| Index: generated/googleapis_beta/lib/genomics/v1beta.dart
|
| diff --git a/generated/googleapis_beta/lib/genomics/v1beta.dart b/generated/googleapis_beta/lib/genomics/v1beta.dart
|
| deleted file mode 100644
|
| index 0aedd5f0d5836e740723176fc5c74d5e5dacdeb6..0000000000000000000000000000000000000000
|
| --- a/generated/googleapis_beta/lib/genomics/v1beta.dart
|
| +++ /dev/null
|
| @@ -1,4567 +0,0 @@
|
| -library googleapis_beta.genomics.v1beta;
|
| -
|
| -import "dart:core" as core;
|
| -import "dart:collection" as collection;
|
| -import "dart:async" as async;
|
| -import "dart:convert" as convert;
|
| -
|
| -import "package:crypto/crypto.dart" as crypto;
|
| -import 'package:http/http.dart' as http;
|
| -import '../src/common_internal.dart' as common_internal;
|
| -import '../common/common.dart' as common;
|
| -
|
| -export '../common/common.dart' show ApiRequestError;
|
| -export '../common/common.dart' show DetailedApiRequestError;
|
| -
|
| -/** Provides access to Genomics data. */
|
| -class GenomicsApi {
|
| - /** View and manage your data in Google BigQuery */
|
| - static const BigqueryScope = "https://www.googleapis.com/auth/bigquery";
|
| -
|
| - /** 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 common_internal.ApiRequester _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);
|
| - ReadsResourceApi get reads => new ReadsResourceApi(_requester);
|
| - ReadsetsResourceApi get readsets => new ReadsetsResourceApi(_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/v1beta/"}) :
|
| - _requester = new common_internal.ApiRequester(client, rootUrl, servicePath);
|
| -}
|
| -
|
| -
|
| -/** Not documented yet. */
|
| -class CallsetsResourceApi {
|
| - final common_internal.ApiRequester _requester;
|
| -
|
| - CallsetsResourceApi(common_internal.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Creates a new call set.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [CallSet].
|
| - *
|
| - * Completes with a [common.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 = common.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 [common.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 = common.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (callSetId == null) {
|
| - throw new core.ArgumentError("Parameter callSetId is required.");
|
| - }
|
| -
|
| - _downloadOptions = null;
|
| -
|
| - _url = 'callsets/' + common_internal.Escaper.ecapeVariable('$callSetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "DELETE",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => null);
|
| - }
|
| -
|
| - /**
|
| - * Gets a call set by ID.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [callSetId] - The ID of the call set.
|
| - *
|
| - * Completes with a [CallSet].
|
| - *
|
| - * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<CallSet> get(core.String callSetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = common.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (callSetId == null) {
|
| - throw new core.ArgumentError("Parameter callSetId is required.");
|
| - }
|
| -
|
| -
|
| - _url = 'callsets/' + common_internal.Escaper.ecapeVariable('$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] - The ID of the call set to be updated.
|
| - *
|
| - * Completes with a [CallSet].
|
| - *
|
| - * Completes with a [common.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 = common.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/' + common_internal.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 [common.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 = common.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] - The ID of the call set to be updated.
|
| - *
|
| - * Completes with a [CallSet].
|
| - *
|
| - * Completes with a [common.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 = common.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/' + common_internal.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));
|
| - }
|
| -
|
| -}
|
| -
|
| -
|
| -/** Not documented yet. */
|
| -class DatasetsResourceApi {
|
| - final common_internal.ApiRequester _requester;
|
| -
|
| - DatasetsResourceApi(common_internal.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Creates a new dataset.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [Dataset].
|
| - *
|
| - * Completes with a [common.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 = common.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.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [datasetId] - The ID of the dataset to be deleted.
|
| - *
|
| - * Completes with a [common.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 = common.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (datasetId == null) {
|
| - throw new core.ArgumentError("Parameter datasetId is required.");
|
| - }
|
| -
|
| - _downloadOptions = null;
|
| -
|
| - _url = 'datasets/' + common_internal.Escaper.ecapeVariable('$datasetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "DELETE",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => null);
|
| - }
|
| -
|
| - /**
|
| - * Gets a dataset by ID.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [datasetId] - The ID of the dataset.
|
| - *
|
| - * Completes with a [Dataset].
|
| - *
|
| - * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<Dataset> get(core.String datasetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = common.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (datasetId == null) {
|
| - throw new core.ArgumentError("Parameter datasetId is required.");
|
| - }
|
| -
|
| -
|
| - _url = 'datasets/' + common_internal.Escaper.ecapeVariable('$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 all datasets.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [maxResults] - The maximum number of results returned by this request.
|
| - *
|
| - * [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.
|
| - *
|
| - * [projectId] - Only return datasets which belong to this Google Developers
|
| - * Console project. Only accepts project numbers. Returns all public projects
|
| - * if no project number is specified.
|
| - *
|
| - * Completes with a [ListDatasetsResponse].
|
| - *
|
| - * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<ListDatasetsResponse> list({core.String maxResults, core.String pageToken, core.String projectId}) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = common.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (maxResults != null) {
|
| - _queryParams["maxResults"] = [maxResults];
|
| - }
|
| - if (pageToken != null) {
|
| - _queryParams["pageToken"] = [pageToken];
|
| - }
|
| - if (projectId != null) {
|
| - _queryParams["projectId"] = [projectId];
|
| - }
|
| -
|
| -
|
| - _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 [common.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 = common.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/' + common_internal.Escaper.ecapeVariable('$datasetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "PATCH",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Dataset.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Undeletes a dataset by restoring a dataset which was deleted via this API.
|
| - * This operation is only possible for a week after the deletion occurred.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [datasetId] - The ID of the dataset to be undeleted.
|
| - *
|
| - * Completes with a [Dataset].
|
| - *
|
| - * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future<Dataset> undelete(core.String datasetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = common.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (datasetId == null) {
|
| - throw new core.ArgumentError("Parameter datasetId is required.");
|
| - }
|
| -
|
| -
|
| - _url = 'datasets/' + common_internal.Escaper.ecapeVariable('$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 [common.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 = common.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/' + common_internal.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));
|
| - }
|
| -
|
| -}
|
| -
|
| -
|
| -/** Not documented yet. */
|
| -class ExperimentalResourceApi {
|
| - final common_internal.ApiRequester _requester;
|
| -
|
| - ExperimentalJobsResourceApi get jobs => new ExperimentalJobsResourceApi(_requester);
|
| -
|
| - ExperimentalResourceApi(common_internal.ApiRequester client) :
|
| - _requester = client;
|
| -}
|
| -
|
| -
|
| -/** Not documented yet. */
|
| -class ExperimentalJobsResourceApi {
|
| - final common_internal.ApiRequester _requester;
|
| -
|
| - ExperimentalJobsResourceApi(common_internal.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 [common.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 = common.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));
|
| - }
|
| -
|
| -}
|
| -
|
| -
|
| -/** Not documented yet. */
|
| -class JobsResourceApi {
|
| - final common_internal.ApiRequester _requester;
|
| -
|
| - JobsResourceApi(common_internal.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 [common.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 = common.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (jobId == null) {
|
| - throw new core.ArgumentError("Parameter jobId is required.");
|
| - }
|
| -
|
| - _downloadOptions = null;
|
| -
|
| - _url = 'jobs/' + common_internal.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 [common.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 = common.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (jobId == null) {
|
| - throw new core.ArgumentError("Parameter jobId is required.");
|
| - }
|
| -
|
| -
|
| - _url = 'jobs/' + common_internal.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 [common.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 = common.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));
|
| - }
|
| -
|
| -}
|
| -
|
| -
|
| -/** Not documented yet. */
|
| -class ReadsResourceApi {
|
| - final common_internal.ApiRequester _requester;
|
| -
|
| - ReadsResourceApi(common_internal.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Gets a list of reads for one or more readsets. Reads search operates over a
|
| - * genomic coordinate space of reference sequence & position defined over the
|
| - * reference sequences to which the requested readsets 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 readset IDs yields all reads in those readsets, including
|
| - * unmapped reads. All reads returned (including reads on subsequent pages)
|
| - * are ordered by genomic coordinate (reference sequence & position). Reads
|
| - * with equivalent genomic coordinates are returned in a deterministic order.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [SearchReadsResponse].
|
| - *
|
| - * Completes with a [common.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 = common.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));
|
| - }
|
| -
|
| -}
|
| -
|
| -
|
| -/** Not documented yet. */
|
| -class ReadsetsResourceApi {
|
| - final common_internal.ApiRequester _requester;
|
| -
|
| - ReadsetsCoveragebucketsResourceApi get coveragebuckets => new ReadsetsCoveragebucketsResourceApi(_requester);
|
| -
|
| - ReadsetsResourceApi(common_internal.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Deletes a readset.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [readsetId] - The ID of the readset to be deleted. The caller must have
|
| - * WRITE permissions to the dataset associated with this readset.
|
| - *
|
| - * Completes with a [common.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 readsetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = common.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (readsetId == null) {
|
| - throw new core.ArgumentError("Parameter readsetId is required.");
|
| - }
|
| -
|
| - _downloadOptions = null;
|
| -
|
| - _url = 'readsets/' + common_internal.Escaper.ecapeVariable('$readsetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "DELETE",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => null);
|
| - }
|
| -
|
| - /**
|
| - * Exports readsets 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. In particular, comments in the input file
|
| - * header will not be preserved, and some custom tags will be converted to
|
| - * strings.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [ExportReadsetsResponse].
|
| - *
|
| - * Completes with a [common.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<ExportReadsetsResponse> export(ExportReadsetsRequest request) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = common.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| -
|
| - _url = 'readsets/export';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ExportReadsetsResponse.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Gets a readset by ID.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [readsetId] - The ID of the readset.
|
| - *
|
| - * Completes with a [Readset].
|
| - *
|
| - * Completes with a [common.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<Readset> get(core.String readsetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = common.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (readsetId == null) {
|
| - throw new core.ArgumentError("Parameter readsetId is required.");
|
| - }
|
| -
|
| -
|
| - _url = 'readsets/' + common_internal.Escaper.ecapeVariable('$readsetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "GET",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Readset.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Creates readsets by asynchronously importing the provided information. Note
|
| - * that currently comments in the input file header are not imported and some
|
| - * custom tags will be converted to strings, rather than preserving tag types.
|
| - * The caller must have WRITE permissions to the dataset.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [ImportReadsetsResponse].
|
| - *
|
| - * Completes with a [common.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<ImportReadsetsResponse> import(ImportReadsetsRequest request) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = common.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| -
|
| - _url = 'readsets/import';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ImportReadsetsResponse.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Updates a readset. This method supports patch semantics.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [readsetId] - The ID of the readset to be updated. The caller must have
|
| - * WRITE permissions to the dataset associated with this readset.
|
| - *
|
| - * Completes with a [Readset].
|
| - *
|
| - * Completes with a [common.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<Readset> patch(Readset request, core.String readsetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = common.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| - if (readsetId == null) {
|
| - throw new core.ArgumentError("Parameter readsetId is required.");
|
| - }
|
| -
|
| -
|
| - _url = 'readsets/' + common_internal.Escaper.ecapeVariable('$readsetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "PATCH",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Readset.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Gets a list of readsets matching the criteria.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [SearchReadsetsResponse].
|
| - *
|
| - * Completes with a [common.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<SearchReadsetsResponse> search(SearchReadsetsRequest request) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = common.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| -
|
| - _url = 'readsets/search';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new SearchReadsetsResponse.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Updates a readset.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [readsetId] - The ID of the readset to be updated. The caller must have
|
| - * WRITE permissions to the dataset associated with this readset.
|
| - *
|
| - * Completes with a [Readset].
|
| - *
|
| - * Completes with a [common.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<Readset> update(Readset request, core.String readsetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = common.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| - if (readsetId == null) {
|
| - throw new core.ArgumentError("Parameter readsetId is required.");
|
| - }
|
| -
|
| -
|
| - _url = 'readsets/' + common_internal.Escaper.ecapeVariable('$readsetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "PUT",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Readset.fromJson(data));
|
| - }
|
| -
|
| -}
|
| -
|
| -
|
| -/** Not documented yet. */
|
| -class ReadsetsCoveragebucketsResourceApi {
|
| - final common_internal.ApiRequester _requester;
|
| -
|
| - ReadsetsCoveragebucketsResourceApi(common_internal.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Lists fixed width coverage buckets for a readset, 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 various bucket widths, enabling
|
| - * various coverage "zoom levels". The caller must have READ permissions for
|
| - * the target readset.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [readsetId] - Required. The ID of the readset over which coverage is
|
| - * requested.
|
| - *
|
| - * [maxResults] - 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_sequenceEnd] - The end position of the range on the reference,
|
| - * 1-based exclusive. If specified, sequenceName must also be specified.
|
| - *
|
| - * [range_sequenceName] - The reference sequence name, for example chr1, 1, or
|
| - * chrX.
|
| - *
|
| - * [range_sequenceStart] - The start position of the range on the reference,
|
| - * 1-based inclusive. If specified, sequenceName 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 [common.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 readsetId, {core.String maxResults, core.String pageToken, core.String range_sequenceEnd, core.String range_sequenceName, core.String range_sequenceStart, core.String targetBucketWidth}) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = common.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (readsetId == null) {
|
| - throw new core.ArgumentError("Parameter readsetId is required.");
|
| - }
|
| - if (maxResults != null) {
|
| - _queryParams["maxResults"] = [maxResults];
|
| - }
|
| - if (pageToken != null) {
|
| - _queryParams["pageToken"] = [pageToken];
|
| - }
|
| - if (range_sequenceEnd != null) {
|
| - _queryParams["range.sequenceEnd"] = [range_sequenceEnd];
|
| - }
|
| - if (range_sequenceName != null) {
|
| - _queryParams["range.sequenceName"] = [range_sequenceName];
|
| - }
|
| - if (range_sequenceStart != null) {
|
| - _queryParams["range.sequenceStart"] = [range_sequenceStart];
|
| - }
|
| - if (targetBucketWidth != null) {
|
| - _queryParams["targetBucketWidth"] = [targetBucketWidth];
|
| - }
|
| -
|
| -
|
| - _url = 'readsets/' + common_internal.Escaper.ecapeVariable('$readsetId') + '/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));
|
| - }
|
| -
|
| -}
|
| -
|
| -
|
| -/** Not documented yet. */
|
| -class VariantsResourceApi {
|
| - final common_internal.ApiRequester _requester;
|
| -
|
| - VariantsResourceApi(common_internal.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Creates a new variant.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [Variant].
|
| - *
|
| - * Completes with a [common.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 = common.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 [common.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 = common.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (variantId == null) {
|
| - throw new core.ArgumentError("Parameter variantId is required.");
|
| - }
|
| -
|
| - _downloadOptions = null;
|
| -
|
| - _url = 'variants/' + common_internal.Escaper.ecapeVariable('$variantId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "DELETE",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => null);
|
| - }
|
| -
|
| - /**
|
| - * Exports variant data to an external destination.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [ExportVariantsResponse].
|
| - *
|
| - * Completes with a [common.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<ExportVariantsResponse> export(ExportVariantsRequest request) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = common.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| -
|
| - _url = 'variants/export';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ExportVariantsResponse.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Gets a variant by ID.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantId] - The ID of the variant.
|
| - *
|
| - * Completes with a [Variant].
|
| - *
|
| - * Completes with a [common.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 = common.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (variantId == null) {
|
| - throw new core.ArgumentError("Parameter variantId is required.");
|
| - }
|
| -
|
| -
|
| - _url = 'variants/' + common_internal.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));
|
| - }
|
| -
|
| - /**
|
| - * 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. As a special case, for single-sample VCF files,
|
| - * QUAL and FILTER fields will be moved to the call level; these are sometimes
|
| - * interpreted in a call-specific context. Imported VCF headers are appended
|
| - * to the metadata already in a variant set.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * Completes with a [ImportVariantsResponse].
|
| - *
|
| - * Completes with a [common.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> import(ImportVariantsRequest request) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = common.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| -
|
| -
|
| - _url = 'variants/import';
|
| -
|
| - var _response = _requester.request(_url,
|
| - "POST",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ImportVariantsResponse.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 [common.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 = common.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 [common.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 = common.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/' + common_internal.Escaper.ecapeVariable('$variantId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "PUT",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Variant.fromJson(data));
|
| - }
|
| -
|
| -}
|
| -
|
| -
|
| -/** Not documented yet. */
|
| -class VariantsetsResourceApi {
|
| - final common_internal.ApiRequester _requester;
|
| -
|
| - VariantsetsResourceApi(common_internal.ApiRequester client) :
|
| - _requester = client;
|
| -
|
| - /**
|
| - * Deletes the contents of a variant set. The variant set object is not
|
| - * deleted.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantSetId] - The ID of the variant set to be deleted.
|
| - *
|
| - * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future delete(core.String variantSetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = common.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (variantSetId == null) {
|
| - throw new core.ArgumentError("Parameter variantSetId is required.");
|
| - }
|
| -
|
| - _downloadOptions = null;
|
| -
|
| - _url = 'variantsets/' + common_internal.Escaper.ecapeVariable('$variantSetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "DELETE",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => null);
|
| - }
|
| -
|
| - /**
|
| - * Gets a variant set by ID.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantSetId] - Required. The ID of the variant set.
|
| - *
|
| - * Completes with a [VariantSet].
|
| - *
|
| - * Completes with a [common.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 = common.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (variantSetId == null) {
|
| - throw new core.ArgumentError("Parameter variantSetId is required.");
|
| - }
|
| -
|
| -
|
| - _url = 'variantsets/' + common_internal.Escaper.ecapeVariable('$variantSetId');
|
| -
|
| - var _response = _requester.request(_url,
|
| - "GET",
|
| - body: _body,
|
| - queryParams: _queryParams,
|
| - uploadOptions: _uploadOptions,
|
| - uploadMedia: _uploadMedia,
|
| - downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new VariantSet.fromJson(data));
|
| - }
|
| -
|
| - /**
|
| - * Merges the given variants with existing variants. Each variant will be
|
| - * merged with an existing variant that matches its reference sequence, start,
|
| - * end, reference bases, and alternative bases. If no such variant exists, a
|
| - * new one will be created.
|
| - *
|
| - * When variants are merged, the call information from the new variant is
|
| - * added to the existing variant, and other fields (such as key/value pairs)
|
| - * are discarded.
|
| - *
|
| - * [request] - The metadata request object.
|
| - *
|
| - * Request parameters:
|
| - *
|
| - * [variantSetId] - The destination variant set.
|
| - *
|
| - * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| - * error.
|
| - *
|
| - * If the used [http.Client] completes with an error when making a REST call,
|
| - * this method will complete with the same error.
|
| - */
|
| - async.Future mergeVariants(MergeVariantsRequest request, core.String variantSetId) {
|
| - var _url = null;
|
| - var _queryParams = new core.Map();
|
| - var _uploadMedia = null;
|
| - var _uploadOptions = null;
|
| - var _downloadOptions = common.DownloadOptions.Metadata;
|
| - var _body = null;
|
| -
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| - }
|
| - if (variantSetId == null) {
|
| - throw new core.ArgumentError("Parameter variantSetId is required.");
|
| - }
|
| -
|
| - _downloadOptions = null;
|
| -
|
| - _url = 'variantsets/' + common_internal.Escaper.ecapeVariable('$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 to be updated.
|
| - *
|
| - * Completes with a [VariantSet].
|
| - *
|
| - * Completes with a [common.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 = common.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/' + common_internal.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 [common.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 = common.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 to be updated.
|
| - *
|
| - * Completes with a [VariantSet].
|
| - *
|
| - * Completes with a [common.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 = common.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/' + common_internal.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));
|
| - }
|
| -
|
| -}
|
| -
|
| -
|
| -
|
| -/**
|
| - * 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 map of additional variant call information. */
|
| - 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 map of additional call set information. */
|
| - 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 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. */
|
| - GenomicRange range;
|
| -
|
| -
|
| - CoverageBucket();
|
| -
|
| - CoverageBucket.fromJson(core.Map _json) {
|
| - if (_json.containsKey("meanCoverage")) {
|
| - meanCoverage = _json["meanCoverage"];
|
| - }
|
| - if (_json.containsKey("range")) {
|
| - range = new GenomicRange.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 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 projectId;
|
| -
|
| -
|
| - Dataset();
|
| -
|
| - Dataset.fromJson(core.Map _json) {
|
| - if (_json.containsKey("id")) {
|
| - id = _json["id"];
|
| - }
|
| - if (_json.containsKey("isPublic")) {
|
| - isPublic = _json["isPublic"];
|
| - }
|
| - if (_json.containsKey("name")) {
|
| - name = _json["name"];
|
| - }
|
| - if (_json.containsKey("projectId")) {
|
| - projectId = _json["projectId"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (id != null) {
|
| - _json["id"] = id;
|
| - }
|
| - if (isPublic != null) {
|
| - _json["isPublic"] = isPublic;
|
| - }
|
| - if (name != null) {
|
| - _json["name"] = name;
|
| - }
|
| - if (projectId != null) {
|
| - _json["projectId"] = projectId;
|
| - }
|
| - 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 projectId;
|
| -
|
| - /**
|
| - * 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("projectId")) {
|
| - projectId = _json["projectId"];
|
| - }
|
| - 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 (projectId != null) {
|
| - _json["projectId"] = projectId;
|
| - }
|
| - 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 readset export request. */
|
| -class ExportReadsetsRequest {
|
| - /**
|
| - * A Google Cloud Storage URI where the exported BAM file will be created. The
|
| - * currently authenticated user must have write access to the new file
|
| - * location. An error will be returned if the URI already contains data.
|
| - */
|
| - core.String exportUri;
|
| -
|
| - /** The Google Developers Console project number that owns this export. */
|
| - core.String projectId;
|
| -
|
| - /** The IDs of the readsets to export. */
|
| - core.List<core.String> readsetIds;
|
| -
|
| - /**
|
| - * 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;
|
| -
|
| -
|
| - ExportReadsetsRequest();
|
| -
|
| - ExportReadsetsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("exportUri")) {
|
| - exportUri = _json["exportUri"];
|
| - }
|
| - if (_json.containsKey("projectId")) {
|
| - projectId = _json["projectId"];
|
| - }
|
| - if (_json.containsKey("readsetIds")) {
|
| - readsetIds = _json["readsetIds"];
|
| - }
|
| - if (_json.containsKey("referenceNames")) {
|
| - referenceNames = _json["referenceNames"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (exportUri != null) {
|
| - _json["exportUri"] = exportUri;
|
| - }
|
| - if (projectId != null) {
|
| - _json["projectId"] = projectId;
|
| - }
|
| - if (readsetIds != null) {
|
| - _json["readsetIds"] = readsetIds;
|
| - }
|
| - if (referenceNames != null) {
|
| - _json["referenceNames"] = referenceNames;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -
|
| -/** The readset export response. */
|
| -class ExportReadsetsResponse {
|
| - /** A job ID that can be used to get status information. */
|
| - core.String jobId;
|
| -
|
| -
|
| - ExportReadsetsResponse();
|
| -
|
| - ExportReadsetsResponse.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 ExportVariantsRequest {
|
| - /**
|
| - * The BigQuery dataset to export data to. Note that this is distinct from the
|
| - * Genomics concept of "dataset".
|
| - */
|
| - core.String bigqueryDataset;
|
| -
|
| - /**
|
| - * 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;
|
| -
|
| - /**
|
| - * 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 projectId;
|
| -
|
| - /**
|
| - * Required. The ID of the variant set that contains variant data which should
|
| - * be exported. The caller must have READ access to this variant set.
|
| - */
|
| - core.String variantSetId;
|
| -
|
| -
|
| - ExportVariantsRequest();
|
| -
|
| - ExportVariantsRequest.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("projectId")) {
|
| - projectId = _json["projectId"];
|
| - }
|
| - if (_json.containsKey("variantSetId")) {
|
| - variantSetId = _json["variantSetId"];
|
| - }
|
| - }
|
| -
|
| - 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 (projectId != null) {
|
| - _json["projectId"] = projectId;
|
| - }
|
| - if (variantSetId != null) {
|
| - _json["variantSetId"] = variantSetId;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -
|
| -/** The variant data export response. */
|
| -class ExportVariantsResponse {
|
| - /** A job ID that can be used to get status information. */
|
| - core.String jobId;
|
| -
|
| -
|
| - ExportVariantsResponse();
|
| -
|
| - ExportVariantsResponse.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;
|
| - }
|
| -}
|
| -
|
| -
|
| -/**
|
| - * An inclusive, exclusive genomic coordinate range over a reference sequence.
|
| - */
|
| -class GenomicRange {
|
| - /**
|
| - * The end position of the range on the reference, 1-based exclusive. If
|
| - * specified, sequenceName must also be specified.
|
| - */
|
| - core.String sequenceEnd;
|
| -
|
| - /** The reference sequence name, for example chr1, 1, or chrX. */
|
| - core.String sequenceName;
|
| -
|
| - /**
|
| - * The start position of the range on the reference, 1-based inclusive. If
|
| - * specified, sequenceName must also be specified.
|
| - */
|
| - core.String sequenceStart;
|
| -
|
| -
|
| - GenomicRange();
|
| -
|
| - GenomicRange.fromJson(core.Map _json) {
|
| - if (_json.containsKey("sequenceEnd")) {
|
| - sequenceEnd = _json["sequenceEnd"];
|
| - }
|
| - if (_json.containsKey("sequenceName")) {
|
| - sequenceName = _json["sequenceName"];
|
| - }
|
| - if (_json.containsKey("sequenceStart")) {
|
| - sequenceStart = _json["sequenceStart"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (sequenceEnd != null) {
|
| - _json["sequenceEnd"] = sequenceEnd;
|
| - }
|
| - if (sequenceName != null) {
|
| - _json["sequenceName"] = sequenceName;
|
| - }
|
| - if (sequenceStart != null) {
|
| - _json["sequenceStart"] = sequenceStart;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -
|
| -/** Not documented yet. */
|
| -class Header {
|
| - /** (SO) Sorting order of alignments. */
|
| - core.String sortingOrder;
|
| -
|
| - /** (VN) BAM format version. */
|
| - core.String version;
|
| -
|
| -
|
| - Header();
|
| -
|
| - Header.fromJson(core.Map _json) {
|
| - if (_json.containsKey("sortingOrder")) {
|
| - sortingOrder = _json["sortingOrder"];
|
| - }
|
| - if (_json.containsKey("version")) {
|
| - version = _json["version"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (sortingOrder != null) {
|
| - _json["sortingOrder"] = sortingOrder;
|
| - }
|
| - if (version != null) {
|
| - _json["version"] = version;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -
|
| -/** The header section of the BAM/SAM file. */
|
| -class HeaderSection {
|
| - /** (@CO) One-line text comments. */
|
| - core.List<core.String> comments;
|
| -
|
| - /**
|
| - * [Deprecated] This field is deprecated and will no longer be populated.
|
| - * Please use filename instead.
|
| - */
|
| - core.String fileUri;
|
| -
|
| - /** The name of the file from which this data was imported. */
|
| - core.String filename;
|
| -
|
| - /** (@HD) The header line. */
|
| - core.List<Header> headers;
|
| -
|
| - /** (@PG) Programs. */
|
| - core.List<Program> programs;
|
| -
|
| - /** (@RG) Read group. */
|
| - core.List<ReadGroup> readGroups;
|
| -
|
| - /** (@SQ) Reference sequence dictionary. */
|
| - core.List<ReferenceSequence> refSequences;
|
| -
|
| -
|
| - HeaderSection();
|
| -
|
| - HeaderSection.fromJson(core.Map _json) {
|
| - if (_json.containsKey("comments")) {
|
| - comments = _json["comments"];
|
| - }
|
| - if (_json.containsKey("fileUri")) {
|
| - fileUri = _json["fileUri"];
|
| - }
|
| - if (_json.containsKey("filename")) {
|
| - filename = _json["filename"];
|
| - }
|
| - if (_json.containsKey("headers")) {
|
| - headers = _json["headers"].map((value) => new Header.fromJson(value)).toList();
|
| - }
|
| - if (_json.containsKey("programs")) {
|
| - programs = _json["programs"].map((value) => new Program.fromJson(value)).toList();
|
| - }
|
| - if (_json.containsKey("readGroups")) {
|
| - readGroups = _json["readGroups"].map((value) => new ReadGroup.fromJson(value)).toList();
|
| - }
|
| - if (_json.containsKey("refSequences")) {
|
| - refSequences = _json["refSequences"].map((value) => new ReferenceSequence.fromJson(value)).toList();
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (comments != null) {
|
| - _json["comments"] = comments;
|
| - }
|
| - if (fileUri != null) {
|
| - _json["fileUri"] = fileUri;
|
| - }
|
| - if (filename != null) {
|
| - _json["filename"] = filename;
|
| - }
|
| - if (headers != null) {
|
| - _json["headers"] = headers.map((value) => (value).toJson()).toList();
|
| - }
|
| - if (programs != null) {
|
| - _json["programs"] = programs.map((value) => (value).toJson()).toList();
|
| - }
|
| - if (readGroups != null) {
|
| - _json["readGroups"] = readGroups.map((value) => (value).toJson()).toList();
|
| - }
|
| - if (refSequences != null) {
|
| - _json["refSequences"] = refSequences.map((value) => (value).toJson()).toList();
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -
|
| -/** The readset import request. */
|
| -class ImportReadsetsRequest {
|
| - /**
|
| - * Required. The ID of the dataset these readsets will belong to. The caller
|
| - * must have WRITE permissions to this dataset.
|
| - */
|
| - core.String datasetId;
|
| -
|
| - /** A list of URIs pointing at BAM files in Google Cloud Storage. */
|
| - core.List<core.String> sourceUris;
|
| -
|
| -
|
| - ImportReadsetsRequest();
|
| -
|
| - ImportReadsetsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("datasetId")) {
|
| - datasetId = _json["datasetId"];
|
| - }
|
| - if (_json.containsKey("sourceUris")) {
|
| - sourceUris = _json["sourceUris"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (datasetId != null) {
|
| - _json["datasetId"] = datasetId;
|
| - }
|
| - if (sourceUris != null) {
|
| - _json["sourceUris"] = sourceUris;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -
|
| -/** The readset import response. */
|
| -class ImportReadsetsResponse {
|
| - /** A job ID that can be used to get status information. */
|
| - core.String jobId;
|
| -
|
| -
|
| - ImportReadsetsResponse();
|
| -
|
| - ImportReadsetsResponse.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.
|
| - * Possible string values are:
|
| - * - "completeGenomics"
|
| - * - "vcf"
|
| - */
|
| - core.String format;
|
| -
|
| - /**
|
| - * A list of URIs pointing at VCF files in Google Cloud Storage. See the VCF
|
| - * Specification for more details on the input format.
|
| - */
|
| - core.List<core.String> sourceUris;
|
| -
|
| - /** Required. The variant set to which variant data should be imported. */
|
| - core.String variantSetId;
|
| -
|
| -
|
| - ImportVariantsRequest();
|
| -
|
| - ImportVariantsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("format")) {
|
| - format = _json["format"];
|
| - }
|
| - if (_json.containsKey("sourceUris")) {
|
| - sourceUris = _json["sourceUris"];
|
| - }
|
| - if (_json.containsKey("variantSetId")) {
|
| - variantSetId = _json["variantSetId"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (format != null) {
|
| - _json["format"] = format;
|
| - }
|
| - if (sourceUris != null) {
|
| - _json["sourceUris"] = sourceUris;
|
| - }
|
| - if (variantSetId != null) {
|
| - _json["variantSetId"] = variantSetId;
|
| - }
|
| - 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;
|
| - }
|
| -}
|
| -
|
| -
|
| -/**
|
| - * 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 description;
|
| -
|
| - /** 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 projectId;
|
| -
|
| - /** 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"
|
| - * - "unknownStatus"
|
| - */
|
| - 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("description")) {
|
| - description = _json["description"];
|
| - }
|
| - if (_json.containsKey("errors")) {
|
| - errors = _json["errors"];
|
| - }
|
| - if (_json.containsKey("id")) {
|
| - id = _json["id"];
|
| - }
|
| - if (_json.containsKey("importedIds")) {
|
| - importedIds = _json["importedIds"];
|
| - }
|
| - if (_json.containsKey("projectId")) {
|
| - projectId = _json["projectId"];
|
| - }
|
| - 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 (description != null) {
|
| - _json["description"] = description;
|
| - }
|
| - if (errors != null) {
|
| - _json["errors"] = errors;
|
| - }
|
| - if (id != null) {
|
| - _json["id"] = id;
|
| - }
|
| - if (importedIds != null) {
|
| - _json["importedIds"] = importedIds;
|
| - }
|
| - if (projectId != null) {
|
| - _json["projectId"] = projectId;
|
| - }
|
| - 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:
|
| - * - "alignReadsets"
|
| - * - "callReadsets"
|
| - * - "experimentalCreateJob"
|
| - * - "exportReadsets"
|
| - * - "exportVariants"
|
| - * - "importReadsets"
|
| - * - "importVariants"
|
| - * - "unknownType"
|
| - */
|
| - 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;
|
| - }
|
| -}
|
| -
|
| -
|
| -/** Not documented yet. */
|
| -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;
|
| - }
|
| -}
|
| -
|
| -
|
| -/** Not documented yet. */
|
| -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;
|
| -
|
| - /** Remaining structured metadata key-value pairs. */
|
| - 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"
|
| - * - "unknownType"
|
| - */
|
| - 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;
|
| - }
|
| -}
|
| -
|
| -
|
| -/** Not documented yet. */
|
| -class Program {
|
| - /** (CL) Command line. */
|
| - core.String commandLine;
|
| -
|
| - /** (ID) Program record identifier. */
|
| - core.String id;
|
| -
|
| - /** (PN) Program name. */
|
| - core.String name;
|
| -
|
| - /** (PP) Previous program ID. */
|
| - core.String prevProgramId;
|
| -
|
| - /** (VN) Program version. */
|
| - core.String version;
|
| -
|
| -
|
| - Program();
|
| -
|
| - Program.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 is a group of bases that may or may not have been aligned to a
|
| - * reference. It contains quality information and other metadata.
|
| - */
|
| -class Read {
|
| - /**
|
| - * The originalBases after the cigar field has been applied. Deletions are
|
| - * represented with '-' and insertions are omitted.
|
| - */
|
| - core.String alignedBases;
|
| -
|
| - /**
|
| - * Represents the quality of each base in this read. Each character represents
|
| - * one base. To get the quality, take the ASCII value of the character and
|
| - * subtract 33. (QUAL)
|
| - */
|
| - core.String baseQuality;
|
| -
|
| - /**
|
| - * A condensed representation of how this read matches up to the reference.
|
| - * (CIGAR)
|
| - */
|
| - core.String cigar;
|
| -
|
| - /**
|
| - * Each bit of this number has a different meaning if enabled. See the full
|
| - * BAM spec for more details. (FLAG)
|
| - */
|
| - core.int flags;
|
| -
|
| - /** The Google generated ID of the read, immutable. */
|
| - core.String id;
|
| -
|
| - /**
|
| - * A score up to 255 that represents how likely this read's aligned position
|
| - * is to be correct. A higher value is better. (MAPQ)
|
| - */
|
| - core.int mappingQuality;
|
| -
|
| - /** The 1-based start position of the paired read. (PNEXT) */
|
| - core.int matePosition;
|
| -
|
| - /**
|
| - * The name of the sequence that the paired read is aligned to. This is
|
| - * usually the same as referenceSequenceName. (RNEXT)
|
| - */
|
| - core.String mateReferenceSequenceName;
|
| -
|
| - /**
|
| - * The name of the read. When imported from a BAM file, this is the query
|
| - * template name. (QNAME)
|
| - */
|
| - core.String name;
|
| -
|
| - /** The list of bases that this read represents (such as "CATCGA"). (SEQ) */
|
| - core.String originalBases;
|
| -
|
| - /**
|
| - * The 1-based start position of the aligned read. If the first base starts at
|
| - * the very beginning of the reference sequence, then the position would be
|
| - * '1'. (POS)
|
| - */
|
| - core.int position;
|
| -
|
| - /** The ID of the readset this read belongs to. */
|
| - core.String readsetId;
|
| -
|
| - /**
|
| - * The name of the sequence that this read is aligned to. This would be, for
|
| - * example, 'X' for the X Chromosome or '20' for Chromosome 20. (RNAME)
|
| - */
|
| - core.String referenceSequenceName;
|
| -
|
| - /** A map of additional read information. (TAG) */
|
| - core.Map<core.String, core.List<core.String>> tags;
|
| -
|
| - /**
|
| - * Length of the original piece of DNA that produced both this read and the
|
| - * paired read. (TLEN)
|
| - */
|
| - core.int templateLength;
|
| -
|
| -
|
| - Read();
|
| -
|
| - Read.fromJson(core.Map _json) {
|
| - if (_json.containsKey("alignedBases")) {
|
| - alignedBases = _json["alignedBases"];
|
| - }
|
| - if (_json.containsKey("baseQuality")) {
|
| - baseQuality = _json["baseQuality"];
|
| - }
|
| - if (_json.containsKey("cigar")) {
|
| - cigar = _json["cigar"];
|
| - }
|
| - if (_json.containsKey("flags")) {
|
| - flags = _json["flags"];
|
| - }
|
| - if (_json.containsKey("id")) {
|
| - id = _json["id"];
|
| - }
|
| - if (_json.containsKey("mappingQuality")) {
|
| - mappingQuality = _json["mappingQuality"];
|
| - }
|
| - if (_json.containsKey("matePosition")) {
|
| - matePosition = _json["matePosition"];
|
| - }
|
| - if (_json.containsKey("mateReferenceSequenceName")) {
|
| - mateReferenceSequenceName = _json["mateReferenceSequenceName"];
|
| - }
|
| - if (_json.containsKey("name")) {
|
| - name = _json["name"];
|
| - }
|
| - if (_json.containsKey("originalBases")) {
|
| - originalBases = _json["originalBases"];
|
| - }
|
| - if (_json.containsKey("position")) {
|
| - position = _json["position"];
|
| - }
|
| - if (_json.containsKey("readsetId")) {
|
| - readsetId = _json["readsetId"];
|
| - }
|
| - if (_json.containsKey("referenceSequenceName")) {
|
| - referenceSequenceName = _json["referenceSequenceName"];
|
| - }
|
| - if (_json.containsKey("tags")) {
|
| - tags = _json["tags"];
|
| - }
|
| - if (_json.containsKey("templateLength")) {
|
| - templateLength = _json["templateLength"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (alignedBases != null) {
|
| - _json["alignedBases"] = alignedBases;
|
| - }
|
| - if (baseQuality != null) {
|
| - _json["baseQuality"] = baseQuality;
|
| - }
|
| - if (cigar != null) {
|
| - _json["cigar"] = cigar;
|
| - }
|
| - if (flags != null) {
|
| - _json["flags"] = flags;
|
| - }
|
| - if (id != null) {
|
| - _json["id"] = id;
|
| - }
|
| - if (mappingQuality != null) {
|
| - _json["mappingQuality"] = mappingQuality;
|
| - }
|
| - if (matePosition != null) {
|
| - _json["matePosition"] = matePosition;
|
| - }
|
| - if (mateReferenceSequenceName != null) {
|
| - _json["mateReferenceSequenceName"] = mateReferenceSequenceName;
|
| - }
|
| - if (name != null) {
|
| - _json["name"] = name;
|
| - }
|
| - if (originalBases != null) {
|
| - _json["originalBases"] = originalBases;
|
| - }
|
| - if (position != null) {
|
| - _json["position"] = position;
|
| - }
|
| - if (readsetId != null) {
|
| - _json["readsetId"] = readsetId;
|
| - }
|
| - if (referenceSequenceName != null) {
|
| - _json["referenceSequenceName"] = referenceSequenceName;
|
| - }
|
| - if (tags != null) {
|
| - _json["tags"] = tags;
|
| - }
|
| - if (templateLength != null) {
|
| - _json["templateLength"] = templateLength;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -
|
| -/** Not documented yet. */
|
| -class ReadGroup {
|
| - /** (DT) Date the run was produced (ISO8601 date or date/time). */
|
| - core.String date;
|
| -
|
| - /** (DS) Description. */
|
| - core.String description;
|
| -
|
| - /**
|
| - * (FO) Flow order. The array of nucleotide bases that correspond to the
|
| - * nucleotides used for each flow of each read.
|
| - */
|
| - core.String flowOrder;
|
| -
|
| - /** (ID) Read group identifier. */
|
| - core.String id;
|
| -
|
| - /**
|
| - * (KS) The array of nucleotide bases that correspond to the key sequence of
|
| - * each read.
|
| - */
|
| - core.String keySequence;
|
| -
|
| - /** (LS) Library. */
|
| - core.String library;
|
| -
|
| - /** (PU) Platform unit. */
|
| - core.String platformUnit;
|
| -
|
| - /** (PI) Predicted median insert size. */
|
| - core.int predictedInsertSize;
|
| -
|
| - /** (PG) Programs used for processing the read group. */
|
| - core.String processingProgram;
|
| -
|
| - /** (SM) Sample. */
|
| - core.String sample;
|
| -
|
| - /** (CN) Name of sequencing center producing the read. */
|
| - core.String sequencingCenterName;
|
| -
|
| - /** (PL) Platform/technology used to produce the reads. */
|
| - core.String sequencingTechnology;
|
| -
|
| -
|
| - ReadGroup();
|
| -
|
| - ReadGroup.fromJson(core.Map _json) {
|
| - if (_json.containsKey("date")) {
|
| - date = _json["date"];
|
| - }
|
| - if (_json.containsKey("description")) {
|
| - description = _json["description"];
|
| - }
|
| - if (_json.containsKey("flowOrder")) {
|
| - flowOrder = _json["flowOrder"];
|
| - }
|
| - if (_json.containsKey("id")) {
|
| - id = _json["id"];
|
| - }
|
| - if (_json.containsKey("keySequence")) {
|
| - keySequence = _json["keySequence"];
|
| - }
|
| - if (_json.containsKey("library")) {
|
| - library = _json["library"];
|
| - }
|
| - if (_json.containsKey("platformUnit")) {
|
| - platformUnit = _json["platformUnit"];
|
| - }
|
| - if (_json.containsKey("predictedInsertSize")) {
|
| - predictedInsertSize = _json["predictedInsertSize"];
|
| - }
|
| - if (_json.containsKey("processingProgram")) {
|
| - processingProgram = _json["processingProgram"];
|
| - }
|
| - if (_json.containsKey("sample")) {
|
| - sample = _json["sample"];
|
| - }
|
| - if (_json.containsKey("sequencingCenterName")) {
|
| - sequencingCenterName = _json["sequencingCenterName"];
|
| - }
|
| - if (_json.containsKey("sequencingTechnology")) {
|
| - sequencingTechnology = _json["sequencingTechnology"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (date != null) {
|
| - _json["date"] = date;
|
| - }
|
| - if (description != null) {
|
| - _json["description"] = description;
|
| - }
|
| - if (flowOrder != null) {
|
| - _json["flowOrder"] = flowOrder;
|
| - }
|
| - if (id != null) {
|
| - _json["id"] = id;
|
| - }
|
| - if (keySequence != null) {
|
| - _json["keySequence"] = keySequence;
|
| - }
|
| - if (library != null) {
|
| - _json["library"] = library;
|
| - }
|
| - if (platformUnit != null) {
|
| - _json["platformUnit"] = platformUnit;
|
| - }
|
| - if (predictedInsertSize != null) {
|
| - _json["predictedInsertSize"] = predictedInsertSize;
|
| - }
|
| - if (processingProgram != null) {
|
| - _json["processingProgram"] = processingProgram;
|
| - }
|
| - if (sample != null) {
|
| - _json["sample"] = sample;
|
| - }
|
| - if (sequencingCenterName != null) {
|
| - _json["sequencingCenterName"] = sequencingCenterName;
|
| - }
|
| - if (sequencingTechnology != null) {
|
| - _json["sequencingTechnology"] = sequencingTechnology;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -
|
| -/** A Readset is a collection of Reads. */
|
| -class Readset {
|
| - /** The ID of the dataset this readset belongs to. */
|
| - core.String datasetId;
|
| -
|
| - /**
|
| - * File information from the original BAM import. See the BAM format
|
| - * specification for additional information on each field.
|
| - */
|
| - core.List<HeaderSection> fileData;
|
| -
|
| - /** The Google generated ID of the readset, immutable. */
|
| - core.String id;
|
| -
|
| - /** The readset name, typically this is the sample name. */
|
| - core.String name;
|
| -
|
| -
|
| - Readset();
|
| -
|
| - Readset.fromJson(core.Map _json) {
|
| - if (_json.containsKey("datasetId")) {
|
| - datasetId = _json["datasetId"];
|
| - }
|
| - if (_json.containsKey("fileData")) {
|
| - fileData = _json["fileData"].map((value) => new HeaderSection.fromJson(value)).toList();
|
| - }
|
| - if (_json.containsKey("id")) {
|
| - id = _json["id"];
|
| - }
|
| - if (_json.containsKey("name")) {
|
| - name = _json["name"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (datasetId != null) {
|
| - _json["datasetId"] = datasetId;
|
| - }
|
| - if (fileData != null) {
|
| - _json["fileData"] = fileData.map((value) => (value).toJson()).toList();
|
| - }
|
| - if (id != null) {
|
| - _json["id"] = id;
|
| - }
|
| - if (name != null) {
|
| - _json["name"] = name;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -
|
| -/**
|
| - * ReferenceBound records an upper bound for the starting coordinate of variants
|
| - * in a particular reference.
|
| - */
|
| -class ReferenceBound {
|
| - /** The reference the bound is associate with. */
|
| - 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;
|
| - }
|
| -}
|
| -
|
| -
|
| -/** Not documented yet. */
|
| -class ReferenceSequence {
|
| - /** (AS) Genome assembly identifier. */
|
| - core.String assemblyId;
|
| -
|
| - /** (LN) Reference sequence length. */
|
| - core.int length;
|
| -
|
| - /**
|
| - * (M5) MD5 checksum of the sequence in the uppercase, excluding spaces but
|
| - * including pads as *.
|
| - */
|
| - core.String md5Checksum;
|
| -
|
| - /** (SN) Reference sequence name. */
|
| - core.String name;
|
| -
|
| - /** (SP) Species. */
|
| - core.String species;
|
| -
|
| - /** (UR) URI of the sequence. */
|
| - core.String uri;
|
| -
|
| -
|
| - ReferenceSequence();
|
| -
|
| - ReferenceSequence.fromJson(core.Map _json) {
|
| - if (_json.containsKey("assemblyId")) {
|
| - assemblyId = _json["assemblyId"];
|
| - }
|
| - if (_json.containsKey("length")) {
|
| - length = _json["length"];
|
| - }
|
| - if (_json.containsKey("md5Checksum")) {
|
| - md5Checksum = _json["md5Checksum"];
|
| - }
|
| - if (_json.containsKey("name")) {
|
| - name = _json["name"];
|
| - }
|
| - if (_json.containsKey("species")) {
|
| - species = _json["species"];
|
| - }
|
| - if (_json.containsKey("uri")) {
|
| - uri = _json["uri"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (assemblyId != null) {
|
| - _json["assemblyId"] = assemblyId;
|
| - }
|
| - if (length != null) {
|
| - _json["length"] = length;
|
| - }
|
| - if (md5Checksum != null) {
|
| - _json["md5Checksum"] = md5Checksum;
|
| - }
|
| - if (name != null) {
|
| - _json["name"] = name;
|
| - }
|
| - if (species != null) {
|
| - _json["species"] = species;
|
| - }
|
| - if (uri != null) {
|
| - _json["uri"] = uri;
|
| - }
|
| - 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 call sets to return. */
|
| - 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;
|
| -
|
| - /**
|
| - * Specifies the number of results to return in a single page. Defaults to
|
| - * 128. The maximum value is 256.
|
| - */
|
| - core.String maxResults;
|
| -
|
| - /**
|
| - * 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 projectId;
|
| -
|
| - /** 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("maxResults")) {
|
| - maxResults = _json["maxResults"];
|
| - }
|
| - if (_json.containsKey("pageToken")) {
|
| - pageToken = _json["pageToken"];
|
| - }
|
| - if (_json.containsKey("projectId")) {
|
| - projectId = _json["projectId"];
|
| - }
|
| - 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 (maxResults != null) {
|
| - _json["maxResults"] = maxResults;
|
| - }
|
| - if (pageToken != null) {
|
| - _json["pageToken"] = pageToken;
|
| - }
|
| - if (projectId != null) {
|
| - _json["projectId"] = projectId;
|
| - }
|
| - 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 search request. */
|
| -class SearchReadsRequest {
|
| - /**
|
| - * Specifies number of results to return in a single page. If unspecified, it
|
| - * will default to 256. The maximum value is 2048.
|
| - */
|
| - core.String maxResults;
|
| -
|
| - /**
|
| - * 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 readsets within which to search for reads. At least one readset ID must
|
| - * be provided. All specified readsets must be aligned against a common set of
|
| - * reference sequences; this defines the genomic coordinates for the query.
|
| - */
|
| - core.List<core.String> readsetIds;
|
| -
|
| - /**
|
| - * The end position (1-based, inclusive) of the target range. If specified,
|
| - * sequenceName must also be specified. Defaults to the end of the target
|
| - * reference sequence, if any.
|
| - */
|
| - core.String sequenceEnd;
|
| -
|
| - /**
|
| - * Restricts the results to a particular reference sequence such as 1, chr1,
|
| - * or X. The set of valid references sequences depends on the readsets
|
| - * specified. If set to *, only unmapped Reads are returned.
|
| - */
|
| - core.String sequenceName;
|
| -
|
| - /**
|
| - * The start position (1-based, inclusive) of the target range. If specified,
|
| - * sequenceName must also be specified. Defaults to the start of the target
|
| - * reference sequence, if any.
|
| - */
|
| - core.String sequenceStart;
|
| -
|
| -
|
| - SearchReadsRequest();
|
| -
|
| - SearchReadsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("maxResults")) {
|
| - maxResults = _json["maxResults"];
|
| - }
|
| - if (_json.containsKey("pageToken")) {
|
| - pageToken = _json["pageToken"];
|
| - }
|
| - if (_json.containsKey("readsetIds")) {
|
| - readsetIds = _json["readsetIds"];
|
| - }
|
| - if (_json.containsKey("sequenceEnd")) {
|
| - sequenceEnd = _json["sequenceEnd"];
|
| - }
|
| - if (_json.containsKey("sequenceName")) {
|
| - sequenceName = _json["sequenceName"];
|
| - }
|
| - if (_json.containsKey("sequenceStart")) {
|
| - sequenceStart = _json["sequenceStart"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (maxResults != null) {
|
| - _json["maxResults"] = maxResults;
|
| - }
|
| - if (pageToken != null) {
|
| - _json["pageToken"] = pageToken;
|
| - }
|
| - if (readsetIds != null) {
|
| - _json["readsetIds"] = readsetIds;
|
| - }
|
| - if (sequenceEnd != null) {
|
| - _json["sequenceEnd"] = sequenceEnd;
|
| - }
|
| - if (sequenceName != null) {
|
| - _json["sequenceName"] = sequenceName;
|
| - }
|
| - if (sequenceStart != null) {
|
| - _json["sequenceStart"] = sequenceStart;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -
|
| -/** The read search response. */
|
| -class SearchReadsResponse {
|
| - /**
|
| - * 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 Reads. The resulting Reads are sorted by position; the
|
| - * smallest positions are returned first. Unmapped reads, which have no
|
| - * position, are returned last and are further sorted alphabetically by name.
|
| - */
|
| - core.List<Read> reads;
|
| -
|
| -
|
| - SearchReadsResponse();
|
| -
|
| - SearchReadsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("nextPageToken")) {
|
| - nextPageToken = _json["nextPageToken"];
|
| - }
|
| - if (_json.containsKey("reads")) {
|
| - reads = _json["reads"].map((value) => new Read.fromJson(value)).toList();
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (nextPageToken != null) {
|
| - _json["nextPageToken"] = nextPageToken;
|
| - }
|
| - if (reads != null) {
|
| - _json["reads"] = reads.map((value) => (value).toJson()).toList();
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -
|
| -/** The readset search request. */
|
| -class SearchReadsetsRequest {
|
| - /**
|
| - * Restricts this query to readsets within the given datasets. At least one ID
|
| - * must be provided.
|
| - */
|
| - core.List<core.String> datasetIds;
|
| -
|
| - /**
|
| - * Specifies number of results to return in a single page. If unspecified, it
|
| - * will default to 128. The maximum value is 1024.
|
| - */
|
| - core.String maxResults;
|
| -
|
| - /**
|
| - * Only return readsets for which a substring of the name matches this string.
|
| - */
|
| - core.String name;
|
| -
|
| - /**
|
| - * 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;
|
| -
|
| -
|
| - SearchReadsetsRequest();
|
| -
|
| - SearchReadsetsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("datasetIds")) {
|
| - datasetIds = _json["datasetIds"];
|
| - }
|
| - if (_json.containsKey("maxResults")) {
|
| - maxResults = _json["maxResults"];
|
| - }
|
| - if (_json.containsKey("name")) {
|
| - name = _json["name"];
|
| - }
|
| - if (_json.containsKey("pageToken")) {
|
| - pageToken = _json["pageToken"];
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (datasetIds != null) {
|
| - _json["datasetIds"] = datasetIds;
|
| - }
|
| - if (maxResults != null) {
|
| - _json["maxResults"] = maxResults;
|
| - }
|
| - if (name != null) {
|
| - _json["name"] = name;
|
| - }
|
| - if (pageToken != null) {
|
| - _json["pageToken"] = pageToken;
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -
|
| -/** The readset search response. */
|
| -class SearchReadsetsResponse {
|
| - /**
|
| - * 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 Readsets. */
|
| - core.List<Readset> readsets;
|
| -
|
| -
|
| - SearchReadsetsResponse();
|
| -
|
| - SearchReadsetsResponse.fromJson(core.Map _json) {
|
| - if (_json.containsKey("nextPageToken")) {
|
| - nextPageToken = _json["nextPageToken"];
|
| - }
|
| - if (_json.containsKey("readsets")) {
|
| - readsets = _json["readsets"].map((value) => new Readset.fromJson(value)).toList();
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (nextPageToken != null) {
|
| - _json["nextPageToken"] = nextPageToken;
|
| - }
|
| - if (readsets != null) {
|
| - _json["readsets"] = readsets.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 variant sets to return in a request. */
|
| - 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. Currently, variants
|
| - * with no calls from any call set will never be returned.
|
| - */
|
| - core.List<core.String> callSetIds;
|
| -
|
| - /**
|
| - * Required. The end of the window (0-based, exclusive) for which overlapping
|
| - * variants should be returned.
|
| - */
|
| - core.String end;
|
| -
|
| - /**
|
| - * The maximum number of calls to return. However, at least one variant will
|
| - * always be returned, even if it has more calls than this limit.
|
| - */
|
| - core.int maxCalls;
|
| -
|
| - /** The maximum number of variants to return. */
|
| - 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;
|
| -
|
| - /**
|
| - * Required. The beginning of the window (0-based, inclusive) for which
|
| - * overlapping variants should be returned.
|
| - */
|
| - core.String start;
|
| -
|
| - /** Only return variants which have exactly this name. */
|
| - core.String variantName;
|
| -
|
| - /**
|
| - * Exactly one variant set ID must be provided. Only variants from this
|
| - * variant set will be returned.
|
| - */
|
| - 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 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 map of additional variant information. */
|
| - 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 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;
|
| -
|
| - /** The Google-generated ID of the variant set. Immutable. */
|
| - core.String id;
|
| -
|
| - /** The metadata associated with this variant set. */
|
| - core.List<Metadata> metadata;
|
| -
|
| - /**
|
| - * 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;
|
| -
|
| -
|
| - VariantSet();
|
| -
|
| - VariantSet.fromJson(core.Map _json) {
|
| - if (_json.containsKey("datasetId")) {
|
| - datasetId = _json["datasetId"];
|
| - }
|
| - if (_json.containsKey("id")) {
|
| - id = _json["id"];
|
| - }
|
| - if (_json.containsKey("metadata")) {
|
| - metadata = _json["metadata"].map((value) => new Metadata.fromJson(value)).toList();
|
| - }
|
| - if (_json.containsKey("referenceBounds")) {
|
| - referenceBounds = _json["referenceBounds"].map((value) => new ReferenceBound.fromJson(value)).toList();
|
| - }
|
| - }
|
| -
|
| - core.Map toJson() {
|
| - var _json = new core.Map();
|
| - if (datasetId != null) {
|
| - _json["datasetId"] = datasetId;
|
| - }
|
| - if (id != null) {
|
| - _json["id"] = id;
|
| - }
|
| - if (metadata != null) {
|
| - _json["metadata"] = metadata.map((value) => (value).toJson()).toList();
|
| - }
|
| - if (referenceBounds != null) {
|
| - _json["referenceBounds"] = referenceBounds.map((value) => (value).toJson()).toList();
|
| - }
|
| - return _json;
|
| - }
|
| -}
|
| -
|
| -
|
|
|
Chromium Code Reviews
Issue 1078053002:
Roll of googleapis as of 4/7/2015. (Closed)
Base URL: https://github.com/dart-lang/googleapis.git@master