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flutter / third_party / googleapis.dart / 3242d2e54b50ee1884ecf8e07aa3fa496e02ecdc / . / generated / googleapis_beta / lib / genomics / v1beta.dart
blob: ef44652c806d243bdd7430cf2d0a99b5c056124b [file] [log] [blame]
library googleapis_beta.genomics.v1beta;
import "dart:core" as core;
import "dart:collection" as collection;
import "dart:async" as async;
import "dart:convert" as convert;
import "package:crypto/crypto.dart" as crypto;
import 'package:http/http.dart' as http;
import '../src/common_internal.dart' as common_internal;
import '../common/common.dart' as common;
export '../common/common.dart' show ApiRequestError;
export '../common/common.dart' show DetailedApiRequestError;
/** Provides access to Genomics data. */
class GenomicsApi {
/** View and manage your data in Google BigQuery */
static const BigqueryScope = "https://www.googleapis.com/auth/bigquery";
/** Manage your data in Google Cloud Storage */
static const DevstorageReadWriteScope = "https://www.googleapis.com/auth/devstorage.read_write";
/** View and manage Genomics data */
static const GenomicsScope = "https://www.googleapis.com/auth/genomics";
/** View Genomics data */
static const GenomicsReadonlyScope = "https://www.googleapis.com/auth/genomics.readonly";
final common_internal.ApiRequester _requester;
BeaconsResourceApi get beacons => new BeaconsResourceApi(_requester);
CallsetsResourceApi get callsets => new CallsetsResourceApi(_requester);
DatasetsResourceApi get datasets => new DatasetsResourceApi(_requester);
ExperimentalResourceApi get experimental => new ExperimentalResourceApi(_requester);
JobsResourceApi get jobs => new JobsResourceApi(_requester);
ReadsResourceApi get reads => new ReadsResourceApi(_requester);
ReadsetsResourceApi get readsets => new ReadsetsResourceApi(_requester);
VariantsResourceApi get variants => new VariantsResourceApi(_requester);
VariantsetsResourceApi get variantsets => new VariantsetsResourceApi(_requester);
GenomicsApi(http.Client client) :
_requester = new common_internal.ApiRequester(client, "https://www.googleapis.com/", "genomics/v1beta/");
}
/** Not documented yet. */
class BeaconsResourceApi {
final common_internal.ApiRequester _requester;
BeaconsResourceApi(common_internal.ApiRequester client) :
_requester = client;
/**
* This is an experimental API that provides a Global Alliance for Genomics
* and Health Beacon. It may change at any time.
*
* Request parameters:
*
* [variantSetId] - The ID of the variant set to query over. It must be
* public. Private variant sets will return an unauthorized exception.
*
* [allele] - Required. The allele to look for ('A', 'C', 'G' or 'T').
*
* [position] - Required. The 0-based position to query.
*
* [referenceName] - Required. The reference to query over.
*
* Completes with a [Beacon].
*
* 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<Beacon> get(core.String variantSetId, {core.String allele, core.String position, core.String referenceName}) {
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.");
}
if (allele != null) {
_queryParams["allele"] = [allele];
}
if (position != null) {
_queryParams["position"] = [position];
}
if (referenceName != null) {
_queryParams["referenceName"] = [referenceName];
}
_url = 'beacons/' + 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 Beacon.fromJson(data));
}
}
/** 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 callset 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 callset.
*
* 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('$callSetId');
var _response = _requester.request(_url,
"GET",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new CallSet.fromJson(data));
}
/**
* Updates a call set. This method supports patch semantics.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* [callSetId] - The ID of the callset to be updated.
*
* Completes with a [CallSet].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<CallSet> patch(CallSet request, core.String callSetId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (request != null) {
_body = convert.JSON.encode((request).toJson());
}
if (callSetId == null) {
throw new core.ArgumentError("Parameter callSetId is required.");
}
_url = 'callsets/' + common_internal.Escaper.ecapeVariable('$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.
*
* [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 callset to be updated.
*
* Completes with a [CallSet].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<CallSet> update(CallSet request, core.String callSetId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (request != null) {
_body = convert.JSON.encode((request).toJson());
}
if (callSetId == null) {
throw new core.ArgumentError("Parameter callSetId is required.");
}
_url = 'callsets/' + common_internal.Escaper.ecapeVariable('$callSetId');
var _response = _requester.request(_url,
"PUT",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new CallSet.fromJson(data));
}
}
/** Not documented yet. */
class DatasetsResourceApi {
final common_internal.ApiRequester _requester;
DatasetsResourceApi(common_internal.ApiRequester client) :
_requester = client;
/**
* Creates a new dataset.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* Completes with a [Dataset].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<Dataset> create(Dataset request) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (request != null) {
_body = convert.JSON.encode((request).toJson());
}
_url = 'datasets';
var _response = _requester.request(_url,
"POST",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new Dataset.fromJson(data));
}
/**
* Deletes a dataset.
*
* Request parameters:
*
* [datasetId] - The ID of the dataset to be deleted.
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future delete(core.String datasetId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (datasetId == null) {
throw new core.ArgumentError("Parameter datasetId is required.");
}
_downloadOptions = null;
_url = 'datasets/' + common_internal.Escaper.ecapeVariable('$datasetId');
var _response = _requester.request(_url,
"DELETE",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => null);
}
/**
* Gets a dataset by ID.
*
* Request parameters:
*
* [datasetId] - The ID of the dataset.
*
* Completes with a [Dataset].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<Dataset> get(core.String datasetId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (datasetId == null) {
throw new core.ArgumentError("Parameter datasetId is required.");
}
_url = 'datasets/' + common_internal.Escaper.ecapeVariable('$datasetId');
var _response = _requester.request(_url,
"GET",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new Dataset.fromJson(data));
}
/**
* Lists all datasets.
*
* Request parameters:
*
* [maxResults] - The maximum number of results returned by this request.
*
* [pageToken] - The continuation token, which is used to page through large
* result sets. To get the next page of results, set this parameter to the
* value of nextPageToken from the previous response.
*
* [projectId] - Only return datasets which belong to this Google Developers
* Console project. Only accepts project numbers. Returns all public projects
* if no project number is specified.
*
* Completes with a [ListDatasetsResponse].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<ListDatasetsResponse> list({core.String maxResults, core.String pageToken, core.String projectId}) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (maxResults != null) {
_queryParams["maxResults"] = [maxResults];
}
if (pageToken != null) {
_queryParams["pageToken"] = [pageToken];
}
if (projectId != null) {
_queryParams["projectId"] = [projectId];
}
_url = 'datasets';
var _response = _requester.request(_url,
"GET",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new ListDatasetsResponse.fromJson(data));
}
/**
* Updates a dataset. This method supports patch semantics.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* [datasetId] - The ID of the dataset to be updated.
*
* Completes with a [Dataset].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<Dataset> patch(Dataset request, core.String datasetId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (request != null) {
_body = convert.JSON.encode((request).toJson());
}
if (datasetId == null) {
throw new core.ArgumentError("Parameter datasetId is required.");
}
_url = 'datasets/' + common_internal.Escaper.ecapeVariable('$datasetId');
var _response = _requester.request(_url,
"PATCH",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new Dataset.fromJson(data));
}
/**
* Undeletes a dataset by restoring a dataset which was deleted via this API.
* This operation is only possible for a week after the deletion occurred.
*
* Request parameters:
*
* [datasetId] - The ID of the dataset to be undeleted.
*
* Completes with a [Dataset].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<Dataset> undelete(core.String datasetId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (datasetId == null) {
throw new core.ArgumentError("Parameter datasetId is required.");
}
_url = 'datasets/' + common_internal.Escaper.ecapeVariable('$datasetId') + '/undelete';
var _response = _requester.request(_url,
"POST",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new Dataset.fromJson(data));
}
/**
* Updates a dataset.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* [datasetId] - The ID of the dataset to be updated.
*
* Completes with a [Dataset].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<Dataset> update(Dataset request, core.String datasetId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (request != null) {
_body = convert.JSON.encode((request).toJson());
}
if (datasetId == null) {
throw new core.ArgumentError("Parameter datasetId is required.");
}
_url = 'datasets/' + common_internal.Escaper.ecapeVariable('$datasetId');
var _response = _requester.request(_url,
"PUT",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new Dataset.fromJson(data));
}
}
/** Not documented yet. */
class ExperimentalResourceApi {
final common_internal.ApiRequester _requester;
ExperimentalJobsResourceApi get jobs => new ExperimentalJobsResourceApi(_requester);
ExperimentalResourceApi(common_internal.ApiRequester client) :
_requester = client;
}
/** Not documented yet. */
class ExperimentalJobsResourceApi {
final common_internal.ApiRequester _requester;
ExperimentalJobsResourceApi(common_internal.ApiRequester client) :
_requester = client;
/**
* Creates and asynchronously runs an ad-hoc job. This is an experimental call
* and may be removed or changed at any time.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* Completes with a [ExperimentalCreateJobResponse].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<ExperimentalCreateJobResponse> create(ExperimentalCreateJobRequest request) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (request != null) {
_body = convert.JSON.encode((request).toJson());
}
_url = 'experimental/jobs/create';
var _response = _requester.request(_url,
"POST",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new ExperimentalCreateJobResponse.fromJson(data));
}
}
/** Not documented yet. */
class JobsResourceApi {
final common_internal.ApiRequester _requester;
JobsResourceApi(common_internal.ApiRequester client) :
_requester = client;
/**
* Cancels a job by ID. Note that it is possible for partial results to be
* generated and stored for cancelled jobs.
*
* Request parameters:
*
* [jobId] - Required. The ID of the job.
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future cancel(core.String jobId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (jobId == null) {
throw new core.ArgumentError("Parameter jobId is required.");
}
_downloadOptions = null;
_url = 'jobs/' + common_internal.Escaper.ecapeVariable('$jobId') + '/cancel';
var _response = _requester.request(_url,
"POST",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => null);
}
/**
* Gets a job by ID.
*
* Request parameters:
*
* [jobId] - Required. The ID of the job.
*
* Completes with a [Job].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<Job> get(core.String jobId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (jobId == null) {
throw new core.ArgumentError("Parameter jobId is required.");
}
_url = 'jobs/' + common_internal.Escaper.ecapeVariable('$jobId');
var _response = _requester.request(_url,
"GET",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new Job.fromJson(data));
}
/**
* Gets a list of jobs matching the criteria.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* Completes with a [SearchJobsResponse].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<SearchJobsResponse> search(SearchJobsRequest request) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (request != null) {
_body = convert.JSON.encode((request).toJson());
}
_url = 'jobs/search';
var _response = _requester.request(_url,
"POST",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new SearchJobsResponse.fromJson(data));
}
}
/** Not documented yet. */
class ReadsResourceApi {
final common_internal.ApiRequester _requester;
ReadsResourceApi(common_internal.ApiRequester client) :
_requester = client;
/**
* Gets a list of reads for one or more readsets. Reads search operates over a
* genomic coordinate space of reference sequence & position defined over the
* reference sequences to which the requested readsets are aligned. If a
* target positional range is specified, search returns all reads whose
* alignment to the reference genome overlap the range. A query which
* specifies only readset IDs yields all reads in those readsets, including
* unmapped reads. All reads returned (including reads on subsequent pages)
* are ordered by genomic coordinate (reference sequence & position). Reads
* with equivalent genomic coordinates are returned in a deterministic order.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* Completes with a [SearchReadsResponse].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<SearchReadsResponse> search(SearchReadsRequest request) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (request != null) {
_body = convert.JSON.encode((request).toJson());
}
_url = 'reads/search';
var _response = _requester.request(_url,
"POST",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new SearchReadsResponse.fromJson(data));
}
}
/** Not documented yet. */
class ReadsetsResourceApi {
final common_internal.ApiRequester _requester;
ReadsetsCoveragebucketsResourceApi get coveragebuckets => new ReadsetsCoveragebucketsResourceApi(_requester);
ReadsetsResourceApi(common_internal.ApiRequester client) :
_requester = client;
/**
* Deletes a readset.
*
* Request parameters:
*
* [readsetId] - The ID of the readset to be deleted. The caller must have
* WRITE permissions to the dataset associated with this readset.
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future delete(core.String readsetId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (readsetId == null) {
throw new core.ArgumentError("Parameter readsetId is required.");
}
_downloadOptions = null;
_url = 'readsets/' + common_internal.Escaper.ecapeVariable('$readsetId');
var _response = _requester.request(_url,
"DELETE",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => null);
}
/**
* Exports readsets to a BAM file in Google Cloud Storage. Note that currently
* there may be some differences between exported BAM files and the original
* BAM file at the time of import. In particular, comments in the input file
* header will not be preserved, and some custom tags will be converted to
* strings.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* Completes with a [ExportReadsetsResponse].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<ExportReadsetsResponse> export(ExportReadsetsRequest request) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (request != null) {
_body = convert.JSON.encode((request).toJson());
}
_url = 'readsets/export';
var _response = _requester.request(_url,
"POST",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new ExportReadsetsResponse.fromJson(data));
}
/**
* Gets a readset by ID.
*
* Request parameters:
*
* [readsetId] - The ID of the readset.
*
* Completes with a [Readset].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<Readset> get(core.String readsetId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (readsetId == null) {
throw new core.ArgumentError("Parameter readsetId is required.");
}
_url = 'readsets/' + common_internal.Escaper.ecapeVariable('$readsetId');
var _response = _requester.request(_url,
"GET",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new Readset.fromJson(data));
}
/**
* Creates readsets by asynchronously importing the provided information. Note
* that currently comments in the input file header are not imported and some
* custom tags will be converted to strings, rather than preserving tag types.
* The caller must have WRITE permissions to the dataset.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* Completes with a [ImportReadsetsResponse].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<ImportReadsetsResponse> import(ImportReadsetsRequest request) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (request != null) {
_body = convert.JSON.encode((request).toJson());
}
_url = 'readsets/import';
var _response = _requester.request(_url,
"POST",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new ImportReadsetsResponse.fromJson(data));
}
/**
* Updates a readset. This method supports patch semantics.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* [readsetId] - The ID of the readset to be updated. The caller must have
* WRITE permissions to the dataset associated with this readset.
*
* Completes with a [Readset].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<Readset> patch(Readset request, core.String readsetId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (request != null) {
_body = convert.JSON.encode((request).toJson());
}
if (readsetId == null) {
throw new core.ArgumentError("Parameter readsetId is required.");
}
_url = 'readsets/' + common_internal.Escaper.ecapeVariable('$readsetId');
var _response = _requester.request(_url,
"PATCH",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new Readset.fromJson(data));
}
/**
* Gets a list of readsets matching the criteria.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* Completes with a [SearchReadsetsResponse].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<SearchReadsetsResponse> search(SearchReadsetsRequest request) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (request != null) {
_body = convert.JSON.encode((request).toJson());
}
_url = 'readsets/search';
var _response = _requester.request(_url,
"POST",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new SearchReadsetsResponse.fromJson(data));
}
/**
* Updates a readset.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* [readsetId] - The ID of the readset to be updated. The caller must have
* WRITE permissions to the dataset associated with this readset.
*
* Completes with a [Readset].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<Readset> update(Readset request, core.String readsetId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (request != null) {
_body = convert.JSON.encode((request).toJson());
}
if (readsetId == null) {
throw new core.ArgumentError("Parameter readsetId is required.");
}
_url = 'readsets/' + common_internal.Escaper.ecapeVariable('$readsetId');
var _response = _requester.request(_url,
"PUT",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new Readset.fromJson(data));
}
}
/** Not documented yet. */
class ReadsetsCoveragebucketsResourceApi {
final common_internal.ApiRequester _requester;
ReadsetsCoveragebucketsResourceApi(common_internal.ApiRequester client) :
_requester = client;
/**
* Lists fixed width coverage buckets for a readset, each of which correspond
* to a range of a reference sequence. Each bucket summarizes coverage
* information across its corresponding genomic range. Coverage is defined as
* the number of reads which are aligned to a given base in the reference
* sequence. Coverage buckets are available at various bucket widths, enabling
* various coverage "zoom levels". The caller must have READ permissions for
* the target readset.
*
* Request parameters:
*
* [readsetId] - Required. The ID of the readset over which coverage is
* requested.
*
* [maxResults] - The maximum number of results to return in a single page. If
* unspecified, defaults to 1024. The maximum value is 2048.
*
* [pageToken] - The continuation token, which is used to page through large
* result sets. To get the next page of results, set this parameter to the
* value of nextPageToken from the previous response.
*
* [range_sequenceEnd] - The end position of the range on the reference,
* 1-based exclusive. If specified, sequenceName must also be specified.
*
* [range_sequenceName] - The reference sequence name, for example chr1, 1, or
* chrX.
*
* [range_sequenceStart] - The start position of the range on the reference,
* 1-based inclusive. If specified, sequenceName must also be specified.
*
* [targetBucketWidth] - The desired width of each reported coverage bucket in
* base pairs. This will be rounded down to the nearest precomputed bucket
* width; the value of which is returned as bucketWidth in the response.
* Defaults to infinity (each bucket spans an entire reference sequence) or
* the length of the target range, if specified. The smallest precomputed
* bucketWidth is currently 2048 base pairs; this is subject to change.
*
* Completes with a [ListCoverageBucketsResponse].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<ListCoverageBucketsResponse> list(core.String readsetId, {core.String maxResults, core.String pageToken, core.String range_sequenceEnd, core.String range_sequenceName, core.String range_sequenceStart, core.String targetBucketWidth}) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (readsetId == null) {
throw new core.ArgumentError("Parameter readsetId is required.");
}
if (maxResults != null) {
_queryParams["maxResults"] = [maxResults];
}
if (pageToken != null) {
_queryParams["pageToken"] = [pageToken];
}
if (range_sequenceEnd != null) {
_queryParams["range.sequenceEnd"] = [range_sequenceEnd];
}
if (range_sequenceName != null) {
_queryParams["range.sequenceName"] = [range_sequenceName];
}
if (range_sequenceStart != null) {
_queryParams["range.sequenceStart"] = [range_sequenceStart];
}
if (targetBucketWidth != null) {
_queryParams["targetBucketWidth"] = [targetBucketWidth];
}
_url = 'readsets/' + common_internal.Escaper.ecapeVariable('$readsetId') + '/coveragebuckets';
var _response = _requester.request(_url,
"GET",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new ListCoverageBucketsResponse.fromJson(data));
}
}
/** Not documented yet. */
class VariantsResourceApi {
final common_internal.ApiRequester _requester;
VariantsResourceApi(common_internal.ApiRequester client) :
_requester = client;
/**
* Creates a new variant.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* Completes with a [Variant].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<Variant> create(Variant request) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (request != null) {
_body = convert.JSON.encode((request).toJson());
}
_url = 'variants';
var _response = _requester.request(_url,
"POST",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new Variant.fromJson(data));
}
/**
* Deletes a variant.
*
* Request parameters:
*
* [variantId] - The ID of the variant to be deleted.
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future delete(core.String variantId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (variantId == null) {
throw new core.ArgumentError("Parameter variantId is required.");
}
_downloadOptions = null;
_url = 'variants/' + common_internal.Escaper.ecapeVariable('$variantId');
var _response = _requester.request(_url,
"DELETE",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => null);
}
/**
* Exports variant data to an external destination.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* Completes with a [ExportVariantsResponse].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<ExportVariantsResponse> export(ExportVariantsRequest request) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (request != null) {
_body = convert.JSON.encode((request).toJson());
}
_url = 'variants/export';
var _response = _requester.request(_url,
"POST",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new ExportVariantsResponse.fromJson(data));
}
/**
* Gets a variant by ID.
*
* Request parameters:
*
* [variantId] - The ID of the variant.
*
* Completes with a [Variant].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<Variant> get(core.String variantId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (variantId == null) {
throw new core.ArgumentError("Parameter variantId is required.");
}
_url = 'variants/' + common_internal.Escaper.ecapeVariable('$variantId');
var _response = _requester.request(_url,
"GET",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new Variant.fromJson(data));
}
/**
* Creates variant data by asynchronously importing the provided information.
* The variants for import will be merged with any existing data and each
* other according to the behavior of mergeVariants. In particular, this means
* for merged VCF variants that have conflicting INFO fields, some data will
* be arbitrarily discarded. As a special case, for single-sample VCF files,
* QUAL and FILTER fields will be moved to the call level; these are sometimes
* interpreted in a call-specific context. Imported VCF headers are appended
* to the metadata already in a VariantSet.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* Completes with a [ImportVariantsResponse].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<ImportVariantsResponse> import(ImportVariantsRequest request) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (request != null) {
_body = convert.JSON.encode((request).toJson());
}
_url = 'variants/import';
var _response = _requester.request(_url,
"POST",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new ImportVariantsResponse.fromJson(data));
}
/**
* Gets a list of variants matching the criteria.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* Completes with a [SearchVariantsResponse].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<SearchVariantsResponse> search(SearchVariantsRequest request) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (request != null) {
_body = convert.JSON.encode((request).toJson());
}
_url = 'variants/search';
var _response = _requester.request(_url,
"POST",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new SearchVariantsResponse.fromJson(data));
}
/**
* Updates a variant's names and info fields. All other modifications are
* silently ignored. Returns the modified variant without its calls.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* [variantId] - The ID of the variant to be updated.
*
* Completes with a [Variant].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<Variant> update(Variant request, core.String variantId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (request != null) {
_body = convert.JSON.encode((request).toJson());
}
if (variantId == null) {
throw new core.ArgumentError("Parameter variantId is required.");
}
_url = 'variants/' + common_internal.Escaper.ecapeVariable('$variantId');
var _response = _requester.request(_url,
"PUT",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new Variant.fromJson(data));
}
}
/** Not documented yet. */
class VariantsetsResourceApi {
final common_internal.ApiRequester _requester;
VariantsetsResourceApi(common_internal.ApiRequester client) :
_requester = client;
/**
* Deletes the contents of a variant set. The variant set object is not
* deleted.
*
* Request parameters:
*
* [variantSetId] - The ID of the variant set to be deleted.
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future delete(core.String variantSetId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (variantSetId == null) {
throw new core.ArgumentError("Parameter variantSetId is required.");
}
_downloadOptions = null;
_url = 'variantsets/' + common_internal.Escaper.ecapeVariable('$variantSetId');
var _response = _requester.request(_url,
"DELETE",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => null);
}
/**
* Gets a variant set by ID.
*
* Request parameters:
*
* [variantSetId] - Required. The ID of the variant set.
*
* Completes with a [VariantSet].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<VariantSet> get(core.String variantSetId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (variantSetId == null) {
throw new core.ArgumentError("Parameter variantSetId is required.");
}
_url = 'variantsets/' + common_internal.Escaper.ecapeVariable('$variantSetId');
var _response = _requester.request(_url,
"GET",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new VariantSet.fromJson(data));
}
/**
* Merges the given variants with existing variants. Each variant will be
* merged with an existing variant that matches its reference sequence, start,
* end, reference bases, and alternative bases. If no such variant exists, a
* new one will be created.
*
* When variants are merged, the call information from the new variant is
* added to the existing variant, and other fields (such as key/value pairs)
* are discarded.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* [variantSetId] - The destination variant set.
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future mergeVariants(MergeVariantsRequest request, core.String variantSetId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (request != null) {
_body = convert.JSON.encode((request).toJson());
}
if (variantSetId == null) {
throw new core.ArgumentError("Parameter variantSetId is required.");
}
_downloadOptions = null;
_url = 'variantsets/' + common_internal.Escaper.ecapeVariable('$variantSetId') + '/mergeVariants';
var _response = _requester.request(_url,
"POST",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => null);
}
/**
* Updates a variant set's metadata. All other modifications are silently
* ignored. Returns the modified variant set. This method supports patch
* semantics.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* [variantSetId] - The ID of the variant to be updated.
*
* Completes with a [VariantSet].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<VariantSet> patch(VariantSet request, core.String variantSetId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (request != null) {
_body = convert.JSON.encode((request).toJson());
}
if (variantSetId == null) {
throw new core.ArgumentError("Parameter variantSetId is required.");
}
_url = 'variantsets/' + common_internal.Escaper.ecapeVariable('$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.
*
* [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. Returns the modified variant set.
*
* [request] - The metadata request object.
*
* Request parameters:
*
* [variantSetId] - The ID of the variant to be updated.
*
* Completes with a [VariantSet].
*
* Completes with a [common.ApiRequestError] if the API endpoint returned an
* error.
*
* If the used [http.Client] completes with an error when making a REST call,
* this method will complete with the same error.
*/
async.Future<VariantSet> update(VariantSet request, core.String variantSetId) {
var _url = null;
var _queryParams = new core.Map();
var _uploadMedia = null;
var _uploadOptions = null;
var _downloadOptions = common.DownloadOptions.Metadata;
var _body = null;
if (request != null) {
_body = convert.JSON.encode((request).toJson());
}
if (variantSetId == null) {
throw new core.ArgumentError("Parameter variantSetId is required.");
}
_url = 'variantsets/' + common_internal.Escaper.ecapeVariable('$variantSetId');
var _response = _requester.request(_url,
"PUT",
body: _body,
queryParams: _queryParams,
uploadOptions: _uploadOptions,
uploadMedia: _uploadMedia,
downloadOptions: _downloadOptions);
return _response.then((data) => new VariantSet.fromJson(data));
}
}
/**
* A beacon represents whether any variant call in a variant set has a specific
* allele at a particular position.
*/
class Beacon {
/** True if the allele exists on any variant call, false otherwise. */
core.bool exists;
Beacon();
Beacon.fromJson(core.Map _json) {
if (_json.containsKey("exists")) {
exists = _json["exists"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (exists != null) {
_json["exists"] = exists;
}
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.
*/
core.List<core.double> genotypeLikelihood;
/** A map of additional variant call information. */
core.Map<core.String, core.List<core.String>> info;
/**
* If this field is present, this variant call's genotype ordering implies the
* phase of the bases and is consistent with any other variant calls in the
* same reference sequence which have the same phaseset value. When importing
* data from VCF, if the genotype data was phased but no phase set was
* specified this field will be set to *.
*/
core.String phaseset;
Call();
Call.fromJson(core.Map _json) {
if (_json.containsKey("callSetId")) {
callSetId = _json["callSetId"];
}
if (_json.containsKey("callSetName")) {
callSetName = _json["callSetName"];
}
if (_json.containsKey("genotype")) {
genotype = _json["genotype"];
}
if (_json.containsKey("genotypeLikelihood")) {
genotypeLikelihood = _json["genotypeLikelihood"];
}
if (_json.containsKey("info")) {
info = _json["info"];
}
if (_json.containsKey("phaseset")) {
phaseset = _json["phaseset"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (callSetId != null) {
_json["callSetId"] = callSetId;
}
if (callSetName != null) {
_json["callSetName"] = callSetName;
}
if (genotype != null) {
_json["genotype"] = genotype;
}
if (genotypeLikelihood != null) {
_json["genotypeLikelihood"] = genotypeLikelihood;
}
if (info != null) {
_json["info"] = info;
}
if (phaseset != null) {
_json["phaseset"] = phaseset;
}
return _json;
}
}
/** A CallSet is a collection of variant calls. 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 callset information. */
core.Map<core.String, core.List<core.String>> info;
/** The callset name. */
core.String name;
/** The sample ID this call set corresponds to. */
core.String sampleId;
/** The IDs of the variant sets this call set belongs to. */
core.List<core.String> variantSetIds;
CallSet();
CallSet.fromJson(core.Map _json) {
if (_json.containsKey("created")) {
created = _json["created"];
}
if (_json.containsKey("id")) {
id = _json["id"];
}
if (_json.containsKey("info")) {
info = _json["info"];
}
if (_json.containsKey("name")) {
name = _json["name"];
}
if (_json.containsKey("sampleId")) {
sampleId = _json["sampleId"];
}
if (_json.containsKey("variantSetIds")) {
variantSetIds = _json["variantSetIds"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (created != null) {
_json["created"] = created;
}
if (id != null) {
_json["id"] = id;
}
if (info != null) {
_json["info"] = info;
}
if (name != null) {
_json["name"] = name;
}
if (sampleId != null) {
_json["sampleId"] = sampleId;
}
if (variantSetIds != null) {
_json["variantSetIds"] = variantSetIds;
}
return _json;
}
}
/**
* A bucket over which read coverage has been precomputed. A bucket corresponds
* to a specific range of the reference sequence.
*/
class CoverageBucket {
/**
* The average number of reads which are aligned to each individual reference
* base in this bucket.
*/
core.double meanCoverage;
/** The genomic coordinate range spanned by this bucket. */
GenomicRange range;
CoverageBucket();
CoverageBucket.fromJson(core.Map _json) {
if (_json.containsKey("meanCoverage")) {
meanCoverage = _json["meanCoverage"];
}
if (_json.containsKey("range")) {
range = new GenomicRange.fromJson(_json["range"]);
}
}
core.Map toJson() {
var _json = new core.Map();
if (meanCoverage != null) {
_json["meanCoverage"] = meanCoverage;
}
if (range != null) {
_json["range"] = (range).toJson();
}
return _json;
}
}
/** A Dataset is a collection of genomic data. */
class Dataset {
/** The Google generated ID of the dataset, immutable. */
core.String id;
/**
* Flag indicating whether or not a dataset is publicly viewable. If a dataset
* is not public, it inherits viewing permissions from its project.
*/
core.bool isPublic;
/** The dataset name. */
core.String name;
/**
* The Google Developers Console project number that this dataset belongs to.
*/
core.String projectId;
Dataset();
Dataset.fromJson(core.Map _json) {
if (_json.containsKey("id")) {
id = _json["id"];
}
if (_json.containsKey("isPublic")) {
isPublic = _json["isPublic"];
}
if (_json.containsKey("name")) {
name = _json["name"];
}
if (_json.containsKey("projectId")) {
projectId = _json["projectId"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (id != null) {
_json["id"] = id;
}
if (isPublic != null) {
_json["isPublic"] = isPublic;
}
if (name != null) {
_json["name"] = name;
}
if (projectId != null) {
_json["projectId"] = projectId;
}
return _json;
}
}
/** The job creation request. */
class ExperimentalCreateJobRequest {
/**
* Specifies whether or not to run the alignment pipeline. At least one of
* align or callVariants must be provided.
*/
core.bool align;
/**
* Specifies whether or not to run the variant calling pipeline. If specified,
* alignment will be performed first and the aligned BAMs will passed as input
* to the variant caller. At least one of align or callVariants must be
* provided.
*/
core.bool callVariants;
/**
* Specifies where to copy the results of certain pipelines. This should be in
* the form of gs://bucket/path.
*/
core.String gcsOutputPath;
/**
* A list of Google Cloud Storage URIs of paired end .fastq files to operate
* upon. If specified, this represents the second file of each paired .fastq
* file. The first file of each pair should be specified in sourceUris.
*/
core.List<core.String> pairedSourceUris;
/**
* Required. The Google Cloud Project ID with which to associate the request.
*/
core.String projectId;
/**
* A list of Google Cloud Storage URIs of data files to operate upon. These
* can be .bam, interleaved .fastq, or paired .fastq. If specifying paired
* .fastq files, the first of each pair of files should be listed here, and
* the second of each pair should be listed in pairedSourceUris.
*/
core.List<core.String> sourceUris;
ExperimentalCreateJobRequest();
ExperimentalCreateJobRequest.fromJson(core.Map _json) {
if (_json.containsKey("align")) {
align = _json["align"];
}
if (_json.containsKey("callVariants")) {
callVariants = _json["callVariants"];
}
if (_json.containsKey("gcsOutputPath")) {
gcsOutputPath = _json["gcsOutputPath"];
}
if (_json.containsKey("pairedSourceUris")) {
pairedSourceUris = _json["pairedSourceUris"];
}
if (_json.containsKey("projectId")) {
projectId = _json["projectId"];
}
if (_json.containsKey("sourceUris")) {
sourceUris = _json["sourceUris"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (align != null) {
_json["align"] = align;
}
if (callVariants != null) {
_json["callVariants"] = callVariants;
}
if (gcsOutputPath != null) {
_json["gcsOutputPath"] = gcsOutputPath;
}
if (pairedSourceUris != null) {
_json["pairedSourceUris"] = pairedSourceUris;
}
if (projectId != null) {
_json["projectId"] = projectId;
}
if (sourceUris != null) {
_json["sourceUris"] = sourceUris;
}
return _json;
}
}
/** The job creation response. */
class ExperimentalCreateJobResponse {
/** A job ID that can be used to get status information. */
core.String jobId;
ExperimentalCreateJobResponse();
ExperimentalCreateJobResponse.fromJson(core.Map _json) {
if (_json.containsKey("jobId")) {
jobId = _json["jobId"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (jobId != null) {
_json["jobId"] = jobId;
}
return _json;
}
}
/** The readset export request. */
class ExportReadsetsRequest {
/**
* A Google Cloud Storage URI where the exported BAM file will be created. The
* currently authenticated user must have write access to the new file
* location. An error will be returned if the URI already contains data.
*/
core.String exportUri;
/** The Google Developers Console project number that owns this export. */
core.String projectId;
/** The IDs of the readsets to export. */
core.List<core.String> readsetIds;
/**
* The reference names to export. If this is not specified, all reference
* sequences, including unmapped reads, are exported. Use * to export only
* unmapped reads.
*/
core.List<core.String> referenceNames;
ExportReadsetsRequest();
ExportReadsetsRequest.fromJson(core.Map _json) {
if (_json.containsKey("exportUri")) {
exportUri = _json["exportUri"];
}
if (_json.containsKey("projectId")) {
projectId = _json["projectId"];
}
if (_json.containsKey("readsetIds")) {
readsetIds = _json["readsetIds"];
}
if (_json.containsKey("referenceNames")) {
referenceNames = _json["referenceNames"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (exportUri != null) {
_json["exportUri"] = exportUri;
}
if (projectId != null) {
_json["projectId"] = projectId;
}
if (readsetIds != null) {
_json["readsetIds"] = readsetIds;
}
if (referenceNames != null) {
_json["referenceNames"] = referenceNames;
}
return _json;
}
}
/** The readset export response. */
class ExportReadsetsResponse {
/** A job ID that can be used to get status information. */
core.String jobId;
ExportReadsetsResponse();
ExportReadsetsResponse.fromJson(core.Map _json) {
if (_json.containsKey("jobId")) {
jobId = _json["jobId"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (jobId != null) {
_json["jobId"] = jobId;
}
return _json;
}
}
/** The variant data export request. */
class ExportVariantsRequest {
/**
* The BigQuery dataset to export data to. Note that this is distinct from the
* Genomics concept of "dataset".
*/
core.String bigqueryDataset;
/**
* The BigQuery table to export data to. If the table doesn't exist, it will
* be created. If it already exists, it will be overwritten.
*/
core.String bigqueryTable;
/**
* If provided, only variant call information from the specified call sets
* will be exported. By default all variant calls are exported.
*/
core.List<core.String> callSetIds;
/**
* The format for the exported data.
* Possible string values are:
* - "bigquery"
*/
core.String format;
/**
* The Google Cloud project number that owns the destination BigQuery dataset.
* The caller must have WRITE access to this project. This project will also
* own the resulting export job.
*/
core.String projectId;
/**
* Required. The ID of the variant set that contains variant data which should
* be exported. The caller must have READ access to this variant set.
*/
core.String variantSetId;
ExportVariantsRequest();
ExportVariantsRequest.fromJson(core.Map _json) {
if (_json.containsKey("bigqueryDataset")) {
bigqueryDataset = _json["bigqueryDataset"];
}
if (_json.containsKey("bigqueryTable")) {
bigqueryTable = _json["bigqueryTable"];
}
if (_json.containsKey("callSetIds")) {
callSetIds = _json["callSetIds"];
}
if (_json.containsKey("format")) {
format = _json["format"];
}
if (_json.containsKey("projectId")) {
projectId = _json["projectId"];
}
if (_json.containsKey("variantSetId")) {
variantSetId = _json["variantSetId"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (bigqueryDataset != null) {
_json["bigqueryDataset"] = bigqueryDataset;
}
if (bigqueryTable != null) {
_json["bigqueryTable"] = bigqueryTable;
}
if (callSetIds != null) {
_json["callSetIds"] = callSetIds;
}
if (format != null) {
_json["format"] = format;
}
if (projectId != null) {
_json["projectId"] = projectId;
}
if (variantSetId != null) {
_json["variantSetId"] = variantSetId;
}
return _json;
}
}
/** The variant data export response. */
class ExportVariantsResponse {
/** A job ID that can be used to get status information. */
core.String jobId;
ExportVariantsResponse();
ExportVariantsResponse.fromJson(core.Map _json) {
if (_json.containsKey("jobId")) {
jobId = _json["jobId"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (jobId != null) {
_json["jobId"] = jobId;
}
return _json;
}
}
/**
* An inclusive, exclusive genomic coordinate range over a reference sequence.
*/
class GenomicRange {
/**
* The end position of the range on the reference, 1-based exclusive. If
* specified, sequenceName must also be specified.
*/
core.String sequenceEnd;
/** The reference sequence name, for example chr1, 1, or chrX. */
core.String sequenceName;
/**
* The start position of the range on the reference, 1-based inclusive. If
* specified, sequenceName must also be specified.
*/
core.String sequenceStart;
GenomicRange();
GenomicRange.fromJson(core.Map _json) {
if (_json.containsKey("sequenceEnd")) {
sequenceEnd = _json["sequenceEnd"];
}
if (_json.containsKey("sequenceName")) {
sequenceName = _json["sequenceName"];
}
if (_json.containsKey("sequenceStart")) {
sequenceStart = _json["sequenceStart"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (sequenceEnd != null) {
_json["sequenceEnd"] = sequenceEnd;
}
if (sequenceName != null) {
_json["sequenceName"] = sequenceName;
}
if (sequenceStart != null) {
_json["sequenceStart"] = sequenceStart;
}
return _json;
}
}
/** Not documented yet. */
class Header {
/** (SO) Sorting order of alignments. */
core.String sortingOrder;
/** (VN) BAM format version. */
core.String version;
Header();
Header.fromJson(core.Map _json) {
if (_json.containsKey("sortingOrder")) {
sortingOrder = _json["sortingOrder"];
}
if (_json.containsKey("version")) {
version = _json["version"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (sortingOrder != null) {
_json["sortingOrder"] = sortingOrder;
}
if (version != null) {
_json["version"] = version;
}
return _json;
}
}
/** The header section of the BAM/SAM file. */
class HeaderSection {
/** (@CO) One-line text comments. */
core.List<core.String> comments;
/**
* [Deprecated] This field is deprecated and will no longer be populated.
* Please use filename instead.
*/
core.String fileUri;
/** The name of the file from which this data was imported. */
core.String filename;
/** (@HD) The header line. */
core.List<Header> headers;
/** (@PG) Programs. */
core.List<Program> programs;
/** (@RG) Read group. */
core.List<ReadGroup> readGroups;
/** (@SQ) Reference sequence dictionary. */
core.List<ReferenceSequence> refSequences;
HeaderSection();
HeaderSection.fromJson(core.Map _json) {
if (_json.containsKey("comments")) {
comments = _json["comments"];
}
if (_json.containsKey("fileUri")) {
fileUri = _json["fileUri"];
}
if (_json.containsKey("filename")) {
filename = _json["filename"];
}
if (_json.containsKey("headers")) {
headers = _json["headers"].map((value) => new Header.fromJson(value)).toList();
}
if (_json.containsKey("programs")) {
programs = _json["programs"].map((value) => new Program.fromJson(value)).toList();
}
if (_json.containsKey("readGroups")) {
readGroups = _json["readGroups"].map((value) => new ReadGroup.fromJson(value)).toList();
}
if (_json.containsKey("refSequences")) {
refSequences = _json["refSequences"].map((value) => new ReferenceSequence.fromJson(value)).toList();
}
}
core.Map toJson() {
var _json = new core.Map();
if (comments != null) {
_json["comments"] = comments;
}
if (fileUri != null) {
_json["fileUri"] = fileUri;
}
if (filename != null) {
_json["filename"] = filename;
}
if (headers != null) {
_json["headers"] = headers.map((value) => (value).toJson()).toList();
}
if (programs != null) {
_json["programs"] = programs.map((value) => (value).toJson()).toList();
}
if (readGroups != null) {
_json["readGroups"] = readGroups.map((value) => (value).toJson()).toList();
}
if (refSequences != null) {
_json["refSequences"] = refSequences.map((value) => (value).toJson()).toList();
}
return _json;
}
}
/** The readset import request. */
class ImportReadsetsRequest {
/**
* Required. The ID of the dataset these readsets will belong to. The caller
* must have WRITE permissions to this dataset.
*/
core.String datasetId;
/** A list of URIs pointing at BAM files in Google Cloud Storage. */
core.List<core.String> sourceUris;
ImportReadsetsRequest();
ImportReadsetsRequest.fromJson(core.Map _json) {
if (_json.containsKey("datasetId")) {
datasetId = _json["datasetId"];
}
if (_json.containsKey("sourceUris")) {
sourceUris = _json["sourceUris"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (datasetId != null) {
_json["datasetId"] = datasetId;
}
if (sourceUris != null) {
_json["sourceUris"] = sourceUris;
}
return _json;
}
}
/** The readset import response. */
class ImportReadsetsResponse {
/** A job ID that can be used to get status information. */
core.String jobId;
ImportReadsetsResponse();
ImportReadsetsResponse.fromJson(core.Map _json) {
if (_json.containsKey("jobId")) {
jobId = _json["jobId"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (jobId != null) {
_json["jobId"] = jobId;
}
return _json;
}
}
/** The variant data import request. */
class ImportVariantsRequest {
/**
* The format of the variant data being imported.
* Possible string values are:
* - "completeGenomics"
* - "vcf"
*/
core.String format;
/**
* A list of URIs pointing at VCF files in Google Cloud Storage. See the VCF
* Specification for more details on the input format.
*/
core.List<core.String> sourceUris;
/** Required. The variant set to which variant data should be imported. */
core.String variantSetId;
ImportVariantsRequest();
ImportVariantsRequest.fromJson(core.Map _json) {
if (_json.containsKey("format")) {
format = _json["format"];
}
if (_json.containsKey("sourceUris")) {
sourceUris = _json["sourceUris"];
}
if (_json.containsKey("variantSetId")) {
variantSetId = _json["variantSetId"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (format != null) {
_json["format"] = format;
}
if (sourceUris != null) {
_json["sourceUris"] = sourceUris;
}
if (variantSetId != null) {
_json["variantSetId"] = variantSetId;
}
return _json;
}
}
/** The variant data import response. */
class ImportVariantsResponse {
/** A job ID that can be used to get status information. */
core.String jobId;
ImportVariantsResponse();
ImportVariantsResponse.fromJson(core.Map _json) {
if (_json.containsKey("jobId")) {
jobId = _json["jobId"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (jobId != null) {
_json["jobId"] = jobId;
}
return _json;
}
}
/**
* A Job represents an ongoing process that can be monitored for status
* information.
*/
class Job {
/** The date this job was created, in milliseconds from the epoch. */
core.String created;
/** A more detailed description of this job's current status. */
core.String description;
/** Any errors that occurred during processing. */
core.List<core.String> errors;
/** The job ID. */
core.String id;
/**
* If this Job represents an import, this field will contain the IDs of the
* objects that were successfully imported.
*/
core.List<core.String> importedIds;
/**
* The Google Developers Console project number to which this job belongs.
*/
core.String projectId;
/** A summarized representation of the original service request. */
JobRequest request;
/**
* The status of this job.
* Possible string values are:
* - "canceled"
* - "failure"
* - "new"
* - "pending"
* - "running"
* - "success"
* - "unknownStatus"
*/
core.String status;
/** Any warnings that occurred during processing. */
core.List<core.String> warnings;
Job();
Job.fromJson(core.Map _json) {
if (_json.containsKey("created")) {
created = _json["created"];
}
if (_json.containsKey("description")) {
description = _json["description"];
}
if (_json.containsKey("errors")) {
errors = _json["errors"];
}
if (_json.containsKey("id")) {
id = _json["id"];
}
if (_json.containsKey("importedIds")) {
importedIds = _json["importedIds"];
}
if (_json.containsKey("projectId")) {
projectId = _json["projectId"];
}
if (_json.containsKey("request")) {
request = new JobRequest.fromJson(_json["request"]);
}
if (_json.containsKey("status")) {
status = _json["status"];
}
if (_json.containsKey("warnings")) {
warnings = _json["warnings"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (created != null) {
_json["created"] = created;
}
if (description != null) {
_json["description"] = description;
}
if (errors != null) {
_json["errors"] = errors;
}
if (id != null) {
_json["id"] = id;
}
if (importedIds != null) {
_json["importedIds"] = importedIds;
}
if (projectId != null) {
_json["projectId"] = projectId;
}
if (request != null) {
_json["request"] = (request).toJson();
}
if (status != null) {
_json["status"] = status;
}
if (warnings != null) {
_json["warnings"] = warnings;
}
return _json;
}
}
/** A summary representation of the service request that spawned the job. */
class JobRequest {
/**
* The data destination of the request, for example, a Google BigQuery Table
* or Dataset ID.
*/
core.List<core.String> destination;
/**
* The data source of the request, for example, a Google Cloud Storage object
* path or Readset ID.
*/
core.List<core.String> source;
/**
* The original request type.
* Possible string values are:
* - "experimentalCreateJob"
* - "exportReadsets"
* - "exportVariants"
* - "importReadsets"
* - "importVariants"
* - "unknownType"
*/
core.String type;
JobRequest();
JobRequest.fromJson(core.Map _json) {
if (_json.containsKey("destination")) {
destination = _json["destination"];
}
if (_json.containsKey("source")) {
source = _json["source"];
}
if (_json.containsKey("type")) {
type = _json["type"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (destination != null) {
_json["destination"] = destination;
}
if (source != null) {
_json["source"] = source;
}
if (type != null) {
_json["type"] = type;
}
return _json;
}
}
/** Not documented yet. */
class ListCoverageBucketsResponse {
/**
* The length of each coverage bucket in base pairs. Note that buckets at the
* end of a reference sequence may be shorter. This value is omitted if the
* bucket width is infinity (the default behaviour, with no range or
* targetBucketWidth).
*/
core.String bucketWidth;
/**
* The coverage buckets. The list of buckets is sparse; a bucket with 0
* overlapping reads is not returned. A bucket never crosses more than one
* reference sequence. Each bucket has width bucketWidth, unless its end is
* the end of the reference sequence.
*/
core.List<CoverageBucket> coverageBuckets;
/**
* The continuation token, which is used to page through large result sets.
* Provide this value in a subsequent request to return the next page of
* results. This field will be empty if there aren't any additional results.
*/
core.String nextPageToken;
ListCoverageBucketsResponse();
ListCoverageBucketsResponse.fromJson(core.Map _json) {
if (_json.containsKey("bucketWidth")) {
bucketWidth = _json["bucketWidth"];
}
if (_json.containsKey("coverageBuckets")) {
coverageBuckets = _json["coverageBuckets"].map((value) => new CoverageBucket.fromJson(value)).toList();
}
if (_json.containsKey("nextPageToken")) {
nextPageToken = _json["nextPageToken"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (bucketWidth != null) {
_json["bucketWidth"] = bucketWidth;
}
if (coverageBuckets != null) {
_json["coverageBuckets"] = coverageBuckets.map((value) => (value).toJson()).toList();
}
if (nextPageToken != null) {
_json["nextPageToken"] = nextPageToken;
}
return _json;
}
}
/** The dataset list response. */
class ListDatasetsResponse {
/** The list of matching Datasets. */
core.List<Dataset> datasets;
/**
* The continuation token, which is used to page through large result sets.
* Provide this value in a subsequent request to return the next page of
* results. This field will be empty if there aren't any additional results.
*/
core.String nextPageToken;
ListDatasetsResponse();
ListDatasetsResponse.fromJson(core.Map _json) {
if (_json.containsKey("datasets")) {
datasets = _json["datasets"].map((value) => new Dataset.fromJson(value)).toList();
}
if (_json.containsKey("nextPageToken")) {
nextPageToken = _json["nextPageToken"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (datasets != null) {
_json["datasets"] = datasets.map((value) => (value).toJson()).toList();
}
if (nextPageToken != null) {
_json["nextPageToken"] = nextPageToken;
}
return _json;
}
}
/** Not documented yet. */
class MergeVariantsRequest {
/** The variants to be merged with existing variants. */
core.List<Variant> variants;
MergeVariantsRequest();
MergeVariantsRequest.fromJson(core.Map _json) {
if (_json.containsKey("variants")) {
variants = _json["variants"].map((value) => new Variant.fromJson(value)).toList();
}
}
core.Map toJson() {
var _json = new core.Map();
if (variants != null) {
_json["variants"] = variants.map((value) => (value).toJson()).toList();
}
return _json;
}
}
/**
* Metadata describes a single piece of variant call metadata. These data
* include a top level key and either a single value string (value) or a list of
* key-value pairs (info.) Value and info are mutually exclusive.
*/
class Metadata {
/** A textual description of this metadata. */
core.String description;
/**
* User-provided ID field, not enforced by this API. Two or more pieces of
* structured metadata with identical id and key fields are considered
* equivalent.
*/
core.String id;
/** Remaining structured metadata key-value pairs. */
core.Map<core.String, core.List<core.String>> info;
/** The top-level key. */
core.String key;
/**
* The number of values that can be included in a field described by this
* metadata.
*/
core.String number;
/**
* The type of data. Possible types include: Integer, Float, Flag, Character,
* and String.
* Possible string values are:
* - "character"
* - "flag"
* - "float"
* - "integer"
* - "string"
* - "unknownType"
*/
core.String type;
/** The value field for simple metadata */
core.String value;
Metadata();
Metadata.fromJson(core.Map _json) {
if (_json.containsKey("description")) {
description = _json["description"];
}
if (_json.containsKey("id")) {
id = _json["id"];
}
if (_json.containsKey("info")) {
info = _json["info"];
}
if (_json.containsKey("key")) {
key = _json["key"];
}
if (_json.containsKey("number")) {
number = _json["number"];
}
if (_json.containsKey("type")) {
type = _json["type"];
}
if (_json.containsKey("value")) {
value = _json["value"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (description != null) {
_json["description"] = description;
}
if (id != null) {
_json["id"] = id;
}
if (info != null) {
_json["info"] = info;
}
if (key != null) {
_json["key"] = key;
}
if (number != null) {
_json["number"] = number;
}
if (type != null) {
_json["type"] = type;
}
if (value != null) {
_json["value"] = value;
}
return _json;
}
}
/** Not documented yet. */
class Program {
/** (CL) Command line. */
core.String commandLine;
/** (ID) Program record identifier. */
core.String id;
/** (PN) Program name. */
core.String name;
/** (PP) Previous program ID. */
core.String prevProgramId;
/** (VN) Program version. */
core.String version;
Program();
Program.fromJson(core.Map _json) {
if (_json.containsKey("commandLine")) {
commandLine = _json["commandLine"];
}
if (_json.containsKey("id")) {
id = _json["id"];
}
if (_json.containsKey("name")) {
name = _json["name"];
}
if (_json.containsKey("prevProgramId")) {
prevProgramId = _json["prevProgramId"];
}
if (_json.containsKey("version")) {
version = _json["version"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (commandLine != null) {
_json["commandLine"] = commandLine;
}
if (id != null) {
_json["id"] = id;
}
if (name != null) {
_json["name"] = name;
}
if (prevProgramId != null) {
_json["prevProgramId"] = prevProgramId;
}
if (version != null) {
_json["version"] = version;
}
return _json;
}
}
/**
* A Read is a group of bases that may or may not have been aligned to a
* reference. It contains quality information and other metadata.
*/
class Read {
/**
* The originalBases after the cigar field has been applied. Deletions are
* represented with '-' and insertions are omitted.
*/
core.String alignedBases;
/**
* Represents the quality of each base in this read. Each character represents
* one base. To get the quality, take the ASCII value of the character and
* subtract 33. (QUAL)
*/
core.String baseQuality;
/**
* A condensed representation of how this read matches up to the reference.
* (CIGAR)
*/
core.String cigar;
/**
* Each bit of this number has a different meaning if enabled. See the full
* BAM spec for more details. (FLAG)
*/
core.int flags;
/** The Google generated ID of the read, immutable. */
core.String id;
/**
* A score up to 255 that represents how likely this read's aligned position
* is to be correct. A higher value is better. (MAPQ)
*/
core.int mappingQuality;
/** The 1-based start position of the paired read. (PNEXT) */
core.int matePosition;
/**
* The name of the sequence that the paired read is aligned to. This is
* usually the same as referenceSequenceName. (RNEXT)
*/
core.String mateReferenceSequenceName;
/**
* The name of the read. When imported from a BAM file, this is the query
* template name. (QNAME)
*/
core.String name;
/** The list of bases that this read represents (such as "CATCGA"). (SEQ) */
core.String originalBases;
/**
* The 1-based start position of the aligned read. If the first base starts at
* the very beginning of the reference sequence, then the position would be
* '1'. (POS)
*/
core.int position;
/** The ID of the readset this read belongs to. */
core.String readsetId;
/**
* The name of the sequence that this read is aligned to. This would be, for
* example, 'X' for the X Chromosome or '20' for Chromosome 20. (RNAME)
*/
core.String referenceSequenceName;
/** A map of additional read information. (TAG) */
core.Map<core.String, core.List<core.String>> tags;
/**
* Length of the original piece of DNA that produced both this read and the
* paired read. (TLEN)
*/
core.int templateLength;
Read();
Read.fromJson(core.Map _json) {
if (_json.containsKey("alignedBases")) {
alignedBases = _json["alignedBases"];
}
if (_json.containsKey("baseQuality")) {
baseQuality = _json["baseQuality"];
}
if (_json.containsKey("cigar")) {
cigar = _json["cigar"];
}
if (_json.containsKey("flags")) {
flags = _json["flags"];
}
if (_json.containsKey("id")) {
id = _json["id"];
}
if (_json.containsKey("mappingQuality")) {
mappingQuality = _json["mappingQuality"];
}
if (_json.containsKey("matePosition")) {
matePosition = _json["matePosition"];
}
if (_json.containsKey("mateReferenceSequenceName")) {
mateReferenceSequenceName = _json["mateReferenceSequenceName"];
}
if (_json.containsKey("name")) {
name = _json["name"];
}
if (_json.containsKey("originalBases")) {
originalBases = _json["originalBases"];
}
if (_json.containsKey("position")) {
position = _json["position"];
}
if (_json.containsKey("readsetId")) {
readsetId = _json["readsetId"];
}
if (_json.containsKey("referenceSequenceName")) {
referenceSequenceName = _json["referenceSequenceName"];
}
if (_json.containsKey("tags")) {
tags = _json["tags"];
}
if (_json.containsKey("templateLength")) {
templateLength = _json["templateLength"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (alignedBases != null) {
_json["alignedBases"] = alignedBases;
}
if (baseQuality != null) {
_json["baseQuality"] = baseQuality;
}
if (cigar != null) {
_json["cigar"] = cigar;
}
if (flags != null) {
_json["flags"] = flags;
}
if (id != null) {
_json["id"] = id;
}
if (mappingQuality != null) {
_json["mappingQuality"] = mappingQuality;
}
if (matePosition != null) {
_json["matePosition"] = matePosition;
}
if (mateReferenceSequenceName != null) {
_json["mateReferenceSequenceName"] = mateReferenceSequenceName;
}
if (name != null) {
_json["name"] = name;
}
if (originalBases != null) {
_json["originalBases"] = originalBases;
}
if (position != null) {
_json["position"] = position;
}
if (readsetId != null) {
_json["readsetId"] = readsetId;
}
if (referenceSequenceName != null) {
_json["referenceSequenceName"] = referenceSequenceName;
}
if (tags != null) {
_json["tags"] = tags;
}
if (templateLength != null) {
_json["templateLength"] = templateLength;
}
return _json;
}
}
/** Not documented yet. */
class ReadGroup {
/** (DT) Date the run was produced (ISO8601 date or date/time). */
core.String date;
/** (DS) Description. */
core.String description;
/**
* (FO) Flow order. The array of nucleotide bases that correspond to the
* nucleotides used for each flow of each read.
*/
core.String flowOrder;
/** (ID) Read group identifier. */
core.String id;
/**
* (KS) The array of nucleotide bases that correspond to the key sequence of
* each read.
*/
core.String keySequence;
/** (LS) Library. */
core.String library;
/** (PU) Platform unit. */
core.String platformUnit;
/** (PI) Predicted median insert size. */
core.int predictedInsertSize;
/** (PG) Programs used for processing the read group. */
core.String processingProgram;
/** (SM) Sample. */
core.String sample;
/** (CN) Name of sequencing center producing the read. */
core.String sequencingCenterName;
/** (PL) Platform/technology used to produce the reads. */
core.String sequencingTechnology;
ReadGroup();
ReadGroup.fromJson(core.Map _json) {
if (_json.containsKey("date")) {
date = _json["date"];
}
if (_json.containsKey("description")) {
description = _json["description"];
}
if (_json.containsKey("flowOrder")) {
flowOrder = _json["flowOrder"];
}
if (_json.containsKey("id")) {
id = _json["id"];
}
if (_json.containsKey("keySequence")) {
keySequence = _json["keySequence"];
}
if (_json.containsKey("library")) {
library = _json["library"];
}
if (_json.containsKey("platformUnit")) {
platformUnit = _json["platformUnit"];
}
if (_json.containsKey("predictedInsertSize")) {
predictedInsertSize = _json["predictedInsertSize"];
}
if (_json.containsKey("processingProgram")) {
processingProgram = _json["processingProgram"];
}
if (_json.containsKey("sample")) {
sample = _json["sample"];
}
if (_json.containsKey("sequencingCenterName")) {
sequencingCenterName = _json["sequencingCenterName"];
}
if (_json.containsKey("sequencingTechnology")) {
sequencingTechnology = _json["sequencingTechnology"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (date != null) {
_json["date"] = date;
}
if (description != null) {
_json["description"] = description;
}
if (flowOrder != null) {
_json["flowOrder"] = flowOrder;
}
if (id != null) {
_json["id"] = id;
}
if (keySequence != null) {
_json["keySequence"] = keySequence;
}
if (library != null) {
_json["library"] = library;
}
if (platformUnit != null) {
_json["platformUnit"] = platformUnit;
}
if (predictedInsertSize != null) {
_json["predictedInsertSize"] = predictedInsertSize;
}
if (processingProgram != null) {
_json["processingProgram"] = processingProgram;
}
if (sample != null) {
_json["sample"] = sample;
}
if (sequencingCenterName != null) {
_json["sequencingCenterName"] = sequencingCenterName;
}
if (sequencingTechnology != null) {
_json["sequencingTechnology"] = sequencingTechnology;
}
return _json;
}
}
/** A Readset is a collection of Reads. */
class Readset {
/** The ID of the dataset this readset belongs to. */
core.String datasetId;
/**
* File information from the original BAM import. See the BAM format
* specification for additional information on each field.
*/
core.List<HeaderSection> fileData;
/** The Google generated ID of the readset, immutable. */
core.String id;
/** The readset name, typically this is the sample name. */
core.String name;
Readset();
Readset.fromJson(core.Map _json) {
if (_json.containsKey("datasetId")) {
datasetId = _json["datasetId"];
}
if (_json.containsKey("fileData")) {
fileData = _json["fileData"].map((value) => new HeaderSection.fromJson(value)).toList();
}
if (_json.containsKey("id")) {
id = _json["id"];
}
if (_json.containsKey("name")) {
name = _json["name"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (datasetId != null) {
_json["datasetId"] = datasetId;
}
if (fileData != null) {
_json["fileData"] = fileData.map((value) => (value).toJson()).toList();
}
if (id != null) {
_json["id"] = id;
}
if (name != null) {
_json["name"] = name;
}
return _json;
}
}
/**
* ReferenceBound records an upper bound for the starting coordinate of variants
* in a particular reference.
*/
class ReferenceBound {
/** The reference the bound is associate with. */
core.String referenceName;
/**
* An upper bound (inclusive) on the starting coordinate of any variant in the
* reference sequence.
*/
core.String upperBound;
ReferenceBound();
ReferenceBound.fromJson(core.Map _json) {
if (_json.containsKey("referenceName")) {
referenceName = _json["referenceName"];
}
if (_json.containsKey("upperBound")) {
upperBound = _json["upperBound"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (referenceName != null) {
_json["referenceName"] = referenceName;
}
if (upperBound != null) {
_json["upperBound"] = upperBound;
}
return _json;
}
}
/** Not documented yet. */
class ReferenceSequence {
/** (AS) Genome assembly identifier. */
core.String assemblyId;
/** (LN) Reference sequence length. */
core.int length;
/**
* (M5) MD5 checksum of the sequence in the uppercase, excluding spaces but
* including pads as *.
*/
core.String md5Checksum;
/** (SN) Reference sequence name. */
core.String name;
/** (SP) Species. */
core.String species;
/** (UR) URI of the sequence. */
core.String uri;
ReferenceSequence();
ReferenceSequence.fromJson(core.Map _json) {
if (_json.containsKey("assemblyId")) {
assemblyId = _json["assemblyId"];
}
if (_json.containsKey("length")) {
length = _json["length"];
}
if (_json.containsKey("md5Checksum")) {
md5Checksum = _json["md5Checksum"];
}
if (_json.containsKey("name")) {
name = _json["name"];
}
if (_json.containsKey("species")) {
species = _json["species"];
}
if (_json.containsKey("uri")) {
uri = _json["uri"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (assemblyId != null) {
_json["assemblyId"] = assemblyId;
}
if (length != null) {
_json["length"] = length;
}
if (md5Checksum != null) {
_json["md5Checksum"] = md5Checksum;
}
if (name != null) {
_json["name"] = name;
}
if (species != null) {
_json["species"] = species;
}
if (uri != null) {
_json["uri"] = uri;
}
return _json;
}
}
/** The call set search request. */
class SearchCallSetsRequest {
/**
* Only return call sets for which a substring of the name matches this
* string.
*/
core.String name;
/** The maximum number of call sets to return. */
core.int pageSize;
/**
* The continuation token, which is used to page through large result sets. To
* get the next page of results, set this parameter to the value of
* nextPageToken from the previous response.
*/
core.String pageToken;
/**
* Restrict the query to call sets within the given variant sets. At least one
* ID must be provided.
*/
core.List<core.String> variantSetIds;
SearchCallSetsRequest();
SearchCallSetsRequest.fromJson(core.Map _json) {
if (_json.containsKey("name")) {
name = _json["name"];
}
if (_json.containsKey("pageSize")) {
pageSize = _json["pageSize"];
}
if (_json.containsKey("pageToken")) {
pageToken = _json["pageToken"];
}
if (_json.containsKey("variantSetIds")) {
variantSetIds = _json["variantSetIds"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (name != null) {
_json["name"] = name;
}
if (pageSize != null) {
_json["pageSize"] = pageSize;
}
if (pageToken != null) {
_json["pageToken"] = pageToken;
}
if (variantSetIds != null) {
_json["variantSetIds"] = variantSetIds;
}
return _json;
}
}
/** The call set search response. */
class SearchCallSetsResponse {
/** The list of matching call sets. */
core.List<CallSet> callSets;
/**
* The continuation token, which is used to page through large result sets.
* Provide this value in a subsequent request to return the next page of
* results. This field will be empty if there aren't any additional results.
*/
core.String nextPageToken;
SearchCallSetsResponse();
SearchCallSetsResponse.fromJson(core.Map _json) {
if (_json.containsKey("callSets")) {
callSets = _json["callSets"].map((value) => new CallSet.fromJson(value)).toList();
}
if (_json.containsKey("nextPageToken")) {
nextPageToken = _json["nextPageToken"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (callSets != null) {
_json["callSets"] = callSets.map((value) => (value).toJson()).toList();
}
if (nextPageToken != null) {
_json["nextPageToken"] = nextPageToken;
}
return _json;
}
}
/** The jobs search request. */
class SearchJobsRequest {
/**
* If specified, only jobs created on or after this date, given in
* milliseconds since Unix epoch, will be returned.
*/
core.String createdAfter;
/**
* If specified, only jobs created prior to this date, given in milliseconds
* since Unix epoch, will be returned.
*/
core.String createdBefore;
/**
* Specifies the number of results to return in a single page. Defaults to
* 128. The maximum value is 256.
*/
core.String maxResults;
/**
* The continuation token which is used to page through large result sets. To
* get the next page of results, set this parameter to the value of the
* nextPageToken from the previous response.
*/
core.String pageToken;
/** Required. Only return jobs which belong to this Google Developers */
core.String projectId;
/** Only return jobs which have a matching status. */
core.List<core.String> status;
SearchJobsRequest();
SearchJobsRequest.fromJson(core.Map _json) {
if (_json.containsKey("createdAfter")) {
createdAfter = _json["createdAfter"];
}
if (_json.containsKey("createdBefore")) {
createdBefore = _json["createdBefore"];
}
if (_json.containsKey("maxResults")) {
maxResults = _json["maxResults"];
}
if (_json.containsKey("pageToken")) {
pageToken = _json["pageToken"];
}
if (_json.containsKey("projectId")) {
projectId = _json["projectId"];
}
if (_json.containsKey("status")) {
status = _json["status"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (createdAfter != null) {
_json["createdAfter"] = createdAfter;
}
if (createdBefore != null) {
_json["createdBefore"] = createdBefore;
}
if (maxResults != null) {
_json["maxResults"] = maxResults;
}
if (pageToken != null) {
_json["pageToken"] = pageToken;
}
if (projectId != null) {
_json["projectId"] = projectId;
}
if (status != null) {
_json["status"] = status;
}
return _json;
}
}
/** The job search response. */
class SearchJobsResponse {
/** The list of jobs results, ordered newest to oldest. */
core.List<Job> jobs;
/**
* The continuation token which is used to page through large result sets.
* Provide this value is a subsequent request to return the next page of
* results. This field will be empty if there are no more results.
*/
core.String nextPageToken;
SearchJobsResponse();
SearchJobsResponse.fromJson(core.Map _json) {
if (_json.containsKey("jobs")) {
jobs = _json["jobs"].map((value) => new Job.fromJson(value)).toList();
}
if (_json.containsKey("nextPageToken")) {
nextPageToken = _json["nextPageToken"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (jobs != null) {
_json["jobs"] = jobs.map((value) => (value).toJson()).toList();
}
if (nextPageToken != null) {
_json["nextPageToken"] = nextPageToken;
}
return _json;
}
}
/** The read search request. */
class SearchReadsRequest {
/**
* Specifies number of results to return in a single page. If unspecified, it
* will default to 256. The maximum value is 2048.
*/
core.String maxResults;
/**
* The continuation token, which is used to page through large result sets. To
* get the next page of results, set this parameter to the value of
* nextPageToken from the previous response.
*/
core.String pageToken;
/**
* The readsets within which to search for reads. At least one readset ID must
* be provided. All specified readsets must be aligned against a common set of
* reference sequences; this defines the genomic coordinates for the query.
*/
core.List<core.String> readsetIds;
/**
* The end position (1-based, inclusive) of the target range. If specified,
* sequenceName must also be specified. Defaults to the end of the target
* reference sequence, if any.
*/
core.String sequenceEnd;
/**
* Restricts the results to a particular reference sequence such as 1, chr1,
* or X. The set of valid references sequences depends on the readsets
* specified. If set to *, only unmapped Reads are returned.
*/
core.String sequenceName;
/**
* The start position (1-based, inclusive) of the target range. If specified,
* sequenceName must also be specified. Defaults to the start of the target
* reference sequence, if any.
*/
core.String sequenceStart;
SearchReadsRequest();
SearchReadsRequest.fromJson(core.Map _json) {
if (_json.containsKey("maxResults")) {
maxResults = _json["maxResults"];
}
if (_json.containsKey("pageToken")) {
pageToken = _json["pageToken"];
}
if (_json.containsKey("readsetIds")) {
readsetIds = _json["readsetIds"];
}
if (_json.containsKey("sequenceEnd")) {
sequenceEnd = _json["sequenceEnd"];
}
if (_json.containsKey("sequenceName")) {
sequenceName = _json["sequenceName"];
}
if (_json.containsKey("sequenceStart")) {
sequenceStart = _json["sequenceStart"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (maxResults != null) {
_json["maxResults"] = maxResults;
}
if (pageToken != null) {
_json["pageToken"] = pageToken;
}
if (readsetIds != null) {
_json["readsetIds"] = readsetIds;
}
if (sequenceEnd != null) {
_json["sequenceEnd"] = sequenceEnd;
}
if (sequenceName != null) {
_json["sequenceName"] = sequenceName;
}
if (sequenceStart != null) {
_json["sequenceStart"] = sequenceStart;
}
return _json;
}
}
/** The read search response. */
class SearchReadsResponse {
/**
* The continuation token, which is used to page through large result sets.
* Provide this value in a subsequent request to return the next page of
* results. This field will be empty if there aren't any additional results.
*/
core.String nextPageToken;
/**
* The list of matching Reads. The resulting Reads are sorted by position; the
* smallest positions are returned first. Unmapped reads, which have no
* position, are returned last and are further sorted alphabetically by name.
*/
core.List<Read> reads;
SearchReadsResponse();
SearchReadsResponse.fromJson(core.Map _json) {
if (_json.containsKey("nextPageToken")) {
nextPageToken = _json["nextPageToken"];
}
if (_json.containsKey("reads")) {
reads = _json["reads"].map((value) => new Read.fromJson(value)).toList();
}
}
core.Map toJson() {
var _json = new core.Map();
if (nextPageToken != null) {
_json["nextPageToken"] = nextPageToken;
}
if (reads != null) {
_json["reads"] = reads.map((value) => (value).toJson()).toList();
}
return _json;
}
}
/** The readset search request. */
class SearchReadsetsRequest {
/**
* Restricts this query to readsets within the given datasets. At least one ID
* must be provided.
*/
core.List<core.String> datasetIds;
/**
* Specifies number of results to return in a single page. If unspecified, it
* will default to 128. The maximum value is 1024.
*/
core.String maxResults;
/**
* Only return readsets for which a substring of the name matches this string.
*/
core.String name;
/**
* The continuation token, which is used to page through large result sets. To
* get the next page of results, set this parameter to the value of
* nextPageToken from the previous response.
*/
core.String pageToken;
SearchReadsetsRequest();
SearchReadsetsRequest.fromJson(core.Map _json) {
if (_json.containsKey("datasetIds")) {
datasetIds = _json["datasetIds"];
}
if (_json.containsKey("maxResults")) {
maxResults = _json["maxResults"];
}
if (_json.containsKey("name")) {
name = _json["name"];
}
if (_json.containsKey("pageToken")) {
pageToken = _json["pageToken"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (datasetIds != null) {
_json["datasetIds"] = datasetIds;
}
if (maxResults != null) {
_json["maxResults"] = maxResults;
}
if (name != null) {
_json["name"] = name;
}
if (pageToken != null) {
_json["pageToken"] = pageToken;
}
return _json;
}
}
/** The readset search response. */
class SearchReadsetsResponse {
/**
* The continuation token, which is used to page through large result sets.
* Provide this value in a subsequent request to return the next page of
* results. This field will be empty if there aren't any additional results.
*/
core.String nextPageToken;
/** The list of matching Readsets. */
core.List<Readset> readsets;
SearchReadsetsResponse();
SearchReadsetsResponse.fromJson(core.Map _json) {
if (_json.containsKey("nextPageToken")) {
nextPageToken = _json["nextPageToken"];
}
if (_json.containsKey("readsets")) {
readsets = _json["readsets"].map((value) => new Readset.fromJson(value)).toList();
}
}
core.Map toJson() {
var _json = new core.Map();
if (nextPageToken != null) {
_json["nextPageToken"] = nextPageToken;
}
if (readsets != null) {
_json["readsets"] = readsets.map((value) => (value).toJson()).toList();
}
return _json;
}
}
/** The search variant sets request. */
class SearchVariantSetsRequest {
/**
* Exactly one dataset ID must be provided here. Only variant sets which
* belong to this dataset will be returned.
*/
core.List<core.String> datasetIds;
/** The maximum number of variant sets to return in a request. */
core.int pageSize;
/**
* The continuation token, which is used to page through large result sets. To
* get the next page of results, set this parameter to the value of
* nextPageToken from the previous response.
*/
core.String pageToken;
SearchVariantSetsRequest();
SearchVariantSetsRequest.fromJson(core.Map _json) {
if (_json.containsKey("datasetIds")) {
datasetIds = _json["datasetIds"];
}
if (_json.containsKey("pageSize")) {
pageSize = _json["pageSize"];
}
if (_json.containsKey("pageToken")) {
pageToken = _json["pageToken"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (datasetIds != null) {
_json["datasetIds"] = datasetIds;
}
if (pageSize != null) {
_json["pageSize"] = pageSize;
}
if (pageToken != null) {
_json["pageToken"] = pageToken;
}
return _json;
}
}
/** The search variant sets response. */
class SearchVariantSetsResponse {
/**
* The continuation token, which is used to page through large result sets.
* Provide this value in a subsequent request to return the next page of
* results. This field will be empty if there aren't any additional results.
*/
core.String nextPageToken;
/** The variant sets belonging to the requested dataset. */
core.List<VariantSet> variantSets;
SearchVariantSetsResponse();
SearchVariantSetsResponse.fromJson(core.Map _json) {
if (_json.containsKey("nextPageToken")) {
nextPageToken = _json["nextPageToken"];
}
if (_json.containsKey("variantSets")) {
variantSets = _json["variantSets"].map((value) => new VariantSet.fromJson(value)).toList();
}
}
core.Map toJson() {
var _json = new core.Map();
if (nextPageToken != null) {
_json["nextPageToken"] = nextPageToken;
}
if (variantSets != null) {
_json["variantSets"] = variantSets.map((value) => (value).toJson()).toList();
}
return _json;
}
}
/** The variant search request. */
class SearchVariantsRequest {
/**
* Only return variant calls which belong to call sets with these ids. Leaving
* this blank returns all variant calls. If a variant has no calls belonging
* to any of these call sets, it won't be returned at all. Currently, variants
* with no calls from any call set will never be returned.
*/
core.List<core.String> callSetIds;
/**
* Required. The end of the window (0-based, exclusive) for which overlapping
* variants should be returned.
*/
core.String end;
/**
* The maximum number of calls to return. However, at least one variant will
* always be returned, even if it has more calls than this limit.
*/
core.int maxCalls;
/** The maximum number of variants to return. */
core.int pageSize;
/**
* The continuation token, which is used to page through large result sets. To
* get the next page of results, set this parameter to the value of
* nextPageToken from the previous response.
*/
core.String pageToken;
/** Required. Only return variants in this reference sequence. */
core.String referenceName;
/**
* Required. The beginning of the window (0-based, inclusive) for which
* overlapping variants should be returned.
*/
core.String start;
/** Only return variants which have exactly this name. */
core.String variantName;
/**
* Exactly one variant set ID must be provided. Only variants from this
* variant set will be returned.
*/
core.List<core.String> variantSetIds;
SearchVariantsRequest();
SearchVariantsRequest.fromJson(core.Map _json) {
if (_json.containsKey("callSetIds")) {
callSetIds = _json["callSetIds"];
}
if (_json.containsKey("end")) {
end = _json["end"];
}
if (_json.containsKey("maxCalls")) {
maxCalls = _json["maxCalls"];
}
if (_json.containsKey("pageSize")) {
pageSize = _json["pageSize"];
}
if (_json.containsKey("pageToken")) {
pageToken = _json["pageToken"];
}
if (_json.containsKey("referenceName")) {
referenceName = _json["referenceName"];
}
if (_json.containsKey("start")) {
start = _json["start"];
}
if (_json.containsKey("variantName")) {
variantName = _json["variantName"];
}
if (_json.containsKey("variantSetIds")) {
variantSetIds = _json["variantSetIds"];
}
}
core.Map toJson() {
var _json = new core.Map();
if (callSetIds != null) {
_json["callSetIds"] = callSetIds;
}
if (end != null) {
_json["end"] = end;
}
if (maxCalls != null) {
_json["maxCalls"] = maxCalls;
}
if (pageSize != null) {
_json["pageSize"] = pageSize;
}
if (pageToken != null) {
_json["pageToken"] = pageToken;
}
if (referenceName != null) {
_json["referenceName"] = referenceName;
}
if (start != null) {
_json["start"] = start;
}
if (variantName != null) {
_json["variantName"] = variantName;
}
if (variantSetIds != null) {
_json["variantSetIds"] = variantSetIds;
}
return _json;
}
}
/** The variant search response. */
class SearchVariantsResponse {
/**
* The continuation token, which is used to page through large result sets.
* Provide this value in a subsequent request to return the next page of
* results. This field will be empty if there aren't any additional results.
*/
core.String nextPageToken;
/** The list of matching Variants. */
core.List<Variant> variants;
SearchVariantsResponse();
SearchVariantsResponse.fromJson(core.Map _json) {
if (_json.containsKey("nextPageToken")) {
nextPageToken = _json["nextPageToken"];
}
if (_json.containsKey("variants")) {
variants = _json["variants"].map((value) => new Variant.fromJson(value)).toList();
}
}
core.Map toJson() {
var _json = new core.Map();
if (nextPageToken != null) {
_json["nextPageToken"] = nextPageToken;
}
if (variants != null) {
_json["variants"] = variants.map((value) => (value).toJson()).toList();
}
return _json;
}
}
/**
* A Variant represents a change in DNA sequence relative to some reference. For
* example, a Variant could represent a SNP or an insertion. Variants belong to
* a variant set.
*/
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 VariantSet represents a collection of Variants and their summary
* statistics.
*/
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;
}
}