| Index: generated/googleapis_beta/lib/genomics/v1beta2.dart
|
| diff --git a/generated/googleapis_beta/lib/genomics/v1beta.dart b/generated/googleapis_beta/lib/genomics/v1beta2.dart
|
| similarity index 61%
|
| copy from generated/googleapis_beta/lib/genomics/v1beta.dart
|
| copy to generated/googleapis_beta/lib/genomics/v1beta2.dart
|
| index ef44652c806d243bdd7430cf2d0a99b5c056124b..a4ab8bbfed2451fb299089c15b4b97bc8fa9420a 100644
|
| --- a/generated/googleapis_beta/lib/genomics/v1beta.dart
|
| +++ b/generated/googleapis_beta/lib/genomics/v1beta2.dart
|
| @@ -1,4 +1,4 @@
|
| -library googleapis_beta.genomics.v1beta;
|
| +library googleapis_beta.genomics.v1beta2;
|
|
|
| import "dart:core" as core;
|
| import "dart:collection" as collection;
|
| @@ -30,85 +30,19 @@ class GenomicsApi {
|
|
|
| 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);
|
| + ReadgroupsetsResourceApi get readgroupsets => new ReadgroupsetsResourceApi(_requester);
|
| ReadsResourceApi get reads => new ReadsResourceApi(_requester);
|
| - ReadsetsResourceApi get readsets => new ReadsetsResourceApi(_requester);
|
| + ReferencesResourceApi get references => new ReferencesResourceApi(_requester);
|
| + ReferencesetsResourceApi get referencesets => new ReferencesetsResourceApi(_requester);
|
| VariantsResourceApi get variants => new VariantsResourceApi(_requester);
|
| VariantsetsResourceApi get variantsets => new VariantsetsResourceApi(_requester);
|
|
|
| GenomicsApi(http.Client client) :
|
| - _requester = new common_internal.ApiRequester(client, "https://www.googleapis.com/", "genomics/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));
|
| - }
|
| -
|
| + _requester = new common_internal.ApiRequester(client, "https://www.googleapis.com/", "genomics/v1beta2/");
|
| }
|
|
|
|
|
| @@ -164,7 +98,7 @@ class CallsetsResourceApi {
|
| *
|
| * Request parameters:
|
| *
|
| - * [callSetId] - The ID of the callset to be deleted.
|
| + * [callSetId] - The ID of the call set to be deleted.
|
| *
|
| * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -203,7 +137,7 @@ class CallsetsResourceApi {
|
| *
|
| * Request parameters:
|
| *
|
| - * [callSetId] - The ID of the callset.
|
| + * [callSetId] - The ID of the call set.
|
| *
|
| * Completes with a [CallSet].
|
| *
|
| @@ -245,7 +179,7 @@ class CallsetsResourceApi {
|
| *
|
| * Request parameters:
|
| *
|
| - * [callSetId] - The ID of the callset to be updated.
|
| + * [callSetId] - The ID of the call set to be updated.
|
| *
|
| * Completes with a [CallSet].
|
| *
|
| @@ -286,6 +220,8 @@ class CallsetsResourceApi {
|
| /**
|
| * Gets a list of call sets matching the criteria.
|
| *
|
| + * Implements GlobalAllianceApi.searchCallSets.
|
| + *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| @@ -330,7 +266,7 @@ class CallsetsResourceApi {
|
| *
|
| * Request parameters:
|
| *
|
| - * [callSetId] - The ID of the callset to be updated.
|
| + * [callSetId] - The ID of the call set to be updated.
|
| *
|
| * Completes with a [CallSet].
|
| *
|
| @@ -502,15 +438,15 @@ class DatasetsResourceApi {
|
| *
|
| * Request parameters:
|
| *
|
| - * [maxResults] - The maximum number of results returned by this request.
|
| + * [pageSize] - The maximum number of results returned by this request.
|
| *
|
| * [pageToken] - The continuation token, which is used to page through large
|
| * result sets. To get the next page of results, set this parameter to the
|
| * value of nextPageToken from the previous response.
|
| *
|
| - * [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.
|
| + * [projectNumber] - Only return datasets which belong to this Google
|
| + * Developers Console project. Only accepts project numbers. Returns all
|
| + * public projects if no project number is specified.
|
| *
|
| * Completes with a [ListDatasetsResponse].
|
| *
|
| @@ -520,7 +456,7 @@ class DatasetsResourceApi {
|
| * 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}) {
|
| + async.Future<ListDatasetsResponse> list({core.int pageSize, core.String pageToken, core.String projectNumber}) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -528,14 +464,14 @@ class DatasetsResourceApi {
|
| var _downloadOptions = common.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (maxResults != null) {
|
| - _queryParams["maxResults"] = [maxResults];
|
| + if (pageSize != null) {
|
| + _queryParams["pageSize"] = ["${pageSize}"];
|
| }
|
| if (pageToken != null) {
|
| _queryParams["pageToken"] = [pageToken];
|
| }
|
| - if (projectId != null) {
|
| - _queryParams["projectId"] = [projectId];
|
| + if (projectNumber != null) {
|
| + _queryParams["projectNumber"] = [projectNumber];
|
| }
|
|
|
|
|
| @@ -878,28 +814,24 @@ class JobsResourceApi {
|
|
|
|
|
| /** Not documented yet. */
|
| -class ReadsResourceApi {
|
| +class ReadgroupsetsResourceApi {
|
| final common_internal.ApiRequester _requester;
|
|
|
| - ReadsResourceApi(common_internal.ApiRequester client) :
|
| + ReadgroupsetsCoveragebucketsResourceApi get coveragebuckets => new ReadgroupsetsCoveragebucketsResourceApi(_requester);
|
| +
|
| + ReadgroupsetsResourceApi(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.
|
| + * Aligns read data from existing read group sets or files from Google Cloud
|
| + * Storage. See the alignment and variant calling documentation for more
|
| + * details.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| - * Completes with a [SearchReadsResponse].
|
| + * Completes with a [AlignReadGroupSetsResponse].
|
| *
|
| * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -907,7 +839,7 @@ class ReadsResourceApi {
|
| * 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) {
|
| + async.Future<AlignReadGroupSetsResponse> align(AlignReadGroupSetsRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -920,7 +852,7 @@ class ReadsResourceApi {
|
| }
|
|
|
|
|
| - _url = 'reads/search';
|
| + _url = 'readgroupsets/align';
|
|
|
| var _response = _requester.request(_url,
|
| "POST",
|
| @@ -929,28 +861,59 @@ class ReadsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new SearchReadsResponse.fromJson(data));
|
| + return _response.then((data) => new AlignReadGroupSetsResponse.fromJson(data));
|
| }
|
|
|
| -}
|
| + /**
|
| + * Calls variants on read data from existing read group sets or files from
|
| + * Google Cloud Storage. See the alignment and variant calling documentation
|
| + * for more details.
|
| + *
|
| + * [request] - The metadata request object.
|
| + *
|
| + * Request parameters:
|
| + *
|
| + * Completes with a [CallReadGroupSetsResponse].
|
| + *
|
| + * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| + * error.
|
| + *
|
| + * If the used [http.Client] completes with an error when making a REST call,
|
| + * this method will complete with the same error.
|
| + */
|
| + async.Future<CallReadGroupSetsResponse> call(CallReadGroupSetsRequest request) {
|
| + var _url = null;
|
| + var _queryParams = new core.Map();
|
| + var _uploadMedia = null;
|
| + var _uploadOptions = null;
|
| + var _downloadOptions = common.DownloadOptions.Metadata;
|
| + var _body = null;
|
|
|
| + if (request != null) {
|
| + _body = convert.JSON.encode((request).toJson());
|
| + }
|
|
|
| -/** Not documented yet. */
|
| -class ReadsetsResourceApi {
|
| - final common_internal.ApiRequester _requester;
|
|
|
| - ReadsetsCoveragebucketsResourceApi get coveragebuckets => new ReadsetsCoveragebucketsResourceApi(_requester);
|
| + _url = 'readgroupsets/call';
|
|
|
| - ReadsetsResourceApi(common_internal.ApiRequester client) :
|
| - _requester = client;
|
| + var _response = _requester.request(_url,
|
| + "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| + return _response.then((data) => new CallReadGroupSetsResponse.fromJson(data));
|
| + }
|
|
|
| /**
|
| - * Deletes a readset.
|
| + * Deletes a read group set.
|
| *
|
| * Request parameters:
|
| *
|
| - * [readsetId] - The ID of the readset to be deleted. The caller must have
|
| - * WRITE permissions to the dataset associated with this readset.
|
| + * [readGroupSetId] - The ID of the read group set to be deleted. The caller
|
| + * must have WRITE permissions to the dataset associated with this read group
|
| + * set.
|
| *
|
| * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -958,7 +921,7 @@ class ReadsetsResourceApi {
|
| * 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) {
|
| + async.Future delete(core.String readGroupSetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -966,13 +929,13 @@ class ReadsetsResourceApi {
|
| var _downloadOptions = common.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (readsetId == null) {
|
| - throw new core.ArgumentError("Parameter readsetId is required.");
|
| + if (readGroupSetId == null) {
|
| + throw new core.ArgumentError("Parameter readGroupSetId is required.");
|
| }
|
|
|
| _downloadOptions = null;
|
|
|
| - _url = 'readsets/' + common_internal.Escaper.ecapeVariable('$readsetId');
|
| + _url = 'readgroupsets/' + common_internal.Escaper.ecapeVariable('$readGroupSetId');
|
|
|
| var _response = _requester.request(_url,
|
| "DELETE",
|
| @@ -985,17 +948,18 @@ class ReadsetsResourceApi {
|
| }
|
|
|
| /**
|
| - * 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.
|
| + * Exports read group sets to a BAM file in Google Cloud Storage.
|
| + *
|
| + * Note that currently there may be some differences between exported BAM
|
| + * files and the original BAM file at the time of import. In particular,
|
| + * comments in the input file header will not be preserved, and some custom
|
| + * tags will be converted to strings.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| - * Completes with a [ExportReadsetsResponse].
|
| + * Completes with a [ExportReadGroupSetsResponse].
|
| *
|
| * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1003,7 +967,7 @@ class ReadsetsResourceApi {
|
| * 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) {
|
| + async.Future<ExportReadGroupSetsResponse> export(ExportReadGroupSetsRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1016,7 +980,7 @@ class ReadsetsResourceApi {
|
| }
|
|
|
|
|
| - _url = 'readsets/export';
|
| + _url = 'readgroupsets/export';
|
|
|
| var _response = _requester.request(_url,
|
| "POST",
|
| @@ -1025,17 +989,17 @@ class ReadsetsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ExportReadsetsResponse.fromJson(data));
|
| + return _response.then((data) => new ExportReadGroupSetsResponse.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Gets a readset by ID.
|
| + * Gets a read group set by ID.
|
| *
|
| * Request parameters:
|
| *
|
| - * [readsetId] - The ID of the readset.
|
| + * [readGroupSetId] - The ID of the read group set.
|
| *
|
| - * Completes with a [Readset].
|
| + * Completes with a [ReadGroupSet].
|
| *
|
| * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1043,7 +1007,7 @@ class ReadsetsResourceApi {
|
| * 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) {
|
| + async.Future<ReadGroupSet> get(core.String readGroupSetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1051,12 +1015,12 @@ class ReadsetsResourceApi {
|
| var _downloadOptions = common.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (readsetId == null) {
|
| - throw new core.ArgumentError("Parameter readsetId is required.");
|
| + if (readGroupSetId == null) {
|
| + throw new core.ArgumentError("Parameter readGroupSetId is required.");
|
| }
|
|
|
|
|
| - _url = 'readsets/' + common_internal.Escaper.ecapeVariable('$readsetId');
|
| + _url = 'readgroupsets/' + common_internal.Escaper.ecapeVariable('$readGroupSetId');
|
|
|
| var _response = _requester.request(_url,
|
| "GET",
|
| @@ -1065,20 +1029,22 @@ class ReadsetsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Readset.fromJson(data));
|
| + return _response.then((data) => new ReadGroupSet.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.
|
| + * Creates read group sets by asynchronously importing the provided
|
| + * information.
|
| + *
|
| + * Note that currently comments in the input file header are not imported and
|
| + * some custom tags will be converted to strings, rather than preserving tag
|
| + * types. The caller must have WRITE permissions to the dataset.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| - * Completes with a [ImportReadsetsResponse].
|
| + * Completes with a [ImportReadGroupSetsResponse].
|
| *
|
| * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1086,7 +1052,7 @@ class ReadsetsResourceApi {
|
| * 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) {
|
| + async.Future<ImportReadGroupSetsResponse> import(ImportReadGroupSetsRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1099,7 +1065,7 @@ class ReadsetsResourceApi {
|
| }
|
|
|
|
|
| - _url = 'readsets/import';
|
| + _url = 'readgroupsets/import';
|
|
|
| var _response = _requester.request(_url,
|
| "POST",
|
| @@ -1108,20 +1074,21 @@ class ReadsetsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ImportReadsetsResponse.fromJson(data));
|
| + return _response.then((data) => new ImportReadGroupSetsResponse.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Updates a readset. This method supports patch semantics.
|
| + * Updates a read group set. 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.
|
| + * [readGroupSetId] - The ID of the read group set to be updated. The caller
|
| + * must have WRITE permissions to the dataset associated with this read group
|
| + * set.
|
| *
|
| - * Completes with a [Readset].
|
| + * Completes with a [ReadGroupSet].
|
| *
|
| * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1129,7 +1096,7 @@ class ReadsetsResourceApi {
|
| * 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) {
|
| + async.Future<ReadGroupSet> patch(ReadGroupSet request, core.String readGroupSetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1140,12 +1107,12 @@ class ReadsetsResourceApi {
|
| if (request != null) {
|
| _body = convert.JSON.encode((request).toJson());
|
| }
|
| - if (readsetId == null) {
|
| - throw new core.ArgumentError("Parameter readsetId is required.");
|
| + if (readGroupSetId == null) {
|
| + throw new core.ArgumentError("Parameter readGroupSetId is required.");
|
| }
|
|
|
|
|
| - _url = 'readsets/' + common_internal.Escaper.ecapeVariable('$readsetId');
|
| + _url = 'readgroupsets/' + common_internal.Escaper.ecapeVariable('$readGroupSetId');
|
|
|
| var _response = _requester.request(_url,
|
| "PATCH",
|
| @@ -1154,17 +1121,19 @@ class ReadsetsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Readset.fromJson(data));
|
| + return _response.then((data) => new ReadGroupSet.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Gets a list of readsets matching the criteria.
|
| + * Searches for read group sets matching the criteria.
|
| + *
|
| + * Implements GlobalAllianceApi.searchReadGroupSets.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| - * Completes with a [SearchReadsetsResponse].
|
| + * Completes with a [SearchReadGroupSetsResponse].
|
| *
|
| * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1172,7 +1141,7 @@ class ReadsetsResourceApi {
|
| * 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) {
|
| + async.Future<SearchReadGroupSetsResponse> search(SearchReadGroupSetsRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1185,7 +1154,7 @@ class ReadsetsResourceApi {
|
| }
|
|
|
|
|
| - _url = 'readsets/search';
|
| + _url = 'readgroupsets/search';
|
|
|
| var _response = _requester.request(_url,
|
| "POST",
|
| @@ -1194,20 +1163,21 @@ class ReadsetsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new SearchReadsetsResponse.fromJson(data));
|
| + return _response.then((data) => new SearchReadGroupSetsResponse.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Updates a readset.
|
| + * Updates a read group set.
|
| *
|
| * [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.
|
| + * [readGroupSetId] - The ID of the read group set to be updated. The caller
|
| + * must have WRITE permissions to the dataset associated with this read group
|
| + * set.
|
| *
|
| - * Completes with a [Readset].
|
| + * Completes with a [ReadGroupSet].
|
| *
|
| * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1215,7 +1185,7 @@ class ReadsetsResourceApi {
|
| * 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) {
|
| + async.Future<ReadGroupSet> update(ReadGroupSet request, core.String readGroupSetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1226,12 +1196,12 @@ class ReadsetsResourceApi {
|
| if (request != null) {
|
| _body = convert.JSON.encode((request).toJson());
|
| }
|
| - if (readsetId == null) {
|
| - throw new core.ArgumentError("Parameter readsetId is required.");
|
| + if (readGroupSetId == null) {
|
| + throw new core.ArgumentError("Parameter readGroupSetId is required.");
|
| }
|
|
|
|
|
| - _url = 'readsets/' + common_internal.Escaper.ecapeVariable('$readsetId');
|
| + _url = 'readgroupsets/' + common_internal.Escaper.ecapeVariable('$readGroupSetId');
|
|
|
| var _response = _requester.request(_url,
|
| "PUT",
|
| @@ -1240,48 +1210,50 @@ class ReadsetsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Readset.fromJson(data));
|
| + return _response.then((data) => new ReadGroupSet.fromJson(data));
|
| }
|
|
|
| }
|
|
|
|
|
| /** Not documented yet. */
|
| -class ReadsetsCoveragebucketsResourceApi {
|
| +class ReadgroupsetsCoveragebucketsResourceApi {
|
| final common_internal.ApiRequester _requester;
|
|
|
| - ReadsetsCoveragebucketsResourceApi(common_internal.ApiRequester client) :
|
| + ReadgroupsetsCoveragebucketsResourceApi(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.
|
| + * Lists fixed width coverage buckets for a read group set, each of which
|
| + * correspond to a range of a reference sequence. Each bucket summarizes
|
| + * coverage information across its corresponding genomic range.
|
| + *
|
| + * Coverage is defined as the number of reads which are aligned to a given
|
| + * base in the reference sequence. Coverage buckets are available at several
|
| + * precomputed bucket widths, enabling retrieval of various coverage 'zoom
|
| + * levels'. The caller must have READ permissions for the target read group
|
| + * set.
|
| *
|
| * Request parameters:
|
| *
|
| - * [readsetId] - Required. The ID of the readset over which coverage is
|
| - * requested.
|
| + * [readGroupSetId] - Required. The ID of the read group set over which
|
| + * coverage is requested.
|
| *
|
| - * [maxResults] - The maximum number of results to return in a single page. If
|
| + * [pageSize] - The maximum number of results to return in a single page. If
|
| * unspecified, defaults to 1024. The maximum value is 2048.
|
| *
|
| * [pageToken] - The continuation token, which is used to page through large
|
| * result sets. To get the next page of results, set this parameter to the
|
| * value of nextPageToken from the previous response.
|
| *
|
| - * [range_sequenceEnd] - The end position of the range on the reference,
|
| - * 1-based exclusive. If specified, sequenceName must also be specified.
|
| + * [range_end] - The end position of the range on the reference, 0-based
|
| + * exclusive. If specified, referenceName must also be specified.
|
| *
|
| - * [range_sequenceName] - The reference sequence name, for example chr1, 1, or
|
| - * chrX.
|
| + * [range_referenceName] - 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.
|
| + * [range_start] - The start position of the range on the reference, 0-based
|
| + * inclusive. If specified, referenceName must also be specified.
|
| *
|
| * [targetBucketWidth] - The desired width of each reported coverage bucket in
|
| * base pairs. This will be rounded down to the nearest precomputed bucket
|
| @@ -1298,7 +1270,7 @@ class ReadsetsCoveragebucketsResourceApi {
|
| * 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}) {
|
| + async.Future<ListCoverageBucketsResponse> list(core.String readGroupSetId, {core.int pageSize, core.String pageToken, core.String range_end, core.String range_referenceName, core.String range_start, core.String targetBucketWidth}) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1306,30 +1278,30 @@ class ReadsetsCoveragebucketsResourceApi {
|
| var _downloadOptions = common.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (readsetId == null) {
|
| - throw new core.ArgumentError("Parameter readsetId is required.");
|
| + if (readGroupSetId == null) {
|
| + throw new core.ArgumentError("Parameter readGroupSetId is required.");
|
| }
|
| - if (maxResults != null) {
|
| - _queryParams["maxResults"] = [maxResults];
|
| + if (pageSize != null) {
|
| + _queryParams["pageSize"] = ["${pageSize}"];
|
| }
|
| if (pageToken != null) {
|
| _queryParams["pageToken"] = [pageToken];
|
| }
|
| - if (range_sequenceEnd != null) {
|
| - _queryParams["range.sequenceEnd"] = [range_sequenceEnd];
|
| + if (range_end != null) {
|
| + _queryParams["range.end"] = [range_end];
|
| }
|
| - if (range_sequenceName != null) {
|
| - _queryParams["range.sequenceName"] = [range_sequenceName];
|
| + if (range_referenceName != null) {
|
| + _queryParams["range.referenceName"] = [range_referenceName];
|
| }
|
| - if (range_sequenceStart != null) {
|
| - _queryParams["range.sequenceStart"] = [range_sequenceStart];
|
| + if (range_start != null) {
|
| + _queryParams["range.start"] = [range_start];
|
| }
|
| if (targetBucketWidth != null) {
|
| _queryParams["targetBucketWidth"] = [targetBucketWidth];
|
| }
|
|
|
|
|
| - _url = 'readsets/' + common_internal.Escaper.ecapeVariable('$readsetId') + '/coveragebuckets';
|
| + _url = 'readgroupsets/' + common_internal.Escaper.ecapeVariable('$readGroupSetId') + '/coveragebuckets';
|
|
|
| var _response = _requester.request(_url,
|
| "GET",
|
| @@ -1345,20 +1317,34 @@ class ReadsetsCoveragebucketsResourceApi {
|
|
|
|
|
| /** Not documented yet. */
|
| -class VariantsResourceApi {
|
| +class ReadsResourceApi {
|
| final common_internal.ApiRequester _requester;
|
|
|
| - VariantsResourceApi(common_internal.ApiRequester client) :
|
| + ReadsResourceApi(common_internal.ApiRequester client) :
|
| _requester = client;
|
|
|
| /**
|
| - * Creates a new variant.
|
| + * Gets a list of reads for one or more read group sets. Reads search operates
|
| + * over a genomic coordinate space of reference sequence & position defined
|
| + * over the reference sequences to which the requested read group sets are
|
| + * aligned.
|
| + *
|
| + * If a target positional range is specified, search returns all reads whose
|
| + * alignment to the reference genome overlap the range. A query which
|
| + * specifies only read group set IDs yields all reads in those read group
|
| + * sets, including unmapped reads.
|
| + *
|
| + * All reads returned (including reads on subsequent pages) are ordered by
|
| + * genomic coordinate (reference sequence & position). Reads with equivalent
|
| + * genomic coordinates are returned in a deterministic order.
|
| + *
|
| + * Implements GlobalAllianceApi.searchReads.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| - * Completes with a [Variant].
|
| + * Completes with a [SearchReadsResponse].
|
| *
|
| * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1366,7 +1352,7 @@ class VariantsResourceApi {
|
| * 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) {
|
| + async.Future<SearchReadsResponse> search(SearchReadsRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1379,7 +1365,7 @@ class VariantsResourceApi {
|
| }
|
|
|
|
|
| - _url = 'variants';
|
| + _url = 'reads/search';
|
|
|
| var _response = _requester.request(_url,
|
| "POST",
|
| @@ -1388,15 +1374,31 @@ class VariantsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Variant.fromJson(data));
|
| + return _response.then((data) => new SearchReadsResponse.fromJson(data));
|
| }
|
|
|
| +}
|
| +
|
| +
|
| +/** Not documented yet. */
|
| +class ReferencesResourceApi {
|
| + final common_internal.ApiRequester _requester;
|
| +
|
| + ReferencesBasesResourceApi get bases => new ReferencesBasesResourceApi(_requester);
|
| +
|
| + ReferencesResourceApi(common_internal.ApiRequester client) :
|
| + _requester = client;
|
| +
|
| /**
|
| - * Deletes a variant.
|
| + * Gets a reference.
|
| + *
|
| + * Implements GlobalAllianceApi.getReference.
|
| *
|
| * Request parameters:
|
| *
|
| - * [variantId] - The ID of the variant to be deleted.
|
| + * [referenceId] - The ID of the reference.
|
| + *
|
| + * Completes with a [Reference].
|
| *
|
| * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1404,7 +1406,7 @@ class VariantsResourceApi {
|
| * 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) {
|
| + async.Future<Reference> get(core.String referenceId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1412,32 +1414,33 @@ class VariantsResourceApi {
|
| var _downloadOptions = common.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (variantId == null) {
|
| - throw new core.ArgumentError("Parameter variantId is required.");
|
| + if (referenceId == null) {
|
| + throw new core.ArgumentError("Parameter referenceId is required.");
|
| }
|
|
|
| - _downloadOptions = null;
|
|
|
| - _url = 'variants/' + common_internal.Escaper.ecapeVariable('$variantId');
|
| + _url = 'references/' + common_internal.Escaper.ecapeVariable('$referenceId');
|
|
|
| var _response = _requester.request(_url,
|
| - "DELETE",
|
| + "GET",
|
| body: _body,
|
| queryParams: _queryParams,
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => null);
|
| + return _response.then((data) => new Reference.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Exports variant data to an external destination.
|
| + * Searches for references which match the given criteria.
|
| + *
|
| + * Implements GlobalAllianceApi.searchReferences.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| - * Completes with a [ExportVariantsResponse].
|
| + * Completes with a [SearchReferencesResponse].
|
| *
|
| * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1445,7 +1448,7 @@ class VariantsResourceApi {
|
| * 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) {
|
| + async.Future<SearchReferencesResponse> search(SearchReferencesRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1458,7 +1461,7 @@ class VariantsResourceApi {
|
| }
|
|
|
|
|
| - _url = 'variants/export';
|
| + _url = 'references/search';
|
|
|
| var _response = _requester.request(_url,
|
| "POST",
|
| @@ -1467,17 +1470,41 @@ class VariantsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ExportVariantsResponse.fromJson(data));
|
| + return _response.then((data) => new SearchReferencesResponse.fromJson(data));
|
| }
|
|
|
| +}
|
| +
|
| +
|
| +/** Not documented yet. */
|
| +class ReferencesBasesResourceApi {
|
| + final common_internal.ApiRequester _requester;
|
| +
|
| + ReferencesBasesResourceApi(common_internal.ApiRequester client) :
|
| + _requester = client;
|
| +
|
| /**
|
| - * Gets a variant by ID.
|
| + * Lists the bases in a reference, optionally restricted to a range.
|
| + *
|
| + * Implements GlobalAllianceApi.getReferenceBases.
|
| *
|
| * Request parameters:
|
| *
|
| - * [variantId] - The ID of the variant.
|
| + * [referenceId] - The ID of the reference.
|
| *
|
| - * Completes with a [Variant].
|
| + * [end] - The end position (0-based, exclusive) of this query. Defaults to
|
| + * the length of this reference.
|
| + *
|
| + * [pageSize] - Specifies the maximum number of bases to return in a single
|
| + * page.
|
| + *
|
| + * [pageToken] - The continuation token, which is used to page through large
|
| + * result sets. To get the next page of results, set this parameter to the
|
| + * value of nextPageToken from the previous response.
|
| + *
|
| + * [start] - The start position (0-based) of this query. Defaults to 0.
|
| + *
|
| + * Completes with a [ListBasesResponse].
|
| *
|
| * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1485,7 +1512,7 @@ class VariantsResourceApi {
|
| * 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) {
|
| + async.Future<ListBasesResponse> list(core.String referenceId, {core.String end, core.int pageSize, core.String pageToken, core.String start}) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1493,12 +1520,24 @@ class VariantsResourceApi {
|
| var _downloadOptions = common.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (variantId == null) {
|
| - throw new core.ArgumentError("Parameter variantId is required.");
|
| + if (referenceId == null) {
|
| + throw new core.ArgumentError("Parameter referenceId is required.");
|
| + }
|
| + if (end != null) {
|
| + _queryParams["end"] = [end];
|
| + }
|
| + if (pageSize != null) {
|
| + _queryParams["pageSize"] = ["${pageSize}"];
|
| + }
|
| + if (pageToken != null) {
|
| + _queryParams["pageToken"] = [pageToken];
|
| + }
|
| + if (start != null) {
|
| + _queryParams["start"] = [start];
|
| }
|
|
|
|
|
| - _url = 'variants/' + common_internal.Escaper.ecapeVariable('$variantId');
|
| + _url = 'references/' + common_internal.Escaper.ecapeVariable('$referenceId') + '/bases';
|
|
|
| var _response = _requester.request(_url,
|
| "GET",
|
| @@ -1507,24 +1546,29 @@ class VariantsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new Variant.fromJson(data));
|
| + return _response.then((data) => new ListBasesResponse.fromJson(data));
|
| }
|
|
|
| +}
|
| +
|
| +
|
| +/** Not documented yet. */
|
| +class ReferencesetsResourceApi {
|
| + final common_internal.ApiRequester _requester;
|
| +
|
| + ReferencesetsResourceApi(common_internal.ApiRequester client) :
|
| + _requester = client;
|
| +
|
| /**
|
| - * 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.
|
| + * Gets a reference set.
|
| *
|
| - * [request] - The metadata request object.
|
| + * Implements GlobalAllianceApi.getReferenceSet.
|
| *
|
| * Request parameters:
|
| *
|
| - * Completes with a [ImportVariantsResponse].
|
| + * [referenceSetId] - The ID of the reference set.
|
| + *
|
| + * Completes with a [ReferenceSet].
|
| *
|
| * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1532,7 +1576,7 @@ class VariantsResourceApi {
|
| * 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) {
|
| + async.Future<ReferenceSet> get(core.String referenceSetId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1540,31 +1584,33 @@ class VariantsResourceApi {
|
| var _downloadOptions = common.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (request != null) {
|
| - _body = convert.JSON.encode((request).toJson());
|
| + if (referenceSetId == null) {
|
| + throw new core.ArgumentError("Parameter referenceSetId is required.");
|
| }
|
|
|
|
|
| - _url = 'variants/import';
|
| + _url = 'referencesets/' + common_internal.Escaper.ecapeVariable('$referenceSetId');
|
|
|
| var _response = _requester.request(_url,
|
| - "POST",
|
| + "GET",
|
| body: _body,
|
| queryParams: _queryParams,
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new ImportVariantsResponse.fromJson(data));
|
| + return _response.then((data) => new ReferenceSet.fromJson(data));
|
| }
|
|
|
| /**
|
| - * Gets a list of variants matching the criteria.
|
| + * Searches for reference sets which match the given criteria.
|
| + *
|
| + * Implements GlobalAllianceApi.searchReferenceSets.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| *
|
| - * Completes with a [SearchVariantsResponse].
|
| + * Completes with a [SearchReferenceSetsResponse].
|
| *
|
| * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1572,7 +1618,7 @@ class VariantsResourceApi {
|
| * 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) {
|
| + async.Future<SearchReferenceSetsResponse> search(SearchReferenceSetsRequest request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1585,7 +1631,7 @@ class VariantsResourceApi {
|
| }
|
|
|
|
|
| - _url = 'variants/search';
|
| + _url = 'referencesets/search';
|
|
|
| var _response = _requester.request(_url,
|
| "POST",
|
| @@ -1594,19 +1640,26 @@ class VariantsResourceApi {
|
| uploadOptions: _uploadOptions,
|
| uploadMedia: _uploadMedia,
|
| downloadOptions: _downloadOptions);
|
| - return _response.then((data) => new SearchVariantsResponse.fromJson(data));
|
| + return _response.then((data) => new SearchReferenceSetsResponse.fromJson(data));
|
| }
|
|
|
| +}
|
| +
|
| +
|
| +/** Not documented yet. */
|
| +class VariantsResourceApi {
|
| + final common_internal.ApiRequester _requester;
|
| +
|
| + VariantsResourceApi(common_internal.ApiRequester client) :
|
| + _requester = client;
|
| +
|
| /**
|
| - * Updates a variant's names and info fields. All other modifications are
|
| - * silently ignored. Returns the modified variant without its calls.
|
| + * Creates a new variant.
|
| *
|
| * [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
|
| @@ -1615,7 +1668,7 @@ class VariantsResourceApi {
|
| * 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) {
|
| + async.Future<Variant> create(Variant request) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1626,15 +1679,12 @@ class VariantsResourceApi {
|
| 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');
|
| + _url = 'variants';
|
|
|
| var _response = _requester.request(_url,
|
| - "PUT",
|
| + "POST",
|
| body: _body,
|
| queryParams: _queryParams,
|
| uploadOptions: _uploadOptions,
|
| @@ -1643,23 +1693,12 @@ class VariantsResourceApi {
|
| 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.
|
| + * Deletes a variant.
|
| *
|
| * Request parameters:
|
| *
|
| - * [variantSetId] - The ID of the variant set to be deleted.
|
| + * [variantId] - The ID of the variant to be deleted.
|
| *
|
| * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1667,7 +1706,7 @@ class VariantsetsResourceApi {
|
| * 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) {
|
| + async.Future delete(core.String variantId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1675,13 +1714,13 @@ class VariantsetsResourceApi {
|
| var _downloadOptions = common.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (variantSetId == null) {
|
| - throw new core.ArgumentError("Parameter variantSetId is required.");
|
| + if (variantId == null) {
|
| + throw new core.ArgumentError("Parameter variantId is required.");
|
| }
|
|
|
| _downloadOptions = null;
|
|
|
| - _url = 'variantsets/' + common_internal.Escaper.ecapeVariable('$variantSetId');
|
| + _url = 'variants/' + common_internal.Escaper.ecapeVariable('$variantId');
|
|
|
| var _response = _requester.request(_url,
|
| "DELETE",
|
| @@ -1694,13 +1733,13 @@ class VariantsetsResourceApi {
|
| }
|
|
|
| /**
|
| - * Gets a variant set by ID.
|
| + * Gets a variant by ID.
|
| *
|
| * Request parameters:
|
| *
|
| - * [variantSetId] - Required. The ID of the variant set.
|
| + * [variantId] - The ID of the variant.
|
| *
|
| - * Completes with a [VariantSet].
|
| + * Completes with a [Variant].
|
| *
|
| * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| * error.
|
| @@ -1708,7 +1747,7 @@ class VariantsetsResourceApi {
|
| * 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) {
|
| + async.Future<Variant> get(core.String variantId) {
|
| var _url = null;
|
| var _queryParams = new core.Map();
|
| var _uploadMedia = null;
|
| @@ -1716,7 +1755,232 @@ class VariantsetsResourceApi {
|
| var _downloadOptions = common.DownloadOptions.Metadata;
|
| var _body = null;
|
|
|
| - if (variantSetId == null) {
|
| + if (variantId == null) {
|
| + throw new core.ArgumentError("Parameter variantId is required.");
|
| + }
|
| +
|
| +
|
| + _url = 'variants/' + common_internal.Escaper.ecapeVariable('$variantId');
|
| +
|
| + var _response = _requester.request(_url,
|
| + "GET",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| + return _response.then((data) => new Variant.fromJson(data));
|
| + }
|
| +
|
| + /**
|
| + * Gets a list of variants matching the criteria.
|
| + *
|
| + * Implements GlobalAllianceApi.searchVariants.
|
| + *
|
| + * [request] - The metadata request object.
|
| + *
|
| + * Request parameters:
|
| + *
|
| + * Completes with a [SearchVariantsResponse].
|
| + *
|
| + * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| + * error.
|
| + *
|
| + * If the used [http.Client] completes with an error when making a REST call,
|
| + * this method will complete with the same error.
|
| + */
|
| + async.Future<SearchVariantsResponse> search(SearchVariantsRequest request) {
|
| + var _url = null;
|
| + var _queryParams = new core.Map();
|
| + var _uploadMedia = null;
|
| + var _uploadOptions = null;
|
| + var _downloadOptions = common.DownloadOptions.Metadata;
|
| + var _body = null;
|
| +
|
| + if (request != null) {
|
| + _body = convert.JSON.encode((request).toJson());
|
| + }
|
| +
|
| +
|
| + _url = 'variants/search';
|
| +
|
| + var _response = _requester.request(_url,
|
| + "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| + return _response.then((data) => new SearchVariantsResponse.fromJson(data));
|
| + }
|
| +
|
| + /**
|
| + * Updates a variant's names and info fields. All other modifications are
|
| + * silently ignored. Returns the modified variant without its calls.
|
| + *
|
| + * [request] - The metadata request object.
|
| + *
|
| + * Request parameters:
|
| + *
|
| + * [variantId] - The ID of the variant to be updated.
|
| + *
|
| + * Completes with a [Variant].
|
| + *
|
| + * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| + * error.
|
| + *
|
| + * If the used [http.Client] completes with an error when making a REST call,
|
| + * this method will complete with the same error.
|
| + */
|
| + async.Future<Variant> update(Variant request, core.String variantId) {
|
| + var _url = null;
|
| + var _queryParams = new core.Map();
|
| + var _uploadMedia = null;
|
| + var _uploadOptions = null;
|
| + var _downloadOptions = common.DownloadOptions.Metadata;
|
| + var _body = null;
|
| +
|
| + if (request != null) {
|
| + _body = convert.JSON.encode((request).toJson());
|
| + }
|
| + if (variantId == null) {
|
| + throw new core.ArgumentError("Parameter variantId is required.");
|
| + }
|
| +
|
| +
|
| + _url = 'variants/' + common_internal.Escaper.ecapeVariable('$variantId');
|
| +
|
| + var _response = _requester.request(_url,
|
| + "PUT",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| + return _response.then((data) => new Variant.fromJson(data));
|
| + }
|
| +
|
| +}
|
| +
|
| +
|
| +/** Not documented yet. */
|
| +class VariantsetsResourceApi {
|
| + final common_internal.ApiRequester _requester;
|
| +
|
| + VariantsetsResourceApi(common_internal.ApiRequester client) :
|
| + _requester = client;
|
| +
|
| + /**
|
| + * Deletes the contents of a variant set. The variant set object is not
|
| + * deleted.
|
| + *
|
| + * Request parameters:
|
| + *
|
| + * [variantSetId] - The ID of the variant set to be deleted.
|
| + *
|
| + * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| + * error.
|
| + *
|
| + * If the used [http.Client] completes with an error when making a REST call,
|
| + * this method will complete with the same error.
|
| + */
|
| + async.Future delete(core.String variantSetId) {
|
| + var _url = null;
|
| + var _queryParams = new core.Map();
|
| + var _uploadMedia = null;
|
| + var _uploadOptions = null;
|
| + var _downloadOptions = common.DownloadOptions.Metadata;
|
| + var _body = null;
|
| +
|
| + if (variantSetId == null) {
|
| + throw new core.ArgumentError("Parameter variantSetId is required.");
|
| + }
|
| +
|
| + _downloadOptions = null;
|
| +
|
| + _url = 'variantsets/' + common_internal.Escaper.ecapeVariable('$variantSetId');
|
| +
|
| + var _response = _requester.request(_url,
|
| + "DELETE",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| + return _response.then((data) => null);
|
| + }
|
| +
|
| + /**
|
| + * Exports variant set data to an external destination.
|
| + *
|
| + * [request] - The metadata request object.
|
| + *
|
| + * Request parameters:
|
| + *
|
| + * [variantSetId] - Required. The ID of the variant set that contains variant
|
| + * data which should be exported. The caller must have READ access to this
|
| + * variant set.
|
| + *
|
| + * Completes with a [ExportVariantSetResponse].
|
| + *
|
| + * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| + * error.
|
| + *
|
| + * If the used [http.Client] completes with an error when making a REST call,
|
| + * this method will complete with the same error.
|
| + */
|
| + async.Future<ExportVariantSetResponse> export(ExportVariantSetRequest request, core.String variantSetId) {
|
| + var _url = null;
|
| + var _queryParams = new core.Map();
|
| + var _uploadMedia = null;
|
| + var _uploadOptions = null;
|
| + var _downloadOptions = common.DownloadOptions.Metadata;
|
| + var _body = null;
|
| +
|
| + if (request != null) {
|
| + _body = convert.JSON.encode((request).toJson());
|
| + }
|
| + if (variantSetId == null) {
|
| + throw new core.ArgumentError("Parameter variantSetId is required.");
|
| + }
|
| +
|
| +
|
| + _url = 'variantsets/' + common_internal.Escaper.ecapeVariable('$variantSetId') + '/export';
|
| +
|
| + var _response = _requester.request(_url,
|
| + "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| + return _response.then((data) => new ExportVariantSetResponse.fromJson(data));
|
| + }
|
| +
|
| + /**
|
| + * Gets a variant set by ID.
|
| + *
|
| + * Request parameters:
|
| + *
|
| + * [variantSetId] - Required. The ID of the variant set.
|
| + *
|
| + * Completes with a [VariantSet].
|
| + *
|
| + * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| + * error.
|
| + *
|
| + * If the used [http.Client] completes with an error when making a REST call,
|
| + * this method will complete with the same error.
|
| + */
|
| + async.Future<VariantSet> get(core.String variantSetId) {
|
| + var _url = null;
|
| + var _queryParams = new core.Map();
|
| + var _uploadMedia = null;
|
| + var _uploadOptions = null;
|
| + var _downloadOptions = common.DownloadOptions.Metadata;
|
| + var _body = null;
|
| +
|
| + if (variantSetId == null) {
|
| throw new core.ArgumentError("Parameter variantSetId is required.");
|
| }
|
|
|
| @@ -1734,6 +1998,60 @@ class VariantsetsResourceApi {
|
| }
|
|
|
| /**
|
| + * Creates variant data by asynchronously importing the provided information.
|
| + *
|
| + * The variants for import will be merged with any existing data and each
|
| + * other according to the behavior of mergeVariants. In particular, this means
|
| + * for merged VCF variants that have conflicting INFO fields, some data will
|
| + * be arbitrarily discarded. As a special case, for single-sample VCF files,
|
| + * QUAL and FILTER fields will be moved to the call level; these are sometimes
|
| + * interpreted in a call-specific context. Imported VCF headers are appended
|
| + * to the metadata already in a variant set.
|
| + *
|
| + * [request] - The metadata request object.
|
| + *
|
| + * Request parameters:
|
| + *
|
| + * [variantSetId] - Required. The variant set to which variant data should be
|
| + * imported.
|
| + *
|
| + * Completes with a [ImportVariantsResponse].
|
| + *
|
| + * Completes with a [common.ApiRequestError] if the API endpoint returned an
|
| + * error.
|
| + *
|
| + * If the used [http.Client] completes with an error when making a REST call,
|
| + * this method will complete with the same error.
|
| + */
|
| + async.Future<ImportVariantsResponse> importVariants(ImportVariantsRequest request, core.String variantSetId) {
|
| + var _url = null;
|
| + var _queryParams = new core.Map();
|
| + var _uploadMedia = null;
|
| + var _uploadOptions = null;
|
| + var _downloadOptions = common.DownloadOptions.Metadata;
|
| + var _body = null;
|
| +
|
| + if (request != null) {
|
| + _body = convert.JSON.encode((request).toJson());
|
| + }
|
| + if (variantSetId == null) {
|
| + throw new core.ArgumentError("Parameter variantSetId is required.");
|
| + }
|
| +
|
| +
|
| + _url = 'variantsets/' + common_internal.Escaper.ecapeVariable('$variantSetId') + '/importVariants';
|
| +
|
| + var _response = _requester.request(_url,
|
| + "POST",
|
| + body: _body,
|
| + queryParams: _queryParams,
|
| + uploadOptions: _uploadOptions,
|
| + uploadMedia: _uploadMedia,
|
| + downloadOptions: _downloadOptions);
|
| + return _response.then((data) => new ImportVariantsResponse.fromJson(data));
|
| + }
|
| +
|
| + /**
|
| * Merges the given variants with existing variants. Each variant will be
|
| * merged with an existing variant that matches its reference sequence, start,
|
| * end, reference bases, and alternative bases. If no such variant exists, a
|
| @@ -1786,8 +2104,7 @@ class VariantsetsResourceApi {
|
|
|
| /**
|
| * Updates a variant set's metadata. All other modifications are silently
|
| - * ignored. Returns the modified variant set. This method supports patch
|
| - * semantics.
|
| + * ignored. This method supports patch semantics.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| @@ -1834,6 +2151,8 @@ class VariantsetsResourceApi {
|
| /**
|
| * Returns a list of all variant sets matching search criteria.
|
| *
|
| + * Implements GlobalAllianceApi.searchVariantSets.
|
| + *
|
| * [request] - The metadata request object.
|
| *
|
| * Request parameters:
|
| @@ -1873,7 +2192,7 @@ class VariantsetsResourceApi {
|
|
|
| /**
|
| * Updates a variant set's metadata. All other modifications are silently
|
| - * ignored. Returns the modified variant set.
|
| + * ignored.
|
| *
|
| * [request] - The metadata request object.
|
| *
|
| @@ -1921,27 +2240,107 @@ class VariantsetsResourceApi {
|
|
|
|
|
|
|
| -/**
|
| - * 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;
|
| +/** The read group set align request. */
|
| +class AlignReadGroupSetsRequest {
|
| + /**
|
| + * The BAM source files for alignment. Exactly one of readGroupSetIds,
|
| + * bamSourceUris, interleavedFastqSource or pairedFastqSource must be
|
| + * provided. The caller must have READ permissions for these files.
|
| + */
|
| + core.List<core.String> bamSourceUris;
|
|
|
| + /**
|
| + * Required. The ID of the dataset the newly aligned read group sets will
|
| + * belong to. The caller must have WRITE permissions to this dataset.
|
| + */
|
| + core.String datasetId;
|
|
|
| - Beacon();
|
| + /**
|
| + * The interleaved FASTQ source files for alignment, where both members of
|
| + * each pair of reads are found on consecutive records within the same FASTQ
|
| + * file. Exactly one of readGroupSetIds, bamSourceUris, interleavedFastqSource
|
| + * or pairedFastqSource must be provided.
|
| + */
|
| + InterleavedFastqSource interleavedFastqSource;
|
| +
|
| + /**
|
| + * The paired end FASTQ source files for alignment, where each member of a
|
| + * pair of reads are found in separate files. Exactly one of readGroupSetIds,
|
| + * bamSourceUris, interleavedFastqSource or pairedFastqSource must be
|
| + * provided.
|
| + */
|
| + PairedFastqSource pairedFastqSource;
|
| +
|
| + /**
|
| + * The IDs of the read group sets which will be aligned. New read group sets
|
| + * will be generated to hold the aligned data, the originals will not be
|
| + * modified. The caller must have READ permissions for these read group sets.
|
| + * Exactly one of readGroupSetIds, bamSourceUris, interleavedFastqSource or
|
| + * pairedFastqSource must be provided.
|
| + */
|
| + core.List<core.String> readGroupSetIds;
|
| +
|
| +
|
| + AlignReadGroupSetsRequest();
|
|
|
| - Beacon.fromJson(core.Map _json) {
|
| - if (_json.containsKey("exists")) {
|
| - exists = _json["exists"];
|
| + AlignReadGroupSetsRequest.fromJson(core.Map _json) {
|
| + if (_json.containsKey("bamSourceUris")) {
|
| + bamSourceUris = _json["bamSourceUris"];
|
| + }
|
| + if (_json.containsKey("datasetId")) {
|
| + datasetId = _json["datasetId"];
|
| + }
|
| + if (_json.containsKey("interleavedFastqSource")) {
|
| + interleavedFastqSource = new InterleavedFastqSource.fromJson(_json["interleavedFastqSource"]);
|
| + }
|
| + if (_json.containsKey("pairedFastqSource")) {
|
| + pairedFastqSource = new PairedFastqSource.fromJson(_json["pairedFastqSource"]);
|
| + }
|
| + if (_json.containsKey("readGroupSetIds")) {
|
| + readGroupSetIds = _json["readGroupSetIds"];
|
| }
|
| }
|
|
|
| core.Map toJson() {
|
| var _json = new core.Map();
|
| - if (exists != null) {
|
| - _json["exists"] = exists;
|
| + if (bamSourceUris != null) {
|
| + _json["bamSourceUris"] = bamSourceUris;
|
| + }
|
| + if (datasetId != null) {
|
| + _json["datasetId"] = datasetId;
|
| + }
|
| + if (interleavedFastqSource != null) {
|
| + _json["interleavedFastqSource"] = (interleavedFastqSource).toJson();
|
| + }
|
| + if (pairedFastqSource != null) {
|
| + _json["pairedFastqSource"] = (pairedFastqSource).toJson();
|
| + }
|
| + if (readGroupSetIds != null) {
|
| + _json["readGroupSetIds"] = readGroupSetIds;
|
| + }
|
| + return _json;
|
| + }
|
| +}
|
| +
|
| +
|
| +/** The read group set align response. */
|
| +class AlignReadGroupSetsResponse {
|
| + /** A job ID that can be used to get status information. */
|
| + core.String jobId;
|
| +
|
| +
|
| + AlignReadGroupSetsResponse();
|
| +
|
| + AlignReadGroupSetsResponse.fromJson(core.Map _json) {
|
| + if (_json.containsKey("jobId")) {
|
| + jobId = _json["jobId"];
|
| + }
|
| + }
|
| +
|
| + core.Map toJson() {
|
| + var _json = new core.Map();
|
| + if (jobId != null) {
|
| + _json["jobId"] = jobId;
|
| }
|
| return _json;
|
| }
|
| @@ -1949,9 +2348,9 @@ class Beacon {
|
|
|
|
|
| /**
|
| - * A Call represents the determination of genotype with respect to a particular
|
| + * 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
|
| + * 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 {
|
| @@ -2041,7 +2440,87 @@ class Call {
|
| }
|
|
|
|
|
| -/** A CallSet is a collection of variant calls. It belongs to a variant set. */
|
| +/** The read group set call request. */
|
| +class CallReadGroupSetsRequest {
|
| + /**
|
| + * Required. The ID of the dataset the called variants will belong to. The
|
| + * caller must have WRITE permissions to this dataset.
|
| + */
|
| + core.String datasetId;
|
| +
|
| + /**
|
| + * The IDs of the read group sets which will be called. The caller must have
|
| + * READ permissions for these read group sets. One of readGroupSetIds or
|
| + * sourceUris must be provided.
|
| + */
|
| + core.List<core.String> readGroupSetIds;
|
| +
|
| + /**
|
| + * A list of URIs pointing at BAM files in Google Cloud Storage which will be
|
| + * called. FASTQ files are not allowed. The caller must have READ permissions
|
| + * for these files. One of readGroupSetIds or sourceUris must be provided.
|
| + */
|
| + core.List<core.String> sourceUris;
|
| +
|
| +
|
| + CallReadGroupSetsRequest();
|
| +
|
| + CallReadGroupSetsRequest.fromJson(core.Map _json) {
|
| + if (_json.containsKey("datasetId")) {
|
| + datasetId = _json["datasetId"];
|
| + }
|
| + if (_json.containsKey("readGroupSetIds")) {
|
| + readGroupSetIds = _json["readGroupSetIds"];
|
| + }
|
| + if (_json.containsKey("sourceUris")) {
|
| + sourceUris = _json["sourceUris"];
|
| + }
|
| + }
|
| +
|
| + core.Map toJson() {
|
| + var _json = new core.Map();
|
| + if (datasetId != null) {
|
| + _json["datasetId"] = datasetId;
|
| + }
|
| + if (readGroupSetIds != null) {
|
| + _json["readGroupSetIds"] = readGroupSetIds;
|
| + }
|
| + if (sourceUris != null) {
|
| + _json["sourceUris"] = sourceUris;
|
| + }
|
| + return _json;
|
| + }
|
| +}
|
| +
|
| +
|
| +/** The read group set call response. */
|
| +class CallReadGroupSetsResponse {
|
| + /** A job ID that can be used to get status information. */
|
| + core.String jobId;
|
| +
|
| +
|
| + CallReadGroupSetsResponse();
|
| +
|
| + CallReadGroupSetsResponse.fromJson(core.Map _json) {
|
| + if (_json.containsKey("jobId")) {
|
| + jobId = _json["jobId"];
|
| + }
|
| + }
|
| +
|
| + core.Map toJson() {
|
| + var _json = new core.Map();
|
| + if (jobId != null) {
|
| + _json["jobId"] = jobId;
|
| + }
|
| + return _json;
|
| + }
|
| +}
|
| +
|
| +
|
| +/**
|
| + * A call set is a collection of variant calls, typically for one sample. It
|
| + * belongs to a variant set.
|
| + */
|
| class CallSet {
|
| /** The date this call set was created in milliseconds from the epoch. */
|
| core.String created;
|
| @@ -2049,10 +2528,10 @@ class CallSet {
|
| /** The Google generated ID of the call set, immutable. */
|
| core.String id;
|
|
|
| - /** A map of additional callset information. */
|
| + /** A map of additional call set information. */
|
| core.Map<core.String, core.List<core.String>> info;
|
|
|
| - /** The callset name. */
|
| + /** The call set name. */
|
| core.String name;
|
|
|
| /** The sample ID this call set corresponds to. */
|
| @@ -2110,6 +2589,64 @@ class CallSet {
|
| }
|
|
|
|
|
| +/** A single CIGAR operation. */
|
| +class CigarUnit {
|
| + /**
|
| + * Not documented yet.
|
| + * Possible string values are:
|
| + * - "ALIGNMENT_MATCH"
|
| + * - "CLIP_HARD"
|
| + * - "CLIP_SOFT"
|
| + * - "DELETE"
|
| + * - "INSERT"
|
| + * - "PAD"
|
| + * - "SEQUENCE_MATCH"
|
| + * - "SEQUENCE_MISMATCH"
|
| + * - "SKIP"
|
| + */
|
| + core.String operation;
|
| +
|
| + /** The number of bases that the operation runs for. Required. */
|
| + core.String operationLength;
|
| +
|
| + /**
|
| + * referenceSequence is only used at mismatches (SEQUENCE_MISMATCH) and
|
| + * deletions (DELETE). Filling this field replaces SAM's MD tag. If the
|
| + * relevant information is not available, this field is unset.
|
| + */
|
| + core.String referenceSequence;
|
| +
|
| +
|
| + CigarUnit();
|
| +
|
| + CigarUnit.fromJson(core.Map _json) {
|
| + if (_json.containsKey("operation")) {
|
| + operation = _json["operation"];
|
| + }
|
| + if (_json.containsKey("operationLength")) {
|
| + operationLength = _json["operationLength"];
|
| + }
|
| + if (_json.containsKey("referenceSequence")) {
|
| + referenceSequence = _json["referenceSequence"];
|
| + }
|
| + }
|
| +
|
| + core.Map toJson() {
|
| + var _json = new core.Map();
|
| + if (operation != null) {
|
| + _json["operation"] = operation;
|
| + }
|
| + if (operationLength != null) {
|
| + _json["operationLength"] = operationLength;
|
| + }
|
| + if (referenceSequence != null) {
|
| + _json["referenceSequence"] = referenceSequence;
|
| + }
|
| + return _json;
|
| + }
|
| +}
|
| +
|
| +
|
| /**
|
| * A bucket over which read coverage has been precomputed. A bucket corresponds
|
| * to a specific range of the reference sequence.
|
| @@ -2122,7 +2659,7 @@ class CoverageBucket {
|
| core.double meanCoverage;
|
|
|
| /** The genomic coordinate range spanned by this bucket. */
|
| - GenomicRange range;
|
| + Range range;
|
|
|
|
|
| CoverageBucket();
|
| @@ -2132,7 +2669,7 @@ class CoverageBucket {
|
| meanCoverage = _json["meanCoverage"];
|
| }
|
| if (_json.containsKey("range")) {
|
| - range = new GenomicRange.fromJson(_json["range"]);
|
| + range = new Range.fromJson(_json["range"]);
|
| }
|
| }
|
|
|
| @@ -2166,7 +2703,7 @@ class Dataset {
|
| /**
|
| * The Google Developers Console project number that this dataset belongs to.
|
| */
|
| - core.String projectId;
|
| + core.String projectNumber;
|
|
|
|
|
| Dataset();
|
| @@ -2181,8 +2718,8 @@ class Dataset {
|
| if (_json.containsKey("name")) {
|
| name = _json["name"];
|
| }
|
| - if (_json.containsKey("projectId")) {
|
| - projectId = _json["projectId"];
|
| + if (_json.containsKey("projectNumber")) {
|
| + projectNumber = _json["projectNumber"];
|
| }
|
| }
|
|
|
| @@ -2197,8 +2734,8 @@ class Dataset {
|
| if (name != null) {
|
| _json["name"] = name;
|
| }
|
| - if (projectId != null) {
|
| - _json["projectId"] = projectId;
|
| + if (projectNumber != null) {
|
| + _json["projectNumber"] = projectNumber;
|
| }
|
| return _json;
|
| }
|
| @@ -2208,16 +2745,14 @@ class Dataset {
|
| /** 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.
|
| + * Specifies whether or not to run the alignment pipeline. Either align or
|
| + * callVariants must be set.
|
| */
|
| core.bool align;
|
|
|
| /**
|
| - * Specifies whether or not to run the variant calling pipeline. 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.
|
| + * Specifies whether or not to run the variant calling pipeline. Either align
|
| + * or callVariants must be set.
|
| */
|
| core.bool callVariants;
|
|
|
| @@ -2237,7 +2772,7 @@ class ExperimentalCreateJobRequest {
|
| /**
|
| * Required. The Google Cloud Project ID with which to associate the request.
|
| */
|
| - core.String projectId;
|
| + core.String projectNumber;
|
|
|
| /**
|
| * A list of Google Cloud Storage URIs of data files to operate upon. These
|
| @@ -2263,8 +2798,8 @@ class ExperimentalCreateJobRequest {
|
| if (_json.containsKey("pairedSourceUris")) {
|
| pairedSourceUris = _json["pairedSourceUris"];
|
| }
|
| - if (_json.containsKey("projectId")) {
|
| - projectId = _json["projectId"];
|
| + if (_json.containsKey("projectNumber")) {
|
| + projectNumber = _json["projectNumber"];
|
| }
|
| if (_json.containsKey("sourceUris")) {
|
| sourceUris = _json["sourceUris"];
|
| @@ -2285,8 +2820,8 @@ class ExperimentalCreateJobRequest {
|
| if (pairedSourceUris != null) {
|
| _json["pairedSourceUris"] = pairedSourceUris;
|
| }
|
| - if (projectId != null) {
|
| - _json["projectId"] = projectId;
|
| + if (projectNumber != null) {
|
| + _json["projectNumber"] = projectNumber;
|
| }
|
| if (sourceUris != null) {
|
| _json["sourceUris"] = sourceUris;
|
| @@ -2320,8 +2855,8 @@ class ExperimentalCreateJobResponse {
|
| }
|
|
|
|
|
| -/** The readset export request. */
|
| -class ExportReadsetsRequest {
|
| +/** The read group set export request. */
|
| +class ExportReadGroupSetsRequest {
|
| /**
|
| * A Google Cloud Storage URI where the exported BAM file will be created. The
|
| * currently authenticated user must have write access to the new file
|
| @@ -2330,10 +2865,10 @@ class ExportReadsetsRequest {
|
| core.String exportUri;
|
|
|
| /** The Google Developers Console project number that owns this export. */
|
| - core.String projectId;
|
| + core.String projectNumber;
|
|
|
| - /** The IDs of the readsets to export. */
|
| - core.List<core.String> readsetIds;
|
| + /** The IDs of the read group sets to export. */
|
| + core.List<core.String> readGroupSetIds;
|
|
|
| /**
|
| * The reference names to export. If this is not specified, all reference
|
| @@ -2343,17 +2878,17 @@ class ExportReadsetsRequest {
|
| core.List<core.String> referenceNames;
|
|
|
|
|
| - ExportReadsetsRequest();
|
| + ExportReadGroupSetsRequest();
|
|
|
| - ExportReadsetsRequest.fromJson(core.Map _json) {
|
| + ExportReadGroupSetsRequest.fromJson(core.Map _json) {
|
| if (_json.containsKey("exportUri")) {
|
| exportUri = _json["exportUri"];
|
| }
|
| - if (_json.containsKey("projectId")) {
|
| - projectId = _json["projectId"];
|
| + if (_json.containsKey("projectNumber")) {
|
| + projectNumber = _json["projectNumber"];
|
| }
|
| - if (_json.containsKey("readsetIds")) {
|
| - readsetIds = _json["readsetIds"];
|
| + if (_json.containsKey("readGroupSetIds")) {
|
| + readGroupSetIds = _json["readGroupSetIds"];
|
| }
|
| if (_json.containsKey("referenceNames")) {
|
| referenceNames = _json["referenceNames"];
|
| @@ -2365,11 +2900,11 @@ class ExportReadsetsRequest {
|
| if (exportUri != null) {
|
| _json["exportUri"] = exportUri;
|
| }
|
| - if (projectId != null) {
|
| - _json["projectId"] = projectId;
|
| + if (projectNumber != null) {
|
| + _json["projectNumber"] = projectNumber;
|
| }
|
| - if (readsetIds != null) {
|
| - _json["readsetIds"] = readsetIds;
|
| + if (readGroupSetIds != null) {
|
| + _json["readGroupSetIds"] = readGroupSetIds;
|
| }
|
| if (referenceNames != null) {
|
| _json["referenceNames"] = referenceNames;
|
| @@ -2379,15 +2914,15 @@ class ExportReadsetsRequest {
|
| }
|
|
|
|
|
| -/** The readset export response. */
|
| -class ExportReadsetsResponse {
|
| +/** The read group set export response. */
|
| +class ExportReadGroupSetsResponse {
|
| /** A job ID that can be used to get status information. */
|
| core.String jobId;
|
|
|
|
|
| - ExportReadsetsResponse();
|
| + ExportReadGroupSetsResponse();
|
|
|
| - ExportReadsetsResponse.fromJson(core.Map _json) {
|
| + ExportReadGroupSetsResponse.fromJson(core.Map _json) {
|
| if (_json.containsKey("jobId")) {
|
| jobId = _json["jobId"];
|
| }
|
| @@ -2404,7 +2939,7 @@ class ExportReadsetsResponse {
|
|
|
|
|
| /** The variant data export request. */
|
| -class ExportVariantsRequest {
|
| +class ExportVariantSetRequest {
|
| /**
|
| * The BigQuery dataset to export data to. Note that this is distinct from the
|
| * Genomics concept of "dataset".
|
| @@ -2426,7 +2961,7 @@ class ExportVariantsRequest {
|
| /**
|
| * The format for the exported data.
|
| * Possible string values are:
|
| - * - "bigquery"
|
| + * - "BIGQUERY"
|
| */
|
| core.String format;
|
|
|
| @@ -2435,18 +2970,12 @@ class ExportVariantsRequest {
|
| * 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;
|
| + core.String projectNumber;
|
|
|
|
|
| - ExportVariantsRequest();
|
| + ExportVariantSetRequest();
|
|
|
| - ExportVariantsRequest.fromJson(core.Map _json) {
|
| + ExportVariantSetRequest.fromJson(core.Map _json) {
|
| if (_json.containsKey("bigqueryDataset")) {
|
| bigqueryDataset = _json["bigqueryDataset"];
|
| }
|
| @@ -2459,11 +2988,8 @@ class ExportVariantsRequest {
|
| if (_json.containsKey("format")) {
|
| format = _json["format"];
|
| }
|
| - if (_json.containsKey("projectId")) {
|
| - projectId = _json["projectId"];
|
| - }
|
| - if (_json.containsKey("variantSetId")) {
|
| - variantSetId = _json["variantSetId"];
|
| + if (_json.containsKey("projectNumber")) {
|
| + projectNumber = _json["projectNumber"];
|
| }
|
| }
|
|
|
| @@ -2475,229 +3001,139 @@ class ExportVariantsRequest {
|
| 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 (callSetIds != null) {
|
| + _json["callSetIds"] = callSetIds;
|
| }
|
| - if (sequenceName != null) {
|
| - _json["sequenceName"] = sequenceName;
|
| + if (format != null) {
|
| + _json["format"] = format;
|
| }
|
| - if (sequenceStart != null) {
|
| - _json["sequenceStart"] = sequenceStart;
|
| + if (projectNumber != null) {
|
| + _json["projectNumber"] = projectNumber;
|
| }
|
| return _json;
|
| }
|
| }
|
|
|
|
|
| -/** Not documented yet. */
|
| -class Header {
|
| - /** (SO) Sorting order of alignments. */
|
| - core.String sortingOrder;
|
| -
|
| - /** (VN) BAM format version. */
|
| - core.String version;
|
| +/** The variant data export response. */
|
| +class ExportVariantSetResponse {
|
| + /** A job ID that can be used to get status information. */
|
| + core.String jobId;
|
|
|
|
|
| - Header();
|
| + ExportVariantSetResponse();
|
|
|
| - Header.fromJson(core.Map _json) {
|
| - if (_json.containsKey("sortingOrder")) {
|
| - sortingOrder = _json["sortingOrder"];
|
| - }
|
| - if (_json.containsKey("version")) {
|
| - version = _json["version"];
|
| + ExportVariantSetResponse.fromJson(core.Map _json) {
|
| + if (_json.containsKey("jobId")) {
|
| + jobId = _json["jobId"];
|
| }
|
| }
|
|
|
| core.Map toJson() {
|
| var _json = new core.Map();
|
| - if (sortingOrder != null) {
|
| - _json["sortingOrder"] = sortingOrder;
|
| - }
|
| - if (version != null) {
|
| - _json["version"] = version;
|
| + if (jobId != null) {
|
| + _json["jobId"] = jobId;
|
| }
|
| return _json;
|
| }
|
| }
|
|
|
|
|
| -/** The header section of the BAM/SAM file. */
|
| -class HeaderSection {
|
| - /** (@CO) One-line text comments. */
|
| - core.List<core.String> comments;
|
| +/** Not documented yet. */
|
| +class FastqMetadata {
|
| + /** Optionally specifies the library name for alignment from FASTQ. */
|
| + core.String libraryName;
|
|
|
| /**
|
| - * [Deprecated] This field is deprecated and will no longer be populated.
|
| - * Please use filename instead.
|
| + * Optionally specifies the platform name for alignment from FASTQ. For
|
| + * example: CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT, PACBIO.
|
| */
|
| - 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;
|
| + core.String platformName;
|
|
|
| - /** (@PG) Programs. */
|
| - core.List<Program> programs;
|
| + /**
|
| + * Optionally specifies the platform unit for alignment from FASTQ. For
|
| + * example: flowcell-barcode.lane for Illumina or slide for SOLID.
|
| + */
|
| + core.String platformUnit;
|
|
|
| - /** (@RG) Read group. */
|
| - core.List<ReadGroup> readGroups;
|
| + /** Optionally specifies the read group name for alignment from FASTQ. */
|
| + core.String readGroupName;
|
|
|
| - /** (@SQ) Reference sequence dictionary. */
|
| - core.List<ReferenceSequence> refSequences;
|
| + /** Optionally specifies the sample name for alignment from FASTQ. */
|
| + core.String sampleName;
|
|
|
|
|
| - HeaderSection();
|
| + FastqMetadata();
|
|
|
| - HeaderSection.fromJson(core.Map _json) {
|
| - if (_json.containsKey("comments")) {
|
| - comments = _json["comments"];
|
| + FastqMetadata.fromJson(core.Map _json) {
|
| + if (_json.containsKey("libraryName")) {
|
| + libraryName = _json["libraryName"];
|
| }
|
| - if (_json.containsKey("fileUri")) {
|
| - fileUri = _json["fileUri"];
|
| + if (_json.containsKey("platformName")) {
|
| + platformName = _json["platformName"];
|
| }
|
| - 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("platformUnit")) {
|
| + platformUnit = _json["platformUnit"];
|
| }
|
| - if (_json.containsKey("readGroups")) {
|
| - readGroups = _json["readGroups"].map((value) => new ReadGroup.fromJson(value)).toList();
|
| + if (_json.containsKey("readGroupName")) {
|
| + readGroupName = _json["readGroupName"];
|
| }
|
| - if (_json.containsKey("refSequences")) {
|
| - refSequences = _json["refSequences"].map((value) => new ReferenceSequence.fromJson(value)).toList();
|
| + if (_json.containsKey("sampleName")) {
|
| + sampleName = _json["sampleName"];
|
| }
|
| }
|
|
|
| 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 (libraryName != null) {
|
| + _json["libraryName"] = libraryName;
|
| }
|
| - if (headers != null) {
|
| - _json["headers"] = headers.map((value) => (value).toJson()).toList();
|
| + if (platformName != null) {
|
| + _json["platformName"] = platformName;
|
| }
|
| - if (programs != null) {
|
| - _json["programs"] = programs.map((value) => (value).toJson()).toList();
|
| + if (platformUnit != null) {
|
| + _json["platformUnit"] = platformUnit;
|
| }
|
| - if (readGroups != null) {
|
| - _json["readGroups"] = readGroups.map((value) => (value).toJson()).toList();
|
| + if (readGroupName != null) {
|
| + _json["readGroupName"] = readGroupName;
|
| }
|
| - if (refSequences != null) {
|
| - _json["refSequences"] = refSequences.map((value) => (value).toJson()).toList();
|
| + if (sampleName != null) {
|
| + _json["sampleName"] = sampleName;
|
| }
|
| return _json;
|
| }
|
| }
|
|
|
|
|
| -/** The readset import request. */
|
| -class ImportReadsetsRequest {
|
| +/** The read group set import request. */
|
| +class ImportReadGroupSetsRequest {
|
| /**
|
| - * Required. The ID of the dataset these readsets will belong to. The caller
|
| - * must have WRITE permissions to this dataset.
|
| + * Required. The ID of the dataset these read group sets will belong to. The
|
| + * caller must have WRITE permissions to this dataset.
|
| */
|
| core.String datasetId;
|
|
|
| + /**
|
| + * The reference set to which the imported read group sets are aligned to, if
|
| + * any. The reference names of this reference set must be a superset of those
|
| + * found in the imported file headers. If no reference set id is provided, a
|
| + * best effort is made to associate with a matching reference set.
|
| + */
|
| + core.String referenceSetId;
|
| +
|
| /** A list of URIs pointing at BAM files in Google Cloud Storage. */
|
| core.List<core.String> sourceUris;
|
|
|
|
|
| - ImportReadsetsRequest();
|
| + ImportReadGroupSetsRequest();
|
|
|
| - ImportReadsetsRequest.fromJson(core.Map _json) {
|
| + ImportReadGroupSetsRequest.fromJson(core.Map _json) {
|
| if (_json.containsKey("datasetId")) {
|
| datasetId = _json["datasetId"];
|
| }
|
| + if (_json.containsKey("referenceSetId")) {
|
| + referenceSetId = _json["referenceSetId"];
|
| + }
|
| if (_json.containsKey("sourceUris")) {
|
| sourceUris = _json["sourceUris"];
|
| }
|
| @@ -2708,6 +3144,9 @@ class ImportReadsetsRequest {
|
| if (datasetId != null) {
|
| _json["datasetId"] = datasetId;
|
| }
|
| + if (referenceSetId != null) {
|
| + _json["referenceSetId"] = referenceSetId;
|
| + }
|
| if (sourceUris != null) {
|
| _json["sourceUris"] = sourceUris;
|
| }
|
| @@ -2716,15 +3155,15 @@ class ImportReadsetsRequest {
|
| }
|
|
|
|
|
| -/** The readset import response. */
|
| -class ImportReadsetsResponse {
|
| +/** The read group set import response. */
|
| +class ImportReadGroupSetsResponse {
|
| /** A job ID that can be used to get status information. */
|
| core.String jobId;
|
|
|
|
|
| - ImportReadsetsResponse();
|
| + ImportReadGroupSetsResponse();
|
|
|
| - ImportReadsetsResponse.fromJson(core.Map _json) {
|
| + ImportReadGroupSetsResponse.fromJson(core.Map _json) {
|
| if (_json.containsKey("jobId")) {
|
| jobId = _json["jobId"];
|
| }
|
| @@ -2745,8 +3184,8 @@ class ImportVariantsRequest {
|
| /**
|
| * The format of the variant data being imported.
|
| * Possible string values are:
|
| - * - "completeGenomics"
|
| - * - "vcf"
|
| + * - "COMPLETE_GENOMICS"
|
| + * - "VCF"
|
| */
|
| core.String format;
|
|
|
| @@ -2756,9 +3195,6 @@ class ImportVariantsRequest {
|
| */
|
| core.List<core.String> sourceUris;
|
|
|
| - /** Required. The variant set to which variant data should be imported. */
|
| - core.String variantSetId;
|
| -
|
|
|
| ImportVariantsRequest();
|
|
|
| @@ -2769,9 +3205,6 @@ class ImportVariantsRequest {
|
| if (_json.containsKey("sourceUris")) {
|
| sourceUris = _json["sourceUris"];
|
| }
|
| - if (_json.containsKey("variantSetId")) {
|
| - variantSetId = _json["variantSetId"];
|
| - }
|
| }
|
|
|
| core.Map toJson() {
|
| @@ -2782,9 +3215,6 @@ class ImportVariantsRequest {
|
| if (sourceUris != null) {
|
| _json["sourceUris"] = sourceUris;
|
| }
|
| - if (variantSetId != null) {
|
| - _json["variantSetId"] = variantSetId;
|
| - }
|
| return _json;
|
| }
|
| }
|
| @@ -2814,6 +3244,46 @@ class ImportVariantsResponse {
|
| }
|
|
|
|
|
| +/** Describes an interleaved FASTQ file source for alignment. */
|
| +class InterleavedFastqSource {
|
| + /**
|
| + * Optionally specifies the metadata to be associated with the final aligned
|
| + * read group set.
|
| + */
|
| + FastqMetadata metadata;
|
| +
|
| + /**
|
| + * A list of URIs pointing at interleaved FASTQ files in Google Cloud Storage
|
| + * which will be aligned. The caller must have READ permissions for these
|
| + * files.
|
| + */
|
| + core.List<core.String> sourceUris;
|
| +
|
| +
|
| + InterleavedFastqSource();
|
| +
|
| + InterleavedFastqSource.fromJson(core.Map _json) {
|
| + if (_json.containsKey("metadata")) {
|
| + metadata = new FastqMetadata.fromJson(_json["metadata"]);
|
| + }
|
| + if (_json.containsKey("sourceUris")) {
|
| + sourceUris = _json["sourceUris"];
|
| + }
|
| + }
|
| +
|
| + core.Map toJson() {
|
| + var _json = new core.Map();
|
| + if (metadata != null) {
|
| + _json["metadata"] = (metadata).toJson();
|
| + }
|
| + if (sourceUris != null) {
|
| + _json["sourceUris"] = sourceUris;
|
| + }
|
| + return _json;
|
| + }
|
| +}
|
| +
|
| +
|
| /**
|
| * A Job represents an ongoing process that can be monitored for status
|
| * information.
|
| @@ -2823,7 +3293,7 @@ class Job {
|
| core.String created;
|
|
|
| /** A more detailed description of this job's current status. */
|
| - core.String description;
|
| + core.String detailedStatus;
|
|
|
| /** Any errors that occurred during processing. */
|
| core.List<core.String> errors;
|
| @@ -2840,7 +3310,7 @@ class Job {
|
| /**
|
| * The Google Developers Console project number to which this job belongs.
|
| */
|
| - core.String projectId;
|
| + core.String projectNumber;
|
|
|
| /** A summarized representation of the original service request. */
|
| JobRequest request;
|
| @@ -2848,13 +3318,13 @@ class Job {
|
| /**
|
| * The status of this job.
|
| * Possible string values are:
|
| - * - "canceled"
|
| - * - "failure"
|
| - * - "new"
|
| - * - "pending"
|
| - * - "running"
|
| - * - "success"
|
| - * - "unknownStatus"
|
| + * - "CANCELED"
|
| + * - "FAILURE"
|
| + * - "NEW"
|
| + * - "PENDING"
|
| + * - "RUNNING"
|
| + * - "SUCCESS"
|
| + * - "UNKNOWN_STATUS"
|
| */
|
| core.String status;
|
|
|
| @@ -2868,8 +3338,8 @@ class Job {
|
| if (_json.containsKey("created")) {
|
| created = _json["created"];
|
| }
|
| - if (_json.containsKey("description")) {
|
| - description = _json["description"];
|
| + if (_json.containsKey("detailedStatus")) {
|
| + detailedStatus = _json["detailedStatus"];
|
| }
|
| if (_json.containsKey("errors")) {
|
| errors = _json["errors"];
|
| @@ -2880,8 +3350,8 @@ class Job {
|
| if (_json.containsKey("importedIds")) {
|
| importedIds = _json["importedIds"];
|
| }
|
| - if (_json.containsKey("projectId")) {
|
| - projectId = _json["projectId"];
|
| + if (_json.containsKey("projectNumber")) {
|
| + projectNumber = _json["projectNumber"];
|
| }
|
| if (_json.containsKey("request")) {
|
| request = new JobRequest.fromJson(_json["request"]);
|
| @@ -2899,8 +3369,8 @@ class Job {
|
| if (created != null) {
|
| _json["created"] = created;
|
| }
|
| - if (description != null) {
|
| - _json["description"] = description;
|
| + if (detailedStatus != null) {
|
| + _json["detailedStatus"] = detailedStatus;
|
| }
|
| if (errors != null) {
|
| _json["errors"] = errors;
|
| @@ -2911,8 +3381,8 @@ class Job {
|
| if (importedIds != null) {
|
| _json["importedIds"] = importedIds;
|
| }
|
| - if (projectId != null) {
|
| - _json["projectId"] = projectId;
|
| + if (projectNumber != null) {
|
| + _json["projectNumber"] = projectNumber;
|
| }
|
| if (request != null) {
|
| _json["request"] = (request).toJson();
|
| @@ -2945,12 +3415,14 @@ class JobRequest {
|
| /**
|
| * The original request type.
|
| * Possible string values are:
|
| - * - "experimentalCreateJob"
|
| - * - "exportReadsets"
|
| - * - "exportVariants"
|
| - * - "importReadsets"
|
| - * - "importVariants"
|
| - * - "unknownType"
|
| + * - "ALIGN_READSETS"
|
| + * - "CALL_READSETS"
|
| + * - "EXPERIMENTAL_CREATE_JOB"
|
| + * - "EXPORT_READSETS"
|
| + * - "EXPORT_VARIANTS"
|
| + * - "IMPORT_READSETS"
|
| + * - "IMPORT_VARIANTS"
|
| + * - "UNKNOWN_TYPE"
|
| */
|
| core.String type;
|
|
|
| @@ -2985,6 +3457,106 @@ class JobRequest {
|
| }
|
|
|
|
|
| +/**
|
| + * A linear alignment can be represented by one CIGAR string. Describes the
|
| + * mapped position and local alignment of the read to the reference.
|
| + */
|
| +class LinearAlignment {
|
| + /**
|
| + * Represents the local alignment of this sequence (alignment matches, indels,
|
| + * etc) against the reference.
|
| + */
|
| + core.List<CigarUnit> cigar;
|
| +
|
| + /**
|
| + * The mapping quality of this alignment. Represents how likely the read maps
|
| + * to this position as opposed to other locations.
|
| + */
|
| + core.int mappingQuality;
|
| +
|
| + /** The position of this alignment. */
|
| + Position position;
|
| +
|
| +
|
| + LinearAlignment();
|
| +
|
| + LinearAlignment.fromJson(core.Map _json) {
|
| + if (_json.containsKey("cigar")) {
|
| + cigar = _json["cigar"].map((value) => new CigarUnit.fromJson(value)).toList();
|
| + }
|
| + if (_json.containsKey("mappingQuality")) {
|
| + mappingQuality = _json["mappingQuality"];
|
| + }
|
| + if (_json.containsKey("position")) {
|
| + position = new Position.fromJson(_json["position"]);
|
| + }
|
| + }
|
| +
|
| + core.Map toJson() {
|
| + var _json = new core.Map();
|
| + if (cigar != null) {
|
| + _json["cigar"] = cigar.map((value) => (value).toJson()).toList();
|
| + }
|
| + if (mappingQuality != null) {
|
| + _json["mappingQuality"] = mappingQuality;
|
| + }
|
| + if (position != null) {
|
| + _json["position"] = (position).toJson();
|
| + }
|
| + return _json;
|
| + }
|
| +}
|
| +
|
| +
|
| +/** Not documented yet. */
|
| +class ListBasesResponse {
|
| + /**
|
| + * The continuation token, which is used to page through large result sets.
|
| + * Provide this value in a subsequent request to return the next page of
|
| + * results. This field will be empty if there aren't any additional results.
|
| + */
|
| + core.String nextPageToken;
|
| +
|
| + /**
|
| + * The offset position (0-based) of the given sequence from the start of this
|
| + * Reference. This value will differ for each page in a paginated request.
|
| + */
|
| + core.String offset;
|
| +
|
| + /** A substring of the bases that make up this reference. */
|
| + core.String sequence;
|
| +
|
| +
|
| + ListBasesResponse();
|
| +
|
| + ListBasesResponse.fromJson(core.Map _json) {
|
| + if (_json.containsKey("nextPageToken")) {
|
| + nextPageToken = _json["nextPageToken"];
|
| + }
|
| + if (_json.containsKey("offset")) {
|
| + offset = _json["offset"];
|
| + }
|
| + if (_json.containsKey("sequence")) {
|
| + sequence = _json["sequence"];
|
| + }
|
| + }
|
| +
|
| + core.Map toJson() {
|
| + var _json = new core.Map();
|
| + if (nextPageToken != null) {
|
| + _json["nextPageToken"] = nextPageToken;
|
| + }
|
| + if (offset != null) {
|
| + _json["offset"] = offset;
|
| + }
|
| + if (sequence != null) {
|
| + _json["sequence"] = sequence;
|
| + }
|
| + return _json;
|
| + }
|
| +}
|
| +
|
| +
|
| /** Not documented yet. */
|
| class ListCoverageBucketsResponse {
|
| /**
|
| @@ -3134,12 +3706,12 @@ class Metadata {
|
| * The type of data. Possible types include: Integer, Float, Flag, Character,
|
| * and String.
|
| * Possible string values are:
|
| - * - "character"
|
| - * - "flag"
|
| - * - "float"
|
| - * - "integer"
|
| - * - "string"
|
| - * - "unknownType"
|
| + * - "CHARACTER"
|
| + * - "FLAG"
|
| + * - "FLOAT"
|
| + * - "INTEGER"
|
| + * - "STRING"
|
| + * - "UNKNOWN_TYPE"
|
| */
|
| core.String type;
|
|
|
| @@ -3201,60 +3773,159 @@ class Metadata {
|
| }
|
|
|
|
|
| -/** Not documented yet. */
|
| -class Program {
|
| - /** (CL) Command line. */
|
| - core.String commandLine;
|
| -
|
| - /** (ID) Program record identifier. */
|
| - core.String id;
|
| +/** Describes a paired-end FASTQ file source for alignment. */
|
| +class PairedFastqSource {
|
| + /**
|
| + * A list of URIs pointing at paired end FASTQ files in Google Cloud Storage
|
| + * which will be aligned. The first of each paired file should be specified
|
| + * here, in an order that matches the second of each paired file specified in
|
| + * secondSourceUris. For example: firstSourceUris: [file1_1.fq, file2_1.fq],
|
| + * secondSourceUris: [file1_2.fq, file2_2.fq]. The caller must have READ
|
| + * permissions for these files.
|
| + */
|
| + core.List<core.String> firstSourceUris;
|
|
|
| - /** (PN) Program name. */
|
| - core.String name;
|
| + /**
|
| + * Optionally specifies the metadata to be associated with the final aligned
|
| + * read group set.
|
| + */
|
| + FastqMetadata metadata;
|
|
|
| - /** (PP) Previous program ID. */
|
| - core.String prevProgramId;
|
| + /**
|
| + * A list of URIs pointing at paired end FASTQ files in Google Cloud Storage
|
| + * which will be aligned. The second of each paired file should be specified
|
| + * here, in an order that matches the first of each paired file specified in
|
| + * firstSourceUris. For example: firstSourceUris: [file1_1.fq, file2_1.fq],
|
| + * secondSourceUris: [file1_2.fq, file2_2.fq]. The caller must have READ
|
| + * permissions for these files.
|
| + */
|
| + core.List<core.String> secondSourceUris;
|
|
|
| - /** (VN) Program version. */
|
| - core.String version;
|
|
|
| + PairedFastqSource();
|
|
|
| - Program();
|
| + PairedFastqSource.fromJson(core.Map _json) {
|
| + if (_json.containsKey("firstSourceUris")) {
|
| + firstSourceUris = _json["firstSourceUris"];
|
| + }
|
| + if (_json.containsKey("metadata")) {
|
| + metadata = new FastqMetadata.fromJson(_json["metadata"]);
|
| + }
|
| + if (_json.containsKey("secondSourceUris")) {
|
| + secondSourceUris = _json["secondSourceUris"];
|
| + }
|
| + }
|
|
|
| - Program.fromJson(core.Map _json) {
|
| - if (_json.containsKey("commandLine")) {
|
| - commandLine = _json["commandLine"];
|
| + core.Map toJson() {
|
| + var _json = new core.Map();
|
| + if (firstSourceUris != null) {
|
| + _json["firstSourceUris"] = firstSourceUris;
|
| }
|
| - if (_json.containsKey("id")) {
|
| - id = _json["id"];
|
| + if (metadata != null) {
|
| + _json["metadata"] = (metadata).toJson();
|
| }
|
| - if (_json.containsKey("name")) {
|
| - name = _json["name"];
|
| + if (secondSourceUris != null) {
|
| + _json["secondSourceUris"] = secondSourceUris;
|
| }
|
| - if (_json.containsKey("prevProgramId")) {
|
| - prevProgramId = _json["prevProgramId"];
|
| + return _json;
|
| + }
|
| +}
|
| +
|
| +
|
| +/**
|
| + * An abstraction for referring to a genomic position, in relation to some
|
| + * already known reference. For now, represents a genomic position as a
|
| + * reference name, a base number on that reference (0-based), and a
|
| + * determination of forward or reverse strand.
|
| + */
|
| +class Position {
|
| + /**
|
| + * The 0-based offset from the start of the forward strand for that reference.
|
| + */
|
| + core.String position;
|
| +
|
| + /** The name of the reference in whatever reference set is being used. */
|
| + core.String referenceName;
|
| +
|
| + /**
|
| + * Whether this position is on the reverse strand, as opposed to the forward
|
| + * strand.
|
| + */
|
| + core.bool reverseStrand;
|
| +
|
| +
|
| + Position();
|
| +
|
| + Position.fromJson(core.Map _json) {
|
| + if (_json.containsKey("position")) {
|
| + position = _json["position"];
|
| }
|
| - if (_json.containsKey("version")) {
|
| - version = _json["version"];
|
| + if (_json.containsKey("referenceName")) {
|
| + referenceName = _json["referenceName"];
|
| + }
|
| + if (_json.containsKey("reverseStrand")) {
|
| + reverseStrand = _json["reverseStrand"];
|
| }
|
| }
|
|
|
| core.Map toJson() {
|
| var _json = new core.Map();
|
| - if (commandLine != null) {
|
| - _json["commandLine"] = commandLine;
|
| + if (position != null) {
|
| + _json["position"] = position;
|
| }
|
| - if (id != null) {
|
| - _json["id"] = id;
|
| + if (referenceName != null) {
|
| + _json["referenceName"] = referenceName;
|
| }
|
| - if (name != null) {
|
| - _json["name"] = name;
|
| + if (reverseStrand != null) {
|
| + _json["reverseStrand"] = reverseStrand;
|
| + }
|
| + return _json;
|
| + }
|
| +}
|
| +
|
| +
|
| +/** A 0-based half-open genomic coordinate range over a reference sequence. */
|
| +class Range {
|
| + /**
|
| + * The end position of the range on the reference, 0-based exclusive. If
|
| + * specified, referenceName must also be specified.
|
| + */
|
| + core.String end;
|
| +
|
| + /** The reference sequence name, for example chr1, 1, or chrX. */
|
| + core.String referenceName;
|
| +
|
| + /**
|
| + * The start position of the range on the reference, 0-based inclusive. If
|
| + * specified, referenceName must also be specified.
|
| + */
|
| + core.String start;
|
| +
|
| +
|
| + Range();
|
| +
|
| + Range.fromJson(core.Map _json) {
|
| + if (_json.containsKey("end")) {
|
| + end = _json["end"];
|
| + }
|
| + if (_json.containsKey("referenceName")) {
|
| + referenceName = _json["referenceName"];
|
| + }
|
| + if (_json.containsKey("start")) {
|
| + start = _json["start"];
|
| + }
|
| + }
|
| +
|
| + core.Map toJson() {
|
| + var _json = new core.Map();
|
| + if (end != null) {
|
| + _json["end"] = end;
|
| }
|
| - if (prevProgramId != null) {
|
| - _json["prevProgramId"] = prevProgramId;
|
| + if (referenceName != null) {
|
| + _json["referenceName"] = referenceName;
|
| }
|
| - if (version != null) {
|
| - _json["version"] = version;
|
| + if (start != null) {
|
| + _json["start"] = start;
|
| }
|
| return _json;
|
| }
|
| @@ -3262,345 +3933,527 @@ class Program {
|
|
|
|
|
| /**
|
| - * 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.
|
| + * A read alignment describes a linear alignment of a string of DNA to a
|
| + * reference sequence, in addition to metadata about the fragment (the molecule
|
| + * of DNA sequenced) and the read (the bases which were read by the sequencer).
|
| + * A read is equivalent to a line in a SAM file. A read belongs to exactly one
|
| + * read group and exactly one read group set.
|
| */
|
| class Read {
|
| /**
|
| - * The originalBases after the cigar field has been applied. Deletions are
|
| - * represented with '-' and insertions are omitted.
|
| + * The quality of the read sequence contained in this alignment record.
|
| + * alignedSequence and alignedQuality may be shorter than the full read
|
| + * sequence and quality. This will occur if the alignment is part of a
|
| + * chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR
|
| + * for this read will begin/end with a hard clip operator that will indicate
|
| + * the length of the excised sequence.
|
| */
|
| - core.String alignedBases;
|
| + core.List<core.int> alignedQuality;
|
|
|
| /**
|
| - * 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)
|
| + * The bases of the read sequence contained in this alignment record.
|
| + * alignedSequence and alignedQuality may be shorter than the full read
|
| + * sequence and quality. This will occur if the alignment is part of a
|
| + * chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR
|
| + * for this read will begin/end with a hard clip operator that will indicate
|
| + * the length of the excised sequence.
|
| */
|
| - core.String baseQuality;
|
| + core.String alignedSequence;
|
|
|
| /**
|
| - * A condensed representation of how this read matches up to the reference.
|
| - * (CIGAR)
|
| + * The linear alignment for this alignment record. This field will be null if
|
| + * the read is unmapped.
|
| */
|
| - core.String cigar;
|
| + LinearAlignment alignment;
|
| +
|
| + /** The fragment is a PCR or optical duplicate (SAM flag 0x400) */
|
| + core.bool duplicateFragment;
|
| +
|
| + /** SAM flag 0x200 */
|
| + core.bool failedVendorQualityChecks;
|
| +
|
| + /** The observed length of the fragment, equivalent to TLEN in SAM. */
|
| + core.int fragmentLength;
|
| +
|
| + /** The fragment name. Equivalent to QNAME (query template name) in SAM. */
|
| + core.String fragmentName;
|
|
|
| /**
|
| - * Each bit of this number has a different meaning if enabled. See the full
|
| - * BAM spec for more details. (FLAG)
|
| + * The unique ID for this read. This is a generated unique ID, not to be
|
| + * confused with fragmentName.
|
| */
|
| - core.int flags;
|
| -
|
| - /** The Google generated ID of the read, immutable. */
|
| core.String id;
|
|
|
| + /** A map of additional read alignment information. */
|
| + core.Map<core.String, core.List<core.String>> info;
|
| +
|
| /**
|
| - * A score up to 255 that represents how likely this read's aligned position
|
| - * is to be correct. A higher value is better. (MAPQ)
|
| + * The mapping of the primary alignment of the (readNumber+1)%numberReads read
|
| + * in the fragment. It replaces mate position and mate strand in SAM.
|
| */
|
| - core.int mappingQuality;
|
| + Position nextMatePosition;
|
|
|
| - /** The 1-based start position of the paired read. (PNEXT) */
|
| - core.int matePosition;
|
| + /** The number of reads in the fragment (extension to SAM flag 0x1). */
|
| + core.int numberReads;
|
|
|
| /**
|
| - * The name of the sequence that the paired read is aligned to. This is
|
| - * usually the same as referenceSequenceName. (RNEXT)
|
| + * The orientation and the distance between reads from the fragment are
|
| + * consistent with the sequencing protocol (extension to SAM flag 0x2)
|
| */
|
| - core.String mateReferenceSequenceName;
|
| + core.bool properPlacement;
|
|
|
| /**
|
| - * The name of the read. When imported from a BAM file, this is the query
|
| - * template name. (QNAME)
|
| + * The ID of the read group this read belongs to. (Every read must belong to
|
| + * exactly one read group.)
|
| */
|
| - core.String name;
|
| -
|
| - /** The list of bases that this read represents (such as "CATCGA"). (SEQ) */
|
| - core.String originalBases;
|
| + core.String readGroupId;
|
|
|
| /**
|
| - * 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)
|
| + * The ID of the read group set this read belongs to. (Every read must belong
|
| + * to exactly one read group set.)
|
| */
|
| - core.int position;
|
| -
|
| - /** The ID of the readset this read belongs to. */
|
| - core.String readsetId;
|
| + core.String readGroupSetId;
|
|
|
| /**
|
| - * 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)
|
| + * The read number in sequencing. 0-based and less than numberReads. This
|
| + * field replaces SAM flag 0x40 and 0x80.
|
| */
|
| - core.String referenceSequenceName;
|
| + core.int readNumber;
|
|
|
| - /** A map of additional read information. (TAG) */
|
| - core.Map<core.String, core.List<core.String>> tags;
|
| + /**
|
| + * Whether this alignment is secondary. Equivalent to SAM flag 0x100. A
|
| + * secondary alignment represents an alternative to the primary alignment for
|
| + * this read. Aligners may return secondary alignments if a read can map
|
| + * ambiguously to multiple coordinates in the genome. By convention, each read
|
| + * has one and only one alignment where both secondaryAlignment and
|
| + * supplementaryAlignment are false.
|
| + */
|
| + core.bool secondaryAlignment;
|
|
|
| /**
|
| - * Length of the original piece of DNA that produced both this read and the
|
| - * paired read. (TLEN)
|
| + * Whether this alignment is supplementary. Equivalent to SAM flag 0x800.
|
| + * Supplementary alignments are used in the representation of a chimeric
|
| + * alignment. In a chimeric alignment, a read is split into multiple linear
|
| + * alignments that map to different reference contigs. The first linear
|
| + * alignment in the read will be designated as the representative alignment;
|
| + * the remaining linear alignments will be designated as supplementary
|
| + * alignments. These alignments may have different mapping quality scores. In
|
| + * each linear alignment in a chimeric alignment, the read will be hard
|
| + * clipped. The alignedSequence and alignedQuality fields in the alignment
|
| + * record will only represent the bases for its respective linear alignment.
|
| */
|
| - core.int templateLength;
|
| + core.bool supplementaryAlignment;
|
|
|
|
|
| Read();
|
|
|
| Read.fromJson(core.Map _json) {
|
| - if (_json.containsKey("alignedBases")) {
|
| - alignedBases = _json["alignedBases"];
|
| + if (_json.containsKey("alignedQuality")) {
|
| + alignedQuality = _json["alignedQuality"];
|
| }
|
| - if (_json.containsKey("baseQuality")) {
|
| - baseQuality = _json["baseQuality"];
|
| + if (_json.containsKey("alignedSequence")) {
|
| + alignedSequence = _json["alignedSequence"];
|
| }
|
| - if (_json.containsKey("cigar")) {
|
| - cigar = _json["cigar"];
|
| + if (_json.containsKey("alignment")) {
|
| + alignment = new LinearAlignment.fromJson(_json["alignment"]);
|
| }
|
| - if (_json.containsKey("flags")) {
|
| - flags = _json["flags"];
|
| + if (_json.containsKey("duplicateFragment")) {
|
| + duplicateFragment = _json["duplicateFragment"];
|
| + }
|
| + if (_json.containsKey("failedVendorQualityChecks")) {
|
| + failedVendorQualityChecks = _json["failedVendorQualityChecks"];
|
| + }
|
| + if (_json.containsKey("fragmentLength")) {
|
| + fragmentLength = _json["fragmentLength"];
|
| + }
|
| + if (_json.containsKey("fragmentName")) {
|
| + fragmentName = _json["fragmentName"];
|
| }
|
| if (_json.containsKey("id")) {
|
| id = _json["id"];
|
| }
|
| - if (_json.containsKey("mappingQuality")) {
|
| - mappingQuality = _json["mappingQuality"];
|
| - }
|
| - if (_json.containsKey("matePosition")) {
|
| - matePosition = _json["matePosition"];
|
| + if (_json.containsKey("info")) {
|
| + info = _json["info"];
|
| }
|
| - if (_json.containsKey("mateReferenceSequenceName")) {
|
| - mateReferenceSequenceName = _json["mateReferenceSequenceName"];
|
| + if (_json.containsKey("nextMatePosition")) {
|
| + nextMatePosition = new Position.fromJson(_json["nextMatePosition"]);
|
| }
|
| - if (_json.containsKey("name")) {
|
| - name = _json["name"];
|
| + if (_json.containsKey("numberReads")) {
|
| + numberReads = _json["numberReads"];
|
| }
|
| - if (_json.containsKey("originalBases")) {
|
| - originalBases = _json["originalBases"];
|
| + if (_json.containsKey("properPlacement")) {
|
| + properPlacement = _json["properPlacement"];
|
| }
|
| - if (_json.containsKey("position")) {
|
| - position = _json["position"];
|
| + if (_json.containsKey("readGroupId")) {
|
| + readGroupId = _json["readGroupId"];
|
| }
|
| - if (_json.containsKey("readsetId")) {
|
| - readsetId = _json["readsetId"];
|
| + if (_json.containsKey("readGroupSetId")) {
|
| + readGroupSetId = _json["readGroupSetId"];
|
| }
|
| - if (_json.containsKey("referenceSequenceName")) {
|
| - referenceSequenceName = _json["referenceSequenceName"];
|
| + if (_json.containsKey("readNumber")) {
|
| + readNumber = _json["readNumber"];
|
| }
|
| - if (_json.containsKey("tags")) {
|
| - tags = _json["tags"];
|
| + if (_json.containsKey("secondaryAlignment")) {
|
| + secondaryAlignment = _json["secondaryAlignment"];
|
| }
|
| - if (_json.containsKey("templateLength")) {
|
| - templateLength = _json["templateLength"];
|
| + if (_json.containsKey("supplementaryAlignment")) {
|
| + supplementaryAlignment = _json["supplementaryAlignment"];
|
| }
|
| }
|
|
|
| core.Map toJson() {
|
| var _json = new core.Map();
|
| - if (alignedBases != null) {
|
| - _json["alignedBases"] = alignedBases;
|
| + if (alignedQuality != null) {
|
| + _json["alignedQuality"] = alignedQuality;
|
| }
|
| - if (baseQuality != null) {
|
| - _json["baseQuality"] = baseQuality;
|
| + if (alignedSequence != null) {
|
| + _json["alignedSequence"] = alignedSequence;
|
| }
|
| - if (cigar != null) {
|
| - _json["cigar"] = cigar;
|
| + if (alignment != null) {
|
| + _json["alignment"] = (alignment).toJson();
|
| + }
|
| + if (duplicateFragment != null) {
|
| + _json["duplicateFragment"] = duplicateFragment;
|
| + }
|
| + if (failedVendorQualityChecks != null) {
|
| + _json["failedVendorQualityChecks"] = failedVendorQualityChecks;
|
| + }
|
| + if (fragmentLength != null) {
|
| + _json["fragmentLength"] = fragmentLength;
|
| }
|
| - if (flags != null) {
|
| - _json["flags"] = flags;
|
| + if (fragmentName != null) {
|
| + _json["fragmentName"] = fragmentName;
|
| }
|
| if (id != null) {
|
| _json["id"] = id;
|
| }
|
| - if (mappingQuality != null) {
|
| - _json["mappingQuality"] = mappingQuality;
|
| - }
|
| - if (matePosition != null) {
|
| - _json["matePosition"] = matePosition;
|
| + if (info != null) {
|
| + _json["info"] = info;
|
| }
|
| - if (mateReferenceSequenceName != null) {
|
| - _json["mateReferenceSequenceName"] = mateReferenceSequenceName;
|
| + if (nextMatePosition != null) {
|
| + _json["nextMatePosition"] = (nextMatePosition).toJson();
|
| }
|
| - if (name != null) {
|
| - _json["name"] = name;
|
| + if (numberReads != null) {
|
| + _json["numberReads"] = numberReads;
|
| }
|
| - if (originalBases != null) {
|
| - _json["originalBases"] = originalBases;
|
| + if (properPlacement != null) {
|
| + _json["properPlacement"] = properPlacement;
|
| }
|
| - if (position != null) {
|
| - _json["position"] = position;
|
| + if (readGroupId != null) {
|
| + _json["readGroupId"] = readGroupId;
|
| }
|
| - if (readsetId != null) {
|
| - _json["readsetId"] = readsetId;
|
| + if (readGroupSetId != null) {
|
| + _json["readGroupSetId"] = readGroupSetId;
|
| }
|
| - if (referenceSequenceName != null) {
|
| - _json["referenceSequenceName"] = referenceSequenceName;
|
| + if (readNumber != null) {
|
| + _json["readNumber"] = readNumber;
|
| }
|
| - if (tags != null) {
|
| - _json["tags"] = tags;
|
| + if (secondaryAlignment != null) {
|
| + _json["secondaryAlignment"] = secondaryAlignment;
|
| }
|
| - if (templateLength != null) {
|
| - _json["templateLength"] = templateLength;
|
| + if (supplementaryAlignment != null) {
|
| + _json["supplementaryAlignment"] = supplementaryAlignment;
|
| }
|
| return _json;
|
| }
|
| }
|
|
|
|
|
| -/** Not documented yet. */
|
| +/**
|
| + * A read group is all the data that's processed the same way by the sequencer.
|
| + */
|
| class ReadGroup {
|
| - /** (DT) Date the run was produced (ISO8601 date or date/time). */
|
| - core.String date;
|
| + /** The ID of the dataset this read group belongs to. */
|
| + core.String datasetId;
|
|
|
| - /** (DS) Description. */
|
| + /** A free-form text description of this read group. */
|
| core.String description;
|
|
|
| + /** The experiment used to generate this read group. */
|
| + ReadGroupExperiment experiment;
|
| +
|
| /**
|
| - * (FO) Flow order. The array of nucleotide bases that correspond to the
|
| - * nucleotides used for each flow of each read.
|
| + * The generated unique read group ID. Note: This is different than the @RG ID
|
| + * field in the SAM spec. For that value, see the name field.
|
| */
|
| - core.String flowOrder;
|
| -
|
| - /** (ID) Read group identifier. */
|
| core.String id;
|
|
|
| + /** A map of additional read group information. */
|
| + core.Map<core.String, core.List<core.String>> info;
|
| +
|
| /**
|
| - * (KS) The array of nucleotide bases that correspond to the key sequence of
|
| - * each read.
|
| + * The read group name. This corresponds to the @RG ID field in the SAM spec.
|
| */
|
| - core.String keySequence;
|
| -
|
| - /** (LS) Library. */
|
| - core.String library;
|
| -
|
| - /** (PU) Platform unit. */
|
| - core.String platformUnit;
|
| + core.String name;
|
|
|
| - /** (PI) Predicted median insert size. */
|
| + /**
|
| + * The predicted insert size of this read group. The insert size is the length
|
| + * the sequenced DNA fragment from end-to-end, not including the adapters.
|
| + */
|
| core.int predictedInsertSize;
|
|
|
| - /** (PG) Programs used for processing the read group. */
|
| - core.String processingProgram;
|
| -
|
| - /** (SM) Sample. */
|
| - core.String sample;
|
| + /**
|
| + * The programs used to generate this read group. Programs are always
|
| + * identical for all read groups within a read group set. For this reason,
|
| + * only the first read group in a returned set will have this field populated.
|
| + */
|
| + core.List<ReadGroupProgram> programs;
|
|
|
| - /** (CN) Name of sequencing center producing the read. */
|
| - core.String sequencingCenterName;
|
| + /**
|
| + * The reference set the reads in this read group are aligned to. Required if
|
| + * there are any read alignments.
|
| + */
|
| + core.String referenceSetId;
|
|
|
| - /** (PL) Platform/technology used to produce the reads. */
|
| - core.String sequencingTechnology;
|
| + /**
|
| + * The sample this read group's data was generated from. Note: This is not an
|
| + * actual ID within this repository, but rather an identifier for a sample
|
| + * which may be meaningful to some external system.
|
| + */
|
| + core.String sampleId;
|
|
|
|
|
| ReadGroup();
|
|
|
| ReadGroup.fromJson(core.Map _json) {
|
| - if (_json.containsKey("date")) {
|
| - date = _json["date"];
|
| + if (_json.containsKey("datasetId")) {
|
| + datasetId = _json["datasetId"];
|
| }
|
| if (_json.containsKey("description")) {
|
| description = _json["description"];
|
| }
|
| - if (_json.containsKey("flowOrder")) {
|
| - flowOrder = _json["flowOrder"];
|
| + if (_json.containsKey("experiment")) {
|
| + experiment = new ReadGroupExperiment.fromJson(_json["experiment"]);
|
| }
|
| if (_json.containsKey("id")) {
|
| id = _json["id"];
|
| }
|
| - if (_json.containsKey("keySequence")) {
|
| - keySequence = _json["keySequence"];
|
| - }
|
| - if (_json.containsKey("library")) {
|
| - library = _json["library"];
|
| + if (_json.containsKey("info")) {
|
| + info = _json["info"];
|
| }
|
| - if (_json.containsKey("platformUnit")) {
|
| - platformUnit = _json["platformUnit"];
|
| + if (_json.containsKey("name")) {
|
| + name = _json["name"];
|
| }
|
| if (_json.containsKey("predictedInsertSize")) {
|
| predictedInsertSize = _json["predictedInsertSize"];
|
| }
|
| - if (_json.containsKey("processingProgram")) {
|
| - processingProgram = _json["processingProgram"];
|
| - }
|
| - if (_json.containsKey("sample")) {
|
| - sample = _json["sample"];
|
| + if (_json.containsKey("programs")) {
|
| + programs = _json["programs"].map((value) => new ReadGroupProgram.fromJson(value)).toList();
|
| }
|
| - if (_json.containsKey("sequencingCenterName")) {
|
| - sequencingCenterName = _json["sequencingCenterName"];
|
| + if (_json.containsKey("referenceSetId")) {
|
| + referenceSetId = _json["referenceSetId"];
|
| }
|
| - if (_json.containsKey("sequencingTechnology")) {
|
| - sequencingTechnology = _json["sequencingTechnology"];
|
| + if (_json.containsKey("sampleId")) {
|
| + sampleId = _json["sampleId"];
|
| }
|
| }
|
|
|
| core.Map toJson() {
|
| var _json = new core.Map();
|
| - if (date != null) {
|
| - _json["date"] = date;
|
| + if (datasetId != null) {
|
| + _json["datasetId"] = datasetId;
|
| }
|
| if (description != null) {
|
| _json["description"] = description;
|
| }
|
| - if (flowOrder != null) {
|
| - _json["flowOrder"] = flowOrder;
|
| + if (experiment != null) {
|
| + _json["experiment"] = (experiment).toJson();
|
| }
|
| if (id != null) {
|
| _json["id"] = id;
|
| }
|
| - if (keySequence != null) {
|
| - _json["keySequence"] = keySequence;
|
| + if (info != null) {
|
| + _json["info"] = info;
|
| + }
|
| + if (name != null) {
|
| + _json["name"] = name;
|
| + }
|
| + if (predictedInsertSize != null) {
|
| + _json["predictedInsertSize"] = predictedInsertSize;
|
| + }
|
| + if (programs != null) {
|
| + _json["programs"] = programs.map((value) => (value).toJson()).toList();
|
| + }
|
| + if (referenceSetId != null) {
|
| + _json["referenceSetId"] = referenceSetId;
|
| + }
|
| + if (sampleId != null) {
|
| + _json["sampleId"] = sampleId;
|
| + }
|
| + return _json;
|
| + }
|
| +}
|
| +
|
| +
|
| +/** Not documented yet. */
|
| +class ReadGroupExperiment {
|
| + /**
|
| + * The instrument model used as part of this experiment. This maps to
|
| + * sequencing technology in BAM.
|
| + */
|
| + core.String instrumentModel;
|
| +
|
| + /**
|
| + * The library used as part of this experiment. Note: This is not an actual ID
|
| + * within this repository, but rather an identifier for a library which may be
|
| + * meaningful to some external system.
|
| + */
|
| + core.String libraryId;
|
| +
|
| + /**
|
| + * The platform unit used as part of this experiment e.g.
|
| + * flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
|
| + */
|
| + core.String platformUnit;
|
| +
|
| + /** The sequencing center used as part of this experiment. */
|
| + core.String sequencingCenter;
|
| +
|
| +
|
| + ReadGroupExperiment();
|
| +
|
| + ReadGroupExperiment.fromJson(core.Map _json) {
|
| + if (_json.containsKey("instrumentModel")) {
|
| + instrumentModel = _json["instrumentModel"];
|
| + }
|
| + if (_json.containsKey("libraryId")) {
|
| + libraryId = _json["libraryId"];
|
| + }
|
| + if (_json.containsKey("platformUnit")) {
|
| + platformUnit = _json["platformUnit"];
|
| + }
|
| + if (_json.containsKey("sequencingCenter")) {
|
| + sequencingCenter = _json["sequencingCenter"];
|
| + }
|
| + }
|
| +
|
| + core.Map toJson() {
|
| + var _json = new core.Map();
|
| + if (instrumentModel != null) {
|
| + _json["instrumentModel"] = instrumentModel;
|
| }
|
| - if (library != null) {
|
| - _json["library"] = library;
|
| + if (libraryId != null) {
|
| + _json["libraryId"] = libraryId;
|
| }
|
| if (platformUnit != null) {
|
| _json["platformUnit"] = platformUnit;
|
| }
|
| - if (predictedInsertSize != null) {
|
| - _json["predictedInsertSize"] = predictedInsertSize;
|
| + if (sequencingCenter != null) {
|
| + _json["sequencingCenter"] = sequencingCenter;
|
| + }
|
| + return _json;
|
| + }
|
| +}
|
| +
|
| +
|
| +/** Not documented yet. */
|
| +class ReadGroupProgram {
|
| + /** The command line used to run this program. */
|
| + core.String commandLine;
|
| +
|
| + /**
|
| + * The user specified locally unique ID of the program. Used along with
|
| + * prevProgramId to define an ordering between programs.
|
| + */
|
| + core.String id;
|
| +
|
| + /** The name of the program. */
|
| + core.String name;
|
| +
|
| + /** The ID of the program run before this one. */
|
| + core.String prevProgramId;
|
| +
|
| + /** The version of the program run. */
|
| + core.String version;
|
| +
|
| +
|
| + ReadGroupProgram();
|
| +
|
| + ReadGroupProgram.fromJson(core.Map _json) {
|
| + if (_json.containsKey("commandLine")) {
|
| + commandLine = _json["commandLine"];
|
| }
|
| - if (processingProgram != null) {
|
| - _json["processingProgram"] = processingProgram;
|
| + 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 (sample != null) {
|
| - _json["sample"] = sample;
|
| + if (name != null) {
|
| + _json["name"] = name;
|
| }
|
| - if (sequencingCenterName != null) {
|
| - _json["sequencingCenterName"] = sequencingCenterName;
|
| + if (prevProgramId != null) {
|
| + _json["prevProgramId"] = prevProgramId;
|
| }
|
| - if (sequencingTechnology != null) {
|
| - _json["sequencingTechnology"] = sequencingTechnology;
|
| + if (version != null) {
|
| + _json["version"] = version;
|
| }
|
| return _json;
|
| }
|
| }
|
|
|
|
|
| -/** A Readset is a collection of Reads. */
|
| -class Readset {
|
| - /** The ID of the dataset this readset belongs to. */
|
| +/**
|
| + * A read group set is a logical collection of read groups, which are
|
| + * collections of reads produced by a sequencer. A read group set typically
|
| + * models reads corresponding to one sample, sequenced one way, and aligned one
|
| + * way.
|
| + * - A read group set belongs to one dataset.
|
| + * - A read group belongs to one read group set.
|
| + * - A read belongs to one read group.
|
| + */
|
| +class ReadGroupSet {
|
| + /** The dataset ID. */
|
| core.String datasetId;
|
|
|
| /**
|
| - * File information from the original BAM import. See the BAM format
|
| - * specification for additional information on each field.
|
| + * The filename of the original source file for this read group set, if any.
|
| */
|
| - core.List<HeaderSection> fileData;
|
| + core.String filename;
|
|
|
| - /** The Google generated ID of the readset, immutable. */
|
| + /** The read group set ID. */
|
| core.String id;
|
|
|
| - /** The readset name, typically this is the sample name. */
|
| + /**
|
| + * The read group set name. By default this will be initialized to the sample
|
| + * name of the sequenced data contained in this set.
|
| + */
|
| core.String name;
|
|
|
| + /**
|
| + * The read groups in this set. There are typically 1-10 read groups in a read
|
| + * group set.
|
| + */
|
| + core.List<ReadGroup> readGroups;
|
| +
|
| + /** The reference set the reads in this read group set are aligned to. */
|
| + core.String referenceSetId;
|
|
|
| - Readset();
|
|
|
| - Readset.fromJson(core.Map _json) {
|
| + ReadGroupSet();
|
| +
|
| + ReadGroupSet.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("filename")) {
|
| + filename = _json["filename"];
|
| }
|
| if (_json.containsKey("id")) {
|
| id = _json["id"];
|
| @@ -3608,6 +4461,12 @@ class Readset {
|
| if (_json.containsKey("name")) {
|
| name = _json["name"];
|
| }
|
| + if (_json.containsKey("readGroups")) {
|
| + readGroups = _json["readGroups"].map((value) => new ReadGroup.fromJson(value)).toList();
|
| + }
|
| + if (_json.containsKey("referenceSetId")) {
|
| + referenceSetId = _json["referenceSetId"];
|
| + }
|
| }
|
|
|
| core.Map toJson() {
|
| @@ -3615,15 +4474,117 @@ class Readset {
|
| if (datasetId != null) {
|
| _json["datasetId"] = datasetId;
|
| }
|
| - if (fileData != null) {
|
| - _json["fileData"] = fileData.map((value) => (value).toJson()).toList();
|
| + if (filename != null) {
|
| + _json["filename"] = filename;
|
| + }
|
| + if (id != null) {
|
| + _json["id"] = id;
|
| + }
|
| + if (name != null) {
|
| + _json["name"] = name;
|
| + }
|
| + if (readGroups != null) {
|
| + _json["readGroups"] = readGroups.map((value) => (value).toJson()).toList();
|
| + }
|
| + if (referenceSetId != null) {
|
| + _json["referenceSetId"] = referenceSetId;
|
| + }
|
| + return _json;
|
| + }
|
| +}
|
| +
|
| +
|
| +/**
|
| + * A reference is a canonical assembled DNA sequence, intended to act as a
|
| + * reference coordinate space for other genomic annotations. A single reference
|
| + * might represent the human chromosome 1 or mitochandrial DNA, for instance. A
|
| + * reference belongs to one or more reference sets.
|
| + */
|
| +class Reference {
|
| + /** The Google generated immutable ID of the reference. */
|
| + core.String id;
|
| +
|
| + /** The length of this reference's sequence. */
|
| + core.String length;
|
| +
|
| + /**
|
| + * MD5 of the upper-case sequence excluding all whitespace characters (this is
|
| + * equivalent to SQ:M5 in SAM). This value is represented in lower case
|
| + * hexadecimal format.
|
| + */
|
| + core.String md5checksum;
|
| +
|
| + /** The name of this reference, for example 22. */
|
| + core.String name;
|
| +
|
| + /**
|
| + * ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human) if not
|
| + * specified by the containing reference set.
|
| + */
|
| + core.int ncbiTaxonId;
|
| +
|
| + /**
|
| + * All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
|
| + * with a version number, for example GCF_000001405.26.
|
| + */
|
| + core.List<core.String> sourceAccessions;
|
| +
|
| + /**
|
| + * The URI from which the sequence was obtained. Specifies a FASTA format
|
| + * file/string with one name, sequence pair.
|
| + */
|
| + core.String sourceURI;
|
| +
|
| +
|
| + Reference();
|
| +
|
| + Reference.fromJson(core.Map _json) {
|
| + if (_json.containsKey("id")) {
|
| + id = _json["id"];
|
| + }
|
| + if (_json.containsKey("length")) {
|
| + length = _json["length"];
|
| + }
|
| + if (_json.containsKey("md5checksum")) {
|
| + md5checksum = _json["md5checksum"];
|
| }
|
| + if (_json.containsKey("name")) {
|
| + name = _json["name"];
|
| + }
|
| + if (_json.containsKey("ncbiTaxonId")) {
|
| + ncbiTaxonId = _json["ncbiTaxonId"];
|
| + }
|
| + if (_json.containsKey("sourceAccessions")) {
|
| + sourceAccessions = _json["sourceAccessions"];
|
| + }
|
| + if (_json.containsKey("sourceURI")) {
|
| + sourceURI = _json["sourceURI"];
|
| + }
|
| + }
|
| +
|
| + core.Map toJson() {
|
| + var _json = new core.Map();
|
| if (id != null) {
|
| _json["id"] = id;
|
| }
|
| + if (length != null) {
|
| + _json["length"] = length;
|
| + }
|
| + if (md5checksum != null) {
|
| + _json["md5checksum"] = md5checksum;
|
| + }
|
| if (name != null) {
|
| _json["name"] = name;
|
| }
|
| + if (ncbiTaxonId != null) {
|
| + _json["ncbiTaxonId"] = ncbiTaxonId;
|
| + }
|
| + if (sourceAccessions != null) {
|
| + _json["sourceAccessions"] = sourceAccessions;
|
| + }
|
| + if (sourceURI != null) {
|
| + _json["sourceURI"] = sourceURI;
|
| + }
|
| return _json;
|
| }
|
| }
|
| @@ -3668,50 +4629,83 @@ class ReferenceBound {
|
| }
|
|
|
|
|
| -/** Not documented yet. */
|
| -class ReferenceSequence {
|
| - /** (AS) Genome assembly identifier. */
|
| +/**
|
| + * A reference set is a set of references which typically comprise a reference
|
| + * assembly for a species, such as GRCh38 which is representative of the human
|
| + * genome. A reference set defines a common coordinate space for comparing
|
| + * reference-aligned experimental data. A reference set contains 1 or more
|
| + * references.
|
| + */
|
| +class ReferenceSet {
|
| + /** Public id of this reference set, such as GRCh37. */
|
| core.String assemblyId;
|
|
|
| - /** (LN) Reference sequence length. */
|
| - core.int length;
|
| + /** Optional free text description of this reference set. */
|
| + core.String description;
|
| +
|
| + /** The Google generated immutable ID of the reference set. */
|
| + core.String id;
|
|
|
| /**
|
| - * (M5) MD5 checksum of the sequence in the uppercase, excluding spaces but
|
| - * including pads as *.
|
| + * Order-independent MD5 checksum which identifies this reference set. The
|
| + * checksum is computed by sorting all lower case hexidecimal string
|
| + * reference.md5checksum (for all reference in this set) in ascending
|
| + * lexicographic order, concatenating, and taking the MD5 of that value. The
|
| + * resulting value is represented in lower case hexadecimal format.
|
| */
|
| - core.String md5Checksum;
|
| + core.String md5checksum;
|
|
|
| - /** (SN) Reference sequence name. */
|
| - core.String name;
|
| + /**
|
| + * ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human) indicating
|
| + * the species which this assembly is intended to model. Note that contained
|
| + * references may specify a different ncbiTaxonId, as assemblies may contain
|
| + * reference sequences which do not belong to the modeled species, e.g. EBV in
|
| + * a human reference genome.
|
| + */
|
| + core.int ncbiTaxonId;
|
| +
|
| + /**
|
| + * The IDs of the reference objects that are part of this set.
|
| + * Reference.md5checksum must be unique within this set.
|
| + */
|
| + core.List<core.String> referenceIds;
|
|
|
| - /** (SP) Species. */
|
| - core.String species;
|
| + /**
|
| + * All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
|
| + * with a version number, for example NC_000001.11.
|
| + */
|
| + core.List<core.String> sourceAccessions;
|
|
|
| - /** (UR) URI of the sequence. */
|
| - core.String uri;
|
| + /** The URI from which the references were obtained. */
|
| + core.String sourceURI;
|
|
|
|
|
| - ReferenceSequence();
|
| + ReferenceSet();
|
|
|
| - ReferenceSequence.fromJson(core.Map _json) {
|
| + ReferenceSet.fromJson(core.Map _json) {
|
| if (_json.containsKey("assemblyId")) {
|
| assemblyId = _json["assemblyId"];
|
| }
|
| - if (_json.containsKey("length")) {
|
| - length = _json["length"];
|
| + if (_json.containsKey("description")) {
|
| + description = _json["description"];
|
| + }
|
| + if (_json.containsKey("id")) {
|
| + id = _json["id"];
|
| }
|
| - if (_json.containsKey("md5Checksum")) {
|
| - md5Checksum = _json["md5Checksum"];
|
| + if (_json.containsKey("md5checksum")) {
|
| + md5checksum = _json["md5checksum"];
|
| }
|
| - if (_json.containsKey("name")) {
|
| - name = _json["name"];
|
| + if (_json.containsKey("ncbiTaxonId")) {
|
| + ncbiTaxonId = _json["ncbiTaxonId"];
|
| }
|
| - if (_json.containsKey("species")) {
|
| - species = _json["species"];
|
| + if (_json.containsKey("referenceIds")) {
|
| + referenceIds = _json["referenceIds"];
|
| }
|
| - if (_json.containsKey("uri")) {
|
| - uri = _json["uri"];
|
| + if (_json.containsKey("sourceAccessions")) {
|
| + sourceAccessions = _json["sourceAccessions"];
|
| + }
|
| + if (_json.containsKey("sourceURI")) {
|
| + sourceURI = _json["sourceURI"];
|
| }
|
| }
|
|
|
| @@ -3720,20 +4714,26 @@ class ReferenceSequence {
|
| if (assemblyId != null) {
|
| _json["assemblyId"] = assemblyId;
|
| }
|
| - if (length != null) {
|
| - _json["length"] = length;
|
| + if (description != null) {
|
| + _json["description"] = description;
|
| }
|
| - if (md5Checksum != null) {
|
| - _json["md5Checksum"] = md5Checksum;
|
| + if (id != null) {
|
| + _json["id"] = id;
|
| }
|
| - if (name != null) {
|
| - _json["name"] = name;
|
| + if (md5checksum != null) {
|
| + _json["md5checksum"] = md5checksum;
|
| + }
|
| + if (ncbiTaxonId != null) {
|
| + _json["ncbiTaxonId"] = ncbiTaxonId;
|
| }
|
| - if (species != null) {
|
| - _json["species"] = species;
|
| + if (referenceIds != null) {
|
| + _json["referenceIds"] = referenceIds;
|
| }
|
| - if (uri != null) {
|
| - _json["uri"] = uri;
|
| + if (sourceAccessions != null) {
|
| + _json["sourceAccessions"] = sourceAccessions;
|
| + }
|
| + if (sourceURI != null) {
|
| + _json["sourceURI"] = sourceURI;
|
| }
|
| return _json;
|
| }
|
| @@ -3856,7 +4856,7 @@ class SearchJobsRequest {
|
| * Specifies the number of results to return in a single page. Defaults to
|
| * 128. The maximum value is 256.
|
| */
|
| - core.String maxResults;
|
| + core.int pageSize;
|
|
|
| /**
|
| * The continuation token which is used to page through large result sets. To
|
| @@ -3866,7 +4866,7 @@ class SearchJobsRequest {
|
| core.String pageToken;
|
|
|
| /** Required. Only return jobs which belong to this Google Developers */
|
| - core.String projectId;
|
| + core.String projectNumber;
|
|
|
| /** Only return jobs which have a matching status. */
|
| core.List<core.String> status;
|
| @@ -3881,14 +4881,14 @@ class SearchJobsRequest {
|
| if (_json.containsKey("createdBefore")) {
|
| createdBefore = _json["createdBefore"];
|
| }
|
| - if (_json.containsKey("maxResults")) {
|
| - maxResults = _json["maxResults"];
|
| + if (_json.containsKey("pageSize")) {
|
| + pageSize = _json["pageSize"];
|
| }
|
| if (_json.containsKey("pageToken")) {
|
| pageToken = _json["pageToken"];
|
| }
|
| - if (_json.containsKey("projectId")) {
|
| - projectId = _json["projectId"];
|
| + if (_json.containsKey("projectNumber")) {
|
| + projectNumber = _json["projectNumber"];
|
| }
|
| if (_json.containsKey("status")) {
|
| status = _json["status"];
|
| @@ -3903,14 +4903,14 @@ class SearchJobsRequest {
|
| if (createdBefore != null) {
|
| _json["createdBefore"] = createdBefore;
|
| }
|
| - if (maxResults != null) {
|
| - _json["maxResults"] = maxResults;
|
| + if (pageSize != null) {
|
| + _json["pageSize"] = pageSize;
|
| }
|
| if (pageToken != null) {
|
| _json["pageToken"] = pageToken;
|
| }
|
| - if (projectId != null) {
|
| - _json["projectId"] = projectId;
|
| + if (projectNumber != null) {
|
| + _json["projectNumber"] = projectNumber;
|
| }
|
| if (status != null) {
|
| _json["status"] = status;
|
| @@ -3957,13 +4957,120 @@ class SearchJobsResponse {
|
| }
|
|
|
|
|
| +/** The read group set search request. */
|
| +class SearchReadGroupSetsRequest {
|
| + /**
|
| + * Restricts this query to read group sets within the given datasets. At least
|
| + * one ID must be provided.
|
| + */
|
| + core.List<core.String> datasetIds;
|
| +
|
| + /**
|
| + * Only return read group sets for which a substring of the name matches this
|
| + * string.
|
| + */
|
| + core.String name;
|
| +
|
| + /**
|
| + * Specifies number of results to return in a single page. If unspecified, it
|
| + * will default to 128. The maximum value is 1024.
|
| + */
|
| + core.int pageSize;
|
| +
|
| + /**
|
| + * The continuation token, which is used to page through large result sets. To
|
| + * get the next page of results, set this parameter to the value of
|
| + * nextPageToken from the previous response.
|
| + */
|
| + core.String pageToken;
|
| +
|
| +
|
| + SearchReadGroupSetsRequest();
|
| +
|
| + SearchReadGroupSetsRequest.fromJson(core.Map _json) {
|
| + if (_json.containsKey("datasetIds")) {
|
| + datasetIds = _json["datasetIds"];
|
| + }
|
| + if (_json.containsKey("name")) {
|
| + name = _json["name"];
|
| + }
|
| + if (_json.containsKey("pageSize")) {
|
| + pageSize = _json["pageSize"];
|
| + }
|
| + if (_json.containsKey("pageToken")) {
|
| + pageToken = _json["pageToken"];
|
| + }
|
| + }
|
| +
|
| + core.Map toJson() {
|
| + var _json = new core.Map();
|
| + if (datasetIds != null) {
|
| + _json["datasetIds"] = datasetIds;
|
| + }
|
| + if (name != null) {
|
| + _json["name"] = name;
|
| + }
|
| + if (pageSize != null) {
|
| + _json["pageSize"] = pageSize;
|
| + }
|
| + if (pageToken != null) {
|
| + _json["pageToken"] = pageToken;
|
| + }
|
| + return _json;
|
| + }
|
| +}
|
| +
|
| +
|
| +/** The read group set search response. */
|
| +class SearchReadGroupSetsResponse {
|
| + /**
|
| + * The continuation token, which is used to page through large result sets.
|
| + * Provide this value in a subsequent request to return the next page of
|
| + * results. This field will be empty if there aren't any additional results.
|
| + */
|
| + core.String nextPageToken;
|
| +
|
| + /** The list of matching read group sets. */
|
| + core.List<ReadGroupSet> readGroupSets;
|
| +
|
| +
|
| + SearchReadGroupSetsResponse();
|
| +
|
| + SearchReadGroupSetsResponse.fromJson(core.Map _json) {
|
| + if (_json.containsKey("nextPageToken")) {
|
| + nextPageToken = _json["nextPageToken"];
|
| + }
|
| + if (_json.containsKey("readGroupSets")) {
|
| + readGroupSets = _json["readGroupSets"].map((value) => new ReadGroupSet.fromJson(value)).toList();
|
| + }
|
| + }
|
| +
|
| + core.Map toJson() {
|
| + var _json = new core.Map();
|
| + if (nextPageToken != null) {
|
| + _json["nextPageToken"] = nextPageToken;
|
| + }
|
| + if (readGroupSets != null) {
|
| + _json["readGroupSets"] = readGroupSets.map((value) => (value).toJson()).toList();
|
| + }
|
| + return _json;
|
| + }
|
| +}
|
| +
|
| +
|
| /** The read search request. */
|
| class SearchReadsRequest {
|
| /**
|
| + * The end position of the range on the reference, 0-based exclusive. If
|
| + * specified, referenceName must also be specified.
|
| + */
|
| + core.String end;
|
| +
|
| + /**
|
| * Specifies number of results to return in a single page. If unspecified, it
|
| * will default to 256. The maximum value is 2048.
|
| */
|
| - core.String maxResults;
|
| + core.int pageSize;
|
|
|
| /**
|
| * The continuation token, which is used to page through large result sets. To
|
| @@ -3973,76 +5080,81 @@ class SearchReadsRequest {
|
| 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.
|
| + * The IDs of the read groups within which to search for reads. All specified
|
| + * read groups must belong to the same read group sets. Must specify one of
|
| + * readGroupSetIds or readGroupIds.
|
| */
|
| - core.List<core.String> readsetIds;
|
| + core.List<core.String> readGroupIds;
|
|
|
| /**
|
| - * 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.
|
| + * The IDs of the read groups sets within which to search for reads. All
|
| + * specified read group sets must be aligned against a common set of reference
|
| + * sequences; this defines the genomic coordinates for the query. Must specify
|
| + * one of readGroupSetIds or readGroupIds.
|
| */
|
| - core.String sequenceEnd;
|
| + core.List<core.String> readGroupSetIds;
|
|
|
| /**
|
| - * 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.
|
| + * The reference sequence name, for example chr1, 1, or chrX. If set to *,
|
| + * only unmapped reads are returned.
|
| */
|
| - core.String sequenceName;
|
| + core.String referenceName;
|
|
|
| /**
|
| - * 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.
|
| + * The start position of the range on the reference, 0-based inclusive. If
|
| + * specified, referenceName must also be specified.
|
| */
|
| - core.String sequenceStart;
|
| + core.String start;
|
|
|
|
|
| SearchReadsRequest();
|
|
|
| SearchReadsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("maxResults")) {
|
| - maxResults = _json["maxResults"];
|
| + if (_json.containsKey("end")) {
|
| + end = _json["end"];
|
| + }
|
| + if (_json.containsKey("pageSize")) {
|
| + pageSize = _json["pageSize"];
|
| }
|
| if (_json.containsKey("pageToken")) {
|
| pageToken = _json["pageToken"];
|
| }
|
| - if (_json.containsKey("readsetIds")) {
|
| - readsetIds = _json["readsetIds"];
|
| + if (_json.containsKey("readGroupIds")) {
|
| + readGroupIds = _json["readGroupIds"];
|
| }
|
| - if (_json.containsKey("sequenceEnd")) {
|
| - sequenceEnd = _json["sequenceEnd"];
|
| + if (_json.containsKey("readGroupSetIds")) {
|
| + readGroupSetIds = _json["readGroupSetIds"];
|
| }
|
| - if (_json.containsKey("sequenceName")) {
|
| - sequenceName = _json["sequenceName"];
|
| + if (_json.containsKey("referenceName")) {
|
| + referenceName = _json["referenceName"];
|
| }
|
| - if (_json.containsKey("sequenceStart")) {
|
| - sequenceStart = _json["sequenceStart"];
|
| + if (_json.containsKey("start")) {
|
| + start = _json["start"];
|
| }
|
| }
|
|
|
| core.Map toJson() {
|
| var _json = new core.Map();
|
| - if (maxResults != null) {
|
| - _json["maxResults"] = maxResults;
|
| + if (end != null) {
|
| + _json["end"] = end;
|
| + }
|
| + if (pageSize != null) {
|
| + _json["pageSize"] = pageSize;
|
| }
|
| if (pageToken != null) {
|
| _json["pageToken"] = pageToken;
|
| }
|
| - if (readsetIds != null) {
|
| - _json["readsetIds"] = readsetIds;
|
| + if (readGroupIds != null) {
|
| + _json["readGroupIds"] = readGroupIds;
|
| }
|
| - if (sequenceEnd != null) {
|
| - _json["sequenceEnd"] = sequenceEnd;
|
| + if (readGroupSetIds != null) {
|
| + _json["readGroupSetIds"] = readGroupSetIds;
|
| }
|
| - if (sequenceName != null) {
|
| - _json["sequenceName"] = sequenceName;
|
| + if (referenceName != null) {
|
| + _json["referenceName"] = referenceName;
|
| }
|
| - if (sequenceStart != null) {
|
| - _json["sequenceStart"] = sequenceStart;
|
| + if (start != null) {
|
| + _json["start"] = start;
|
| }
|
| return _json;
|
| }
|
| @@ -4052,62 +5164,165 @@ class SearchReadsRequest {
|
| /** The read search response. */
|
| class SearchReadsResponse {
|
| /**
|
| + * The list of matching alignments sorted by mapped genomic coordinate, if
|
| + * any, ascending in position within the same reference. Unmapped reads, which
|
| + * have no position, are returned last and are further sorted in ascending
|
| + * lexicographic order by fragment name.
|
| + */
|
| + core.List<Read> alignments;
|
| +
|
| + /**
|
| * The continuation token, which is used to page through large result sets.
|
| * Provide this value in a subsequent request to return the next page of
|
| * results. This field will be empty if there aren't any additional results.
|
| */
|
| core.String nextPageToken;
|
|
|
| - /**
|
| - * 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("alignments")) {
|
| + alignments = _json["alignments"].map((value) => new Read.fromJson(value)).toList();
|
| + }
|
| 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 (alignments != null) {
|
| + _json["alignments"] = alignments.map((value) => (value).toJson()).toList();
|
| + }
|
| if (nextPageToken != null) {
|
| _json["nextPageToken"] = nextPageToken;
|
| }
|
| - if (reads != null) {
|
| - _json["reads"] = reads.map((value) => (value).toJson()).toList();
|
| + return _json;
|
| + }
|
| +}
|
| +
|
| +
|
| +/** Not documented yet. */
|
| +class SearchReferenceSetsRequest {
|
| + /**
|
| + * If present, return references for which the accession matches any of these
|
| + * strings. Best to give a version number, for example GCF_000001405.26. If
|
| + * only the main accession number is given then all records with that main
|
| + * accession will be returned, whichever version. Note that different versions
|
| + * will have different sequences.
|
| + */
|
| + core.List<core.String> accessions;
|
| +
|
| + /**
|
| + * If present, return references for which the md5checksum matches. See
|
| + * ReferenceSet.md5checksum for details.
|
| + */
|
| + core.List<core.String> md5checksums;
|
| +
|
| + /** Specifies the maximum number of results to return in a single page. */
|
| + core.int pageSize;
|
| +
|
| + /**
|
| + * The continuation token, which is used to page through large result sets. To
|
| + * get the next page of results, set this parameter to the value of
|
| + * nextPageToken from the previous response.
|
| + */
|
| + core.String pageToken;
|
| +
|
| +
|
| + SearchReferenceSetsRequest();
|
| +
|
| + SearchReferenceSetsRequest.fromJson(core.Map _json) {
|
| + if (_json.containsKey("accessions")) {
|
| + accessions = _json["accessions"];
|
| + }
|
| + if (_json.containsKey("md5checksums")) {
|
| + md5checksums = _json["md5checksums"];
|
| + }
|
| + if (_json.containsKey("pageSize")) {
|
| + pageSize = _json["pageSize"];
|
| + }
|
| + if (_json.containsKey("pageToken")) {
|
| + pageToken = _json["pageToken"];
|
| + }
|
| + }
|
| +
|
| + core.Map toJson() {
|
| + var _json = new core.Map();
|
| + if (accessions != null) {
|
| + _json["accessions"] = accessions;
|
| + }
|
| + if (md5checksums != null) {
|
| + _json["md5checksums"] = md5checksums;
|
| + }
|
| + if (pageSize != null) {
|
| + _json["pageSize"] = pageSize;
|
| + }
|
| + if (pageToken != null) {
|
| + _json["pageToken"] = pageToken;
|
| }
|
| return _json;
|
| }
|
| }
|
|
|
|
|
| -/** The readset search request. */
|
| -class SearchReadsetsRequest {
|
| +/** Not documented yet. */
|
| +class SearchReferenceSetsResponse {
|
| /**
|
| - * Restricts this query to readsets within the given datasets. At least one ID
|
| - * must be provided.
|
| + * 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.List<core.String> datasetIds;
|
| + core.String nextPageToken;
|
| +
|
| + /** The matching references sets. */
|
| + core.List<ReferenceSet> referenceSets;
|
| +
|
| +
|
| + SearchReferenceSetsResponse();
|
| +
|
| + SearchReferenceSetsResponse.fromJson(core.Map _json) {
|
| + if (_json.containsKey("nextPageToken")) {
|
| + nextPageToken = _json["nextPageToken"];
|
| + }
|
| + if (_json.containsKey("referenceSets")) {
|
| + referenceSets = _json["referenceSets"].map((value) => new ReferenceSet.fromJson(value)).toList();
|
| + }
|
| + }
|
| +
|
| + core.Map toJson() {
|
| + var _json = new core.Map();
|
| + if (nextPageToken != null) {
|
| + _json["nextPageToken"] = nextPageToken;
|
| + }
|
| + if (referenceSets != null) {
|
| + _json["referenceSets"] = referenceSets.map((value) => (value).toJson()).toList();
|
| + }
|
| + return _json;
|
| + }
|
| +}
|
| +
|
|
|
| +/** Not documented yet. */
|
| +class SearchReferencesRequest {
|
| /**
|
| - * Specifies number of results to return in a single page. If unspecified, it
|
| - * will default to 128. The maximum value is 1024.
|
| + * If present, return references for which the accession matches this string.
|
| + * Best to give a version number, for example GCF_000001405.26. If only the
|
| + * main accession number is given then all records with that main accession
|
| + * will be returned, whichever version. Note that different versions will have
|
| + * different sequences.
|
| */
|
| - core.String maxResults;
|
| + core.List<core.String> accessions;
|
|
|
| /**
|
| - * Only return readsets for which a substring of the name matches this string.
|
| + * If present, return references for which the md5checksum matches. See
|
| + * Reference.md5checksum for construction details.
|
| */
|
| - core.String name;
|
| + core.List<core.String> md5checksums;
|
| +
|
| + /** Specifies the maximum number of results to return in a single page. */
|
| + core.int pageSize;
|
|
|
| /**
|
| * The continuation token, which is used to page through large result sets. To
|
| @@ -4116,45 +5331,54 @@ class SearchReadsetsRequest {
|
| */
|
| core.String pageToken;
|
|
|
| + /** If present, return only references which belong to this reference set. */
|
| + core.String referenceSetId;
|
|
|
| - SearchReadsetsRequest();
|
|
|
| - SearchReadsetsRequest.fromJson(core.Map _json) {
|
| - if (_json.containsKey("datasetIds")) {
|
| - datasetIds = _json["datasetIds"];
|
| + SearchReferencesRequest();
|
| +
|
| + SearchReferencesRequest.fromJson(core.Map _json) {
|
| + if (_json.containsKey("accessions")) {
|
| + accessions = _json["accessions"];
|
| }
|
| - if (_json.containsKey("maxResults")) {
|
| - maxResults = _json["maxResults"];
|
| + if (_json.containsKey("md5checksums")) {
|
| + md5checksums = _json["md5checksums"];
|
| }
|
| - if (_json.containsKey("name")) {
|
| - name = _json["name"];
|
| + if (_json.containsKey("pageSize")) {
|
| + pageSize = _json["pageSize"];
|
| }
|
| if (_json.containsKey("pageToken")) {
|
| pageToken = _json["pageToken"];
|
| }
|
| + if (_json.containsKey("referenceSetId")) {
|
| + referenceSetId = _json["referenceSetId"];
|
| + }
|
| }
|
|
|
| core.Map toJson() {
|
| var _json = new core.Map();
|
| - if (datasetIds != null) {
|
| - _json["datasetIds"] = datasetIds;
|
| + if (accessions != null) {
|
| + _json["accessions"] = accessions;
|
| }
|
| - if (maxResults != null) {
|
| - _json["maxResults"] = maxResults;
|
| + if (md5checksums != null) {
|
| + _json["md5checksums"] = md5checksums;
|
| }
|
| - if (name != null) {
|
| - _json["name"] = name;
|
| + if (pageSize != null) {
|
| + _json["pageSize"] = pageSize;
|
| }
|
| if (pageToken != null) {
|
| _json["pageToken"] = pageToken;
|
| }
|
| + if (referenceSetId != null) {
|
| + _json["referenceSetId"] = referenceSetId;
|
| + }
|
| return _json;
|
| }
|
| }
|
|
|
|
|
| -/** The readset search response. */
|
| -class SearchReadsetsResponse {
|
| +/** Not documented yet. */
|
| +class SearchReferencesResponse {
|
| /**
|
| * The continuation token, which is used to page through large result sets.
|
| * Provide this value in a subsequent request to return the next page of
|
| @@ -4162,18 +5386,18 @@ class SearchReadsetsResponse {
|
| */
|
| core.String nextPageToken;
|
|
|
| - /** The list of matching Readsets. */
|
| - core.List<Readset> readsets;
|
| + /** The matching references. */
|
| + core.List<Reference> references;
|
|
|
|
|
| - SearchReadsetsResponse();
|
| + SearchReferencesResponse();
|
|
|
| - SearchReadsetsResponse.fromJson(core.Map _json) {
|
| + SearchReferencesResponse.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();
|
| + if (_json.containsKey("references")) {
|
| + references = _json["references"].map((value) => new Reference.fromJson(value)).toList();
|
| }
|
| }
|
|
|
| @@ -4182,8 +5406,8 @@ class SearchReadsetsResponse {
|
| if (nextPageToken != null) {
|
| _json["nextPageToken"] = nextPageToken;
|
| }
|
| - if (readsets != null) {
|
| - _json["readsets"] = readsets.map((value) => (value).toJson()).toList();
|
| + if (references != null) {
|
| + _json["references"] = references.map((value) => (value).toJson()).toList();
|
| }
|
| return _json;
|
| }
|
| @@ -4431,9 +5655,13 @@ class SearchVariantsResponse {
|
|
|
|
|
| /**
|
| - * 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.
|
| + * A variant represents a change in DNA sequence relative to a reference
|
| + * sequence. For example, a variant could represent a SNP or an insertion.
|
| + * Variants belong to a variant set. Each of the calls on a variant represent a
|
| + * determination of genotype with respect to that variant. For example, a call
|
| + * might assign probability of 0.32 to the occurrence of a SNP named rs1234 in a
|
| + * sample named NA12345. A call belongs to a call set, which contains related
|
| + * calls typically from one sample.
|
| */
|
| class Variant {
|
| /** The bases that appear instead of the reference bases. */
|
| @@ -4586,8 +5814,8 @@ class Variant {
|
|
|
|
|
| /**
|
| - * A VariantSet represents a collection of Variants and their summary
|
| - * statistics.
|
| + * A variant set is a collection of call sets and variants. It contains summary
|
| + * statistics of those contents. A variant set belongs to a dataset.
|
| */
|
| class VariantSet {
|
| /** The dataset to which this variant set belongs. Immutable. */
|
|
|
Chromium Code Reviews
Issue 698403003:
Api roll 5: 2014-11-05 (Closed)
Base URL: git@github.com:dart-lang/googleapis.git@master