
|
|
|
| -/** The search variant sets request. */
|
| +/// The search variant sets request.
|
| class SearchVariantSetsRequest {
|
| - /**
|
| - * Exactly one dataset ID must be provided here. Only variant sets which
|
| - * belong to this dataset will be returned.
|
| - */
|
| + /// Exactly one dataset ID must be provided here. Only variant sets which
|
| + /// belong to this dataset will be returned.
|
| core.List<core.String> datasetIds;
|
| - /**
|
| - * The maximum number of results to return in a single page. If unspecified,
|
| - * defaults to 1024.
|
| - */
|
| +
|
| + /// The maximum number of results to return in a single page. If unspecified,
|
| + /// defaults to 1024.
|
| core.int pageSize;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String pageToken;
|
|
|
| SearchVariantSetsRequest();
|
| @@ -6629,7 +6517,8 @@ class SearchVariantSetsRequest {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (datasetIds != null) {
|
| _json["datasetIds"] = datasetIds;
|
| }
|
| @@ -6643,15 +6532,14 @@ class SearchVariantSetsRequest {
|
| }
|
| }
|
|
|
| -/** The search variant sets response. */
|
| +/// The search variant sets response.
|
| class SearchVariantSetsResponse {
|
| - /**
|
| - * 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.
|
| - */
|
| + /// 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.
|
| core.String nextPageToken;
|
| - /** The variant sets belonging to the requested dataset. */
|
| +
|
| + /// The variant sets belonging to the requested dataset.
|
| core.List<VariantSet> variantSets;
|
|
|
| SearchVariantSetsResponse();
|
| @@ -6661,67 +6549,68 @@ class SearchVariantSetsResponse {
|
| nextPageToken = _json["nextPageToken"];
|
| }
|
| if (_json.containsKey("variantSets")) {
|
| - variantSets = _json["variantSets"].map((value) => new VariantSet.fromJson(value)).toList();
|
| + variantSets = _json["variantSets"]
|
| + .map((value) => new VariantSet.fromJson(value))
|
| + .toList();
|
| }
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (nextPageToken != null) {
|
| _json["nextPageToken"] = nextPageToken;
|
| }
|
| if (variantSets != null) {
|
| - _json["variantSets"] = variantSets.map((value) => (value).toJson()).toList();
|
| + _json["variantSets"] =
|
| + variantSets.map((value) => (value).toJson()).toList();
|
| }
|
| return _json;
|
| }
|
| }
|
|
|
| -/** The variant search request. */
|
| +/// The variant search request.
|
| class SearchVariantsRequest {
|
| - /**
|
| - * 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.
|
| - */
|
| + /// 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.
|
| core.List<core.String> callSetIds;
|
| - /**
|
| - * The end of the window, 0-based exclusive. If unspecified or 0, defaults to
|
| - * the length of the reference.
|
| - */
|
| +
|
| + /// The end of the window, 0-based exclusive. If unspecified or 0, defaults
|
| + /// to
|
| + /// the length of the reference.
|
| core.String end;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.int maxCalls;
|
| - /**
|
| - * The maximum number of variants to return in a single page. If unspecified,
|
| - * defaults to 5000. The maximum value is 10000.
|
| - */
|
| +
|
| + /// The maximum number of variants to return in a single page. If
|
| + /// unspecified,
|
| + /// defaults to 5000. The maximum value is 10000.
|
| core.int pageSize;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String pageToken;
|
| - /** Required. Only return variants in this reference sequence. */
|
| +
|
| + /// Required. Only return variants in this reference sequence.
|
| core.String referenceName;
|
| - /**
|
| - * The beginning of the window (0-based, inclusive) for which
|
| - * overlapping variants should be returned. If unspecified, defaults to 0.
|
| - */
|
| +
|
| + /// The beginning of the window (0-based, inclusive) for which
|
| + /// overlapping variants should be returned. If unspecified, defaults to 0.
|
| core.String start;
|
| - /** Only return variants which have exactly this name. */
|
| +
|
| + /// Only return variants which have exactly this name.
|
| core.String variantName;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.List<core.String> variantSetIds;
|
|
|
| SearchVariantsRequest();
|
| @@ -6757,7 +6646,8 @@ class SearchVariantsRequest {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (callSetIds != null) {
|
| _json["callSetIds"] = callSetIds;
|
| }
|
| @@ -6789,15 +6679,14 @@ class SearchVariantsRequest {
|
| }
|
| }
|
|
|
| -/** The variant search response. */
|
| +/// The variant search response.
|
| class SearchVariantsResponse {
|
| - /**
|
| - * 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.
|
| - */
|
| + /// 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.
|
| core.String nextPageToken;
|
| - /** The list of matching Variants. */
|
| +
|
| + /// The list of matching Variants.
|
| core.List<Variant> variants;
|
|
|
| SearchVariantsResponse();
|
| @@ -6807,12 +6696,15 @@ class SearchVariantsResponse {
|
| nextPageToken = _json["nextPageToken"];
|
| }
|
| if (_json.containsKey("variants")) {
|
| - variants = _json["variants"].map((value) => new Variant.fromJson(value)).toList();
|
| + variants = _json["variants"]
|
| + .map((value) => new Variant.fromJson(value))
|
| + .toList();
|
| }
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (nextPageToken != null) {
|
| _json["nextPageToken"] = nextPageToken;
|
| }
|
| @@ -6823,14 +6715,13 @@ class SearchVariantsResponse {
|
| }
|
| }
|
|
|
| -/** Request message for `SetIamPolicy` method. */
|
| +/// Request message for `SetIamPolicy` method.
|
| class SetIamPolicyRequest {
|
| - /**
|
| - * 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.
|
| - */
|
| + /// 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.
|
| Policy policy;
|
|
|
| SetIamPolicyRequest();
|
| @@ -6842,7 +6733,8 @@ class SetIamPolicyRequest {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (policy != null) {
|
| _json["policy"] = (policy).toJson();
|
| }
|
| @@ -6850,78 +6742,81 @@ class SetIamPolicyRequest {
|
| }
|
| }
|
|
|
| -/**
|
| - * 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](https://github.com/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` that 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.
|
| - *
|
| - * - 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.
|
| - */
|
| +/// 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](https://github.com/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` that 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.
|
| +///
|
| +/// - 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.
|
| class Status {
|
| - /** The status code, which should be an enum value of google.rpc.Code. */
|
| + /// The status code, which should be an enum value of google.rpc.Code.
|
| core.int code;
|
| - /**
|
| - * A list of messages that carry the error details. There is a common set of
|
| - * message types for APIs to use.
|
| - *
|
| - * The values for Object must be JSON objects. It can consist of `num`,
|
| - * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| - */
|
| +
|
| + /// A list of messages that carry the error details. There is a common set
|
| + /// of
|
| + /// message types for APIs to use.
|
| + ///
|
| + /// The values for Object must be JSON objects. It can consist of `num`,
|
| + /// `String`, `bool` and `null` as well as `Map` and `List` values.
|
| core.List<core.Map<core.String, core.Object>> details;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String message;
|
|
|
| Status();
|
| @@ -6939,7 +6834,8 @@ class Status {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (code != null) {
|
| _json["code"] = code;
|
| }
|
| @@ -6953,21 +6849,19 @@ class Status {
|
| }
|
| }
|
|
|
| -/** Request message for `TestIamPermissions` method. */
|
| +/// Request message for `TestIamPermissions` method.
|
| class TestIamPermissionsRequest {
|
| - /**
|
| - * 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`
|
| - */
|
| + /// 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`
|
| core.List<core.String> permissions;
|
|
|
| TestIamPermissionsRequest();
|
| @@ -6979,7 +6873,8 @@ class TestIamPermissionsRequest {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (permissions != null) {
|
| _json["permissions"] = permissions;
|
| }
|
| @@ -6987,12 +6882,10 @@ class TestIamPermissionsRequest {
|
| }
|
| }
|
|
|
| -/** Response message for `TestIamPermissions` method. */
|
| +/// Response message for `TestIamPermissions` method.
|
| class TestIamPermissionsResponse {
|
| - /**
|
| - * A subset of `TestPermissionsRequest.permissions` that the caller is
|
| - * allowed.
|
| - */
|
| + /// A subset of `TestPermissionsRequest.permissions` that the caller is
|
| + /// allowed.
|
| core.List<core.String> permissions;
|
|
|
| TestIamPermissionsResponse();
|
| @@ -7004,7 +6897,8 @@ class TestIamPermissionsResponse {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (permissions != null) {
|
| _json["permissions"] = permissions;
|
| }
|
| @@ -7012,47 +6906,47 @@ class TestIamPermissionsResponse {
|
| }
|
| }
|
|
|
| -/**
|
| - * A transcript represents the assertion that a particular region of the
|
| - * reference genome may be transcribed as RNA.
|
| - */
|
| +/// A transcript represents the assertion that a particular region of the
|
| +/// reference genome may be transcribed as RNA.
|
| class Transcript {
|
| - /**
|
| - * 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.
|
| - */
|
| + /// 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.
|
| CodingSequence codingSequence;
|
| - /**
|
| - * The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> 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.
|
| - */
|
| +
|
| + /// The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> 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.
|
| core.List<Exon> exons;
|
| - /**
|
| - * The annotation ID of the gene from which this transcript is transcribed.
|
| - */
|
| +
|
| + /// The annotation ID of the gene from which this transcript is transcribed.
|
| core.String geneId;
|
|
|
| Transcript();
|
| @@ -7070,7 +6964,8 @@ class Transcript {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (codingSequence != null) {
|
| _json["codingSequence"] = (codingSequence).toJson();
|
| }
|
| @@ -7085,87 +6980,81 @@ class Transcript {
|
| }
|
|
|
| class UndeleteDatasetRequest {
|
| -
|
| UndeleteDatasetRequest();
|
|
|
| - UndeleteDatasetRequest.fromJson(core.Map _json) {
|
| - }
|
| + UndeleteDatasetRequest.fromJson(core.Map _json) {}
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| return _json;
|
| }
|
| }
|
|
|
| -/**
|
| - * 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](https://cloud.google.com/genomics/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.
|
| - */
|
| +/// 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](https://cloud.google.com/genomics/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.
|
| class Variant {
|
| - /** The bases that appear instead of the reference bases. */
|
| + /// The bases that appear instead of the reference bases.
|
| core.List<core.String> alternateBases;
|
| - /**
|
| - * The variant calls for this particular variant. Each one represents the
|
| - * determination of genotype with respect to this variant.
|
| - */
|
| +
|
| + /// The variant calls for this particular variant. Each one represents the
|
| + /// determination of genotype with respect to this variant.
|
| core.List<VariantCall> calls;
|
| - /** The date this variant was created, in milliseconds from the epoch. */
|
| +
|
| + /// The date this variant was created, in milliseconds from the epoch.
|
| core.String created;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String end;
|
| - /**
|
| - * A list of filters (normally quality filters) this variant has failed.
|
| - * `PASS` indicates this variant has passed all filters.
|
| - */
|
| +
|
| + /// A list of filters (normally quality filters) this variant has failed.
|
| + /// `PASS` indicates this variant has passed all filters.
|
| core.List<core.String> filter;
|
| - /** The server-generated variant ID, unique across all variants. */
|
| +
|
| + /// The server-generated variant ID, unique across all variants.
|
| core.String id;
|
| - /**
|
| - * A map of additional variant information. This must be of the form
|
| - * map<string, string[]> (string key mapping to a list of string values).
|
| - *
|
| - * The values for Object must be JSON objects. It can consist of `num`,
|
| - * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| - */
|
| +
|
| + /// A map of additional variant information. This must be of the form
|
| + /// map<string, string[]> (string key mapping to a list of string values).
|
| + ///
|
| + /// The values for Object must be JSON objects. It can consist of `num`,
|
| + /// `String`, `bool` and `null` as well as `Map` and `List` values.
|
| core.Map<core.String, core.List<core.Object>> info;
|
| - /** Names for the variant, for example a RefSNP ID. */
|
| +
|
| + /// Names for the variant, for example a RefSNP ID.
|
| core.List<core.String> names;
|
| - /**
|
| - * A measure of how likely this variant is to be real.
|
| - * A higher value is better.
|
| - */
|
| +
|
| + /// A measure of how likely this variant is to be real.
|
| + /// A higher value is better.
|
| core.double quality;
|
| - /**
|
| - * The reference bases for this variant. They start at the given
|
| - * position.
|
| - */
|
| +
|
| + /// The reference bases for this variant. They start at the given
|
| + /// position.
|
| core.String referenceBases;
|
| - /**
|
| - * The reference on which this variant occurs.
|
| - * (such as `chr20` or `X`)
|
| - */
|
| +
|
| + /// The reference on which this variant occurs.
|
| + /// (such as `chr20` or `X`)
|
| core.String referenceName;
|
| - /**
|
| - * The position at which this variant occurs (0-based).
|
| - * This corresponds to the first base of the string of reference bases.
|
| - */
|
| +
|
| + /// The position at which this variant occurs (0-based).
|
| + /// This corresponds to the first base of the string of reference bases.
|
| core.String start;
|
| - /** The ID of the variant set this variant belongs to. */
|
| +
|
| + /// The ID of the variant set this variant belongs to.
|
| core.String variantSetId;
|
|
|
| Variant();
|
| @@ -7175,7 +7064,9 @@ class Variant {
|
| alternateBases = _json["alternateBases"];
|
| }
|
| if (_json.containsKey("calls")) {
|
| - calls = _json["calls"].map((value) => new VariantCall.fromJson(value)).toList();
|
| + calls = _json["calls"]
|
| + .map((value) => new VariantCall.fromJson(value))
|
| + .toList();
|
| }
|
| if (_json.containsKey("created")) {
|
| created = _json["created"];
|
| @@ -7213,7 +7104,8 @@ class Variant {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (alternateBases != null) {
|
| _json["alternateBases"] = alternateBases;
|
| }
|
| @@ -7258,100 +7150,93 @@ class Variant {
|
| }
|
|
|
| class VariantAnnotation {
|
| - /**
|
| - * 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.
|
| - */
|
| + /// 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.
|
| core.String alternateBases;
|
| - /**
|
| - * 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/
|
| - * Possible string values are:
|
| - * - "CLINICAL_SIGNIFICANCE_UNSPECIFIED"
|
| - * - "CLINICAL_SIGNIFICANCE_OTHER" : `OTHER` should be used when no other
|
| - * clinical significance
|
| - * value will suffice.
|
| - * - "UNCERTAIN"
|
| - * - "BENIGN"
|
| - * - "LIKELY_BENIGN"
|
| - * - "LIKELY_PATHOGENIC"
|
| - * - "PATHOGENIC"
|
| - * - "DRUG_RESPONSE"
|
| - * - "HISTOCOMPATIBILITY"
|
| - * - "CONFERS_SENSITIVITY"
|
| - * - "RISK_FACTOR"
|
| - * - "ASSOCIATION"
|
| - * - "PROTECTIVE"
|
| - * - "MULTIPLE_REPORTED" : `MULTIPLE_REPORTED` should be used when multiple
|
| - * clinical
|
| - * signficances are reported for a variant. The original clinical
|
| - * significance values may be provided in the `info` field.
|
| - */
|
| +
|
| + /// 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/
|
| + /// Possible string values are:
|
| + /// - "CLINICAL_SIGNIFICANCE_UNSPECIFIED"
|
| + /// - "CLINICAL_SIGNIFICANCE_OTHER" : `OTHER` should be used when no other
|
| + /// clinical significance
|
| + /// value will suffice.
|
| + /// - "UNCERTAIN"
|
| + /// - "BENIGN"
|
| + /// - "LIKELY_BENIGN"
|
| + /// - "LIKELY_PATHOGENIC"
|
| + /// - "PATHOGENIC"
|
| + /// - "DRUG_RESPONSE"
|
| + /// - "HISTOCOMPATIBILITY"
|
| + /// - "CONFERS_SENSITIVITY"
|
| + /// - "RISK_FACTOR"
|
| + /// - "ASSOCIATION"
|
| + /// - "PROTECTIVE"
|
| + /// - "MULTIPLE_REPORTED" : `MULTIPLE_REPORTED` should be used when multiple
|
| + /// clinical
|
| + /// signficances are reported for a variant. The original clinical
|
| + /// significance values may be provided in the `info` field.
|
| core.String clinicalSignificance;
|
| - /**
|
| - * The set of conditions associated with this variant.
|
| - * A condition describes the way a variant influences human health.
|
| - */
|
| +
|
| + /// The set of conditions associated with this variant.
|
| + /// A condition describes the way a variant influences human health.
|
| core.List<ClinicalCondition> conditions;
|
| - /**
|
| - * Effect of the variant on the coding sequence.
|
| - * Possible string values are:
|
| - * - "EFFECT_UNSPECIFIED"
|
| - * - "EFFECT_OTHER" : `EFFECT_OTHER` should be used when no other Effect
|
| - * will suffice.
|
| - * - "FRAMESHIFT" : `FRAMESHIFT` indicates a mutation in which the insertion
|
| - * or
|
| - * deletion of nucleotides resulted in a frameshift change.
|
| - * - "FRAME_PRESERVING_INDEL" : `FRAME_PRESERVING_INDEL` indicates a mutation
|
| - * in which a
|
| - * multiple of three nucleotides has been inserted or deleted, resulting
|
| - * in no change to the reading frame of the coding sequence.
|
| - * - "SYNONYMOUS_SNP" : `SYNONYMOUS_SNP` indicates a single nucleotide
|
| - * polymorphism
|
| - * mutation that results in no amino acid change.
|
| - * - "NONSYNONYMOUS_SNP" : `NONSYNONYMOUS_SNP` indicates a single nucleotide
|
| - * polymorphism mutation that results in an amino acid change.
|
| - * - "STOP_GAIN" : `STOP_GAIN` indicates a mutation that leads to the creation
|
| - * of a stop codon at the variant site. Frameshift mutations creating
|
| - * downstream stop codons do not count as `STOP_GAIN`.
|
| - * - "STOP_LOSS" : `STOP_LOSS` indicates a mutation that eliminates a
|
| - * stop codon at the variant site.
|
| - * - "SPLICE_SITE_DISRUPTION" : `SPLICE_SITE_DISRUPTION` indicates that this
|
| - * variant is
|
| - * found in a splice site for the associated transcript, and alters the
|
| - * normal splicing pattern.
|
| - */
|
| +
|
| + /// Effect of the variant on the coding sequence.
|
| + /// Possible string values are:
|
| + /// - "EFFECT_UNSPECIFIED"
|
| + /// - "EFFECT_OTHER" : `EFFECT_OTHER` should be used when no other Effect
|
| + /// will suffice.
|
| + /// - "FRAMESHIFT" : `FRAMESHIFT` indicates a mutation in which the insertion
|
| + /// or
|
| + /// deletion of nucleotides resulted in a frameshift change.
|
| + /// - "FRAME_PRESERVING_INDEL" : `FRAME_PRESERVING_INDEL` indicates a
|
| + /// mutation in which a
|
| + /// multiple of three nucleotides has been inserted or deleted, resulting
|
| + /// in no change to the reading frame of the coding sequence.
|
| + /// - "SYNONYMOUS_SNP" : `SYNONYMOUS_SNP` indicates a single nucleotide
|
| + /// polymorphism
|
| + /// mutation that results in no amino acid change.
|
| + /// - "NONSYNONYMOUS_SNP" : `NONSYNONYMOUS_SNP` indicates a single nucleotide
|
| + /// polymorphism mutation that results in an amino acid change.
|
| + /// - "STOP_GAIN" : `STOP_GAIN` indicates a mutation that leads to the
|
| + /// creation
|
| + /// of a stop codon at the variant site. Frameshift mutations creating
|
| + /// downstream stop codons do not count as `STOP_GAIN`.
|
| + /// - "STOP_LOSS" : `STOP_LOSS` indicates a mutation that eliminates a
|
| + /// stop codon at the variant site.
|
| + /// - "SPLICE_SITE_DISRUPTION" : `SPLICE_SITE_DISRUPTION` indicates that this
|
| + /// variant is
|
| + /// found in a splice site for the associated transcript, and alters the
|
| + /// normal splicing pattern.
|
| core.String effect;
|
| - /**
|
| - * Google annotation ID of the gene affected by this variant. This should
|
| - * be provided when the variant is created.
|
| - */
|
| +
|
| + /// Google annotation ID of the gene affected by this variant. This should
|
| + /// be provided when the variant is created.
|
| core.String geneId;
|
| - /**
|
| - * Google annotation IDs of the transcripts affected by this variant. These
|
| - * should be provided when the variant is created.
|
| - */
|
| +
|
| + /// Google annotation IDs of the transcripts affected by this variant. These
|
| + /// should be provided when the variant is created.
|
| core.List<core.String> transcriptIds;
|
| - /**
|
| - * Type has been adapted from ClinVar's list of variant types.
|
| - * Possible string values are:
|
| - * - "TYPE_UNSPECIFIED"
|
| - * - "TYPE_OTHER" : `TYPE_OTHER` should be used when no other Type will
|
| - * suffice.
|
| - * Further explanation of the variant type may be included in the
|
| - * info field.
|
| - * - "INSERTION" : `INSERTION` indicates an insertion.
|
| - * - "DELETION" : `DELETION` indicates a deletion.
|
| - * - "SUBSTITUTION" : `SUBSTITUTION` indicates a block substitution of
|
| - * two or more nucleotides.
|
| - * - "SNP" : `SNP` indicates a single nucleotide polymorphism.
|
| - * - "STRUCTURAL" : `STRUCTURAL` indicates a large structural variant,
|
| - * including chromosomal fusions, inversions, etc.
|
| - * - "CNV" : `CNV` indicates a variation in copy number.
|
| - */
|
| +
|
| + /// Type has been adapted from ClinVar's list of variant types.
|
| + /// Possible string values are:
|
| + /// - "TYPE_UNSPECIFIED"
|
| + /// - "TYPE_OTHER" : `TYPE_OTHER` should be used when no other Type will
|
| + /// suffice.
|
| + /// Further explanation of the variant type may be included in the
|
| + /// info field.
|
| + /// - "INSERTION" : `INSERTION` indicates an insertion.
|
| + /// - "DELETION" : `DELETION` indicates a deletion.
|
| + /// - "SUBSTITUTION" : `SUBSTITUTION` indicates a block substitution of
|
| + /// two or more nucleotides.
|
| + /// - "SNP" : `SNP` indicates a single nucleotide polymorphism.
|
| + /// - "STRUCTURAL" : `STRUCTURAL` indicates a large structural variant,
|
| + /// including chromosomal fusions, inversions, etc.
|
| + /// - "CNV" : `CNV` indicates a variation in copy number.
|
| core.String type;
|
|
|
| VariantAnnotation();
|
| @@ -7364,7 +7249,9 @@ class VariantAnnotation {
|
| clinicalSignificance = _json["clinicalSignificance"];
|
| }
|
| if (_json.containsKey("conditions")) {
|
| - conditions = _json["conditions"].map((value) => new ClinicalCondition.fromJson(value)).toList();
|
| + conditions = _json["conditions"]
|
| + .map((value) => new ClinicalCondition.fromJson(value))
|
| + .toList();
|
| }
|
| if (_json.containsKey("effect")) {
|
| effect = _json["effect"];
|
| @@ -7381,7 +7268,8 @@ class VariantAnnotation {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (alternateBases != null) {
|
| _json["alternateBases"] = alternateBases;
|
| }
|
| @@ -7389,7 +7277,8 @@ class VariantAnnotation {
|
| _json["clinicalSignificance"] = clinicalSignificance;
|
| }
|
| if (conditions != null) {
|
| - _json["conditions"] = conditions.map((value) => (value).toJson()).toList();
|
| + _json["conditions"] =
|
| + conditions.map((value) => (value).toJson()).toList();
|
| }
|
| if (effect != null) {
|
| _json["effect"] = effect;
|
| @@ -7407,56 +7296,52 @@ class VariantAnnotation {
|
| }
|
| }
|
|
|
| -/**
|
| - * 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.
|
| - */
|
| +/// 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.
|
| class VariantCall {
|
| - /** The ID of the call set this variant call belongs to. */
|
| + /// The ID of the call set this variant call belongs to.
|
| core.String callSetId;
|
| - /** The name of the call set this variant call belongs to. */
|
| +
|
| + /// The name of the call set this variant call belongs to.
|
| core.String callSetName;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.List<core.int> genotype;
|
| - /**
|
| - * 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`.
|
| - */
|
| +
|
| + /// 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`.
|
| core.List<core.double> genotypeLikelihood;
|
| - /**
|
| - * A map of additional variant call information. This must be of the form
|
| - * map<string, string[]> (string key mapping to a list of string values).
|
| - *
|
| - * The values for Object must be JSON objects. It can consist of `num`,
|
| - * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| - */
|
| +
|
| + /// A map of additional variant call information. This must be of the form
|
| + /// map<string, string[]> (string key mapping to a list of string values).
|
| + ///
|
| + /// The values for Object must be JSON objects. It can consist of `num`,
|
| + /// `String`, `bool` and `null` as well as `Map` and `List` values.
|
| core.Map<core.String, core.List<core.Object>> info;
|
| - /**
|
| - * 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 `*`.
|
| - */
|
| +
|
| + /// 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 `*`.
|
| core.String phaseset;
|
|
|
| VariantCall();
|
| @@ -7483,7 +7368,8 @@ class VariantCall {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (callSetId != null) {
|
| _json["callSetId"] = callSetId;
|
| }
|
| @@ -7506,41 +7392,43 @@ class VariantCall {
|
| }
|
| }
|
|
|
| -/**
|
| - * 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](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| - */
|
| +/// 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](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
|
| class VariantSet {
|
| - /** The dataset to which this variant set belongs. */
|
| + /// The dataset to which this variant set belongs.
|
| core.String datasetId;
|
| - /** A textual description of this variant set. */
|
| +
|
| + /// A textual description of this variant set.
|
| core.String description;
|
| - /** The server-generated variant set ID, unique across all variant sets. */
|
| +
|
| + /// The server-generated variant set ID, unique across all variant sets.
|
| core.String id;
|
| - /** The metadata associated with this variant set. */
|
| +
|
| + /// The metadata associated with this variant set.
|
| core.List<VariantSetMetadata> metadata;
|
| - /** User-specified, mutable name. */
|
| +
|
| + /// User-specified, mutable name.
|
| core.String name;
|
| - /**
|
| - * A list of all references used by the variants in a variant set
|
| - * with associated coordinate upper bounds for each one.
|
| - */
|
| +
|
| + /// A list of all references used by the variants in a variant set
|
| + /// with associated coordinate upper bounds for each one.
|
| core.List<ReferenceBound> referenceBounds;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String referenceSetId;
|
|
|
| VariantSet();
|
| @@ -7556,13 +7444,17 @@ class VariantSet {
|
| id = _json["id"];
|
| }
|
| if (_json.containsKey("metadata")) {
|
| - metadata = _json["metadata"].map((value) => new VariantSetMetadata.fromJson(value)).toList();
|
| + metadata = _json["metadata"]
|
| + .map((value) => new VariantSetMetadata.fromJson(value))
|
| + .toList();
|
| }
|
| if (_json.containsKey("name")) {
|
| name = _json["name"];
|
| }
|
| if (_json.containsKey("referenceBounds")) {
|
| - referenceBounds = _json["referenceBounds"].map((value) => new ReferenceBound.fromJson(value)).toList();
|
| + referenceBounds = _json["referenceBounds"]
|
| + .map((value) => new ReferenceBound.fromJson(value))
|
| + .toList();
|
| }
|
| if (_json.containsKey("referenceSetId")) {
|
| referenceSetId = _json["referenceSetId"];
|
| @@ -7570,7 +7462,8 @@ class VariantSet {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (datasetId != null) {
|
| _json["datasetId"] = datasetId;
|
| }
|
| @@ -7587,7 +7480,8 @@ class VariantSet {
|
| _json["name"] = name;
|
| }
|
| if (referenceBounds != null) {
|
| - _json["referenceBounds"] = referenceBounds.map((value) => (value).toJson()).toList();
|
| + _json["referenceBounds"] =
|
| + referenceBounds.map((value) => (value).toJson()).toList();
|
| }
|
| if (referenceSetId != null) {
|
| _json["referenceSetId"] = referenceSetId;
|
| @@ -7596,49 +7490,45 @@ class VariantSet {
|
| }
|
| }
|
|
|
| -/**
|
| - * 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.
|
| - */
|
| +/// 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.
|
| class VariantSetMetadata {
|
| - /** A textual description of this metadata. */
|
| + /// A textual description of this metadata.
|
| core.String description;
|
| - /**
|
| - * 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.
|
| - */
|
| +
|
| + /// 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.
|
| core.String id;
|
| - /**
|
| - * Remaining structured metadata key-value pairs. This must be of the form
|
| - * map<string, string[]> (string key mapping to a list of string values).
|
| - *
|
| - * The values for Object must be JSON objects. It can consist of `num`,
|
| - * `String`, `bool` and `null` as well as `Map` and `List` values.
|
| - */
|
| +
|
| + /// Remaining structured metadata key-value pairs. This must be of the form
|
| + /// map<string, string[]> (string key mapping to a list of string values).
|
| + ///
|
| + /// The values for Object must be JSON objects. It can consist of `num`,
|
| + /// `String`, `bool` and `null` as well as `Map` and `List` values.
|
| core.Map<core.String, core.List<core.Object>> info;
|
| - /** The top-level key. */
|
| +
|
| + /// The top-level key.
|
| core.String key;
|
| - /**
|
| - * The number of values that can be included in a field described by this
|
| - * metadata.
|
| - */
|
| +
|
| + /// The number of values that can be included in a field described by this
|
| + /// metadata.
|
| core.String number;
|
| - /**
|
| - * The type of data. Possible types include: Integer, Float,
|
| - * Flag, Character, and String.
|
| - * Possible string values are:
|
| - * - "TYPE_UNSPECIFIED"
|
| - * - "INTEGER"
|
| - * - "FLOAT"
|
| - * - "FLAG"
|
| - * - "CHARACTER"
|
| - * - "STRING"
|
| - */
|
| +
|
| + /// The type of data. Possible types include: Integer, Float,
|
| + /// Flag, Character, and String.
|
| + /// Possible string values are:
|
| + /// - "TYPE_UNSPECIFIED"
|
| + /// - "INTEGER"
|
| + /// - "FLOAT"
|
| + /// - "FLAG"
|
| + /// - "CHARACTER"
|
| + /// - "STRING"
|
| core.String type;
|
| - /** The value field for simple metadata */
|
| +
|
| + /// The value field for simple metadata
|
| core.String value;
|
|
|
| VariantSetMetadata();
|
| @@ -7668,7 +7558,8 @@ class VariantSetMetadata {
|
| }
|
|
|
| core.Map<core.String, core.Object> toJson() {
|
| - final core.Map<core.String, core.Object> _json = new core.Map<core.String, core.Object>();
|
| + final core.Map<core.String, core.Object> _json =
|
| + new core.Map<core.String, core.Object>();
|
| if (description != null) {
|
| _json["description"] = description;
|
| }
|
|
|
Chromium Code Reviews
Issue 3006323002:
Api-Roll 54: 2017-09-11 (Closed)
