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flutter / third_party / googleapis.dart / 42f961558737d1fcce0403bffa583e2bf678aee3 / . / generated / googleapis_beta / lib / genomics / v1beta2.dart
blob: 7386460c551dbeb11d0dbfacc21ea9be7de013c8 [file] [log] [blame]
library googleapis_beta.genomics.v1beta2;
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);
ReadgroupsetsResourceApi get readgroupsets => new ReadgroupsetsResourceApi(_requester);
ReadsResourceApi get reads => new ReadsResourceApi(_requester);
ReferencesResourceApi get references => new ReferencesResourceApi(_requester);
ReferencesetsResourceApi get referencesets => new ReferencesetsResourceApi(_requester);
VariantsResourceApi get variants => new VariantsResourceApi(_requester);
VariantsetsResourceApi get variantsets => new VariantsetsResourceApi(_requester);
GenomicsApi(http.Client client) :
_requester = new common_internal.ApiRequester(client, "https://www.googleapis.com/", "genomics/v1beta2/");
}
/** 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:
*
* [pageSize] - 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.
*
* [projectNumber] - 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.int pageSize, core.String pageToken, core.String projectNumber}) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (pageSize != null) {
_queryParams["pageSize"] = ["${pageSize}"];
}
if (pageToken != null) {
_queryParams["pageToken"] = [pageToken];
}
if (projectNumber != null) {
_queryParams["projectNumber"] = [projectNumber];
}
_url = 'datasets';
var _response = _requester.request(_url,
"GET",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new ListDatasetsResponse.fromJson(data));
}
/**
* Updates a dataset. This method supports patch semantics.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* [datasetId] - The ID of the dataset to be updated.
*
* Completes with a [Dataset].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<Dataset> patch(Dataset request, core.String datasetId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (request != null) {
_body = convert.JSON.encode((request).toJson());
}
if (datasetId == null) {
throw new core.ArgumentError("Parameter datasetId is required.");
}
_url = 'datasets/' + common_internal.Escaper.ecapeVariable('$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 ReadgroupsetsResourceApi {
final common_internal.ApiRequester _requester;
ReadgroupsetsCoveragebucketsResourceApi get coveragebuckets => new ReadgroupsetsCoveragebucketsResourceApi(_requester);
ReadgroupsetsResourceApi(common_internal.ApiRequester client) :
_requester = client;
/**
* Aligns read data from existing read group sets or files from Google Cloud
* Storage. See the alignment and variant calling documentation for more
* details.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* Completes with a [AlignReadGroupSetsResponse].
*
* 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<AlignReadGroupSetsResponse> align(AlignReadGroupSetsRequest 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 = 'readgroupsets/align';
var _response = _requester.request(_url,
"POST",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new AlignReadGroupSetsResponse.fromJson(data));
}
/**
* Calls variants on read data from existing read group sets or files from
* Google Cloud Storage. See the alignment and variant calling documentation
* for more details.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* Completes with a [CallReadGroupSetsResponse].
*
* 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<CallReadGroupSetsResponse> call(CallReadGroupSetsRequest 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 = 'readgroupsets/call';
var _response = _requester.request(_url,
"POST",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new CallReadGroupSetsResponse.fromJson(data));
}
/**
* Deletes a read group set.
*
* Request parameters:
*
* [readGroupSetId] - The ID of the read group set to be deleted. The caller
* must have WRITE permissions to the dataset associated with this read group
* set.
*
* Completes with a [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 readGroupSetId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (readGroupSetId == null) {
throw new core.ArgumentError("Parameter readGroupSetId is required.");
}
_downloadOptions = null;
_url = 'readgroupsets/' + common_internal.Escaper.ecapeVariable('$readGroupSetId');
var _response = _requester.request(_url,
"DELETE",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => null);
}
/**
* Exports read group sets to a BAM file in Google Cloud Storage.
*
* Note that currently there may be some differences between exported BAM
* files and the original BAM file at the time of import. 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 [ExportReadGroupSetsResponse].
*
* 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<ExportReadGroupSetsResponse> export(ExportReadGroupSetsRequest 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 = 'readgroupsets/export';
var _response = _requester.request(_url,
"POST",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new ExportReadGroupSetsResponse.fromJson(data));
}
/**
* Gets a read group set by ID.
*
* Request parameters:
*
* [readGroupSetId] - The ID of the read group set.
*
* Completes with a [ReadGroupSet].
*
* Completes with a [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<ReadGroupSet> get(core.String readGroupSetId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (readGroupSetId == null) {
throw new core.ArgumentError("Parameter readGroupSetId is required.");
}
_url = 'readgroupsets/' + common_internal.Escaper.ecapeVariable('$readGroupSetId');
var _response = _requester.request(_url,
"GET",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new ReadGroupSet.fromJson(data));
}
/**
* Creates read group sets by asynchronously importing the provided
* information.
*
* 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 [ImportReadGroupSetsResponse].
*
* 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<ImportReadGroupSetsResponse> import(ImportReadGroupSetsRequest 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 = 'readgroupsets/import';
var _response = _requester.request(_url,
"POST",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new ImportReadGroupSetsResponse.fromJson(data));
}
/**
* Updates a read group set. This method supports patch semantics.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* [readGroupSetId] - The ID of the read group set to be updated. The caller
* must have WRITE permissions to the dataset associated with this read group
* set.
*
* Completes with a [ReadGroupSet].
*
* Completes with a [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<ReadGroupSet> patch(ReadGroupSet request, core.String readGroupSetId) {
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 (readGroupSetId == null) {
throw new core.ArgumentError("Parameter readGroupSetId is required.");
}
_url = 'readgroupsets/' + common_internal.Escaper.ecapeVariable('$readGroupSetId');
var _response = _requester.request(_url,
"PATCH",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new ReadGroupSet.fromJson(data));
}
/**
* Searches for read group sets matching the criteria.
*
* Implements GlobalAllianceApi.searchReadGroupSets.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* Completes with a [SearchReadGroupSetsResponse].
*
* Completes with a [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<SearchReadGroupSetsResponse> search(SearchReadGroupSetsRequest 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 = 'readgroupsets/search';
var _response = _requester.request(_url,
"POST",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new SearchReadGroupSetsResponse.fromJson(data));
}
/**
* Updates a read group set.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* [readGroupSetId] - The ID of the read group set to be updated. The caller
* must have WRITE permissions to the dataset associated with this read group
* set.
*
* Completes with a [ReadGroupSet].
*
* Completes with a [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<ReadGroupSet> update(ReadGroupSet request, core.String readGroupSetId) {
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 (readGroupSetId == null) {
throw new core.ArgumentError("Parameter readGroupSetId is required.");
}
_url = 'readgroupsets/' + common_internal.Escaper.ecapeVariable('$readGroupSetId');
var _response = _requester.request(_url,
"PUT",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new ReadGroupSet.fromJson(data));
}
}
/** Not documented yet. */
class ReadgroupsetsCoveragebucketsResourceApi {
final common_internal.ApiRequester _requester;
ReadgroupsetsCoveragebucketsResourceApi(common_internal.ApiRequester client) :
_requester = client;
/**
* Lists fixed width coverage buckets for a read group set, each of which
* correspond to a range of a reference sequence. Each bucket summarizes
* coverage information across its corresponding genomic range.
*
* Coverage is defined as the number of reads which are aligned to a given
* base in the reference sequence. Coverage buckets are available at several
* precomputed bucket widths, enabling retrieval of various coverage 'zoom
* levels'. The caller must have READ permissions for the target read group
* set.
*
* Request parameters:
*
* [readGroupSetId] - Required. The ID of the read group set over which
* coverage is requested.
*
* [pageSize] - The maximum number of results to return in a single page. If
* unspecified, defaults to 1024. The maximum value is 2048.
*
* [pageToken] - The continuation token, which is used to page through large
* result sets. To get the next page of results, set this parameter to the
* value of nextPageToken from the previous response.
*
* [range_end] - The end position of the range on the reference, 0-based
* exclusive. If specified, referenceName must also be specified.
*
* [range_referenceName] - The reference sequence name, for example chr1, 1,
* or chrX.
*
* [range_start] - The start position of the range on the reference, 0-based
* inclusive. If specified, referenceName must also be specified.
*
* [targetBucketWidth] - The desired width of each reported coverage bucket in
* base pairs. This will be rounded down to the nearest precomputed bucket
* width; the value of which is returned as bucketWidth in the response.
* Defaults to infinity (each bucket spans an entire reference sequence) or
* the length of the target range, if specified. The smallest precomputed
* bucketWidth is currently 2048 base pairs; this is subject to change.
*
* Completes with a [ListCoverageBucketsResponse].
*
* Completes with a [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 readGroupSetId, {core.int pageSize, core.String pageToken, core.String range_end, core.String range_referenceName, core.String range_start, core.String targetBucketWidth}) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (readGroupSetId == null) {
throw new core.ArgumentError("Parameter readGroupSetId is required.");
}
if (pageSize != null) {
_queryParams["pageSize"] = ["${pageSize}"];
}
if (pageToken != null) {
_queryParams["pageToken"] = [pageToken];
}
if (range_end != null) {
_queryParams["range.end"] = [range_end];
}
if (range_referenceName != null) {
_queryParams["range.referenceName"] = [range_referenceName];
}
if (range_start != null) {
_queryParams["range.start"] = [range_start];
}
if (targetBucketWidth != null) {
_queryParams["targetBucketWidth"] = [targetBucketWidth];
}
_url = 'readgroupsets/' + common_internal.Escaper.ecapeVariable('$readGroupSetId') + '/coveragebuckets';
var _response = _requester.request(_url,
"GET",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new ListCoverageBucketsResponse.fromJson(data));
}
}
/** 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 read group sets. Reads search operates
* over a genomic coordinate space of reference sequence & position defined
* over the reference sequences to which the requested read group sets are
* aligned.
*
* If a target positional range is specified, search returns all reads whose
* alignment to the reference genome overlap the range. A query which
* specifies only read group set IDs yields all reads in those read group
* sets, including unmapped reads.
*
* All reads returned (including reads on subsequent pages) are ordered by
* genomic coordinate (reference sequence & position). Reads with equivalent
* genomic coordinates are returned in a deterministic order.
*
* Implements GlobalAllianceApi.searchReads.
*
* [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 ReferencesResourceApi {
final common_internal.ApiRequester _requester;
ReferencesBasesResourceApi get bases => new ReferencesBasesResourceApi(_requester);
ReferencesResourceApi(common_internal.ApiRequester client) :
_requester = client;
/**
* Gets a reference.
*
* Implements GlobalAllianceApi.getReference.
*
* Request parameters:
*
* [referenceId] - The ID of the reference.
*
* Completes with a [Reference].
*
* Completes with a [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<Reference> get(core.String referenceId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (referenceId == null) {
throw new core.ArgumentError("Parameter referenceId is required.");
}
_url = 'references/' + common_internal.Escaper.ecapeVariable('$referenceId');
var _response = _requester.request(_url,
"GET",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new Reference.fromJson(data));
}
/**
* Searches for references which match the given criteria.
*
* Implements GlobalAllianceApi.searchReferences.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* Completes with a [SearchReferencesResponse].
*
* Completes with a [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<SearchReferencesResponse> search(SearchReferencesRequest 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 = 'references/search';
var _response = _requester.request(_url,
"POST",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new SearchReferencesResponse.fromJson(data));
}
}
/** Not documented yet. */
class ReferencesBasesResourceApi {
final common_internal.ApiRequester _requester;
ReferencesBasesResourceApi(common_internal.ApiRequester client) :
_requester = client;
/**
* Lists the bases in a reference, optionally restricted to a range.
*
* Implements GlobalAllianceApi.getReferenceBases.
*
* Request parameters:
*
* [referenceId] - The ID of the reference.
*
* [end] - The end position (0-based, exclusive) of this query. Defaults to
* the length of this reference.
*
* [pageSize] - Specifies the maximum number of bases to return in a single
* page.
*
* [pageToken] - The continuation token, which is used to page through large
* result sets. To get the next page of results, set this parameter to the
* value of nextPageToken from the previous response.
*
* [start] - The start position (0-based) of this query. Defaults to 0.
*
* Completes with a [ListBasesResponse].
*
* Completes with a [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<ListBasesResponse> list(core.String referenceId, {core.String end, core.int pageSize, core.String pageToken, core.String start}) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (referenceId == null) {
throw new core.ArgumentError("Parameter referenceId is required.");
}
if (end != null) {
_queryParams["end"] = [end];
}
if (pageSize != null) {
_queryParams["pageSize"] = ["${pageSize}"];
}
if (pageToken != null) {
_queryParams["pageToken"] = [pageToken];
}
if (start != null) {
_queryParams["start"] = [start];
}
_url = 'references/' + common_internal.Escaper.ecapeVariable('$referenceId') + '/bases';
var _response = _requester.request(_url,
"GET",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new ListBasesResponse.fromJson(data));
}
}
/** Not documented yet. */
class ReferencesetsResourceApi {
final common_internal.ApiRequester _requester;
ReferencesetsResourceApi(common_internal.ApiRequester client) :
_requester = client;
/**
* Gets a reference set.
*
* Implements GlobalAllianceApi.getReferenceSet.
*
* Request parameters:
*
* [referenceSetId] - The ID of the reference set.
*
* Completes with a [ReferenceSet].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<ReferenceSet> get(core.String referenceSetId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (referenceSetId == null) {
throw new core.ArgumentError("Parameter referenceSetId is required.");
}
_url = 'referencesets/' + common_internal.Escaper.ecapeVariable('$referenceSetId');
var _response = _requester.request(_url,
"GET",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new ReferenceSet.fromJson(data));
}
/**
* Searches for reference sets which match the given criteria.
*
* Implements GlobalAllianceApi.searchReferenceSets.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* Completes with a [SearchReferenceSetsResponse].
*
* Completes with a [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<SearchReferenceSetsResponse> search(SearchReferenceSetsRequest 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 = 'referencesets/search';
var _response = _requester.request(_url,
"POST",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new SearchReferenceSetsResponse.fromJson(data));
}
}
/** 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('$variantId');
var _response = _requester.request(_url,
"DELETE",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => null);
}
/**
* Gets a variant by ID.
*
* Request parameters:
*
* [variantId] - The ID of the variant.
*
* Completes with a [Variant].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<Variant> get(core.String variantId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (variantId == null) {
throw new core.ArgumentError("Parameter variantId is required.");
}
_url = 'variants/' + common_internal.Escaper.ecapeVariable('$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));
}
/**
* 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);
}
/**
* Exports variant set data to an external destination.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* [variantSetId] - Required. The ID of the variant set that contains variant
* data which should be exported. The caller must have READ access to this
* variant set.
*
* Completes with a [ExportVariantSetResponse].
*
* 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<ExportVariantSetResponse> export(ExportVariantSetRequest 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('$variantSetId') + '/export';
var _response = _requester.request(_url,
"POST",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new ExportVariantSetResponse.fromJson(data));
}
/**
* Gets a variant set by ID.
*
* Request parameters:
*
* [variantSetId] - Required. The ID of the variant set.
*
* Completes with a [VariantSet].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<VariantSet> get(core.String variantSetId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (variantSetId == null) {
throw new core.ArgumentError("Parameter variantSetId is required.");
}
_url = 'variantsets/' + common_internal.Escaper.ecapeVariable('$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));
}
/**
* 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:
*
* [variantSetId] - Required. The variant set to which variant data should be
* imported.
*
* 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> importVariants(ImportVariantsRequest 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('$variantSetId') + '/importVariants';
var _response = _requester.request(_url,
"POST",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new ImportVariantsResponse.fromJson(data));
}
/**
* Merges the given variants with existing variants. Each variant will be
* merged with an existing variant that matches its reference sequence, start,
* end, reference bases, and alternative bases. If no such variant exists, a
* new one will be created.
*
* When variants are merged, the call information from the new variant is
* added to the existing variant, and other fields (such as key/value pairs)
* are discarded.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* [variantSetId] - The destination variant set.
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future mergeVariants(MergeVariantsRequest request, core.String variantSetId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (request != null) {
_body = convert.JSON.encode((request).toJson());
}
if (variantSetId == null) {
throw new core.ArgumentError("Parameter variantSetId is required.");
}
_downloadOptions = null;
_url = 'variantsets/' + common_internal.Escaper.ecapeVariable('$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));
}
}
/** The read group set align request. */
class AlignReadGroupSetsRequest {
/**
* The BAM source files for alignment. Exactly one of readGroupSetIds,
* bamSourceUris, interleavedFastqSource or pairedFastqSource must be
* provided. The caller must have READ permissions for these files.
*/
core.List<core.String> bamSourceUris;
/**
* Required. The ID of the dataset the newly aligned read group sets will
* belong to. The caller must have WRITE permissions to this dataset.
*/
core.String datasetId;
/**
* The interleaved FASTQ source files for alignment, where both members of
* each pair of reads are found on consecutive records within the same FASTQ
* file. Exactly one of readGroupSetIds, bamSourceUris, interleavedFastqSource
* or pairedFastqSource must be provided.
*/
InterleavedFastqSource interleavedFastqSource;
/**
* The paired end FASTQ source files for alignment, where each member of a
* pair of reads are found in separate files. Exactly one of readGroupSetIds,
* bamSourceUris, interleavedFastqSource or pairedFastqSource must be
* provided.
*/
PairedFastqSource pairedFastqSource;
/**
* The IDs of the read group sets which will be aligned. New read group sets
* will be generated to hold the aligned data, the originals will not be
* modified. The caller must have READ permissions for these read group sets.
* Exactly one of readGroupSetIds, bamSourceUris, interleavedFastqSource or
* pairedFastqSource must be provided.
*/
core.List<core.String> readGroupSetIds;
AlignReadGroupSetsRequest();
AlignReadGroupSetsRequest.fromJson(core.Map _json) {
if (_json.containsKey("bamSourceUris")) {
bamSourceUris = _json["bamSourceUris"];
}
if (_json.containsKey("datasetId")) {
datasetId = _json["datasetId"];
}
if (_json.containsKey("interleavedFastqSource")) {
interleavedFastqSource = new InterleavedFastqSource.fromJson(_json["interleavedFastqSource"]);
}
if (_json.containsKey("pairedFastqSource")) {
pairedFastqSource = new PairedFastqSource.fromJson(_json["pairedFastqSource"]);
}
if (_json.containsKey("readGroupSetIds")) {
readGroupSetIds = _json["readGroupSetIds"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (bamSourceUris != null) {
_json["bamSourceUris"] = bamSourceUris;
}
if (datasetId != null) {
_json["datasetId"] = datasetId;
}
if (interleavedFastqSource != null) {
_json["interleavedFastqSource"] = (interleavedFastqSource).toJson();
}
if (pairedFastqSource != null) {
_json["pairedFastqSource"] = (pairedFastqSource).toJson();
}
if (readGroupSetIds != null) {
_json["readGroupSetIds"] = readGroupSetIds;
}
return _json;
}
}
/** The read group set align response. */
class AlignReadGroupSetsResponse {
/** A job ID that can be used to get status information. */
core.String jobId;
AlignReadGroupSetsResponse();
AlignReadGroupSetsResponse.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 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;
}
}
/** The read group set call request. */
class CallReadGroupSetsRequest {
/**
* Required. The ID of the dataset the called variants will belong to. The
* caller must have WRITE permissions to this dataset.
*/
core.String datasetId;
/**
* The IDs of the read group sets which will be called. The caller must have
* READ permissions for these read group sets. One of readGroupSetIds or
* sourceUris must be provided.
*/
core.List<core.String> readGroupSetIds;
/**
* A list of URIs pointing at BAM files in Google Cloud Storage which will be
* called. FASTQ files are not allowed. The caller must have READ permissions
* for these files. One of readGroupSetIds or sourceUris must be provided.
*/
core.List<core.String> sourceUris;
CallReadGroupSetsRequest();
CallReadGroupSetsRequest.fromJson(core.Map _json) {
if (_json.containsKey("datasetId")) {
datasetId = _json["datasetId"];
}
if (_json.containsKey("readGroupSetIds")) {
readGroupSetIds = _json["readGroupSetIds"];
}
if (_json.containsKey("sourceUris")) {
sourceUris = _json["sourceUris"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (datasetId != null) {
_json["datasetId"] = datasetId;
}
if (readGroupSetIds != null) {
_json["readGroupSetIds"] = readGroupSetIds;
}
if (sourceUris != null) {
_json["sourceUris"] = sourceUris;
}
return _json;
}
}
/** The read group set call response. */
class CallReadGroupSetsResponse {
/** A job ID that can be used to get status information. */
core.String jobId;
CallReadGroupSetsResponse();
CallReadGroupSetsResponse.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 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 single CIGAR operation. */
class CigarUnit {
/**
* Not documented yet.
* Possible string values are:
* - "ALIGNMENT_MATCH"
* - "CLIP_HARD"
* - "CLIP_SOFT"
* - "DELETE"
* - "INSERT"
* - "PAD"
* - "SEQUENCE_MATCH"
* - "SEQUENCE_MISMATCH"
* - "SKIP"
*/
core.String operation;
/** The number of bases that the operation runs for. Required. */
core.String operationLength;
/**
* referenceSequence is only used at mismatches (SEQUENCE_MISMATCH) and
* deletions (DELETE). Filling this field replaces SAM's MD tag. If the
* relevant information is not available, this field is unset.
*/
core.String referenceSequence;
CigarUnit();
CigarUnit.fromJson(core.Map _json) {
if (_json.containsKey("operation")) {
operation = _json["operation"];
}
if (_json.containsKey("operationLength")) {
operationLength = _json["operationLength"];
}
if (_json.containsKey("referenceSequence")) {
referenceSequence = _json["referenceSequence"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (operation != null) {
_json["operation"] = operation;
}
if (operationLength != null) {
_json["operationLength"] = operationLength;
}
if (referenceSequence != null) {
_json["referenceSequence"] = referenceSequence;
}
return _json;
}
}
/**
* A bucket over which read coverage has been precomputed. A bucket corresponds
* to a specific range of the reference sequence.
*/
class CoverageBucket {
/**
* The average number of reads which are aligned to each individual reference
* base in this bucket.
*/
core.double meanCoverage;
/** The genomic coordinate range spanned by this bucket. */
Range range;
CoverageBucket();
CoverageBucket.fromJson(core.Map _json) {
if (_json.containsKey("meanCoverage")) {
meanCoverage = _json["meanCoverage"];
}
if (_json.containsKey("range")) {
range = new Range.fromJson(_json["range"]);
}
}
core.Map toJson() {
var _json = new core.Map();
if (meanCoverage != null) {
_json["meanCoverage"] = meanCoverage;
}
if (range != null) {
_json["range"] = (range).toJson();
}
return _json;
}
}
/** A Dataset is a collection of genomic data. */
class Dataset {
/** The Google generated ID of the dataset, immutable. */
core.String id;
/**
* Flag indicating whether or not a dataset is publicly viewable. If a dataset
* is not public, it inherits viewing permissions from its project.
*/
core.bool isPublic;
/** The dataset name. */
core.String name;
/**
* The Google Developers Console project number that this dataset belongs to.
*/
core.String projectNumber;
Dataset();
Dataset.fromJson(core.Map _json) {
if (_json.containsKey("id")) {
id = _json["id"];
}
if (_json.containsKey("isPublic")) {
isPublic = _json["isPublic"];
}
if (_json.containsKey("name")) {
name = _json["name"];
}
if (_json.containsKey("projectNumber")) {
projectNumber = _json["projectNumber"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (id != null) {
_json["id"] = id;
}
if (isPublic != null) {
_json["isPublic"] = isPublic;
}
if (name != null) {
_json["name"] = name;
}
if (projectNumber != null) {
_json["projectNumber"] = projectNumber;
}
return _json;
}
}
/** The job creation request. */
class ExperimentalCreateJobRequest {
/**
* Specifies whether or not to run the alignment pipeline. Either align or
* callVariants must be set.
*/
core.bool align;
/**
* Specifies whether or not to run the variant calling pipeline. Either align
* or callVariants must be set.
*/
core.bool callVariants;
/**
* Specifies where to copy the results of certain pipelines. This should be in
* the form of gs://bucket/path.
*/
core.String gcsOutputPath;
/**
* A list of Google Cloud Storage URIs of paired end .fastq files to operate
* upon. If specified, this represents the second file of each paired .fastq
* file. The first file of each pair should be specified in sourceUris.
*/
core.List<core.String> pairedSourceUris;
/**
* Required. The Google Cloud Project ID with which to associate the request.
*/
core.String projectNumber;
/**
* A list of Google Cloud Storage URIs of data files to operate upon. These
* can be .bam, interleaved .fastq, or paired .fastq. If specifying paired
* .fastq files, the first of each pair of files should be listed here, and
* the second of each pair should be listed in pairedSourceUris.
*/
core.List<core.String> sourceUris;
ExperimentalCreateJobRequest();
ExperimentalCreateJobRequest.fromJson(core.Map _json) {
if (_json.containsKey("align")) {
align = _json["align"];
}
if (_json.containsKey("callVariants")) {
callVariants = _json["callVariants"];
}
if (_json.containsKey("gcsOutputPath")) {
gcsOutputPath = _json["gcsOutputPath"];
}
if (_json.containsKey("pairedSourceUris")) {
pairedSourceUris = _json["pairedSourceUris"];
}
if (_json.containsKey("projectNumber")) {
projectNumber = _json["projectNumber"];
}
if (_json.containsKey("sourceUris")) {
sourceUris = _json["sourceUris"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (align != null) {
_json["align"] = align;
}
if (callVariants != null) {
_json["callVariants"] = callVariants;
}
if (gcsOutputPath != null) {
_json["gcsOutputPath"] = gcsOutputPath;
}
if (pairedSourceUris != null) {
_json["pairedSourceUris"] = pairedSourceUris;
}
if (projectNumber != null) {
_json["projectNumber"] = projectNumber;
}
if (sourceUris != null) {
_json["sourceUris"] = sourceUris;
}
return _json;
}
}
/** The job creation response. */
class ExperimentalCreateJobResponse {
/** A job ID that can be used to get status information. */
core.String jobId;
ExperimentalCreateJobResponse();
ExperimentalCreateJobResponse.fromJson(core.Map _json) {
if (_json.containsKey("jobId")) {
jobId = _json["jobId"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (jobId != null) {
_json["jobId"] = jobId;
}
return _json;
}
}
/** The read group set export request. */
class ExportReadGroupSetsRequest {
/**
* 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 projectNumber;
/** The IDs of the read group sets to export. */
core.List<core.String> readGroupSetIds;
/**
* The reference names to export. If this is not specified, all reference
* sequences, including unmapped reads, are exported. Use * to export only
* unmapped reads.
*/
core.List<core.String> referenceNames;
ExportReadGroupSetsRequest();
ExportReadGroupSetsRequest.fromJson(core.Map _json) {
if (_json.containsKey("exportUri")) {
exportUri = _json["exportUri"];
}
if (_json.containsKey("projectNumber")) {
projectNumber = _json["projectNumber"];
}
if (_json.containsKey("readGroupSetIds")) {
readGroupSetIds = _json["readGroupSetIds"];
}
if (_json.containsKey("referenceNames")) {
referenceNames = _json["referenceNames"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (exportUri != null) {
_json["exportUri"] = exportUri;
}
if (projectNumber != null) {
_json["projectNumber"] = projectNumber;
}
if (readGroupSetIds != null) {
_json["readGroupSetIds"] = readGroupSetIds;
}
if (referenceNames != null) {
_json["referenceNames"] = referenceNames;
}
return _json;
}
}
/** The read group set export response. */
class ExportReadGroupSetsResponse {
/** A job ID that can be used to get status information. */
core.String jobId;
ExportReadGroupSetsResponse();
ExportReadGroupSetsResponse.fromJson(core.Map _json) {
if (_json.containsKey("jobId")) {
jobId = _json["jobId"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (jobId != null) {
_json["jobId"] = jobId;
}
return _json;
}
}
/** The variant data export request. */
class ExportVariantSetRequest {
/**
* 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 projectNumber;
ExportVariantSetRequest();
ExportVariantSetRequest.fromJson(core.Map _json) {
if (_json.containsKey("bigqueryDataset")) {
bigqueryDataset = _json["bigqueryDataset"];
}
if (_json.containsKey("bigqueryTable")) {
bigqueryTable = _json["bigqueryTable"];
}
if (_json.containsKey("callSetIds")) {
callSetIds = _json["callSetIds"];
}
if (_json.containsKey("format")) {
format = _json["format"];
}
if (_json.containsKey("projectNumber")) {
projectNumber = _json["projectNumber"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (bigqueryDataset != null) {
_json["bigqueryDataset"] = bigqueryDataset;
}
if (bigqueryTable != null) {
_json["bigqueryTable"] = bigqueryTable;
}
if (callSetIds != null) {
_json["callSetIds"] = callSetIds;
}
if (format != null) {
_json["format"] = format;
}
if (projectNumber != null) {
_json["projectNumber"] = projectNumber;
}
return _json;
}
}
/** The variant data export response. */
class ExportVariantSetResponse {
/** A job ID that can be used to get status information. */
core.String jobId;
ExportVariantSetResponse();
ExportVariantSetResponse.fromJson(core.Map _json) {
if (_json.containsKey("jobId")) {
jobId = _json["jobId"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (jobId != null) {
_json["jobId"] = jobId;
}
return _json;
}
}
/** Not documented yet. */
class FastqMetadata {
/** Optionally specifies the library name for alignment from FASTQ. */
core.String libraryName;
/**
* Optionally specifies the platform name for alignment from FASTQ. For
* example: CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT, PACBIO.
*/
core.String platformName;
/**
* Optionally specifies the platform unit for alignment from FASTQ. For
* example: flowcell-barcode.lane for Illumina or slide for SOLID.
*/
core.String platformUnit;
/** Optionally specifies the read group name for alignment from FASTQ. */
core.String readGroupName;
/** Optionally specifies the sample name for alignment from FASTQ. */
core.String sampleName;
FastqMetadata();
FastqMetadata.fromJson(core.Map _json) {
if (_json.containsKey("libraryName")) {
libraryName = _json["libraryName"];
}
if (_json.containsKey("platformName")) {
platformName = _json["platformName"];
}
if (_json.containsKey("platformUnit")) {
platformUnit = _json["platformUnit"];
}
if (_json.containsKey("readGroupName")) {
readGroupName = _json["readGroupName"];
}
if (_json.containsKey("sampleName")) {
sampleName = _json["sampleName"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (libraryName != null) {
_json["libraryName"] = libraryName;
}
if (platformName != null) {
_json["platformName"] = platformName;
}
if (platformUnit != null) {
_json["platformUnit"] = platformUnit;
}
if (readGroupName != null) {
_json["readGroupName"] = readGroupName;
}
if (sampleName != null) {
_json["sampleName"] = sampleName;
}
return _json;
}
}
/** The read group set import request. */
class ImportReadGroupSetsRequest {
/**
* Required. The ID of the dataset these read group sets will belong to. The
* caller must have WRITE permissions to this dataset.
*/
core.String datasetId;
/**
* The reference set to which the imported read group sets are aligned to, if
* any. The reference names of this reference set must be a superset of those
* found in the imported file headers. If no reference set id is provided, a
* best effort is made to associate with a matching reference set.
*/
core.String referenceSetId;
/** A list of URIs pointing at BAM files in Google Cloud Storage. */
core.List<core.String> sourceUris;
ImportReadGroupSetsRequest();
ImportReadGroupSetsRequest.fromJson(core.Map _json) {
if (_json.containsKey("datasetId")) {
datasetId = _json["datasetId"];
}
if (_json.containsKey("referenceSetId")) {
referenceSetId = _json["referenceSetId"];
}
if (_json.containsKey("sourceUris")) {
sourceUris = _json["sourceUris"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (datasetId != null) {
_json["datasetId"] = datasetId;
}
if (referenceSetId != null) {
_json["referenceSetId"] = referenceSetId;
}
if (sourceUris != null) {
_json["sourceUris"] = sourceUris;
}
return _json;
}
}
/** The read group set import response. */
class ImportReadGroupSetsResponse {
/** A job ID that can be used to get status information. */
core.String jobId;
ImportReadGroupSetsResponse();
ImportReadGroupSetsResponse.fromJson(core.Map _json) {
if (_json.containsKey("jobId")) {
jobId = _json["jobId"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (jobId != null) {
_json["jobId"] = jobId;
}
return _json;
}
}
/** The variant data import request. */
class ImportVariantsRequest {
/**
* The format of the variant data being imported.
* Possible string values are:
* - "COMPLETE_GENOMICS"
* - "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;
ImportVariantsRequest();
ImportVariantsRequest.fromJson(core.Map _json) {
if (_json.containsKey("format")) {
format = _json["format"];
}
if (_json.containsKey("sourceUris")) {
sourceUris = _json["sourceUris"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (format != null) {
_json["format"] = format;
}
if (sourceUris != null) {
_json["sourceUris"] = sourceUris;
}
return _json;
}
}
/** The variant data import response. */
class ImportVariantsResponse {
/** A job ID that can be used to get status information. */
core.String jobId;
ImportVariantsResponse();
ImportVariantsResponse.fromJson(core.Map _json) {
if (_json.containsKey("jobId")) {
jobId = _json["jobId"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (jobId != null) {
_json["jobId"] = jobId;
}
return _json;
}
}
/** Describes an interleaved FASTQ file source for alignment. */
class InterleavedFastqSource {
/**
* Optionally specifies the metadata to be associated with the final aligned
* read group set.
*/
FastqMetadata metadata;
/**
* A list of URIs pointing at interleaved FASTQ files in Google Cloud Storage
* which will be aligned. The caller must have READ permissions for these
* files.
*/
core.List<core.String> sourceUris;
InterleavedFastqSource();
InterleavedFastqSource.fromJson(core.Map _json) {
if (_json.containsKey("metadata")) {
metadata = new FastqMetadata.fromJson(_json["metadata"]);
}
if (_json.containsKey("sourceUris")) {
sourceUris = _json["sourceUris"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (metadata != null) {
_json["metadata"] = (metadata).toJson();
}
if (sourceUris != null) {
_json["sourceUris"] = sourceUris;
}
return _json;
}
}
/**
* A Job represents an ongoing process that can be monitored for status
* information.
*/
class Job {
/** The date this job was created, in milliseconds from the epoch. */
core.String created;
/** A more detailed description of this job's current status. */
core.String detailedStatus;
/** Any errors that occurred during processing. */
core.List<core.String> errors;
/** The job ID. */
core.String id;
/**
* If this Job represents an import, this field will contain the IDs of the
* objects that were successfully imported.
*/
core.List<core.String> importedIds;
/**
* The Google Developers Console project number to which this job belongs.
*/
core.String projectNumber;
/** A summarized representation of the original service request. */
JobRequest request;
/**
* The status of this job.
* Possible string values are:
* - "CANCELED"
* - "FAILURE"
* - "NEW"
* - "PENDING"
* - "RUNNING"
* - "SUCCESS"
* - "UNKNOWN_STATUS"
*/
core.String status;
/** Any warnings that occurred during processing. */
core.List<core.String> warnings;
Job();
Job.fromJson(core.Map _json) {
if (_json.containsKey("created")) {
created = _json["created"];
}
if (_json.containsKey("detailedStatus")) {
detailedStatus = _json["detailedStatus"];
}
if (_json.containsKey("errors")) {
errors = _json["errors"];
}
if (_json.containsKey("id")) {
id = _json["id"];
}
if (_json.containsKey("importedIds")) {
importedIds = _json["importedIds"];
}
if (_json.containsKey("projectNumber")) {
projectNumber = _json["projectNumber"];
}
if (_json.containsKey("request")) {
request = new JobRequest.fromJson(_json["request"]);
}
if (_json.containsKey("status")) {
status = _json["status"];
}
if (_json.containsKey("warnings")) {
warnings = _json["warnings"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (created != null) {
_json["created"] = created;
}
if (detailedStatus != null) {
_json["detailedStatus"] = detailedStatus;
}
if (errors != null) {
_json["errors"] = errors;
}
if (id != null) {
_json["id"] = id;
}
if (importedIds != null) {
_json["importedIds"] = importedIds;
}
if (projectNumber != null) {
_json["projectNumber"] = projectNumber;
}
if (request != null) {
_json["request"] = (request).toJson();
}
if (status != null) {
_json["status"] = status;
}
if (warnings != null) {
_json["warnings"] = warnings;
}
return _json;
}
}
/** A summary representation of the service request that spawned the job. */
class JobRequest {
/**
* The data destination of the request, for example, a Google BigQuery Table
* or Dataset ID.
*/
core.List<core.String> destination;
/**
* The data source of the request, for example, a Google Cloud Storage object
* path or Readset ID.
*/
core.List<core.String> source;
/**
* The original request type.
* Possible string values are:
* - "ALIGN_READSETS"
* - "CALL_READSETS"
* - "EXPERIMENTAL_CREATE_JOB"
* - "EXPORT_READSETS"
* - "EXPORT_VARIANTS"
* - "IMPORT_READSETS"
* - "IMPORT_VARIANTS"
* - "UNKNOWN_TYPE"
*/
core.String type;
JobRequest();
JobRequest.fromJson(core.Map _json) {
if (_json.containsKey("destination")) {
destination = _json["destination"];
}
if (_json.containsKey("source")) {
source = _json["source"];
}
if (_json.containsKey("type")) {
type = _json["type"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (destination != null) {
_json["destination"] = destination;
}
if (source != null) {
_json["source"] = source;
}
if (type != null) {
_json["type"] = type;
}
return _json;
}
}
/**
* A linear alignment can be represented by one CIGAR string. Describes the
* mapped position and local alignment of the read to the reference.
*/
class LinearAlignment {
/**
* Represents the local alignment of this sequence (alignment matches, indels,
* etc) against the reference.
*/
core.List<CigarUnit> cigar;
/**
* The mapping quality of this alignment. Represents how likely the read maps
* to this position as opposed to other locations.
*/
core.int mappingQuality;
/** The position of this alignment. */
Position position;
LinearAlignment();
LinearAlignment.fromJson(core.Map _json) {
if (_json.containsKey("cigar")) {
cigar = _json["cigar"].map((value) => new CigarUnit.fromJson(value)).toList();
}
if (_json.containsKey("mappingQuality")) {
mappingQuality = _json["mappingQuality"];
}
if (_json.containsKey("position")) {
position = new Position.fromJson(_json["position"]);
}
}
core.Map toJson() {
var _json = new core.Map();
if (cigar != null) {
_json["cigar"] = cigar.map((value) => (value).toJson()).toList();
}
if (mappingQuality != null) {
_json["mappingQuality"] = mappingQuality;
}
if (position != null) {
_json["position"] = (position).toJson();
}
return _json;
}
}
/** Not documented yet. */
class ListBasesResponse {
/**
* The continuation token, which is used to page through large result sets.
* Provide this value in a subsequent request to return the next page of
* results. This field will be empty if there aren't any additional results.
*/
core.String nextPageToken;
/**
* The offset position (0-based) of the given sequence from the start of this
* Reference. This value will differ for each page in a paginated request.
*/
core.String offset;
/** A substring of the bases that make up this reference. */
core.String sequence;
ListBasesResponse();
ListBasesResponse.fromJson(core.Map _json) {
if (_json.containsKey("nextPageToken")) {
nextPageToken = _json["nextPageToken"];
}
if (_json.containsKey("offset")) {
offset = _json["offset"];
}
if (_json.containsKey("sequence")) {
sequence = _json["sequence"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (nextPageToken != null) {
_json["nextPageToken"] = nextPageToken;
}
if (offset != null) {
_json["offset"] = offset;
}
if (sequence != null) {
_json["sequence"] = sequence;
}
return _json;
}
}
/** 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"
* - "UNKNOWN_TYPE"
*/
core.String type;
/** The value field for simple metadata */
core.String value;
Metadata();
Metadata.fromJson(core.Map _json) {
if (_json.containsKey("description")) {
description = _json["description"];
}
if (_json.containsKey("id")) {
id = _json["id"];
}
if (_json.containsKey("info")) {
info = _json["info"];
}
if (_json.containsKey("key")) {
key = _json["key"];
}
if (_json.containsKey("number")) {
number = _json["number"];
}
if (_json.containsKey("type")) {
type = _json["type"];
}
if (_json.containsKey("value")) {
value = _json["value"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (description != null) {
_json["description"] = description;
}
if (id != null) {
_json["id"] = id;
}
if (info != null) {
_json["info"] = info;
}
if (key != null) {
_json["key"] = key;
}
if (number != null) {
_json["number"] = number;
}
if (type != null) {
_json["type"] = type;
}
if (value != null) {
_json["value"] = value;
}
return _json;
}
}
/** Describes a paired-end FASTQ file source for alignment. */
class PairedFastqSource {
/**
* A list of URIs pointing at paired end FASTQ files in Google Cloud Storage
* which will be aligned. The first of each paired file should be specified
* here, in an order that matches the second of each paired file specified in
* secondSourceUris. For example: firstSourceUris: [file1_1.fq, file2_1.fq],
* secondSourceUris: [file1_2.fq, file2_2.fq]. The caller must have READ
* permissions for these files.
*/
core.List<core.String> firstSourceUris;
/**
* Optionally specifies the metadata to be associated with the final aligned
* read group set.
*/
FastqMetadata metadata;
/**
* A list of URIs pointing at paired end FASTQ files in Google Cloud Storage
* which will be aligned. The second of each paired file should be specified
* here, in an order that matches the first of each paired file specified in
* firstSourceUris. For example: firstSourceUris: [file1_1.fq, file2_1.fq],
* secondSourceUris: [file1_2.fq, file2_2.fq]. The caller must have READ
* permissions for these files.
*/
core.List<core.String> secondSourceUris;
PairedFastqSource();
PairedFastqSource.fromJson(core.Map _json) {
if (_json.containsKey("firstSourceUris")) {
firstSourceUris = _json["firstSourceUris"];
}
if (_json.containsKey("metadata")) {
metadata = new FastqMetadata.fromJson(_json["metadata"]);
}
if (_json.containsKey("secondSourceUris")) {
secondSourceUris = _json["secondSourceUris"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (firstSourceUris != null) {
_json["firstSourceUris"] = firstSourceUris;
}
if (metadata != null) {
_json["metadata"] = (metadata).toJson();
}
if (secondSourceUris != null) {
_json["secondSourceUris"] = secondSourceUris;
}
return _json;
}
}
/**
* An abstraction for referring to a genomic position, in relation to some
* already known reference. For now, represents a genomic position as a
* reference name, a base number on that reference (0-based), and a
* determination of forward or reverse strand.
*/
class Position {
/**
* The 0-based offset from the start of the forward strand for that reference.
*/
core.String position;
/** The name of the reference in whatever reference set is being used. */
core.String referenceName;
/**
* Whether this position is on the reverse strand, as opposed to the forward
* strand.
*/
core.bool reverseStrand;
Position();
Position.fromJson(core.Map _json) {
if (_json.containsKey("position")) {
position = _json["position"];
}
if (_json.containsKey("referenceName")) {
referenceName = _json["referenceName"];
}
if (_json.containsKey("reverseStrand")) {
reverseStrand = _json["reverseStrand"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (position != null) {
_json["position"] = position;
}
if (referenceName != null) {
_json["referenceName"] = referenceName;
}
if (reverseStrand != null) {
_json["reverseStrand"] = reverseStrand;
}
return _json;
}
}
/** A 0-based half-open genomic coordinate range over a reference sequence. */
class Range {
/**
* The end position of the range on the reference, 0-based exclusive. If
* specified, referenceName must also be specified.
*/
core.String end;
/** The reference sequence name, for example chr1, 1, or chrX. */
core.String referenceName;
/**
* The start position of the range on the reference, 0-based inclusive. If
* specified, referenceName must also be specified.
*/
core.String start;
Range();
Range.fromJson(core.Map _json) {
if (_json.containsKey("end")) {
end = _json["end"];
}
if (_json.containsKey("referenceName")) {
referenceName = _json["referenceName"];
}
if (_json.containsKey("start")) {
start = _json["start"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (end != null) {
_json["end"] = end;
}
if (referenceName != null) {
_json["referenceName"] = referenceName;
}
if (start != null) {
_json["start"] = start;
}
return _json;
}
}
/**
* A read alignment describes a linear alignment of a string of DNA to a
* reference sequence, in addition to metadata about the fragment (the molecule
* of DNA sequenced) and the read (the bases which were read by the sequencer).
* A read is equivalent to a line in a SAM file. A read belongs to exactly one
* read group and exactly one read group set. Generating a reference-aligned
* sequence string When interacting with mapped reads, it's often useful to
* produce a string representing the local alignment of the read to reference.
* The following pseudocode demonstrates one way of doing this:
* out = "" offset = 0 for c in read.alignment.cigar { switch c.operation { case
* "ALIGNMENT_MATCH", "SEQUENCE_MATCH", "SEQUENCE_MISMATCH": out +=
* read.alignedSequence[offset:offset+c.operationLength] offset +=
* c.operationLength break case "CLIP_SOFT", "INSERT": offset +=
* c.operationLength break case "PAD": out += repeat("*", c.operationLength)
* break case "DELETE": out += repeat("-", c.operationLength) break case "SKIP":
* out += repeat(" ", c.operationLength) break case "CLIP_HARD": break } }
* return out
* Converting to SAM's CIGAR string The following pseudocode generates a SAM
* CIGAR string from the cigar field. Note that this is a lossy conversion
* (cigar.referenceSequence is lost).
* cigarMap = { "ALIGNMENT_MATCH": "M", "INSERT": "I", "DELETE": "D", "SKIP":
* "N", "CLIP_SOFT": "S", "CLIP_HARD": "H", "PAD": "P", "SEQUENCE_MATCH": "=",
* "SEQUENCE_MISMATCH": "X", } cigarStr = "" for c in read.alignment.cigar {
* cigarStr += c.operationLength + cigarMap[c.operation] } return cigarStr
*/
class Read {
/**
* The quality of the read sequence contained in this alignment record.
* alignedSequence and alignedQuality may be shorter than the full read
* sequence and quality. This will occur if the alignment is part of a
* chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR
* for this read will begin/end with a hard clip operator that will indicate
* the length of the excised sequence.
*/
core.List<core.int> alignedQuality;
/**
* The bases of the read sequence contained in this alignment record, without
* CIGAR operations applied. alignedSequence and alignedQuality may be shorter
* than the full read sequence and quality. This will occur if the alignment
* is part of a chimeric alignment, or if the read was trimmed. When this
* occurs, the CIGAR for this read will begin/end with a hard clip operator
* that will indicate the length of the excised sequence.
*/
core.String alignedSequence;
/**
* The linear alignment for this alignment record. This field will be null if
* the read is unmapped.
*/
LinearAlignment alignment;
/** The fragment is a PCR or optical duplicate (SAM flag 0x400) */
core.bool duplicateFragment;
/** SAM flag 0x200 */
core.bool failedVendorQualityChecks;
/** The observed length of the fragment, equivalent to TLEN in SAM. */
core.int fragmentLength;
/** The fragment name. Equivalent to QNAME (query template name) in SAM. */
core.String fragmentName;
/**
* The unique ID for this read. This is a generated unique ID, not to be
* confused with fragmentName.
*/
core.String id;
/** A map of additional read alignment information. */
core.Map<core.String, core.List<core.String>> info;
/**
* The mapping of the primary alignment of the (readNumber+1)%numberReads read
* in the fragment. It replaces mate position and mate strand in SAM.
*/
Position nextMatePosition;
/** The number of reads in the fragment (extension to SAM flag 0x1). */
core.int numberReads;
/**
* The orientation and the distance between reads from the fragment are
* consistent with the sequencing protocol (SAM flag 0x2)
*/
core.bool properPlacement;
/**
* The ID of the read group this read belongs to. (Every read must belong to
* exactly one read group.)
*/
core.String readGroupId;
/**
* The ID of the read group set this read belongs to. (Every read must belong
* to exactly one read group set.)
*/
core.String readGroupSetId;
/**
* The read number in sequencing. 0-based and less than numberReads. This
* field replaces SAM flag 0x40 and 0x80.
*/
core.int readNumber;
/**
* Whether this alignment is secondary. Equivalent to SAM flag 0x100. A
* secondary alignment represents an alternative to the primary alignment for
* this read. Aligners may return secondary alignments if a read can map
* ambiguously to multiple coordinates in the genome. By convention, each read
* has one and only one alignment where both secondaryAlignment and
* supplementaryAlignment are false.
*/
core.bool secondaryAlignment;
/**
* Whether this alignment is supplementary. Equivalent to SAM flag 0x800.
* Supplementary alignments are used in the representation of a chimeric
* alignment. In a chimeric alignment, a read is split into multiple linear
* alignments that map to different reference contigs. The first linear
* alignment in the read will be designated as the representative alignment;
* the remaining linear alignments will be designated as supplementary
* alignments. These alignments may have different mapping quality scores. In
* each linear alignment in a chimeric alignment, the read will be hard
* clipped. The alignedSequence and alignedQuality fields in the alignment
* record will only represent the bases for its respective linear alignment.
*/
core.bool supplementaryAlignment;
Read();
Read.fromJson(core.Map _json) {
if (_json.containsKey("alignedQuality")) {
alignedQuality = _json["alignedQuality"];
}
if (_json.containsKey("alignedSequence")) {
alignedSequence = _json["alignedSequence"];
}
if (_json.containsKey("alignment")) {
alignment = new LinearAlignment.fromJson(_json["alignment"]);
}
if (_json.containsKey("duplicateFragment")) {
duplicateFragment = _json["duplicateFragment"];
}
if (_json.containsKey("failedVendorQualityChecks")) {
failedVendorQualityChecks = _json["failedVendorQualityChecks"];
}
if (_json.containsKey("fragmentLength")) {
fragmentLength = _json["fragmentLength"];
}
if (_json.containsKey("fragmentName")) {
fragmentName = _json["fragmentName"];
}
if (_json.containsKey("id")) {
id = _json["id"];
}
if (_json.containsKey("info")) {
info = _json["info"];
}
if (_json.containsKey("nextMatePosition")) {
nextMatePosition = new Position.fromJson(_json["nextMatePosition"]);
}
if (_json.containsKey("numberReads")) {
numberReads = _json["numberReads"];
}
if (_json.containsKey("properPlacement")) {
properPlacement = _json["properPlacement"];
}
if (_json.containsKey("readGroupId")) {
readGroupId = _json["readGroupId"];
}
if (_json.containsKey("readGroupSetId")) {
readGroupSetId = _json["readGroupSetId"];
}
if (_json.containsKey("readNumber")) {
readNumber = _json["readNumber"];
}
if (_json.containsKey("secondaryAlignment")) {
secondaryAlignment = _json["secondaryAlignment"];
}
if (_json.containsKey("supplementaryAlignment")) {
supplementaryAlignment = _json["supplementaryAlignment"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (alignedQuality != null) {
_json["alignedQuality"] = alignedQuality;
}
if (alignedSequence != null) {
_json["alignedSequence"] = alignedSequence;
}
if (alignment != null) {
_json["alignment"] = (alignment).toJson();
}
if (duplicateFragment != null) {
_json["duplicateFragment"] = duplicateFragment;
}
if (failedVendorQualityChecks != null) {
_json["failedVendorQualityChecks"] = failedVendorQualityChecks;
}
if (fragmentLength != null) {
_json["fragmentLength"] = fragmentLength;
}
if (fragmentName != null) {
_json["fragmentName"] = fragmentName;
}
if (id != null) {
_json["id"] = id;
}
if (info != null) {
_json["info"] = info;
}
if (nextMatePosition != null) {
_json["nextMatePosition"] = (nextMatePosition).toJson();
}
if (numberReads != null) {
_json["numberReads"] = numberReads;
}
if (properPlacement != null) {
_json["properPlacement"] = properPlacement;
}
if (readGroupId != null) {
_json["readGroupId"] = readGroupId;
}
if (readGroupSetId != null) {
_json["readGroupSetId"] = readGroupSetId;
}
if (readNumber != null) {
_json["readNumber"] = readNumber;
}
if (secondaryAlignment != null) {
_json["secondaryAlignment"] = secondaryAlignment;
}
if (supplementaryAlignment != null) {
_json["supplementaryAlignment"] = supplementaryAlignment;
}
return _json;
}
}
/**
* A read group is all the data that's processed the same way by the sequencer.
*/
class ReadGroup {
/** The ID of the dataset this read group belongs to. */
core.String datasetId;
/** A free-form text description of this read group. */
core.String description;
/** The experiment used to generate this read group. */
ReadGroupExperiment experiment;
/**
* The generated unique read group ID. Note: This is different than the @RG ID
* field in the SAM spec. For that value, see the name field.
*/
core.String id;
/** A map of additional read group information. */
core.Map<core.String, core.List<core.String>> info;
/**
* The read group name. This corresponds to the @RG ID field in the SAM spec.
*/
core.String name;
/**
* The predicted insert size of this read group. The insert size is the length
* the sequenced DNA fragment from end-to-end, not including the adapters.
*/
core.int predictedInsertSize;
/**
* The programs used to generate this read group. Programs are always
* identical for all read groups within a read group set. For this reason,
* only the first read group in a returned set will have this field populated.
*/
core.List<ReadGroupProgram> programs;
/**
* The reference set the reads in this read group are aligned to. Required if
* there are any read alignments.
*/
core.String referenceSetId;
/**
* The sample this read group's data was generated from. Note: This is not an
* actual ID within this repository, but rather an identifier for a sample
* which may be meaningful to some external system.
*/
core.String sampleId;
ReadGroup();
ReadGroup.fromJson(core.Map _json) {
if (_json.containsKey("datasetId")) {
datasetId = _json["datasetId"];
}
if (_json.containsKey("description")) {
description = _json["description"];
}
if (_json.containsKey("experiment")) {
experiment = new ReadGroupExperiment.fromJson(_json["experiment"]);
}
if (_json.containsKey("id")) {
id = _json["id"];
}
if (_json.containsKey("info")) {
info = _json["info"];
}
if (_json.containsKey("name")) {
name = _json["name"];
}
if (_json.containsKey("predictedInsertSize")) {
predictedInsertSize = _json["predictedInsertSize"];
}
if (_json.containsKey("programs")) {
programs = _json["programs"].map((value) => new ReadGroupProgram.fromJson(value)).toList();
}
if (_json.containsKey("referenceSetId")) {
referenceSetId = _json["referenceSetId"];
}
if (_json.containsKey("sampleId")) {
sampleId = _json["sampleId"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (datasetId != null) {
_json["datasetId"] = datasetId;
}
if (description != null) {
_json["description"] = description;
}
if (experiment != null) {
_json["experiment"] = (experiment).toJson();
}
if (id != null) {
_json["id"] = id;
}
if (info != null) {
_json["info"] = info;
}
if (name != null) {
_json["name"] = name;
}
if (predictedInsertSize != null) {
_json["predictedInsertSize"] = predictedInsertSize;
}
if (programs != null) {
_json["programs"] = programs.map((value) => (value).toJson()).toList();
}
if (referenceSetId != null) {
_json["referenceSetId"] = referenceSetId;
}
if (sampleId != null) {
_json["sampleId"] = sampleId;
}
return _json;
}
}
/** Not documented yet. */
class ReadGroupExperiment {
/**
* The instrument model used as part of this experiment. This maps to
* sequencing technology in BAM.
*/
core.String instrumentModel;
/**
* The library used as part of this experiment. Note: This is not an actual ID
* within this repository, but rather an identifier for a library which may be
* meaningful to some external system.
*/
core.String libraryId;
/**
* The platform unit used as part of this experiment e.g.
* flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
*/
core.String platformUnit;
/** The sequencing center used as part of this experiment. */
core.String sequencingCenter;
ReadGroupExperiment();
ReadGroupExperiment.fromJson(core.Map _json) {
if (_json.containsKey("instrumentModel")) {
instrumentModel = _json["instrumentModel"];
}
if (_json.containsKey("libraryId")) {
libraryId = _json["libraryId"];
}
if (_json.containsKey("platformUnit")) {
platformUnit = _json["platformUnit"];
}
if (_json.containsKey("sequencingCenter")) {
sequencingCenter = _json["sequencingCenter"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (instrumentModel != null) {
_json["instrumentModel"] = instrumentModel;
}
if (libraryId != null) {
_json["libraryId"] = libraryId;
}
if (platformUnit != null) {
_json["platformUnit"] = platformUnit;
}
if (sequencingCenter != null) {
_json["sequencingCenter"] = sequencingCenter;
}
return _json;
}
}
/** Not documented yet. */
class ReadGroupProgram {
/** The command line used to run this program. */
core.String commandLine;
/**
* The user specified locally unique ID of the program. Used along with
* prevProgramId to define an ordering between programs.
*/
core.String id;
/** The name of the program. */
core.String name;
/** The ID of the program run before this one. */
core.String prevProgramId;
/** The version of the program run. */
core.String version;
ReadGroupProgram();
ReadGroupProgram.fromJson(core.Map _json) {
if (_json.containsKey("commandLine")) {
commandLine = _json["commandLine"];
}
if (_json.containsKey("id")) {
id = _json["id"];
}
if (_json.containsKey("name")) {
name = _json["name"];
}
if (_json.containsKey("prevProgramId")) {
prevProgramId = _json["prevProgramId"];
}
if (_json.containsKey("version")) {
version = _json["version"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (commandLine != null) {
_json["commandLine"] = commandLine;
}
if (id != null) {
_json["id"] = id;
}
if (name != null) {
_json["name"] = name;
}
if (prevProgramId != null) {
_json["prevProgramId"] = prevProgramId;
}
if (version != null) {
_json["version"] = version;
}
return _json;
}
}
/**
* A read group set is a logical collection of read groups, which are
* collections of reads produced by a sequencer. A read group set typically
* models reads corresponding to one sample, sequenced one way, and aligned one
* way.
* - A read group set belongs to one dataset.
* - A read group belongs to one read group set.
* - A read belongs to one read group.
*/
class ReadGroupSet {
/** The dataset ID. */
core.String datasetId;
/**
* The filename of the original source file for this read group set, if any.
*/
core.String filename;
/** The read group set ID. */
core.String id;
/**
* The read group set name. By default this will be initialized to the sample
* name of the sequenced data contained in this set.
*/
core.String name;
/**
* The read groups in this set. There are typically 1-10 read groups in a read
* group set.
*/
core.List<ReadGroup> readGroups;
/** The reference set the reads in this read group set are aligned to. */
core.String referenceSetId;
ReadGroupSet();
ReadGroupSet.fromJson(core.Map _json) {
if (_json.containsKey("datasetId")) {
datasetId = _json["datasetId"];
}
if (_json.containsKey("filename")) {
filename = _json["filename"];
}
if (_json.containsKey("id")) {
id = _json["id"];
}
if (_json.containsKey("name")) {
name = _json["name"];
}
if (_json.containsKey("readGroups")) {
readGroups = _json["readGroups"].map((value) => new ReadGroup.fromJson(value)).toList();
}
if (_json.containsKey("referenceSetId")) {
referenceSetId = _json["referenceSetId"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (datasetId != null) {
_json["datasetId"] = datasetId;
}
if (filename != null) {
_json["filename"] = filename;
}
if (id != null) {
_json["id"] = id;
}
if (name != null) {
_json["name"] = name;
}
if (readGroups != null) {
_json["readGroups"] = readGroups.map((value) => (value).toJson()).toList();
}
if (referenceSetId != null) {
_json["referenceSetId"] = referenceSetId;
}
return _json;
}
}
/**
* A reference is a canonical assembled DNA sequence, intended to act as a
* reference coordinate space for other genomic annotations. A single reference
* might represent the human chromosome 1 or mitochandrial DNA, for instance. A
* reference belongs to one or more reference sets.
*/
class Reference {
/** The Google generated immutable ID of the reference. */
core.String id;
/** The length of this reference's sequence. */
core.String length;
/**
* MD5 of the upper-case sequence excluding all whitespace characters (this is
* equivalent to SQ:M5 in SAM). This value is represented in lower case
* hexadecimal format.
*/
core.String md5checksum;
/** The name of this reference, for example 22. */
core.String name;
/**
* ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human) if not
* specified by the containing reference set.
*/
core.int ncbiTaxonId;
/**
* All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
* with a version number, for example GCF_000001405.26.
*/
core.List<core.String> sourceAccessions;
/**
* The URI from which the sequence was obtained. Specifies a FASTA format
* file/string with one name, sequence pair.
*/
core.String sourceURI;
Reference();
Reference.fromJson(core.Map _json) {
if (_json.containsKey("id")) {
id = _json["id"];
}
if (_json.containsKey("length")) {
length = _json["length"];
}
if (_json.containsKey("md5checksum")) {
md5checksum = _json["md5checksum"];
}
if (_json.containsKey("name")) {
name = _json["name"];
}
if (_json.containsKey("ncbiTaxonId")) {
ncbiTaxonId = _json["ncbiTaxonId"];
}
if (_json.containsKey("sourceAccessions")) {
sourceAccessions = _json["sourceAccessions"];
}
if (_json.containsKey("sourceURI")) {
sourceURI = _json["sourceURI"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (id != null) {
_json["id"] = id;
}
if (length != null) {
_json["length"] = length;
}
if (md5checksum != null) {
_json["md5checksum"] = md5checksum;
}
if (name != null) {
_json["name"] = name;
}
if (ncbiTaxonId != null) {
_json["ncbiTaxonId"] = ncbiTaxonId;
}
if (sourceAccessions != null) {
_json["sourceAccessions"] = sourceAccessions;
}
if (sourceURI != null) {
_json["sourceURI"] = sourceURI;
}
return _json;
}
}
/**
* ReferenceBound records an upper bound for the starting coordinate of variants
* in a particular reference.
*/
class ReferenceBound {
/** The 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;
}
}
/**
* A reference set is a set of references which typically comprise a reference
* assembly for a species, such as GRCh38 which is representative of the human
* genome. A reference set defines a common coordinate space for comparing
* reference-aligned experimental data. A reference set contains 1 or more
* references.
*/
class ReferenceSet {
/** Public id of this reference set, such as GRCh37. */
core.String assemblyId;
/** Optional free text description of this reference set. */
core.String description;
/** The Google generated immutable ID of the reference set. */
core.String id;
/**
* Order-independent MD5 checksum which identifies this reference set. The
* checksum is computed by sorting all lower case hexidecimal string
* reference.md5checksum (for all reference in this set) in ascending
* lexicographic order, concatenating, and taking the MD5 of that value. The
* resulting value is represented in lower case hexadecimal format.
*/
core.String md5checksum;
/**
* ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human) indicating
* the species which this assembly is intended to model. Note that contained
* references may specify a different ncbiTaxonId, as assemblies may contain
* reference sequences which do not belong to the modeled species, e.g. EBV in
* a human reference genome.
*/
core.int ncbiTaxonId;
/**
* The IDs of the reference objects that are part of this set.
* Reference.md5checksum must be unique within this set.
*/
core.List<core.String> referenceIds;
/**
* All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
* with a version number, for example NC_000001.11.
*/
core.List<core.String> sourceAccessions;
/** The URI from which the references were obtained. */
core.String sourceURI;
ReferenceSet();
ReferenceSet.fromJson(core.Map _json) {
if (_json.containsKey("assemblyId")) {
assemblyId = _json["assemblyId"];
}
if (_json.containsKey("description")) {
description = _json["description"];
}
if (_json.containsKey("id")) {
id = _json["id"];
}
if (_json.containsKey("md5checksum")) {
md5checksum = _json["md5checksum"];
}
if (_json.containsKey("ncbiTaxonId")) {
ncbiTaxonId = _json["ncbiTaxonId"];
}
if (_json.containsKey("referenceIds")) {
referenceIds = _json["referenceIds"];
}
if (_json.containsKey("sourceAccessions")) {
sourceAccessions = _json["sourceAccessions"];
}
if (_json.containsKey("sourceURI")) {
sourceURI = _json["sourceURI"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (assemblyId != null) {
_json["assemblyId"] = assemblyId;
}
if (description != null) {
_json["description"] = description;
}
if (id != null) {
_json["id"] = id;
}
if (md5checksum != null) {
_json["md5checksum"] = md5checksum;
}
if (ncbiTaxonId != null) {
_json["ncbiTaxonId"] = ncbiTaxonId;
}
if (referenceIds != null) {
_json["referenceIds"] = referenceIds;
}
if (sourceAccessions != null) {
_json["sourceAccessions"] = sourceAccessions;
}
if (sourceURI != null) {
_json["sourceURI"] = sourceURI;
}
return _json;
}
}
/** 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.int pageSize;
/**
* The continuation token which is used to page through large result sets. To
* get the next page of results, set this parameter to the value of the
* nextPageToken from the previous response.
*/
core.String pageToken;
/** Required. Only return jobs which belong to this Google Developers */
core.String projectNumber;
/** Only return jobs which have a matching status. */
core.List<core.String> status;
SearchJobsRequest();
SearchJobsRequest.fromJson(core.Map _json) {
if (_json.containsKey("createdAfter")) {
createdAfter = _json["createdAfter"];
}
if (_json.containsKey("createdBefore")) {
createdBefore = _json["createdBefore"];
}
if (_json.containsKey("pageSize")) {
pageSize = _json["pageSize"];
}
if (_json.containsKey("pageToken")) {
pageToken = _json["pageToken"];
}
if (_json.containsKey("projectNumber")) {
projectNumber = _json["projectNumber"];
}
if (_json.containsKey("status")) {
status = _json["status"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (createdAfter != null) {
_json["createdAfter"] = createdAfter;
}
if (createdBefore != null) {
_json["createdBefore"] = createdBefore;
}
if (pageSize != null) {
_json["pageSize"] = pageSize;
}
if (pageToken != null) {
_json["pageToken"] = pageToken;
}
if (projectNumber != null) {
_json["projectNumber"] = projectNumber;
}
if (status != null) {
_json["status"] = status;
}
return _json;
}
}
/** The job search response. */
class SearchJobsResponse {
/** The list of jobs results, ordered newest to oldest. */
core.List<Job> jobs;
/**
* The continuation token which is used to page through large result sets.
* Provide this value is a subsequent request to return the next page of
* results. This field will be empty if there are no more results.
*/
core.String nextPageToken;
SearchJobsResponse();
SearchJobsResponse.fromJson(core.Map _json) {
if (_json.containsKey("jobs")) {
jobs = _json["jobs"].map((value) => new Job.fromJson(value)).toList();
}
if (_json.containsKey("nextPageToken")) {
nextPageToken = _json["nextPageToken"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (jobs != null) {
_json["jobs"] = jobs.map((value) => (value).toJson()).toList();
}
if (nextPageToken != null) {
_json["nextPageToken"] = nextPageToken;
}
return _json;
}
}
/** The read group set search request. */
class SearchReadGroupSetsRequest {
/**
* Restricts this query to read group sets within the given datasets. At least
* one ID must be provided.
*/
core.List<core.String> datasetIds;
/**
* Only return read group sets for which a substring of the name matches this
* string.
*/
core.String name;
/**
* Specifies number of results to return in a single page. If unspecified, it
* will default to 128. The maximum value is 1024.
*/
core.int pageSize;
/**
* The continuation token, which is used to page through large result sets. To
* get the next page of results, set this parameter to the value of
* nextPageToken from the previous response.
*/
core.String pageToken;
SearchReadGroupSetsRequest();
SearchReadGroupSetsRequest.fromJson(core.Map _json) {
if (_json.containsKey("datasetIds")) {
datasetIds = _json["datasetIds"];
}
if (_json.containsKey("name")) {
name = _json["name"];
}
if (_json.containsKey("pageSize")) {
pageSize = _json["pageSize"];
}
if (_json.containsKey("pageToken")) {
pageToken = _json["pageToken"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (datasetIds != null) {
_json["datasetIds"] = datasetIds;
}
if (name != null) {
_json["name"] = name;
}
if (pageSize != null) {
_json["pageSize"] = pageSize;
}
if (pageToken != null) {
_json["pageToken"] = pageToken;
}
return _json;
}
}
/** The read group set search response. */
class SearchReadGroupSetsResponse {
/**
* The continuation token, which is used to page through large result sets.
* Provide this value in a subsequent request to return the next page of
* results. This field will be empty if there aren't any additional results.
*/
core.String nextPageToken;
/** The list of matching read group sets. */
core.List<ReadGroupSet> readGroupSets;
SearchReadGroupSetsResponse();
SearchReadGroupSetsResponse.fromJson(core.Map _json) {
if (_json.containsKey("nextPageToken")) {
nextPageToken = _json["nextPageToken"];
}
if (_json.containsKey("readGroupSets")) {
readGroupSets = _json["readGroupSets"].map((value) => new ReadGroupSet.fromJson(value)).toList();
}
}
core.Map toJson() {
var _json = new core.Map();
if (nextPageToken != null) {
_json["nextPageToken"] = nextPageToken;
}
if (readGroupSets != null) {
_json["readGroupSets"] = readGroupSets.map((value) => (value).toJson()).toList();
}
return _json;
}
}
/** The read search request. */
class SearchReadsRequest {
/**
* The end position of the range on the reference, 0-based exclusive. If
* specified, referenceName must also be specified.
*/
core.String end;
/**
* Specifies number of results to return in a single page. If unspecified, it
* will default to 256. The maximum value is 2048.
*/
core.int pageSize;
/**
* The continuation token, which is used to page through large result sets. To
* get the next page of results, set this parameter to the value of
* nextPageToken from the previous response.
*/
core.String pageToken;
/**
* The IDs of the read groups within which to search for reads. All specified
* read groups must belong to the same read group sets. Must specify one of
* readGroupSetIds or readGroupIds.
*/
core.List<core.String> readGroupIds;
/**
* The IDs of the read groups sets within which to search for reads. All
* specified read group sets must be aligned against a common set of reference
* sequences; this defines the genomic coordinates for the query. Must specify
* one of readGroupSetIds or readGroupIds.
*/
core.List<core.String> readGroupSetIds;
/**
* The reference sequence name, for example chr1, 1, or chrX. If set to *,
* only unmapped reads are returned.
*/
core.String referenceName;
/**
* The start position of the range on the reference, 0-based inclusive. If
* specified, referenceName must also be specified.
*/
core.String start;
SearchReadsRequest();
SearchReadsRequest.fromJson(core.Map _json) {
if (_json.containsKey("end")) {
end = _json["end"];
}
if (_json.containsKey("pageSize")) {
pageSize = _json["pageSize"];
}
if (_json.containsKey("pageToken")) {
pageToken = _json["pageToken"];
}
if (_json.containsKey("readGroupIds")) {
readGroupIds = _json["readGroupIds"];
}
if (_json.containsKey("readGroupSetIds")) {
readGroupSetIds = _json["readGroupSetIds"];
}
if (_json.containsKey("referenceName")) {
referenceName = _json["referenceName"];
}
if (_json.containsKey("start")) {
start = _json["start"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (end != null) {
_json["end"] = end;
}
if (pageSize != null) {
_json["pageSize"] = pageSize;
}
if (pageToken != null) {
_json["pageToken"] = pageToken;
}
if (readGroupIds != null) {
_json["readGroupIds"] = readGroupIds;
}
if (readGroupSetIds != null) {
_json["readGroupSetIds"] = readGroupSetIds;
}
if (referenceName != null) {
_json["referenceName"] = referenceName;
}
if (start != null) {
_json["start"] = start;
}
return _json;
}
}
/** The read search response. */
class SearchReadsResponse {
/**
* The list of matching alignments sorted by mapped genomic coordinate, if
* any, ascending in position within the same reference. Unmapped reads, which
* have no position, are returned last and are further sorted in ascending
* lexicographic order by fragment name.
*/
core.List<Read> alignments;
/**
* The continuation token, which is used to page through large result sets.
* Provide this value in a subsequent request to return the next page of
* results. This field will be empty if there aren't any additional results.
*/
core.String nextPageToken;
SearchReadsResponse();
SearchReadsResponse.fromJson(core.Map _json) {
if (_json.containsKey("alignments")) {
alignments = _json["alignments"].map((value) => new Read.fromJson(value)).toList();
}
if (_json.containsKey("nextPageToken")) {
nextPageToken = _json["nextPageToken"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (alignments != null) {
_json["alignments"] = alignments.map((value) => (value).toJson()).toList();
}
if (nextPageToken != null) {
_json["nextPageToken"] = nextPageToken;
}
return _json;
}
}
/** Not documented yet. */
class SearchReferenceSetsRequest {
/**
* If present, return references for which the accession matches any of these
* strings. Best to give a version number, for example GCF_000001405.26. If
* only the main accession number is given then all records with that main
* accession will be returned, whichever version. Note that different versions
* will have different sequences.
*/
core.List<core.String> accessions;
/**
* If present, return references for which the md5checksum matches. See
* ReferenceSet.md5checksum for details.
*/
core.List<core.String> md5checksums;
/** Specifies the maximum number of results to return in a single page. */
core.int pageSize;
/**
* The continuation token, which is used to page through large result sets. To
* get the next page of results, set this parameter to the value of
* nextPageToken from the previous response.
*/
core.String pageToken;
SearchReferenceSetsRequest();
SearchReferenceSetsRequest.fromJson(core.Map _json) {
if (_json.containsKey("accessions")) {
accessions = _json["accessions"];
}
if (_json.containsKey("md5checksums")) {
md5checksums = _json["md5checksums"];
}
if (_json.containsKey("pageSize")) {
pageSize = _json["pageSize"];
}
if (_json.containsKey("pageToken")) {
pageToken = _json["pageToken"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (accessions != null) {
_json["accessions"] = accessions;
}
if (md5checksums != null) {
_json["md5checksums"] = md5checksums;
}
if (pageSize != null) {
_json["pageSize"] = pageSize;
}
if (pageToken != null) {
_json["pageToken"] = pageToken;
}
return _json;
}
}
/** Not documented yet. */
class SearchReferenceSetsResponse {
/**
* The continuation token, which is used to page through large result sets.
* Provide this value in a subsequent request to return the next page of
* results. This field will be empty if there aren't any additional results.
*/
core.String nextPageToken;
/** The matching references sets. */
core.List<ReferenceSet> referenceSets;
SearchReferenceSetsResponse();
SearchReferenceSetsResponse.fromJson(core.Map _json) {
if (_json.containsKey("nextPageToken")) {
nextPageToken = _json["nextPageToken"];
}
if (_json.containsKey("referenceSets")) {
referenceSets = _json["referenceSets"].map((value) => new ReferenceSet.fromJson(value)).toList();
}
}
core.Map toJson() {
var _json = new core.Map();
if (nextPageToken != null) {
_json["nextPageToken"] = nextPageToken;
}
if (referenceSets != null) {
_json["referenceSets"] = referenceSets.map((value) => (value).toJson()).toList();
}
return _json;
}
}
/** Not documented yet. */
class SearchReferencesRequest {
/**
* If present, return references for which the accession matches this string.
* Best to give a version number, for example GCF_000001405.26. If only the
* main accession number is given then all records with that main accession
* will be returned, whichever version. Note that different versions will have
* different sequences.
*/
core.List<core.String> accessions;
/**
* If present, return references for which the md5checksum matches. See
* Reference.md5checksum for construction details.
*/
core.List<core.String> md5checksums;
/** Specifies the maximum number of results to return in a single page. */
core.int pageSize;
/**
* The continuation token, which is used to page through large result sets. To
* get the next page of results, set this parameter to the value of
* nextPageToken from the previous response.
*/
core.String pageToken;
/** If present, return only references which belong to this reference set. */
core.String referenceSetId;
SearchReferencesRequest();
SearchReferencesRequest.fromJson(core.Map _json) {
if (_json.containsKey("accessions")) {
accessions = _json["accessions"];
}
if (_json.containsKey("md5checksums")) {
md5checksums = _json["md5checksums"];
}
if (_json.containsKey("pageSize")) {
pageSize = _json["pageSize"];
}
if (_json.containsKey("pageToken")) {
pageToken = _json["pageToken"];
}
if (_json.containsKey("referenceSetId")) {
referenceSetId = _json["referenceSetId"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (accessions != null) {
_json["accessions"] = accessions;
}
if (md5checksums != null) {
_json["md5checksums"] = md5checksums;
}
if (pageSize != null) {
_json["pageSize"] = pageSize;
}
if (pageToken != null) {
_json["pageToken"] = pageToken;
}
if (referenceSetId != null) {
_json["referenceSetId"] = referenceSetId;
}
return _json;
}
}
/** Not documented yet. */
class SearchReferencesResponse {
/**
* The continuation token, which is used to page through large result sets.
* Provide this value in a subsequent request to return the next page of
* results. This field will be empty if there aren't any additional results.
*/
core.String nextPageToken;
/** The matching references. */
core.List<Reference> references;
SearchReferencesResponse();
SearchReferencesResponse.fromJson(core.Map _json) {
if (_json.containsKey("nextPageToken")) {
nextPageToken = _json["nextPageToken"];
}
if (_json.containsKey("references")) {
references = _json["references"].map((value) => new Reference.fromJson(value)).toList();
}
}
core.Map toJson() {
var _json = new core.Map();
if (nextPageToken != null) {
_json["nextPageToken"] = nextPageToken;
}
if (references != null) {
_json["references"] = references.map((value) => (value).toJson()).toList();
}
return _json;
}
}
/** The search variant sets request. */
class SearchVariantSetsRequest {
/**
* Exactly one dataset ID must be provided here. Only variant sets which
* belong to this dataset will be returned.
*/
core.List<core.String> datasetIds;
/** The maximum number of 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;
}
}