| Index: generated/googleapis_beta/lib/genomics/v1beta2.dart
|
| diff --git a/generated/googleapis_beta/lib/genomics/v1beta2.dart b/generated/googleapis_beta/lib/genomics/v1beta2.dart
|
| deleted file mode 100644
|
| index 73a9eac1a3a4f46aaa94e86ff5fc5bceecc2d614..0000000000000000000000000000000000000000
|
| --- a/generated/googleapis_beta/lib/genomics/v1beta2.dart
|
| +++ /dev/null
|
| @@ -1,6974 +0,0 @@
|
| -// This is a generated file (see the discoveryapis_generator project).
|
| -
|
| -library googleapis_beta.genomics.v1beta2;
|
| -
|
| -import 'dart:core' as core;
|
| -import 'dart:async' as async;
|
| -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;
|
| -
|
| -const core.String USER_AGENT = 'dart-api-client genomics/v1beta2';
|
| -
|
| -/** Provides access to Genomics data. */
|
| -class GenomicsApi {
|
| - /** 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";
|
| -
|
| - /** Manage your data in Google Cloud Storage */
|
| - static const DevstorageReadWriteScope = "https://www.googleapis.com/auth/devstorage.read_write";
|
| -
|
| - /** 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";
|
| -
|
| -
|
| - final commons.ApiRequester _requester;
|
| -
|
| - AnnotationSetsResourceApi get annotationSets => new AnnotationSetsResourceApi(_requester);
|
| - AnnotationsResourceApi get annotations => new AnnotationsResourceApi(_requester);
|
| - CallsetsResourceApi get callsets => new CallsetsResourceApi(_requester);
|
| - DatasetsResourceApi get datasets => new DatasetsResourceApi(_requester);
|
| - ExperimentalResourceApi get experimental => new ExperimentalResourceApi(_requester);
|
| - JobsResourceApi get jobs => new JobsResourceApi(_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);
|
| - VariantsResourceApi get variants => new VariantsResourceApi(_requester);
|
| - VariantsetsResourceApi get variantsets => new VariantsetsResourceApi(_requester);
|
| -
|
| - GenomicsApi(http.Client client, {core.String rootUrl: "https://www.googleapis.com/", core.String servicePath: "genomics/v1beta2/"}) :
|
| - _requester = new commons.ApiRequester(client, rootUrl, servicePath, USER_AGENT);
|
| -}
|
| -
|
| -
|
| -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 must be provided when creating an annotation set:
|
| - * - 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();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| - _url = 'annotationSets';
|
| -
|
| - 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 [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 delete(core.String annotationSetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (annotationSetId == null) {
|
| - throw new core.ArgumentError("Parameter annotationSetId is required.");
|
| - }
|
| -
|
| - _downloadOptions = null;
|
| -
|
| - _url = 'annotationSets/' + commons.Escaper.ecapeVariable('$annotationSetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "DELETE",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => null);
|
| - }
|
| -
|
| - /**
|
| - * Gets an annotation set. Caller must have READ permission for the associated
|
| - * dataset.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [annotationSetId] - The ID of the annotation set to be retrieved.
|
| - *
|
| - * Completes with a [AnnotationSet].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<AnnotationSet> get(core.String annotationSetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (annotationSetId == null) {
|
| - throw new core.ArgumentError("Parameter annotationSetId is required.");
|
| - }
|
| -
|
| - _url = 'annotationSets/' + commons.Escaper.ecapeVariable('$annotationSetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "GET",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new AnnotationSet.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. This method
|
| - * supports patch semantics.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [annotationSetId] - The ID of the annotation set to 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> patch(AnnotationSet request, core.String annotationSetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| - if (annotationSetId == null) {
|
| - throw new core.ArgumentError("Parameter annotationSetId is required.");
|
| - }
|
| -
|
| - _url = 'annotationSets/' + commons.Escaper.ecapeVariable('$annotationSetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "PATCH",
|
| - 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) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| - _url = '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.
|
| - *
|
| - * 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) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| - if (annotationSetId == null) {
|
| - throw new core.ArgumentError("Parameter annotationSetId is required.");
|
| - }
|
| -
|
| - _url = 'annotationSets/' + commons.Escaper.ecapeVariable('$annotationSetId');
|
| -
|
| - 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 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 annotations.create.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [BatchAnnotationsResponse].
|
| - *
|
| - * 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<BatchAnnotationsResponse> batchCreate(BatchCreateAnnotationsRequest request) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| - _url = 'annotations:batchCreate';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new BatchAnnotationsResponse.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Creates a new annotation. Caller must have WRITE permission for the
|
| - * associated annotation set.
|
| - *
|
| - *
|
| - * The following fields must be provided when creating an annotation:
|
| - * - annotationSetId
|
| - * - position.referenceName or position.referenceId Transcripts
|
| - * For annotations of type TRANSCRIPT, the following fields of
|
| - * annotation.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();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| - _url = 'annotations';
|
| -
|
| - 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 [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 delete(core.String annotationId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (annotationId == null) {
|
| - throw new core.ArgumentError("Parameter annotationId is required.");
|
| - }
|
| -
|
| - _downloadOptions = null;
|
| -
|
| - _url = 'annotations/' + commons.Escaper.ecapeVariable('$annotationId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "DELETE",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => null);
|
| - }
|
| -
|
| - /**
|
| - * Gets an annotation. Caller must have READ permission for the associated
|
| - * annotation set.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [annotationId] - The ID of the annotation to be retrieved.
|
| - *
|
| - * Completes with a [Annotation].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<Annotation> get(core.String annotationId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (annotationId == null) {
|
| - throw new core.ArgumentError("Parameter annotationId is required.");
|
| - }
|
| -
|
| - _url = 'annotations/' + commons.Escaper.ecapeVariable('$annotationId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "GET",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Annotation.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Updates an annotation. The update must respect all mutability restrictions
|
| - * and other invariants described on the annotation resource. Caller must have
|
| - * WRITE permission for the associated dataset. This method supports patch
|
| - * semantics.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [annotationId] - The ID of the annotation to 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> patch(Annotation request, core.String annotationId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| - if (annotationId == null) {
|
| - throw new core.ArgumentError("Parameter annotationId is required.");
|
| - }
|
| -
|
| - _url = 'annotations/' + commons.Escaper.ecapeVariable('$annotationId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "PATCH",
|
| - 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) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| - _url = '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. The update must respect all mutability restrictions
|
| - * and other invariants described on the annotation resource. 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.
|
| - *
|
| - * 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) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| - if (annotationId == null) {
|
| - throw new core.ArgumentError("Parameter annotationId is required.");
|
| - }
|
| -
|
| - _url = 'annotations/' + commons.Escaper.ecapeVariable('$annotationId');
|
| -
|
| - 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 CallsetsResourceApi {
|
| - final commons.ApiRequester _requester;
|
| -
|
| - CallsetsResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Creates a new call set.
|
| - *
|
| - * [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();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| - _url = 'callsets';
|
| -
|
| - 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.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [callSetId] - The ID of the call set to be deleted.
|
| - *
|
| - * 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 delete(core.String callSetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (callSetId == null) {
|
| - throw new core.ArgumentError("Parameter callSetId is required.");
|
| - }
|
| -
|
| - _downloadOptions = null;
|
| -
|
| - _url = 'callsets/' + commons.Escaper.ecapeVariable('$callSetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "DELETE",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => null);
|
| - }
|
| -
|
| - /**
|
| - * Gets a call set by ID.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [callSetId] - The ID of the call set.
|
| - *
|
| - * Completes with a [CallSet].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<CallSet> get(core.String callSetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (callSetId == null) {
|
| - throw new core.ArgumentError("Parameter callSetId is required.");
|
| - }
|
| -
|
| - _url = 'callsets/' + commons.Escaper.ecapeVariable('$callSetId');
|
| -
|
| - 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. This method supports patch semantics.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [callSetId] - Required. The ID of the call set to 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) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| - if (callSetId == null) {
|
| - throw new core.ArgumentError("Parameter callSetId is required.");
|
| - }
|
| -
|
| - _url = 'callsets/' + commons.Escaper.ecapeVariable('$callSetId');
|
| -
|
| - 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.
|
| - *
|
| - * Implements GlobalAllianceApi.searchCallSets.
|
| - *
|
| - * [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();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| - _url = 'callsets/search';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new SearchCallSetsResponse.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Updates a call set.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [callSetId] - Required. The ID of the call set to 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> update(CallSet request, core.String callSetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| - if (callSetId == null) {
|
| - throw new core.ArgumentError("Parameter callSetId is required.");
|
| - }
|
| -
|
| - _url = 'callsets/' + commons.Escaper.ecapeVariable('$callSetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "PUT",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new CallSet.fromJson(data));
|
| - }
|
| -
|
| -}
|
| -
|
| -
|
| -class DatasetsResourceApi {
|
| - final commons.ApiRequester _requester;
|
| -
|
| - DatasetsResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Creates a new dataset.
|
| - *
|
| - * [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();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| - _url = 'datasets';
|
| -
|
| - 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 UndeleteDataset operation.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [datasetId] - The ID of the dataset to be deleted.
|
| - *
|
| - * 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 delete(core.String datasetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (datasetId == null) {
|
| - throw new core.ArgumentError("Parameter datasetId is required.");
|
| - }
|
| -
|
| - _downloadOptions = null;
|
| -
|
| - _url = 'datasets/' + commons.Escaper.ecapeVariable('$datasetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "DELETE",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => null);
|
| - }
|
| -
|
| - /**
|
| - * Gets a dataset by ID.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [datasetId] - The ID of the dataset.
|
| - *
|
| - * Completes with a [Dataset].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<Dataset> get(core.String datasetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (datasetId == null) {
|
| - throw new core.ArgumentError("Parameter datasetId is required.");
|
| - }
|
| -
|
| - _url = 'datasets/' + commons.Escaper.ecapeVariable('$datasetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "GET",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Dataset.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Lists datasets within a project.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [pageSize] - The maximum number of results to return in a single page. If
|
| - * unspecified, defaults to 50. The maximum value is 1024.
|
| - *
|
| - * [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.
|
| - *
|
| - * [projectNumber] - Required. The project 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.int pageSize, core.String pageToken, core.String projectNumber}) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (pageSize != null) {
|
| - _queryParams["pageSize"] = ["${pageSize}"];
|
| - }
|
| - if (pageToken != null) {
|
| - _queryParams["pageToken"] = [pageToken];
|
| - }
|
| - if (projectNumber != null) {
|
| - _queryParams["projectNumber"] = [projectNumber];
|
| - }
|
| -
|
| - _url = 'datasets';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "GET",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ListDatasetsResponse.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Updates a dataset. This method supports patch semantics.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [datasetId] - The ID of the dataset to be updated.
|
| - *
|
| - * Completes with a [Dataset].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<Dataset> patch(Dataset request, core.String datasetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| - if (datasetId == null) {
|
| - throw new core.ArgumentError("Parameter datasetId is required.");
|
| - }
|
| -
|
| - _url = 'datasets/' + commons.Escaper.ecapeVariable('$datasetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "PATCH",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Dataset.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Undeletes a dataset by restoring a dataset which was deleted via this API.
|
| - * This operation is only possible for a week after the deletion occurred.
|
| - *
|
| - * 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(core.String datasetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (datasetId == null) {
|
| - throw new core.ArgumentError("Parameter datasetId is required.");
|
| - }
|
| -
|
| - _url = 'datasets/' + commons.Escaper.ecapeVariable('$datasetId') + '/undelete';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Dataset.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Updates a dataset.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [datasetId] - The ID of the dataset to be updated.
|
| - *
|
| - * Completes with a [Dataset].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<Dataset> update(Dataset request, core.String datasetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| - if (datasetId == null) {
|
| - throw new core.ArgumentError("Parameter datasetId is required.");
|
| - }
|
| -
|
| - _url = 'datasets/' + commons.Escaper.ecapeVariable('$datasetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "PUT",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Dataset.fromJson(data));
|
| - }
|
| -
|
| -}
|
| -
|
| -
|
| -class ExperimentalResourceApi {
|
| - final commons.ApiRequester _requester;
|
| -
|
| - ExperimentalJobsResourceApi get jobs => new ExperimentalJobsResourceApi(_requester);
|
| -
|
| - ExperimentalResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -}
|
| -
|
| -
|
| -class ExperimentalJobsResourceApi {
|
| - final commons.ApiRequester _requester;
|
| -
|
| - ExperimentalJobsResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Creates and asynchronously runs an ad-hoc job. This is an experimental call
|
| - * and may be removed or changed at any time.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [ExperimentalCreateJobResponse].
|
| - *
|
| - * 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<ExperimentalCreateJobResponse> create(ExperimentalCreateJobRequest request) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| - _url = 'experimental/jobs/create';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ExperimentalCreateJobResponse.fromJson(data));
|
| - }
|
| -
|
| -}
|
| -
|
| -
|
| -class JobsResourceApi {
|
| - final commons.ApiRequester _requester;
|
| -
|
| - JobsResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Cancels a job by ID. Note that it is possible for partial results to be
|
| - * generated and stored for cancelled jobs.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [jobId] - Required. The ID of the job.
|
| - *
|
| - * 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 cancel(core.String jobId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (jobId == null) {
|
| - throw new core.ArgumentError("Parameter jobId is required.");
|
| - }
|
| -
|
| - _downloadOptions = null;
|
| -
|
| - _url = 'jobs/' + commons.Escaper.ecapeVariable('$jobId') + '/cancel';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => null);
|
| - }
|
| -
|
| - /**
|
| - * Gets a job by ID.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [jobId] - Required. The ID of the job.
|
| - *
|
| - * Completes with a [Job].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<Job> get(core.String jobId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (jobId == null) {
|
| - throw new core.ArgumentError("Parameter jobId is required.");
|
| - }
|
| -
|
| - _url = 'jobs/' + commons.Escaper.ecapeVariable('$jobId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "GET",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Job.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Gets a list of jobs matching the criteria.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [SearchJobsResponse].
|
| - *
|
| - * 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<SearchJobsResponse> search(SearchJobsRequest request) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| - _url = 'jobs/search';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new SearchJobsResponse.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.
|
| - *
|
| - * 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 [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 delete(core.String readGroupSetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (readGroupSetId == null) {
|
| - throw new core.ArgumentError("Parameter readGroupSetId is required.");
|
| - }
|
| -
|
| - _downloadOptions = null;
|
| -
|
| - _url = 'readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "DELETE",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => null);
|
| - }
|
| -
|
| - /**
|
| - * Exports read group sets to a BAM file in Google Cloud Storage.
|
| - *
|
| - * 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 details.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [ExportReadGroupSetsResponse].
|
| - *
|
| - * 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<ExportReadGroupSetsResponse> export(ExportReadGroupSetsRequest request) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| - _url = 'readgroupsets/export';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ExportReadGroupSetsResponse.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Gets a read group set by ID.
|
| - *
|
| - * 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();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (readGroupSetId == null) {
|
| - throw new core.ArgumentError("Parameter readGroupSetId is required.");
|
| - }
|
| -
|
| - _url = 'readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId');
|
| -
|
| - 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. The caller must have WRITE permissions to the dataset.
|
| - *
|
| - * Notes on BAM import:
|
| - * - Tags will be converted to strings - tag types are not preserved
|
| - * - Comments (@CO) in the input file header are not imported
|
| - * - Original order of reference headers is not 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 (referenceName
|
| - * and position)
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [ImportReadGroupSetsResponse].
|
| - *
|
| - * 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<ImportReadGroupSetsResponse> import(ImportReadGroupSetsRequest request) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| - _url = 'readgroupsets/import';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ImportReadGroupSetsResponse.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Updates a read group set. 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.
|
| - *
|
| - * 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) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| - if (readGroupSetId == null) {
|
| - throw new core.ArgumentError("Parameter readGroupSetId is required.");
|
| - }
|
| -
|
| - _url = 'readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId');
|
| -
|
| - 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.
|
| - *
|
| - * Implements GlobalAllianceApi.searchReadGroupSets.
|
| - *
|
| - * [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;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| - _url = '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));
|
| - }
|
| -
|
| - /**
|
| - * Updates a read group set.
|
| - *
|
| - * [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.
|
| - *
|
| - * 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> update(ReadGroupSet request, core.String readGroupSetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| - if (readGroupSetId == null) {
|
| - throw new core.ArgumentError("Parameter readGroupSetId is required.");
|
| - }
|
| -
|
| - _url = 'readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "PUT",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ReadGroupSet.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.
|
| - *
|
| - * 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.
|
| - *
|
| - * [pageSize] - The maximum number of results to return in a single page. If
|
| - * unspecified, defaults to 1024. The maximum value is 2048.
|
| - *
|
| - * [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.
|
| - *
|
| - * [range_end] - The end position of the range on the reference, 0-based
|
| - * exclusive. If specified, referenceName must also be specified.
|
| - *
|
| - * [range_referenceName] - The reference sequence name, for example chr1, 1,
|
| - * or chrX.
|
| - *
|
| - * [range_start] - The start position of the range on the reference, 0-based
|
| - * inclusive. If specified, referenceName must also be specified.
|
| - *
|
| - * [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.
|
| - *
|
| - * 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.int pageSize, core.String pageToken, core.String range_end, core.String range_referenceName, core.String range_start, core.String targetBucketWidth}) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (readGroupSetId == null) {
|
| - throw new core.ArgumentError("Parameter readGroupSetId is required.");
|
| - }
|
| - if (pageSize != null) {
|
| - _queryParams["pageSize"] = ["${pageSize}"];
|
| - }
|
| - if (pageToken != null) {
|
| - _queryParams["pageToken"] = [pageToken];
|
| - }
|
| - if (range_end != null) {
|
| - _queryParams["range.end"] = [range_end];
|
| - }
|
| - if (range_referenceName != null) {
|
| - _queryParams["range.referenceName"] = [range_referenceName];
|
| - }
|
| - if (range_start != null) {
|
| - _queryParams["range.start"] = [range_start];
|
| - }
|
| - if (targetBucketWidth != null) {
|
| - _queryParams["targetBucketWidth"] = [targetBucketWidth];
|
| - }
|
| -
|
| - _url = 'readgroupsets/' + commons.Escaper.ecapeVariable('$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));
|
| - }
|
| -
|
| -}
|
| -
|
| -
|
| -class ReadsResourceApi {
|
| - final commons.ApiRequester _requester;
|
| -
|
| - ReadsResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Gets a list of reads for one or more read group sets. 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.
|
| - *
|
| - * [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();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| - _url = 'reads/search';
|
| -
|
| - 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.
|
| - *
|
| - * Implements GlobalAllianceApi.getReference.
|
| - *
|
| - * 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();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (referenceId == null) {
|
| - throw new core.ArgumentError("Parameter referenceId is required.");
|
| - }
|
| -
|
| - _url = 'references/' + commons.Escaper.ecapeVariable('$referenceId');
|
| -
|
| - 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.
|
| - *
|
| - * Implements GlobalAllianceApi.searchReferences.
|
| - *
|
| - * [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;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| - _url = '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));
|
| - }
|
| -
|
| -}
|
| -
|
| -
|
| -class ReferencesBasesResourceApi {
|
| - final commons.ApiRequester _requester;
|
| -
|
| - ReferencesBasesResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Lists the bases in a reference, optionally restricted to a range.
|
| - *
|
| - * Implements GlobalAllianceApi.getReferenceBases.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [referenceId] - The ID of the reference.
|
| - *
|
| - * [end] - The end position (0-based, exclusive) of this query. Defaults to
|
| - * the length of this 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).
|
| - *
|
| - * [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.
|
| - *
|
| - * [start] - The start position (0-based) of this query. Defaults to 0.
|
| - *
|
| - * 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 end, core.int pageSize, core.String pageToken, core.String start}) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (referenceId == null) {
|
| - throw new core.ArgumentError("Parameter referenceId is required.");
|
| - }
|
| - if (end != null) {
|
| - _queryParams["end"] = [end];
|
| - }
|
| - if (pageSize != null) {
|
| - _queryParams["pageSize"] = ["${pageSize}"];
|
| - }
|
| - if (pageToken != null) {
|
| - _queryParams["pageToken"] = [pageToken];
|
| - }
|
| - if (start != null) {
|
| - _queryParams["start"] = [start];
|
| - }
|
| -
|
| - _url = 'references/' + commons.Escaper.ecapeVariable('$referenceId') + '/bases';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "GET",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ListBasesResponse.fromJson(data));
|
| - }
|
| -
|
| -}
|
| -
|
| -
|
| -class ReferencesetsResourceApi {
|
| - final commons.ApiRequester _requester;
|
| -
|
| - ReferencesetsResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Gets a reference set.
|
| - *
|
| - * Implements GlobalAllianceApi.getReferenceSet.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [referenceSetId] - The ID of the reference set.
|
| - *
|
| - * Completes with a [ReferenceSet].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<ReferenceSet> get(core.String referenceSetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (referenceSetId == null) {
|
| - throw new core.ArgumentError("Parameter referenceSetId is required.");
|
| - }
|
| -
|
| - _url = 'referencesets/' + commons.Escaper.ecapeVariable('$referenceSetId');
|
| -
|
| - 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.
|
| - *
|
| - * Implements GlobalAllianceApi.searchReferenceSets.
|
| - *
|
| - * [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;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| - _url = '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));
|
| - }
|
| -
|
| -}
|
| -
|
| -
|
| -class VariantsResourceApi {
|
| - final commons.ApiRequester _requester;
|
| -
|
| - VariantsResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Creates a new variant.
|
| - *
|
| - * [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();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| - _url = 'variants';
|
| -
|
| - 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.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantId] - The ID of the variant to be deleted.
|
| - *
|
| - * 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 delete(core.String variantId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (variantId == null) {
|
| - throw new core.ArgumentError("Parameter variantId is required.");
|
| - }
|
| -
|
| - _downloadOptions = null;
|
| -
|
| - _url = 'variants/' + commons.Escaper.ecapeVariable('$variantId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "DELETE",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => null);
|
| - }
|
| -
|
| - /**
|
| - * Gets a variant by ID.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantId] - Required.
|
| - *
|
| - * Completes with a [Variant].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<Variant> get(core.String variantId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (variantId == null) {
|
| - throw new core.ArgumentError("Parameter variantId is required.");
|
| - }
|
| -
|
| - _url = 'variants/' + commons.Escaper.ecapeVariable('$variantId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "GET",
|
| - 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.
|
| - *
|
| - * Implements GlobalAllianceApi.searchVariants.
|
| - *
|
| - * [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();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| - _url = 'variants/search';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new SearchVariantsResponse.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Updates a variant's names and info fields. All other modifications are
|
| - * silently ignored. Returns the modified variant without its calls.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantId] - The ID of the variant to 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> update(Variant request, core.String variantId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| - if (variantId == null) {
|
| - throw new core.ArgumentError("Parameter variantId is required.");
|
| - }
|
| -
|
| - _url = 'variants/' + commons.Escaper.ecapeVariable('$variantId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "PUT",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Variant.fromJson(data));
|
| - }
|
| -
|
| -}
|
| -
|
| -
|
| -class VariantsetsResourceApi {
|
| - final commons.ApiRequester _requester;
|
| -
|
| - VariantsetsResourceApi(commons.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Creates a new variant set (only necessary in v1).
|
| - *
|
| - * 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();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| - _url = 'variantsets';
|
| -
|
| - 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.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantSetId] - The ID of the variant set to be deleted. Required.
|
| - *
|
| - * 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 delete(core.String variantSetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (variantSetId == null) {
|
| - throw new core.ArgumentError("Parameter variantSetId is required.");
|
| - }
|
| -
|
| - _downloadOptions = null;
|
| -
|
| - _url = 'variantsets/' + commons.Escaper.ecapeVariable('$variantSetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "DELETE",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => null);
|
| - }
|
| -
|
| - /**
|
| - * Exports variant set data to an external destination.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantSetId] - The ID of the variant set that contains variant data which
|
| - * should be exported. Required. The caller must have READ access to this
|
| - * variant set.
|
| - *
|
| - * Completes with a [ExportVariantSetResponse].
|
| - *
|
| - * 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<ExportVariantSetResponse> export(ExportVariantSetRequest request, core.String variantSetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| - if (variantSetId == null) {
|
| - throw new core.ArgumentError("Parameter variantSetId is required.");
|
| - }
|
| -
|
| - _url = 'variantsets/' + commons.Escaper.ecapeVariable('$variantSetId') + '/export';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ExportVariantSetResponse.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Gets a variant set by ID.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantSetId] - The ID of the variant set. Required.
|
| - *
|
| - * Completes with a [VariantSet].
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<VariantSet> get(core.String variantSetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (variantSetId == null) {
|
| - throw new core.ArgumentError("Parameter variantSetId is required.");
|
| - }
|
| -
|
| - _url = 'variantsets/' + commons.Escaper.ecapeVariable('$variantSetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "GET",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new VariantSet.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Creates variant data by asynchronously importing the provided information.
|
| - *
|
| - * The variants for import will be merged with any existing data and each
|
| - * other according to the behavior of mergeVariants. In particular, this means
|
| - * for merged VCF variants that have conflicting info fields, some data will
|
| - * be arbitrarily discarded unless otherwise specified in the InfoMergeConfig
|
| - * field of ImportVariantsRequest. 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:
|
| - *
|
| - * [variantSetId] - Required. The variant set to which variant data should be
|
| - * imported.
|
| - *
|
| - * Completes with a [ImportVariantsResponse].
|
| - *
|
| - * 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<ImportVariantsResponse> importVariants(ImportVariantsRequest request, core.String variantSetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| - if (variantSetId == null) {
|
| - throw new core.ArgumentError("Parameter variantSetId is required.");
|
| - }
|
| -
|
| - _url = 'variantsets/' + commons.Escaper.ecapeVariable('$variantSetId') + '/importVariants';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ImportVariantsResponse.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Merges the given variants with existing variants. Each variant will be
|
| - * merged with an existing variant that matches its reference sequence, start,
|
| - * end, reference bases, and alternative bases. If no such variant exists, a
|
| - * new one will be created.
|
| - *
|
| - * When variants are merged, the call information from the new variant is
|
| - * added to the existing variant. Variant info fields are merged as specified
|
| - * in the InfoMergeConfig field of the MergeVariantsRequest.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantSetId] - The destination variant set.
|
| - *
|
| - * Completes with a [commons.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future mergeVariants(MergeVariantsRequest request, core.String variantSetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| - if (variantSetId == null) {
|
| - throw new core.ArgumentError("Parameter variantSetId is required.");
|
| - }
|
| -
|
| - _downloadOptions = null;
|
| -
|
| - _url = 'variantsets/' + commons.Escaper.ecapeVariable('$variantSetId') + '/mergeVariants';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => null);
|
| - }
|
| -
|
| - /**
|
| - * Updates a variant set's metadata. All other modifications are silently
|
| - * ignored. This method supports patch semantics.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantSetId] - The ID of the variant set to be updated (must already
|
| - * exist).
|
| - *
|
| - * 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) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| - if (variantSetId == null) {
|
| - throw new core.ArgumentError("Parameter variantSetId is required.");
|
| - }
|
| -
|
| - _url = 'variantsets/' + commons.Escaper.ecapeVariable('$variantSetId');
|
| -
|
| - 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.
|
| - *
|
| - * Implements GlobalAllianceApi.searchVariantSets.
|
| - *
|
| - * [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;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| - _url = '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));
|
| - }
|
| -
|
| - /**
|
| - * Updates a variant set's metadata. All other modifications are silently
|
| - * ignored.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantSetId] - The ID of the variant set to be updated (must already
|
| - * exist).
|
| - *
|
| - * 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> update(VariantSet request, core.String variantSetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = commons.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| - if (variantSetId == null) {
|
| - throw new core.ArgumentError("Parameter variantSetId is required.");
|
| - }
|
| -
|
| - _url = 'variantsets/' + commons.Escaper.ecapeVariable('$variantSetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "PUT",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new VariantSet.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.
|
| - */
|
| -class Annotation {
|
| - /** The annotation set to which this annotation belongs. */
|
| - core.String annotationSetId;
|
| - /** The server-generated annotation ID, unique across all annotations. */
|
| - core.String id;
|
| - /** A string which maps to an array of values. */
|
| - core.Map<core.String, core.List<core.String>> info;
|
| - /** The display name of this annotation. */
|
| - core.String name;
|
| - /** The position of this annotation on the reference sequence. */
|
| - RangePosition position;
|
| - /**
|
| - * 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:
|
| - * - "GENE"
|
| - * - "GENERIC"
|
| - * - "TRANSCRIPT"
|
| - * - "VARIANT"
|
| - */
|
| - 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.
|
| - */
|
| - VariantAnnotation variant;
|
| -
|
| - Annotation();
|
| -
|
| - Annotation.fromJson(core.Map _json) {
|
| - if (_json.containsKey("annotationSetId")) {
|
| - annotationSetId = _json["annotationSetId"];
|
| - }
|
| - if (_json.containsKey("id")) {
|
| - id = _json["id"];
|
| - }
|
| - if (_json.containsKey("info")) {
|
| - info = _json["info"];
|
| - }
|
| - if (_json.containsKey("name")) {
|
| - name = _json["name"];
|
| - }
|
| - if (_json.containsKey("position")) {
|
| - position = new RangePosition.fromJson(_json["position"]);
|
| - }
|
| - if (_json.containsKey("transcript")) {
|
| - transcript = new Transcript.fromJson(_json["transcript"]);
|
| - }
|
| - if (_json.containsKey("type")) {
|
| - type = _json["type"];
|
| - }
|
| - if (_json.containsKey("variant")) {
|
| - variant = new VariantAnnotation.fromJson(_json["variant"]);
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (annotationSetId != null) {
|
| - _json["annotationSetId"] = annotationSetId;
|
| - }
|
| - if (id != null) {
|
| - _json["id"] = id;
|
| - }
|
| - if (info != null) {
|
| - _json["info"] = info;
|
| - }
|
| - if (name != null) {
|
| - _json["name"] = name;
|
| - }
|
| - if (position != null) {
|
| - _json["position"] = (position).toJson();
|
| - }
|
| - if (transcript != null) {
|
| - _json["transcript"] = (transcript).toJson();
|
| - }
|
| - if (type != null) {
|
| - _json["type"] = type;
|
| - }
|
| - if (variant != null) {
|
| - _json["variant"] = (variant).toJson();
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/**
|
| - * 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. */
|
| - core.String datasetId;
|
| - /**
|
| - * The server-generated annotation set ID, unique across all annotation sets.
|
| - */
|
| - core.String id;
|
| - /** A string which maps to an array of values. */
|
| - core.Map<core.String, core.List<core.String>> info;
|
| - /** 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.
|
| - */
|
| - core.String referenceSetId;
|
| - /**
|
| - * 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:
|
| - * - "GENE"
|
| - * - "GENERIC"
|
| - * - "TRANSCRIPT"
|
| - * - "VARIANT"
|
| - */
|
| - core.String type;
|
| -
|
| - AnnotationSet();
|
| -
|
| - AnnotationSet.fromJson(core.Map _json) {
|
| - if (_json.containsKey("datasetId")) {
|
| - datasetId = _json["datasetId"];
|
| - }
|
| - if (_json.containsKey("id")) {
|
| - id = _json["id"];
|
| - }
|
| - if (_json.containsKey("info")) {
|
| - info = _json["info"];
|
| - }
|
| - if (_json.containsKey("name")) {
|
| - name = _json["name"];
|
| - }
|
| - if (_json.containsKey("referenceSetId")) {
|
| - referenceSetId = _json["referenceSetId"];
|
| - }
|
| - if (_json.containsKey("sourceUri")) {
|
| - sourceUri = _json["sourceUri"];
|
| - }
|
| - if (_json.containsKey("type")) {
|
| - type = _json["type"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (datasetId != null) {
|
| - _json["datasetId"] = datasetId;
|
| - }
|
| - if (id != null) {
|
| - _json["id"] = id;
|
| - }
|
| - if (info != null) {
|
| - _json["info"] = info;
|
| - }
|
| - if (name != null) {
|
| - _json["name"] = name;
|
| - }
|
| - if (referenceSetId != null) {
|
| - _json["referenceSetId"] = referenceSetId;
|
| - }
|
| - if (sourceUri != null) {
|
| - _json["sourceUri"] = sourceUri;
|
| - }
|
| - if (type != null) {
|
| - _json["type"] = type;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class BatchAnnotationsResponse {
|
| - /**
|
| - * The resulting per-annotation entries, ordered consistently with the
|
| - * original request.
|
| - */
|
| - core.List<BatchAnnotationsResponseEntry> entries;
|
| -
|
| - BatchAnnotationsResponse();
|
| -
|
| - BatchAnnotationsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("entries")) {
|
| - entries = _json["entries"].map((value) => new BatchAnnotationsResponseEntry.fromJson(value)).toList();
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (entries != null) {
|
| - _json["entries"] = entries.map((value) => (value).toJson()).toList();
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class BatchAnnotationsResponseEntry {
|
| - /** The annotation, if any. */
|
| - Annotation annotation;
|
| - /** The resulting status for this annotation operation. */
|
| - BatchAnnotationsResponseEntryStatus status;
|
| -
|
| - BatchAnnotationsResponseEntry();
|
| -
|
| - BatchAnnotationsResponseEntry.fromJson(core.Map _json) {
|
| - if (_json.containsKey("annotation")) {
|
| - annotation = new Annotation.fromJson(_json["annotation"]);
|
| - }
|
| - if (_json.containsKey("status")) {
|
| - status = new BatchAnnotationsResponseEntryStatus.fromJson(_json["status"]);
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (annotation != null) {
|
| - _json["annotation"] = (annotation).toJson();
|
| - }
|
| - if (status != null) {
|
| - _json["status"] = (status).toJson();
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class BatchAnnotationsResponseEntryStatus {
|
| - /** The HTTP status code for this operation. */
|
| - core.int code;
|
| - /** Error message for this status, if any. */
|
| - core.String message;
|
| -
|
| - BatchAnnotationsResponseEntryStatus();
|
| -
|
| - BatchAnnotationsResponseEntryStatus.fromJson(core.Map _json) {
|
| - if (_json.containsKey("code")) {
|
| - code = _json["code"];
|
| - }
|
| - if (_json.containsKey("message")) {
|
| - message = _json["message"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (code != null) {
|
| - _json["code"] = code;
|
| - }
|
| - if (message != null) {
|
| - _json["message"] = message;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class BatchCreateAnnotationsRequest {
|
| - /**
|
| - * The annotations to be created. At most 4096 can be specified in a single
|
| - * request.
|
| - */
|
| - core.List<Annotation> annotations;
|
| -
|
| - BatchCreateAnnotationsRequest();
|
| -
|
| - BatchCreateAnnotationsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("annotations")) {
|
| - annotations = _json["annotations"].map((value) => new Annotation.fromJson(value)).toList();
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (annotations != null) {
|
| - _json["annotations"] = annotations.map((value) => (value).toJson()).toList();
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/**
|
| - * 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 Call {
|
| - /** 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. */
|
| - 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.
|
| - */
|
| - 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.
|
| - */
|
| - core.List<core.double> genotypeLikelihood;
|
| - /** A string which maps to an array of values. */
|
| - core.Map<core.String, core.List<core.String>> 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 *.
|
| - */
|
| - core.String phaseset;
|
| -
|
| - Call();
|
| -
|
| - Call.fromJson(core.Map _json) {
|
| - if (_json.containsKey("callSetId")) {
|
| - callSetId = _json["callSetId"];
|
| - }
|
| - if (_json.containsKey("callSetName")) {
|
| - callSetName = _json["callSetName"];
|
| - }
|
| - if (_json.containsKey("genotype")) {
|
| - genotype = _json["genotype"];
|
| - }
|
| - if (_json.containsKey("genotypeLikelihood")) {
|
| - genotypeLikelihood = _json["genotypeLikelihood"];
|
| - }
|
| - if (_json.containsKey("info")) {
|
| - info = _json["info"];
|
| - }
|
| - if (_json.containsKey("phaseset")) {
|
| - phaseset = _json["phaseset"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (callSetId != null) {
|
| - _json["callSetId"] = callSetId;
|
| - }
|
| - if (callSetName != null) {
|
| - _json["callSetName"] = callSetName;
|
| - }
|
| - if (genotype != null) {
|
| - _json["genotype"] = genotype;
|
| - }
|
| - if (genotypeLikelihood != null) {
|
| - _json["genotypeLikelihood"] = genotypeLikelihood;
|
| - }
|
| - if (info != null) {
|
| - _json["info"] = info;
|
| - }
|
| - if (phaseset != null) {
|
| - _json["phaseset"] = phaseset;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/**
|
| - * A call set is a collection of variant calls, typically for one sample. It
|
| - * belongs to a variant set.
|
| - */
|
| -class CallSet {
|
| - /** The date this call set was created in milliseconds from the epoch. */
|
| - core.String created;
|
| - /** The Google generated ID of the call set, immutable. */
|
| - core.String id;
|
| - /** A string which maps to an array of values. */
|
| - core.Map<core.String, core.List<core.String>> info;
|
| - /** The call set name. */
|
| - core.String name;
|
| - /** The sample ID this call set corresponds to. */
|
| - core.String sampleId;
|
| - /** The IDs of the variant sets this call set belongs to. */
|
| - core.List<core.String> variantSetIds;
|
| -
|
| - CallSet();
|
| -
|
| - CallSet.fromJson(core.Map _json) {
|
| - if (_json.containsKey("created")) {
|
| - created = _json["created"];
|
| - }
|
| - if (_json.containsKey("id")) {
|
| - id = _json["id"];
|
| - }
|
| - if (_json.containsKey("info")) {
|
| - info = _json["info"];
|
| - }
|
| - if (_json.containsKey("name")) {
|
| - name = _json["name"];
|
| - }
|
| - if (_json.containsKey("sampleId")) {
|
| - sampleId = _json["sampleId"];
|
| - }
|
| - if (_json.containsKey("variantSetIds")) {
|
| - variantSetIds = _json["variantSetIds"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (created != null) {
|
| - _json["created"] = created;
|
| - }
|
| - if (id != null) {
|
| - _json["id"] = id;
|
| - }
|
| - if (info != null) {
|
| - _json["info"] = info;
|
| - }
|
| - if (name != null) {
|
| - _json["name"] = name;
|
| - }
|
| - if (sampleId != null) {
|
| - _json["sampleId"] = sampleId;
|
| - }
|
| - if (variantSetIds != null) {
|
| - _json["variantSetIds"] = variantSetIds;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** A single CIGAR operation. */
|
| -class CigarUnit {
|
| - /**
|
| - *
|
| - * Possible string values are:
|
| - * - "ALIGNMENT_MATCH"
|
| - * - "CLIP_HARD"
|
| - * - "CLIP_SOFT"
|
| - * - "DELETE"
|
| - * - "INSERT"
|
| - * - "OPERATION_UNSPECIFIED"
|
| - * - "PAD"
|
| - * - "SEQUENCE_MATCH"
|
| - * - "SEQUENCE_MISMATCH"
|
| - * - "SKIP"
|
| - */
|
| - core.String operation;
|
| - /** The number of 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.
|
| - */
|
| - core.String referenceSequence;
|
| -
|
| - CigarUnit();
|
| -
|
| - CigarUnit.fromJson(core.Map _json) {
|
| - if (_json.containsKey("operation")) {
|
| - operation = _json["operation"];
|
| - }
|
| - if (_json.containsKey("operationLength")) {
|
| - operationLength = _json["operationLength"];
|
| - }
|
| - if (_json.containsKey("referenceSequence")) {
|
| - referenceSequence = _json["referenceSequence"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (operation != null) {
|
| - _json["operation"] = operation;
|
| - }
|
| - if (operationLength != null) {
|
| - _json["operationLength"] = operationLength;
|
| - }
|
| - if (referenceSequence != null) {
|
| - _json["referenceSequence"] = referenceSequence;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/**
|
| - * 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.
|
| - */
|
| - core.double meanCoverage;
|
| - /** The genomic coordinate range spanned by this bucket. */
|
| - Range range;
|
| -
|
| - CoverageBucket();
|
| -
|
| - CoverageBucket.fromJson(core.Map _json) {
|
| - if (_json.containsKey("meanCoverage")) {
|
| - meanCoverage = _json["meanCoverage"];
|
| - }
|
| - if (_json.containsKey("range")) {
|
| - range = new Range.fromJson(_json["range"]);
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (meanCoverage != null) {
|
| - _json["meanCoverage"] = meanCoverage;
|
| - }
|
| - if (range != null) {
|
| - _json["range"] = (range).toJson();
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** A Dataset is a collection of genomic data. */
|
| -class Dataset {
|
| - /** The time this dataset was created, in seconds from the epoch. */
|
| - core.String createTime;
|
| - /** The Google generated ID of the dataset, immutable. */
|
| - core.String id;
|
| - /**
|
| - * Flag indicating whether or not a dataset is publicly viewable. If a dataset
|
| - * is not public, it inherits viewing permissions from its project.
|
| - */
|
| - core.bool isPublic;
|
| - /** The dataset name. */
|
| - core.String name;
|
| - /**
|
| - * The Google Developers Console project number that this dataset belongs to.
|
| - */
|
| - core.String projectNumber;
|
| -
|
| - Dataset();
|
| -
|
| - Dataset.fromJson(core.Map _json) {
|
| - if (_json.containsKey("createTime")) {
|
| - createTime = _json["createTime"];
|
| - }
|
| - if (_json.containsKey("id")) {
|
| - id = _json["id"];
|
| - }
|
| - if (_json.containsKey("isPublic")) {
|
| - isPublic = _json["isPublic"];
|
| - }
|
| - if (_json.containsKey("name")) {
|
| - name = _json["name"];
|
| - }
|
| - if (_json.containsKey("projectNumber")) {
|
| - projectNumber = _json["projectNumber"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (createTime != null) {
|
| - _json["createTime"] = createTime;
|
| - }
|
| - if (id != null) {
|
| - _json["id"] = id;
|
| - }
|
| - if (isPublic != null) {
|
| - _json["isPublic"] = isPublic;
|
| - }
|
| - if (name != null) {
|
| - _json["name"] = name;
|
| - }
|
| - if (projectNumber != null) {
|
| - _json["projectNumber"] = projectNumber;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** The job creation request. */
|
| -class ExperimentalCreateJobRequest {
|
| - /**
|
| - * Specifies whether or not to run the alignment pipeline. Either align or
|
| - * callVariants must be set.
|
| - */
|
| - core.bool align;
|
| - /**
|
| - * Specifies whether or not to run the variant calling pipeline. Either align
|
| - * or callVariants must be set.
|
| - */
|
| - core.bool callVariants;
|
| - /**
|
| - * Specifies where to copy the results of certain pipelines. This should be in
|
| - * the form of gs://bucket/path.
|
| - */
|
| - core.String gcsOutputPath;
|
| - /**
|
| - * A list of Google Cloud Storage URIs of paired end .fastq files to operate
|
| - * upon. If specified, this represents the second file of each paired .fastq
|
| - * file. The first file of each pair should be specified in sourceUris.
|
| - */
|
| - core.List<core.String> pairedSourceUris;
|
| - /**
|
| - * Required. The Google Cloud Project ID with which to associate the request.
|
| - */
|
| - core.String projectNumber;
|
| - /**
|
| - * A list of Google Cloud Storage URIs of data files to operate upon. These
|
| - * can be .bam, interleaved .fastq, or paired .fastq. If specifying paired
|
| - * .fastq files, the first of each pair of files should be listed here, and
|
| - * the second of each pair should be listed in pairedSourceUris.
|
| - */
|
| - core.List<core.String> sourceUris;
|
| -
|
| - ExperimentalCreateJobRequest();
|
| -
|
| - ExperimentalCreateJobRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("align")) {
|
| - align = _json["align"];
|
| - }
|
| - if (_json.containsKey("callVariants")) {
|
| - callVariants = _json["callVariants"];
|
| - }
|
| - if (_json.containsKey("gcsOutputPath")) {
|
| - gcsOutputPath = _json["gcsOutputPath"];
|
| - }
|
| - if (_json.containsKey("pairedSourceUris")) {
|
| - pairedSourceUris = _json["pairedSourceUris"];
|
| - }
|
| - if (_json.containsKey("projectNumber")) {
|
| - projectNumber = _json["projectNumber"];
|
| - }
|
| - if (_json.containsKey("sourceUris")) {
|
| - sourceUris = _json["sourceUris"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (align != null) {
|
| - _json["align"] = align;
|
| - }
|
| - if (callVariants != null) {
|
| - _json["callVariants"] = callVariants;
|
| - }
|
| - if (gcsOutputPath != null) {
|
| - _json["gcsOutputPath"] = gcsOutputPath;
|
| - }
|
| - if (pairedSourceUris != null) {
|
| - _json["pairedSourceUris"] = pairedSourceUris;
|
| - }
|
| - if (projectNumber != null) {
|
| - _json["projectNumber"] = projectNumber;
|
| - }
|
| - if (sourceUris != null) {
|
| - _json["sourceUris"] = sourceUris;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** The job creation response. */
|
| -class ExperimentalCreateJobResponse {
|
| - /** A job ID that can be used to get status information. */
|
| - core.String jobId;
|
| -
|
| - ExperimentalCreateJobResponse();
|
| -
|
| - ExperimentalCreateJobResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("jobId")) {
|
| - jobId = _json["jobId"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (jobId != null) {
|
| - _json["jobId"] = jobId;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** The read group set export request. */
|
| -class ExportReadGroupSetsRequest {
|
| - /**
|
| - * 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 Developers Console project number that owns this
|
| - * export. The caller must have WRITE access to this project.
|
| - */
|
| - core.String projectNumber;
|
| - /**
|
| - * Required. The IDs of the read group sets to export. The caller must have
|
| - * READ access to these read group sets.
|
| - */
|
| - core.List<core.String> readGroupSetIds;
|
| - /**
|
| - * 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;
|
| -
|
| - ExportReadGroupSetsRequest();
|
| -
|
| - ExportReadGroupSetsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("exportUri")) {
|
| - exportUri = _json["exportUri"];
|
| - }
|
| - if (_json.containsKey("projectNumber")) {
|
| - projectNumber = _json["projectNumber"];
|
| - }
|
| - if (_json.containsKey("readGroupSetIds")) {
|
| - readGroupSetIds = _json["readGroupSetIds"];
|
| - }
|
| - if (_json.containsKey("referenceNames")) {
|
| - referenceNames = _json["referenceNames"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (exportUri != null) {
|
| - _json["exportUri"] = exportUri;
|
| - }
|
| - if (projectNumber != null) {
|
| - _json["projectNumber"] = projectNumber;
|
| - }
|
| - if (readGroupSetIds != null) {
|
| - _json["readGroupSetIds"] = readGroupSetIds;
|
| - }
|
| - if (referenceNames != null) {
|
| - _json["referenceNames"] = referenceNames;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** The read group set export response. */
|
| -class ExportReadGroupSetsResponse {
|
| - /** A job ID that can be used to get status information. */
|
| - core.String jobId;
|
| -
|
| - ExportReadGroupSetsResponse();
|
| -
|
| - ExportReadGroupSetsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("jobId")) {
|
| - jobId = _json["jobId"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (jobId != null) {
|
| - _json["jobId"] = jobId;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** 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".
|
| - */
|
| - 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.
|
| - */
|
| - core.String bigqueryTable;
|
| - /**
|
| - * 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:
|
| - * - "BIGQUERY"
|
| - */
|
| - core.String format;
|
| - /**
|
| - * Required. The Google Cloud project number 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 projectNumber;
|
| -
|
| - ExportVariantSetRequest();
|
| -
|
| - ExportVariantSetRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("bigqueryDataset")) {
|
| - bigqueryDataset = _json["bigqueryDataset"];
|
| - }
|
| - if (_json.containsKey("bigqueryTable")) {
|
| - bigqueryTable = _json["bigqueryTable"];
|
| - }
|
| - if (_json.containsKey("callSetIds")) {
|
| - callSetIds = _json["callSetIds"];
|
| - }
|
| - if (_json.containsKey("format")) {
|
| - format = _json["format"];
|
| - }
|
| - if (_json.containsKey("projectNumber")) {
|
| - projectNumber = _json["projectNumber"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (bigqueryDataset != null) {
|
| - _json["bigqueryDataset"] = bigqueryDataset;
|
| - }
|
| - if (bigqueryTable != null) {
|
| - _json["bigqueryTable"] = bigqueryTable;
|
| - }
|
| - if (callSetIds != null) {
|
| - _json["callSetIds"] = callSetIds;
|
| - }
|
| - if (format != null) {
|
| - _json["format"] = format;
|
| - }
|
| - if (projectNumber != null) {
|
| - _json["projectNumber"] = projectNumber;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** The variant data export response. */
|
| -class ExportVariantSetResponse {
|
| - /** A job ID that can be used to get status information. */
|
| - core.String jobId;
|
| -
|
| - ExportVariantSetResponse();
|
| -
|
| - ExportVariantSetResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("jobId")) {
|
| - jobId = _json["jobId"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (jobId != null) {
|
| - _json["jobId"] = jobId;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class ExternalId {
|
| - /** The id used by the source of this data. */
|
| - core.String id;
|
| - /** The name of the source of this data. */
|
| - core.String sourceName;
|
| -
|
| - ExternalId();
|
| -
|
| - ExternalId.fromJson(core.Map _json) {
|
| - if (_json.containsKey("id")) {
|
| - id = _json["id"];
|
| - }
|
| - if (_json.containsKey("sourceName")) {
|
| - sourceName = _json["sourceName"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (id != null) {
|
| - _json["id"] = id;
|
| - }
|
| - if (sourceName != null) {
|
| - _json["sourceName"] = sourceName;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** 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.
|
| - */
|
| - core.String datasetId;
|
| - /**
|
| - * The partition strategy describes how read groups are partitioned into read
|
| - * group sets.
|
| - * Possible string values are:
|
| - * - "MERGE_ALL"
|
| - * - "PER_FILE_PER_SAMPLE"
|
| - */
|
| - 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.
|
| - */
|
| - core.String referenceSetId;
|
| - /** A list of URIs pointing at BAM files in Google Cloud Storage. */
|
| - core.List<core.String> sourceUris;
|
| -
|
| - ImportReadGroupSetsRequest();
|
| -
|
| - ImportReadGroupSetsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("datasetId")) {
|
| - datasetId = _json["datasetId"];
|
| - }
|
| - if (_json.containsKey("partitionStrategy")) {
|
| - partitionStrategy = _json["partitionStrategy"];
|
| - }
|
| - if (_json.containsKey("referenceSetId")) {
|
| - referenceSetId = _json["referenceSetId"];
|
| - }
|
| - if (_json.containsKey("sourceUris")) {
|
| - sourceUris = _json["sourceUris"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (datasetId != null) {
|
| - _json["datasetId"] = datasetId;
|
| - }
|
| - if (partitionStrategy != null) {
|
| - _json["partitionStrategy"] = partitionStrategy;
|
| - }
|
| - if (referenceSetId != null) {
|
| - _json["referenceSetId"] = referenceSetId;
|
| - }
|
| - if (sourceUris != null) {
|
| - _json["sourceUris"] = sourceUris;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** The read group set import response. */
|
| -class ImportReadGroupSetsResponse {
|
| - /** A job ID that can be used to get status information. */
|
| - core.String jobId;
|
| -
|
| - ImportReadGroupSetsResponse();
|
| -
|
| - ImportReadGroupSetsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("jobId")) {
|
| - jobId = _json["jobId"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (jobId != null) {
|
| - _json["jobId"] = jobId;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** The variant data import request. */
|
| -class ImportVariantsRequest {
|
| - /**
|
| - * The format of the variant data being imported. If unspecified, defaults to
|
| - * "VCF".
|
| - * Possible string values are:
|
| - * - "COMPLETE_GENOMICS"
|
| - * - "VCF"
|
| - */
|
| - core.String format;
|
| - /**
|
| - * 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. Note that recursive wildcards ('**')
|
| - * are not supported.
|
| - */
|
| - core.List<core.String> sourceUris;
|
| -
|
| - ImportVariantsRequest();
|
| -
|
| - ImportVariantsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("format")) {
|
| - format = _json["format"];
|
| - }
|
| - if (_json.containsKey("normalizeReferenceNames")) {
|
| - normalizeReferenceNames = _json["normalizeReferenceNames"];
|
| - }
|
| - if (_json.containsKey("sourceUris")) {
|
| - sourceUris = _json["sourceUris"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (format != null) {
|
| - _json["format"] = format;
|
| - }
|
| - if (normalizeReferenceNames != null) {
|
| - _json["normalizeReferenceNames"] = normalizeReferenceNames;
|
| - }
|
| - if (sourceUris != null) {
|
| - _json["sourceUris"] = sourceUris;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** The variant data import response. */
|
| -class ImportVariantsResponse {
|
| - /** A job ID that can be used to get status information. */
|
| - core.String jobId;
|
| -
|
| - ImportVariantsResponse();
|
| -
|
| - ImportVariantsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("jobId")) {
|
| - jobId = _json["jobId"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (jobId != null) {
|
| - _json["jobId"] = jobId;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/**
|
| - * Wrapper message for `int32`.
|
| - *
|
| - * The JSON representation for `Int32Value` is JSON number.
|
| - */
|
| -class Int32Value {
|
| - /** The int32 value. */
|
| - core.int value;
|
| -
|
| - Int32Value();
|
| -
|
| - Int32Value.fromJson(core.Map _json) {
|
| - if (_json.containsKey("value")) {
|
| - value = _json["value"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (value != null) {
|
| - _json["value"] = value;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/**
|
| - * A Job represents an ongoing process that can be monitored for status
|
| - * information.
|
| - */
|
| -class Job {
|
| - /** The date this job was created, in milliseconds from the epoch. */
|
| - core.String created;
|
| - /** A more detailed description of this job's current status. */
|
| - core.String detailedStatus;
|
| - /** Any errors that occurred during processing. */
|
| - core.List<core.String> errors;
|
| - /** The job ID. */
|
| - core.String id;
|
| - /**
|
| - * If this Job represents an import, this field will contain the IDs of the
|
| - * objects that were successfully imported.
|
| - */
|
| - core.List<core.String> importedIds;
|
| - /**
|
| - * The Google Developers Console project number to which this job belongs.
|
| - */
|
| - core.String projectNumber;
|
| - /** A summarized representation of the original service request. */
|
| - JobRequest request;
|
| - /**
|
| - * The status of this job.
|
| - * Possible string values are:
|
| - * - "CANCELED"
|
| - * - "FAILURE"
|
| - * - "NEW"
|
| - * - "PENDING"
|
| - * - "RUNNING"
|
| - * - "SUCCESS"
|
| - * - "UNKNOWN_STATUS"
|
| - */
|
| - core.String status;
|
| - /** Any warnings that occurred during processing. */
|
| - core.List<core.String> warnings;
|
| -
|
| - Job();
|
| -
|
| - Job.fromJson(core.Map _json) {
|
| - if (_json.containsKey("created")) {
|
| - created = _json["created"];
|
| - }
|
| - if (_json.containsKey("detailedStatus")) {
|
| - detailedStatus = _json["detailedStatus"];
|
| - }
|
| - if (_json.containsKey("errors")) {
|
| - errors = _json["errors"];
|
| - }
|
| - if (_json.containsKey("id")) {
|
| - id = _json["id"];
|
| - }
|
| - if (_json.containsKey("importedIds")) {
|
| - importedIds = _json["importedIds"];
|
| - }
|
| - if (_json.containsKey("projectNumber")) {
|
| - projectNumber = _json["projectNumber"];
|
| - }
|
| - if (_json.containsKey("request")) {
|
| - request = new JobRequest.fromJson(_json["request"]);
|
| - }
|
| - if (_json.containsKey("status")) {
|
| - status = _json["status"];
|
| - }
|
| - if (_json.containsKey("warnings")) {
|
| - warnings = _json["warnings"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (created != null) {
|
| - _json["created"] = created;
|
| - }
|
| - if (detailedStatus != null) {
|
| - _json["detailedStatus"] = detailedStatus;
|
| - }
|
| - if (errors != null) {
|
| - _json["errors"] = errors;
|
| - }
|
| - if (id != null) {
|
| - _json["id"] = id;
|
| - }
|
| - if (importedIds != null) {
|
| - _json["importedIds"] = importedIds;
|
| - }
|
| - if (projectNumber != null) {
|
| - _json["projectNumber"] = projectNumber;
|
| - }
|
| - if (request != null) {
|
| - _json["request"] = (request).toJson();
|
| - }
|
| - if (status != null) {
|
| - _json["status"] = status;
|
| - }
|
| - if (warnings != null) {
|
| - _json["warnings"] = warnings;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** A summary representation of the service request that spawned the job. */
|
| -class JobRequest {
|
| - /**
|
| - * The data destination of the request, for example, a Google BigQuery Table
|
| - * or Dataset ID.
|
| - */
|
| - core.List<core.String> destination;
|
| - /**
|
| - * The data source of the request, for example, a Google Cloud Storage object
|
| - * path or Readset ID.
|
| - */
|
| - core.List<core.String> source;
|
| - /**
|
| - * The original request type.
|
| - * Possible string values are:
|
| - * - "ALIGN_READSETS"
|
| - * - "CALL_READSETS"
|
| - * - "EXPERIMENTAL_CREATE_JOB"
|
| - * - "EXPORT_READSETS"
|
| - * - "EXPORT_VARIANTS"
|
| - * - "IMPORT_READSETS"
|
| - * - "IMPORT_VARIANTS"
|
| - * - "UNKNOWN_TYPE"
|
| - */
|
| - core.String type;
|
| -
|
| - JobRequest();
|
| -
|
| - JobRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("destination")) {
|
| - destination = _json["destination"];
|
| - }
|
| - if (_json.containsKey("source")) {
|
| - source = _json["source"];
|
| - }
|
| - if (_json.containsKey("type")) {
|
| - type = _json["type"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (destination != null) {
|
| - _json["destination"] = destination;
|
| - }
|
| - if (source != null) {
|
| - _json["source"] = source;
|
| - }
|
| - if (type != null) {
|
| - _json["type"] = type;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** Used to hold basic key value information. */
|
| -class KeyValue {
|
| - /** A string which maps to an array of values. */
|
| - core.String key;
|
| - /** The string values. */
|
| - core.List<core.String> value;
|
| -
|
| - KeyValue();
|
| -
|
| - KeyValue.fromJson(core.Map _json) {
|
| - if (_json.containsKey("key")) {
|
| - key = _json["key"];
|
| - }
|
| - if (_json.containsKey("value")) {
|
| - value = _json["value"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (key != null) {
|
| - _json["key"] = key;
|
| - }
|
| - if (value != null) {
|
| - _json["value"] = value;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/**
|
| - * 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.
|
| - */
|
| - 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.
|
| - */
|
| - core.int mappingQuality;
|
| - /** 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();
|
| - }
|
| - if (_json.containsKey("mappingQuality")) {
|
| - mappingQuality = _json["mappingQuality"];
|
| - }
|
| - if (_json.containsKey("position")) {
|
| - position = new Position.fromJson(_json["position"]);
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (cigar != null) {
|
| - _json["cigar"] = cigar.map((value) => (value).toJson()).toList();
|
| - }
|
| - if (mappingQuality != null) {
|
| - _json["mappingQuality"] = mappingQuality;
|
| - }
|
| - if (position != null) {
|
| - _json["position"] = (position).toJson();
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -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.
|
| - */
|
| - 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.
|
| - */
|
| - core.String offset;
|
| - /** A substring of the bases that make up this reference. */
|
| - core.String sequence;
|
| -
|
| - ListBasesResponse();
|
| -
|
| - ListBasesResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("nextPageToken")) {
|
| - nextPageToken = _json["nextPageToken"];
|
| - }
|
| - if (_json.containsKey("offset")) {
|
| - offset = _json["offset"];
|
| - }
|
| - if (_json.containsKey("sequence")) {
|
| - sequence = _json["sequence"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (nextPageToken != null) {
|
| - _json["nextPageToken"] = nextPageToken;
|
| - }
|
| - if (offset != null) {
|
| - _json["offset"] = offset;
|
| - }
|
| - if (sequence != null) {
|
| - _json["sequence"] = sequence;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -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).
|
| - */
|
| - 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.
|
| - */
|
| - 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.
|
| - */
|
| - core.String nextPageToken;
|
| -
|
| - ListCoverageBucketsResponse();
|
| -
|
| - ListCoverageBucketsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("bucketWidth")) {
|
| - bucketWidth = _json["bucketWidth"];
|
| - }
|
| - if (_json.containsKey("coverageBuckets")) {
|
| - coverageBuckets = _json["coverageBuckets"].map((value) => new CoverageBucket.fromJson(value)).toList();
|
| - }
|
| - if (_json.containsKey("nextPageToken")) {
|
| - nextPageToken = _json["nextPageToken"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (bucketWidth != null) {
|
| - _json["bucketWidth"] = bucketWidth;
|
| - }
|
| - if (coverageBuckets != null) {
|
| - _json["coverageBuckets"] = coverageBuckets.map((value) => (value).toJson()).toList();
|
| - }
|
| - if (nextPageToken != null) {
|
| - _json["nextPageToken"] = nextPageToken;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** The dataset list response. */
|
| -class ListDatasetsResponse {
|
| - /** 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.
|
| - */
|
| - core.String nextPageToken;
|
| -
|
| - ListDatasetsResponse();
|
| -
|
| - ListDatasetsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("datasets")) {
|
| - datasets = _json["datasets"].map((value) => new Dataset.fromJson(value)).toList();
|
| - }
|
| - if (_json.containsKey("nextPageToken")) {
|
| - nextPageToken = _json["nextPageToken"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (datasets != null) {
|
| - _json["datasets"] = datasets.map((value) => (value).toJson()).toList();
|
| - }
|
| - if (nextPageToken != null) {
|
| - _json["nextPageToken"] = nextPageToken;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class MergeVariantsRequest {
|
| - /** The variants to be merged with existing variants. */
|
| - core.List<Variant> variants;
|
| -
|
| - MergeVariantsRequest();
|
| -
|
| - MergeVariantsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("variants")) {
|
| - variants = _json["variants"].map((value) => new Variant.fromJson(value)).toList();
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (variants != null) {
|
| - _json["variants"] = variants.map((value) => (value).toJson()).toList();
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/**
|
| - * 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 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.
|
| - */
|
| - core.String id;
|
| - /** A string which maps to an array of values. */
|
| - core.Map<core.String, core.List<core.String>> info;
|
| - /** The top-level key. */
|
| - core.String key;
|
| - /**
|
| - * 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:
|
| - * - "CHARACTER"
|
| - * - "FLAG"
|
| - * - "FLOAT"
|
| - * - "INTEGER"
|
| - * - "STRING"
|
| - * - "UNKNOWN_TYPE"
|
| - */
|
| - core.String type;
|
| - /** The value field for simple metadata */
|
| - core.String value;
|
| -
|
| - Metadata();
|
| -
|
| - Metadata.fromJson(core.Map _json) {
|
| - if (_json.containsKey("description")) {
|
| - description = _json["description"];
|
| - }
|
| - if (_json.containsKey("id")) {
|
| - id = _json["id"];
|
| - }
|
| - if (_json.containsKey("info")) {
|
| - info = _json["info"];
|
| - }
|
| - if (_json.containsKey("key")) {
|
| - key = _json["key"];
|
| - }
|
| - if (_json.containsKey("number")) {
|
| - number = _json["number"];
|
| - }
|
| - if (_json.containsKey("type")) {
|
| - type = _json["type"];
|
| - }
|
| - if (_json.containsKey("value")) {
|
| - value = _json["value"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (description != null) {
|
| - _json["description"] = description;
|
| - }
|
| - if (id != null) {
|
| - _json["id"] = id;
|
| - }
|
| - if (info != null) {
|
| - _json["info"] = info;
|
| - }
|
| - if (key != null) {
|
| - _json["key"] = key;
|
| - }
|
| - if (number != null) {
|
| - _json["number"] = number;
|
| - }
|
| - if (type != null) {
|
| - _json["type"] = type;
|
| - }
|
| - if (value != null) {
|
| - _json["value"] = value;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/**
|
| - * 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.
|
| - */
|
| - core.String position;
|
| - /** 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.
|
| - */
|
| - core.bool reverseStrand;
|
| -
|
| - Position();
|
| -
|
| - Position.fromJson(core.Map _json) {
|
| - if (_json.containsKey("position")) {
|
| - position = _json["position"];
|
| - }
|
| - if (_json.containsKey("referenceName")) {
|
| - referenceName = _json["referenceName"];
|
| - }
|
| - if (_json.containsKey("reverseStrand")) {
|
| - reverseStrand = _json["reverseStrand"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (position != null) {
|
| - _json["position"] = position;
|
| - }
|
| - if (referenceName != null) {
|
| - _json["referenceName"] = referenceName;
|
| - }
|
| - if (reverseStrand != null) {
|
| - _json["reverseStrand"] = reverseStrand;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/**
|
| - * A 0-based half-open genomic coordinate range for search requests.
|
| - * reference_id or reference_name must be set.
|
| - */
|
| -class QueryRange {
|
| - /**
|
| - * The end position of the range on the reference, 0-based exclusive. If
|
| - * specified, referenceId or referenceName must also be specified. If unset or
|
| - * 0, defaults to the length of the reference.
|
| - */
|
| - core.String end;
|
| - /** 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.
|
| - */
|
| - core.String referenceName;
|
| - /**
|
| - * The start position of the range on the reference, 0-based inclusive. If
|
| - * specified, referenceId or referenceName must also be specified. Defaults to
|
| - * 0.
|
| - */
|
| - core.String start;
|
| -
|
| - QueryRange();
|
| -
|
| - QueryRange.fromJson(core.Map _json) {
|
| - if (_json.containsKey("end")) {
|
| - end = _json["end"];
|
| - }
|
| - if (_json.containsKey("referenceId")) {
|
| - referenceId = _json["referenceId"];
|
| - }
|
| - if (_json.containsKey("referenceName")) {
|
| - referenceName = _json["referenceName"];
|
| - }
|
| - if (_json.containsKey("start")) {
|
| - start = _json["start"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (end != null) {
|
| - _json["end"] = end;
|
| - }
|
| - if (referenceId != null) {
|
| - _json["referenceId"] = referenceId;
|
| - }
|
| - if (referenceName != null) {
|
| - _json["referenceName"] = referenceName;
|
| - }
|
| - if (start != null) {
|
| - _json["start"] = start;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** A 0-based half-open genomic coordinate range over a reference sequence. */
|
| -class Range {
|
| - /**
|
| - * The end position of the range on the reference, 0-based exclusive. If
|
| - * specified, referenceName must also be specified.
|
| - */
|
| - core.String end;
|
| - /** 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. If
|
| - * specified, referenceName must also be specified.
|
| - */
|
| - core.String start;
|
| -
|
| - Range();
|
| -
|
| - Range.fromJson(core.Map _json) {
|
| - if (_json.containsKey("end")) {
|
| - end = _json["end"];
|
| - }
|
| - if (_json.containsKey("referenceName")) {
|
| - referenceName = _json["referenceName"];
|
| - }
|
| - if (_json.containsKey("start")) {
|
| - start = _json["start"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (end != null) {
|
| - _json["end"] = end;
|
| - }
|
| - if (referenceName != null) {
|
| - _json["referenceName"] = referenceName;
|
| - }
|
| - if (start != null) {
|
| - _json["start"] = start;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/**
|
| - * A 0-based half-open genomic coordinate range over a reference sequence, for
|
| - * representing the position of a genomic resource.
|
| - */
|
| -class RangePosition {
|
| - /** The end position of the range on the reference, 0-based exclusive. */
|
| - core.String end;
|
| - /** 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.
|
| - */
|
| - 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.
|
| - */
|
| - core.bool reverseStrand;
|
| - /** The start position of the range on the reference, 0-based inclusive. */
|
| - core.String start;
|
| -
|
| - RangePosition();
|
| -
|
| - RangePosition.fromJson(core.Map _json) {
|
| - if (_json.containsKey("end")) {
|
| - end = _json["end"];
|
| - }
|
| - if (_json.containsKey("referenceId")) {
|
| - referenceId = _json["referenceId"];
|
| - }
|
| - if (_json.containsKey("referenceName")) {
|
| - referenceName = _json["referenceName"];
|
| - }
|
| - if (_json.containsKey("reverseStrand")) {
|
| - reverseStrand = _json["reverseStrand"];
|
| - }
|
| - if (_json.containsKey("start")) {
|
| - start = _json["start"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (end != null) {
|
| - _json["end"] = end;
|
| - }
|
| - if (referenceId != null) {
|
| - _json["referenceId"] = referenceId;
|
| - }
|
| - if (referenceName != null) {
|
| - _json["referenceName"] = referenceName;
|
| - }
|
| - if (reverseStrand != null) {
|
| - _json["reverseStrand"] = reverseStrand;
|
| - }
|
| - if (start != null) {
|
| - _json["start"] = start;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/**
|
| - * 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. 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.
|
| - */
|
| - 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.
|
| - */
|
| - core.String alignedSequence;
|
| - /**
|
| - * 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). */
|
| - core.bool duplicateFragment;
|
| - /**
|
| - * 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. */
|
| - core.int fragmentLength;
|
| - /** The fragment name. Equivalent to QNAME (query template name) in SAM. */
|
| - core.String fragmentName;
|
| - /**
|
| - * The unique ID for this read. This is a generated unique ID, not to be
|
| - * confused with fragmentName.
|
| - */
|
| - core.String id;
|
| - /** A string which maps to an array of values. */
|
| - core.Map<core.String, core.List<core.String>> info;
|
| - /**
|
| - * The position of the primary alignment of the (readNumber+1)%numberReads
|
| - * read in the fragment. It replaces mate position and mate strand in SAM.
|
| - * This field will be unset if that read is unmapped or if the fragment only
|
| - * has a single read.
|
| - */
|
| - Position nextMatePosition;
|
| - /** 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).
|
| - */
|
| - 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 (not SAM's RG tag).
|
| - */
|
| - core.String readGroupId;
|
| - /**
|
| - * 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.
|
| - */
|
| - 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.
|
| - */
|
| - 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.
|
| - */
|
| - core.bool supplementaryAlignment;
|
| -
|
| - Read();
|
| -
|
| - Read.fromJson(core.Map _json) {
|
| - if (_json.containsKey("alignedQuality")) {
|
| - alignedQuality = _json["alignedQuality"];
|
| - }
|
| - if (_json.containsKey("alignedSequence")) {
|
| - alignedSequence = _json["alignedSequence"];
|
| - }
|
| - if (_json.containsKey("alignment")) {
|
| - alignment = new LinearAlignment.fromJson(_json["alignment"]);
|
| - }
|
| - if (_json.containsKey("duplicateFragment")) {
|
| - duplicateFragment = _json["duplicateFragment"];
|
| - }
|
| - if (_json.containsKey("failedVendorQualityChecks")) {
|
| - failedVendorQualityChecks = _json["failedVendorQualityChecks"];
|
| - }
|
| - if (_json.containsKey("fragmentLength")) {
|
| - fragmentLength = _json["fragmentLength"];
|
| - }
|
| - if (_json.containsKey("fragmentName")) {
|
| - fragmentName = _json["fragmentName"];
|
| - }
|
| - if (_json.containsKey("id")) {
|
| - id = _json["id"];
|
| - }
|
| - if (_json.containsKey("info")) {
|
| - info = _json["info"];
|
| - }
|
| - if (_json.containsKey("nextMatePosition")) {
|
| - nextMatePosition = new Position.fromJson(_json["nextMatePosition"]);
|
| - }
|
| - if (_json.containsKey("numberReads")) {
|
| - numberReads = _json["numberReads"];
|
| - }
|
| - if (_json.containsKey("properPlacement")) {
|
| - properPlacement = _json["properPlacement"];
|
| - }
|
| - if (_json.containsKey("readGroupId")) {
|
| - readGroupId = _json["readGroupId"];
|
| - }
|
| - if (_json.containsKey("readGroupSetId")) {
|
| - readGroupSetId = _json["readGroupSetId"];
|
| - }
|
| - if (_json.containsKey("readNumber")) {
|
| - readNumber = _json["readNumber"];
|
| - }
|
| - if (_json.containsKey("secondaryAlignment")) {
|
| - secondaryAlignment = _json["secondaryAlignment"];
|
| - }
|
| - if (_json.containsKey("supplementaryAlignment")) {
|
| - supplementaryAlignment = _json["supplementaryAlignment"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (alignedQuality != null) {
|
| - _json["alignedQuality"] = alignedQuality;
|
| - }
|
| - if (alignedSequence != null) {
|
| - _json["alignedSequence"] = alignedSequence;
|
| - }
|
| - if (alignment != null) {
|
| - _json["alignment"] = (alignment).toJson();
|
| - }
|
| - if (duplicateFragment != null) {
|
| - _json["duplicateFragment"] = duplicateFragment;
|
| - }
|
| - if (failedVendorQualityChecks != null) {
|
| - _json["failedVendorQualityChecks"] = failedVendorQualityChecks;
|
| - }
|
| - if (fragmentLength != null) {
|
| - _json["fragmentLength"] = fragmentLength;
|
| - }
|
| - if (fragmentName != null) {
|
| - _json["fragmentName"] = fragmentName;
|
| - }
|
| - if (id != null) {
|
| - _json["id"] = id;
|
| - }
|
| - if (info != null) {
|
| - _json["info"] = info;
|
| - }
|
| - if (nextMatePosition != null) {
|
| - _json["nextMatePosition"] = (nextMatePosition).toJson();
|
| - }
|
| - if (numberReads != null) {
|
| - _json["numberReads"] = numberReads;
|
| - }
|
| - if (properPlacement != null) {
|
| - _json["properPlacement"] = properPlacement;
|
| - }
|
| - if (readGroupId != null) {
|
| - _json["readGroupId"] = readGroupId;
|
| - }
|
| - if (readGroupSetId != null) {
|
| - _json["readGroupSetId"] = readGroupSetId;
|
| - }
|
| - if (readNumber != null) {
|
| - _json["readNumber"] = readNumber;
|
| - }
|
| - if (secondaryAlignment != null) {
|
| - _json["secondaryAlignment"] = secondaryAlignment;
|
| - }
|
| - if (supplementaryAlignment != null) {
|
| - _json["supplementaryAlignment"] = supplementaryAlignment;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/**
|
| - * A read group is all the data that's processed the same way by the sequencer.
|
| - */
|
| -class ReadGroup {
|
| - /** The ID of the dataset this read group belongs to. */
|
| - core.String datasetId;
|
| - /** A free-form text description of this read group. */
|
| - core.String description;
|
| - /** The experiment used to generate this read group. */
|
| - ReadGroupExperiment experiment;
|
| - /**
|
| - * The generated unique read group ID. Note: This is different than the @RG ID
|
| - * field in the SAM spec. For that value, see the name field.
|
| - */
|
| - core.String id;
|
| - /** A string which maps to an array of values. */
|
| - core.Map<core.String, core.List<core.String>> info;
|
| - /**
|
| - * 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.
|
| - */
|
| - 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.
|
| - */
|
| - core.List<ReadGroupProgram> programs;
|
| - /** The reference set to which the reads in this read group are aligned. */
|
| - core.String referenceSetId;
|
| - /**
|
| - * The sample this read group's data was generated from. Note: This is not an
|
| - * actual ID within this repository, but rather an identifier for a sample
|
| - * which may be meaningful to some external system.
|
| - */
|
| - core.String sampleId;
|
| -
|
| - ReadGroup();
|
| -
|
| - ReadGroup.fromJson(core.Map _json) {
|
| - if (_json.containsKey("datasetId")) {
|
| - datasetId = _json["datasetId"];
|
| - }
|
| - if (_json.containsKey("description")) {
|
| - description = _json["description"];
|
| - }
|
| - if (_json.containsKey("experiment")) {
|
| - experiment = new ReadGroupExperiment.fromJson(_json["experiment"]);
|
| - }
|
| - if (_json.containsKey("id")) {
|
| - id = _json["id"];
|
| - }
|
| - if (_json.containsKey("info")) {
|
| - info = _json["info"];
|
| - }
|
| - if (_json.containsKey("name")) {
|
| - name = _json["name"];
|
| - }
|
| - if (_json.containsKey("predictedInsertSize")) {
|
| - predictedInsertSize = _json["predictedInsertSize"];
|
| - }
|
| - if (_json.containsKey("programs")) {
|
| - programs = _json["programs"].map((value) => new ReadGroupProgram.fromJson(value)).toList();
|
| - }
|
| - if (_json.containsKey("referenceSetId")) {
|
| - referenceSetId = _json["referenceSetId"];
|
| - }
|
| - if (_json.containsKey("sampleId")) {
|
| - sampleId = _json["sampleId"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (datasetId != null) {
|
| - _json["datasetId"] = datasetId;
|
| - }
|
| - if (description != null) {
|
| - _json["description"] = description;
|
| - }
|
| - if (experiment != null) {
|
| - _json["experiment"] = (experiment).toJson();
|
| - }
|
| - if (id != null) {
|
| - _json["id"] = id;
|
| - }
|
| - if (info != null) {
|
| - _json["info"] = info;
|
| - }
|
| - if (name != null) {
|
| - _json["name"] = name;
|
| - }
|
| - if (predictedInsertSize != null) {
|
| - _json["predictedInsertSize"] = predictedInsertSize;
|
| - }
|
| - if (programs != null) {
|
| - _json["programs"] = programs.map((value) => (value).toJson()).toList();
|
| - }
|
| - if (referenceSetId != null) {
|
| - _json["referenceSetId"] = referenceSetId;
|
| - }
|
| - if (sampleId != null) {
|
| - _json["sampleId"] = sampleId;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class ReadGroupExperiment {
|
| - /**
|
| - * The instrument model used as part of this experiment. This maps to
|
| - * sequencing technology in BAM.
|
| - */
|
| - core.String instrumentModel;
|
| - /**
|
| - * The library used as part of this experiment. Note: This is not an actual ID
|
| - * within this repository, but rather an identifier for a library which may be
|
| - * meaningful to some external system.
|
| - */
|
| - core.String libraryId;
|
| - /**
|
| - * The platform unit used as part of this experiment e.g.
|
| - * flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
|
| - */
|
| - core.String platformUnit;
|
| - /** The sequencing center used as part of this experiment. */
|
| - core.String sequencingCenter;
|
| -
|
| - ReadGroupExperiment();
|
| -
|
| - ReadGroupExperiment.fromJson(core.Map _json) {
|
| - if (_json.containsKey("instrumentModel")) {
|
| - instrumentModel = _json["instrumentModel"];
|
| - }
|
| - if (_json.containsKey("libraryId")) {
|
| - libraryId = _json["libraryId"];
|
| - }
|
| - if (_json.containsKey("platformUnit")) {
|
| - platformUnit = _json["platformUnit"];
|
| - }
|
| - if (_json.containsKey("sequencingCenter")) {
|
| - sequencingCenter = _json["sequencingCenter"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (instrumentModel != null) {
|
| - _json["instrumentModel"] = instrumentModel;
|
| - }
|
| - if (libraryId != null) {
|
| - _json["libraryId"] = libraryId;
|
| - }
|
| - if (platformUnit != null) {
|
| - _json["platformUnit"] = platformUnit;
|
| - }
|
| - if (sequencingCenter != null) {
|
| - _json["sequencingCenter"] = sequencingCenter;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class ReadGroupProgram {
|
| - /** 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.
|
| - */
|
| - core.String id;
|
| - /**
|
| - * 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. */
|
| - core.String prevProgramId;
|
| - /** The version of the program run. */
|
| - core.String version;
|
| -
|
| - ReadGroupProgram();
|
| -
|
| - ReadGroupProgram.fromJson(core.Map _json) {
|
| - if (_json.containsKey("commandLine")) {
|
| - commandLine = _json["commandLine"];
|
| - }
|
| - if (_json.containsKey("id")) {
|
| - id = _json["id"];
|
| - }
|
| - if (_json.containsKey("name")) {
|
| - name = _json["name"];
|
| - }
|
| - if (_json.containsKey("prevProgramId")) {
|
| - prevProgramId = _json["prevProgramId"];
|
| - }
|
| - if (_json.containsKey("version")) {
|
| - version = _json["version"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (commandLine != null) {
|
| - _json["commandLine"] = commandLine;
|
| - }
|
| - if (id != null) {
|
| - _json["id"] = id;
|
| - }
|
| - if (name != null) {
|
| - _json["name"] = name;
|
| - }
|
| - if (prevProgramId != null) {
|
| - _json["prevProgramId"] = prevProgramId;
|
| - }
|
| - if (version != null) {
|
| - _json["version"] = version;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/**
|
| - * 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.
|
| - */
|
| -class ReadGroupSet {
|
| - /** The dataset ID. */
|
| - core.String datasetId;
|
| - /**
|
| - * The filename of the original source file for this read group set, if any.
|
| - */
|
| - core.String filename;
|
| - /** The read group set ID. */
|
| - core.String id;
|
| - /** A string which maps to an array of values. */
|
| - core.Map<core.String, core.List<core.String>> info;
|
| - /**
|
| - * 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.
|
| - */
|
| - core.List<ReadGroup> readGroups;
|
| - /** The reference set the reads in this read group set are aligned to. */
|
| - core.String referenceSetId;
|
| -
|
| - ReadGroupSet();
|
| -
|
| - ReadGroupSet.fromJson(core.Map _json) {
|
| - if (_json.containsKey("datasetId")) {
|
| - datasetId = _json["datasetId"];
|
| - }
|
| - if (_json.containsKey("filename")) {
|
| - filename = _json["filename"];
|
| - }
|
| - if (_json.containsKey("id")) {
|
| - id = _json["id"];
|
| - }
|
| - if (_json.containsKey("info")) {
|
| - info = _json["info"];
|
| - }
|
| - if (_json.containsKey("name")) {
|
| - name = _json["name"];
|
| - }
|
| - if (_json.containsKey("readGroups")) {
|
| - readGroups = _json["readGroups"].map((value) => new ReadGroup.fromJson(value)).toList();
|
| - }
|
| - if (_json.containsKey("referenceSetId")) {
|
| - referenceSetId = _json["referenceSetId"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (datasetId != null) {
|
| - _json["datasetId"] = datasetId;
|
| - }
|
| - if (filename != null) {
|
| - _json["filename"] = filename;
|
| - }
|
| - if (id != null) {
|
| - _json["id"] = id;
|
| - }
|
| - if (info != null) {
|
| - _json["info"] = info;
|
| - }
|
| - if (name != null) {
|
| - _json["name"] = name;
|
| - }
|
| - if (readGroups != null) {
|
| - _json["readGroups"] = readGroups.map((value) => (value).toJson()).toList();
|
| - }
|
| - if (referenceSetId != null) {
|
| - _json["referenceSetId"] = referenceSetId;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/**
|
| - * 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.
|
| - */
|
| -class Reference {
|
| - /** The Google generated immutable ID of the reference. */
|
| - core.String id;
|
| - /** 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.
|
| - */
|
| - core.String md5checksum;
|
| - /** 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.
|
| - */
|
| - core.int ncbiTaxonId;
|
| - /**
|
| - * 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.
|
| - */
|
| - core.String sourceURI;
|
| -
|
| - Reference();
|
| -
|
| - Reference.fromJson(core.Map _json) {
|
| - if (_json.containsKey("id")) {
|
| - id = _json["id"];
|
| - }
|
| - if (_json.containsKey("length")) {
|
| - length = _json["length"];
|
| - }
|
| - if (_json.containsKey("md5checksum")) {
|
| - md5checksum = _json["md5checksum"];
|
| - }
|
| - if (_json.containsKey("name")) {
|
| - name = _json["name"];
|
| - }
|
| - if (_json.containsKey("ncbiTaxonId")) {
|
| - ncbiTaxonId = _json["ncbiTaxonId"];
|
| - }
|
| - if (_json.containsKey("sourceAccessions")) {
|
| - sourceAccessions = _json["sourceAccessions"];
|
| - }
|
| - if (_json.containsKey("sourceURI")) {
|
| - sourceURI = _json["sourceURI"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (id != null) {
|
| - _json["id"] = id;
|
| - }
|
| - if (length != null) {
|
| - _json["length"] = length;
|
| - }
|
| - if (md5checksum != null) {
|
| - _json["md5checksum"] = md5checksum;
|
| - }
|
| - if (name != null) {
|
| - _json["name"] = name;
|
| - }
|
| - if (ncbiTaxonId != null) {
|
| - _json["ncbiTaxonId"] = ncbiTaxonId;
|
| - }
|
| - if (sourceAccessions != null) {
|
| - _json["sourceAccessions"] = sourceAccessions;
|
| - }
|
| - if (sourceURI != null) {
|
| - _json["sourceURI"] = sourceURI;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/**
|
| - * 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. */
|
| - core.String referenceName;
|
| - /**
|
| - * An upper bound (inclusive) on the starting coordinate of any variant in the
|
| - * reference sequence.
|
| - */
|
| - core.String upperBound;
|
| -
|
| - ReferenceBound();
|
| -
|
| - ReferenceBound.fromJson(core.Map _json) {
|
| - if (_json.containsKey("referenceName")) {
|
| - referenceName = _json["referenceName"];
|
| - }
|
| - if (_json.containsKey("upperBound")) {
|
| - upperBound = _json["upperBound"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (referenceName != null) {
|
| - _json["referenceName"] = referenceName;
|
| - }
|
| - if (upperBound != null) {
|
| - _json["upperBound"] = upperBound;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/**
|
| - * 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.
|
| - */
|
| -class ReferenceSet {
|
| - /** Public id of this reference set, such as GRCh37. */
|
| - core.String assemblyId;
|
| - /** Free text description of this reference set. */
|
| - core.String description;
|
| - /** The Google generated immutable ID of the reference set. */
|
| - 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.
|
| - */
|
| - 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.
|
| - */
|
| - core.int ncbiTaxonId;
|
| - /**
|
| - * 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.
|
| - */
|
| - core.List<core.String> sourceAccessions;
|
| - /** The URI from which the references were obtained. */
|
| - core.String sourceURI;
|
| -
|
| - ReferenceSet();
|
| -
|
| - ReferenceSet.fromJson(core.Map _json) {
|
| - if (_json.containsKey("assemblyId")) {
|
| - assemblyId = _json["assemblyId"];
|
| - }
|
| - if (_json.containsKey("description")) {
|
| - description = _json["description"];
|
| - }
|
| - if (_json.containsKey("id")) {
|
| - id = _json["id"];
|
| - }
|
| - if (_json.containsKey("md5checksum")) {
|
| - md5checksum = _json["md5checksum"];
|
| - }
|
| - if (_json.containsKey("ncbiTaxonId")) {
|
| - ncbiTaxonId = _json["ncbiTaxonId"];
|
| - }
|
| - if (_json.containsKey("referenceIds")) {
|
| - referenceIds = _json["referenceIds"];
|
| - }
|
| - if (_json.containsKey("sourceAccessions")) {
|
| - sourceAccessions = _json["sourceAccessions"];
|
| - }
|
| - if (_json.containsKey("sourceURI")) {
|
| - sourceURI = _json["sourceURI"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (assemblyId != null) {
|
| - _json["assemblyId"] = assemblyId;
|
| - }
|
| - if (description != null) {
|
| - _json["description"] = description;
|
| - }
|
| - if (id != null) {
|
| - _json["id"] = id;
|
| - }
|
| - if (md5checksum != null) {
|
| - _json["md5checksum"] = md5checksum;
|
| - }
|
| - if (ncbiTaxonId != null) {
|
| - _json["ncbiTaxonId"] = ncbiTaxonId;
|
| - }
|
| - if (referenceIds != null) {
|
| - _json["referenceIds"] = referenceIds;
|
| - }
|
| - if (sourceAccessions != null) {
|
| - _json["sourceAccessions"] = sourceAccessions;
|
| - }
|
| - if (sourceURI != null) {
|
| - _json["sourceURI"] = sourceURI;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class SearchAnnotationSetsRequest {
|
| - /**
|
| - * 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).
|
| - */
|
| - core.String name;
|
| - /**
|
| - * 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.
|
| - */
|
| - core.String pageToken;
|
| - /**
|
| - * 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.
|
| - */
|
| - core.List<core.String> types;
|
| -
|
| - SearchAnnotationSetsRequest();
|
| -
|
| - SearchAnnotationSetsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("datasetIds")) {
|
| - datasetIds = _json["datasetIds"];
|
| - }
|
| - if (_json.containsKey("name")) {
|
| - name = _json["name"];
|
| - }
|
| - if (_json.containsKey("pageSize")) {
|
| - pageSize = _json["pageSize"];
|
| - }
|
| - if (_json.containsKey("pageToken")) {
|
| - pageToken = _json["pageToken"];
|
| - }
|
| - if (_json.containsKey("referenceSetId")) {
|
| - referenceSetId = _json["referenceSetId"];
|
| - }
|
| - if (_json.containsKey("types")) {
|
| - types = _json["types"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (datasetIds != null) {
|
| - _json["datasetIds"] = datasetIds;
|
| - }
|
| - if (name != null) {
|
| - _json["name"] = name;
|
| - }
|
| - if (pageSize != null) {
|
| - _json["pageSize"] = pageSize;
|
| - }
|
| - if (pageToken != null) {
|
| - _json["pageToken"] = pageToken;
|
| - }
|
| - if (referenceSetId != null) {
|
| - _json["referenceSetId"] = referenceSetId;
|
| - }
|
| - if (types != null) {
|
| - _json["types"] = types;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class SearchAnnotationSetsResponse {
|
| - /** 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.
|
| - */
|
| - core.String nextPageToken;
|
| -
|
| - SearchAnnotationSetsResponse();
|
| -
|
| - SearchAnnotationSetsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("annotationSets")) {
|
| - annotationSets = _json["annotationSets"].map((value) => new AnnotationSet.fromJson(value)).toList();
|
| - }
|
| - if (_json.containsKey("nextPageToken")) {
|
| - nextPageToken = _json["nextPageToken"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (annotationSets != null) {
|
| - _json["annotationSets"] = annotationSets.map((value) => (value).toJson()).toList();
|
| - }
|
| - if (nextPageToken != null) {
|
| - _json["nextPageToken"] = nextPageToken;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class SearchAnnotationsRequest {
|
| - /**
|
| - * The annotation sets to search within. The caller must have READ access to
|
| - * these annotation sets. Required. All queried annotation sets must have the
|
| - * same type.
|
| - */
|
| - core.List<core.String> annotationSetIds;
|
| - /**
|
| - * 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.
|
| - */
|
| - core.String pageToken;
|
| - /**
|
| - * If specified, this query matches only annotations that overlap this range.
|
| - */
|
| - QueryRange range;
|
| -
|
| - SearchAnnotationsRequest();
|
| -
|
| - SearchAnnotationsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("annotationSetIds")) {
|
| - annotationSetIds = _json["annotationSetIds"];
|
| - }
|
| - if (_json.containsKey("pageSize")) {
|
| - pageSize = _json["pageSize"];
|
| - }
|
| - if (_json.containsKey("pageToken")) {
|
| - pageToken = _json["pageToken"];
|
| - }
|
| - if (_json.containsKey("range")) {
|
| - range = new QueryRange.fromJson(_json["range"]);
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (annotationSetIds != null) {
|
| - _json["annotationSetIds"] = annotationSetIds;
|
| - }
|
| - if (pageSize != null) {
|
| - _json["pageSize"] = pageSize;
|
| - }
|
| - if (pageToken != null) {
|
| - _json["pageToken"] = pageToken;
|
| - }
|
| - if (range != null) {
|
| - _json["range"] = (range).toJson();
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class SearchAnnotationsResponse {
|
| - /** 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.
|
| - */
|
| - core.String nextPageToken;
|
| -
|
| - SearchAnnotationsResponse();
|
| -
|
| - SearchAnnotationsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("annotations")) {
|
| - annotations = _json["annotations"].map((value) => new Annotation.fromJson(value)).toList();
|
| - }
|
| - if (_json.containsKey("nextPageToken")) {
|
| - nextPageToken = _json["nextPageToken"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (annotations != null) {
|
| - _json["annotations"] = annotations.map((value) => (value).toJson()).toList();
|
| - }
|
| - if (nextPageToken != null) {
|
| - _json["nextPageToken"] = nextPageToken;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** The call set search request. */
|
| -class SearchCallSetsRequest {
|
| - /**
|
| - * 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.
|
| - */
|
| - 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.
|
| - */
|
| - core.String pageToken;
|
| - /**
|
| - * Restrict the query to call sets within the given variant sets. At least one
|
| - * ID must be provided.
|
| - */
|
| - core.List<core.String> variantSetIds;
|
| -
|
| - SearchCallSetsRequest();
|
| -
|
| - SearchCallSetsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("name")) {
|
| - name = _json["name"];
|
| - }
|
| - if (_json.containsKey("pageSize")) {
|
| - pageSize = _json["pageSize"];
|
| - }
|
| - if (_json.containsKey("pageToken")) {
|
| - pageToken = _json["pageToken"];
|
| - }
|
| - if (_json.containsKey("variantSetIds")) {
|
| - variantSetIds = _json["variantSetIds"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (name != null) {
|
| - _json["name"] = name;
|
| - }
|
| - if (pageSize != null) {
|
| - _json["pageSize"] = pageSize;
|
| - }
|
| - if (pageToken != null) {
|
| - _json["pageToken"] = pageToken;
|
| - }
|
| - if (variantSetIds != null) {
|
| - _json["variantSetIds"] = variantSetIds;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** The call set search response. */
|
| -class SearchCallSetsResponse {
|
| - /** 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.
|
| - */
|
| - core.String nextPageToken;
|
| -
|
| - SearchCallSetsResponse();
|
| -
|
| - SearchCallSetsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("callSets")) {
|
| - callSets = _json["callSets"].map((value) => new CallSet.fromJson(value)).toList();
|
| - }
|
| - if (_json.containsKey("nextPageToken")) {
|
| - nextPageToken = _json["nextPageToken"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (callSets != null) {
|
| - _json["callSets"] = callSets.map((value) => (value).toJson()).toList();
|
| - }
|
| - if (nextPageToken != null) {
|
| - _json["nextPageToken"] = nextPageToken;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** The jobs search request. */
|
| -class SearchJobsRequest {
|
| - /**
|
| - * If specified, only jobs created on or after this date, given in
|
| - * milliseconds since Unix epoch, will be returned.
|
| - */
|
| - core.String createdAfter;
|
| - /**
|
| - * If specified, only jobs created prior to this date, given in milliseconds
|
| - * since Unix epoch, will be returned.
|
| - */
|
| - core.String createdBefore;
|
| - /**
|
| - * The maximum number of results to return in a single page. If unspecified,
|
| - * defaults to 128. The maximum value is 256.
|
| - */
|
| - 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 the
|
| - * nextPageToken from the previous response.
|
| - */
|
| - core.String pageToken;
|
| - /**
|
| - * Required. Only return jobs which belong to this Google Developers Console
|
| - * project.
|
| - */
|
| - core.String projectNumber;
|
| - /** Only return jobs which have a matching status. */
|
| - core.List<core.String> status;
|
| -
|
| - SearchJobsRequest();
|
| -
|
| - SearchJobsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("createdAfter")) {
|
| - createdAfter = _json["createdAfter"];
|
| - }
|
| - if (_json.containsKey("createdBefore")) {
|
| - createdBefore = _json["createdBefore"];
|
| - }
|
| - if (_json.containsKey("pageSize")) {
|
| - pageSize = _json["pageSize"];
|
| - }
|
| - if (_json.containsKey("pageToken")) {
|
| - pageToken = _json["pageToken"];
|
| - }
|
| - if (_json.containsKey("projectNumber")) {
|
| - projectNumber = _json["projectNumber"];
|
| - }
|
| - if (_json.containsKey("status")) {
|
| - status = _json["status"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (createdAfter != null) {
|
| - _json["createdAfter"] = createdAfter;
|
| - }
|
| - if (createdBefore != null) {
|
| - _json["createdBefore"] = createdBefore;
|
| - }
|
| - if (pageSize != null) {
|
| - _json["pageSize"] = pageSize;
|
| - }
|
| - if (pageToken != null) {
|
| - _json["pageToken"] = pageToken;
|
| - }
|
| - if (projectNumber != null) {
|
| - _json["projectNumber"] = projectNumber;
|
| - }
|
| - if (status != null) {
|
| - _json["status"] = status;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** The job search response. */
|
| -class SearchJobsResponse {
|
| - /** The list of jobs results, ordered newest to oldest. */
|
| - core.List<Job> jobs;
|
| - /**
|
| - * The continuation token which is used to page through large result sets.
|
| - * Provide this value is a subsequent request to return the next page of
|
| - * results. This field will be empty if there are no more results.
|
| - */
|
| - core.String nextPageToken;
|
| -
|
| - SearchJobsResponse();
|
| -
|
| - SearchJobsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("jobs")) {
|
| - jobs = _json["jobs"].map((value) => new Job.fromJson(value)).toList();
|
| - }
|
| - if (_json.containsKey("nextPageToken")) {
|
| - nextPageToken = _json["nextPageToken"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (jobs != null) {
|
| - _json["jobs"] = jobs.map((value) => (value).toJson()).toList();
|
| - }
|
| - if (nextPageToken != null) {
|
| - _json["nextPageToken"] = nextPageToken;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** 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.
|
| - */
|
| - core.List<core.String> datasetIds;
|
| - /**
|
| - * 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.
|
| - */
|
| - 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.
|
| - */
|
| - core.String pageToken;
|
| -
|
| - SearchReadGroupSetsRequest();
|
| -
|
| - SearchReadGroupSetsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("datasetIds")) {
|
| - datasetIds = _json["datasetIds"];
|
| - }
|
| - if (_json.containsKey("name")) {
|
| - name = _json["name"];
|
| - }
|
| - if (_json.containsKey("pageSize")) {
|
| - pageSize = _json["pageSize"];
|
| - }
|
| - if (_json.containsKey("pageToken")) {
|
| - pageToken = _json["pageToken"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (datasetIds != null) {
|
| - _json["datasetIds"] = datasetIds;
|
| - }
|
| - if (name != null) {
|
| - _json["name"] = name;
|
| - }
|
| - if (pageSize != null) {
|
| - _json["pageSize"] = pageSize;
|
| - }
|
| - if (pageToken != null) {
|
| - _json["pageToken"] = pageToken;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** 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.
|
| - */
|
| - core.String nextPageToken;
|
| - /** The list of matching read group sets. */
|
| - core.List<ReadGroupSet> readGroupSets;
|
| -
|
| - SearchReadGroupSetsResponse();
|
| -
|
| - SearchReadGroupSetsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("nextPageToken")) {
|
| - nextPageToken = _json["nextPageToken"];
|
| - }
|
| - if (_json.containsKey("readGroupSets")) {
|
| - readGroupSets = _json["readGroupSets"].map((value) => new ReadGroupSet.fromJson(value)).toList();
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (nextPageToken != null) {
|
| - _json["nextPageToken"] = nextPageToken;
|
| - }
|
| - if (readGroupSets != null) {
|
| - _json["readGroupSets"] = readGroupSets.map((value) => (value).toJson()).toList();
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** 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.
|
| - */
|
| - core.String end;
|
| - /**
|
| - * 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.
|
| - */
|
| - 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.
|
| - */
|
| - 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.
|
| - */
|
| - 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) returned.
|
| - */
|
| - core.String referenceName;
|
| - /**
|
| - * The start position of the range on the reference, 0-based inclusive. If
|
| - * specified, referenceName must also be specified.
|
| - */
|
| - core.String start;
|
| -
|
| - SearchReadsRequest();
|
| -
|
| - SearchReadsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("end")) {
|
| - end = _json["end"];
|
| - }
|
| - if (_json.containsKey("pageSize")) {
|
| - pageSize = _json["pageSize"];
|
| - }
|
| - if (_json.containsKey("pageToken")) {
|
| - pageToken = _json["pageToken"];
|
| - }
|
| - if (_json.containsKey("readGroupIds")) {
|
| - readGroupIds = _json["readGroupIds"];
|
| - }
|
| - if (_json.containsKey("readGroupSetIds")) {
|
| - readGroupSetIds = _json["readGroupSetIds"];
|
| - }
|
| - if (_json.containsKey("referenceName")) {
|
| - referenceName = _json["referenceName"];
|
| - }
|
| - if (_json.containsKey("start")) {
|
| - start = _json["start"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (end != null) {
|
| - _json["end"] = end;
|
| - }
|
| - if (pageSize != null) {
|
| - _json["pageSize"] = pageSize;
|
| - }
|
| - if (pageToken != null) {
|
| - _json["pageToken"] = pageToken;
|
| - }
|
| - if (readGroupIds != null) {
|
| - _json["readGroupIds"] = readGroupIds;
|
| - }
|
| - if (readGroupSetIds != null) {
|
| - _json["readGroupSetIds"] = readGroupSetIds;
|
| - }
|
| - if (referenceName != null) {
|
| - _json["referenceName"] = referenceName;
|
| - }
|
| - if (start != null) {
|
| - _json["start"] = start;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** 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.
|
| - */
|
| - 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.
|
| - */
|
| - core.String nextPageToken;
|
| -
|
| - SearchReadsResponse();
|
| -
|
| - SearchReadsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("alignments")) {
|
| - alignments = _json["alignments"].map((value) => new Read.fromJson(value)).toList();
|
| - }
|
| - if (_json.containsKey("nextPageToken")) {
|
| - nextPageToken = _json["nextPageToken"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (alignments != null) {
|
| - _json["alignments"] = alignments.map((value) => (value).toJson()).toList();
|
| - }
|
| - if (nextPageToken != null) {
|
| - _json["nextPageToken"] = nextPageToken;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class SearchReferenceSetsRequest {
|
| - /**
|
| - * If present, return references for which the accession matches any of these
|
| - * strings. Best to give a version number, for example GCF_000001405.26. If
|
| - * only the main accession number is given then all records with that main
|
| - * accession will be returned, whichever version. Note that different versions
|
| - * will have different sequences.
|
| - */
|
| - core.List<core.String> accessions;
|
| - /**
|
| - * If present, return reference sets for which a substring of their assemblyId
|
| - * matches this string (case insensitive).
|
| - */
|
| - core.String assemblyId;
|
| - /**
|
| - * If present, return references for which the md5checksum matches. See
|
| - * ReferenceSet.md5checksum for details.
|
| - */
|
| - 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.
|
| - */
|
| - 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.
|
| - */
|
| - core.String pageToken;
|
| -
|
| - SearchReferenceSetsRequest();
|
| -
|
| - SearchReferenceSetsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("accessions")) {
|
| - accessions = _json["accessions"];
|
| - }
|
| - if (_json.containsKey("assemblyId")) {
|
| - assemblyId = _json["assemblyId"];
|
| - }
|
| - if (_json.containsKey("md5checksums")) {
|
| - md5checksums = _json["md5checksums"];
|
| - }
|
| - if (_json.containsKey("pageSize")) {
|
| - pageSize = _json["pageSize"];
|
| - }
|
| - if (_json.containsKey("pageToken")) {
|
| - pageToken = _json["pageToken"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (accessions != null) {
|
| - _json["accessions"] = accessions;
|
| - }
|
| - if (assemblyId != null) {
|
| - _json["assemblyId"] = assemblyId;
|
| - }
|
| - if (md5checksums != null) {
|
| - _json["md5checksums"] = md5checksums;
|
| - }
|
| - if (pageSize != null) {
|
| - _json["pageSize"] = pageSize;
|
| - }
|
| - if (pageToken != null) {
|
| - _json["pageToken"] = pageToken;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -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.
|
| - */
|
| - core.String nextPageToken;
|
| - /** The matching references sets. */
|
| - core.List<ReferenceSet> referenceSets;
|
| -
|
| - SearchReferenceSetsResponse();
|
| -
|
| - SearchReferenceSetsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("nextPageToken")) {
|
| - nextPageToken = _json["nextPageToken"];
|
| - }
|
| - if (_json.containsKey("referenceSets")) {
|
| - referenceSets = _json["referenceSets"].map((value) => new ReferenceSet.fromJson(value)).toList();
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (nextPageToken != null) {
|
| - _json["nextPageToken"] = nextPageToken;
|
| - }
|
| - if (referenceSets != null) {
|
| - _json["referenceSets"] = referenceSets.map((value) => (value).toJson()).toList();
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class SearchReferencesRequest {
|
| - /**
|
| - * If present, return references for which the accession matches this string.
|
| - * Best to give a version number, for example GCF_000001405.26. If only the
|
| - * main accession number is given then all records with that main accession
|
| - * will be returned, whichever version. Note that different versions will have
|
| - * different sequences.
|
| - */
|
| - core.List<core.String> accessions;
|
| - /**
|
| - * If present, return references for which the md5checksum matches. See
|
| - * Reference.md5checksum for construction details.
|
| - */
|
| - 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.
|
| - */
|
| - 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.
|
| - */
|
| - core.String pageToken;
|
| - /** If present, return only references which belong to this reference set. */
|
| - core.String referenceSetId;
|
| -
|
| - SearchReferencesRequest();
|
| -
|
| - SearchReferencesRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("accessions")) {
|
| - accessions = _json["accessions"];
|
| - }
|
| - if (_json.containsKey("md5checksums")) {
|
| - md5checksums = _json["md5checksums"];
|
| - }
|
| - if (_json.containsKey("pageSize")) {
|
| - pageSize = _json["pageSize"];
|
| - }
|
| - if (_json.containsKey("pageToken")) {
|
| - pageToken = _json["pageToken"];
|
| - }
|
| - if (_json.containsKey("referenceSetId")) {
|
| - referenceSetId = _json["referenceSetId"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (accessions != null) {
|
| - _json["accessions"] = accessions;
|
| - }
|
| - if (md5checksums != null) {
|
| - _json["md5checksums"] = md5checksums;
|
| - }
|
| - if (pageSize != null) {
|
| - _json["pageSize"] = pageSize;
|
| - }
|
| - if (pageToken != null) {
|
| - _json["pageToken"] = pageToken;
|
| - }
|
| - if (referenceSetId != null) {
|
| - _json["referenceSetId"] = referenceSetId;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -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.
|
| - */
|
| - core.String nextPageToken;
|
| - /** The matching references. */
|
| - core.List<Reference> references;
|
| -
|
| - SearchReferencesResponse();
|
| -
|
| - SearchReferencesResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("nextPageToken")) {
|
| - nextPageToken = _json["nextPageToken"];
|
| - }
|
| - if (_json.containsKey("references")) {
|
| - references = _json["references"].map((value) => new Reference.fromJson(value)).toList();
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (nextPageToken != null) {
|
| - _json["nextPageToken"] = nextPageToken;
|
| - }
|
| - if (references != null) {
|
| - _json["references"] = references.map((value) => (value).toJson()).toList();
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** 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.
|
| - */
|
| - core.List<core.String> datasetIds;
|
| - /**
|
| - * 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.
|
| - */
|
| - core.String pageToken;
|
| -
|
| - SearchVariantSetsRequest();
|
| -
|
| - SearchVariantSetsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("datasetIds")) {
|
| - datasetIds = _json["datasetIds"];
|
| - }
|
| - if (_json.containsKey("pageSize")) {
|
| - pageSize = _json["pageSize"];
|
| - }
|
| - if (_json.containsKey("pageToken")) {
|
| - pageToken = _json["pageToken"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (datasetIds != null) {
|
| - _json["datasetIds"] = datasetIds;
|
| - }
|
| - if (pageSize != null) {
|
| - _json["pageSize"] = pageSize;
|
| - }
|
| - if (pageToken != null) {
|
| - _json["pageToken"] = pageToken;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** 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.
|
| - */
|
| - core.String nextPageToken;
|
| - /** The variant sets belonging to the requested dataset. */
|
| - core.List<VariantSet> variantSets;
|
| -
|
| - SearchVariantSetsResponse();
|
| -
|
| - SearchVariantSetsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("nextPageToken")) {
|
| - nextPageToken = _json["nextPageToken"];
|
| - }
|
| - if (_json.containsKey("variantSets")) {
|
| - variantSets = _json["variantSets"].map((value) => new VariantSet.fromJson(value)).toList();
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (nextPageToken != null) {
|
| - _json["nextPageToken"] = nextPageToken;
|
| - }
|
| - if (variantSets != null) {
|
| - _json["variantSets"] = variantSets.map((value) => (value).toJson()).toList();
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** 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.
|
| - */
|
| - core.List<core.String> callSetIds;
|
| - /**
|
| - * 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.
|
| - */
|
| - core.int maxCalls;
|
| - /**
|
| - * 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.
|
| - */
|
| - core.String pageToken;
|
| - /** 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.
|
| - */
|
| - core.String start;
|
| - /** 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. Both this and call_set_ids may be set.
|
| - */
|
| - core.List<core.String> variantSetIds;
|
| -
|
| - SearchVariantsRequest();
|
| -
|
| - SearchVariantsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("callSetIds")) {
|
| - callSetIds = _json["callSetIds"];
|
| - }
|
| - if (_json.containsKey("end")) {
|
| - end = _json["end"];
|
| - }
|
| - if (_json.containsKey("maxCalls")) {
|
| - maxCalls = _json["maxCalls"];
|
| - }
|
| - if (_json.containsKey("pageSize")) {
|
| - pageSize = _json["pageSize"];
|
| - }
|
| - if (_json.containsKey("pageToken")) {
|
| - pageToken = _json["pageToken"];
|
| - }
|
| - if (_json.containsKey("referenceName")) {
|
| - referenceName = _json["referenceName"];
|
| - }
|
| - if (_json.containsKey("start")) {
|
| - start = _json["start"];
|
| - }
|
| - if (_json.containsKey("variantName")) {
|
| - variantName = _json["variantName"];
|
| - }
|
| - if (_json.containsKey("variantSetIds")) {
|
| - variantSetIds = _json["variantSetIds"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (callSetIds != null) {
|
| - _json["callSetIds"] = callSetIds;
|
| - }
|
| - if (end != null) {
|
| - _json["end"] = end;
|
| - }
|
| - if (maxCalls != null) {
|
| - _json["maxCalls"] = maxCalls;
|
| - }
|
| - if (pageSize != null) {
|
| - _json["pageSize"] = pageSize;
|
| - }
|
| - if (pageToken != null) {
|
| - _json["pageToken"] = pageToken;
|
| - }
|
| - if (referenceName != null) {
|
| - _json["referenceName"] = referenceName;
|
| - }
|
| - if (start != null) {
|
| - _json["start"] = start;
|
| - }
|
| - if (variantName != null) {
|
| - _json["variantName"] = variantName;
|
| - }
|
| - if (variantSetIds != null) {
|
| - _json["variantSetIds"] = variantSetIds;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** 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.
|
| - */
|
| - core.String nextPageToken;
|
| - /** The list of matching Variants. */
|
| - core.List<Variant> variants;
|
| -
|
| - SearchVariantsResponse();
|
| -
|
| - SearchVariantsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("nextPageToken")) {
|
| - nextPageToken = _json["nextPageToken"];
|
| - }
|
| - if (_json.containsKey("variants")) {
|
| - variants = _json["variants"].map((value) => new Variant.fromJson(value)).toList();
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (nextPageToken != null) {
|
| - _json["nextPageToken"] = nextPageToken;
|
| - }
|
| - if (variants != null) {
|
| - _json["variants"] = variants.map((value) => (value).toJson()).toList();
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/**
|
| - * 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.
|
| - */
|
| - TranscriptCodingSequence codingSequence;
|
| - /**
|
| - * The exons that compose this transcript. This field should be unset for
|
| - * genomes where transcript splicing does not occur, for example prokaryotes.
|
| - *
|
| - *
|
| - * Introns are regions of the transcript that are not included in the spliced
|
| - * RNA product. Though not explicitly modeled here, intron ranges can be
|
| - * deduced; all regions of this transcript that are not exons are introns.
|
| - *
|
| - *
|
| - * Exonic sequences do not necessarily code for a translational product (amino
|
| - * acids). Only the regions of exons bounded by the codingSequence correspond
|
| - * to coding DNA sequence.
|
| - *
|
| - *
|
| - * Exons are ordered by start position and may not overlap.
|
| - */
|
| - core.List<TranscriptExon> exons;
|
| - /**
|
| - * The annotation ID of the gene from which this transcript is transcribed.
|
| - */
|
| - core.String geneId;
|
| -
|
| - Transcript();
|
| -
|
| - Transcript.fromJson(core.Map _json) {
|
| - if (_json.containsKey("codingSequence")) {
|
| - codingSequence = new TranscriptCodingSequence.fromJson(_json["codingSequence"]);
|
| - }
|
| - if (_json.containsKey("exons")) {
|
| - exons = _json["exons"].map((value) => new TranscriptExon.fromJson(value)).toList();
|
| - }
|
| - if (_json.containsKey("geneId")) {
|
| - geneId = _json["geneId"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (codingSequence != null) {
|
| - _json["codingSequence"] = (codingSequence).toJson();
|
| - }
|
| - if (exons != null) {
|
| - _json["exons"] = exons.map((value) => (value).toJson()).toList();
|
| - }
|
| - if (geneId != null) {
|
| - _json["geneId"] = geneId;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class TranscriptCodingSequence {
|
| - /**
|
| - * 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.
|
| - */
|
| - core.String start;
|
| -
|
| - TranscriptCodingSequence();
|
| -
|
| - TranscriptCodingSequence.fromJson(core.Map _json) {
|
| - if (_json.containsKey("end")) {
|
| - end = _json["end"];
|
| - }
|
| - if (_json.containsKey("start")) {
|
| - start = _json["start"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (end != null) {
|
| - _json["end"] = end;
|
| - }
|
| - if (start != null) {
|
| - _json["start"] = start;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class TranscriptExon {
|
| - /**
|
| - * 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.position.reverseStrand). 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.
|
| - */
|
| - Int32Value 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.
|
| - */
|
| - core.String start;
|
| -
|
| - TranscriptExon();
|
| -
|
| - TranscriptExon.fromJson(core.Map _json) {
|
| - if (_json.containsKey("end")) {
|
| - end = _json["end"];
|
| - }
|
| - if (_json.containsKey("frame")) {
|
| - frame = new Int32Value.fromJson(_json["frame"]);
|
| - }
|
| - if (_json.containsKey("start")) {
|
| - start = _json["start"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (end != null) {
|
| - _json["end"] = end;
|
| - }
|
| - if (frame != null) {
|
| - _json["frame"] = (frame).toJson();
|
| - }
|
| - if (start != null) {
|
| - _json["start"] = start;
|
| - }
|
| - 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. 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. */
|
| - core.List<core.String> alternateBases;
|
| - /**
|
| - * The variant calls for this particular variant. Each one represents the
|
| - * determination of genotype with respect to this variant.
|
| - */
|
| - core.List<Call> calls;
|
| - /** 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.
|
| - */
|
| - core.String end;
|
| - /**
|
| - * 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 Google generated ID of the variant, immutable. */
|
| - core.String id;
|
| - /** A string which maps to an array of values. */
|
| - core.Map<core.String, core.List<core.String>> info;
|
| - /** 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.
|
| - */
|
| - core.double quality;
|
| - /**
|
| - * 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) */
|
| - core.String referenceName;
|
| - /**
|
| - * 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. */
|
| - core.String variantSetId;
|
| -
|
| - Variant();
|
| -
|
| - Variant.fromJson(core.Map _json) {
|
| - if (_json.containsKey("alternateBases")) {
|
| - alternateBases = _json["alternateBases"];
|
| - }
|
| - if (_json.containsKey("calls")) {
|
| - calls = _json["calls"].map((value) => new Call.fromJson(value)).toList();
|
| - }
|
| - if (_json.containsKey("created")) {
|
| - created = _json["created"];
|
| - }
|
| - if (_json.containsKey("end")) {
|
| - end = _json["end"];
|
| - }
|
| - if (_json.containsKey("filter")) {
|
| - filter = _json["filter"];
|
| - }
|
| - if (_json.containsKey("id")) {
|
| - id = _json["id"];
|
| - }
|
| - if (_json.containsKey("info")) {
|
| - info = _json["info"];
|
| - }
|
| - if (_json.containsKey("names")) {
|
| - names = _json["names"];
|
| - }
|
| - if (_json.containsKey("quality")) {
|
| - quality = _json["quality"];
|
| - }
|
| - if (_json.containsKey("referenceBases")) {
|
| - referenceBases = _json["referenceBases"];
|
| - }
|
| - if (_json.containsKey("referenceName")) {
|
| - referenceName = _json["referenceName"];
|
| - }
|
| - if (_json.containsKey("start")) {
|
| - start = _json["start"];
|
| - }
|
| - if (_json.containsKey("variantSetId")) {
|
| - variantSetId = _json["variantSetId"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (alternateBases != null) {
|
| - _json["alternateBases"] = alternateBases;
|
| - }
|
| - if (calls != null) {
|
| - _json["calls"] = calls.map((value) => (value).toJson()).toList();
|
| - }
|
| - if (created != null) {
|
| - _json["created"] = created;
|
| - }
|
| - if (end != null) {
|
| - _json["end"] = end;
|
| - }
|
| - if (filter != null) {
|
| - _json["filter"] = filter;
|
| - }
|
| - if (id != null) {
|
| - _json["id"] = id;
|
| - }
|
| - if (info != null) {
|
| - _json["info"] = info;
|
| - }
|
| - if (names != null) {
|
| - _json["names"] = names;
|
| - }
|
| - if (quality != null) {
|
| - _json["quality"] = quality;
|
| - }
|
| - if (referenceBases != null) {
|
| - _json["referenceBases"] = referenceBases;
|
| - }
|
| - if (referenceName != null) {
|
| - _json["referenceName"] = referenceName;
|
| - }
|
| - if (start != null) {
|
| - _json["start"] = start;
|
| - }
|
| - if (variantSetId != null) {
|
| - _json["variantSetId"] = variantSetId;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/** A Variant annotation. */
|
| -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.
|
| - */
|
| - 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:
|
| - * - "ASSOCIATION"
|
| - * - "BENIGN"
|
| - * - "CLINICAL_SIGNIFICANCE_UNSPECIFIED"
|
| - * - "CONFERS_SENSITIVITY"
|
| - * - "DRUG_RESPONSE"
|
| - * - "HISTOCOMPATIBILITY"
|
| - * - "LIKELY_BENIGN"
|
| - * - "LIKELY_PATHOGENIC"
|
| - * - "MULTIPLE_REPORTED"
|
| - * - "OTHER"
|
| - * - "PATHOGENIC"
|
| - * - "PROTECTIVE"
|
| - * - "RISK_FACTOR"
|
| - * - "UNCERTAIN"
|
| - */
|
| - core.String clinicalSignificance;
|
| - /**
|
| - * The set of conditions associated with this variant. A condition describes
|
| - * the way a variant influences human health.
|
| - */
|
| - core.List<VariantAnnotationCondition> conditions;
|
| - /**
|
| - * Effect of the variant on the coding sequence.
|
| - * Possible string values are:
|
| - * - "EFFECT_UNSPECIFIED"
|
| - * - "FRAMESHIFT"
|
| - * - "FRAME_PRESERVING_INDEL"
|
| - * - "NONSYNONYMOUS_SNP"
|
| - * - "OTHER"
|
| - * - "SPLICE_SITE_DISRUPTION"
|
| - * - "STOP_GAIN"
|
| - * - "STOP_LOSS"
|
| - * - "SYNONYMOUS_SNP"
|
| - */
|
| - core.String effect;
|
| - /**
|
| - * 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.
|
| - */
|
| - core.List<core.String> transcriptIds;
|
| - /**
|
| - * Type has been adapted from ClinVar's list of variant types.
|
| - * Possible string values are:
|
| - * - "CNV"
|
| - * - "DELETION"
|
| - * - "INSERTION"
|
| - * - "OTHER"
|
| - * - "SNP"
|
| - * - "STRUCTURAL"
|
| - * - "SUBSTITUTION"
|
| - * - "TYPE_UNSPECIFIED"
|
| - */
|
| - core.String type;
|
| -
|
| - VariantAnnotation();
|
| -
|
| - VariantAnnotation.fromJson(core.Map _json) {
|
| - if (_json.containsKey("alternateBases")) {
|
| - alternateBases = _json["alternateBases"];
|
| - }
|
| - if (_json.containsKey("clinicalSignificance")) {
|
| - clinicalSignificance = _json["clinicalSignificance"];
|
| - }
|
| - if (_json.containsKey("conditions")) {
|
| - conditions = _json["conditions"].map((value) => new VariantAnnotationCondition.fromJson(value)).toList();
|
| - }
|
| - if (_json.containsKey("effect")) {
|
| - effect = _json["effect"];
|
| - }
|
| - if (_json.containsKey("geneId")) {
|
| - geneId = _json["geneId"];
|
| - }
|
| - if (_json.containsKey("transcriptIds")) {
|
| - transcriptIds = _json["transcriptIds"];
|
| - }
|
| - if (_json.containsKey("type")) {
|
| - type = _json["type"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (alternateBases != null) {
|
| - _json["alternateBases"] = alternateBases;
|
| - }
|
| - if (clinicalSignificance != null) {
|
| - _json["clinicalSignificance"] = clinicalSignificance;
|
| - }
|
| - if (conditions != null) {
|
| - _json["conditions"] = conditions.map((value) => (value).toJson()).toList();
|
| - }
|
| - if (effect != null) {
|
| - _json["effect"] = effect;
|
| - }
|
| - if (geneId != null) {
|
| - _json["geneId"] = geneId;
|
| - }
|
| - if (transcriptIds != null) {
|
| - _json["transcriptIds"] = transcriptIds;
|
| - }
|
| - if (type != null) {
|
| - _json["type"] = type;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -class VariantAnnotationCondition {
|
| - /**
|
| - * 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. */
|
| - core.List<ExternalId> externalIds;
|
| - /** 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/
|
| - */
|
| - core.String omimId;
|
| -
|
| - VariantAnnotationCondition();
|
| -
|
| - VariantAnnotationCondition.fromJson(core.Map _json) {
|
| - if (_json.containsKey("conceptId")) {
|
| - conceptId = _json["conceptId"];
|
| - }
|
| - if (_json.containsKey("externalIds")) {
|
| - externalIds = _json["externalIds"].map((value) => new ExternalId.fromJson(value)).toList();
|
| - }
|
| - if (_json.containsKey("names")) {
|
| - names = _json["names"];
|
| - }
|
| - if (_json.containsKey("omimId")) {
|
| - omimId = _json["omimId"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (conceptId != null) {
|
| - _json["conceptId"] = conceptId;
|
| - }
|
| - if (externalIds != null) {
|
| - _json["externalIds"] = externalIds.map((value) => (value).toJson()).toList();
|
| - }
|
| - if (names != null) {
|
| - _json["names"] = names;
|
| - }
|
| - if (omimId != null) {
|
| - _json["omimId"] = omimId;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -/**
|
| - * 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.
|
| - */
|
| -class VariantSet {
|
| - /** The dataset to which this variant set belongs. Immutable. */
|
| - core.String datasetId;
|
| - /** A textual description of this variant set. */
|
| - core.String description;
|
| - /** The Google-generated ID of the variant set. Immutable. */
|
| - core.String id;
|
| - /** The metadata associated with this variant set. */
|
| - core.List<Metadata> metadata;
|
| - /** 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.
|
| - */
|
| - 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.
|
| - */
|
| - core.String referenceSetId;
|
| -
|
| - VariantSet();
|
| -
|
| - VariantSet.fromJson(core.Map _json) {
|
| - if (_json.containsKey("datasetId")) {
|
| - datasetId = _json["datasetId"];
|
| - }
|
| - if (_json.containsKey("description")) {
|
| - description = _json["description"];
|
| - }
|
| - if (_json.containsKey("id")) {
|
| - id = _json["id"];
|
| - }
|
| - if (_json.containsKey("metadata")) {
|
| - metadata = _json["metadata"].map((value) => new Metadata.fromJson(value)).toList();
|
| - }
|
| - if (_json.containsKey("name")) {
|
| - name = _json["name"];
|
| - }
|
| - if (_json.containsKey("referenceBounds")) {
|
| - referenceBounds = _json["referenceBounds"].map((value) => new ReferenceBound.fromJson(value)).toList();
|
| - }
|
| - if (_json.containsKey("referenceSetId")) {
|
| - referenceSetId = _json["referenceSetId"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (datasetId != null) {
|
| - _json["datasetId"] = datasetId;
|
| - }
|
| - if (description != null) {
|
| - _json["description"] = description;
|
| - }
|
| - if (id != null) {
|
| - _json["id"] = id;
|
| - }
|
| - if (metadata != null) {
|
| - _json["metadata"] = metadata.map((value) => (value).toJson()).toList();
|
| - }
|
| - if (name != null) {
|
| - _json["name"] = name;
|
| - }
|
| - if (referenceBounds != null) {
|
| - _json["referenceBounds"] = referenceBounds.map((value) => (value).toJson()).toList();
|
| - }
|
| - if (referenceSetId != null) {
|
| - _json["referenceSetId"] = referenceSetId;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
|
|
Chromium Code Reviews
Issue 2571553005:
Api-roll 43: 2016-12-13 (Closed)
