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Side by Side Diff: generated/googleapis/lib/genomics/v1.dart

Issue 3006323002: Api-Roll 54: 2017-09-11 (Closed)
Patch Set: use 2.0.0-dev.infinity sdk constraint in pubspecs Created 3 years, 3 months ago
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1 // This is a generated file (see the discoveryapis_generator project). 1 // This is a generated file (see the discoveryapis_generator project).
2 2
3 library googleapis.genomics.v1; 3 library googleapis.genomics.v1;
4 4
5 import 'dart:core' as core; 5 import 'dart:core' as core;
6 import 'dart:async' as async; 6 import 'dart:async' as async;
7 import 'dart:convert' as convert; 7 import 'dart:convert' as convert;
8 8
9 import 'package:_discoveryapis_commons/_discoveryapis_commons.dart' as commons; 9 import 'package:_discoveryapis_commons/_discoveryapis_commons.dart' as commons;
10 import 'package:http/http.dart' as http; 10 import 'package:http/http.dart' as http;
11 11
12 export 'package:_discoveryapis_commons/_discoveryapis_commons.dart' show 12 export 'package:_discoveryapis_commons/_discoveryapis_commons.dart'
13 ApiRequestError, DetailedApiRequestError; 13 show ApiRequestError, DetailedApiRequestError;
14 14
15 const core.String USER_AGENT = 'dart-api-client genomics/v1'; 15 const core.String USER_AGENT = 'dart-api-client genomics/v1';
16 16
17 /** Upload, process, query, and search Genomics data in the cloud. */ 17 /// Upload, process, query, and search Genomics data in the cloud.
18 class GenomicsApi { 18 class GenomicsApi {
19 /** View and manage your data in Google BigQuery */ 19 /// View and manage your data in Google BigQuery
20 static const BigqueryScope = "https://www.googleapis.com/auth/bigquery"; 20 static const BigqueryScope = "https://www.googleapis.com/auth/bigquery";
21 21
22 /** View and manage your data across Google Cloud Platform services */ 22 /// View and manage your data across Google Cloud Platform services
23 static const CloudPlatformScope = "https://www.googleapis.com/auth/cloud-platf orm"; 23 static const CloudPlatformScope =
24 "https://www.googleapis.com/auth/cloud-platform";
24 25
25 /** Manage your data in Google Cloud Storage */ 26 /// Manage your data in Google Cloud Storage
26 static const DevstorageReadWriteScope = "https://www.googleapis.com/auth/devst orage.read_write"; 27 static const DevstorageReadWriteScope =
28 "https://www.googleapis.com/auth/devstorage.read_write";
27 29
28 /** View and manage Genomics data */ 30 /// View and manage Genomics data
29 static const GenomicsScope = "https://www.googleapis.com/auth/genomics"; 31 static const GenomicsScope = "https://www.googleapis.com/auth/genomics";
30 32
31 /** View Genomics data */ 33 /// View Genomics data
32 static const GenomicsReadonlyScope = "https://www.googleapis.com/auth/genomics .readonly"; 34 static const GenomicsReadonlyScope =
33 35 "https://www.googleapis.com/auth/genomics.readonly";
34 36
35 final commons.ApiRequester _requester; 37 final commons.ApiRequester _requester;
36 38
37 AnnotationsResourceApi get annotations => new AnnotationsResourceApi(_requeste r); 39 AnnotationsResourceApi get annotations =>
38 AnnotationsetsResourceApi get annotationsets => new AnnotationsetsResourceApi( _requester); 40 new AnnotationsResourceApi(_requester);
41 AnnotationsetsResourceApi get annotationsets =>
42 new AnnotationsetsResourceApi(_requester);
39 CallsetsResourceApi get callsets => new CallsetsResourceApi(_requester); 43 CallsetsResourceApi get callsets => new CallsetsResourceApi(_requester);
40 DatasetsResourceApi get datasets => new DatasetsResourceApi(_requester); 44 DatasetsResourceApi get datasets => new DatasetsResourceApi(_requester);
41 OperationsResourceApi get operations => new OperationsResourceApi(_requester); 45 OperationsResourceApi get operations => new OperationsResourceApi(_requester);
42 ReadgroupsetsResourceApi get readgroupsets => new ReadgroupsetsResourceApi(_re quester); 46 ReadgroupsetsResourceApi get readgroupsets =>
47 new ReadgroupsetsResourceApi(_requester);
43 ReadsResourceApi get reads => new ReadsResourceApi(_requester); 48 ReadsResourceApi get reads => new ReadsResourceApi(_requester);
44 ReferencesResourceApi get references => new ReferencesResourceApi(_requester); 49 ReferencesResourceApi get references => new ReferencesResourceApi(_requester);
45 ReferencesetsResourceApi get referencesets => new ReferencesetsResourceApi(_re quester); 50 ReferencesetsResourceApi get referencesets =>
51 new ReferencesetsResourceApi(_requester);
46 VariantsResourceApi get variants => new VariantsResourceApi(_requester); 52 VariantsResourceApi get variants => new VariantsResourceApi(_requester);
47 VariantsetsResourceApi get variantsets => new VariantsetsResourceApi(_requeste r); 53 VariantsetsResourceApi get variantsets =>
54 new VariantsetsResourceApi(_requester);
48 55
49 GenomicsApi(http.Client client, {core.String rootUrl: "https://genomics.google apis.com/", core.String servicePath: ""}) : 56 GenomicsApi(http.Client client,
50 _requester = new commons.ApiRequester(client, rootUrl, servicePath, USER_A GENT); 57 {core.String rootUrl: "https://genomics.googleapis.com/",
58 core.String servicePath: ""})
59 : _requester =
60 new commons.ApiRequester(client, rootUrl, servicePath, USER_AGENT);
51 } 61 }
52 62
53
54 class AnnotationsResourceApi { 63 class AnnotationsResourceApi {
55 final commons.ApiRequester _requester; 64 final commons.ApiRequester _requester;
56 65
57 AnnotationsResourceApi(commons.ApiRequester client) : 66 AnnotationsResourceApi(commons.ApiRequester client) : _requester = client;
58 _requester = client;
59 67
60 /** 68 /// Creates one or more new annotations atomically. All annotations must
61 * Creates one or more new annotations atomically. All annotations must 69 /// belong to the same annotation set. Caller must have WRITE
62 * belong to the same annotation set. Caller must have WRITE 70 /// permission for this annotation set. For optimal performance, batch
63 * permission for this annotation set. For optimal performance, batch 71 /// positionally adjacent annotations together.
64 * positionally adjacent annotations together. 72 ///
65 * 73 /// If the request has a systemic issue, such as an attempt to write to
66 * If the request has a systemic issue, such as an attempt to write to 74 /// an inaccessible annotation set, the entire RPC will fail accordingly. For
67 * an inaccessible annotation set, the entire RPC will fail accordingly. For 75 /// lesser data issues, when possible an error will be isolated to the
68 * lesser data issues, when possible an error will be isolated to the 76 /// corresponding batch entry in the response; the remaining well formed
69 * corresponding batch entry in the response; the remaining well formed 77 /// annotations will be created normally.
70 * annotations will be created normally. 78 ///
71 * 79 /// For details on the requirements for each individual annotation resource,
72 * For details on the requirements for each individual annotation resource, 80 /// see
73 * see 81 /// CreateAnnotation.
74 * CreateAnnotation. 82 ///
75 * 83 /// [request] - The metadata request object.
76 * [request] - The metadata request object. 84 ///
77 * 85 /// Request parameters:
78 * Request parameters: 86 ///
79 * 87 /// Completes with a [BatchCreateAnnotationsResponse].
80 * Completes with a [BatchCreateAnnotationsResponse]. 88 ///
81 * 89 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
82 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 90 /// an error.
83 * error. 91 ///
84 * 92 /// If the used [http.Client] completes with an error when making a REST
85 * If the used [http.Client] completes with an error when making a REST call, 93 /// call, this method will complete with the same error.
86 * this method will complete with the same error. 94 async.Future<BatchCreateAnnotationsResponse> batchCreate(
87 */ 95 BatchCreateAnnotationsRequest request) {
88 async.Future<BatchCreateAnnotationsResponse> batchCreate(BatchCreateAnnotation sRequest request) {
89 var _url = null; 96 var _url = null;
90 var _queryParams = new core.Map(); 97 var _queryParams = new core.Map();
91 var _uploadMedia = null; 98 var _uploadMedia = null;
92 var _uploadOptions = null; 99 var _uploadOptions = null;
93 var _downloadOptions = commons.DownloadOptions.Metadata; 100 var _downloadOptions = commons.DownloadOptions.Metadata;
94 var _body = null; 101 var _body = null;
95 102
96 if (request != null) { 103 if (request != null) {
97 _body = convert.JSON.encode((request).toJson()); 104 _body = convert.JSON.encode((request).toJson());
98 } 105 }
99 106
100 _url = 'v1/annotations:batchCreate'; 107 _url = 'v1/annotations:batchCreate';
101 108
102 var _response = _requester.request(_url, 109 var _response = _requester.request(_url, "POST",
103 "POST", 110 body: _body,
104 body: _body, 111 queryParams: _queryParams,
105 queryParams: _queryParams, 112 uploadOptions: _uploadOptions,
106 uploadOptions: _uploadOptions, 113 uploadMedia: _uploadMedia,
107 uploadMedia: _uploadMedia, 114 downloadOptions: _downloadOptions);
108 downloadOptions: _downloadOptions); 115 return _response
109 return _response.then((data) => new BatchCreateAnnotationsResponse.fromJson( data)); 116 .then((data) => new BatchCreateAnnotationsResponse.fromJson(data));
110 } 117 }
111 118
112 /** 119 /// Creates a new annotation. Caller must have WRITE permission
113 * Creates a new annotation. Caller must have WRITE permission 120 /// for the associated annotation set.
114 * for the associated annotation set. 121 ///
115 * 122 /// The following fields are required:
116 * The following fields are required: 123 ///
117 * 124 /// * annotationSetId
118 * * annotationSetId 125 /// * referenceName or
119 * * referenceName or 126 /// referenceId
120 * referenceId 127 ///
121 * 128 /// ### Transcripts
122 * ### Transcripts 129 ///
123 * 130 /// For annotations of type TRANSCRIPT, the following fields of
124 * For annotations of type TRANSCRIPT, the following fields of 131 /// transcript must be provided:
125 * transcript must be provided: 132 ///
126 * 133 /// * exons.start
127 * * exons.start 134 /// * exons.end
128 * * exons.end 135 ///
129 * 136 /// All other fields may be optionally specified, unless documented as being
130 * All other fields may be optionally specified, unless documented as being 137 /// server-generated (for example, the `id` field). The annotated
131 * server-generated (for example, the `id` field). The annotated 138 /// range must be no longer than 100Mbp (mega base pairs). See the
132 * range must be no longer than 100Mbp (mega base pairs). See the 139 /// Annotation resource
133 * Annotation resource 140 /// for additional restrictions on each field.
134 * for additional restrictions on each field. 141 ///
135 * 142 /// [request] - The metadata request object.
136 * [request] - The metadata request object. 143 ///
137 * 144 /// Request parameters:
138 * Request parameters: 145 ///
139 * 146 /// Completes with a [Annotation].
140 * Completes with a [Annotation]. 147 ///
141 * 148 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
142 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 149 /// an error.
143 * error. 150 ///
144 * 151 /// If the used [http.Client] completes with an error when making a REST
145 * If the used [http.Client] completes with an error when making a REST call, 152 /// call, this method will complete with the same error.
146 * this method will complete with the same error.
147 */
148 async.Future<Annotation> create(Annotation request) { 153 async.Future<Annotation> create(Annotation request) {
149 var _url = null; 154 var _url = null;
150 var _queryParams = new core.Map(); 155 var _queryParams = new core.Map();
151 var _uploadMedia = null; 156 var _uploadMedia = null;
152 var _uploadOptions = null; 157 var _uploadOptions = null;
153 var _downloadOptions = commons.DownloadOptions.Metadata; 158 var _downloadOptions = commons.DownloadOptions.Metadata;
154 var _body = null; 159 var _body = null;
155 160
156 if (request != null) { 161 if (request != null) {
157 _body = convert.JSON.encode((request).toJson()); 162 _body = convert.JSON.encode((request).toJson());
158 } 163 }
159 164
160 _url = 'v1/annotations'; 165 _url = 'v1/annotations';
161 166
162 var _response = _requester.request(_url, 167 var _response = _requester.request(_url, "POST",
163 "POST", 168 body: _body,
164 body: _body, 169 queryParams: _queryParams,
165 queryParams: _queryParams, 170 uploadOptions: _uploadOptions,
166 uploadOptions: _uploadOptions, 171 uploadMedia: _uploadMedia,
167 uploadMedia: _uploadMedia, 172 downloadOptions: _downloadOptions);
168 downloadOptions: _downloadOptions);
169 return _response.then((data) => new Annotation.fromJson(data)); 173 return _response.then((data) => new Annotation.fromJson(data));
170 } 174 }
171 175
172 /** 176 /// Deletes an annotation. Caller must have WRITE permission for
173 * Deletes an annotation. Caller must have WRITE permission for 177 /// the associated annotation set.
174 * the associated annotation set. 178 ///
175 * 179 /// Request parameters:
176 * Request parameters: 180 ///
177 * 181 /// [annotationId] - The ID of the annotation to be deleted.
178 * [annotationId] - The ID of the annotation to be deleted. 182 ///
179 * 183 /// Completes with a [Empty].
180 * Completes with a [Empty]. 184 ///
181 * 185 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
182 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 186 /// an error.
183 * error. 187 ///
184 * 188 /// If the used [http.Client] completes with an error when making a REST
185 * If the used [http.Client] completes with an error when making a REST call, 189 /// call, this method will complete with the same error.
186 * this method will complete with the same error.
187 */
188 async.Future<Empty> delete(core.String annotationId) { 190 async.Future<Empty> delete(core.String annotationId) {
189 var _url = null; 191 var _url = null;
190 var _queryParams = new core.Map(); 192 var _queryParams = new core.Map();
191 var _uploadMedia = null; 193 var _uploadMedia = null;
192 var _uploadOptions = null; 194 var _uploadOptions = null;
193 var _downloadOptions = commons.DownloadOptions.Metadata; 195 var _downloadOptions = commons.DownloadOptions.Metadata;
194 var _body = null; 196 var _body = null;
195 197
196 if (annotationId == null) { 198 if (annotationId == null) {
197 throw new core.ArgumentError("Parameter annotationId is required."); 199 throw new core.ArgumentError("Parameter annotationId is required.");
198 } 200 }
199 201
200 _url = 'v1/annotations/' + commons.Escaper.ecapeVariable('$annotationId'); 202 _url = 'v1/annotations/' + commons.Escaper.ecapeVariable('$annotationId');
201 203
202 var _response = _requester.request(_url, 204 var _response = _requester.request(_url, "DELETE",
203 "DELETE", 205 body: _body,
204 body: _body, 206 queryParams: _queryParams,
205 queryParams: _queryParams, 207 uploadOptions: _uploadOptions,
206 uploadOptions: _uploadOptions, 208 uploadMedia: _uploadMedia,
207 uploadMedia: _uploadMedia, 209 downloadOptions: _downloadOptions);
208 downloadOptions: _downloadOptions);
209 return _response.then((data) => new Empty.fromJson(data)); 210 return _response.then((data) => new Empty.fromJson(data));
210 } 211 }
211 212
212 /** 213 /// Gets an annotation. Caller must have READ permission
213 * Gets an annotation. Caller must have READ permission 214 /// for the associated annotation set.
214 * for the associated annotation set. 215 ///
215 * 216 /// Request parameters:
216 * Request parameters: 217 ///
217 * 218 /// [annotationId] - The ID of the annotation to be retrieved.
218 * [annotationId] - The ID of the annotation to be retrieved. 219 ///
219 * 220 /// Completes with a [Annotation].
220 * Completes with a [Annotation]. 221 ///
221 * 222 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
222 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 223 /// an error.
223 * error. 224 ///
224 * 225 /// If the used [http.Client] completes with an error when making a REST
225 * If the used [http.Client] completes with an error when making a REST call, 226 /// call, this method will complete with the same error.
226 * this method will complete with the same error.
227 */
228 async.Future<Annotation> get(core.String annotationId) { 227 async.Future<Annotation> get(core.String annotationId) {
229 var _url = null; 228 var _url = null;
230 var _queryParams = new core.Map(); 229 var _queryParams = new core.Map();
231 var _uploadMedia = null; 230 var _uploadMedia = null;
232 var _uploadOptions = null; 231 var _uploadOptions = null;
233 var _downloadOptions = commons.DownloadOptions.Metadata; 232 var _downloadOptions = commons.DownloadOptions.Metadata;
234 var _body = null; 233 var _body = null;
235 234
236 if (annotationId == null) { 235 if (annotationId == null) {
237 throw new core.ArgumentError("Parameter annotationId is required."); 236 throw new core.ArgumentError("Parameter annotationId is required.");
238 } 237 }
239 238
240 _url = 'v1/annotations/' + commons.Escaper.ecapeVariable('$annotationId'); 239 _url = 'v1/annotations/' + commons.Escaper.ecapeVariable('$annotationId');
241 240
242 var _response = _requester.request(_url, 241 var _response = _requester.request(_url, "GET",
243 "GET", 242 body: _body,
244 body: _body, 243 queryParams: _queryParams,
245 queryParams: _queryParams, 244 uploadOptions: _uploadOptions,
246 uploadOptions: _uploadOptions, 245 uploadMedia: _uploadMedia,
247 uploadMedia: _uploadMedia, 246 downloadOptions: _downloadOptions);
248 downloadOptions: _downloadOptions);
249 return _response.then((data) => new Annotation.fromJson(data)); 247 return _response.then((data) => new Annotation.fromJson(data));
250 } 248 }
251 249
252 /** 250 /// Searches for annotations that match the given criteria. Results are
253 * Searches for annotations that match the given criteria. Results are 251 /// ordered by genomic coordinate (by reference sequence, then position).
254 * ordered by genomic coordinate (by reference sequence, then position). 252 /// Annotations with equivalent genomic coordinates are returned in an
255 * Annotations with equivalent genomic coordinates are returned in an 253 /// unspecified order. This order is consistent, such that two queries for
256 * unspecified order. This order is consistent, such that two queries for the 254 /// the
257 * same content (regardless of page size) yield annotations in the same order 255 /// same content (regardless of page size) yield annotations in the same
258 * across their respective streams of paginated responses. Caller must have 256 /// order
259 * READ permission for the queried annotation sets. 257 /// across their respective streams of paginated responses. Caller must have
260 * 258 /// READ permission for the queried annotation sets.
261 * [request] - The metadata request object. 259 ///
262 * 260 /// [request] - The metadata request object.
263 * Request parameters: 261 ///
264 * 262 /// Request parameters:
265 * Completes with a [SearchAnnotationsResponse]. 263 ///
266 * 264 /// Completes with a [SearchAnnotationsResponse].
267 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 265 ///
268 * error. 266 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
269 * 267 /// an error.
270 * If the used [http.Client] completes with an error when making a REST call, 268 ///
271 * this method will complete with the same error. 269 /// If the used [http.Client] completes with an error when making a REST
272 */ 270 /// call, this method will complete with the same error.
273 async.Future<SearchAnnotationsResponse> search(SearchAnnotationsRequest reques t) { 271 async.Future<SearchAnnotationsResponse> search(
272 SearchAnnotationsRequest request) {
274 var _url = null; 273 var _url = null;
275 var _queryParams = new core.Map(); 274 var _queryParams = new core.Map();
276 var _uploadMedia = null; 275 var _uploadMedia = null;
277 var _uploadOptions = null; 276 var _uploadOptions = null;
278 var _downloadOptions = commons.DownloadOptions.Metadata; 277 var _downloadOptions = commons.DownloadOptions.Metadata;
279 var _body = null; 278 var _body = null;
280 279
281 if (request != null) { 280 if (request != null) {
282 _body = convert.JSON.encode((request).toJson()); 281 _body = convert.JSON.encode((request).toJson());
283 } 282 }
284 283
285 _url = 'v1/annotations/search'; 284 _url = 'v1/annotations/search';
286 285
287 var _response = _requester.request(_url, 286 var _response = _requester.request(_url, "POST",
288 "POST", 287 body: _body,
289 body: _body, 288 queryParams: _queryParams,
290 queryParams: _queryParams, 289 uploadOptions: _uploadOptions,
291 uploadOptions: _uploadOptions, 290 uploadMedia: _uploadMedia,
292 uploadMedia: _uploadMedia, 291 downloadOptions: _downloadOptions);
293 downloadOptions: _downloadOptions); 292 return _response
294 return _response.then((data) => new SearchAnnotationsResponse.fromJson(data) ); 293 .then((data) => new SearchAnnotationsResponse.fromJson(data));
295 } 294 }
296 295
297 /** 296 /// Updates an annotation. Caller must have
298 * Updates an annotation. Caller must have 297 /// WRITE permission for the associated dataset.
299 * WRITE permission for the associated dataset. 298 ///
300 * 299 /// [request] - The metadata request object.
301 * [request] - The metadata request object. 300 ///
302 * 301 /// Request parameters:
303 * Request parameters: 302 ///
304 * 303 /// [annotationId] - The ID of the annotation to be updated.
305 * [annotationId] - The ID of the annotation to be updated. 304 ///
306 * 305 /// [updateMask] - An optional mask specifying which fields to update.
307 * [updateMask] - An optional mask specifying which fields to update. Mutable 306 /// Mutable fields are
308 * fields are 307 /// name,
309 * name, 308 /// variant,
310 * variant, 309 /// transcript, and
311 * transcript, and 310 /// info. If unspecified, all mutable
312 * info. If unspecified, all mutable 311 /// fields will be updated.
313 * fields will be updated. 312 ///
314 * 313 /// Completes with a [Annotation].
315 * Completes with a [Annotation]. 314 ///
316 * 315 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
317 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 316 /// an error.
318 * error. 317 ///
319 * 318 /// If the used [http.Client] completes with an error when making a REST
320 * If the used [http.Client] completes with an error when making a REST call, 319 /// call, this method will complete with the same error.
321 * this method will complete with the same error. 320 async.Future<Annotation> update(Annotation request, core.String annotationId,
322 */ 321 {core.String updateMask}) {
323 async.Future<Annotation> update(Annotation request, core.String annotationId, {core.String updateMask}) {
324 var _url = null; 322 var _url = null;
325 var _queryParams = new core.Map(); 323 var _queryParams = new core.Map();
326 var _uploadMedia = null; 324 var _uploadMedia = null;
327 var _uploadOptions = null; 325 var _uploadOptions = null;
328 var _downloadOptions = commons.DownloadOptions.Metadata; 326 var _downloadOptions = commons.DownloadOptions.Metadata;
329 var _body = null; 327 var _body = null;
330 328
331 if (request != null) { 329 if (request != null) {
332 _body = convert.JSON.encode((request).toJson()); 330 _body = convert.JSON.encode((request).toJson());
333 } 331 }
334 if (annotationId == null) { 332 if (annotationId == null) {
335 throw new core.ArgumentError("Parameter annotationId is required."); 333 throw new core.ArgumentError("Parameter annotationId is required.");
336 } 334 }
337 if (updateMask != null) { 335 if (updateMask != null) {
338 _queryParams["updateMask"] = [updateMask]; 336 _queryParams["updateMask"] = [updateMask];
339 } 337 }
340 338
341 _url = 'v1/annotations/' + commons.Escaper.ecapeVariable('$annotationId'); 339 _url = 'v1/annotations/' + commons.Escaper.ecapeVariable('$annotationId');
342 340
343 var _response = _requester.request(_url, 341 var _response = _requester.request(_url, "PUT",
344 "PUT", 342 body: _body,
345 body: _body, 343 queryParams: _queryParams,
346 queryParams: _queryParams, 344 uploadOptions: _uploadOptions,
347 uploadOptions: _uploadOptions, 345 uploadMedia: _uploadMedia,
348 uploadMedia: _uploadMedia, 346 downloadOptions: _downloadOptions);
349 downloadOptions: _downloadOptions);
350 return _response.then((data) => new Annotation.fromJson(data)); 347 return _response.then((data) => new Annotation.fromJson(data));
351 } 348 }
352
353 } 349 }
354 350
355
356 class AnnotationsetsResourceApi { 351 class AnnotationsetsResourceApi {
357 final commons.ApiRequester _requester; 352 final commons.ApiRequester _requester;
358 353
359 AnnotationsetsResourceApi(commons.ApiRequester client) : 354 AnnotationsetsResourceApi(commons.ApiRequester client) : _requester = client;
360 _requester = client;
361 355
362 /** 356 /// Creates a new annotation set. Caller must have WRITE permission for the
363 * Creates a new annotation set. Caller must have WRITE permission for the 357 /// associated dataset.
364 * associated dataset. 358 ///
365 * 359 /// The following fields are required:
366 * The following fields are required: 360 ///
367 * 361 /// * datasetId
368 * * datasetId 362 /// * referenceSetId
369 * * referenceSetId 363 ///
370 * 364 /// All other fields may be optionally specified, unless documented as being
371 * All other fields may be optionally specified, unless documented as being 365 /// server-generated (for example, the `id` field).
372 * server-generated (for example, the `id` field). 366 ///
373 * 367 /// [request] - The metadata request object.
374 * [request] - The metadata request object. 368 ///
375 * 369 /// Request parameters:
376 * Request parameters: 370 ///
377 * 371 /// Completes with a [AnnotationSet].
378 * Completes with a [AnnotationSet]. 372 ///
379 * 373 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
380 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 374 /// an error.
381 * error. 375 ///
382 * 376 /// If the used [http.Client] completes with an error when making a REST
383 * If the used [http.Client] completes with an error when making a REST call, 377 /// call, this method will complete with the same error.
384 * this method will complete with the same error.
385 */
386 async.Future<AnnotationSet> create(AnnotationSet request) { 378 async.Future<AnnotationSet> create(AnnotationSet request) {
387 var _url = null; 379 var _url = null;
388 var _queryParams = new core.Map(); 380 var _queryParams = new core.Map();
389 var _uploadMedia = null; 381 var _uploadMedia = null;
390 var _uploadOptions = null; 382 var _uploadOptions = null;
391 var _downloadOptions = commons.DownloadOptions.Metadata; 383 var _downloadOptions = commons.DownloadOptions.Metadata;
392 var _body = null; 384 var _body = null;
393 385
394 if (request != null) { 386 if (request != null) {
395 _body = convert.JSON.encode((request).toJson()); 387 _body = convert.JSON.encode((request).toJson());
396 } 388 }
397 389
398 _url = 'v1/annotationsets'; 390 _url = 'v1/annotationsets';
399 391
400 var _response = _requester.request(_url, 392 var _response = _requester.request(_url, "POST",
401 "POST", 393 body: _body,
402 body: _body, 394 queryParams: _queryParams,
403 queryParams: _queryParams, 395 uploadOptions: _uploadOptions,
404 uploadOptions: _uploadOptions, 396 uploadMedia: _uploadMedia,
405 uploadMedia: _uploadMedia, 397 downloadOptions: _downloadOptions);
406 downloadOptions: _downloadOptions);
407 return _response.then((data) => new AnnotationSet.fromJson(data)); 398 return _response.then((data) => new AnnotationSet.fromJson(data));
408 } 399 }
409 400
410 /** 401 /// Deletes an annotation set. Caller must have WRITE permission
411 * Deletes an annotation set. Caller must have WRITE permission 402 /// for the associated annotation set.
412 * for the associated annotation set. 403 ///
413 * 404 /// Request parameters:
414 * Request parameters: 405 ///
415 * 406 /// [annotationSetId] - The ID of the annotation set to be deleted.
416 * [annotationSetId] - The ID of the annotation set to be deleted. 407 ///
417 * 408 /// Completes with a [Empty].
418 * Completes with a [Empty]. 409 ///
419 * 410 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
420 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 411 /// an error.
421 * error. 412 ///
422 * 413 /// If the used [http.Client] completes with an error when making a REST
423 * If the used [http.Client] completes with an error when making a REST call, 414 /// call, this method will complete with the same error.
424 * this method will complete with the same error.
425 */
426 async.Future<Empty> delete(core.String annotationSetId) { 415 async.Future<Empty> delete(core.String annotationSetId) {
427 var _url = null; 416 var _url = null;
428 var _queryParams = new core.Map(); 417 var _queryParams = new core.Map();
429 var _uploadMedia = null; 418 var _uploadMedia = null;
430 var _uploadOptions = null; 419 var _uploadOptions = null;
431 var _downloadOptions = commons.DownloadOptions.Metadata; 420 var _downloadOptions = commons.DownloadOptions.Metadata;
432 var _body = null; 421 var _body = null;
433 422
434 if (annotationSetId == null) { 423 if (annotationSetId == null) {
435 throw new core.ArgumentError("Parameter annotationSetId is required."); 424 throw new core.ArgumentError("Parameter annotationSetId is required.");
436 } 425 }
437 426
438 _url = 'v1/annotationsets/' + commons.Escaper.ecapeVariable('$annotationSetI d'); 427 _url = 'v1/annotationsets/' +
428 commons.Escaper.ecapeVariable('$annotationSetId');
439 429
440 var _response = _requester.request(_url, 430 var _response = _requester.request(_url, "DELETE",
441 "DELETE", 431 body: _body,
442 body: _body, 432 queryParams: _queryParams,
443 queryParams: _queryParams, 433 uploadOptions: _uploadOptions,
444 uploadOptions: _uploadOptions, 434 uploadMedia: _uploadMedia,
445 uploadMedia: _uploadMedia, 435 downloadOptions: _downloadOptions);
446 downloadOptions: _downloadOptions);
447 return _response.then((data) => new Empty.fromJson(data)); 436 return _response.then((data) => new Empty.fromJson(data));
448 } 437 }
449 438
450 /** 439 /// Gets an annotation set. Caller must have READ permission for
451 * Gets an annotation set. Caller must have READ permission for 440 /// the associated dataset.
452 * the associated dataset. 441 ///
453 * 442 /// Request parameters:
454 * Request parameters: 443 ///
455 * 444 /// [annotationSetId] - The ID of the annotation set to be retrieved.
456 * [annotationSetId] - The ID of the annotation set to be retrieved. 445 ///
457 * 446 /// Completes with a [AnnotationSet].
458 * Completes with a [AnnotationSet]. 447 ///
459 * 448 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
460 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 449 /// an error.
461 * error. 450 ///
462 * 451 /// If the used [http.Client] completes with an error when making a REST
463 * If the used [http.Client] completes with an error when making a REST call, 452 /// call, this method will complete with the same error.
464 * this method will complete with the same error.
465 */
466 async.Future<AnnotationSet> get(core.String annotationSetId) { 453 async.Future<AnnotationSet> get(core.String annotationSetId) {
467 var _url = null; 454 var _url = null;
468 var _queryParams = new core.Map(); 455 var _queryParams = new core.Map();
469 var _uploadMedia = null; 456 var _uploadMedia = null;
470 var _uploadOptions = null; 457 var _uploadOptions = null;
471 var _downloadOptions = commons.DownloadOptions.Metadata; 458 var _downloadOptions = commons.DownloadOptions.Metadata;
472 var _body = null; 459 var _body = null;
473 460
474 if (annotationSetId == null) { 461 if (annotationSetId == null) {
475 throw new core.ArgumentError("Parameter annotationSetId is required."); 462 throw new core.ArgumentError("Parameter annotationSetId is required.");
476 } 463 }
477 464
478 _url = 'v1/annotationsets/' + commons.Escaper.ecapeVariable('$annotationSetI d'); 465 _url = 'v1/annotationsets/' +
466 commons.Escaper.ecapeVariable('$annotationSetId');
479 467
480 var _response = _requester.request(_url, 468 var _response = _requester.request(_url, "GET",
481 "GET", 469 body: _body,
482 body: _body, 470 queryParams: _queryParams,
483 queryParams: _queryParams, 471 uploadOptions: _uploadOptions,
484 uploadOptions: _uploadOptions, 472 uploadMedia: _uploadMedia,
485 uploadMedia: _uploadMedia, 473 downloadOptions: _downloadOptions);
486 downloadOptions: _downloadOptions);
487 return _response.then((data) => new AnnotationSet.fromJson(data)); 474 return _response.then((data) => new AnnotationSet.fromJson(data));
488 } 475 }
489 476
490 /** 477 /// Searches for annotation sets that match the given criteria. Annotation
491 * Searches for annotation sets that match the given criteria. Annotation sets 478 /// sets
492 * are returned in an unspecified order. This order is consistent, such that 479 /// are returned in an unspecified order. This order is consistent, such that
493 * two queries for the same content (regardless of page size) yield annotation 480 /// two queries for the same content (regardless of page size) yield
494 * sets in the same order across their respective streams of paginated 481 /// annotation
495 * responses. Caller must have READ permission for the queried datasets. 482 /// sets in the same order across their respective streams of paginated
496 * 483 /// responses. Caller must have READ permission for the queried datasets.
497 * [request] - The metadata request object. 484 ///
498 * 485 /// [request] - The metadata request object.
499 * Request parameters: 486 ///
500 * 487 /// Request parameters:
501 * Completes with a [SearchAnnotationSetsResponse]. 488 ///
502 * 489 /// Completes with a [SearchAnnotationSetsResponse].
503 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 490 ///
504 * error. 491 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
505 * 492 /// an error.
506 * If the used [http.Client] completes with an error when making a REST call, 493 ///
507 * this method will complete with the same error. 494 /// If the used [http.Client] completes with an error when making a REST
508 */ 495 /// call, this method will complete with the same error.
509 async.Future<SearchAnnotationSetsResponse> search(SearchAnnotationSetsRequest request) { 496 async.Future<SearchAnnotationSetsResponse> search(
497 SearchAnnotationSetsRequest request) {
510 var _url = null; 498 var _url = null;
511 var _queryParams = new core.Map(); 499 var _queryParams = new core.Map();
512 var _uploadMedia = null; 500 var _uploadMedia = null;
513 var _uploadOptions = null; 501 var _uploadOptions = null;
514 var _downloadOptions = commons.DownloadOptions.Metadata; 502 var _downloadOptions = commons.DownloadOptions.Metadata;
515 var _body = null; 503 var _body = null;
516 504
517 if (request != null) { 505 if (request != null) {
518 _body = convert.JSON.encode((request).toJson()); 506 _body = convert.JSON.encode((request).toJson());
519 } 507 }
520 508
521 _url = 'v1/annotationsets/search'; 509 _url = 'v1/annotationsets/search';
522 510
523 var _response = _requester.request(_url, 511 var _response = _requester.request(_url, "POST",
524 "POST", 512 body: _body,
525 body: _body, 513 queryParams: _queryParams,
526 queryParams: _queryParams, 514 uploadOptions: _uploadOptions,
527 uploadOptions: _uploadOptions, 515 uploadMedia: _uploadMedia,
528 uploadMedia: _uploadMedia, 516 downloadOptions: _downloadOptions);
529 downloadOptions: _downloadOptions); 517 return _response
530 return _response.then((data) => new SearchAnnotationSetsResponse.fromJson(da ta)); 518 .then((data) => new SearchAnnotationSetsResponse.fromJson(data));
531 } 519 }
532 520
533 /** 521 /// Updates an annotation set. The update must respect all mutability
534 * Updates an annotation set. The update must respect all mutability 522 /// restrictions and other invariants described on the annotation set
535 * restrictions and other invariants described on the annotation set resource. 523 /// resource.
536 * Caller must have WRITE permission for the associated dataset. 524 /// Caller must have WRITE permission for the associated dataset.
537 * 525 ///
538 * [request] - The metadata request object. 526 /// [request] - The metadata request object.
539 * 527 ///
540 * Request parameters: 528 /// Request parameters:
541 * 529 ///
542 * [annotationSetId] - The ID of the annotation set to be updated. 530 /// [annotationSetId] - The ID of the annotation set to be updated.
543 * 531 ///
544 * [updateMask] - An optional mask specifying which fields to update. Mutable 532 /// [updateMask] - An optional mask specifying which fields to update.
545 * fields are 533 /// Mutable fields are
546 * name, 534 /// name,
547 * source_uri, and 535 /// source_uri, and
548 * info. If unspecified, all 536 /// info. If unspecified, all
549 * mutable fields will be updated. 537 /// mutable fields will be updated.
550 * 538 ///
551 * Completes with a [AnnotationSet]. 539 /// Completes with a [AnnotationSet].
552 * 540 ///
553 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 541 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
554 * error. 542 /// an error.
555 * 543 ///
556 * If the used [http.Client] completes with an error when making a REST call, 544 /// If the used [http.Client] completes with an error when making a REST
557 * this method will complete with the same error. 545 /// call, this method will complete with the same error.
558 */ 546 async.Future<AnnotationSet> update(
559 async.Future<AnnotationSet> update(AnnotationSet request, core.String annotati onSetId, {core.String updateMask}) { 547 AnnotationSet request, core.String annotationSetId,
548 {core.String updateMask}) {
560 var _url = null; 549 var _url = null;
561 var _queryParams = new core.Map(); 550 var _queryParams = new core.Map();
562 var _uploadMedia = null; 551 var _uploadMedia = null;
563 var _uploadOptions = null; 552 var _uploadOptions = null;
564 var _downloadOptions = commons.DownloadOptions.Metadata; 553 var _downloadOptions = commons.DownloadOptions.Metadata;
565 var _body = null; 554 var _body = null;
566 555
567 if (request != null) { 556 if (request != null) {
568 _body = convert.JSON.encode((request).toJson()); 557 _body = convert.JSON.encode((request).toJson());
569 } 558 }
570 if (annotationSetId == null) { 559 if (annotationSetId == null) {
571 throw new core.ArgumentError("Parameter annotationSetId is required."); 560 throw new core.ArgumentError("Parameter annotationSetId is required.");
572 } 561 }
573 if (updateMask != null) { 562 if (updateMask != null) {
574 _queryParams["updateMask"] = [updateMask]; 563 _queryParams["updateMask"] = [updateMask];
575 } 564 }
576 565
577 _url = 'v1/annotationsets/' + commons.Escaper.ecapeVariable('$annotationSetI d'); 566 _url = 'v1/annotationsets/' +
567 commons.Escaper.ecapeVariable('$annotationSetId');
578 568
579 var _response = _requester.request(_url, 569 var _response = _requester.request(_url, "PUT",
580 "PUT", 570 body: _body,
581 body: _body, 571 queryParams: _queryParams,
582 queryParams: _queryParams, 572 uploadOptions: _uploadOptions,
583 uploadOptions: _uploadOptions, 573 uploadMedia: _uploadMedia,
584 uploadMedia: _uploadMedia, 574 downloadOptions: _downloadOptions);
585 downloadOptions: _downloadOptions);
586 return _response.then((data) => new AnnotationSet.fromJson(data)); 575 return _response.then((data) => new AnnotationSet.fromJson(data));
587 } 576 }
588
589 } 577 }
590 578
591
592 class CallsetsResourceApi { 579 class CallsetsResourceApi {
593 final commons.ApiRequester _requester; 580 final commons.ApiRequester _requester;
594 581
595 CallsetsResourceApi(commons.ApiRequester client) : 582 CallsetsResourceApi(commons.ApiRequester client) : _requester = client;
596 _requester = client;
597 583
598 /** 584 /// Creates a new call set.
599 * Creates a new call set. 585 ///
600 * 586 /// For the definitions of call sets and other genomics resources, see
601 * For the definitions of call sets and other genomics resources, see 587 /// [Fundamentals of Google
602 * [Fundamentals of Google 588 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
603 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 589 ///
604 * 590 /// [request] - The metadata request object.
605 * [request] - The metadata request object. 591 ///
606 * 592 /// Request parameters:
607 * Request parameters: 593 ///
608 * 594 /// Completes with a [CallSet].
609 * Completes with a [CallSet]. 595 ///
610 * 596 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
611 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 597 /// an error.
612 * error. 598 ///
613 * 599 /// If the used [http.Client] completes with an error when making a REST
614 * If the used [http.Client] completes with an error when making a REST call, 600 /// call, this method will complete with the same error.
615 * this method will complete with the same error.
616 */
617 async.Future<CallSet> create(CallSet request) { 601 async.Future<CallSet> create(CallSet request) {
618 var _url = null; 602 var _url = null;
619 var _queryParams = new core.Map(); 603 var _queryParams = new core.Map();
620 var _uploadMedia = null; 604 var _uploadMedia = null;
621 var _uploadOptions = null; 605 var _uploadOptions = null;
622 var _downloadOptions = commons.DownloadOptions.Metadata; 606 var _downloadOptions = commons.DownloadOptions.Metadata;
623 var _body = null; 607 var _body = null;
624 608
625 if (request != null) { 609 if (request != null) {
626 _body = convert.JSON.encode((request).toJson()); 610 _body = convert.JSON.encode((request).toJson());
627 } 611 }
628 612
629 _url = 'v1/callsets'; 613 _url = 'v1/callsets';
630 614
631 var _response = _requester.request(_url, 615 var _response = _requester.request(_url, "POST",
632 "POST", 616 body: _body,
633 body: _body, 617 queryParams: _queryParams,
634 queryParams: _queryParams, 618 uploadOptions: _uploadOptions,
635 uploadOptions: _uploadOptions, 619 uploadMedia: _uploadMedia,
636 uploadMedia: _uploadMedia, 620 downloadOptions: _downloadOptions);
637 downloadOptions: _downloadOptions);
638 return _response.then((data) => new CallSet.fromJson(data)); 621 return _response.then((data) => new CallSet.fromJson(data));
639 } 622 }
640 623
641 /** 624 /// Deletes a call set.
642 * Deletes a call set. 625 ///
643 * 626 /// For the definitions of call sets and other genomics resources, see
644 * For the definitions of call sets and other genomics resources, see 627 /// [Fundamentals of Google
645 * [Fundamentals of Google 628 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
646 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 629 ///
647 * 630 /// Request parameters:
648 * Request parameters: 631 ///
649 * 632 /// [callSetId] - The ID of the call set to be deleted.
650 * [callSetId] - The ID of the call set to be deleted. 633 ///
651 * 634 /// Completes with a [Empty].
652 * Completes with a [Empty]. 635 ///
653 * 636 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
654 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 637 /// an error.
655 * error. 638 ///
656 * 639 /// If the used [http.Client] completes with an error when making a REST
657 * If the used [http.Client] completes with an error when making a REST call, 640 /// call, this method will complete with the same error.
658 * this method will complete with the same error.
659 */
660 async.Future<Empty> delete(core.String callSetId) { 641 async.Future<Empty> delete(core.String callSetId) {
661 var _url = null; 642 var _url = null;
662 var _queryParams = new core.Map(); 643 var _queryParams = new core.Map();
663 var _uploadMedia = null; 644 var _uploadMedia = null;
664 var _uploadOptions = null; 645 var _uploadOptions = null;
665 var _downloadOptions = commons.DownloadOptions.Metadata; 646 var _downloadOptions = commons.DownloadOptions.Metadata;
666 var _body = null; 647 var _body = null;
667 648
668 if (callSetId == null) { 649 if (callSetId == null) {
669 throw new core.ArgumentError("Parameter callSetId is required."); 650 throw new core.ArgumentError("Parameter callSetId is required.");
670 } 651 }
671 652
672 _url = 'v1/callsets/' + commons.Escaper.ecapeVariable('$callSetId'); 653 _url = 'v1/callsets/' + commons.Escaper.ecapeVariable('$callSetId');
673 654
674 var _response = _requester.request(_url, 655 var _response = _requester.request(_url, "DELETE",
675 "DELETE", 656 body: _body,
676 body: _body, 657 queryParams: _queryParams,
677 queryParams: _queryParams, 658 uploadOptions: _uploadOptions,
678 uploadOptions: _uploadOptions, 659 uploadMedia: _uploadMedia,
679 uploadMedia: _uploadMedia, 660 downloadOptions: _downloadOptions);
680 downloadOptions: _downloadOptions);
681 return _response.then((data) => new Empty.fromJson(data)); 661 return _response.then((data) => new Empty.fromJson(data));
682 } 662 }
683 663
684 /** 664 /// Gets a call set by ID.
685 * Gets a call set by ID. 665 ///
686 * 666 /// For the definitions of call sets and other genomics resources, see
687 * For the definitions of call sets and other genomics resources, see 667 /// [Fundamentals of Google
688 * [Fundamentals of Google 668 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
689 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 669 ///
690 * 670 /// Request parameters:
691 * Request parameters: 671 ///
692 * 672 /// [callSetId] - The ID of the call set.
693 * [callSetId] - The ID of the call set. 673 ///
694 * 674 /// Completes with a [CallSet].
695 * Completes with a [CallSet]. 675 ///
696 * 676 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
697 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 677 /// an error.
698 * error. 678 ///
699 * 679 /// If the used [http.Client] completes with an error when making a REST
700 * If the used [http.Client] completes with an error when making a REST call, 680 /// call, this method will complete with the same error.
701 * this method will complete with the same error.
702 */
703 async.Future<CallSet> get(core.String callSetId) { 681 async.Future<CallSet> get(core.String callSetId) {
704 var _url = null; 682 var _url = null;
705 var _queryParams = new core.Map(); 683 var _queryParams = new core.Map();
706 var _uploadMedia = null; 684 var _uploadMedia = null;
707 var _uploadOptions = null; 685 var _uploadOptions = null;
708 var _downloadOptions = commons.DownloadOptions.Metadata; 686 var _downloadOptions = commons.DownloadOptions.Metadata;
709 var _body = null; 687 var _body = null;
710 688
711 if (callSetId == null) { 689 if (callSetId == null) {
712 throw new core.ArgumentError("Parameter callSetId is required."); 690 throw new core.ArgumentError("Parameter callSetId is required.");
713 } 691 }
714 692
715 _url = 'v1/callsets/' + commons.Escaper.ecapeVariable('$callSetId'); 693 _url = 'v1/callsets/' + commons.Escaper.ecapeVariable('$callSetId');
716 694
717 var _response = _requester.request(_url, 695 var _response = _requester.request(_url, "GET",
718 "GET", 696 body: _body,
719 body: _body, 697 queryParams: _queryParams,
720 queryParams: _queryParams, 698 uploadOptions: _uploadOptions,
721 uploadOptions: _uploadOptions, 699 uploadMedia: _uploadMedia,
722 uploadMedia: _uploadMedia, 700 downloadOptions: _downloadOptions);
723 downloadOptions: _downloadOptions);
724 return _response.then((data) => new CallSet.fromJson(data)); 701 return _response.then((data) => new CallSet.fromJson(data));
725 } 702 }
726 703
727 /** 704 /// Updates a call set.
728 * Updates a call set. 705 ///
729 * 706 /// For the definitions of call sets and other genomics resources, see
730 * For the definitions of call sets and other genomics resources, see 707 /// [Fundamentals of Google
731 * [Fundamentals of Google 708 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
732 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 709 ///
733 * 710 /// This method supports patch semantics.
734 * This method supports patch semantics. 711 ///
735 * 712 /// [request] - The metadata request object.
736 * [request] - The metadata request object. 713 ///
737 * 714 /// Request parameters:
738 * Request parameters: 715 ///
739 * 716 /// [callSetId] - The ID of the call set to be updated.
740 * [callSetId] - The ID of the call set to be updated. 717 ///
741 * 718 /// [updateMask] - An optional mask specifying which fields to update. At
742 * [updateMask] - An optional mask specifying which fields to update. At this 719 /// this time, the only
743 * time, the only 720 /// mutable field is name. The only
744 * mutable field is name. The only 721 /// acceptable value is "name". If unspecified, all mutable fields will be
745 * acceptable value is "name". If unspecified, all mutable fields will be 722 /// updated.
746 * updated. 723 ///
747 * 724 /// Completes with a [CallSet].
748 * Completes with a [CallSet]. 725 ///
749 * 726 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
750 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 727 /// an error.
751 * error. 728 ///
752 * 729 /// If the used [http.Client] completes with an error when making a REST
753 * If the used [http.Client] completes with an error when making a REST call, 730 /// call, this method will complete with the same error.
754 * this method will complete with the same error. 731 async.Future<CallSet> patch(CallSet request, core.String callSetId,
755 */ 732 {core.String updateMask}) {
756 async.Future<CallSet> patch(CallSet request, core.String callSetId, {core.Stri ng updateMask}) {
757 var _url = null; 733 var _url = null;
758 var _queryParams = new core.Map(); 734 var _queryParams = new core.Map();
759 var _uploadMedia = null; 735 var _uploadMedia = null;
760 var _uploadOptions = null; 736 var _uploadOptions = null;
761 var _downloadOptions = commons.DownloadOptions.Metadata; 737 var _downloadOptions = commons.DownloadOptions.Metadata;
762 var _body = null; 738 var _body = null;
763 739
764 if (request != null) { 740 if (request != null) {
765 _body = convert.JSON.encode((request).toJson()); 741 _body = convert.JSON.encode((request).toJson());
766 } 742 }
767 if (callSetId == null) { 743 if (callSetId == null) {
768 throw new core.ArgumentError("Parameter callSetId is required."); 744 throw new core.ArgumentError("Parameter callSetId is required.");
769 } 745 }
770 if (updateMask != null) { 746 if (updateMask != null) {
771 _queryParams["updateMask"] = [updateMask]; 747 _queryParams["updateMask"] = [updateMask];
772 } 748 }
773 749
774 _url = 'v1/callsets/' + commons.Escaper.ecapeVariable('$callSetId'); 750 _url = 'v1/callsets/' + commons.Escaper.ecapeVariable('$callSetId');
775 751
776 var _response = _requester.request(_url, 752 var _response = _requester.request(_url, "PATCH",
777 "PATCH", 753 body: _body,
778 body: _body, 754 queryParams: _queryParams,
779 queryParams: _queryParams, 755 uploadOptions: _uploadOptions,
780 uploadOptions: _uploadOptions, 756 uploadMedia: _uploadMedia,
781 uploadMedia: _uploadMedia, 757 downloadOptions: _downloadOptions);
782 downloadOptions: _downloadOptions);
783 return _response.then((data) => new CallSet.fromJson(data)); 758 return _response.then((data) => new CallSet.fromJson(data));
784 } 759 }
785 760
786 /** 761 /// Gets a list of call sets matching the criteria.
787 * Gets a list of call sets matching the criteria. 762 ///
788 * 763 /// For the definitions of call sets and other genomics resources, see
789 * For the definitions of call sets and other genomics resources, see 764 /// [Fundamentals of Google
790 * [Fundamentals of Google 765 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
791 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 766 ///
792 * 767 /// Implements
793 * Implements 768 /// [GlobalAllianceApi.searchCallSets](https://github.com/ga4gh/schemas/blob/v 0.5.1/src/main/resources/avro/variantmethods.avdl#L178).
794 * [GlobalAllianceApi.searchCallSets](https://github.com/ga4gh/schemas/blob/v0 .5.1/src/main/resources/avro/variantmethods.avdl#L178). 769 ///
795 * 770 /// [request] - The metadata request object.
796 * [request] - The metadata request object. 771 ///
797 * 772 /// Request parameters:
798 * Request parameters: 773 ///
799 * 774 /// Completes with a [SearchCallSetsResponse].
800 * Completes with a [SearchCallSetsResponse]. 775 ///
801 * 776 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
802 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 777 /// an error.
803 * error. 778 ///
804 * 779 /// If the used [http.Client] completes with an error when making a REST
805 * If the used [http.Client] completes with an error when making a REST call, 780 /// call, this method will complete with the same error.
806 * this method will complete with the same error.
807 */
808 async.Future<SearchCallSetsResponse> search(SearchCallSetsRequest request) { 781 async.Future<SearchCallSetsResponse> search(SearchCallSetsRequest request) {
809 var _url = null; 782 var _url = null;
810 var _queryParams = new core.Map(); 783 var _queryParams = new core.Map();
811 var _uploadMedia = null; 784 var _uploadMedia = null;
812 var _uploadOptions = null; 785 var _uploadOptions = null;
813 var _downloadOptions = commons.DownloadOptions.Metadata; 786 var _downloadOptions = commons.DownloadOptions.Metadata;
814 var _body = null; 787 var _body = null;
815 788
816 if (request != null) { 789 if (request != null) {
817 _body = convert.JSON.encode((request).toJson()); 790 _body = convert.JSON.encode((request).toJson());
818 } 791 }
819 792
820 _url = 'v1/callsets/search'; 793 _url = 'v1/callsets/search';
821 794
822 var _response = _requester.request(_url, 795 var _response = _requester.request(_url, "POST",
823 "POST", 796 body: _body,
824 body: _body, 797 queryParams: _queryParams,
825 queryParams: _queryParams, 798 uploadOptions: _uploadOptions,
826 uploadOptions: _uploadOptions, 799 uploadMedia: _uploadMedia,
827 uploadMedia: _uploadMedia, 800 downloadOptions: _downloadOptions);
828 downloadOptions: _downloadOptions);
829 return _response.then((data) => new SearchCallSetsResponse.fromJson(data)); 801 return _response.then((data) => new SearchCallSetsResponse.fromJson(data));
830 } 802 }
831
832 } 803 }
833 804
834
835 class DatasetsResourceApi { 805 class DatasetsResourceApi {
836 final commons.ApiRequester _requester; 806 final commons.ApiRequester _requester;
837 807
838 DatasetsResourceApi(commons.ApiRequester client) : 808 DatasetsResourceApi(commons.ApiRequester client) : _requester = client;
839 _requester = client;
840 809
841 /** 810 /// Creates a new dataset.
842 * Creates a new dataset. 811 ///
843 * 812 /// For the definitions of datasets and other genomics resources, see
844 * For the definitions of datasets and other genomics resources, see 813 /// [Fundamentals of Google
845 * [Fundamentals of Google 814 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
846 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 815 ///
847 * 816 /// [request] - The metadata request object.
848 * [request] - The metadata request object. 817 ///
849 * 818 /// Request parameters:
850 * Request parameters: 819 ///
851 * 820 /// Completes with a [Dataset].
852 * Completes with a [Dataset]. 821 ///
853 * 822 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
854 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 823 /// an error.
855 * error. 824 ///
856 * 825 /// If the used [http.Client] completes with an error when making a REST
857 * If the used [http.Client] completes with an error when making a REST call, 826 /// call, this method will complete with the same error.
858 * this method will complete with the same error.
859 */
860 async.Future<Dataset> create(Dataset request) { 827 async.Future<Dataset> create(Dataset request) {
861 var _url = null; 828 var _url = null;
862 var _queryParams = new core.Map(); 829 var _queryParams = new core.Map();
863 var _uploadMedia = null; 830 var _uploadMedia = null;
864 var _uploadOptions = null; 831 var _uploadOptions = null;
865 var _downloadOptions = commons.DownloadOptions.Metadata; 832 var _downloadOptions = commons.DownloadOptions.Metadata;
866 var _body = null; 833 var _body = null;
867 834
868 if (request != null) { 835 if (request != null) {
869 _body = convert.JSON.encode((request).toJson()); 836 _body = convert.JSON.encode((request).toJson());
870 } 837 }
871 838
872 _url = 'v1/datasets'; 839 _url = 'v1/datasets';
873 840
874 var _response = _requester.request(_url, 841 var _response = _requester.request(_url, "POST",
875 "POST", 842 body: _body,
876 body: _body, 843 queryParams: _queryParams,
877 queryParams: _queryParams, 844 uploadOptions: _uploadOptions,
878 uploadOptions: _uploadOptions, 845 uploadMedia: _uploadMedia,
879 uploadMedia: _uploadMedia, 846 downloadOptions: _downloadOptions);
880 downloadOptions: _downloadOptions);
881 return _response.then((data) => new Dataset.fromJson(data)); 847 return _response.then((data) => new Dataset.fromJson(data));
882 } 848 }
883 849
884 /** 850 /// Deletes a dataset and all of its contents (all read group sets,
885 * Deletes a dataset and all of its contents (all read group sets, 851 /// reference sets, variant sets, call sets, annotation sets, etc.)
886 * reference sets, variant sets, call sets, annotation sets, etc.) 852 /// This is reversible (up to one week after the deletion) via
887 * This is reversible (up to one week after the deletion) via 853 /// the
888 * the 854 /// datasets.undelete
889 * datasets.undelete 855 /// operation.
890 * operation. 856 ///
891 * 857 /// For the definitions of datasets and other genomics resources, see
892 * For the definitions of datasets and other genomics resources, see 858 /// [Fundamentals of Google
893 * [Fundamentals of Google 859 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
894 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 860 ///
895 * 861 /// Request parameters:
896 * Request parameters: 862 ///
897 * 863 /// [datasetId] - The ID of the dataset to be deleted.
898 * [datasetId] - The ID of the dataset to be deleted. 864 ///
899 * 865 /// Completes with a [Empty].
900 * Completes with a [Empty]. 866 ///
901 * 867 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
902 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 868 /// an error.
903 * error. 869 ///
904 * 870 /// If the used [http.Client] completes with an error when making a REST
905 * If the used [http.Client] completes with an error when making a REST call, 871 /// call, this method will complete with the same error.
906 * this method will complete with the same error.
907 */
908 async.Future<Empty> delete(core.String datasetId) { 872 async.Future<Empty> delete(core.String datasetId) {
909 var _url = null; 873 var _url = null;
910 var _queryParams = new core.Map(); 874 var _queryParams = new core.Map();
911 var _uploadMedia = null; 875 var _uploadMedia = null;
912 var _uploadOptions = null; 876 var _uploadOptions = null;
913 var _downloadOptions = commons.DownloadOptions.Metadata; 877 var _downloadOptions = commons.DownloadOptions.Metadata;
914 var _body = null; 878 var _body = null;
915 879
916 if (datasetId == null) { 880 if (datasetId == null) {
917 throw new core.ArgumentError("Parameter datasetId is required."); 881 throw new core.ArgumentError("Parameter datasetId is required.");
918 } 882 }
919 883
920 _url = 'v1/datasets/' + commons.Escaper.ecapeVariable('$datasetId'); 884 _url = 'v1/datasets/' + commons.Escaper.ecapeVariable('$datasetId');
921 885
922 var _response = _requester.request(_url, 886 var _response = _requester.request(_url, "DELETE",
923 "DELETE", 887 body: _body,
924 body: _body, 888 queryParams: _queryParams,
925 queryParams: _queryParams, 889 uploadOptions: _uploadOptions,
926 uploadOptions: _uploadOptions, 890 uploadMedia: _uploadMedia,
927 uploadMedia: _uploadMedia, 891 downloadOptions: _downloadOptions);
928 downloadOptions: _downloadOptions);
929 return _response.then((data) => new Empty.fromJson(data)); 892 return _response.then((data) => new Empty.fromJson(data));
930 } 893 }
931 894
932 /** 895 /// Gets a dataset by ID.
933 * Gets a dataset by ID. 896 ///
934 * 897 /// For the definitions of datasets and other genomics resources, see
935 * For the definitions of datasets and other genomics resources, see 898 /// [Fundamentals of Google
936 * [Fundamentals of Google 899 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
937 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 900 ///
938 * 901 /// Request parameters:
939 * Request parameters: 902 ///
940 * 903 /// [datasetId] - The ID of the dataset.
941 * [datasetId] - The ID of the dataset. 904 ///
942 * 905 /// Completes with a [Dataset].
943 * Completes with a [Dataset]. 906 ///
944 * 907 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
945 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 908 /// an error.
946 * error. 909 ///
947 * 910 /// If the used [http.Client] completes with an error when making a REST
948 * If the used [http.Client] completes with an error when making a REST call, 911 /// call, this method will complete with the same error.
949 * this method will complete with the same error.
950 */
951 async.Future<Dataset> get(core.String datasetId) { 912 async.Future<Dataset> get(core.String datasetId) {
952 var _url = null; 913 var _url = null;
953 var _queryParams = new core.Map(); 914 var _queryParams = new core.Map();
954 var _uploadMedia = null; 915 var _uploadMedia = null;
955 var _uploadOptions = null; 916 var _uploadOptions = null;
956 var _downloadOptions = commons.DownloadOptions.Metadata; 917 var _downloadOptions = commons.DownloadOptions.Metadata;
957 var _body = null; 918 var _body = null;
958 919
959 if (datasetId == null) { 920 if (datasetId == null) {
960 throw new core.ArgumentError("Parameter datasetId is required."); 921 throw new core.ArgumentError("Parameter datasetId is required.");
961 } 922 }
962 923
963 _url = 'v1/datasets/' + commons.Escaper.ecapeVariable('$datasetId'); 924 _url = 'v1/datasets/' + commons.Escaper.ecapeVariable('$datasetId');
964 925
965 var _response = _requester.request(_url, 926 var _response = _requester.request(_url, "GET",
966 "GET", 927 body: _body,
967 body: _body, 928 queryParams: _queryParams,
968 queryParams: _queryParams, 929 uploadOptions: _uploadOptions,
969 uploadOptions: _uploadOptions, 930 uploadMedia: _uploadMedia,
970 uploadMedia: _uploadMedia, 931 downloadOptions: _downloadOptions);
971 downloadOptions: _downloadOptions);
972 return _response.then((data) => new Dataset.fromJson(data)); 932 return _response.then((data) => new Dataset.fromJson(data));
973 } 933 }
974 934
975 /** 935 /// Gets the access control policy for the dataset. This is empty if the
976 * Gets the access control policy for the dataset. This is empty if the 936 /// policy or resource does not exist.
977 * policy or resource does not exist. 937 ///
978 * 938 /// See <a href="/iam/docs/managing-policies#getting_a_policy">Getting a
979 * See <a href="/iam/docs/managing-policies#getting_a_policy">Getting a 939 /// Policy</a> for more information.
980 * Policy</a> for more information. 940 ///
981 * 941 /// For the definitions of datasets and other genomics resources, see
982 * For the definitions of datasets and other genomics resources, see 942 /// [Fundamentals of Google
983 * [Fundamentals of Google 943 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
984 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 944 ///
985 * 945 /// [request] - The metadata request object.
986 * [request] - The metadata request object. 946 ///
987 * 947 /// Request parameters:
988 * Request parameters: 948 ///
989 * 949 /// [resource] - REQUIRED: The resource for which policy is being specified.
990 * [resource] - REQUIRED: The resource for which policy is being specified. 950 /// Format is
991 * Format is 951 /// `datasets/<dataset ID>`.
992 * `datasets/<dataset ID>`. 952 /// Value must have pattern "^datasets/[^/]+$".
993 * Value must have pattern "^datasets/[^/]+$". 953 ///
994 * 954 /// Completes with a [Policy].
995 * Completes with a [Policy]. 955 ///
996 * 956 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
997 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 957 /// an error.
998 * error. 958 ///
999 * 959 /// If the used [http.Client] completes with an error when making a REST
1000 * If the used [http.Client] completes with an error when making a REST call, 960 /// call, this method will complete with the same error.
1001 * this method will complete with the same error. 961 async.Future<Policy> getIamPolicy(
1002 */ 962 GetIamPolicyRequest request, core.String resource) {
1003 async.Future<Policy> getIamPolicy(GetIamPolicyRequest request, core.String res ource) {
1004 var _url = null; 963 var _url = null;
1005 var _queryParams = new core.Map(); 964 var _queryParams = new core.Map();
1006 var _uploadMedia = null; 965 var _uploadMedia = null;
1007 var _uploadOptions = null; 966 var _uploadOptions = null;
1008 var _downloadOptions = commons.DownloadOptions.Metadata; 967 var _downloadOptions = commons.DownloadOptions.Metadata;
1009 var _body = null; 968 var _body = null;
1010 969
1011 if (request != null) { 970 if (request != null) {
1012 _body = convert.JSON.encode((request).toJson()); 971 _body = convert.JSON.encode((request).toJson());
1013 } 972 }
1014 if (resource == null) { 973 if (resource == null) {
1015 throw new core.ArgumentError("Parameter resource is required."); 974 throw new core.ArgumentError("Parameter resource is required.");
1016 } 975 }
1017 976
1018 _url = 'v1/' + commons.Escaper.ecapeVariableReserved('$resource') + ':getIam Policy'; 977 _url = 'v1/' +
978 commons.Escaper.ecapeVariableReserved('$resource') +
979 ':getIamPolicy';
1019 980
1020 var _response = _requester.request(_url, 981 var _response = _requester.request(_url, "POST",
1021 "POST", 982 body: _body,
1022 body: _body, 983 queryParams: _queryParams,
1023 queryParams: _queryParams, 984 uploadOptions: _uploadOptions,
1024 uploadOptions: _uploadOptions, 985 uploadMedia: _uploadMedia,
1025 uploadMedia: _uploadMedia, 986 downloadOptions: _downloadOptions);
1026 downloadOptions: _downloadOptions);
1027 return _response.then((data) => new Policy.fromJson(data)); 987 return _response.then((data) => new Policy.fromJson(data));
1028 } 988 }
1029 989
1030 /** 990 /// Lists datasets within a project.
1031 * Lists datasets within a project. 991 ///
1032 * 992 /// For the definitions of datasets and other genomics resources, see
1033 * For the definitions of datasets and other genomics resources, see 993 /// [Fundamentals of Google
1034 * [Fundamentals of Google 994 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
1035 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 995 ///
1036 * 996 /// Request parameters:
1037 * Request parameters: 997 ///
1038 * 998 /// [pageToken] - The continuation token, which is used to page through large
1039 * [projectId] - Required. The Google Cloud project ID to list datasets for. 999 /// result sets.
1040 * 1000 /// To get the next page of results, set this parameter to the value of
1041 * [pageToken] - The continuation token, which is used to page through large 1001 /// `nextPageToken` from the previous response.
1042 * result sets. 1002 ///
1043 * To get the next page of results, set this parameter to the value of 1003 /// [pageSize] - The maximum number of results to return in a single page. If
1044 * `nextPageToken` from the previous response. 1004 /// unspecified,
1045 * 1005 /// defaults to 50. The maximum value is 1024.
1046 * [pageSize] - The maximum number of results to return in a single page. If 1006 ///
1047 * unspecified, 1007 /// [projectId] - Required. The Google Cloud project ID to list datasets for.
1048 * defaults to 50. The maximum value is 1024. 1008 ///
1049 * 1009 /// Completes with a [ListDatasetsResponse].
1050 * Completes with a [ListDatasetsResponse]. 1010 ///
1051 * 1011 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
1052 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 1012 /// an error.
1053 * error. 1013 ///
1054 * 1014 /// If the used [http.Client] completes with an error when making a REST
1055 * If the used [http.Client] completes with an error when making a REST call, 1015 /// call, this method will complete with the same error.
1056 * this method will complete with the same error. 1016 async.Future<ListDatasetsResponse> list(
1057 */ 1017 {core.String pageToken, core.int pageSize, core.String projectId}) {
1058 async.Future<ListDatasetsResponse> list({core.String projectId, core.String pa geToken, core.int pageSize}) {
1059 var _url = null; 1018 var _url = null;
1060 var _queryParams = new core.Map(); 1019 var _queryParams = new core.Map();
1061 var _uploadMedia = null; 1020 var _uploadMedia = null;
1062 var _uploadOptions = null; 1021 var _uploadOptions = null;
1063 var _downloadOptions = commons.DownloadOptions.Metadata; 1022 var _downloadOptions = commons.DownloadOptions.Metadata;
1064 var _body = null; 1023 var _body = null;
1065 1024
1066 if (projectId != null) {
1067 _queryParams["projectId"] = [projectId];
1068 }
1069 if (pageToken != null) { 1025 if (pageToken != null) {
1070 _queryParams["pageToken"] = [pageToken]; 1026 _queryParams["pageToken"] = [pageToken];
1071 } 1027 }
1072 if (pageSize != null) { 1028 if (pageSize != null) {
1073 _queryParams["pageSize"] = ["${pageSize}"]; 1029 _queryParams["pageSize"] = ["${pageSize}"];
1074 } 1030 }
1031 if (projectId != null) {
1032 _queryParams["projectId"] = [projectId];
1033 }
1075 1034
1076 _url = 'v1/datasets'; 1035 _url = 'v1/datasets';
1077 1036
1078 var _response = _requester.request(_url, 1037 var _response = _requester.request(_url, "GET",
1079 "GET", 1038 body: _body,
1080 body: _body, 1039 queryParams: _queryParams,
1081 queryParams: _queryParams, 1040 uploadOptions: _uploadOptions,
1082 uploadOptions: _uploadOptions, 1041 uploadMedia: _uploadMedia,
1083 uploadMedia: _uploadMedia, 1042 downloadOptions: _downloadOptions);
1084 downloadOptions: _downloadOptions);
1085 return _response.then((data) => new ListDatasetsResponse.fromJson(data)); 1043 return _response.then((data) => new ListDatasetsResponse.fromJson(data));
1086 } 1044 }
1087 1045
1088 /** 1046 /// Updates a dataset.
1089 * Updates a dataset. 1047 ///
1090 * 1048 /// For the definitions of datasets and other genomics resources, see
1091 * For the definitions of datasets and other genomics resources, see 1049 /// [Fundamentals of Google
1092 * [Fundamentals of Google 1050 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
1093 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 1051 ///
1094 * 1052 /// This method supports patch semantics.
1095 * This method supports patch semantics. 1053 ///
1096 * 1054 /// [request] - The metadata request object.
1097 * [request] - The metadata request object. 1055 ///
1098 * 1056 /// Request parameters:
1099 * Request parameters: 1057 ///
1100 * 1058 /// [datasetId] - The ID of the dataset to be updated.
1101 * [datasetId] - The ID of the dataset to be updated. 1059 ///
1102 * 1060 /// [updateMask] - An optional mask specifying which fields to update. At
1103 * [updateMask] - An optional mask specifying which fields to update. At this 1061 /// this time, the only
1104 * time, the only 1062 /// mutable field is name. The only
1105 * mutable field is name. The only 1063 /// acceptable value is "name". If unspecified, all mutable fields will be
1106 * acceptable value is "name". If unspecified, all mutable fields will be 1064 /// updated.
1107 * updated. 1065 ///
1108 * 1066 /// Completes with a [Dataset].
1109 * Completes with a [Dataset]. 1067 ///
1110 * 1068 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
1111 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 1069 /// an error.
1112 * error. 1070 ///
1113 * 1071 /// If the used [http.Client] completes with an error when making a REST
1114 * If the used [http.Client] completes with an error when making a REST call, 1072 /// call, this method will complete with the same error.
1115 * this method will complete with the same error. 1073 async.Future<Dataset> patch(Dataset request, core.String datasetId,
1116 */ 1074 {core.String updateMask}) {
1117 async.Future<Dataset> patch(Dataset request, core.String datasetId, {core.Stri ng updateMask}) {
1118 var _url = null; 1075 var _url = null;
1119 var _queryParams = new core.Map(); 1076 var _queryParams = new core.Map();
1120 var _uploadMedia = null; 1077 var _uploadMedia = null;
1121 var _uploadOptions = null; 1078 var _uploadOptions = null;
1122 var _downloadOptions = commons.DownloadOptions.Metadata; 1079 var _downloadOptions = commons.DownloadOptions.Metadata;
1123 var _body = null; 1080 var _body = null;
1124 1081
1125 if (request != null) { 1082 if (request != null) {
1126 _body = convert.JSON.encode((request).toJson()); 1083 _body = convert.JSON.encode((request).toJson());
1127 } 1084 }
1128 if (datasetId == null) { 1085 if (datasetId == null) {
1129 throw new core.ArgumentError("Parameter datasetId is required."); 1086 throw new core.ArgumentError("Parameter datasetId is required.");
1130 } 1087 }
1131 if (updateMask != null) { 1088 if (updateMask != null) {
1132 _queryParams["updateMask"] = [updateMask]; 1089 _queryParams["updateMask"] = [updateMask];
1133 } 1090 }
1134 1091
1135 _url = 'v1/datasets/' + commons.Escaper.ecapeVariable('$datasetId'); 1092 _url = 'v1/datasets/' + commons.Escaper.ecapeVariable('$datasetId');
1136 1093
1137 var _response = _requester.request(_url, 1094 var _response = _requester.request(_url, "PATCH",
1138 "PATCH", 1095 body: _body,
1139 body: _body, 1096 queryParams: _queryParams,
1140 queryParams: _queryParams, 1097 uploadOptions: _uploadOptions,
1141 uploadOptions: _uploadOptions, 1098 uploadMedia: _uploadMedia,
1142 uploadMedia: _uploadMedia, 1099 downloadOptions: _downloadOptions);
1143 downloadOptions: _downloadOptions);
1144 return _response.then((data) => new Dataset.fromJson(data)); 1100 return _response.then((data) => new Dataset.fromJson(data));
1145 } 1101 }
1146 1102
1147 /** 1103 /// Sets the access control policy on the specified dataset. Replaces any
1148 * Sets the access control policy on the specified dataset. Replaces any 1104 /// existing policy.
1149 * existing policy. 1105 ///
1150 * 1106 /// For the definitions of datasets and other genomics resources, see
1151 * For the definitions of datasets and other genomics resources, see 1107 /// [Fundamentals of Google
1152 * [Fundamentals of Google 1108 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
1153 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 1109 ///
1154 * 1110 /// See <a href="/iam/docs/managing-policies#setting_a_policy">Setting a
1155 * See <a href="/iam/docs/managing-policies#setting_a_policy">Setting a 1111 /// Policy</a> for more information.
1156 * Policy</a> for more information. 1112 ///
1157 * 1113 /// [request] - The metadata request object.
1158 * [request] - The metadata request object. 1114 ///
1159 * 1115 /// Request parameters:
1160 * Request parameters: 1116 ///
1161 * 1117 /// [resource] - REQUIRED: The resource for which policy is being specified.
1162 * [resource] - REQUIRED: The resource for which policy is being specified. 1118 /// Format is
1163 * Format is 1119 /// `datasets/<dataset ID>`.
1164 * `datasets/<dataset ID>`. 1120 /// Value must have pattern "^datasets/[^/]+$".
1165 * Value must have pattern "^datasets/[^/]+$". 1121 ///
1166 * 1122 /// Completes with a [Policy].
1167 * Completes with a [Policy]. 1123 ///
1168 * 1124 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
1169 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 1125 /// an error.
1170 * error. 1126 ///
1171 * 1127 /// If the used [http.Client] completes with an error when making a REST
1172 * If the used [http.Client] completes with an error when making a REST call, 1128 /// call, this method will complete with the same error.
1173 * this method will complete with the same error. 1129 async.Future<Policy> setIamPolicy(
1174 */ 1130 SetIamPolicyRequest request, core.String resource) {
1175 async.Future<Policy> setIamPolicy(SetIamPolicyRequest request, core.String res ource) {
1176 var _url = null; 1131 var _url = null;
1177 var _queryParams = new core.Map(); 1132 var _queryParams = new core.Map();
1178 var _uploadMedia = null; 1133 var _uploadMedia = null;
1179 var _uploadOptions = null; 1134 var _uploadOptions = null;
1180 var _downloadOptions = commons.DownloadOptions.Metadata; 1135 var _downloadOptions = commons.DownloadOptions.Metadata;
1181 var _body = null; 1136 var _body = null;
1182 1137
1183 if (request != null) { 1138 if (request != null) {
1184 _body = convert.JSON.encode((request).toJson()); 1139 _body = convert.JSON.encode((request).toJson());
1185 } 1140 }
1186 if (resource == null) { 1141 if (resource == null) {
1187 throw new core.ArgumentError("Parameter resource is required."); 1142 throw new core.ArgumentError("Parameter resource is required.");
1188 } 1143 }
1189 1144
1190 _url = 'v1/' + commons.Escaper.ecapeVariableReserved('$resource') + ':setIam Policy'; 1145 _url = 'v1/' +
1146 commons.Escaper.ecapeVariableReserved('$resource') +
1147 ':setIamPolicy';
1191 1148
1192 var _response = _requester.request(_url, 1149 var _response = _requester.request(_url, "POST",
1193 "POST", 1150 body: _body,
1194 body: _body, 1151 queryParams: _queryParams,
1195 queryParams: _queryParams, 1152 uploadOptions: _uploadOptions,
1196 uploadOptions: _uploadOptions, 1153 uploadMedia: _uploadMedia,
1197 uploadMedia: _uploadMedia, 1154 downloadOptions: _downloadOptions);
1198 downloadOptions: _downloadOptions);
1199 return _response.then((data) => new Policy.fromJson(data)); 1155 return _response.then((data) => new Policy.fromJson(data));
1200 } 1156 }
1201 1157
1202 /** 1158 /// Returns permissions that a caller has on the specified resource.
1203 * Returns permissions that a caller has on the specified resource. 1159 /// See <a href="/iam/docs/managing-policies#testing_permissions">Testing
1204 * See <a href="/iam/docs/managing-policies#testing_permissions">Testing 1160 /// Permissions</a> for more information.
1205 * Permissions</a> for more information. 1161 ///
1206 * 1162 /// For the definitions of datasets and other genomics resources, see
1207 * For the definitions of datasets and other genomics resources, see 1163 /// [Fundamentals of Google
1208 * [Fundamentals of Google 1164 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
1209 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 1165 ///
1210 * 1166 /// [request] - The metadata request object.
1211 * [request] - The metadata request object. 1167 ///
1212 * 1168 /// Request parameters:
1213 * Request parameters: 1169 ///
1214 * 1170 /// [resource] - REQUIRED: The resource for which policy is being specified.
1215 * [resource] - REQUIRED: The resource for which policy is being specified. 1171 /// Format is
1216 * Format is 1172 /// `datasets/<dataset ID>`.
1217 * `datasets/<dataset ID>`. 1173 /// Value must have pattern "^datasets/[^/]+$".
1218 * Value must have pattern "^datasets/[^/]+$". 1174 ///
1219 * 1175 /// Completes with a [TestIamPermissionsResponse].
1220 * Completes with a [TestIamPermissionsResponse]. 1176 ///
1221 * 1177 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
1222 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 1178 /// an error.
1223 * error. 1179 ///
1224 * 1180 /// If the used [http.Client] completes with an error when making a REST
1225 * If the used [http.Client] completes with an error when making a REST call, 1181 /// call, this method will complete with the same error.
1226 * this method will complete with the same error. 1182 async.Future<TestIamPermissionsResponse> testIamPermissions(
1227 */ 1183 TestIamPermissionsRequest request, core.String resource) {
1228 async.Future<TestIamPermissionsResponse> testIamPermissions(TestIamPermissions Request request, core.String resource) {
1229 var _url = null; 1184 var _url = null;
1230 var _queryParams = new core.Map(); 1185 var _queryParams = new core.Map();
1231 var _uploadMedia = null; 1186 var _uploadMedia = null;
1232 var _uploadOptions = null; 1187 var _uploadOptions = null;
1233 var _downloadOptions = commons.DownloadOptions.Metadata; 1188 var _downloadOptions = commons.DownloadOptions.Metadata;
1234 var _body = null; 1189 var _body = null;
1235 1190
1236 if (request != null) { 1191 if (request != null) {
1237 _body = convert.JSON.encode((request).toJson()); 1192 _body = convert.JSON.encode((request).toJson());
1238 } 1193 }
1239 if (resource == null) { 1194 if (resource == null) {
1240 throw new core.ArgumentError("Parameter resource is required."); 1195 throw new core.ArgumentError("Parameter resource is required.");
1241 } 1196 }
1242 1197
1243 _url = 'v1/' + commons.Escaper.ecapeVariableReserved('$resource') + ':testIa mPermissions'; 1198 _url = 'v1/' +
1199 commons.Escaper.ecapeVariableReserved('$resource') +
1200 ':testIamPermissions';
1244 1201
1245 var _response = _requester.request(_url, 1202 var _response = _requester.request(_url, "POST",
1246 "POST", 1203 body: _body,
1247 body: _body, 1204 queryParams: _queryParams,
1248 queryParams: _queryParams, 1205 uploadOptions: _uploadOptions,
1249 uploadOptions: _uploadOptions, 1206 uploadMedia: _uploadMedia,
1250 uploadMedia: _uploadMedia, 1207 downloadOptions: _downloadOptions);
1251 downloadOptions: _downloadOptions); 1208 return _response
1252 return _response.then((data) => new TestIamPermissionsResponse.fromJson(data )); 1209 .then((data) => new TestIamPermissionsResponse.fromJson(data));
1253 } 1210 }
1254 1211
1255 /** 1212 /// Undeletes a dataset by restoring a dataset which was deleted via this
1256 * Undeletes a dataset by restoring a dataset which was deleted via this API. 1213 /// API.
1257 * 1214 ///
1258 * For the definitions of datasets and other genomics resources, see 1215 /// For the definitions of datasets and other genomics resources, see
1259 * [Fundamentals of Google 1216 /// [Fundamentals of Google
1260 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 1217 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
1261 * 1218 ///
1262 * This operation is only possible for a week after the deletion occurred. 1219 /// This operation is only possible for a week after the deletion occurred.
1263 * 1220 ///
1264 * [request] - The metadata request object. 1221 /// [request] - The metadata request object.
1265 * 1222 ///
1266 * Request parameters: 1223 /// Request parameters:
1267 * 1224 ///
1268 * [datasetId] - The ID of the dataset to be undeleted. 1225 /// [datasetId] - The ID of the dataset to be undeleted.
1269 * 1226 ///
1270 * Completes with a [Dataset]. 1227 /// Completes with a [Dataset].
1271 * 1228 ///
1272 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 1229 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
1273 * error. 1230 /// an error.
1274 * 1231 ///
1275 * If the used [http.Client] completes with an error when making a REST call, 1232 /// If the used [http.Client] completes with an error when making a REST
1276 * this method will complete with the same error. 1233 /// call, this method will complete with the same error.
1277 */ 1234 async.Future<Dataset> undelete(
1278 async.Future<Dataset> undelete(UndeleteDatasetRequest request, core.String dat asetId) { 1235 UndeleteDatasetRequest request, core.String datasetId) {
1279 var _url = null; 1236 var _url = null;
1280 var _queryParams = new core.Map(); 1237 var _queryParams = new core.Map();
1281 var _uploadMedia = null; 1238 var _uploadMedia = null;
1282 var _uploadOptions = null; 1239 var _uploadOptions = null;
1283 var _downloadOptions = commons.DownloadOptions.Metadata; 1240 var _downloadOptions = commons.DownloadOptions.Metadata;
1284 var _body = null; 1241 var _body = null;
1285 1242
1286 if (request != null) { 1243 if (request != null) {
1287 _body = convert.JSON.encode((request).toJson()); 1244 _body = convert.JSON.encode((request).toJson());
1288 } 1245 }
1289 if (datasetId == null) { 1246 if (datasetId == null) {
1290 throw new core.ArgumentError("Parameter datasetId is required."); 1247 throw new core.ArgumentError("Parameter datasetId is required.");
1291 } 1248 }
1292 1249
1293 _url = 'v1/datasets/' + commons.Escaper.ecapeVariable('$datasetId') + ':unde lete'; 1250 _url = 'v1/datasets/' +
1251 commons.Escaper.ecapeVariable('$datasetId') +
1252 ':undelete';
1294 1253
1295 var _response = _requester.request(_url, 1254 var _response = _requester.request(_url, "POST",
1296 "POST", 1255 body: _body,
1297 body: _body, 1256 queryParams: _queryParams,
1298 queryParams: _queryParams, 1257 uploadOptions: _uploadOptions,
1299 uploadOptions: _uploadOptions, 1258 uploadMedia: _uploadMedia,
1300 uploadMedia: _uploadMedia, 1259 downloadOptions: _downloadOptions);
1301 downloadOptions: _downloadOptions);
1302 return _response.then((data) => new Dataset.fromJson(data)); 1260 return _response.then((data) => new Dataset.fromJson(data));
1303 } 1261 }
1304
1305 } 1262 }
1306 1263
1307
1308 class OperationsResourceApi { 1264 class OperationsResourceApi {
1309 final commons.ApiRequester _requester; 1265 final commons.ApiRequester _requester;
1310 1266
1311 OperationsResourceApi(commons.ApiRequester client) : 1267 OperationsResourceApi(commons.ApiRequester client) : _requester = client;
1312 _requester = client;
1313 1268
1314 /** 1269 /// Starts asynchronous cancellation on a long-running operation. The server
1315 * Starts asynchronous cancellation on a long-running operation. The server 1270 /// makes a best effort to cancel the operation, but success is not
1316 * makes a best effort to cancel the operation, but success is not guaranteed. 1271 /// guaranteed. Clients may use Operations.GetOperation or
1317 * Clients may use Operations.GetOperation or Operations.ListOperations to 1272 /// Operations.ListOperations to check whether the cancellation succeeded or
1318 * check whether the cancellation succeeded or the operation completed despite 1273 /// the operation completed despite cancellation.
1319 * cancellation. 1274 ///
1320 * 1275 /// [request] - The metadata request object.
1321 * [request] - The metadata request object. 1276 ///
1322 * 1277 /// Request parameters:
1323 * Request parameters: 1278 ///
1324 * 1279 /// [name] - The name of the operation resource to be cancelled.
1325 * [name] - The name of the operation resource to be cancelled. 1280 /// Value must have pattern "^operations/.+$".
1326 * Value must have pattern "^operations/.+$". 1281 ///
1327 * 1282 /// Completes with a [Empty].
1328 * Completes with a [Empty]. 1283 ///
1329 * 1284 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
1330 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 1285 /// an error.
1331 * error. 1286 ///
1332 * 1287 /// If the used [http.Client] completes with an error when making a REST
1333 * If the used [http.Client] completes with an error when making a REST call, 1288 /// call, this method will complete with the same error.
1334 * this method will complete with the same error.
1335 */
1336 async.Future<Empty> cancel(CancelOperationRequest request, core.String name) { 1289 async.Future<Empty> cancel(CancelOperationRequest request, core.String name) {
1337 var _url = null; 1290 var _url = null;
1338 var _queryParams = new core.Map(); 1291 var _queryParams = new core.Map();
1339 var _uploadMedia = null; 1292 var _uploadMedia = null;
1340 var _uploadOptions = null; 1293 var _uploadOptions = null;
1341 var _downloadOptions = commons.DownloadOptions.Metadata; 1294 var _downloadOptions = commons.DownloadOptions.Metadata;
1342 var _body = null; 1295 var _body = null;
1343 1296
1344 if (request != null) { 1297 if (request != null) {
1345 _body = convert.JSON.encode((request).toJson()); 1298 _body = convert.JSON.encode((request).toJson());
1346 } 1299 }
1347 if (name == null) { 1300 if (name == null) {
1348 throw new core.ArgumentError("Parameter name is required."); 1301 throw new core.ArgumentError("Parameter name is required.");
1349 } 1302 }
1350 1303
1351 _url = 'v1/' + commons.Escaper.ecapeVariableReserved('$name') + ':cancel'; 1304 _url = 'v1/' + commons.Escaper.ecapeVariableReserved('$name') + ':cancel';
1352 1305
1353 var _response = _requester.request(_url, 1306 var _response = _requester.request(_url, "POST",
1354 "POST", 1307 body: _body,
1355 body: _body, 1308 queryParams: _queryParams,
1356 queryParams: _queryParams, 1309 uploadOptions: _uploadOptions,
1357 uploadOptions: _uploadOptions, 1310 uploadMedia: _uploadMedia,
1358 uploadMedia: _uploadMedia, 1311 downloadOptions: _downloadOptions);
1359 downloadOptions: _downloadOptions);
1360 return _response.then((data) => new Empty.fromJson(data)); 1312 return _response.then((data) => new Empty.fromJson(data));
1361 } 1313 }
1362 1314
1363 /** 1315 /// Gets the latest state of a long-running operation. Clients can use this
1364 * Gets the latest state of a long-running operation. Clients can use this 1316 /// method to poll the operation result at intervals as recommended by the
1365 * method to poll the operation result at intervals as recommended by the API 1317 /// API
1366 * service. 1318 /// service.
1367 * 1319 ///
1368 * Request parameters: 1320 /// Request parameters:
1369 * 1321 ///
1370 * [name] - The name of the operation resource. 1322 /// [name] - The name of the operation resource.
1371 * Value must have pattern "^operations/.+$". 1323 /// Value must have pattern "^operations/.+$".
1372 * 1324 ///
1373 * Completes with a [Operation]. 1325 /// Completes with a [Operation].
1374 * 1326 ///
1375 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 1327 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
1376 * error. 1328 /// an error.
1377 * 1329 ///
1378 * If the used [http.Client] completes with an error when making a REST call, 1330 /// If the used [http.Client] completes with an error when making a REST
1379 * this method will complete with the same error. 1331 /// call, this method will complete with the same error.
1380 */
1381 async.Future<Operation> get(core.String name) { 1332 async.Future<Operation> get(core.String name) {
1382 var _url = null; 1333 var _url = null;
1383 var _queryParams = new core.Map(); 1334 var _queryParams = new core.Map();
1384 var _uploadMedia = null; 1335 var _uploadMedia = null;
1385 var _uploadOptions = null; 1336 var _uploadOptions = null;
1386 var _downloadOptions = commons.DownloadOptions.Metadata; 1337 var _downloadOptions = commons.DownloadOptions.Metadata;
1387 var _body = null; 1338 var _body = null;
1388 1339
1389 if (name == null) { 1340 if (name == null) {
1390 throw new core.ArgumentError("Parameter name is required."); 1341 throw new core.ArgumentError("Parameter name is required.");
1391 } 1342 }
1392 1343
1393 _url = 'v1/' + commons.Escaper.ecapeVariableReserved('$name'); 1344 _url = 'v1/' + commons.Escaper.ecapeVariableReserved('$name');
1394 1345
1395 var _response = _requester.request(_url, 1346 var _response = _requester.request(_url, "GET",
1396 "GET", 1347 body: _body,
1397 body: _body, 1348 queryParams: _queryParams,
1398 queryParams: _queryParams, 1349 uploadOptions: _uploadOptions,
1399 uploadOptions: _uploadOptions, 1350 uploadMedia: _uploadMedia,
1400 uploadMedia: _uploadMedia, 1351 downloadOptions: _downloadOptions);
1401 downloadOptions: _downloadOptions);
1402 return _response.then((data) => new Operation.fromJson(data)); 1352 return _response.then((data) => new Operation.fromJson(data));
1403 } 1353 }
1404 1354
1405 /** 1355 /// Lists operations that match the specified filter in the request.
1406 * Lists operations that match the specified filter in the request. 1356 ///
1407 * 1357 /// Request parameters:
1408 * Request parameters: 1358 ///
1409 * 1359 /// [name] - The name of the operation's parent resource.
1410 * [name] - The name of the operation's parent resource. 1360 /// Value must have pattern "^operations$".
1411 * Value must have pattern "^operations$". 1361 ///
1412 * 1362 /// [pageToken] - The standard list page token.
1413 * [pageToken] - The standard list page token. 1363 ///
1414 * 1364 /// [pageSize] - The maximum number of results to return. If unspecified,
1415 * [pageSize] - The maximum number of results to return. If unspecified, 1365 /// defaults to
1416 * defaults to 1366 /// 256. The maximum value is 2048.
1417 * 256. The maximum value is 2048. 1367 ///
1418 * 1368 /// [filter] - A string for filtering Operations.
1419 * [filter] - A string for filtering Operations. 1369 /// The following filter fields are supported&#58;
1420 * The following filter fields are supported&#58; 1370 ///
1421 * 1371 /// * projectId&#58; Required. Corresponds to
1422 * * projectId&#58; Required. Corresponds to 1372 /// OperationMetadata.projectId.
1423 * OperationMetadata.projectId. 1373 /// * createTime&#58; The time this job was created, in seconds from the
1424 * * createTime&#58; The time this job was created, in seconds from the 1374 /// [epoch](http://en.wikipedia.org/wiki/Unix_time). Can use `>=` and/or `<=`
1425 * [epoch](http://en.wikipedia.org/wiki/Unix_time). Can use `>=` and/or `<=` 1375 /// operators.
1426 * operators. 1376 /// * status&#58; Can be `RUNNING`, `SUCCESS`, `FAILURE`, or `CANCELED`. Only
1427 * * status&#58; Can be `RUNNING`, `SUCCESS`, `FAILURE`, or `CANCELED`. Only 1377 /// one status may be specified.
1428 * one status may be specified. 1378 /// * labels.key where key is a label key.
1429 * * labels.key where key is a label key. 1379 ///
1430 * 1380 /// Examples&#58;
1431 * Examples&#58; 1381 ///
1432 * 1382 /// * `projectId = my-project AND createTime >= 1432140000`
1433 * * `projectId = my-project AND createTime >= 1432140000` 1383 /// * `projectId = my-project AND createTime >= 1432140000 AND createTime <=
1434 * * `projectId = my-project AND createTime >= 1432140000 AND createTime <= 1384 /// 1432150000 AND status = RUNNING`
1435 * 1432150000 AND status = RUNNING` 1385 /// * `projectId = my-project AND labels.color = *`
1436 * * `projectId = my-project AND labels.color = *` 1386 /// * `projectId = my-project AND labels.color = red`
1437 * * `projectId = my-project AND labels.color = red` 1387 ///
1438 * 1388 /// Completes with a [ListOperationsResponse].
1439 * Completes with a [ListOperationsResponse]. 1389 ///
1440 * 1390 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
1441 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 1391 /// an error.
1442 * error. 1392 ///
1443 * 1393 /// If the used [http.Client] completes with an error when making a REST
1444 * If the used [http.Client] completes with an error when making a REST call, 1394 /// call, this method will complete with the same error.
1445 * this method will complete with the same error. 1395 async.Future<ListOperationsResponse> list(core.String name,
1446 */ 1396 {core.String pageToken, core.int pageSize, core.String filter}) {
1447 async.Future<ListOperationsResponse> list(core.String name, {core.String pageT oken, core.int pageSize, core.String filter}) {
1448 var _url = null; 1397 var _url = null;
1449 var _queryParams = new core.Map(); 1398 var _queryParams = new core.Map();
1450 var _uploadMedia = null; 1399 var _uploadMedia = null;
1451 var _uploadOptions = null; 1400 var _uploadOptions = null;
1452 var _downloadOptions = commons.DownloadOptions.Metadata; 1401 var _downloadOptions = commons.DownloadOptions.Metadata;
1453 var _body = null; 1402 var _body = null;
1454 1403
1455 if (name == null) { 1404 if (name == null) {
1456 throw new core.ArgumentError("Parameter name is required."); 1405 throw new core.ArgumentError("Parameter name is required.");
1457 } 1406 }
1458 if (pageToken != null) { 1407 if (pageToken != null) {
1459 _queryParams["pageToken"] = [pageToken]; 1408 _queryParams["pageToken"] = [pageToken];
1460 } 1409 }
1461 if (pageSize != null) { 1410 if (pageSize != null) {
1462 _queryParams["pageSize"] = ["${pageSize}"]; 1411 _queryParams["pageSize"] = ["${pageSize}"];
1463 } 1412 }
1464 if (filter != null) { 1413 if (filter != null) {
1465 _queryParams["filter"] = [filter]; 1414 _queryParams["filter"] = [filter];
1466 } 1415 }
1467 1416
1468 _url = 'v1/' + commons.Escaper.ecapeVariableReserved('$name'); 1417 _url = 'v1/' + commons.Escaper.ecapeVariableReserved('$name');
1469 1418
1470 var _response = _requester.request(_url, 1419 var _response = _requester.request(_url, "GET",
1471 "GET", 1420 body: _body,
1472 body: _body, 1421 queryParams: _queryParams,
1473 queryParams: _queryParams, 1422 uploadOptions: _uploadOptions,
1474 uploadOptions: _uploadOptions, 1423 uploadMedia: _uploadMedia,
1475 uploadMedia: _uploadMedia, 1424 downloadOptions: _downloadOptions);
1476 downloadOptions: _downloadOptions);
1477 return _response.then((data) => new ListOperationsResponse.fromJson(data)); 1425 return _response.then((data) => new ListOperationsResponse.fromJson(data));
1478 } 1426 }
1479
1480 } 1427 }
1481 1428
1482
1483 class ReadgroupsetsResourceApi { 1429 class ReadgroupsetsResourceApi {
1484 final commons.ApiRequester _requester; 1430 final commons.ApiRequester _requester;
1485 1431
1486 ReadgroupsetsCoveragebucketsResourceApi get coveragebuckets => new Readgroupse tsCoveragebucketsResourceApi(_requester); 1432 ReadgroupsetsCoveragebucketsResourceApi get coveragebuckets =>
1433 new ReadgroupsetsCoveragebucketsResourceApi(_requester);
1487 1434
1488 ReadgroupsetsResourceApi(commons.ApiRequester client) : 1435 ReadgroupsetsResourceApi(commons.ApiRequester client) : _requester = client;
1489 _requester = client;
1490 1436
1491 /** 1437 /// Deletes a read group set.
1492 * Deletes a read group set. 1438 ///
1493 * 1439 /// For the definitions of read group sets and other genomics resources, see
1494 * For the definitions of read group sets and other genomics resources, see 1440 /// [Fundamentals of Google
1495 * [Fundamentals of Google 1441 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
1496 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 1442 ///
1497 * 1443 /// Request parameters:
1498 * Request parameters: 1444 ///
1499 * 1445 /// [readGroupSetId] - The ID of the read group set to be deleted. The caller
1500 * [readGroupSetId] - The ID of the read group set to be deleted. The caller 1446 /// must have WRITE
1501 * must have WRITE 1447 /// permissions to the dataset associated with this read group set.
1502 * permissions to the dataset associated with this read group set. 1448 ///
1503 * 1449 /// Completes with a [Empty].
1504 * Completes with a [Empty]. 1450 ///
1505 * 1451 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
1506 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 1452 /// an error.
1507 * error. 1453 ///
1508 * 1454 /// If the used [http.Client] completes with an error when making a REST
1509 * If the used [http.Client] completes with an error when making a REST call, 1455 /// call, this method will complete with the same error.
1510 * this method will complete with the same error.
1511 */
1512 async.Future<Empty> delete(core.String readGroupSetId) { 1456 async.Future<Empty> delete(core.String readGroupSetId) {
1513 var _url = null; 1457 var _url = null;
1514 var _queryParams = new core.Map(); 1458 var _queryParams = new core.Map();
1515 var _uploadMedia = null; 1459 var _uploadMedia = null;
1516 var _uploadOptions = null; 1460 var _uploadOptions = null;
1517 var _downloadOptions = commons.DownloadOptions.Metadata; 1461 var _downloadOptions = commons.DownloadOptions.Metadata;
1518 var _body = null; 1462 var _body = null;
1519 1463
1520 if (readGroupSetId == null) { 1464 if (readGroupSetId == null) {
1521 throw new core.ArgumentError("Parameter readGroupSetId is required."); 1465 throw new core.ArgumentError("Parameter readGroupSetId is required.");
1522 } 1466 }
1523 1467
1524 _url = 'v1/readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId' ); 1468 _url =
1469 'v1/readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId');
1525 1470
1526 var _response = _requester.request(_url, 1471 var _response = _requester.request(_url, "DELETE",
1527 "DELETE", 1472 body: _body,
1528 body: _body, 1473 queryParams: _queryParams,
1529 queryParams: _queryParams, 1474 uploadOptions: _uploadOptions,
1530 uploadOptions: _uploadOptions, 1475 uploadMedia: _uploadMedia,
1531 uploadMedia: _uploadMedia, 1476 downloadOptions: _downloadOptions);
1532 downloadOptions: _downloadOptions);
1533 return _response.then((data) => new Empty.fromJson(data)); 1477 return _response.then((data) => new Empty.fromJson(data));
1534 } 1478 }
1535 1479
1536 /** 1480 /// Exports a read group set to a BAM file in Google Cloud Storage.
1537 * Exports a read group set to a BAM file in Google Cloud Storage. 1481 ///
1538 * 1482 /// For the definitions of read group sets and other genomics resources, see
1539 * For the definitions of read group sets and other genomics resources, see 1483 /// [Fundamentals of Google
1540 * [Fundamentals of Google 1484 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
1541 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 1485 ///
1542 * 1486 /// Note that currently there may be some differences between exported BAM
1543 * Note that currently there may be some differences between exported BAM 1487 /// files and the original BAM file at the time of import. See
1544 * files and the original BAM file at the time of import. See 1488 /// ImportReadGroupSets
1545 * ImportReadGroupSets 1489 /// for caveats.
1546 * for caveats. 1490 ///
1547 * 1491 /// [request] - The metadata request object.
1548 * [request] - The metadata request object. 1492 ///
1549 * 1493 /// Request parameters:
1550 * Request parameters: 1494 ///
1551 * 1495 /// [readGroupSetId] - Required. The ID of the read group set to export. The
1552 * [readGroupSetId] - Required. The ID of the read group set to export. The 1496 /// caller must have
1553 * caller must have 1497 /// READ access to this read group set.
1554 * READ access to this read group set. 1498 ///
1555 * 1499 /// Completes with a [Operation].
1556 * Completes with a [Operation]. 1500 ///
1557 * 1501 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
1558 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 1502 /// an error.
1559 * error. 1503 ///
1560 * 1504 /// If the used [http.Client] completes with an error when making a REST
1561 * If the used [http.Client] completes with an error when making a REST call, 1505 /// call, this method will complete with the same error.
1562 * this method will complete with the same error. 1506 async.Future<Operation> export(
1563 */ 1507 ExportReadGroupSetRequest request, core.String readGroupSetId) {
1564 async.Future<Operation> export(ExportReadGroupSetRequest request, core.String readGroupSetId) {
1565 var _url = null; 1508 var _url = null;
1566 var _queryParams = new core.Map(); 1509 var _queryParams = new core.Map();
1567 var _uploadMedia = null; 1510 var _uploadMedia = null;
1568 var _uploadOptions = null; 1511 var _uploadOptions = null;
1569 var _downloadOptions = commons.DownloadOptions.Metadata; 1512 var _downloadOptions = commons.DownloadOptions.Metadata;
1570 var _body = null; 1513 var _body = null;
1571 1514
1572 if (request != null) { 1515 if (request != null) {
1573 _body = convert.JSON.encode((request).toJson()); 1516 _body = convert.JSON.encode((request).toJson());
1574 } 1517 }
1575 if (readGroupSetId == null) { 1518 if (readGroupSetId == null) {
1576 throw new core.ArgumentError("Parameter readGroupSetId is required."); 1519 throw new core.ArgumentError("Parameter readGroupSetId is required.");
1577 } 1520 }
1578 1521
1579 _url = 'v1/readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId' ) + ':export'; 1522 _url = 'v1/readgroupsets/' +
1523 commons.Escaper.ecapeVariable('$readGroupSetId') +
1524 ':export';
1580 1525
1581 var _response = _requester.request(_url, 1526 var _response = _requester.request(_url, "POST",
1582 "POST", 1527 body: _body,
1583 body: _body, 1528 queryParams: _queryParams,
1584 queryParams: _queryParams, 1529 uploadOptions: _uploadOptions,
1585 uploadOptions: _uploadOptions, 1530 uploadMedia: _uploadMedia,
1586 uploadMedia: _uploadMedia, 1531 downloadOptions: _downloadOptions);
1587 downloadOptions: _downloadOptions);
1588 return _response.then((data) => new Operation.fromJson(data)); 1532 return _response.then((data) => new Operation.fromJson(data));
1589 } 1533 }
1590 1534
1591 /** 1535 /// Gets a read group set by ID.
1592 * Gets a read group set by ID. 1536 ///
1593 * 1537 /// For the definitions of read group sets and other genomics resources, see
1594 * For the definitions of read group sets and other genomics resources, see 1538 /// [Fundamentals of Google
1595 * [Fundamentals of Google 1539 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
1596 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 1540 ///
1597 * 1541 /// Request parameters:
1598 * Request parameters: 1542 ///
1599 * 1543 /// [readGroupSetId] - The ID of the read group set.
1600 * [readGroupSetId] - The ID of the read group set. 1544 ///
1601 * 1545 /// Completes with a [ReadGroupSet].
1602 * Completes with a [ReadGroupSet]. 1546 ///
1603 * 1547 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
1604 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 1548 /// an error.
1605 * error. 1549 ///
1606 * 1550 /// If the used [http.Client] completes with an error when making a REST
1607 * If the used [http.Client] completes with an error when making a REST call, 1551 /// call, this method will complete with the same error.
1608 * this method will complete with the same error.
1609 */
1610 async.Future<ReadGroupSet> get(core.String readGroupSetId) { 1552 async.Future<ReadGroupSet> get(core.String readGroupSetId) {
1611 var _url = null; 1553 var _url = null;
1612 var _queryParams = new core.Map(); 1554 var _queryParams = new core.Map();
1613 var _uploadMedia = null; 1555 var _uploadMedia = null;
1614 var _uploadOptions = null; 1556 var _uploadOptions = null;
1615 var _downloadOptions = commons.DownloadOptions.Metadata; 1557 var _downloadOptions = commons.DownloadOptions.Metadata;
1616 var _body = null; 1558 var _body = null;
1617 1559
1618 if (readGroupSetId == null) { 1560 if (readGroupSetId == null) {
1619 throw new core.ArgumentError("Parameter readGroupSetId is required."); 1561 throw new core.ArgumentError("Parameter readGroupSetId is required.");
1620 } 1562 }
1621 1563
1622 _url = 'v1/readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId' ); 1564 _url =
1565 'v1/readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId');
1623 1566
1624 var _response = _requester.request(_url, 1567 var _response = _requester.request(_url, "GET",
1625 "GET", 1568 body: _body,
1626 body: _body, 1569 queryParams: _queryParams,
1627 queryParams: _queryParams, 1570 uploadOptions: _uploadOptions,
1628 uploadOptions: _uploadOptions, 1571 uploadMedia: _uploadMedia,
1629 uploadMedia: _uploadMedia, 1572 downloadOptions: _downloadOptions);
1630 downloadOptions: _downloadOptions);
1631 return _response.then((data) => new ReadGroupSet.fromJson(data)); 1573 return _response.then((data) => new ReadGroupSet.fromJson(data));
1632 } 1574 }
1633 1575
1634 /** 1576 /// Creates read group sets by asynchronously importing the provided
1635 * Creates read group sets by asynchronously importing the provided 1577 /// information.
1636 * information. 1578 ///
1637 * 1579 /// For the definitions of read group sets and other genomics resources, see
1638 * For the definitions of read group sets and other genomics resources, see 1580 /// [Fundamentals of Google
1639 * [Fundamentals of Google 1581 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
1640 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 1582 ///
1641 * 1583 /// The caller must have WRITE permissions to the dataset.
1642 * The caller must have WRITE permissions to the dataset. 1584 ///
1643 * 1585 /// ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import
1644 * ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import 1586 ///
1645 * 1587 /// - Tags will be converted to strings - tag types are not preserved
1646 * - Tags will be converted to strings - tag types are not preserved 1588 /// - Comments (`@CO`) in the input file header will not be preserved
1647 * - Comments (`@CO`) in the input file header will not be preserved 1589 /// - Original header order of references (`@SQ`) will not be preserved
1648 * - Original header order of references (`@SQ`) will not be preserved 1590 /// - Any reverse stranded unmapped reads will be reverse complemented, and
1649 * - Any reverse stranded unmapped reads will be reverse complemented, and 1591 /// their qualities (also the "BQ" and "OQ" tags, if any) will be reversed
1650 * their qualities (also the "BQ" and "OQ" tags, if any) will be reversed 1592 /// - Unmapped reads will be stripped of positional information (reference
1651 * - Unmapped reads will be stripped of positional information (reference name 1593 /// name
1652 * and position) 1594 /// and position)
1653 * 1595 ///
1654 * [request] - The metadata request object. 1596 /// [request] - The metadata request object.
1655 * 1597 ///
1656 * Request parameters: 1598 /// Request parameters:
1657 * 1599 ///
1658 * Completes with a [Operation]. 1600 /// Completes with a [Operation].
1659 * 1601 ///
1660 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 1602 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
1661 * error. 1603 /// an error.
1662 * 1604 ///
1663 * If the used [http.Client] completes with an error when making a REST call, 1605 /// If the used [http.Client] completes with an error when making a REST
1664 * this method will complete with the same error. 1606 /// call, this method will complete with the same error.
1665 */
1666 async.Future<Operation> import(ImportReadGroupSetsRequest request) { 1607 async.Future<Operation> import(ImportReadGroupSetsRequest request) {
1667 var _url = null; 1608 var _url = null;
1668 var _queryParams = new core.Map(); 1609 var _queryParams = new core.Map();
1669 var _uploadMedia = null; 1610 var _uploadMedia = null;
1670 var _uploadOptions = null; 1611 var _uploadOptions = null;
1671 var _downloadOptions = commons.DownloadOptions.Metadata; 1612 var _downloadOptions = commons.DownloadOptions.Metadata;
1672 var _body = null; 1613 var _body = null;
1673 1614
1674 if (request != null) { 1615 if (request != null) {
1675 _body = convert.JSON.encode((request).toJson()); 1616 _body = convert.JSON.encode((request).toJson());
1676 } 1617 }
1677 1618
1678 _url = 'v1/readgroupsets:import'; 1619 _url = 'v1/readgroupsets:import';
1679 1620
1680 var _response = _requester.request(_url, 1621 var _response = _requester.request(_url, "POST",
1681 "POST", 1622 body: _body,
1682 body: _body, 1623 queryParams: _queryParams,
1683 queryParams: _queryParams, 1624 uploadOptions: _uploadOptions,
1684 uploadOptions: _uploadOptions, 1625 uploadMedia: _uploadMedia,
1685 uploadMedia: _uploadMedia, 1626 downloadOptions: _downloadOptions);
1686 downloadOptions: _downloadOptions);
1687 return _response.then((data) => new Operation.fromJson(data)); 1627 return _response.then((data) => new Operation.fromJson(data));
1688 } 1628 }
1689 1629
1690 /** 1630 /// Updates a read group set.
1691 * Updates a read group set. 1631 ///
1692 * 1632 /// For the definitions of read group sets and other genomics resources, see
1693 * For the definitions of read group sets and other genomics resources, see 1633 /// [Fundamentals of Google
1694 * [Fundamentals of Google 1634 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
1695 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 1635 ///
1696 * 1636 /// This method supports patch semantics.
1697 * This method supports patch semantics. 1637 ///
1698 * 1638 /// [request] - The metadata request object.
1699 * [request] - The metadata request object. 1639 ///
1700 * 1640 /// Request parameters:
1701 * Request parameters: 1641 ///
1702 * 1642 /// [readGroupSetId] - The ID of the read group set to be updated. The caller
1703 * [readGroupSetId] - The ID of the read group set to be updated. The caller 1643 /// must have WRITE
1704 * must have WRITE 1644 /// permissions to the dataset associated with this read group set.
1705 * permissions to the dataset associated with this read group set. 1645 ///
1706 * 1646 /// [updateMask] - An optional mask specifying which fields to update.
1707 * [updateMask] - An optional mask specifying which fields to update. 1647 /// Supported fields:
1708 * Supported fields: 1648 ///
1709 * 1649 /// * name.
1710 * * name. 1650 /// * referenceSetId.
1711 * * referenceSetId. 1651 ///
1712 * 1652 /// Leaving `updateMask` unset is equivalent to specifying all mutable
1713 * Leaving `updateMask` unset is equivalent to specifying all mutable 1653 /// fields.
1714 * fields. 1654 ///
1715 * 1655 /// Completes with a [ReadGroupSet].
1716 * Completes with a [ReadGroupSet]. 1656 ///
1717 * 1657 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
1718 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 1658 /// an error.
1719 * error. 1659 ///
1720 * 1660 /// If the used [http.Client] completes with an error when making a REST
1721 * If the used [http.Client] completes with an error when making a REST call, 1661 /// call, this method will complete with the same error.
1722 * this method will complete with the same error. 1662 async.Future<ReadGroupSet> patch(
1723 */ 1663 ReadGroupSet request, core.String readGroupSetId,
1724 async.Future<ReadGroupSet> patch(ReadGroupSet request, core.String readGroupSe tId, {core.String updateMask}) { 1664 {core.String updateMask}) {
1725 var _url = null; 1665 var _url = null;
1726 var _queryParams = new core.Map(); 1666 var _queryParams = new core.Map();
1727 var _uploadMedia = null; 1667 var _uploadMedia = null;
1728 var _uploadOptions = null; 1668 var _uploadOptions = null;
1729 var _downloadOptions = commons.DownloadOptions.Metadata; 1669 var _downloadOptions = commons.DownloadOptions.Metadata;
1730 var _body = null; 1670 var _body = null;
1731 1671
1732 if (request != null) { 1672 if (request != null) {
1733 _body = convert.JSON.encode((request).toJson()); 1673 _body = convert.JSON.encode((request).toJson());
1734 } 1674 }
1735 if (readGroupSetId == null) { 1675 if (readGroupSetId == null) {
1736 throw new core.ArgumentError("Parameter readGroupSetId is required."); 1676 throw new core.ArgumentError("Parameter readGroupSetId is required.");
1737 } 1677 }
1738 if (updateMask != null) { 1678 if (updateMask != null) {
1739 _queryParams["updateMask"] = [updateMask]; 1679 _queryParams["updateMask"] = [updateMask];
1740 } 1680 }
1741 1681
1742 _url = 'v1/readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId' ); 1682 _url =
1683 'v1/readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId');
1743 1684
1744 var _response = _requester.request(_url, 1685 var _response = _requester.request(_url, "PATCH",
1745 "PATCH", 1686 body: _body,
1746 body: _body, 1687 queryParams: _queryParams,
1747 queryParams: _queryParams, 1688 uploadOptions: _uploadOptions,
1748 uploadOptions: _uploadOptions, 1689 uploadMedia: _uploadMedia,
1749 uploadMedia: _uploadMedia, 1690 downloadOptions: _downloadOptions);
1750 downloadOptions: _downloadOptions);
1751 return _response.then((data) => new ReadGroupSet.fromJson(data)); 1691 return _response.then((data) => new ReadGroupSet.fromJson(data));
1752 } 1692 }
1753 1693
1754 /** 1694 /// Searches for read group sets matching the criteria.
1755 * Searches for read group sets matching the criteria. 1695 ///
1756 * 1696 /// For the definitions of read group sets and other genomics resources, see
1757 * For the definitions of read group sets and other genomics resources, see 1697 /// [Fundamentals of Google
1758 * [Fundamentals of Google 1698 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
1759 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 1699 ///
1760 * 1700 /// Implements
1761 * Implements 1701 /// [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/b lob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135).
1762 * [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/bl ob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135). 1702 ///
1763 * 1703 /// [request] - The metadata request object.
1764 * [request] - The metadata request object. 1704 ///
1765 * 1705 /// Request parameters:
1766 * Request parameters: 1706 ///
1767 * 1707 /// Completes with a [SearchReadGroupSetsResponse].
1768 * Completes with a [SearchReadGroupSetsResponse]. 1708 ///
1769 * 1709 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
1770 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 1710 /// an error.
1771 * error. 1711 ///
1772 * 1712 /// If the used [http.Client] completes with an error when making a REST
1773 * If the used [http.Client] completes with an error when making a REST call, 1713 /// call, this method will complete with the same error.
1774 * this method will complete with the same error. 1714 async.Future<SearchReadGroupSetsResponse> search(
1775 */ 1715 SearchReadGroupSetsRequest request) {
1776 async.Future<SearchReadGroupSetsResponse> search(SearchReadGroupSetsRequest re quest) {
1777 var _url = null; 1716 var _url = null;
1778 var _queryParams = new core.Map(); 1717 var _queryParams = new core.Map();
1779 var _uploadMedia = null; 1718 var _uploadMedia = null;
1780 var _uploadOptions = null; 1719 var _uploadOptions = null;
1781 var _downloadOptions = commons.DownloadOptions.Metadata; 1720 var _downloadOptions = commons.DownloadOptions.Metadata;
1782 var _body = null; 1721 var _body = null;
1783 1722
1784 if (request != null) { 1723 if (request != null) {
1785 _body = convert.JSON.encode((request).toJson()); 1724 _body = convert.JSON.encode((request).toJson());
1786 } 1725 }
1787 1726
1788 _url = 'v1/readgroupsets/search'; 1727 _url = 'v1/readgroupsets/search';
1789 1728
1790 var _response = _requester.request(_url, 1729 var _response = _requester.request(_url, "POST",
1791 "POST", 1730 body: _body,
1792 body: _body, 1731 queryParams: _queryParams,
1793 queryParams: _queryParams, 1732 uploadOptions: _uploadOptions,
1794 uploadOptions: _uploadOptions, 1733 uploadMedia: _uploadMedia,
1795 uploadMedia: _uploadMedia, 1734 downloadOptions: _downloadOptions);
1796 downloadOptions: _downloadOptions); 1735 return _response
1797 return _response.then((data) => new SearchReadGroupSetsResponse.fromJson(dat a)); 1736 .then((data) => new SearchReadGroupSetsResponse.fromJson(data));
1798 } 1737 }
1799
1800 } 1738 }
1801 1739
1802
1803 class ReadgroupsetsCoveragebucketsResourceApi { 1740 class ReadgroupsetsCoveragebucketsResourceApi {
1804 final commons.ApiRequester _requester; 1741 final commons.ApiRequester _requester;
1805 1742
1806 ReadgroupsetsCoveragebucketsResourceApi(commons.ApiRequester client) : 1743 ReadgroupsetsCoveragebucketsResourceApi(commons.ApiRequester client)
1807 _requester = client; 1744 : _requester = client;
1808 1745
1809 /** 1746 /// Lists fixed width coverage buckets for a read group set, each of which
1810 * Lists fixed width coverage buckets for a read group set, each of which 1747 /// correspond to a range of a reference sequence. Each bucket summarizes
1811 * correspond to a range of a reference sequence. Each bucket summarizes 1748 /// coverage information across its corresponding genomic range.
1812 * coverage information across its corresponding genomic range. 1749 ///
1813 * 1750 /// For the definitions of read group sets and other genomics resources, see
1814 * For the definitions of read group sets and other genomics resources, see 1751 /// [Fundamentals of Google
1815 * [Fundamentals of Google 1752 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
1816 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 1753 ///
1817 * 1754 /// Coverage is defined as the number of reads which are aligned to a given
1818 * Coverage is defined as the number of reads which are aligned to a given 1755 /// base in the reference sequence. Coverage buckets are available at several
1819 * base in the reference sequence. Coverage buckets are available at several 1756 /// precomputed bucket widths, enabling retrieval of various coverage 'zoom
1820 * precomputed bucket widths, enabling retrieval of various coverage 'zoom 1757 /// levels'. The caller must have READ permissions for the target read group
1821 * levels'. The caller must have READ permissions for the target read group 1758 /// set.
1822 * set. 1759 ///
1823 * 1760 /// Request parameters:
1824 * Request parameters: 1761 ///
1825 * 1762 /// [readGroupSetId] - Required. The ID of the read group set over which
1826 * [readGroupSetId] - Required. The ID of the read group set over which 1763 /// coverage is requested.
1827 * coverage is requested. 1764 ///
1828 * 1765 /// [start] - The start position of the range on the reference, 0-based
1829 * [end] - The end position of the range on the reference, 0-based exclusive. 1766 /// inclusive. If
1830 * If 1767 /// specified, `referenceName` must also be specified. Defaults to 0.
1831 * specified, `referenceName` must also be specified. If unset or 0, defaults 1768 ///
1832 * to the length of the reference. 1769 /// [targetBucketWidth] - The desired width of each reported coverage bucket
1833 * 1770 /// in base pairs. This
1834 * [pageToken] - The continuation token, which is used to page through large 1771 /// will be rounded down to the nearest precomputed bucket width; the value
1835 * result sets. 1772 /// of which is returned as `bucketWidth` in the response. Defaults
1836 * To get the next page of results, set this parameter to the value of 1773 /// to infinity (each bucket spans an entire reference sequence) or the
1837 * `nextPageToken` from the previous response. 1774 /// length
1838 * 1775 /// of the target range, if specified. The smallest precomputed
1839 * [pageSize] - The maximum number of results to return in a single page. If 1776 /// `bucketWidth` is currently 2048 base pairs; this is subject to
1840 * unspecified, 1777 /// change.
1841 * defaults to 1024. The maximum value is 2048. 1778 ///
1842 * 1779 /// [referenceName] - The name of the reference to query, within the
1843 * [start] - The start position of the range on the reference, 0-based 1780 /// reference set associated
1844 * inclusive. If 1781 /// with this query. Optional.
1845 * specified, `referenceName` must also be specified. Defaults to 0. 1782 ///
1846 * 1783 /// [end] - The end position of the range on the reference, 0-based
1847 * [targetBucketWidth] - The desired width of each reported coverage bucket in 1784 /// exclusive. If
1848 * base pairs. This 1785 /// specified, `referenceName` must also be specified. If unset or 0,
1849 * will be rounded down to the nearest precomputed bucket width; the value 1786 /// defaults
1850 * of which is returned as `bucketWidth` in the response. Defaults 1787 /// to the length of the reference.
1851 * to infinity (each bucket spans an entire reference sequence) or the length 1788 ///
1852 * of the target range, if specified. The smallest precomputed 1789 /// [pageToken] - The continuation token, which is used to page through large
1853 * `bucketWidth` is currently 2048 base pairs; this is subject to 1790 /// result sets.
1854 * change. 1791 /// To get the next page of results, set this parameter to the value of
1855 * 1792 /// `nextPageToken` from the previous response.
1856 * [referenceName] - The name of the reference to query, within the reference 1793 ///
1857 * set associated 1794 /// [pageSize] - The maximum number of results to return in a single page. If
1858 * with this query. Optional. 1795 /// unspecified,
1859 * 1796 /// defaults to 1024. The maximum value is 2048.
1860 * Completes with a [ListCoverageBucketsResponse]. 1797 ///
1861 * 1798 /// Completes with a [ListCoverageBucketsResponse].
1862 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 1799 ///
1863 * error. 1800 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
1864 * 1801 /// an error.
1865 * If the used [http.Client] completes with an error when making a REST call, 1802 ///
1866 * this method will complete with the same error. 1803 /// If the used [http.Client] completes with an error when making a REST
1867 */ 1804 /// call, this method will complete with the same error.
1868 async.Future<ListCoverageBucketsResponse> list(core.String readGroupSetId, {co re.String end, core.String pageToken, core.int pageSize, core.String start, core .String targetBucketWidth, core.String referenceName}) { 1805 async.Future<ListCoverageBucketsResponse> list(core.String readGroupSetId,
1806 {core.String start,
1807 core.String targetBucketWidth,
1808 core.String referenceName,
1809 core.String end,
1810 core.String pageToken,
1811 core.int pageSize}) {
1869 var _url = null; 1812 var _url = null;
1870 var _queryParams = new core.Map(); 1813 var _queryParams = new core.Map();
1871 var _uploadMedia = null; 1814 var _uploadMedia = null;
1872 var _uploadOptions = null; 1815 var _uploadOptions = null;
1873 var _downloadOptions = commons.DownloadOptions.Metadata; 1816 var _downloadOptions = commons.DownloadOptions.Metadata;
1874 var _body = null; 1817 var _body = null;
1875 1818
1876 if (readGroupSetId == null) { 1819 if (readGroupSetId == null) {
1877 throw new core.ArgumentError("Parameter readGroupSetId is required."); 1820 throw new core.ArgumentError("Parameter readGroupSetId is required.");
1878 } 1821 }
1879 if (end != null) {
1880 _queryParams["end"] = [end];
1881 }
1882 if (pageToken != null) {
1883 _queryParams["pageToken"] = [pageToken];
1884 }
1885 if (pageSize != null) {
1886 _queryParams["pageSize"] = ["${pageSize}"];
1887 }
1888 if (start != null) { 1822 if (start != null) {
1889 _queryParams["start"] = [start]; 1823 _queryParams["start"] = [start];
1890 } 1824 }
1891 if (targetBucketWidth != null) { 1825 if (targetBucketWidth != null) {
1892 _queryParams["targetBucketWidth"] = [targetBucketWidth]; 1826 _queryParams["targetBucketWidth"] = [targetBucketWidth];
1893 } 1827 }
1894 if (referenceName != null) { 1828 if (referenceName != null) {
1895 _queryParams["referenceName"] = [referenceName]; 1829 _queryParams["referenceName"] = [referenceName];
1896 } 1830 }
1831 if (end != null) {
1832 _queryParams["end"] = [end];
1833 }
1834 if (pageToken != null) {
1835 _queryParams["pageToken"] = [pageToken];
1836 }
1837 if (pageSize != null) {
1838 _queryParams["pageSize"] = ["${pageSize}"];
1839 }
1897 1840
1898 _url = 'v1/readgroupsets/' + commons.Escaper.ecapeVariable('$readGroupSetId' ) + '/coveragebuckets'; 1841 _url = 'v1/readgroupsets/' +
1842 commons.Escaper.ecapeVariable('$readGroupSetId') +
1843 '/coveragebuckets';
1899 1844
1900 var _response = _requester.request(_url, 1845 var _response = _requester.request(_url, "GET",
1901 "GET", 1846 body: _body,
1902 body: _body, 1847 queryParams: _queryParams,
1903 queryParams: _queryParams, 1848 uploadOptions: _uploadOptions,
1904 uploadOptions: _uploadOptions, 1849 uploadMedia: _uploadMedia,
1905 uploadMedia: _uploadMedia, 1850 downloadOptions: _downloadOptions);
1906 downloadOptions: _downloadOptions); 1851 return _response
1907 return _response.then((data) => new ListCoverageBucketsResponse.fromJson(dat a)); 1852 .then((data) => new ListCoverageBucketsResponse.fromJson(data));
1908 } 1853 }
1909
1910 } 1854 }
1911 1855
1912
1913 class ReadsResourceApi { 1856 class ReadsResourceApi {
1914 final commons.ApiRequester _requester; 1857 final commons.ApiRequester _requester;
1915 1858
1916 ReadsResourceApi(commons.ApiRequester client) : 1859 ReadsResourceApi(commons.ApiRequester client) : _requester = client;
1917 _requester = client;
1918 1860
1919 /** 1861 /// Gets a list of reads for one or more read group sets.
1920 * Gets a list of reads for one or more read group sets. 1862 ///
1921 * 1863 /// For the definitions of read group sets and other genomics resources, see
1922 * For the definitions of read group sets and other genomics resources, see 1864 /// [Fundamentals of Google
1923 * [Fundamentals of Google 1865 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
1924 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 1866 ///
1925 * 1867 /// Reads search operates over a genomic coordinate space of reference
1926 * Reads search operates over a genomic coordinate space of reference sequence 1868 /// sequence
1927 * & position defined over the reference sequences to which the requested 1869 /// & position defined over the reference sequences to which the requested
1928 * read group sets are aligned. 1870 /// read group sets are aligned.
1929 * 1871 ///
1930 * If a target positional range is specified, search returns all reads whose 1872 /// If a target positional range is specified, search returns all reads whose
1931 * alignment to the reference genome overlap the range. A query which 1873 /// alignment to the reference genome overlap the range. A query which
1932 * specifies only read group set IDs yields all reads in those read group 1874 /// specifies only read group set IDs yields all reads in those read group
1933 * sets, including unmapped reads. 1875 /// sets, including unmapped reads.
1934 * 1876 ///
1935 * All reads returned (including reads on subsequent pages) are ordered by 1877 /// All reads returned (including reads on subsequent pages) are ordered by
1936 * genomic coordinate (by reference sequence, then position). Reads with 1878 /// genomic coordinate (by reference sequence, then position). Reads with
1937 * equivalent genomic coordinates are returned in an unspecified order. This 1879 /// equivalent genomic coordinates are returned in an unspecified order. This
1938 * order is consistent, such that two queries for the same content (regardless 1880 /// order is consistent, such that two queries for the same content
1939 * of page size) yield reads in the same order across their respective streams 1881 /// (regardless
1940 * of paginated responses. 1882 /// of page size) yield reads in the same order across their respective
1941 * 1883 /// streams
1942 * Implements 1884 /// of paginated responses.
1943 * [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5. 1/src/main/resources/avro/readmethods.avdl#L85). 1885 ///
1944 * 1886 /// Implements
1945 * [request] - The metadata request object. 1887 /// [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5 .1/src/main/resources/avro/readmethods.avdl#L85).
1946 * 1888 ///
1947 * Request parameters: 1889 /// [request] - The metadata request object.
1948 * 1890 ///
1949 * Completes with a [SearchReadsResponse]. 1891 /// Request parameters:
1950 * 1892 ///
1951 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 1893 /// Completes with a [SearchReadsResponse].
1952 * error. 1894 ///
1953 * 1895 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
1954 * If the used [http.Client] completes with an error when making a REST call, 1896 /// an error.
1955 * this method will complete with the same error. 1897 ///
1956 */ 1898 /// If the used [http.Client] completes with an error when making a REST
1899 /// call, this method will complete with the same error.
1957 async.Future<SearchReadsResponse> search(SearchReadsRequest request) { 1900 async.Future<SearchReadsResponse> search(SearchReadsRequest request) {
1958 var _url = null; 1901 var _url = null;
1959 var _queryParams = new core.Map(); 1902 var _queryParams = new core.Map();
1960 var _uploadMedia = null; 1903 var _uploadMedia = null;
1961 var _uploadOptions = null; 1904 var _uploadOptions = null;
1962 var _downloadOptions = commons.DownloadOptions.Metadata; 1905 var _downloadOptions = commons.DownloadOptions.Metadata;
1963 var _body = null; 1906 var _body = null;
1964 1907
1965 if (request != null) { 1908 if (request != null) {
1966 _body = convert.JSON.encode((request).toJson()); 1909 _body = convert.JSON.encode((request).toJson());
1967 } 1910 }
1968 1911
1969 _url = 'v1/reads/search'; 1912 _url = 'v1/reads/search';
1970 1913
1971 var _response = _requester.request(_url, 1914 var _response = _requester.request(_url, "POST",
1972 "POST", 1915 body: _body,
1973 body: _body, 1916 queryParams: _queryParams,
1974 queryParams: _queryParams, 1917 uploadOptions: _uploadOptions,
1975 uploadOptions: _uploadOptions, 1918 uploadMedia: _uploadMedia,
1976 uploadMedia: _uploadMedia, 1919 downloadOptions: _downloadOptions);
1977 downloadOptions: _downloadOptions);
1978 return _response.then((data) => new SearchReadsResponse.fromJson(data)); 1920 return _response.then((data) => new SearchReadsResponse.fromJson(data));
1979 } 1921 }
1980
1981 } 1922 }
1982 1923
1983
1984 class ReferencesResourceApi { 1924 class ReferencesResourceApi {
1985 final commons.ApiRequester _requester; 1925 final commons.ApiRequester _requester;
1986 1926
1987 ReferencesBasesResourceApi get bases => new ReferencesBasesResourceApi(_reques ter); 1927 ReferencesBasesResourceApi get bases =>
1928 new ReferencesBasesResourceApi(_requester);
1988 1929
1989 ReferencesResourceApi(commons.ApiRequester client) : 1930 ReferencesResourceApi(commons.ApiRequester client) : _requester = client;
1990 _requester = client;
1991 1931
1992 /** 1932 /// Gets a reference.
1993 * Gets a reference. 1933 ///
1994 * 1934 /// For the definitions of references and other genomics resources, see
1995 * For the definitions of references and other genomics resources, see 1935 /// [Fundamentals of Google
1996 * [Fundamentals of Google 1936 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
1997 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 1937 ///
1998 * 1938 /// Implements
1999 * Implements 1939 /// [GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob/v0. 5.1/src/main/resources/avro/referencemethods.avdl#L158).
2000 * [GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob/v0.5 .1/src/main/resources/avro/referencemethods.avdl#L158). 1940 ///
2001 * 1941 /// Request parameters:
2002 * Request parameters: 1942 ///
2003 * 1943 /// [referenceId] - The ID of the reference.
2004 * [referenceId] - The ID of the reference. 1944 ///
2005 * 1945 /// Completes with a [Reference].
2006 * Completes with a [Reference]. 1946 ///
2007 * 1947 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
2008 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 1948 /// an error.
2009 * error. 1949 ///
2010 * 1950 /// If the used [http.Client] completes with an error when making a REST
2011 * If the used [http.Client] completes with an error when making a REST call, 1951 /// call, this method will complete with the same error.
2012 * this method will complete with the same error.
2013 */
2014 async.Future<Reference> get(core.String referenceId) { 1952 async.Future<Reference> get(core.String referenceId) {
2015 var _url = null; 1953 var _url = null;
2016 var _queryParams = new core.Map(); 1954 var _queryParams = new core.Map();
2017 var _uploadMedia = null; 1955 var _uploadMedia = null;
2018 var _uploadOptions = null; 1956 var _uploadOptions = null;
2019 var _downloadOptions = commons.DownloadOptions.Metadata; 1957 var _downloadOptions = commons.DownloadOptions.Metadata;
2020 var _body = null; 1958 var _body = null;
2021 1959
2022 if (referenceId == null) { 1960 if (referenceId == null) {
2023 throw new core.ArgumentError("Parameter referenceId is required."); 1961 throw new core.ArgumentError("Parameter referenceId is required.");
2024 } 1962 }
2025 1963
2026 _url = 'v1/references/' + commons.Escaper.ecapeVariable('$referenceId'); 1964 _url = 'v1/references/' + commons.Escaper.ecapeVariable('$referenceId');
2027 1965
2028 var _response = _requester.request(_url, 1966 var _response = _requester.request(_url, "GET",
2029 "GET", 1967 body: _body,
2030 body: _body, 1968 queryParams: _queryParams,
2031 queryParams: _queryParams, 1969 uploadOptions: _uploadOptions,
2032 uploadOptions: _uploadOptions, 1970 uploadMedia: _uploadMedia,
2033 uploadMedia: _uploadMedia, 1971 downloadOptions: _downloadOptions);
2034 downloadOptions: _downloadOptions);
2035 return _response.then((data) => new Reference.fromJson(data)); 1972 return _response.then((data) => new Reference.fromJson(data));
2036 } 1973 }
2037 1974
2038 /** 1975 /// Searches for references which match the given criteria.
2039 * Searches for references which match the given criteria. 1976 ///
2040 * 1977 /// For the definitions of references and other genomics resources, see
2041 * For the definitions of references and other genomics resources, see 1978 /// [Fundamentals of Google
2042 * [Fundamentals of Google 1979 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
2043 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 1980 ///
2044 * 1981 /// Implements
2045 * Implements 1982 /// [GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob /v0.5.1/src/main/resources/avro/referencemethods.avdl#L146).
2046 * [GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/ v0.5.1/src/main/resources/avro/referencemethods.avdl#L146). 1983 ///
2047 * 1984 /// [request] - The metadata request object.
2048 * [request] - The metadata request object. 1985 ///
2049 * 1986 /// Request parameters:
2050 * Request parameters: 1987 ///
2051 * 1988 /// Completes with a [SearchReferencesResponse].
2052 * Completes with a [SearchReferencesResponse]. 1989 ///
2053 * 1990 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
2054 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 1991 /// an error.
2055 * error. 1992 ///
2056 * 1993 /// If the used [http.Client] completes with an error when making a REST
2057 * If the used [http.Client] completes with an error when making a REST call, 1994 /// call, this method will complete with the same error.
2058 * this method will complete with the same error. 1995 async.Future<SearchReferencesResponse> search(
2059 */ 1996 SearchReferencesRequest request) {
2060 async.Future<SearchReferencesResponse> search(SearchReferencesRequest request) {
2061 var _url = null; 1997 var _url = null;
2062 var _queryParams = new core.Map(); 1998 var _queryParams = new core.Map();
2063 var _uploadMedia = null; 1999 var _uploadMedia = null;
2064 var _uploadOptions = null; 2000 var _uploadOptions = null;
2065 var _downloadOptions = commons.DownloadOptions.Metadata; 2001 var _downloadOptions = commons.DownloadOptions.Metadata;
2066 var _body = null; 2002 var _body = null;
2067 2003
2068 if (request != null) { 2004 if (request != null) {
2069 _body = convert.JSON.encode((request).toJson()); 2005 _body = convert.JSON.encode((request).toJson());
2070 } 2006 }
2071 2007
2072 _url = 'v1/references/search'; 2008 _url = 'v1/references/search';
2073 2009
2074 var _response = _requester.request(_url, 2010 var _response = _requester.request(_url, "POST",
2075 "POST", 2011 body: _body,
2076 body: _body, 2012 queryParams: _queryParams,
2077 queryParams: _queryParams, 2013 uploadOptions: _uploadOptions,
2078 uploadOptions: _uploadOptions, 2014 uploadMedia: _uploadMedia,
2079 uploadMedia: _uploadMedia, 2015 downloadOptions: _downloadOptions);
2080 downloadOptions: _downloadOptions); 2016 return _response
2081 return _response.then((data) => new SearchReferencesResponse.fromJson(data)) ; 2017 .then((data) => new SearchReferencesResponse.fromJson(data));
2082 } 2018 }
2083
2084 } 2019 }
2085 2020
2086
2087 class ReferencesBasesResourceApi { 2021 class ReferencesBasesResourceApi {
2088 final commons.ApiRequester _requester; 2022 final commons.ApiRequester _requester;
2089 2023
2090 ReferencesBasesResourceApi(commons.ApiRequester client) : 2024 ReferencesBasesResourceApi(commons.ApiRequester client) : _requester = client;
2091 _requester = client;
2092 2025
2093 /** 2026 /// Lists the bases in a reference, optionally restricted to a range.
2094 * Lists the bases in a reference, optionally restricted to a range. 2027 ///
2095 * 2028 /// For the definitions of references and other genomics resources, see
2096 * For the definitions of references and other genomics resources, see 2029 /// [Fundamentals of Google
2097 * [Fundamentals of Google 2030 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
2098 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 2031 ///
2099 * 2032 /// Implements
2100 * Implements 2033 /// [GlobalAllianceApi.getReferenceBases](https://github.com/ga4gh/schemas/blo b/v0.5.1/src/main/resources/avro/referencemethods.avdl#L221).
2101 * [GlobalAllianceApi.getReferenceBases](https://github.com/ga4gh/schemas/blob /v0.5.1/src/main/resources/avro/referencemethods.avdl#L221). 2034 ///
2102 * 2035 /// Request parameters:
2103 * Request parameters: 2036 ///
2104 * 2037 /// [referenceId] - The ID of the reference.
2105 * [referenceId] - The ID of the reference. 2038 ///
2106 * 2039 /// [start] - The start position (0-based) of this query. Defaults to 0.
2107 * [pageSize] - The maximum number of bases to return in a single page. If 2040 ///
2108 * unspecified, 2041 /// [end] - The end position (0-based, exclusive) of this query. Defaults to
2109 * defaults to 200Kbp (kilo base pairs). The maximum value is 10Mbp (mega base 2042 /// the length
2110 * pairs). 2043 /// of this reference.
2111 * 2044 ///
2112 * [start] - The start position (0-based) of this query. Defaults to 0. 2045 /// [pageToken] - The continuation token, which is used to page through large
2113 * 2046 /// result sets.
2114 * [end] - The end position (0-based, exclusive) of this query. Defaults to 2047 /// To get the next page of results, set this parameter to the value of
2115 * the length 2048 /// `nextPageToken` from the previous response.
2116 * of this reference. 2049 ///
2117 * 2050 /// [pageSize] - The maximum number of bases to return in a single page. If
2118 * [pageToken] - The continuation token, which is used to page through large 2051 /// unspecified,
2119 * result sets. 2052 /// defaults to 200Kbp (kilo base pairs). The maximum value is 10Mbp (mega
2120 * To get the next page of results, set this parameter to the value of 2053 /// base
2121 * `nextPageToken` from the previous response. 2054 /// pairs).
2122 * 2055 ///
2123 * Completes with a [ListBasesResponse]. 2056 /// Completes with a [ListBasesResponse].
2124 * 2057 ///
2125 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 2058 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
2126 * error. 2059 /// an error.
2127 * 2060 ///
2128 * If the used [http.Client] completes with an error when making a REST call, 2061 /// If the used [http.Client] completes with an error when making a REST
2129 * this method will complete with the same error. 2062 /// call, this method will complete with the same error.
2130 */ 2063 async.Future<ListBasesResponse> list(core.String referenceId,
2131 async.Future<ListBasesResponse> list(core.String referenceId, {core.int pageSi ze, core.String start, core.String end, core.String pageToken}) { 2064 {core.String start,
2065 core.String end,
2066 core.String pageToken,
2067 core.int pageSize}) {
2132 var _url = null; 2068 var _url = null;
2133 var _queryParams = new core.Map(); 2069 var _queryParams = new core.Map();
2134 var _uploadMedia = null; 2070 var _uploadMedia = null;
2135 var _uploadOptions = null; 2071 var _uploadOptions = null;
2136 var _downloadOptions = commons.DownloadOptions.Metadata; 2072 var _downloadOptions = commons.DownloadOptions.Metadata;
2137 var _body = null; 2073 var _body = null;
2138 2074
2139 if (referenceId == null) { 2075 if (referenceId == null) {
2140 throw new core.ArgumentError("Parameter referenceId is required."); 2076 throw new core.ArgumentError("Parameter referenceId is required.");
2141 } 2077 }
2142 if (pageSize != null) {
2143 _queryParams["pageSize"] = ["${pageSize}"];
2144 }
2145 if (start != null) { 2078 if (start != null) {
2146 _queryParams["start"] = [start]; 2079 _queryParams["start"] = [start];
2147 } 2080 }
2148 if (end != null) { 2081 if (end != null) {
2149 _queryParams["end"] = [end]; 2082 _queryParams["end"] = [end];
2150 } 2083 }
2151 if (pageToken != null) { 2084 if (pageToken != null) {
2152 _queryParams["pageToken"] = [pageToken]; 2085 _queryParams["pageToken"] = [pageToken];
2153 } 2086 }
2087 if (pageSize != null) {
2088 _queryParams["pageSize"] = ["${pageSize}"];
2089 }
2154 2090
2155 _url = 'v1/references/' + commons.Escaper.ecapeVariable('$referenceId') + '/ bases'; 2091 _url = 'v1/references/' +
2092 commons.Escaper.ecapeVariable('$referenceId') +
2093 '/bases';
2156 2094
2157 var _response = _requester.request(_url, 2095 var _response = _requester.request(_url, "GET",
2158 "GET", 2096 body: _body,
2159 body: _body, 2097 queryParams: _queryParams,
2160 queryParams: _queryParams, 2098 uploadOptions: _uploadOptions,
2161 uploadOptions: _uploadOptions, 2099 uploadMedia: _uploadMedia,
2162 uploadMedia: _uploadMedia, 2100 downloadOptions: _downloadOptions);
2163 downloadOptions: _downloadOptions);
2164 return _response.then((data) => new ListBasesResponse.fromJson(data)); 2101 return _response.then((data) => new ListBasesResponse.fromJson(data));
2165 } 2102 }
2166
2167 } 2103 }
2168 2104
2169
2170 class ReferencesetsResourceApi { 2105 class ReferencesetsResourceApi {
2171 final commons.ApiRequester _requester; 2106 final commons.ApiRequester _requester;
2172 2107
2173 ReferencesetsResourceApi(commons.ApiRequester client) : 2108 ReferencesetsResourceApi(commons.ApiRequester client) : _requester = client;
2174 _requester = client;
2175 2109
2176 /** 2110 /// Gets a reference set.
2177 * Gets a reference set. 2111 ///
2178 * 2112 /// For the definitions of references and other genomics resources, see
2179 * For the definitions of references and other genomics resources, see 2113 /// [Fundamentals of Google
2180 * [Fundamentals of Google 2114 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
2181 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 2115 ///
2182 * 2116 /// Implements
2183 * Implements 2117 /// [GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob/ v0.5.1/src/main/resources/avro/referencemethods.avdl#L83).
2184 * [GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob/v 0.5.1/src/main/resources/avro/referencemethods.avdl#L83). 2118 ///
2185 * 2119 /// Request parameters:
2186 * Request parameters: 2120 ///
2187 * 2121 /// [referenceSetId] - The ID of the reference set.
2188 * [referenceSetId] - The ID of the reference set. 2122 ///
2189 * 2123 /// Completes with a [ReferenceSet].
2190 * Completes with a [ReferenceSet]. 2124 ///
2191 * 2125 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
2192 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 2126 /// an error.
2193 * error. 2127 ///
2194 * 2128 /// If the used [http.Client] completes with an error when making a REST
2195 * If the used [http.Client] completes with an error when making a REST call, 2129 /// call, this method will complete with the same error.
2196 * this method will complete with the same error.
2197 */
2198 async.Future<ReferenceSet> get(core.String referenceSetId) { 2130 async.Future<ReferenceSet> get(core.String referenceSetId) {
2199 var _url = null; 2131 var _url = null;
2200 var _queryParams = new core.Map(); 2132 var _queryParams = new core.Map();
2201 var _uploadMedia = null; 2133 var _uploadMedia = null;
2202 var _uploadOptions = null; 2134 var _uploadOptions = null;
2203 var _downloadOptions = commons.DownloadOptions.Metadata; 2135 var _downloadOptions = commons.DownloadOptions.Metadata;
2204 var _body = null; 2136 var _body = null;
2205 2137
2206 if (referenceSetId == null) { 2138 if (referenceSetId == null) {
2207 throw new core.ArgumentError("Parameter referenceSetId is required."); 2139 throw new core.ArgumentError("Parameter referenceSetId is required.");
2208 } 2140 }
2209 2141
2210 _url = 'v1/referencesets/' + commons.Escaper.ecapeVariable('$referenceSetId' ); 2142 _url =
2143 'v1/referencesets/' + commons.Escaper.ecapeVariable('$referenceSetId');
2211 2144
2212 var _response = _requester.request(_url, 2145 var _response = _requester.request(_url, "GET",
2213 "GET", 2146 body: _body,
2214 body: _body, 2147 queryParams: _queryParams,
2215 queryParams: _queryParams, 2148 uploadOptions: _uploadOptions,
2216 uploadOptions: _uploadOptions, 2149 uploadMedia: _uploadMedia,
2217 uploadMedia: _uploadMedia, 2150 downloadOptions: _downloadOptions);
2218 downloadOptions: _downloadOptions);
2219 return _response.then((data) => new ReferenceSet.fromJson(data)); 2151 return _response.then((data) => new ReferenceSet.fromJson(data));
2220 } 2152 }
2221 2153
2222 /** 2154 /// Searches for reference sets which match the given criteria.
2223 * Searches for reference sets which match the given criteria. 2155 ///
2224 * 2156 /// For the definitions of references and other genomics resources, see
2225 * For the definitions of references and other genomics resources, see 2157 /// [Fundamentals of Google
2226 * [Fundamentals of Google 2158 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
2227 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 2159 ///
2228 * 2160 /// Implements
2229 * Implements 2161 /// [GlobalAllianceApi.searchReferenceSets](https://github.com/ga4gh/schemas/b lob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L71)
2230 * [GlobalAllianceApi.searchReferenceSets](https://github.com/ga4gh/schemas/bl ob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L71) 2162 ///
2231 * 2163 /// [request] - The metadata request object.
2232 * [request] - The metadata request object. 2164 ///
2233 * 2165 /// Request parameters:
2234 * Request parameters: 2166 ///
2235 * 2167 /// Completes with a [SearchReferenceSetsResponse].
2236 * Completes with a [SearchReferenceSetsResponse]. 2168 ///
2237 * 2169 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
2238 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 2170 /// an error.
2239 * error. 2171 ///
2240 * 2172 /// If the used [http.Client] completes with an error when making a REST
2241 * If the used [http.Client] completes with an error when making a REST call, 2173 /// call, this method will complete with the same error.
2242 * this method will complete with the same error. 2174 async.Future<SearchReferenceSetsResponse> search(
2243 */ 2175 SearchReferenceSetsRequest request) {
2244 async.Future<SearchReferenceSetsResponse> search(SearchReferenceSetsRequest re quest) {
2245 var _url = null; 2176 var _url = null;
2246 var _queryParams = new core.Map(); 2177 var _queryParams = new core.Map();
2247 var _uploadMedia = null; 2178 var _uploadMedia = null;
2248 var _uploadOptions = null; 2179 var _uploadOptions = null;
2249 var _downloadOptions = commons.DownloadOptions.Metadata; 2180 var _downloadOptions = commons.DownloadOptions.Metadata;
2250 var _body = null; 2181 var _body = null;
2251 2182
2252 if (request != null) { 2183 if (request != null) {
2253 _body = convert.JSON.encode((request).toJson()); 2184 _body = convert.JSON.encode((request).toJson());
2254 } 2185 }
2255 2186
2256 _url = 'v1/referencesets/search'; 2187 _url = 'v1/referencesets/search';
2257 2188
2258 var _response = _requester.request(_url, 2189 var _response = _requester.request(_url, "POST",
2259 "POST", 2190 body: _body,
2260 body: _body, 2191 queryParams: _queryParams,
2261 queryParams: _queryParams, 2192 uploadOptions: _uploadOptions,
2262 uploadOptions: _uploadOptions, 2193 uploadMedia: _uploadMedia,
2263 uploadMedia: _uploadMedia, 2194 downloadOptions: _downloadOptions);
2264 downloadOptions: _downloadOptions); 2195 return _response
2265 return _response.then((data) => new SearchReferenceSetsResponse.fromJson(dat a)); 2196 .then((data) => new SearchReferenceSetsResponse.fromJson(data));
2266 } 2197 }
2267
2268 } 2198 }
2269 2199
2270
2271 class VariantsResourceApi { 2200 class VariantsResourceApi {
2272 final commons.ApiRequester _requester; 2201 final commons.ApiRequester _requester;
2273 2202
2274 VariantsResourceApi(commons.ApiRequester client) : 2203 VariantsResourceApi(commons.ApiRequester client) : _requester = client;
2275 _requester = client;
2276 2204
2277 /** 2205 /// Creates a new variant.
2278 * Creates a new variant. 2206 ///
2279 * 2207 /// For the definitions of variants and other genomics resources, see
2280 * For the definitions of variants and other genomics resources, see 2208 /// [Fundamentals of Google
2281 * [Fundamentals of Google 2209 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
2282 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 2210 ///
2283 * 2211 /// [request] - The metadata request object.
2284 * [request] - The metadata request object. 2212 ///
2285 * 2213 /// Request parameters:
2286 * Request parameters: 2214 ///
2287 * 2215 /// Completes with a [Variant].
2288 * Completes with a [Variant]. 2216 ///
2289 * 2217 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
2290 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 2218 /// an error.
2291 * error. 2219 ///
2292 * 2220 /// If the used [http.Client] completes with an error when making a REST
2293 * If the used [http.Client] completes with an error when making a REST call, 2221 /// call, this method will complete with the same error.
2294 * this method will complete with the same error.
2295 */
2296 async.Future<Variant> create(Variant request) { 2222 async.Future<Variant> create(Variant request) {
2297 var _url = null; 2223 var _url = null;
2298 var _queryParams = new core.Map(); 2224 var _queryParams = new core.Map();
2299 var _uploadMedia = null; 2225 var _uploadMedia = null;
2300 var _uploadOptions = null; 2226 var _uploadOptions = null;
2301 var _downloadOptions = commons.DownloadOptions.Metadata; 2227 var _downloadOptions = commons.DownloadOptions.Metadata;
2302 var _body = null; 2228 var _body = null;
2303 2229
2304 if (request != null) { 2230 if (request != null) {
2305 _body = convert.JSON.encode((request).toJson()); 2231 _body = convert.JSON.encode((request).toJson());
2306 } 2232 }
2307 2233
2308 _url = 'v1/variants'; 2234 _url = 'v1/variants';
2309 2235
2310 var _response = _requester.request(_url, 2236 var _response = _requester.request(_url, "POST",
2311 "POST", 2237 body: _body,
2312 body: _body, 2238 queryParams: _queryParams,
2313 queryParams: _queryParams, 2239 uploadOptions: _uploadOptions,
2314 uploadOptions: _uploadOptions, 2240 uploadMedia: _uploadMedia,
2315 uploadMedia: _uploadMedia, 2241 downloadOptions: _downloadOptions);
2316 downloadOptions: _downloadOptions);
2317 return _response.then((data) => new Variant.fromJson(data)); 2242 return _response.then((data) => new Variant.fromJson(data));
2318 } 2243 }
2319 2244
2320 /** 2245 /// Deletes a variant.
2321 * Deletes a variant. 2246 ///
2322 * 2247 /// For the definitions of variants and other genomics resources, see
2323 * For the definitions of variants and other genomics resources, see 2248 /// [Fundamentals of Google
2324 * [Fundamentals of Google 2249 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
2325 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 2250 ///
2326 * 2251 /// Request parameters:
2327 * Request parameters: 2252 ///
2328 * 2253 /// [variantId] - The ID of the variant to be deleted.
2329 * [variantId] - The ID of the variant to be deleted. 2254 ///
2330 * 2255 /// Completes with a [Empty].
2331 * Completes with a [Empty]. 2256 ///
2332 * 2257 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
2333 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 2258 /// an error.
2334 * error. 2259 ///
2335 * 2260 /// If the used [http.Client] completes with an error when making a REST
2336 * If the used [http.Client] completes with an error when making a REST call, 2261 /// call, this method will complete with the same error.
2337 * this method will complete with the same error.
2338 */
2339 async.Future<Empty> delete(core.String variantId) { 2262 async.Future<Empty> delete(core.String variantId) {
2340 var _url = null; 2263 var _url = null;
2341 var _queryParams = new core.Map(); 2264 var _queryParams = new core.Map();
2342 var _uploadMedia = null; 2265 var _uploadMedia = null;
2343 var _uploadOptions = null; 2266 var _uploadOptions = null;
2344 var _downloadOptions = commons.DownloadOptions.Metadata; 2267 var _downloadOptions = commons.DownloadOptions.Metadata;
2345 var _body = null; 2268 var _body = null;
2346 2269
2347 if (variantId == null) { 2270 if (variantId == null) {
2348 throw new core.ArgumentError("Parameter variantId is required."); 2271 throw new core.ArgumentError("Parameter variantId is required.");
2349 } 2272 }
2350 2273
2351 _url = 'v1/variants/' + commons.Escaper.ecapeVariable('$variantId'); 2274 _url = 'v1/variants/' + commons.Escaper.ecapeVariable('$variantId');
2352 2275
2353 var _response = _requester.request(_url, 2276 var _response = _requester.request(_url, "DELETE",
2354 "DELETE", 2277 body: _body,
2355 body: _body, 2278 queryParams: _queryParams,
2356 queryParams: _queryParams, 2279 uploadOptions: _uploadOptions,
2357 uploadOptions: _uploadOptions, 2280 uploadMedia: _uploadMedia,
2358 uploadMedia: _uploadMedia, 2281 downloadOptions: _downloadOptions);
2359 downloadOptions: _downloadOptions);
2360 return _response.then((data) => new Empty.fromJson(data)); 2282 return _response.then((data) => new Empty.fromJson(data));
2361 } 2283 }
2362 2284
2363 /** 2285 /// Gets a variant by ID.
2364 * Gets a variant by ID. 2286 ///
2365 * 2287 /// For the definitions of variants and other genomics resources, see
2366 * For the definitions of variants and other genomics resources, see 2288 /// [Fundamentals of Google
2367 * [Fundamentals of Google 2289 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
2368 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 2290 ///
2369 * 2291 /// Request parameters:
2370 * Request parameters: 2292 ///
2371 * 2293 /// [variantId] - The ID of the variant.
2372 * [variantId] - The ID of the variant. 2294 ///
2373 * 2295 /// Completes with a [Variant].
2374 * Completes with a [Variant]. 2296 ///
2375 * 2297 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
2376 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 2298 /// an error.
2377 * error. 2299 ///
2378 * 2300 /// If the used [http.Client] completes with an error when making a REST
2379 * If the used [http.Client] completes with an error when making a REST call, 2301 /// call, this method will complete with the same error.
2380 * this method will complete with the same error.
2381 */
2382 async.Future<Variant> get(core.String variantId) { 2302 async.Future<Variant> get(core.String variantId) {
2383 var _url = null; 2303 var _url = null;
2384 var _queryParams = new core.Map(); 2304 var _queryParams = new core.Map();
2385 var _uploadMedia = null; 2305 var _uploadMedia = null;
2386 var _uploadOptions = null; 2306 var _uploadOptions = null;
2387 var _downloadOptions = commons.DownloadOptions.Metadata; 2307 var _downloadOptions = commons.DownloadOptions.Metadata;
2388 var _body = null; 2308 var _body = null;
2389 2309
2390 if (variantId == null) { 2310 if (variantId == null) {
2391 throw new core.ArgumentError("Parameter variantId is required."); 2311 throw new core.ArgumentError("Parameter variantId is required.");
2392 } 2312 }
2393 2313
2394 _url = 'v1/variants/' + commons.Escaper.ecapeVariable('$variantId'); 2314 _url = 'v1/variants/' + commons.Escaper.ecapeVariable('$variantId');
2395 2315
2396 var _response = _requester.request(_url, 2316 var _response = _requester.request(_url, "GET",
2397 "GET", 2317 body: _body,
2398 body: _body, 2318 queryParams: _queryParams,
2399 queryParams: _queryParams, 2319 uploadOptions: _uploadOptions,
2400 uploadOptions: _uploadOptions, 2320 uploadMedia: _uploadMedia,
2401 uploadMedia: _uploadMedia, 2321 downloadOptions: _downloadOptions);
2402 downloadOptions: _downloadOptions);
2403 return _response.then((data) => new Variant.fromJson(data)); 2322 return _response.then((data) => new Variant.fromJson(data));
2404 } 2323 }
2405 2324
2406 /** 2325 /// Creates variant data by asynchronously importing the provided
2407 * Creates variant data by asynchronously importing the provided information. 2326 /// information.
2408 * 2327 ///
2409 * For the definitions of variant sets and other genomics resources, see 2328 /// For the definitions of variant sets and other genomics resources, see
2410 * [Fundamentals of Google 2329 /// [Fundamentals of Google
2411 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 2330 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
2412 * 2331 ///
2413 * The variants for import will be merged with any existing variant that 2332 /// The variants for import will be merged with any existing variant that
2414 * matches its reference sequence, start, end, reference bases, and 2333 /// matches its reference sequence, start, end, reference bases, and
2415 * alternative bases. If no such variant exists, a new one will be created. 2334 /// alternative bases. If no such variant exists, a new one will be created.
2416 * 2335 ///
2417 * When variants are merged, the call information from the new variant 2336 /// When variants are merged, the call information from the new variant
2418 * is added to the existing variant, and Variant info fields are merged 2337 /// is added to the existing variant, and Variant info fields are merged
2419 * as specified in 2338 /// as specified in
2420 * infoMergeConfig. 2339 /// infoMergeConfig.
2421 * As a special case, for single-sample VCF files, QUAL and FILTER fields will 2340 /// As a special case, for single-sample VCF files, QUAL and FILTER fields
2422 * be moved to the call level; these are sometimes interpreted in a 2341 /// will
2423 * call-specific context. 2342 /// be moved to the call level; these are sometimes interpreted in a
2424 * Imported VCF headers are appended to the metadata already in a variant set. 2343 /// call-specific context.
2425 * 2344 /// Imported VCF headers are appended to the metadata already in a variant
2426 * [request] - The metadata request object. 2345 /// set.
2427 * 2346 ///
2428 * Request parameters: 2347 /// [request] - The metadata request object.
2429 * 2348 ///
2430 * Completes with a [Operation]. 2349 /// Request parameters:
2431 * 2350 ///
2432 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 2351 /// Completes with a [Operation].
2433 * error. 2352 ///
2434 * 2353 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
2435 * If the used [http.Client] completes with an error when making a REST call, 2354 /// an error.
2436 * this method will complete with the same error. 2355 ///
2437 */ 2356 /// If the used [http.Client] completes with an error when making a REST
2357 /// call, this method will complete with the same error.
2438 async.Future<Operation> import(ImportVariantsRequest request) { 2358 async.Future<Operation> import(ImportVariantsRequest request) {
2439 var _url = null; 2359 var _url = null;
2440 var _queryParams = new core.Map(); 2360 var _queryParams = new core.Map();
2441 var _uploadMedia = null; 2361 var _uploadMedia = null;
2442 var _uploadOptions = null; 2362 var _uploadOptions = null;
2443 var _downloadOptions = commons.DownloadOptions.Metadata; 2363 var _downloadOptions = commons.DownloadOptions.Metadata;
2444 var _body = null; 2364 var _body = null;
2445 2365
2446 if (request != null) { 2366 if (request != null) {
2447 _body = convert.JSON.encode((request).toJson()); 2367 _body = convert.JSON.encode((request).toJson());
2448 } 2368 }
2449 2369
2450 _url = 'v1/variants:import'; 2370 _url = 'v1/variants:import';
2451 2371
2452 var _response = _requester.request(_url, 2372 var _response = _requester.request(_url, "POST",
2453 "POST", 2373 body: _body,
2454 body: _body, 2374 queryParams: _queryParams,
2455 queryParams: _queryParams, 2375 uploadOptions: _uploadOptions,
2456 uploadOptions: _uploadOptions, 2376 uploadMedia: _uploadMedia,
2457 uploadMedia: _uploadMedia, 2377 downloadOptions: _downloadOptions);
2458 downloadOptions: _downloadOptions);
2459 return _response.then((data) => new Operation.fromJson(data)); 2378 return _response.then((data) => new Operation.fromJson(data));
2460 } 2379 }
2461 2380
2462 /** 2381 /// Merges the given variants with existing variants.
2463 * Merges the given variants with existing variants. 2382 ///
2464 * 2383 /// For the definitions of variants and other genomics resources, see
2465 * For the definitions of variants and other genomics resources, see 2384 /// [Fundamentals of Google
2466 * [Fundamentals of Google 2385 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
2467 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 2386 ///
2468 * 2387 /// Each variant will be
2469 * Each variant will be 2388 /// merged with an existing variant that matches its reference sequence,
2470 * merged with an existing variant that matches its reference sequence, 2389 /// start, end, reference bases, and alternative bases. If no such variant
2471 * start, end, reference bases, and alternative bases. If no such variant 2390 /// exists, a new one will be created.
2472 * exists, a new one will be created. 2391 ///
2473 * 2392 /// When variants are merged, the call information from the new variant
2474 * When variants are merged, the call information from the new variant 2393 /// is added to the existing variant. Variant info fields are merged as
2475 * is added to the existing variant. Variant info fields are merged as 2394 /// specified in the
2476 * specified in the 2395 /// infoMergeConfig
2477 * infoMergeConfig 2396 /// field of the MergeVariantsRequest.
2478 * field of the MergeVariantsRequest. 2397 ///
2479 * 2398 /// Please exercise caution when using this method! It is easy to introduce
2480 * Please exercise caution when using this method! It is easy to introduce 2399 /// mistakes in existing variants and difficult to back out of them. For
2481 * mistakes in existing variants and difficult to back out of them. For 2400 /// example,
2482 * example, 2401 /// suppose you were trying to merge a new variant with an existing one and
2483 * suppose you were trying to merge a new variant with an existing one and 2402 /// both
2484 * both 2403 /// variants contain calls that belong to callsets with the same callset ID.
2485 * variants contain calls that belong to callsets with the same callset ID. 2404 ///
2486 * 2405 /// // Existing variant - irrelevant fields trimmed for clarity
2487 * // Existing variant - irrelevant fields trimmed for clarity 2406 /// {
2488 * { 2407 /// "variantSetId": "10473108253681171589",
2489 * "variantSetId": "10473108253681171589", 2408 /// "referenceName": "1",
2490 * "referenceName": "1", 2409 /// "start": "10582",
2491 * "start": "10582", 2410 /// "referenceBases": "G",
2492 * "referenceBases": "G", 2411 /// "alternateBases": [
2493 * "alternateBases": [ 2412 /// "A"
2494 * "A" 2413 /// ],
2495 * ], 2414 /// "calls": [
2496 * "calls": [ 2415 /// {
2497 * { 2416 /// "callSetId": "10473108253681171589-0",
2498 * "callSetId": "10473108253681171589-0", 2417 /// "callSetName": "CALLSET0",
2499 * "callSetName": "CALLSET0", 2418 /// "genotype": [
2500 * "genotype": [ 2419 /// 0,
2501 * 0, 2420 /// 1
2502 * 1 2421 /// ],
2503 * ], 2422 /// }
2504 * } 2423 /// ]
2505 * ] 2424 /// }
2506 * } 2425 ///
2507 * 2426 /// // New variant with conflicting call information
2508 * // New variant with conflicting call information 2427 /// {
2509 * { 2428 /// "variantSetId": "10473108253681171589",
2510 * "variantSetId": "10473108253681171589", 2429 /// "referenceName": "1",
2511 * "referenceName": "1", 2430 /// "start": "10582",
2512 * "start": "10582", 2431 /// "referenceBases": "G",
2513 * "referenceBases": "G", 2432 /// "alternateBases": [
2514 * "alternateBases": [ 2433 /// "A"
2515 * "A" 2434 /// ],
2516 * ], 2435 /// "calls": [
2517 * "calls": [ 2436 /// {
2518 * { 2437 /// "callSetId": "10473108253681171589-0",
2519 * "callSetId": "10473108253681171589-0", 2438 /// "callSetName": "CALLSET0",
2520 * "callSetName": "CALLSET0", 2439 /// "genotype": [
2521 * "genotype": [ 2440 /// 1,
2522 * 1, 2441 /// 1
2523 * 1 2442 /// ],
2524 * ], 2443 /// }
2525 * } 2444 /// ]
2526 * ] 2445 /// }
2527 * } 2446 ///
2528 * 2447 /// The resulting merged variant would overwrite the existing calls with
2529 * The resulting merged variant would overwrite the existing calls with those 2448 /// those
2530 * from the new variant: 2449 /// from the new variant:
2531 * 2450 ///
2532 * { 2451 /// {
2533 * "variantSetId": "10473108253681171589", 2452 /// "variantSetId": "10473108253681171589",
2534 * "referenceName": "1", 2453 /// "referenceName": "1",
2535 * "start": "10582", 2454 /// "start": "10582",
2536 * "referenceBases": "G", 2455 /// "referenceBases": "G",
2537 * "alternateBases": [ 2456 /// "alternateBases": [
2538 * "A" 2457 /// "A"
2539 * ], 2458 /// ],
2540 * "calls": [ 2459 /// "calls": [
2541 * { 2460 /// {
2542 * "callSetId": "10473108253681171589-0", 2461 /// "callSetId": "10473108253681171589-0",
2543 * "callSetName": "CALLSET0", 2462 /// "callSetName": "CALLSET0",
2544 * "genotype": [ 2463 /// "genotype": [
2545 * 1, 2464 /// 1,
2546 * 1 2465 /// 1
2547 * ], 2466 /// ],
2548 * } 2467 /// }
2549 * ] 2468 /// ]
2550 * } 2469 /// }
2551 * 2470 ///
2552 * This may be the desired outcome, but it is up to the user to determine if 2471 /// This may be the desired outcome, but it is up to the user to determine if
2553 * if that is indeed the case. 2472 /// if that is indeed the case.
2554 * 2473 ///
2555 * [request] - The metadata request object. 2474 /// [request] - The metadata request object.
2556 * 2475 ///
2557 * Request parameters: 2476 /// Request parameters:
2558 * 2477 ///
2559 * Completes with a [Empty]. 2478 /// Completes with a [Empty].
2560 * 2479 ///
2561 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 2480 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
2562 * error. 2481 /// an error.
2563 * 2482 ///
2564 * If the used [http.Client] completes with an error when making a REST call, 2483 /// If the used [http.Client] completes with an error when making a REST
2565 * this method will complete with the same error. 2484 /// call, this method will complete with the same error.
2566 */
2567 async.Future<Empty> merge(MergeVariantsRequest request) { 2485 async.Future<Empty> merge(MergeVariantsRequest request) {
2568 var _url = null; 2486 var _url = null;
2569 var _queryParams = new core.Map(); 2487 var _queryParams = new core.Map();
2570 var _uploadMedia = null; 2488 var _uploadMedia = null;
2571 var _uploadOptions = null; 2489 var _uploadOptions = null;
2572 var _downloadOptions = commons.DownloadOptions.Metadata; 2490 var _downloadOptions = commons.DownloadOptions.Metadata;
2573 var _body = null; 2491 var _body = null;
2574 2492
2575 if (request != null) { 2493 if (request != null) {
2576 _body = convert.JSON.encode((request).toJson()); 2494 _body = convert.JSON.encode((request).toJson());
2577 } 2495 }
2578 2496
2579 _url = 'v1/variants:merge'; 2497 _url = 'v1/variants:merge';
2580 2498
2581 var _response = _requester.request(_url, 2499 var _response = _requester.request(_url, "POST",
2582 "POST", 2500 body: _body,
2583 body: _body, 2501 queryParams: _queryParams,
2584 queryParams: _queryParams, 2502 uploadOptions: _uploadOptions,
2585 uploadOptions: _uploadOptions, 2503 uploadMedia: _uploadMedia,
2586 uploadMedia: _uploadMedia, 2504 downloadOptions: _downloadOptions);
2587 downloadOptions: _downloadOptions);
2588 return _response.then((data) => new Empty.fromJson(data)); 2505 return _response.then((data) => new Empty.fromJson(data));
2589 } 2506 }
2590 2507
2591 /** 2508 /// Updates a variant.
2592 * Updates a variant. 2509 ///
2593 * 2510 /// For the definitions of variants and other genomics resources, see
2594 * For the definitions of variants and other genomics resources, see 2511 /// [Fundamentals of Google
2595 * [Fundamentals of Google 2512 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
2596 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 2513 ///
2597 * 2514 /// This method supports patch semantics. Returns the modified variant
2598 * This method supports patch semantics. Returns the modified variant without 2515 /// without
2599 * its calls. 2516 /// its calls.
2600 * 2517 ///
2601 * [request] - The metadata request object. 2518 /// [request] - The metadata request object.
2602 * 2519 ///
2603 * Request parameters: 2520 /// Request parameters:
2604 * 2521 ///
2605 * [variantId] - The ID of the variant to be updated. 2522 /// [variantId] - The ID of the variant to be updated.
2606 * 2523 ///
2607 * [updateMask] - An optional mask specifying which fields to update. At this 2524 /// [updateMask] - An optional mask specifying which fields to update. At
2608 * time, mutable 2525 /// this time, mutable
2609 * fields are names and 2526 /// fields are names and
2610 * info. Acceptable values are "names" and 2527 /// info. Acceptable values are "names" and
2611 * "info". If unspecified, all mutable fields will be updated. 2528 /// "info". If unspecified, all mutable fields will be updated.
2612 * 2529 ///
2613 * Completes with a [Variant]. 2530 /// Completes with a [Variant].
2614 * 2531 ///
2615 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 2532 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
2616 * error. 2533 /// an error.
2617 * 2534 ///
2618 * If the used [http.Client] completes with an error when making a REST call, 2535 /// If the used [http.Client] completes with an error when making a REST
2619 * this method will complete with the same error. 2536 /// call, this method will complete with the same error.
2620 */ 2537 async.Future<Variant> patch(Variant request, core.String variantId,
2621 async.Future<Variant> patch(Variant request, core.String variantId, {core.Stri ng updateMask}) { 2538 {core.String updateMask}) {
2622 var _url = null; 2539 var _url = null;
2623 var _queryParams = new core.Map(); 2540 var _queryParams = new core.Map();
2624 var _uploadMedia = null; 2541 var _uploadMedia = null;
2625 var _uploadOptions = null; 2542 var _uploadOptions = null;
2626 var _downloadOptions = commons.DownloadOptions.Metadata; 2543 var _downloadOptions = commons.DownloadOptions.Metadata;
2627 var _body = null; 2544 var _body = null;
2628 2545
2629 if (request != null) { 2546 if (request != null) {
2630 _body = convert.JSON.encode((request).toJson()); 2547 _body = convert.JSON.encode((request).toJson());
2631 } 2548 }
2632 if (variantId == null) { 2549 if (variantId == null) {
2633 throw new core.ArgumentError("Parameter variantId is required."); 2550 throw new core.ArgumentError("Parameter variantId is required.");
2634 } 2551 }
2635 if (updateMask != null) { 2552 if (updateMask != null) {
2636 _queryParams["updateMask"] = [updateMask]; 2553 _queryParams["updateMask"] = [updateMask];
2637 } 2554 }
2638 2555
2639 _url = 'v1/variants/' + commons.Escaper.ecapeVariable('$variantId'); 2556 _url = 'v1/variants/' + commons.Escaper.ecapeVariable('$variantId');
2640 2557
2641 var _response = _requester.request(_url, 2558 var _response = _requester.request(_url, "PATCH",
2642 "PATCH", 2559 body: _body,
2643 body: _body, 2560 queryParams: _queryParams,
2644 queryParams: _queryParams, 2561 uploadOptions: _uploadOptions,
2645 uploadOptions: _uploadOptions, 2562 uploadMedia: _uploadMedia,
2646 uploadMedia: _uploadMedia, 2563 downloadOptions: _downloadOptions);
2647 downloadOptions: _downloadOptions);
2648 return _response.then((data) => new Variant.fromJson(data)); 2564 return _response.then((data) => new Variant.fromJson(data));
2649 } 2565 }
2650 2566
2651 /** 2567 /// Gets a list of variants matching the criteria.
2652 * Gets a list of variants matching the criteria. 2568 ///
2653 * 2569 /// For the definitions of variants and other genomics resources, see
2654 * For the definitions of variants and other genomics resources, see 2570 /// [Fundamentals of Google
2655 * [Fundamentals of Google 2571 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
2656 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 2572 ///
2657 * 2573 /// Implements
2658 * Implements 2574 /// [GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schemas/blob/v 0.5.1/src/main/resources/avro/variantmethods.avdl#L126).
2659 * [GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schemas/blob/v0 .5.1/src/main/resources/avro/variantmethods.avdl#L126). 2575 ///
2660 * 2576 /// [request] - The metadata request object.
2661 * [request] - The metadata request object. 2577 ///
2662 * 2578 /// Request parameters:
2663 * Request parameters: 2579 ///
2664 * 2580 /// Completes with a [SearchVariantsResponse].
2665 * Completes with a [SearchVariantsResponse]. 2581 ///
2666 * 2582 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
2667 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 2583 /// an error.
2668 * error. 2584 ///
2669 * 2585 /// If the used [http.Client] completes with an error when making a REST
2670 * If the used [http.Client] completes with an error when making a REST call, 2586 /// call, this method will complete with the same error.
2671 * this method will complete with the same error.
2672 */
2673 async.Future<SearchVariantsResponse> search(SearchVariantsRequest request) { 2587 async.Future<SearchVariantsResponse> search(SearchVariantsRequest request) {
2674 var _url = null; 2588 var _url = null;
2675 var _queryParams = new core.Map(); 2589 var _queryParams = new core.Map();
2676 var _uploadMedia = null; 2590 var _uploadMedia = null;
2677 var _uploadOptions = null; 2591 var _uploadOptions = null;
2678 var _downloadOptions = commons.DownloadOptions.Metadata; 2592 var _downloadOptions = commons.DownloadOptions.Metadata;
2679 var _body = null; 2593 var _body = null;
2680 2594
2681 if (request != null) { 2595 if (request != null) {
2682 _body = convert.JSON.encode((request).toJson()); 2596 _body = convert.JSON.encode((request).toJson());
2683 } 2597 }
2684 2598
2685 _url = 'v1/variants/search'; 2599 _url = 'v1/variants/search';
2686 2600
2687 var _response = _requester.request(_url, 2601 var _response = _requester.request(_url, "POST",
2688 "POST", 2602 body: _body,
2689 body: _body, 2603 queryParams: _queryParams,
2690 queryParams: _queryParams, 2604 uploadOptions: _uploadOptions,
2691 uploadOptions: _uploadOptions, 2605 uploadMedia: _uploadMedia,
2692 uploadMedia: _uploadMedia, 2606 downloadOptions: _downloadOptions);
2693 downloadOptions: _downloadOptions);
2694 return _response.then((data) => new SearchVariantsResponse.fromJson(data)); 2607 return _response.then((data) => new SearchVariantsResponse.fromJson(data));
2695 } 2608 }
2696
2697 } 2609 }
2698 2610
2699
2700 class VariantsetsResourceApi { 2611 class VariantsetsResourceApi {
2701 final commons.ApiRequester _requester; 2612 final commons.ApiRequester _requester;
2702 2613
2703 VariantsetsResourceApi(commons.ApiRequester client) : 2614 VariantsetsResourceApi(commons.ApiRequester client) : _requester = client;
2704 _requester = client;
2705 2615
2706 /** 2616 /// Creates a new variant set.
2707 * Creates a new variant set. 2617 ///
2708 * 2618 /// For the definitions of variant sets and other genomics resources, see
2709 * For the definitions of variant sets and other genomics resources, see 2619 /// [Fundamentals of Google
2710 * [Fundamentals of Google 2620 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
2711 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 2621 ///
2712 * 2622 /// The provided variant set must have a valid `datasetId` set - all other
2713 * The provided variant set must have a valid `datasetId` set - all other 2623 /// fields are optional. Note that the `id` field will be ignored, as this is
2714 * fields are optional. Note that the `id` field will be ignored, as this is 2624 /// assigned by the server.
2715 * assigned by the server. 2625 ///
2716 * 2626 /// [request] - The metadata request object.
2717 * [request] - The metadata request object. 2627 ///
2718 * 2628 /// Request parameters:
2719 * Request parameters: 2629 ///
2720 * 2630 /// Completes with a [VariantSet].
2721 * Completes with a [VariantSet]. 2631 ///
2722 * 2632 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
2723 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 2633 /// an error.
2724 * error. 2634 ///
2725 * 2635 /// If the used [http.Client] completes with an error when making a REST
2726 * If the used [http.Client] completes with an error when making a REST call, 2636 /// call, this method will complete with the same error.
2727 * this method will complete with the same error.
2728 */
2729 async.Future<VariantSet> create(VariantSet request) { 2637 async.Future<VariantSet> create(VariantSet request) {
2730 var _url = null; 2638 var _url = null;
2731 var _queryParams = new core.Map(); 2639 var _queryParams = new core.Map();
2732 var _uploadMedia = null; 2640 var _uploadMedia = null;
2733 var _uploadOptions = null; 2641 var _uploadOptions = null;
2734 var _downloadOptions = commons.DownloadOptions.Metadata; 2642 var _downloadOptions = commons.DownloadOptions.Metadata;
2735 var _body = null; 2643 var _body = null;
2736 2644
2737 if (request != null) { 2645 if (request != null) {
2738 _body = convert.JSON.encode((request).toJson()); 2646 _body = convert.JSON.encode((request).toJson());
2739 } 2647 }
2740 2648
2741 _url = 'v1/variantsets'; 2649 _url = 'v1/variantsets';
2742 2650
2743 var _response = _requester.request(_url, 2651 var _response = _requester.request(_url, "POST",
2744 "POST", 2652 body: _body,
2745 body: _body, 2653 queryParams: _queryParams,
2746 queryParams: _queryParams, 2654 uploadOptions: _uploadOptions,
2747 uploadOptions: _uploadOptions, 2655 uploadMedia: _uploadMedia,
2748 uploadMedia: _uploadMedia, 2656 downloadOptions: _downloadOptions);
2749 downloadOptions: _downloadOptions);
2750 return _response.then((data) => new VariantSet.fromJson(data)); 2657 return _response.then((data) => new VariantSet.fromJson(data));
2751 } 2658 }
2752 2659
2753 /** 2660 /// Deletes a variant set including all variants, call sets, and calls
2754 * Deletes a variant set including all variants, call sets, and calls within. 2661 /// within.
2755 * This is not reversible. 2662 /// This is not reversible.
2756 * 2663 ///
2757 * For the definitions of variant sets and other genomics resources, see 2664 /// For the definitions of variant sets and other genomics resources, see
2758 * [Fundamentals of Google 2665 /// [Fundamentals of Google
2759 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 2666 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
2760 * 2667 ///
2761 * Request parameters: 2668 /// Request parameters:
2762 * 2669 ///
2763 * [variantSetId] - The ID of the variant set to be deleted. 2670 /// [variantSetId] - The ID of the variant set to be deleted.
2764 * 2671 ///
2765 * Completes with a [Empty]. 2672 /// Completes with a [Empty].
2766 * 2673 ///
2767 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 2674 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
2768 * error. 2675 /// an error.
2769 * 2676 ///
2770 * If the used [http.Client] completes with an error when making a REST call, 2677 /// If the used [http.Client] completes with an error when making a REST
2771 * this method will complete with the same error. 2678 /// call, this method will complete with the same error.
2772 */
2773 async.Future<Empty> delete(core.String variantSetId) { 2679 async.Future<Empty> delete(core.String variantSetId) {
2774 var _url = null; 2680 var _url = null;
2775 var _queryParams = new core.Map(); 2681 var _queryParams = new core.Map();
2776 var _uploadMedia = null; 2682 var _uploadMedia = null;
2777 var _uploadOptions = null; 2683 var _uploadOptions = null;
2778 var _downloadOptions = commons.DownloadOptions.Metadata; 2684 var _downloadOptions = commons.DownloadOptions.Metadata;
2779 var _body = null; 2685 var _body = null;
2780 2686
2781 if (variantSetId == null) { 2687 if (variantSetId == null) {
2782 throw new core.ArgumentError("Parameter variantSetId is required."); 2688 throw new core.ArgumentError("Parameter variantSetId is required.");
2783 } 2689 }
2784 2690
2785 _url = 'v1/variantsets/' + commons.Escaper.ecapeVariable('$variantSetId'); 2691 _url = 'v1/variantsets/' + commons.Escaper.ecapeVariable('$variantSetId');
2786 2692
2787 var _response = _requester.request(_url, 2693 var _response = _requester.request(_url, "DELETE",
2788 "DELETE", 2694 body: _body,
2789 body: _body, 2695 queryParams: _queryParams,
2790 queryParams: _queryParams, 2696 uploadOptions: _uploadOptions,
2791 uploadOptions: _uploadOptions, 2697 uploadMedia: _uploadMedia,
2792 uploadMedia: _uploadMedia, 2698 downloadOptions: _downloadOptions);
2793 downloadOptions: _downloadOptions);
2794 return _response.then((data) => new Empty.fromJson(data)); 2699 return _response.then((data) => new Empty.fromJson(data));
2795 } 2700 }
2796 2701
2797 /** 2702 /// Exports variant set data to an external destination.
2798 * Exports variant set data to an external destination. 2703 ///
2799 * 2704 /// For the definitions of variant sets and other genomics resources, see
2800 * For the definitions of variant sets and other genomics resources, see 2705 /// [Fundamentals of Google
2801 * [Fundamentals of Google 2706 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
2802 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 2707 ///
2803 * 2708 /// [request] - The metadata request object.
2804 * [request] - The metadata request object. 2709 ///
2805 * 2710 /// Request parameters:
2806 * Request parameters: 2711 ///
2807 * 2712 /// [variantSetId] - Required. The ID of the variant set that contains
2808 * [variantSetId] - Required. The ID of the variant set that contains variant 2713 /// variant data which
2809 * data which 2714 /// should be exported. The caller must have READ access to this variant set.
2810 * should be exported. The caller must have READ access to this variant set. 2715 ///
2811 * 2716 /// Completes with a [Operation].
2812 * Completes with a [Operation]. 2717 ///
2813 * 2718 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
2814 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 2719 /// an error.
2815 * error. 2720 ///
2816 * 2721 /// If the used [http.Client] completes with an error when making a REST
2817 * If the used [http.Client] completes with an error when making a REST call, 2722 /// call, this method will complete with the same error.
2818 * this method will complete with the same error. 2723 async.Future<Operation> export(
2819 */ 2724 ExportVariantSetRequest request, core.String variantSetId) {
2820 async.Future<Operation> export(ExportVariantSetRequest request, core.String va riantSetId) {
2821 var _url = null; 2725 var _url = null;
2822 var _queryParams = new core.Map(); 2726 var _queryParams = new core.Map();
2823 var _uploadMedia = null; 2727 var _uploadMedia = null;
2824 var _uploadOptions = null; 2728 var _uploadOptions = null;
2825 var _downloadOptions = commons.DownloadOptions.Metadata; 2729 var _downloadOptions = commons.DownloadOptions.Metadata;
2826 var _body = null; 2730 var _body = null;
2827 2731
2828 if (request != null) { 2732 if (request != null) {
2829 _body = convert.JSON.encode((request).toJson()); 2733 _body = convert.JSON.encode((request).toJson());
2830 } 2734 }
2831 if (variantSetId == null) { 2735 if (variantSetId == null) {
2832 throw new core.ArgumentError("Parameter variantSetId is required."); 2736 throw new core.ArgumentError("Parameter variantSetId is required.");
2833 } 2737 }
2834 2738
2835 _url = 'v1/variantsets/' + commons.Escaper.ecapeVariable('$variantSetId') + ':export'; 2739 _url = 'v1/variantsets/' +
2740 commons.Escaper.ecapeVariable('$variantSetId') +
2741 ':export';
2836 2742
2837 var _response = _requester.request(_url, 2743 var _response = _requester.request(_url, "POST",
2838 "POST", 2744 body: _body,
2839 body: _body, 2745 queryParams: _queryParams,
2840 queryParams: _queryParams, 2746 uploadOptions: _uploadOptions,
2841 uploadOptions: _uploadOptions, 2747 uploadMedia: _uploadMedia,
2842 uploadMedia: _uploadMedia, 2748 downloadOptions: _downloadOptions);
2843 downloadOptions: _downloadOptions);
2844 return _response.then((data) => new Operation.fromJson(data)); 2749 return _response.then((data) => new Operation.fromJson(data));
2845 } 2750 }
2846 2751
2847 /** 2752 /// Gets a variant set by ID.
2848 * Gets a variant set by ID. 2753 ///
2849 * 2754 /// For the definitions of variant sets and other genomics resources, see
2850 * For the definitions of variant sets and other genomics resources, see 2755 /// [Fundamentals of Google
2851 * [Fundamentals of Google 2756 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
2852 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 2757 ///
2853 * 2758 /// Request parameters:
2854 * Request parameters: 2759 ///
2855 * 2760 /// [variantSetId] - Required. The ID of the variant set.
2856 * [variantSetId] - Required. The ID of the variant set. 2761 ///
2857 * 2762 /// Completes with a [VariantSet].
2858 * Completes with a [VariantSet]. 2763 ///
2859 * 2764 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
2860 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 2765 /// an error.
2861 * error. 2766 ///
2862 * 2767 /// If the used [http.Client] completes with an error when making a REST
2863 * If the used [http.Client] completes with an error when making a REST call, 2768 /// call, this method will complete with the same error.
2864 * this method will complete with the same error.
2865 */
2866 async.Future<VariantSet> get(core.String variantSetId) { 2769 async.Future<VariantSet> get(core.String variantSetId) {
2867 var _url = null; 2770 var _url = null;
2868 var _queryParams = new core.Map(); 2771 var _queryParams = new core.Map();
2869 var _uploadMedia = null; 2772 var _uploadMedia = null;
2870 var _uploadOptions = null; 2773 var _uploadOptions = null;
2871 var _downloadOptions = commons.DownloadOptions.Metadata; 2774 var _downloadOptions = commons.DownloadOptions.Metadata;
2872 var _body = null; 2775 var _body = null;
2873 2776
2874 if (variantSetId == null) { 2777 if (variantSetId == null) {
2875 throw new core.ArgumentError("Parameter variantSetId is required."); 2778 throw new core.ArgumentError("Parameter variantSetId is required.");
2876 } 2779 }
2877 2780
2878 _url = 'v1/variantsets/' + commons.Escaper.ecapeVariable('$variantSetId'); 2781 _url = 'v1/variantsets/' + commons.Escaper.ecapeVariable('$variantSetId');
2879 2782
2880 var _response = _requester.request(_url, 2783 var _response = _requester.request(_url, "GET",
2881 "GET", 2784 body: _body,
2882 body: _body, 2785 queryParams: _queryParams,
2883 queryParams: _queryParams, 2786 uploadOptions: _uploadOptions,
2884 uploadOptions: _uploadOptions, 2787 uploadMedia: _uploadMedia,
2885 uploadMedia: _uploadMedia, 2788 downloadOptions: _downloadOptions);
2886 downloadOptions: _downloadOptions);
2887 return _response.then((data) => new VariantSet.fromJson(data)); 2789 return _response.then((data) => new VariantSet.fromJson(data));
2888 } 2790 }
2889 2791
2890 /** 2792 /// Updates a variant set using patch semantics.
2891 * Updates a variant set using patch semantics. 2793 ///
2892 * 2794 /// For the definitions of variant sets and other genomics resources, see
2893 * For the definitions of variant sets and other genomics resources, see 2795 /// [Fundamentals of Google
2894 * [Fundamentals of Google 2796 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
2895 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 2797 ///
2896 * 2798 /// [request] - The metadata request object.
2897 * [request] - The metadata request object. 2799 ///
2898 * 2800 /// Request parameters:
2899 * Request parameters: 2801 ///
2900 * 2802 /// [variantSetId] - The ID of the variant to be updated (must already
2901 * [variantSetId] - The ID of the variant to be updated (must already exist). 2803 /// exist).
2902 * 2804 ///
2903 * [updateMask] - An optional mask specifying which fields to update. 2805 /// [updateMask] - An optional mask specifying which fields to update.
2904 * Supported fields: 2806 /// Supported fields:
2905 * 2807 ///
2906 * * metadata. 2808 /// * metadata.
2907 * * name. 2809 /// * name.
2908 * * description. 2810 /// * description.
2909 * 2811 ///
2910 * Leaving `updateMask` unset is equivalent to specifying all mutable 2812 /// Leaving `updateMask` unset is equivalent to specifying all mutable
2911 * fields. 2813 /// fields.
2912 * 2814 ///
2913 * Completes with a [VariantSet]. 2815 /// Completes with a [VariantSet].
2914 * 2816 ///
2915 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 2817 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
2916 * error. 2818 /// an error.
2917 * 2819 ///
2918 * If the used [http.Client] completes with an error when making a REST call, 2820 /// If the used [http.Client] completes with an error when making a REST
2919 * this method will complete with the same error. 2821 /// call, this method will complete with the same error.
2920 */ 2822 async.Future<VariantSet> patch(VariantSet request, core.String variantSetId,
2921 async.Future<VariantSet> patch(VariantSet request, core.String variantSetId, { core.String updateMask}) { 2823 {core.String updateMask}) {
2922 var _url = null; 2824 var _url = null;
2923 var _queryParams = new core.Map(); 2825 var _queryParams = new core.Map();
2924 var _uploadMedia = null; 2826 var _uploadMedia = null;
2925 var _uploadOptions = null; 2827 var _uploadOptions = null;
2926 var _downloadOptions = commons.DownloadOptions.Metadata; 2828 var _downloadOptions = commons.DownloadOptions.Metadata;
2927 var _body = null; 2829 var _body = null;
2928 2830
2929 if (request != null) { 2831 if (request != null) {
2930 _body = convert.JSON.encode((request).toJson()); 2832 _body = convert.JSON.encode((request).toJson());
2931 } 2833 }
2932 if (variantSetId == null) { 2834 if (variantSetId == null) {
2933 throw new core.ArgumentError("Parameter variantSetId is required."); 2835 throw new core.ArgumentError("Parameter variantSetId is required.");
2934 } 2836 }
2935 if (updateMask != null) { 2837 if (updateMask != null) {
2936 _queryParams["updateMask"] = [updateMask]; 2838 _queryParams["updateMask"] = [updateMask];
2937 } 2839 }
2938 2840
2939 _url = 'v1/variantsets/' + commons.Escaper.ecapeVariable('$variantSetId'); 2841 _url = 'v1/variantsets/' + commons.Escaper.ecapeVariable('$variantSetId');
2940 2842
2941 var _response = _requester.request(_url, 2843 var _response = _requester.request(_url, "PATCH",
2942 "PATCH", 2844 body: _body,
2943 body: _body, 2845 queryParams: _queryParams,
2944 queryParams: _queryParams, 2846 uploadOptions: _uploadOptions,
2945 uploadOptions: _uploadOptions, 2847 uploadMedia: _uploadMedia,
2946 uploadMedia: _uploadMedia, 2848 downloadOptions: _downloadOptions);
2947 downloadOptions: _downloadOptions);
2948 return _response.then((data) => new VariantSet.fromJson(data)); 2849 return _response.then((data) => new VariantSet.fromJson(data));
2949 } 2850 }
2950 2851
2951 /** 2852 /// Returns a list of all variant sets matching search criteria.
2952 * Returns a list of all variant sets matching search criteria. 2853 ///
2953 * 2854 /// For the definitions of variant sets and other genomics resources, see
2954 * For the definitions of variant sets and other genomics resources, see 2855 /// [Fundamentals of Google
2955 * [Fundamentals of Google 2856 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomic s)
2956 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics ) 2857 ///
2957 * 2858 /// Implements
2958 * Implements 2859 /// [GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blo b/v0.5.1/src/main/resources/avro/variantmethods.avdl#L49).
2959 * [GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blob /v0.5.1/src/main/resources/avro/variantmethods.avdl#L49). 2860 ///
2960 * 2861 /// [request] - The metadata request object.
2961 * [request] - The metadata request object. 2862 ///
2962 * 2863 /// Request parameters:
2963 * Request parameters: 2864 ///
2964 * 2865 /// Completes with a [SearchVariantSetsResponse].
2965 * Completes with a [SearchVariantSetsResponse]. 2866 ///
2966 * 2867 /// Completes with a [commons.ApiRequestError] if the API endpoint returned
2967 * Completes with a [commons.ApiRequestError] if the API endpoint returned an 2868 /// an error.
2968 * error. 2869 ///
2969 * 2870 /// If the used [http.Client] completes with an error when making a REST
2970 * If the used [http.Client] completes with an error when making a REST call, 2871 /// call, this method will complete with the same error.
2971 * this method will complete with the same error. 2872 async.Future<SearchVariantSetsResponse> search(
2972 */ 2873 SearchVariantSetsRequest request) {
2973 async.Future<SearchVariantSetsResponse> search(SearchVariantSetsRequest reques t) {
2974 var _url = null; 2874 var _url = null;
2975 var _queryParams = new core.Map(); 2875 var _queryParams = new core.Map();
2976 var _uploadMedia = null; 2876 var _uploadMedia = null;
2977 var _uploadOptions = null; 2877 var _uploadOptions = null;
2978 var _downloadOptions = commons.DownloadOptions.Metadata; 2878 var _downloadOptions = commons.DownloadOptions.Metadata;
2979 var _body = null; 2879 var _body = null;
2980 2880
2981 if (request != null) { 2881 if (request != null) {
2982 _body = convert.JSON.encode((request).toJson()); 2882 _body = convert.JSON.encode((request).toJson());
2983 } 2883 }
2984 2884
2985 _url = 'v1/variantsets/search'; 2885 _url = 'v1/variantsets/search';
2986 2886
2987 var _response = _requester.request(_url, 2887 var _response = _requester.request(_url, "POST",
2988 "POST", 2888 body: _body,
2989 body: _body, 2889 queryParams: _queryParams,
2990 queryParams: _queryParams, 2890 uploadOptions: _uploadOptions,
2991 uploadOptions: _uploadOptions, 2891 uploadMedia: _uploadMedia,
2992 uploadMedia: _uploadMedia, 2892 downloadOptions: _downloadOptions);
2993 downloadOptions: _downloadOptions); 2893 return _response
2994 return _response.then((data) => new SearchVariantSetsResponse.fromJson(data) ); 2894 .then((data) => new SearchVariantSetsResponse.fromJson(data));
2995 } 2895 }
2996
2997 } 2896 }
2998 2897
2898 /// An annotation describes a region of reference genome. The value of an
2899 /// annotation may be one of several canonical types, supplemented by arbitrary
2900 /// info tags. An annotation is not inherently associated with a specific
2901 /// sample or individual (though a client could choose to use annotations in
2902 /// this way). Example canonical annotation types are `GENE` and
2903 /// `VARIANT`.
2904 class Annotation {
2905 /// The annotation set to which this annotation belongs.
2906 core.String annotationSetId;
2999 2907
2908 /// The end position of the range on the reference, 0-based exclusive.
2909 core.String end;
3000 2910
3001 /** 2911 /// The server-generated annotation ID, unique across all annotations.
3002 * An annotation describes a region of reference genome. The value of an
3003 * annotation may be one of several canonical types, supplemented by arbitrary
3004 * info tags. An annotation is not inherently associated with a specific
3005 * sample or individual (though a client could choose to use annotations in
3006 * this way). Example canonical annotation types are `GENE` and
3007 * `VARIANT`.
3008 */
3009 class Annotation {
3010 /** The annotation set to which this annotation belongs. */
3011 core.String annotationSetId;
3012 /** The end position of the range on the reference, 0-based exclusive. */
3013 core.String end;
3014 /** The server-generated annotation ID, unique across all annotations. */
3015 core.String id; 2912 core.String id;
3016 /** 2913
3017 * A map of additional read alignment information. This must be of the form 2914 /// A map of additional read alignment information. This must be of the form
3018 * map<string, string[]> (string key mapping to a list of string values). 2915 /// map<string, string[]> (string key mapping to a list of string values).
3019 * 2916 ///
3020 * The values for Object must be JSON objects. It can consist of `num`, 2917 /// The values for Object must be JSON objects. It can consist of `num`,
3021 * `String`, `bool` and `null` as well as `Map` and `List` values. 2918 /// `String`, `bool` and `null` as well as `Map` and `List` values.
3022 */
3023 core.Map<core.String, core.List<core.Object>> info; 2919 core.Map<core.String, core.List<core.Object>> info;
3024 /** The display name of this annotation. */ 2920
2921 /// The display name of this annotation.
3025 core.String name; 2922 core.String name;
3026 /** The ID of the Google Genomics reference associated with this range. */ 2923
2924 /// The ID of the Google Genomics reference associated with this range.
3027 core.String referenceId; 2925 core.String referenceId;
3028 /** 2926
3029 * The display name corresponding to the reference specified by 2927 /// The display name corresponding to the reference specified by
3030 * `referenceId`, for example `chr1`, `1`, or `chrX`. 2928 /// `referenceId`, for example `chr1`, `1`, or `chrX`.
3031 */
3032 core.String referenceName; 2929 core.String referenceName;
3033 /** 2930
3034 * Whether this range refers to the reverse strand, as opposed to the forward 2931 /// Whether this range refers to the reverse strand, as opposed to the
3035 * strand. Note that regardless of this field, the start/end position of the 2932 /// forward
3036 * range always refer to the forward strand. 2933 /// strand. Note that regardless of this field, the start/end position of the
3037 */ 2934 /// range always refer to the forward strand.
3038 core.bool reverseStrand; 2935 core.bool reverseStrand;
3039 /** The start position of the range on the reference, 0-based inclusive. */ 2936
2937 /// The start position of the range on the reference, 0-based inclusive.
3040 core.String start; 2938 core.String start;
3041 /** 2939
3042 * A transcript value represents the assertion that a particular region of 2940 /// A transcript value represents the assertion that a particular region of
3043 * the reference genome may be transcribed as RNA. An alternative splicing 2941 /// the reference genome may be transcribed as RNA. An alternative splicing
3044 * pattern would be represented as a separate transcript object. This field 2942 /// pattern would be represented as a separate transcript object. This field
3045 * is only set for annotations of type `TRANSCRIPT`. 2943 /// is only set for annotations of type `TRANSCRIPT`.
3046 */
3047 Transcript transcript; 2944 Transcript transcript;
3048 /** 2945
3049 * The data type for this annotation. Must match the containing annotation 2946 /// The data type for this annotation. Must match the containing annotation
3050 * set's type. 2947 /// set's type.
3051 * Possible string values are: 2948 /// Possible string values are:
3052 * - "ANNOTATION_TYPE_UNSPECIFIED" 2949 /// - "ANNOTATION_TYPE_UNSPECIFIED"
3053 * - "GENERIC" : A `GENERIC` annotation type should be used when no other 2950 /// - "GENERIC" : A `GENERIC` annotation type should be used when no other
3054 * annotation 2951 /// annotation
3055 * type will suffice. This represents an untyped annotation of the reference 2952 /// type will suffice. This represents an untyped annotation of the reference
3056 * genome. 2953 /// genome.
3057 * - "VARIANT" : A `VARIANT` annotation type. 2954 /// - "VARIANT" : A `VARIANT` annotation type.
3058 * - "GENE" : A `GENE` annotation type represents the existence of a gene at 2955 /// - "GENE" : A `GENE` annotation type represents the existence of a gene at
3059 * the 2956 /// the
3060 * associated reference coordinates. The start coordinate is typically the 2957 /// associated reference coordinates. The start coordinate is typically the
3061 * gene's transcription start site and the end is typically the end of the 2958 /// gene's transcription start site and the end is typically the end of the
3062 * gene's last exon. 2959 /// gene's last exon.
3063 * - "TRANSCRIPT" : A `TRANSCRIPT` annotation type represents the assertion 2960 /// - "TRANSCRIPT" : A `TRANSCRIPT` annotation type represents the assertion
3064 * that a 2961 /// that a
3065 * particular region of the reference genome may be transcribed as RNA. 2962 /// particular region of the reference genome may be transcribed as RNA.
3066 */
3067 core.String type; 2963 core.String type;
3068 /** 2964
3069 * A variant annotation, which describes the effect of a variant on the 2965 /// A variant annotation, which describes the effect of a variant on the
3070 * genome, the coding sequence, and/or higher level consequences at the 2966 /// genome, the coding sequence, and/or higher level consequences at the
3071 * organism level e.g. pathogenicity. This field is only set for annotations 2967 /// organism level e.g. pathogenicity. This field is only set for annotations
3072 * of type `VARIANT`. 2968 /// of type `VARIANT`.
3073 */
3074 VariantAnnotation variant; 2969 VariantAnnotation variant;
3075 2970
3076 Annotation(); 2971 Annotation();
3077 2972
3078 Annotation.fromJson(core.Map _json) { 2973 Annotation.fromJson(core.Map _json) {
3079 if (_json.containsKey("annotationSetId")) { 2974 if (_json.containsKey("annotationSetId")) {
3080 annotationSetId = _json["annotationSetId"]; 2975 annotationSetId = _json["annotationSetId"];
3081 } 2976 }
3082 if (_json.containsKey("end")) { 2977 if (_json.containsKey("end")) {
3083 end = _json["end"]; 2978 end = _json["end"];
(...skipping 24 matching lines...) Expand all
3108 } 3003 }
3109 if (_json.containsKey("type")) { 3004 if (_json.containsKey("type")) {
3110 type = _json["type"]; 3005 type = _json["type"];
3111 } 3006 }
3112 if (_json.containsKey("variant")) { 3007 if (_json.containsKey("variant")) {
3113 variant = new VariantAnnotation.fromJson(_json["variant"]); 3008 variant = new VariantAnnotation.fromJson(_json["variant"]);
3114 } 3009 }
3115 } 3010 }
3116 3011
3117 core.Map<core.String, core.Object> toJson() { 3012 core.Map<core.String, core.Object> toJson() {
3118 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 3013 final core.Map<core.String, core.Object> _json =
3014 new core.Map<core.String, core.Object>();
3119 if (annotationSetId != null) { 3015 if (annotationSetId != null) {
3120 _json["annotationSetId"] = annotationSetId; 3016 _json["annotationSetId"] = annotationSetId;
3121 } 3017 }
3122 if (end != null) { 3018 if (end != null) {
3123 _json["end"] = end; 3019 _json["end"] = end;
3124 } 3020 }
3125 if (id != null) { 3021 if (id != null) {
3126 _json["id"] = id; 3022 _json["id"] = id;
3127 } 3023 }
3128 if (info != null) { 3024 if (info != null) {
(...skipping 20 matching lines...) Expand all
3149 if (type != null) { 3045 if (type != null) {
3150 _json["type"] = type; 3046 _json["type"] = type;
3151 } 3047 }
3152 if (variant != null) { 3048 if (variant != null) {
3153 _json["variant"] = (variant).toJson(); 3049 _json["variant"] = (variant).toJson();
3154 } 3050 }
3155 return _json; 3051 return _json;
3156 } 3052 }
3157 } 3053 }
3158 3054
3159 /** 3055 /// An annotation set is a logical grouping of annotations that share
3160 * An annotation set is a logical grouping of annotations that share consistent 3056 /// consistent
3161 * type information and provenance. Examples of annotation sets include 'all 3057 /// type information and provenance. Examples of annotation sets include 'all
3162 * genes from refseq', and 'all variant annotations from ClinVar'. 3058 /// genes from refseq', and 'all variant annotations from ClinVar'.
3163 */
3164 class AnnotationSet { 3059 class AnnotationSet {
3165 /** The dataset to which this annotation set belongs. */ 3060 /// The dataset to which this annotation set belongs.
3166 core.String datasetId; 3061 core.String datasetId;
3167 /** 3062
3168 * The server-generated annotation set ID, unique across all annotation sets. 3063 /// The server-generated annotation set ID, unique across all annotation
3169 */ 3064 /// sets.
3170 core.String id; 3065 core.String id;
3171 /** 3066
3172 * A map of additional read alignment information. This must be of the form 3067 /// A map of additional read alignment information. This must be of the form
3173 * map<string, string[]> (string key mapping to a list of string values). 3068 /// map<string, string[]> (string key mapping to a list of string values).
3174 * 3069 ///
3175 * The values for Object must be JSON objects. It can consist of `num`, 3070 /// The values for Object must be JSON objects. It can consist of `num`,
3176 * `String`, `bool` and `null` as well as `Map` and `List` values. 3071 /// `String`, `bool` and `null` as well as `Map` and `List` values.
3177 */
3178 core.Map<core.String, core.List<core.Object>> info; 3072 core.Map<core.String, core.List<core.Object>> info;
3179 /** The display name for this annotation set. */ 3073
3074 /// The display name for this annotation set.
3180 core.String name; 3075 core.String name;
3181 /** 3076
3182 * The ID of the reference set that defines the coordinate space for this 3077 /// The ID of the reference set that defines the coordinate space for this
3183 * set's annotations. 3078 /// set's annotations.
3184 */
3185 core.String referenceSetId; 3079 core.String referenceSetId;
3186 /** 3080
3187 * The source URI describing the file from which this annotation set was 3081 /// The source URI describing the file from which this annotation set was
3188 * generated, if any. 3082 /// generated, if any.
3189 */
3190 core.String sourceUri; 3083 core.String sourceUri;
3191 /** 3084
3192 * The type of annotations contained within this set. 3085 /// The type of annotations contained within this set.
3193 * Possible string values are: 3086 /// Possible string values are:
3194 * - "ANNOTATION_TYPE_UNSPECIFIED" 3087 /// - "ANNOTATION_TYPE_UNSPECIFIED"
3195 * - "GENERIC" : A `GENERIC` annotation type should be used when no other 3088 /// - "GENERIC" : A `GENERIC` annotation type should be used when no other
3196 * annotation 3089 /// annotation
3197 * type will suffice. This represents an untyped annotation of the reference 3090 /// type will suffice. This represents an untyped annotation of the reference
3198 * genome. 3091 /// genome.
3199 * - "VARIANT" : A `VARIANT` annotation type. 3092 /// - "VARIANT" : A `VARIANT` annotation type.
3200 * - "GENE" : A `GENE` annotation type represents the existence of a gene at 3093 /// - "GENE" : A `GENE` annotation type represents the existence of a gene at
3201 * the 3094 /// the
3202 * associated reference coordinates. The start coordinate is typically the 3095 /// associated reference coordinates. The start coordinate is typically the
3203 * gene's transcription start site and the end is typically the end of the 3096 /// gene's transcription start site and the end is typically the end of the
3204 * gene's last exon. 3097 /// gene's last exon.
3205 * - "TRANSCRIPT" : A `TRANSCRIPT` annotation type represents the assertion 3098 /// - "TRANSCRIPT" : A `TRANSCRIPT` annotation type represents the assertion
3206 * that a 3099 /// that a
3207 * particular region of the reference genome may be transcribed as RNA. 3100 /// particular region of the reference genome may be transcribed as RNA.
3208 */
3209 core.String type; 3101 core.String type;
3210 3102
3211 AnnotationSet(); 3103 AnnotationSet();
3212 3104
3213 AnnotationSet.fromJson(core.Map _json) { 3105 AnnotationSet.fromJson(core.Map _json) {
3214 if (_json.containsKey("datasetId")) { 3106 if (_json.containsKey("datasetId")) {
3215 datasetId = _json["datasetId"]; 3107 datasetId = _json["datasetId"];
3216 } 3108 }
3217 if (_json.containsKey("id")) { 3109 if (_json.containsKey("id")) {
3218 id = _json["id"]; 3110 id = _json["id"];
3219 } 3111 }
3220 if (_json.containsKey("info")) { 3112 if (_json.containsKey("info")) {
3221 info = _json["info"]; 3113 info = _json["info"];
3222 } 3114 }
3223 if (_json.containsKey("name")) { 3115 if (_json.containsKey("name")) {
3224 name = _json["name"]; 3116 name = _json["name"];
3225 } 3117 }
3226 if (_json.containsKey("referenceSetId")) { 3118 if (_json.containsKey("referenceSetId")) {
3227 referenceSetId = _json["referenceSetId"]; 3119 referenceSetId = _json["referenceSetId"];
3228 } 3120 }
3229 if (_json.containsKey("sourceUri")) { 3121 if (_json.containsKey("sourceUri")) {
3230 sourceUri = _json["sourceUri"]; 3122 sourceUri = _json["sourceUri"];
3231 } 3123 }
3232 if (_json.containsKey("type")) { 3124 if (_json.containsKey("type")) {
3233 type = _json["type"]; 3125 type = _json["type"];
3234 } 3126 }
3235 } 3127 }
3236 3128
3237 core.Map<core.String, core.Object> toJson() { 3129 core.Map<core.String, core.Object> toJson() {
3238 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 3130 final core.Map<core.String, core.Object> _json =
3131 new core.Map<core.String, core.Object>();
3239 if (datasetId != null) { 3132 if (datasetId != null) {
3240 _json["datasetId"] = datasetId; 3133 _json["datasetId"] = datasetId;
3241 } 3134 }
3242 if (id != null) { 3135 if (id != null) {
3243 _json["id"] = id; 3136 _json["id"] = id;
3244 } 3137 }
3245 if (info != null) { 3138 if (info != null) {
3246 _json["info"] = info; 3139 _json["info"] = info;
3247 } 3140 }
3248 if (name != null) { 3141 if (name != null) {
3249 _json["name"] = name; 3142 _json["name"] = name;
3250 } 3143 }
3251 if (referenceSetId != null) { 3144 if (referenceSetId != null) {
3252 _json["referenceSetId"] = referenceSetId; 3145 _json["referenceSetId"] = referenceSetId;
3253 } 3146 }
3254 if (sourceUri != null) { 3147 if (sourceUri != null) {
3255 _json["sourceUri"] = sourceUri; 3148 _json["sourceUri"] = sourceUri;
3256 } 3149 }
3257 if (type != null) { 3150 if (type != null) {
3258 _json["type"] = type; 3151 _json["type"] = type;
3259 } 3152 }
3260 return _json; 3153 return _json;
3261 } 3154 }
3262 } 3155 }
3263 3156
3264 class BatchCreateAnnotationsRequest { 3157 class BatchCreateAnnotationsRequest {
3265 /** 3158 /// The annotations to be created. At most 4096 can be specified in a single
3266 * The annotations to be created. At most 4096 can be specified in a single 3159 /// request.
3267 * request.
3268 */
3269 core.List<Annotation> annotations; 3160 core.List<Annotation> annotations;
3270 /** 3161
3271 * A unique request ID which enables the server to detect duplicated requests. 3162 /// A unique request ID which enables the server to detect duplicated
3272 * If provided, duplicated requests will result in the same response; if not 3163 /// requests.
3273 * provided, duplicated requests may result in duplicated data. For a given 3164 /// If provided, duplicated requests will result in the same response; if not
3274 * annotation set, callers should not reuse `request_id`s when writing 3165 /// provided, duplicated requests may result in duplicated data. For a given
3275 * different batches of annotations - behavior in this case is undefined. 3166 /// annotation set, callers should not reuse `request_id`s when writing
3276 * A common approach is to use a UUID. For batch jobs where worker crashes are 3167 /// different batches of annotations - behavior in this case is undefined.
3277 * a possibility, consider using some unique variant of a worker or run ID. 3168 /// A common approach is to use a UUID. For batch jobs where worker crashes
3278 */ 3169 /// are
3170 /// a possibility, consider using some unique variant of a worker or run ID.
3279 core.String requestId; 3171 core.String requestId;
3280 3172
3281 BatchCreateAnnotationsRequest(); 3173 BatchCreateAnnotationsRequest();
3282 3174
3283 BatchCreateAnnotationsRequest.fromJson(core.Map _json) { 3175 BatchCreateAnnotationsRequest.fromJson(core.Map _json) {
3284 if (_json.containsKey("annotations")) { 3176 if (_json.containsKey("annotations")) {
3285 annotations = _json["annotations"].map((value) => new Annotation.fromJson( value)).toList(); 3177 annotations = _json["annotations"]
3178 .map((value) => new Annotation.fromJson(value))
3179 .toList();
3286 } 3180 }
3287 if (_json.containsKey("requestId")) { 3181 if (_json.containsKey("requestId")) {
3288 requestId = _json["requestId"]; 3182 requestId = _json["requestId"];
3289 } 3183 }
3290 } 3184 }
3291 3185
3292 core.Map<core.String, core.Object> toJson() { 3186 core.Map<core.String, core.Object> toJson() {
3293 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 3187 final core.Map<core.String, core.Object> _json =
3188 new core.Map<core.String, core.Object>();
3294 if (annotations != null) { 3189 if (annotations != null) {
3295 _json["annotations"] = annotations.map((value) => (value).toJson()).toList (); 3190 _json["annotations"] =
3191 annotations.map((value) => (value).toJson()).toList();
3296 } 3192 }
3297 if (requestId != null) { 3193 if (requestId != null) {
3298 _json["requestId"] = requestId; 3194 _json["requestId"] = requestId;
3299 } 3195 }
3300 return _json; 3196 return _json;
3301 } 3197 }
3302 } 3198 }
3303 3199
3304 class BatchCreateAnnotationsResponse { 3200 class BatchCreateAnnotationsResponse {
3305 /** 3201 /// The resulting per-annotation entries, ordered consistently with the
3306 * The resulting per-annotation entries, ordered consistently with the 3202 /// original request.
3307 * original request.
3308 */
3309 core.List<Entry> entries; 3203 core.List<Entry> entries;
3310 3204
3311 BatchCreateAnnotationsResponse(); 3205 BatchCreateAnnotationsResponse();
3312 3206
3313 BatchCreateAnnotationsResponse.fromJson(core.Map _json) { 3207 BatchCreateAnnotationsResponse.fromJson(core.Map _json) {
3314 if (_json.containsKey("entries")) { 3208 if (_json.containsKey("entries")) {
3315 entries = _json["entries"].map((value) => new Entry.fromJson(value)).toLis t(); 3209 entries =
3210 _json["entries"].map((value) => new Entry.fromJson(value)).toList();
3316 } 3211 }
3317 } 3212 }
3318 3213
3319 core.Map<core.String, core.Object> toJson() { 3214 core.Map<core.String, core.Object> toJson() {
3320 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 3215 final core.Map<core.String, core.Object> _json =
3216 new core.Map<core.String, core.Object>();
3321 if (entries != null) { 3217 if (entries != null) {
3322 _json["entries"] = entries.map((value) => (value).toJson()).toList(); 3218 _json["entries"] = entries.map((value) => (value).toJson()).toList();
3323 } 3219 }
3324 return _json; 3220 return _json;
3325 } 3221 }
3326 } 3222 }
3327 3223
3328 /** Associates `members` with a `role`. */ 3224 /// Associates `members` with a `role`.
3329 class Binding { 3225 class Binding {
3330 /** 3226 /// Specifies the identities requesting access for a Cloud Platform resource.
3331 * Specifies the identities requesting access for a Cloud Platform resource. 3227 /// `members` can have the following values:
3332 * `members` can have the following values: 3228 ///
3333 * 3229 /// * `allUsers`: A special identifier that represents anyone who is
3334 * * `allUsers`: A special identifier that represents anyone who is 3230 /// on the internet; with or without a Google account.
3335 * on the internet; with or without a Google account. 3231 ///
3336 * 3232 /// * `allAuthenticatedUsers`: A special identifier that represents anyone
3337 * * `allAuthenticatedUsers`: A special identifier that represents anyone 3233 /// who is authenticated with a Google account or a service account.
3338 * who is authenticated with a Google account or a service account. 3234 ///
3339 * 3235 /// * `user:{emailid}`: An email address that represents a specific Google
3340 * * `user:{emailid}`: An email address that represents a specific Google 3236 /// account. For example, `alice@gmail.com` or `joe@example.com`.
3341 * account. For example, `alice@gmail.com` or `joe@example.com`. 3237 ///
3342 * 3238 ///
3343 * 3239 /// * `serviceAccount:{emailid}`: An email address that represents a service
3344 * * `serviceAccount:{emailid}`: An email address that represents a service 3240 /// account. For example, `my-other-app@appspot.gserviceaccount.com`.
3345 * account. For example, `my-other-app@appspot.gserviceaccount.com`. 3241 ///
3346 * 3242 /// * `group:{emailid}`: An email address that represents a Google group.
3347 * * `group:{emailid}`: An email address that represents a Google group. 3243 /// For example, `admins@example.com`.
3348 * For example, `admins@example.com`. 3244 ///
3349 * 3245 ///
3350 * 3246 /// * `domain:{domain}`: A Google Apps domain name that represents all the
3351 * * `domain:{domain}`: A Google Apps domain name that represents all the 3247 /// users of that domain. For example, `google.com` or `example.com`.
3352 * users of that domain. For example, `google.com` or `example.com`.
3353 */
3354 core.List<core.String> members; 3248 core.List<core.String> members;
3355 /** 3249
3356 * Role that is assigned to `members`. 3250 /// Role that is assigned to `members`.
3357 * For example, `roles/viewer`, `roles/editor`, or `roles/owner`. 3251 /// For example, `roles/viewer`, `roles/editor`, or `roles/owner`.
3358 * Required 3252 /// Required
3359 */
3360 core.String role; 3253 core.String role;
3361 3254
3362 Binding(); 3255 Binding();
3363 3256
3364 Binding.fromJson(core.Map _json) { 3257 Binding.fromJson(core.Map _json) {
3365 if (_json.containsKey("members")) { 3258 if (_json.containsKey("members")) {
3366 members = _json["members"]; 3259 members = _json["members"];
3367 } 3260 }
3368 if (_json.containsKey("role")) { 3261 if (_json.containsKey("role")) {
3369 role = _json["role"]; 3262 role = _json["role"];
3370 } 3263 }
3371 } 3264 }
3372 3265
3373 core.Map<core.String, core.Object> toJson() { 3266 core.Map<core.String, core.Object> toJson() {
3374 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 3267 final core.Map<core.String, core.Object> _json =
3268 new core.Map<core.String, core.Object>();
3375 if (members != null) { 3269 if (members != null) {
3376 _json["members"] = members; 3270 _json["members"] = members;
3377 } 3271 }
3378 if (role != null) { 3272 if (role != null) {
3379 _json["role"] = role; 3273 _json["role"] = role;
3380 } 3274 }
3381 return _json; 3275 return _json;
3382 } 3276 }
3383 } 3277 }
3384 3278
3385 /** 3279 /// A call set is a collection of variant calls, typically for one sample. It
3386 * A call set is a collection of variant calls, typically for one sample. It 3280 /// belongs to a variant set.
3387 * belongs to a variant set. 3281 ///
3388 * 3282 /// For more genomics resource definitions, see [Fundamentals of Google
3389 * For more genomics resource definitions, see [Fundamentals of Google 3283 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
3390 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
3391 */
3392 class CallSet { 3284 class CallSet {
3393 /** The date this call set was created in milliseconds from the epoch. */ 3285 /// The date this call set was created in milliseconds from the epoch.
3394 core.String created; 3286 core.String created;
3395 /** The server-generated call set ID, unique across all call sets. */ 3287
3288 /// The server-generated call set ID, unique across all call sets.
3396 core.String id; 3289 core.String id;
3397 /** 3290
3398 * A map of additional call set information. This must be of the form 3291 /// A map of additional call set information. This must be of the form
3399 * map<string, string[]> (string key mapping to a list of string values). 3292 /// map<string, string[]> (string key mapping to a list of string values).
3400 * 3293 ///
3401 * The values for Object must be JSON objects. It can consist of `num`, 3294 /// The values for Object must be JSON objects. It can consist of `num`,
3402 * `String`, `bool` and `null` as well as `Map` and `List` values. 3295 /// `String`, `bool` and `null` as well as `Map` and `List` values.
3403 */
3404 core.Map<core.String, core.List<core.Object>> info; 3296 core.Map<core.String, core.List<core.Object>> info;
3405 /** The call set name. */ 3297
3298 /// The call set name.
3406 core.String name; 3299 core.String name;
3407 /** The sample ID this call set corresponds to. */ 3300
3301 /// The sample ID this call set corresponds to.
3408 core.String sampleId; 3302 core.String sampleId;
3409 /** 3303
3410 * The IDs of the variant sets this call set belongs to. This field must 3304 /// The IDs of the variant sets this call set belongs to. This field must
3411 * have exactly length one, as a call set belongs to a single variant set. 3305 /// have exactly length one, as a call set belongs to a single variant set.
3412 * This field is repeated for compatibility with the 3306 /// This field is repeated for compatibility with the
3413 * [GA4GH 0.5.1 3307 /// [GA4GH 0.5.1
3414 * API](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/v ariants.avdl#L76). 3308 /// API](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/ variants.avdl#L76).
3415 */
3416 core.List<core.String> variantSetIds; 3309 core.List<core.String> variantSetIds;
3417 3310
3418 CallSet(); 3311 CallSet();
3419 3312
3420 CallSet.fromJson(core.Map _json) { 3313 CallSet.fromJson(core.Map _json) {
3421 if (_json.containsKey("created")) { 3314 if (_json.containsKey("created")) {
3422 created = _json["created"]; 3315 created = _json["created"];
3423 } 3316 }
3424 if (_json.containsKey("id")) { 3317 if (_json.containsKey("id")) {
3425 id = _json["id"]; 3318 id = _json["id"];
3426 } 3319 }
3427 if (_json.containsKey("info")) { 3320 if (_json.containsKey("info")) {
3428 info = _json["info"]; 3321 info = _json["info"];
3429 } 3322 }
3430 if (_json.containsKey("name")) { 3323 if (_json.containsKey("name")) {
3431 name = _json["name"]; 3324 name = _json["name"];
3432 } 3325 }
3433 if (_json.containsKey("sampleId")) { 3326 if (_json.containsKey("sampleId")) {
3434 sampleId = _json["sampleId"]; 3327 sampleId = _json["sampleId"];
3435 } 3328 }
3436 if (_json.containsKey("variantSetIds")) { 3329 if (_json.containsKey("variantSetIds")) {
3437 variantSetIds = _json["variantSetIds"]; 3330 variantSetIds = _json["variantSetIds"];
3438 } 3331 }
3439 } 3332 }
3440 3333
3441 core.Map<core.String, core.Object> toJson() { 3334 core.Map<core.String, core.Object> toJson() {
3442 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 3335 final core.Map<core.String, core.Object> _json =
3336 new core.Map<core.String, core.Object>();
3443 if (created != null) { 3337 if (created != null) {
3444 _json["created"] = created; 3338 _json["created"] = created;
3445 } 3339 }
3446 if (id != null) { 3340 if (id != null) {
3447 _json["id"] = id; 3341 _json["id"] = id;
3448 } 3342 }
3449 if (info != null) { 3343 if (info != null) {
3450 _json["info"] = info; 3344 _json["info"] = info;
3451 } 3345 }
3452 if (name != null) { 3346 if (name != null) {
3453 _json["name"] = name; 3347 _json["name"] = name;
3454 } 3348 }
3455 if (sampleId != null) { 3349 if (sampleId != null) {
3456 _json["sampleId"] = sampleId; 3350 _json["sampleId"] = sampleId;
3457 } 3351 }
3458 if (variantSetIds != null) { 3352 if (variantSetIds != null) {
3459 _json["variantSetIds"] = variantSetIds; 3353 _json["variantSetIds"] = variantSetIds;
3460 } 3354 }
3461 return _json; 3355 return _json;
3462 } 3356 }
3463 } 3357 }
3464 3358
3465 /** The request message for Operations.CancelOperation. */ 3359 /// The request message for Operations.CancelOperation.
3466 class CancelOperationRequest { 3360 class CancelOperationRequest {
3467
3468 CancelOperationRequest(); 3361 CancelOperationRequest();
3469 3362
3470 CancelOperationRequest.fromJson(core.Map _json) { 3363 CancelOperationRequest.fromJson(core.Map _json) {}
3471 }
3472 3364
3473 core.Map<core.String, core.Object> toJson() { 3365 core.Map<core.String, core.Object> toJson() {
3474 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 3366 final core.Map<core.String, core.Object> _json =
3367 new core.Map<core.String, core.Object>();
3475 return _json; 3368 return _json;
3476 } 3369 }
3477 } 3370 }
3478 3371
3479 /** A single CIGAR operation. */ 3372 /// A single CIGAR operation.
3480 class CigarUnit { 3373 class CigarUnit {
3481 /** 3374 ///
3482 * 3375 /// Possible string values are:
3483 * Possible string values are: 3376 /// - "OPERATION_UNSPECIFIED"
3484 * - "OPERATION_UNSPECIFIED" 3377 /// - "ALIGNMENT_MATCH" : An alignment match indicates that a sequence can be
3485 * - "ALIGNMENT_MATCH" : An alignment match indicates that a sequence can be 3378 /// aligned to the
3486 * aligned to the 3379 /// reference without evidence of an INDEL. Unlike the
3487 * reference without evidence of an INDEL. Unlike the 3380 /// `SEQUENCE_MATCH` and `SEQUENCE_MISMATCH` operators,
3488 * `SEQUENCE_MATCH` and `SEQUENCE_MISMATCH` operators, 3381 /// the `ALIGNMENT_MATCH` operator does not indicate whether the
3489 * the `ALIGNMENT_MATCH` operator does not indicate whether the 3382 /// reference and read sequences are an exact match. This operator is
3490 * reference and read sequences are an exact match. This operator is 3383 /// equivalent to SAM's `M`.
3491 * equivalent to SAM's `M`. 3384 /// - "INSERT" : The insert operator indicates that the read contains
3492 * - "INSERT" : The insert operator indicates that the read contains evidence 3385 /// evidence of bases
3493 * of bases 3386 /// being inserted into the reference. This operator is equivalent to SAM's
3494 * being inserted into the reference. This operator is equivalent to SAM's 3387 /// `I`.
3495 * `I`. 3388 /// - "DELETE" : The delete operator indicates that the read contains
3496 * - "DELETE" : The delete operator indicates that the read contains evidence 3389 /// evidence of bases
3497 * of bases 3390 /// being deleted from the reference. This operator is equivalent to SAM's
3498 * being deleted from the reference. This operator is equivalent to SAM's 3391 /// `D`.
3499 * `D`. 3392 /// - "SKIP" : The skip operator indicates that this read skips a long
3500 * - "SKIP" : The skip operator indicates that this read skips a long segment 3393 /// segment of the
3501 * of the 3394 /// reference, but the bases have not been deleted. This operator is commonly
3502 * reference, but the bases have not been deleted. This operator is commonly 3395 /// used when working with RNA-seq data, where reads may skip long segments
3503 * used when working with RNA-seq data, where reads may skip long segments 3396 /// of the reference between exons. This operator is equivalent to SAM's
3504 * of the reference between exons. This operator is equivalent to SAM's 3397 /// `N`.
3505 * `N`. 3398 /// - "CLIP_SOFT" : The soft clip operator indicates that bases at the
3506 * - "CLIP_SOFT" : The soft clip operator indicates that bases at the 3399 /// start/end of a read
3507 * start/end of a read 3400 /// have not been considered during alignment. This may occur if the majority
3508 * have not been considered during alignment. This may occur if the majority 3401 /// of a read maps, except for low quality bases at the start/end of a read.
3509 * of a read maps, except for low quality bases at the start/end of a read. 3402 /// This operator is equivalent to SAM's `S`. Bases that are soft
3510 * This operator is equivalent to SAM's `S`. Bases that are soft 3403 /// clipped will still be stored in the read.
3511 * clipped will still be stored in the read. 3404 /// - "CLIP_HARD" : The hard clip operator indicates that bases at the
3512 * - "CLIP_HARD" : The hard clip operator indicates that bases at the 3405 /// start/end of a read
3513 * start/end of a read 3406 /// have been omitted from this alignment. This may occur if this linear
3514 * have been omitted from this alignment. This may occur if this linear 3407 /// alignment is part of a chimeric alignment, or if the read has been
3515 * alignment is part of a chimeric alignment, or if the read has been 3408 /// trimmed (for example, during error correction or to trim poly-A tails for
3516 * trimmed (for example, during error correction or to trim poly-A tails for 3409 /// RNA-seq). This operator is equivalent to SAM's `H`.
3517 * RNA-seq). This operator is equivalent to SAM's `H`. 3410 /// - "PAD" : The pad operator indicates that there is padding in an
3518 * - "PAD" : The pad operator indicates that there is padding in an alignment. 3411 /// alignment. This
3519 * This 3412 /// operator is equivalent to SAM's `P`.
3520 * operator is equivalent to SAM's `P`. 3413 /// - "SEQUENCE_MATCH" : This operator indicates that this portion of the
3521 * - "SEQUENCE_MATCH" : This operator indicates that this portion of the 3414 /// aligned sequence exactly
3522 * aligned sequence exactly 3415 /// matches the reference. This operator is equivalent to SAM's `=`.
3523 * matches the reference. This operator is equivalent to SAM's `=`. 3416 /// - "SEQUENCE_MISMATCH" : This operator indicates that this portion of the
3524 * - "SEQUENCE_MISMATCH" : This operator indicates that this portion of the 3417 /// aligned sequence is an
3525 * aligned sequence is an 3418 /// alignment match to the reference, but a sequence mismatch. This can
3526 * alignment match to the reference, but a sequence mismatch. This can 3419 /// indicate a SNP or a read error. This operator is equivalent to SAM's
3527 * indicate a SNP or a read error. This operator is equivalent to SAM's 3420 /// `X`.
3528 * `X`.
3529 */
3530 core.String operation; 3421 core.String operation;
3531 /** The number of genomic bases that the operation runs for. Required. */ 3422
3423 /// The number of genomic bases that the operation runs for. Required.
3532 core.String operationLength; 3424 core.String operationLength;
3533 /** 3425
3534 * `referenceSequence` is only used at mismatches 3426 /// `referenceSequence` is only used at mismatches
3535 * (`SEQUENCE_MISMATCH`) and deletions (`DELETE`). 3427 /// (`SEQUENCE_MISMATCH`) and deletions (`DELETE`).
3536 * Filling this field replaces SAM's MD tag. If the relevant information is 3428 /// Filling this field replaces SAM's MD tag. If the relevant information is
3537 * not available, this field is unset. 3429 /// not available, this field is unset.
3538 */
3539 core.String referenceSequence; 3430 core.String referenceSequence;
3540 3431
3541 CigarUnit(); 3432 CigarUnit();
3542 3433
3543 CigarUnit.fromJson(core.Map _json) { 3434 CigarUnit.fromJson(core.Map _json) {
3544 if (_json.containsKey("operation")) { 3435 if (_json.containsKey("operation")) {
3545 operation = _json["operation"]; 3436 operation = _json["operation"];
3546 } 3437 }
3547 if (_json.containsKey("operationLength")) { 3438 if (_json.containsKey("operationLength")) {
3548 operationLength = _json["operationLength"]; 3439 operationLength = _json["operationLength"];
3549 } 3440 }
3550 if (_json.containsKey("referenceSequence")) { 3441 if (_json.containsKey("referenceSequence")) {
3551 referenceSequence = _json["referenceSequence"]; 3442 referenceSequence = _json["referenceSequence"];
3552 } 3443 }
3553 } 3444 }
3554 3445
3555 core.Map<core.String, core.Object> toJson() { 3446 core.Map<core.String, core.Object> toJson() {
3556 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 3447 final core.Map<core.String, core.Object> _json =
3448 new core.Map<core.String, core.Object>();
3557 if (operation != null) { 3449 if (operation != null) {
3558 _json["operation"] = operation; 3450 _json["operation"] = operation;
3559 } 3451 }
3560 if (operationLength != null) { 3452 if (operationLength != null) {
3561 _json["operationLength"] = operationLength; 3453 _json["operationLength"] = operationLength;
3562 } 3454 }
3563 if (referenceSequence != null) { 3455 if (referenceSequence != null) {
3564 _json["referenceSequence"] = referenceSequence; 3456 _json["referenceSequence"] = referenceSequence;
3565 } 3457 }
3566 return _json; 3458 return _json;
3567 } 3459 }
3568 } 3460 }
3569 3461
3570 class ClinicalCondition { 3462 class ClinicalCondition {
3571 /** 3463 /// The MedGen concept id associated with this gene.
3572 * The MedGen concept id associated with this gene. 3464 /// Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
3573 * Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/
3574 */
3575 core.String conceptId; 3465 core.String conceptId;
3576 /** The set of external IDs for this condition. */ 3466
3467 /// The set of external IDs for this condition.
3577 core.List<ExternalId> externalIds; 3468 core.List<ExternalId> externalIds;
3578 /** A set of names for the condition. */ 3469
3470 /// A set of names for the condition.
3579 core.List<core.String> names; 3471 core.List<core.String> names;
3580 /** 3472
3581 * The OMIM id for this condition. 3473 /// The OMIM id for this condition.
3582 * Search for these IDs at http://omim.org/ 3474 /// Search for these IDs at http://omim.org/
3583 */
3584 core.String omimId; 3475 core.String omimId;
3585 3476
3586 ClinicalCondition(); 3477 ClinicalCondition();
3587 3478
3588 ClinicalCondition.fromJson(core.Map _json) { 3479 ClinicalCondition.fromJson(core.Map _json) {
3589 if (_json.containsKey("conceptId")) { 3480 if (_json.containsKey("conceptId")) {
3590 conceptId = _json["conceptId"]; 3481 conceptId = _json["conceptId"];
3591 } 3482 }
3592 if (_json.containsKey("externalIds")) { 3483 if (_json.containsKey("externalIds")) {
3593 externalIds = _json["externalIds"].map((value) => new ExternalId.fromJson( value)).toList(); 3484 externalIds = _json["externalIds"]
3485 .map((value) => new ExternalId.fromJson(value))
3486 .toList();
3594 } 3487 }
3595 if (_json.containsKey("names")) { 3488 if (_json.containsKey("names")) {
3596 names = _json["names"]; 3489 names = _json["names"];
3597 } 3490 }
3598 if (_json.containsKey("omimId")) { 3491 if (_json.containsKey("omimId")) {
3599 omimId = _json["omimId"]; 3492 omimId = _json["omimId"];
3600 } 3493 }
3601 } 3494 }
3602 3495
3603 core.Map<core.String, core.Object> toJson() { 3496 core.Map<core.String, core.Object> toJson() {
3604 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 3497 final core.Map<core.String, core.Object> _json =
3498 new core.Map<core.String, core.Object>();
3605 if (conceptId != null) { 3499 if (conceptId != null) {
3606 _json["conceptId"] = conceptId; 3500 _json["conceptId"] = conceptId;
3607 } 3501 }
3608 if (externalIds != null) { 3502 if (externalIds != null) {
3609 _json["externalIds"] = externalIds.map((value) => (value).toJson()).toList (); 3503 _json["externalIds"] =
3504 externalIds.map((value) => (value).toJson()).toList();
3610 } 3505 }
3611 if (names != null) { 3506 if (names != null) {
3612 _json["names"] = names; 3507 _json["names"] = names;
3613 } 3508 }
3614 if (omimId != null) { 3509 if (omimId != null) {
3615 _json["omimId"] = omimId; 3510 _json["omimId"] = omimId;
3616 } 3511 }
3617 return _json; 3512 return _json;
3618 } 3513 }
3619 } 3514 }
3620 3515
3621 class CodingSequence { 3516 class CodingSequence {
3622 /** 3517 /// The end of the coding sequence on this annotation's reference sequence,
3623 * The end of the coding sequence on this annotation's reference sequence, 3518 /// 0-based exclusive. Note that this position is relative to the reference
3624 * 0-based exclusive. Note that this position is relative to the reference 3519 /// start, and *not* the containing annotation start.
3625 * start, and *not* the containing annotation start.
3626 */
3627 core.String end; 3520 core.String end;
3628 /** 3521
3629 * The start of the coding sequence on this annotation's reference sequence, 3522 /// The start of the coding sequence on this annotation's reference sequence,
3630 * 0-based inclusive. Note that this position is relative to the reference 3523 /// 0-based inclusive. Note that this position is relative to the reference
3631 * start, and *not* the containing annotation start. 3524 /// start, and *not* the containing annotation start.
3632 */
3633 core.String start; 3525 core.String start;
3634 3526
3635 CodingSequence(); 3527 CodingSequence();
3636 3528
3637 CodingSequence.fromJson(core.Map _json) { 3529 CodingSequence.fromJson(core.Map _json) {
3638 if (_json.containsKey("end")) { 3530 if (_json.containsKey("end")) {
3639 end = _json["end"]; 3531 end = _json["end"];
3640 } 3532 }
3641 if (_json.containsKey("start")) { 3533 if (_json.containsKey("start")) {
3642 start = _json["start"]; 3534 start = _json["start"];
3643 } 3535 }
3644 } 3536 }
3645 3537
3646 core.Map<core.String, core.Object> toJson() { 3538 core.Map<core.String, core.Object> toJson() {
3647 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 3539 final core.Map<core.String, core.Object> _json =
3540 new core.Map<core.String, core.Object>();
3648 if (end != null) { 3541 if (end != null) {
3649 _json["end"] = end; 3542 _json["end"] = end;
3650 } 3543 }
3651 if (start != null) { 3544 if (start != null) {
3652 _json["start"] = start; 3545 _json["start"] = start;
3653 } 3546 }
3654 return _json; 3547 return _json;
3655 } 3548 }
3656 } 3549 }
3657 3550
3658 /** 3551 /// Describes a Compute Engine resource that is being managed by a running
3659 * Describes a Compute Engine resource that is being managed by a running 3552 /// pipeline.
3660 * pipeline.
3661 */
3662 class ComputeEngine { 3553 class ComputeEngine {
3663 /** The names of the disks that were created for this pipeline. */ 3554 /// The names of the disks that were created for this pipeline.
3664 core.List<core.String> diskNames; 3555 core.List<core.String> diskNames;
3665 /** The instance on which the operation is running. */ 3556
3557 /// The instance on which the operation is running.
3666 core.String instanceName; 3558 core.String instanceName;
3667 /** The machine type of the instance. */ 3559
3560 /// The machine type of the instance.
3668 core.String machineType; 3561 core.String machineType;
3669 /** The availability zone in which the instance resides. */ 3562
3563 /// The availability zone in which the instance resides.
3670 core.String zone; 3564 core.String zone;
3671 3565
3672 ComputeEngine(); 3566 ComputeEngine();
3673 3567
3674 ComputeEngine.fromJson(core.Map _json) { 3568 ComputeEngine.fromJson(core.Map _json) {
3675 if (_json.containsKey("diskNames")) { 3569 if (_json.containsKey("diskNames")) {
3676 diskNames = _json["diskNames"]; 3570 diskNames = _json["diskNames"];
3677 } 3571 }
3678 if (_json.containsKey("instanceName")) { 3572 if (_json.containsKey("instanceName")) {
3679 instanceName = _json["instanceName"]; 3573 instanceName = _json["instanceName"];
3680 } 3574 }
3681 if (_json.containsKey("machineType")) { 3575 if (_json.containsKey("machineType")) {
3682 machineType = _json["machineType"]; 3576 machineType = _json["machineType"];
3683 } 3577 }
3684 if (_json.containsKey("zone")) { 3578 if (_json.containsKey("zone")) {
3685 zone = _json["zone"]; 3579 zone = _json["zone"];
3686 } 3580 }
3687 } 3581 }
3688 3582
3689 core.Map<core.String, core.Object> toJson() { 3583 core.Map<core.String, core.Object> toJson() {
3690 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 3584 final core.Map<core.String, core.Object> _json =
3585 new core.Map<core.String, core.Object>();
3691 if (diskNames != null) { 3586 if (diskNames != null) {
3692 _json["diskNames"] = diskNames; 3587 _json["diskNames"] = diskNames;
3693 } 3588 }
3694 if (instanceName != null) { 3589 if (instanceName != null) {
3695 _json["instanceName"] = instanceName; 3590 _json["instanceName"] = instanceName;
3696 } 3591 }
3697 if (machineType != null) { 3592 if (machineType != null) {
3698 _json["machineType"] = machineType; 3593 _json["machineType"] = machineType;
3699 } 3594 }
3700 if (zone != null) { 3595 if (zone != null) {
3701 _json["zone"] = zone; 3596 _json["zone"] = zone;
3702 } 3597 }
3703 return _json; 3598 return _json;
3704 } 3599 }
3705 } 3600 }
3706 3601
3707 /** 3602 /// A bucket over which read coverage has been precomputed. A bucket
3708 * A bucket over which read coverage has been precomputed. A bucket corresponds 3603 /// corresponds
3709 * to a specific range of the reference sequence. 3604 /// to a specific range of the reference sequence.
3710 */
3711 class CoverageBucket { 3605 class CoverageBucket {
3712 /** 3606 /// The average number of reads which are aligned to each individual
3713 * The average number of reads which are aligned to each individual 3607 /// reference base in this bucket.
3714 * reference base in this bucket.
3715 */
3716 core.double meanCoverage; 3608 core.double meanCoverage;
3717 /** The genomic coordinate range spanned by this bucket. */ 3609
3610 /// The genomic coordinate range spanned by this bucket.
3718 Range range; 3611 Range range;
3719 3612
3720 CoverageBucket(); 3613 CoverageBucket();
3721 3614
3722 CoverageBucket.fromJson(core.Map _json) { 3615 CoverageBucket.fromJson(core.Map _json) {
3723 if (_json.containsKey("meanCoverage")) { 3616 if (_json.containsKey("meanCoverage")) {
3724 meanCoverage = _json["meanCoverage"]; 3617 meanCoverage = _json["meanCoverage"];
3725 } 3618 }
3726 if (_json.containsKey("range")) { 3619 if (_json.containsKey("range")) {
3727 range = new Range.fromJson(_json["range"]); 3620 range = new Range.fromJson(_json["range"]);
3728 } 3621 }
3729 } 3622 }
3730 3623
3731 core.Map<core.String, core.Object> toJson() { 3624 core.Map<core.String, core.Object> toJson() {
3732 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 3625 final core.Map<core.String, core.Object> _json =
3626 new core.Map<core.String, core.Object>();
3733 if (meanCoverage != null) { 3627 if (meanCoverage != null) {
3734 _json["meanCoverage"] = meanCoverage; 3628 _json["meanCoverage"] = meanCoverage;
3735 } 3629 }
3736 if (range != null) { 3630 if (range != null) {
3737 _json["range"] = (range).toJson(); 3631 _json["range"] = (range).toJson();
3738 } 3632 }
3739 return _json; 3633 return _json;
3740 } 3634 }
3741 } 3635 }
3742 3636
3743 /** 3637 /// A Dataset is a collection of genomic data.
3744 * A Dataset is a collection of genomic data. 3638 ///
3745 * 3639 /// For more genomics resource definitions, see [Fundamentals of Google
3746 * For more genomics resource definitions, see [Fundamentals of Google 3640 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
3747 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
3748 */
3749 class Dataset { 3641 class Dataset {
3750 /** The time this dataset was created, in seconds from the epoch. */ 3642 /// The time this dataset was created, in seconds from the epoch.
3751 core.String createTime; 3643 core.String createTime;
3752 /** The server-generated dataset ID, unique across all datasets. */ 3644
3645 /// The server-generated dataset ID, unique across all datasets.
3753 core.String id; 3646 core.String id;
3754 /** The dataset name. */ 3647
3648 /// The dataset name.
3755 core.String name; 3649 core.String name;
3756 /** The Google Cloud project ID that this dataset belongs to. */ 3650
3651 /// The Google Cloud project ID that this dataset belongs to.
3757 core.String projectId; 3652 core.String projectId;
3758 3653
3759 Dataset(); 3654 Dataset();
3760 3655
3761 Dataset.fromJson(core.Map _json) { 3656 Dataset.fromJson(core.Map _json) {
3762 if (_json.containsKey("createTime")) { 3657 if (_json.containsKey("createTime")) {
3763 createTime = _json["createTime"]; 3658 createTime = _json["createTime"];
3764 } 3659 }
3765 if (_json.containsKey("id")) { 3660 if (_json.containsKey("id")) {
3766 id = _json["id"]; 3661 id = _json["id"];
3767 } 3662 }
3768 if (_json.containsKey("name")) { 3663 if (_json.containsKey("name")) {
3769 name = _json["name"]; 3664 name = _json["name"];
3770 } 3665 }
3771 if (_json.containsKey("projectId")) { 3666 if (_json.containsKey("projectId")) {
3772 projectId = _json["projectId"]; 3667 projectId = _json["projectId"];
3773 } 3668 }
3774 } 3669 }
3775 3670
3776 core.Map<core.String, core.Object> toJson() { 3671 core.Map<core.String, core.Object> toJson() {
3777 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 3672 final core.Map<core.String, core.Object> _json =
3673 new core.Map<core.String, core.Object>();
3778 if (createTime != null) { 3674 if (createTime != null) {
3779 _json["createTime"] = createTime; 3675 _json["createTime"] = createTime;
3780 } 3676 }
3781 if (id != null) { 3677 if (id != null) {
3782 _json["id"] = id; 3678 _json["id"] = id;
3783 } 3679 }
3784 if (name != null) { 3680 if (name != null) {
3785 _json["name"] = name; 3681 _json["name"] = name;
3786 } 3682 }
3787 if (projectId != null) { 3683 if (projectId != null) {
3788 _json["projectId"] = projectId; 3684 _json["projectId"] = projectId;
3789 } 3685 }
3790 return _json; 3686 return _json;
3791 } 3687 }
3792 } 3688 }
3793 3689
3794 /** 3690 /// A generic empty message that you can re-use to avoid defining duplicated
3795 * A generic empty message that you can re-use to avoid defining duplicated 3691 /// empty messages in your APIs. A typical example is to use it as the request
3796 * empty messages in your APIs. A typical example is to use it as the request 3692 /// or the response type of an API method. For instance:
3797 * or the response type of an API method. For instance: 3693 ///
3798 * 3694 /// service Foo {
3799 * service Foo { 3695 /// rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty);
3800 * rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty); 3696 /// }
3801 * } 3697 ///
3802 * 3698 /// The JSON representation for `Empty` is empty JSON object `{}`.
3803 * The JSON representation for `Empty` is empty JSON object `{}`.
3804 */
3805 class Empty { 3699 class Empty {
3806
3807 Empty(); 3700 Empty();
3808 3701
3809 Empty.fromJson(core.Map _json) { 3702 Empty.fromJson(core.Map _json) {}
3810 }
3811 3703
3812 core.Map<core.String, core.Object> toJson() { 3704 core.Map<core.String, core.Object> toJson() {
3813 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 3705 final core.Map<core.String, core.Object> _json =
3706 new core.Map<core.String, core.Object>();
3814 return _json; 3707 return _json;
3815 } 3708 }
3816 } 3709 }
3817 3710
3818 class Entry { 3711 class Entry {
3819 /** The created annotation, if creation was successful. */ 3712 /// The created annotation, if creation was successful.
3820 Annotation annotation; 3713 Annotation annotation;
3821 /** The creation status. */ 3714
3715 /// The creation status.
3822 Status status; 3716 Status status;
3823 3717
3824 Entry(); 3718 Entry();
3825 3719
3826 Entry.fromJson(core.Map _json) { 3720 Entry.fromJson(core.Map _json) {
3827 if (_json.containsKey("annotation")) { 3721 if (_json.containsKey("annotation")) {
3828 annotation = new Annotation.fromJson(_json["annotation"]); 3722 annotation = new Annotation.fromJson(_json["annotation"]);
3829 } 3723 }
3830 if (_json.containsKey("status")) { 3724 if (_json.containsKey("status")) {
3831 status = new Status.fromJson(_json["status"]); 3725 status = new Status.fromJson(_json["status"]);
3832 } 3726 }
3833 } 3727 }
3834 3728
3835 core.Map<core.String, core.Object> toJson() { 3729 core.Map<core.String, core.Object> toJson() {
3836 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 3730 final core.Map<core.String, core.Object> _json =
3731 new core.Map<core.String, core.Object>();
3837 if (annotation != null) { 3732 if (annotation != null) {
3838 _json["annotation"] = (annotation).toJson(); 3733 _json["annotation"] = (annotation).toJson();
3839 } 3734 }
3840 if (status != null) { 3735 if (status != null) {
3841 _json["status"] = (status).toJson(); 3736 _json["status"] = (status).toJson();
3842 } 3737 }
3843 return _json; 3738 return _json;
3844 } 3739 }
3845 } 3740 }
3846 3741
3847 class Exon { 3742 class Exon {
3848 /** 3743 /// The end position of the exon on this annotation's reference sequence,
3849 * The end position of the exon on this annotation's reference sequence, 3744 /// 0-based exclusive. Note that this is relative to the reference start, and
3850 * 0-based exclusive. Note that this is relative to the reference start, and 3745 /// *not* the containing annotation start.
3851 * *not* the containing annotation start.
3852 */
3853 core.String end; 3746 core.String end;
3854 /** 3747
3855 * The frame of this exon. Contains a value of 0, 1, or 2, which indicates 3748 /// The frame of this exon. Contains a value of 0, 1, or 2, which indicates
3856 * the offset of the first coding base of the exon within the reading frame 3749 /// the offset of the first coding base of the exon within the reading frame
3857 * of the coding DNA sequence, if any. This field is dependent on the 3750 /// of the coding DNA sequence, if any. This field is dependent on the
3858 * strandedness of this annotation (see 3751 /// strandedness of this annotation (see
3859 * Annotation.reverse_strand). 3752 /// Annotation.reverse_strand).
3860 * For forward stranded annotations, this offset is relative to the 3753 /// For forward stranded annotations, this offset is relative to the
3861 * exon.start. For reverse 3754 /// exon.start. For reverse
3862 * strand annotations, this offset is relative to the 3755 /// strand annotations, this offset is relative to the
3863 * exon.end `- 1`. 3756 /// exon.end `- 1`.
3864 * 3757 ///
3865 * Unset if this exon does not intersect the coding sequence. Upon creation 3758 /// Unset if this exon does not intersect the coding sequence. Upon creation
3866 * of a transcript, the frame must be populated for all or none of the 3759 /// of a transcript, the frame must be populated for all or none of the
3867 * coding exons. 3760 /// coding exons.
3868 */
3869 core.int frame; 3761 core.int frame;
3870 /** 3762
3871 * The start position of the exon on this annotation's reference sequence, 3763 /// The start position of the exon on this annotation's reference sequence,
3872 * 0-based inclusive. Note that this is relative to the reference start, and 3764 /// 0-based inclusive. Note that this is relative to the reference start, and
3873 * **not** the containing annotation start. 3765 /// **not** the containing annotation start.
3874 */
3875 core.String start; 3766 core.String start;
3876 3767
3877 Exon(); 3768 Exon();
3878 3769
3879 Exon.fromJson(core.Map _json) { 3770 Exon.fromJson(core.Map _json) {
3880 if (_json.containsKey("end")) { 3771 if (_json.containsKey("end")) {
3881 end = _json["end"]; 3772 end = _json["end"];
3882 } 3773 }
3883 if (_json.containsKey("frame")) { 3774 if (_json.containsKey("frame")) {
3884 frame = _json["frame"]; 3775 frame = _json["frame"];
3885 } 3776 }
3886 if (_json.containsKey("start")) { 3777 if (_json.containsKey("start")) {
3887 start = _json["start"]; 3778 start = _json["start"];
3888 } 3779 }
3889 } 3780 }
3890 3781
3891 core.Map<core.String, core.Object> toJson() { 3782 core.Map<core.String, core.Object> toJson() {
3892 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 3783 final core.Map<core.String, core.Object> _json =
3784 new core.Map<core.String, core.Object>();
3893 if (end != null) { 3785 if (end != null) {
3894 _json["end"] = end; 3786 _json["end"] = end;
3895 } 3787 }
3896 if (frame != null) { 3788 if (frame != null) {
3897 _json["frame"] = frame; 3789 _json["frame"] = frame;
3898 } 3790 }
3899 if (start != null) { 3791 if (start != null) {
3900 _json["start"] = start; 3792 _json["start"] = start;
3901 } 3793 }
3902 return _json; 3794 return _json;
3903 } 3795 }
3904 } 3796 }
3905 3797
3906 class Experiment { 3798 class Experiment {
3907 /** 3799 /// The instrument model used as part of this experiment. This maps to
3908 * The instrument model used as part of this experiment. This maps to 3800 /// sequencing technology in the SAM spec.
3909 * sequencing technology in the SAM spec.
3910 */
3911 core.String instrumentModel; 3801 core.String instrumentModel;
3912 /** 3802
3913 * A client-supplied library identifier; a library is a collection of DNA 3803 /// A client-supplied library identifier; a library is a collection of DNA
3914 * fragments which have been prepared for sequencing from a sample. This 3804 /// fragments which have been prepared for sequencing from a sample. This
3915 * field is important for quality control as error or bias can be introduced 3805 /// field is important for quality control as error or bias can be introduced
3916 * during sample preparation. 3806 /// during sample preparation.
3917 */
3918 core.String libraryId; 3807 core.String libraryId;
3919 /** 3808
3920 * The platform unit used as part of this experiment, for example 3809 /// The platform unit used as part of this experiment, for example
3921 * flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the 3810 /// flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
3922 * @RG PU field in the SAM spec. 3811 /// @RG PU field in the SAM spec.
3923 */
3924 core.String platformUnit; 3812 core.String platformUnit;
3925 /** The sequencing center used as part of this experiment. */ 3813
3814 /// The sequencing center used as part of this experiment.
3926 core.String sequencingCenter; 3815 core.String sequencingCenter;
3927 3816
3928 Experiment(); 3817 Experiment();
3929 3818
3930 Experiment.fromJson(core.Map _json) { 3819 Experiment.fromJson(core.Map _json) {
3931 if (_json.containsKey("instrumentModel")) { 3820 if (_json.containsKey("instrumentModel")) {
3932 instrumentModel = _json["instrumentModel"]; 3821 instrumentModel = _json["instrumentModel"];
3933 } 3822 }
3934 if (_json.containsKey("libraryId")) { 3823 if (_json.containsKey("libraryId")) {
3935 libraryId = _json["libraryId"]; 3824 libraryId = _json["libraryId"];
3936 } 3825 }
3937 if (_json.containsKey("platformUnit")) { 3826 if (_json.containsKey("platformUnit")) {
3938 platformUnit = _json["platformUnit"]; 3827 platformUnit = _json["platformUnit"];
3939 } 3828 }
3940 if (_json.containsKey("sequencingCenter")) { 3829 if (_json.containsKey("sequencingCenter")) {
3941 sequencingCenter = _json["sequencingCenter"]; 3830 sequencingCenter = _json["sequencingCenter"];
3942 } 3831 }
3943 } 3832 }
3944 3833
3945 core.Map<core.String, core.Object> toJson() { 3834 core.Map<core.String, core.Object> toJson() {
3946 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 3835 final core.Map<core.String, core.Object> _json =
3836 new core.Map<core.String, core.Object>();
3947 if (instrumentModel != null) { 3837 if (instrumentModel != null) {
3948 _json["instrumentModel"] = instrumentModel; 3838 _json["instrumentModel"] = instrumentModel;
3949 } 3839 }
3950 if (libraryId != null) { 3840 if (libraryId != null) {
3951 _json["libraryId"] = libraryId; 3841 _json["libraryId"] = libraryId;
3952 } 3842 }
3953 if (platformUnit != null) { 3843 if (platformUnit != null) {
3954 _json["platformUnit"] = platformUnit; 3844 _json["platformUnit"] = platformUnit;
3955 } 3845 }
3956 if (sequencingCenter != null) { 3846 if (sequencingCenter != null) {
3957 _json["sequencingCenter"] = sequencingCenter; 3847 _json["sequencingCenter"] = sequencingCenter;
3958 } 3848 }
3959 return _json; 3849 return _json;
3960 } 3850 }
3961 } 3851 }
3962 3852
3963 /** The read group set export request. */ 3853 /// The read group set export request.
3964 class ExportReadGroupSetRequest { 3854 class ExportReadGroupSetRequest {
3965 /** 3855 /// Required. A Google Cloud Storage URI for the exported BAM file.
3966 * Required. A Google Cloud Storage URI for the exported BAM file. 3856 /// The currently authenticated user must have write access to the new file.
3967 * The currently authenticated user must have write access to the new file. 3857 /// An error will be returned if the URI already contains data.
3968 * An error will be returned if the URI already contains data.
3969 */
3970 core.String exportUri; 3858 core.String exportUri;
3971 /** 3859
3972 * Required. The Google Cloud project ID that owns this 3860 /// Required. The Google Cloud project ID that owns this
3973 * export. The caller must have WRITE access to this project. 3861 /// export. The caller must have WRITE access to this project.
3974 */
3975 core.String projectId; 3862 core.String projectId;
3976 /** 3863
3977 * The reference names to export. If this is not specified, all reference 3864 /// The reference names to export. If this is not specified, all reference
3978 * sequences, including unmapped reads, are exported. 3865 /// sequences, including unmapped reads, are exported.
3979 * Use `*` to export only unmapped reads. 3866 /// Use `*` to export only unmapped reads.
3980 */
3981 core.List<core.String> referenceNames; 3867 core.List<core.String> referenceNames;
3982 3868
3983 ExportReadGroupSetRequest(); 3869 ExportReadGroupSetRequest();
3984 3870
3985 ExportReadGroupSetRequest.fromJson(core.Map _json) { 3871 ExportReadGroupSetRequest.fromJson(core.Map _json) {
3986 if (_json.containsKey("exportUri")) { 3872 if (_json.containsKey("exportUri")) {
3987 exportUri = _json["exportUri"]; 3873 exportUri = _json["exportUri"];
3988 } 3874 }
3989 if (_json.containsKey("projectId")) { 3875 if (_json.containsKey("projectId")) {
3990 projectId = _json["projectId"]; 3876 projectId = _json["projectId"];
3991 } 3877 }
3992 if (_json.containsKey("referenceNames")) { 3878 if (_json.containsKey("referenceNames")) {
3993 referenceNames = _json["referenceNames"]; 3879 referenceNames = _json["referenceNames"];
3994 } 3880 }
3995 } 3881 }
3996 3882
3997 core.Map<core.String, core.Object> toJson() { 3883 core.Map<core.String, core.Object> toJson() {
3998 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 3884 final core.Map<core.String, core.Object> _json =
3885 new core.Map<core.String, core.Object>();
3999 if (exportUri != null) { 3886 if (exportUri != null) {
4000 _json["exportUri"] = exportUri; 3887 _json["exportUri"] = exportUri;
4001 } 3888 }
4002 if (projectId != null) { 3889 if (projectId != null) {
4003 _json["projectId"] = projectId; 3890 _json["projectId"] = projectId;
4004 } 3891 }
4005 if (referenceNames != null) { 3892 if (referenceNames != null) {
4006 _json["referenceNames"] = referenceNames; 3893 _json["referenceNames"] = referenceNames;
4007 } 3894 }
4008 return _json; 3895 return _json;
4009 } 3896 }
4010 } 3897 }
4011 3898
4012 /** The variant data export request. */ 3899 /// The variant data export request.
4013 class ExportVariantSetRequest { 3900 class ExportVariantSetRequest {
4014 /** 3901 /// Required. The BigQuery dataset to export data to. This dataset must
4015 * Required. The BigQuery dataset to export data to. This dataset must already 3902 /// already
4016 * exist. Note that this is distinct from the Genomics concept of "dataset". 3903 /// exist. Note that this is distinct from the Genomics concept of "dataset".
4017 */
4018 core.String bigqueryDataset; 3904 core.String bigqueryDataset;
4019 /** 3905
4020 * Required. The BigQuery table to export data to. 3906 /// Required. The BigQuery table to export data to.
4021 * If the table doesn't exist, it will be created. If it already exists, it 3907 /// If the table doesn't exist, it will be created. If it already exists, it
4022 * will be overwritten. 3908 /// will be overwritten.
4023 */
4024 core.String bigqueryTable; 3909 core.String bigqueryTable;
4025 /** 3910
4026 * If provided, only variant call information from the specified call sets 3911 /// If provided, only variant call information from the specified call sets
4027 * will be exported. By default all variant calls are exported. 3912 /// will be exported. By default all variant calls are exported.
4028 */
4029 core.List<core.String> callSetIds; 3913 core.List<core.String> callSetIds;
4030 /** 3914
4031 * The format for the exported data. 3915 /// The format for the exported data.
4032 * Possible string values are: 3916 /// Possible string values are:
4033 * - "FORMAT_UNSPECIFIED" 3917 /// - "FORMAT_UNSPECIFIED"
4034 * - "FORMAT_BIGQUERY" : Export the data to Google BigQuery. 3918 /// - "FORMAT_BIGQUERY" : Export the data to Google BigQuery.
4035 */
4036 core.String format; 3919 core.String format;
4037 /** 3920
4038 * Required. The Google Cloud project ID that owns the destination 3921 /// Required. The Google Cloud project ID that owns the destination
4039 * BigQuery dataset. The caller must have WRITE access to this project. This 3922 /// BigQuery dataset. The caller must have WRITE access to this project.
4040 * project will also own the resulting export job. 3923 /// This
4041 */ 3924 /// project will also own the resulting export job.
4042 core.String projectId; 3925 core.String projectId;
4043 3926
4044 ExportVariantSetRequest(); 3927 ExportVariantSetRequest();
4045 3928
4046 ExportVariantSetRequest.fromJson(core.Map _json) { 3929 ExportVariantSetRequest.fromJson(core.Map _json) {
4047 if (_json.containsKey("bigqueryDataset")) { 3930 if (_json.containsKey("bigqueryDataset")) {
4048 bigqueryDataset = _json["bigqueryDataset"]; 3931 bigqueryDataset = _json["bigqueryDataset"];
4049 } 3932 }
4050 if (_json.containsKey("bigqueryTable")) { 3933 if (_json.containsKey("bigqueryTable")) {
4051 bigqueryTable = _json["bigqueryTable"]; 3934 bigqueryTable = _json["bigqueryTable"];
4052 } 3935 }
4053 if (_json.containsKey("callSetIds")) { 3936 if (_json.containsKey("callSetIds")) {
4054 callSetIds = _json["callSetIds"]; 3937 callSetIds = _json["callSetIds"];
4055 } 3938 }
4056 if (_json.containsKey("format")) { 3939 if (_json.containsKey("format")) {
4057 format = _json["format"]; 3940 format = _json["format"];
4058 } 3941 }
4059 if (_json.containsKey("projectId")) { 3942 if (_json.containsKey("projectId")) {
4060 projectId = _json["projectId"]; 3943 projectId = _json["projectId"];
4061 } 3944 }
4062 } 3945 }
4063 3946
4064 core.Map<core.String, core.Object> toJson() { 3947 core.Map<core.String, core.Object> toJson() {
4065 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 3948 final core.Map<core.String, core.Object> _json =
3949 new core.Map<core.String, core.Object>();
4066 if (bigqueryDataset != null) { 3950 if (bigqueryDataset != null) {
4067 _json["bigqueryDataset"] = bigqueryDataset; 3951 _json["bigqueryDataset"] = bigqueryDataset;
4068 } 3952 }
4069 if (bigqueryTable != null) { 3953 if (bigqueryTable != null) {
4070 _json["bigqueryTable"] = bigqueryTable; 3954 _json["bigqueryTable"] = bigqueryTable;
4071 } 3955 }
4072 if (callSetIds != null) { 3956 if (callSetIds != null) {
4073 _json["callSetIds"] = callSetIds; 3957 _json["callSetIds"] = callSetIds;
4074 } 3958 }
4075 if (format != null) { 3959 if (format != null) {
4076 _json["format"] = format; 3960 _json["format"] = format;
4077 } 3961 }
4078 if (projectId != null) { 3962 if (projectId != null) {
4079 _json["projectId"] = projectId; 3963 _json["projectId"] = projectId;
4080 } 3964 }
4081 return _json; 3965 return _json;
4082 } 3966 }
4083 } 3967 }
4084 3968
4085 class ExternalId { 3969 class ExternalId {
4086 /** The id used by the source of this data. */ 3970 /// The id used by the source of this data.
4087 core.String id; 3971 core.String id;
4088 /** The name of the source of this data. */ 3972
3973 /// The name of the source of this data.
4089 core.String sourceName; 3974 core.String sourceName;
4090 3975
4091 ExternalId(); 3976 ExternalId();
4092 3977
4093 ExternalId.fromJson(core.Map _json) { 3978 ExternalId.fromJson(core.Map _json) {
4094 if (_json.containsKey("id")) { 3979 if (_json.containsKey("id")) {
4095 id = _json["id"]; 3980 id = _json["id"];
4096 } 3981 }
4097 if (_json.containsKey("sourceName")) { 3982 if (_json.containsKey("sourceName")) {
4098 sourceName = _json["sourceName"]; 3983 sourceName = _json["sourceName"];
4099 } 3984 }
4100 } 3985 }
4101 3986
4102 core.Map<core.String, core.Object> toJson() { 3987 core.Map<core.String, core.Object> toJson() {
4103 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 3988 final core.Map<core.String, core.Object> _json =
3989 new core.Map<core.String, core.Object>();
4104 if (id != null) { 3990 if (id != null) {
4105 _json["id"] = id; 3991 _json["id"] = id;
4106 } 3992 }
4107 if (sourceName != null) { 3993 if (sourceName != null) {
4108 _json["sourceName"] = sourceName; 3994 _json["sourceName"] = sourceName;
4109 } 3995 }
4110 return _json; 3996 return _json;
4111 } 3997 }
4112 } 3998 }
4113 3999
4114 /** Request message for `GetIamPolicy` method. */ 4000 /// Request message for `GetIamPolicy` method.
4115 class GetIamPolicyRequest { 4001 class GetIamPolicyRequest {
4116
4117 GetIamPolicyRequest(); 4002 GetIamPolicyRequest();
4118 4003
4119 GetIamPolicyRequest.fromJson(core.Map _json) { 4004 GetIamPolicyRequest.fromJson(core.Map _json) {}
4120 }
4121 4005
4122 core.Map<core.String, core.Object> toJson() { 4006 core.Map<core.String, core.Object> toJson() {
4123 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 4007 final core.Map<core.String, core.Object> _json =
4008 new core.Map<core.String, core.Object>();
4124 return _json; 4009 return _json;
4125 } 4010 }
4126 } 4011 }
4127 4012
4128 /** The read group set import request. */ 4013 /// The read group set import request.
4129 class ImportReadGroupSetsRequest { 4014 class ImportReadGroupSetsRequest {
4130 /** 4015 /// Required. The ID of the dataset these read group sets will belong to. The
4131 * Required. The ID of the dataset these read group sets will belong to. The 4016 /// caller must have WRITE permissions to this dataset.
4132 * caller must have WRITE permissions to this dataset.
4133 */
4134 core.String datasetId; 4017 core.String datasetId;
4135 /** 4018
4136 * The partition strategy describes how read groups are partitioned into read 4019 /// The partition strategy describes how read groups are partitioned into
4137 * group sets. 4020 /// read
4138 * Possible string values are: 4021 /// group sets.
4139 * - "PARTITION_STRATEGY_UNSPECIFIED" 4022 /// Possible string values are:
4140 * - "PER_FILE_PER_SAMPLE" : In most cases, this strategy yields one read 4023 /// - "PARTITION_STRATEGY_UNSPECIFIED"
4141 * group set per file. This is 4024 /// - "PER_FILE_PER_SAMPLE" : In most cases, this strategy yields one read
4142 * the default behavior. 4025 /// group set per file. This is
4143 * 4026 /// the default behavior.
4144 * Allocate one read group set per file per sample. For BAM files, read 4027 ///
4145 * groups are considered to share a sample if they have identical sample 4028 /// Allocate one read group set per file per sample. For BAM files, read
4146 * names. Furthermore, all reads for each file which do not belong to a read 4029 /// groups are considered to share a sample if they have identical sample
4147 * group, if any, will be grouped into a single read group set per-file. 4030 /// names. Furthermore, all reads for each file which do not belong to a read
4148 * - "MERGE_ALL" : Includes all read groups in all imported files into a 4031 /// group, if any, will be grouped into a single read group set per-file.
4149 * single read group 4032 /// - "MERGE_ALL" : Includes all read groups in all imported files into a
4150 * set. Requires that the headers for all imported files are equivalent. All 4033 /// single read group
4151 * reads which do not belong to a read group, if any, will be grouped into a 4034 /// set. Requires that the headers for all imported files are equivalent. All
4152 * separate read group set. 4035 /// reads which do not belong to a read group, if any, will be grouped into a
4153 */ 4036 /// separate read group set.
4154 core.String partitionStrategy; 4037 core.String partitionStrategy;
4155 /** 4038
4156 * The reference set to which the imported read group sets are aligned to, if 4039 /// The reference set to which the imported read group sets are aligned to,
4157 * any. The reference names of this reference set must be a superset of those 4040 /// if
4158 * found in the imported file headers. If no reference set id is provided, a 4041 /// any. The reference names of this reference set must be a superset of
4159 * best effort is made to associate with a matching reference set. 4042 /// those
4160 */ 4043 /// found in the imported file headers. If no reference set id is provided, a
4044 /// best effort is made to associate with a matching reference set.
4161 core.String referenceSetId; 4045 core.String referenceSetId;
4162 /** 4046
4163 * A list of URIs pointing at [BAM 4047 /// A list of URIs pointing at [BAM
4164 * files](https://samtools.github.io/hts-specs/SAMv1.pdf) 4048 /// files](https://samtools.github.io/hts-specs/SAMv1.pdf)
4165 * in Google Cloud Storage. 4049 /// in Google Cloud Storage.
4166 * Those URIs can include wildcards (*), but do not add or remove 4050 /// Those URIs can include wildcards (*), but do not add or remove
4167 * matching files before import has completed. 4051 /// matching files before import has completed.
4168 * 4052 ///
4169 * Note that Google Cloud Storage object listing is only eventually 4053 /// Note that Google Cloud Storage object listing is only eventually
4170 * consistent: files added may be not be immediately visible to 4054 /// consistent: files added may be not be immediately visible to
4171 * everyone. Thus, if using a wildcard it is preferable not to start 4055 /// everyone. Thus, if using a wildcard it is preferable not to start
4172 * the import immediately after the files are created. 4056 /// the import immediately after the files are created.
4173 */
4174 core.List<core.String> sourceUris; 4057 core.List<core.String> sourceUris;
4175 4058
4176 ImportReadGroupSetsRequest(); 4059 ImportReadGroupSetsRequest();
4177 4060
4178 ImportReadGroupSetsRequest.fromJson(core.Map _json) { 4061 ImportReadGroupSetsRequest.fromJson(core.Map _json) {
4179 if (_json.containsKey("datasetId")) { 4062 if (_json.containsKey("datasetId")) {
4180 datasetId = _json["datasetId"]; 4063 datasetId = _json["datasetId"];
4181 } 4064 }
4182 if (_json.containsKey("partitionStrategy")) { 4065 if (_json.containsKey("partitionStrategy")) {
4183 partitionStrategy = _json["partitionStrategy"]; 4066 partitionStrategy = _json["partitionStrategy"];
4184 } 4067 }
4185 if (_json.containsKey("referenceSetId")) { 4068 if (_json.containsKey("referenceSetId")) {
4186 referenceSetId = _json["referenceSetId"]; 4069 referenceSetId = _json["referenceSetId"];
4187 } 4070 }
4188 if (_json.containsKey("sourceUris")) { 4071 if (_json.containsKey("sourceUris")) {
4189 sourceUris = _json["sourceUris"]; 4072 sourceUris = _json["sourceUris"];
4190 } 4073 }
4191 } 4074 }
4192 4075
4193 core.Map<core.String, core.Object> toJson() { 4076 core.Map<core.String, core.Object> toJson() {
4194 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 4077 final core.Map<core.String, core.Object> _json =
4078 new core.Map<core.String, core.Object>();
4195 if (datasetId != null) { 4079 if (datasetId != null) {
4196 _json["datasetId"] = datasetId; 4080 _json["datasetId"] = datasetId;
4197 } 4081 }
4198 if (partitionStrategy != null) { 4082 if (partitionStrategy != null) {
4199 _json["partitionStrategy"] = partitionStrategy; 4083 _json["partitionStrategy"] = partitionStrategy;
4200 } 4084 }
4201 if (referenceSetId != null) { 4085 if (referenceSetId != null) {
4202 _json["referenceSetId"] = referenceSetId; 4086 _json["referenceSetId"] = referenceSetId;
4203 } 4087 }
4204 if (sourceUris != null) { 4088 if (sourceUris != null) {
4205 _json["sourceUris"] = sourceUris; 4089 _json["sourceUris"] = sourceUris;
4206 } 4090 }
4207 return _json; 4091 return _json;
4208 } 4092 }
4209 } 4093 }
4210 4094
4211 /** The read group set import response. */ 4095 /// The read group set import response.
4212 class ImportReadGroupSetsResponse { 4096 class ImportReadGroupSetsResponse {
4213 /** IDs of the read group sets that were created. */ 4097 /// IDs of the read group sets that were created.
4214 core.List<core.String> readGroupSetIds; 4098 core.List<core.String> readGroupSetIds;
4215 4099
4216 ImportReadGroupSetsResponse(); 4100 ImportReadGroupSetsResponse();
4217 4101
4218 ImportReadGroupSetsResponse.fromJson(core.Map _json) { 4102 ImportReadGroupSetsResponse.fromJson(core.Map _json) {
4219 if (_json.containsKey("readGroupSetIds")) { 4103 if (_json.containsKey("readGroupSetIds")) {
4220 readGroupSetIds = _json["readGroupSetIds"]; 4104 readGroupSetIds = _json["readGroupSetIds"];
4221 } 4105 }
4222 } 4106 }
4223 4107
4224 core.Map<core.String, core.Object> toJson() { 4108 core.Map<core.String, core.Object> toJson() {
4225 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 4109 final core.Map<core.String, core.Object> _json =
4110 new core.Map<core.String, core.Object>();
4226 if (readGroupSetIds != null) { 4111 if (readGroupSetIds != null) {
4227 _json["readGroupSetIds"] = readGroupSetIds; 4112 _json["readGroupSetIds"] = readGroupSetIds;
4228 } 4113 }
4229 return _json; 4114 return _json;
4230 } 4115 }
4231 } 4116 }
4232 4117
4233 /** The variant data import request. */ 4118 /// The variant data import request.
4234 class ImportVariantsRequest { 4119 class ImportVariantsRequest {
4235 /** 4120 /// The format of the variant data being imported. If unspecified, defaults
4236 * The format of the variant data being imported. If unspecified, defaults to 4121 /// to
4237 * to `VCF`. 4122 /// to `VCF`.
4238 * Possible string values are: 4123 /// Possible string values are:
4239 * - "FORMAT_UNSPECIFIED" 4124 /// - "FORMAT_UNSPECIFIED"
4240 * - "FORMAT_VCF" : VCF (Variant Call Format). The VCF files may be gzip 4125 /// - "FORMAT_VCF" : VCF (Variant Call Format). The VCF files may be gzip
4241 * compressed. gVCF is 4126 /// compressed. gVCF is
4242 * also supported. Disclaimer: gzip VCF imports are currently much slower 4127 /// also supported. Disclaimer: gzip VCF imports are currently much slower
4243 * than equivalent uncompressed VCF imports. For this reason, uncompressed 4128 /// than equivalent uncompressed VCF imports. For this reason, uncompressed
4244 * VCF is currently recommended for imports with more than 1GB combined 4129 /// VCF is currently recommended for imports with more than 1GB combined
4245 * uncompressed size, or for time sensitive imports. 4130 /// uncompressed size, or for time sensitive imports.
4246 * - "FORMAT_COMPLETE_GENOMICS" : Complete Genomics masterVarBeta format. The 4131 /// - "FORMAT_COMPLETE_GENOMICS" : Complete Genomics masterVarBeta format.
4247 * masterVarBeta files may 4132 /// The masterVarBeta files may
4248 * be bzip2 compressed. 4133 /// be bzip2 compressed.
4249 */
4250 core.String format; 4134 core.String format;
4251 /** 4135
4252 * A mapping between info field keys and the InfoMergeOperations to 4136 /// A mapping between info field keys and the InfoMergeOperations to
4253 * be performed on them. This is plumbed down to the MergeVariantRequests 4137 /// be performed on them. This is plumbed down to the MergeVariantRequests
4254 * generated by the resulting import job. 4138 /// generated by the resulting import job.
4255 */
4256 core.Map<core.String, core.String> infoMergeConfig; 4139 core.Map<core.String, core.String> infoMergeConfig;
4257 /** 4140
4258 * Convert reference names to the canonical representation. 4141 /// Convert reference names to the canonical representation.
4259 * hg19 haploytypes (those reference names containing "_hap") 4142 /// hg19 haploytypes (those reference names containing "_hap")
4260 * are not modified in any way. 4143 /// are not modified in any way.
4261 * All other reference names are modified according to the following rules: 4144 /// All other reference names are modified according to the following rules:
4262 * The reference name is capitalized. 4145 /// The reference name is capitalized.
4263 * The "chr" prefix is dropped for all autosomes and sex chromsomes. 4146 /// The "chr" prefix is dropped for all autosomes and sex chromsomes.
4264 * For example "chr17" becomes "17" and "chrX" becomes "X". 4147 /// For example "chr17" becomes "17" and "chrX" becomes "X".
4265 * All mitochondrial chromosomes ("chrM", "chrMT", etc) become "MT". 4148 /// All mitochondrial chromosomes ("chrM", "chrMT", etc) become "MT".
4266 */
4267 core.bool normalizeReferenceNames; 4149 core.bool normalizeReferenceNames;
4268 /** 4150
4269 * A list of URIs referencing variant files in Google Cloud Storage. URIs can 4151 /// A list of URIs referencing variant files in Google Cloud Storage. URIs
4270 * include wildcards [as described 4152 /// can
4271 * here](https://cloud.google.com/storage/docs/gsutil/addlhelp/WildcardNames). 4153 /// include wildcards [as described
4272 * Note that recursive wildcards ('**') are not supported. 4154 /// here](https://cloud.google.com/storage/docs/gsutil/addlhelp/WildcardNames) .
4273 */ 4155 /// Note that recursive wildcards ('**') are not supported.
4274 core.List<core.String> sourceUris; 4156 core.List<core.String> sourceUris;
4275 /** Required. The variant set to which variant data should be imported. */ 4157
4158 /// Required. The variant set to which variant data should be imported.
4276 core.String variantSetId; 4159 core.String variantSetId;
4277 4160
4278 ImportVariantsRequest(); 4161 ImportVariantsRequest();
4279 4162
4280 ImportVariantsRequest.fromJson(core.Map _json) { 4163 ImportVariantsRequest.fromJson(core.Map _json) {
4281 if (_json.containsKey("format")) { 4164 if (_json.containsKey("format")) {
4282 format = _json["format"]; 4165 format = _json["format"];
4283 } 4166 }
4284 if (_json.containsKey("infoMergeConfig")) { 4167 if (_json.containsKey("infoMergeConfig")) {
4285 infoMergeConfig = _json["infoMergeConfig"]; 4168 infoMergeConfig = _json["infoMergeConfig"];
4286 } 4169 }
4287 if (_json.containsKey("normalizeReferenceNames")) { 4170 if (_json.containsKey("normalizeReferenceNames")) {
4288 normalizeReferenceNames = _json["normalizeReferenceNames"]; 4171 normalizeReferenceNames = _json["normalizeReferenceNames"];
4289 } 4172 }
4290 if (_json.containsKey("sourceUris")) { 4173 if (_json.containsKey("sourceUris")) {
4291 sourceUris = _json["sourceUris"]; 4174 sourceUris = _json["sourceUris"];
4292 } 4175 }
4293 if (_json.containsKey("variantSetId")) { 4176 if (_json.containsKey("variantSetId")) {
4294 variantSetId = _json["variantSetId"]; 4177 variantSetId = _json["variantSetId"];
4295 } 4178 }
4296 } 4179 }
4297 4180
4298 core.Map<core.String, core.Object> toJson() { 4181 core.Map<core.String, core.Object> toJson() {
4299 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 4182 final core.Map<core.String, core.Object> _json =
4183 new core.Map<core.String, core.Object>();
4300 if (format != null) { 4184 if (format != null) {
4301 _json["format"] = format; 4185 _json["format"] = format;
4302 } 4186 }
4303 if (infoMergeConfig != null) { 4187 if (infoMergeConfig != null) {
4304 _json["infoMergeConfig"] = infoMergeConfig; 4188 _json["infoMergeConfig"] = infoMergeConfig;
4305 } 4189 }
4306 if (normalizeReferenceNames != null) { 4190 if (normalizeReferenceNames != null) {
4307 _json["normalizeReferenceNames"] = normalizeReferenceNames; 4191 _json["normalizeReferenceNames"] = normalizeReferenceNames;
4308 } 4192 }
4309 if (sourceUris != null) { 4193 if (sourceUris != null) {
4310 _json["sourceUris"] = sourceUris; 4194 _json["sourceUris"] = sourceUris;
4311 } 4195 }
4312 if (variantSetId != null) { 4196 if (variantSetId != null) {
4313 _json["variantSetId"] = variantSetId; 4197 _json["variantSetId"] = variantSetId;
4314 } 4198 }
4315 return _json; 4199 return _json;
4316 } 4200 }
4317 } 4201 }
4318 4202
4319 /** The variant data import response. */ 4203 /// The variant data import response.
4320 class ImportVariantsResponse { 4204 class ImportVariantsResponse {
4321 /** IDs of the call sets created during the import. */ 4205 /// IDs of the call sets created during the import.
4322 core.List<core.String> callSetIds; 4206 core.List<core.String> callSetIds;
4323 4207
4324 ImportVariantsResponse(); 4208 ImportVariantsResponse();
4325 4209
4326 ImportVariantsResponse.fromJson(core.Map _json) { 4210 ImportVariantsResponse.fromJson(core.Map _json) {
4327 if (_json.containsKey("callSetIds")) { 4211 if (_json.containsKey("callSetIds")) {
4328 callSetIds = _json["callSetIds"]; 4212 callSetIds = _json["callSetIds"];
4329 } 4213 }
4330 } 4214 }
4331 4215
4332 core.Map<core.String, core.Object> toJson() { 4216 core.Map<core.String, core.Object> toJson() {
4333 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 4217 final core.Map<core.String, core.Object> _json =
4218 new core.Map<core.String, core.Object>();
4334 if (callSetIds != null) { 4219 if (callSetIds != null) {
4335 _json["callSetIds"] = callSetIds; 4220 _json["callSetIds"] = callSetIds;
4336 } 4221 }
4337 return _json; 4222 return _json;
4338 } 4223 }
4339 } 4224 }
4340 4225
4341 /** 4226 /// A linear alignment can be represented by one CIGAR string. Describes the
4342 * A linear alignment can be represented by one CIGAR string. Describes the 4227 /// mapped position and local alignment of the read to the reference.
4343 * mapped position and local alignment of the read to the reference.
4344 */
4345 class LinearAlignment { 4228 class LinearAlignment {
4346 /** 4229 /// Represents the local alignment of this sequence (alignment matches,
4347 * Represents the local alignment of this sequence (alignment matches, indels, 4230 /// indels,
4348 * etc) against the reference. 4231 /// etc) against the reference.
4349 */
4350 core.List<CigarUnit> cigar; 4232 core.List<CigarUnit> cigar;
4351 /** 4233
4352 * The mapping quality of this alignment. Represents how likely 4234 /// The mapping quality of this alignment. Represents how likely
4353 * the read maps to this position as opposed to other locations. 4235 /// the read maps to this position as opposed to other locations.
4354 * 4236 ///
4355 * Specifically, this is -10 log10 Pr(mapping position is wrong), rounded to 4237 /// Specifically, this is -10 log10 Pr(mapping position is wrong), rounded to
4356 * the nearest integer. 4238 /// the nearest integer.
4357 */
4358 core.int mappingQuality; 4239 core.int mappingQuality;
4359 /** The position of this alignment. */ 4240
4241 /// The position of this alignment.
4360 Position position; 4242 Position position;
4361 4243
4362 LinearAlignment(); 4244 LinearAlignment();
4363 4245
4364 LinearAlignment.fromJson(core.Map _json) { 4246 LinearAlignment.fromJson(core.Map _json) {
4365 if (_json.containsKey("cigar")) { 4247 if (_json.containsKey("cigar")) {
4366 cigar = _json["cigar"].map((value) => new CigarUnit.fromJson(value)).toLis t(); 4248 cigar =
4249 _json["cigar"].map((value) => new CigarUnit.fromJson(value)).toList();
4367 } 4250 }
4368 if (_json.containsKey("mappingQuality")) { 4251 if (_json.containsKey("mappingQuality")) {
4369 mappingQuality = _json["mappingQuality"]; 4252 mappingQuality = _json["mappingQuality"];
4370 } 4253 }
4371 if (_json.containsKey("position")) { 4254 if (_json.containsKey("position")) {
4372 position = new Position.fromJson(_json["position"]); 4255 position = new Position.fromJson(_json["position"]);
4373 } 4256 }
4374 } 4257 }
4375 4258
4376 core.Map<core.String, core.Object> toJson() { 4259 core.Map<core.String, core.Object> toJson() {
4377 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 4260 final core.Map<core.String, core.Object> _json =
4261 new core.Map<core.String, core.Object>();
4378 if (cigar != null) { 4262 if (cigar != null) {
4379 _json["cigar"] = cigar.map((value) => (value).toJson()).toList(); 4263 _json["cigar"] = cigar.map((value) => (value).toJson()).toList();
4380 } 4264 }
4381 if (mappingQuality != null) { 4265 if (mappingQuality != null) {
4382 _json["mappingQuality"] = mappingQuality; 4266 _json["mappingQuality"] = mappingQuality;
4383 } 4267 }
4384 if (position != null) { 4268 if (position != null) {
4385 _json["position"] = (position).toJson(); 4269 _json["position"] = (position).toJson();
4386 } 4270 }
4387 return _json; 4271 return _json;
4388 } 4272 }
4389 } 4273 }
4390 4274
4391 class ListBasesResponse { 4275 class ListBasesResponse {
4392 /** 4276 /// The continuation token, which is used to page through large result sets.
4393 * The continuation token, which is used to page through large result sets. 4277 /// Provide this value in a subsequent request to return the next page of
4394 * Provide this value in a subsequent request to return the next page of 4278 /// results. This field will be empty if there aren't any additional results.
4395 * results. This field will be empty if there aren't any additional results.
4396 */
4397 core.String nextPageToken; 4279 core.String nextPageToken;
4398 /** 4280
4399 * The offset position (0-based) of the given `sequence` from the 4281 /// The offset position (0-based) of the given `sequence` from the
4400 * start of this `Reference`. This value will differ for each page 4282 /// start of this `Reference`. This value will differ for each page
4401 * in a paginated request. 4283 /// in a paginated request.
4402 */
4403 core.String offset; 4284 core.String offset;
4404 /** A substring of the bases that make up this reference. */ 4285
4286 /// A substring of the bases that make up this reference.
4405 core.String sequence; 4287 core.String sequence;
4406 4288
4407 ListBasesResponse(); 4289 ListBasesResponse();
4408 4290
4409 ListBasesResponse.fromJson(core.Map _json) { 4291 ListBasesResponse.fromJson(core.Map _json) {
4410 if (_json.containsKey("nextPageToken")) { 4292 if (_json.containsKey("nextPageToken")) {
4411 nextPageToken = _json["nextPageToken"]; 4293 nextPageToken = _json["nextPageToken"];
4412 } 4294 }
4413 if (_json.containsKey("offset")) { 4295 if (_json.containsKey("offset")) {
4414 offset = _json["offset"]; 4296 offset = _json["offset"];
4415 } 4297 }
4416 if (_json.containsKey("sequence")) { 4298 if (_json.containsKey("sequence")) {
4417 sequence = _json["sequence"]; 4299 sequence = _json["sequence"];
4418 } 4300 }
4419 } 4301 }
4420 4302
4421 core.Map<core.String, core.Object> toJson() { 4303 core.Map<core.String, core.Object> toJson() {
4422 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 4304 final core.Map<core.String, core.Object> _json =
4305 new core.Map<core.String, core.Object>();
4423 if (nextPageToken != null) { 4306 if (nextPageToken != null) {
4424 _json["nextPageToken"] = nextPageToken; 4307 _json["nextPageToken"] = nextPageToken;
4425 } 4308 }
4426 if (offset != null) { 4309 if (offset != null) {
4427 _json["offset"] = offset; 4310 _json["offset"] = offset;
4428 } 4311 }
4429 if (sequence != null) { 4312 if (sequence != null) {
4430 _json["sequence"] = sequence; 4313 _json["sequence"] = sequence;
4431 } 4314 }
4432 return _json; 4315 return _json;
4433 } 4316 }
4434 } 4317 }
4435 4318
4436 class ListCoverageBucketsResponse { 4319 class ListCoverageBucketsResponse {
4437 /** 4320 /// The length of each coverage bucket in base pairs. Note that buckets at
4438 * The length of each coverage bucket in base pairs. Note that buckets at the 4321 /// the
4439 * end of a reference sequence may be shorter. This value is omitted if the 4322 /// end of a reference sequence may be shorter. This value is omitted if the
4440 * bucket width is infinity (the default behaviour, with no range or 4323 /// bucket width is infinity (the default behaviour, with no range or
4441 * `targetBucketWidth`). 4324 /// `targetBucketWidth`).
4442 */
4443 core.String bucketWidth; 4325 core.String bucketWidth;
4444 /** 4326
4445 * The coverage buckets. The list of buckets is sparse; a bucket with 0 4327 /// The coverage buckets. The list of buckets is sparse; a bucket with 0
4446 * overlapping reads is not returned. A bucket never crosses more than one 4328 /// overlapping reads is not returned. A bucket never crosses more than one
4447 * reference sequence. Each bucket has width `bucketWidth`, unless 4329 /// reference sequence. Each bucket has width `bucketWidth`, unless
4448 * its end is the end of the reference sequence. 4330 /// its end is the end of the reference sequence.
4449 */
4450 core.List<CoverageBucket> coverageBuckets; 4331 core.List<CoverageBucket> coverageBuckets;
4451 /** 4332
4452 * The continuation token, which is used to page through large result sets. 4333 /// The continuation token, which is used to page through large result sets.
4453 * Provide this value in a subsequent request to return the next page of 4334 /// Provide this value in a subsequent request to return the next page of
4454 * results. This field will be empty if there aren't any additional results. 4335 /// results. This field will be empty if there aren't any additional results.
4455 */
4456 core.String nextPageToken; 4336 core.String nextPageToken;
4457 4337
4458 ListCoverageBucketsResponse(); 4338 ListCoverageBucketsResponse();
4459 4339
4460 ListCoverageBucketsResponse.fromJson(core.Map _json) { 4340 ListCoverageBucketsResponse.fromJson(core.Map _json) {
4461 if (_json.containsKey("bucketWidth")) { 4341 if (_json.containsKey("bucketWidth")) {
4462 bucketWidth = _json["bucketWidth"]; 4342 bucketWidth = _json["bucketWidth"];
4463 } 4343 }
4464 if (_json.containsKey("coverageBuckets")) { 4344 if (_json.containsKey("coverageBuckets")) {
4465 coverageBuckets = _json["coverageBuckets"].map((value) => new CoverageBuck et.fromJson(value)).toList(); 4345 coverageBuckets = _json["coverageBuckets"]
4346 .map((value) => new CoverageBucket.fromJson(value))
4347 .toList();
4466 } 4348 }
4467 if (_json.containsKey("nextPageToken")) { 4349 if (_json.containsKey("nextPageToken")) {
4468 nextPageToken = _json["nextPageToken"]; 4350 nextPageToken = _json["nextPageToken"];
4469 } 4351 }
4470 } 4352 }
4471 4353
4472 core.Map<core.String, core.Object> toJson() { 4354 core.Map<core.String, core.Object> toJson() {
4473 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 4355 final core.Map<core.String, core.Object> _json =
4356 new core.Map<core.String, core.Object>();
4474 if (bucketWidth != null) { 4357 if (bucketWidth != null) {
4475 _json["bucketWidth"] = bucketWidth; 4358 _json["bucketWidth"] = bucketWidth;
4476 } 4359 }
4477 if (coverageBuckets != null) { 4360 if (coverageBuckets != null) {
4478 _json["coverageBuckets"] = coverageBuckets.map((value) => (value).toJson() ).toList(); 4361 _json["coverageBuckets"] =
4362 coverageBuckets.map((value) => (value).toJson()).toList();
4479 } 4363 }
4480 if (nextPageToken != null) { 4364 if (nextPageToken != null) {
4481 _json["nextPageToken"] = nextPageToken; 4365 _json["nextPageToken"] = nextPageToken;
4482 } 4366 }
4483 return _json; 4367 return _json;
4484 } 4368 }
4485 } 4369 }
4486 4370
4487 /** The dataset list response. */ 4371 /// The dataset list response.
4488 class ListDatasetsResponse { 4372 class ListDatasetsResponse {
4489 /** The list of matching Datasets. */ 4373 /// The list of matching Datasets.
4490 core.List<Dataset> datasets; 4374 core.List<Dataset> datasets;
4491 /** 4375
4492 * The continuation token, which is used to page through large result sets. 4376 /// The continuation token, which is used to page through large result sets.
4493 * Provide this value in a subsequent request to return the next page of 4377 /// Provide this value in a subsequent request to return the next page of
4494 * results. This field will be empty if there aren't any additional results. 4378 /// results. This field will be empty if there aren't any additional results.
4495 */
4496 core.String nextPageToken; 4379 core.String nextPageToken;
4497 4380
4498 ListDatasetsResponse(); 4381 ListDatasetsResponse();
4499 4382
4500 ListDatasetsResponse.fromJson(core.Map _json) { 4383 ListDatasetsResponse.fromJson(core.Map _json) {
4501 if (_json.containsKey("datasets")) { 4384 if (_json.containsKey("datasets")) {
4502 datasets = _json["datasets"].map((value) => new Dataset.fromJson(value)).t oList(); 4385 datasets = _json["datasets"]
4386 .map((value) => new Dataset.fromJson(value))
4387 .toList();
4503 } 4388 }
4504 if (_json.containsKey("nextPageToken")) { 4389 if (_json.containsKey("nextPageToken")) {
4505 nextPageToken = _json["nextPageToken"]; 4390 nextPageToken = _json["nextPageToken"];
4506 } 4391 }
4507 } 4392 }
4508 4393
4509 core.Map<core.String, core.Object> toJson() { 4394 core.Map<core.String, core.Object> toJson() {
4510 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 4395 final core.Map<core.String, core.Object> _json =
4396 new core.Map<core.String, core.Object>();
4511 if (datasets != null) { 4397 if (datasets != null) {
4512 _json["datasets"] = datasets.map((value) => (value).toJson()).toList(); 4398 _json["datasets"] = datasets.map((value) => (value).toJson()).toList();
4513 } 4399 }
4514 if (nextPageToken != null) { 4400 if (nextPageToken != null) {
4515 _json["nextPageToken"] = nextPageToken; 4401 _json["nextPageToken"] = nextPageToken;
4516 } 4402 }
4517 return _json; 4403 return _json;
4518 } 4404 }
4519 } 4405 }
4520 4406
4521 /** The response message for Operations.ListOperations. */ 4407 /// The response message for Operations.ListOperations.
4522 class ListOperationsResponse { 4408 class ListOperationsResponse {
4523 /** The standard List next-page token. */ 4409 /// The standard List next-page token.
4524 core.String nextPageToken; 4410 core.String nextPageToken;
4525 /** A list of operations that matches the specified filter in the request. */ 4411
4412 /// A list of operations that matches the specified filter in the request.
4526 core.List<Operation> operations; 4413 core.List<Operation> operations;
4527 4414
4528 ListOperationsResponse(); 4415 ListOperationsResponse();
4529 4416
4530 ListOperationsResponse.fromJson(core.Map _json) { 4417 ListOperationsResponse.fromJson(core.Map _json) {
4531 if (_json.containsKey("nextPageToken")) { 4418 if (_json.containsKey("nextPageToken")) {
4532 nextPageToken = _json["nextPageToken"]; 4419 nextPageToken = _json["nextPageToken"];
4533 } 4420 }
4534 if (_json.containsKey("operations")) { 4421 if (_json.containsKey("operations")) {
4535 operations = _json["operations"].map((value) => new Operation.fromJson(val ue)).toList(); 4422 operations = _json["operations"]
4423 .map((value) => new Operation.fromJson(value))
4424 .toList();
4536 } 4425 }
4537 } 4426 }
4538 4427
4539 core.Map<core.String, core.Object> toJson() { 4428 core.Map<core.String, core.Object> toJson() {
4540 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 4429 final core.Map<core.String, core.Object> _json =
4430 new core.Map<core.String, core.Object>();
4541 if (nextPageToken != null) { 4431 if (nextPageToken != null) {
4542 _json["nextPageToken"] = nextPageToken; 4432 _json["nextPageToken"] = nextPageToken;
4543 } 4433 }
4544 if (operations != null) { 4434 if (operations != null) {
4545 _json["operations"] = operations.map((value) => (value).toJson()).toList() ; 4435 _json["operations"] =
4436 operations.map((value) => (value).toJson()).toList();
4546 } 4437 }
4547 return _json; 4438 return _json;
4548 } 4439 }
4549 } 4440 }
4550 4441
4551 class MergeVariantsRequest { 4442 class MergeVariantsRequest {
4552 /** 4443 /// A mapping between info field keys and the InfoMergeOperations to
4553 * A mapping between info field keys and the InfoMergeOperations to 4444 /// be performed on them.
4554 * be performed on them.
4555 */
4556 core.Map<core.String, core.String> infoMergeConfig; 4445 core.Map<core.String, core.String> infoMergeConfig;
4557 /** The destination variant set. */ 4446
4447 /// The destination variant set.
4558 core.String variantSetId; 4448 core.String variantSetId;
4559 /** The variants to be merged with existing variants. */ 4449
4450 /// The variants to be merged with existing variants.
4560 core.List<Variant> variants; 4451 core.List<Variant> variants;
4561 4452
4562 MergeVariantsRequest(); 4453 MergeVariantsRequest();
4563 4454
4564 MergeVariantsRequest.fromJson(core.Map _json) { 4455 MergeVariantsRequest.fromJson(core.Map _json) {
4565 if (_json.containsKey("infoMergeConfig")) { 4456 if (_json.containsKey("infoMergeConfig")) {
4566 infoMergeConfig = _json["infoMergeConfig"]; 4457 infoMergeConfig = _json["infoMergeConfig"];
4567 } 4458 }
4568 if (_json.containsKey("variantSetId")) { 4459 if (_json.containsKey("variantSetId")) {
4569 variantSetId = _json["variantSetId"]; 4460 variantSetId = _json["variantSetId"];
4570 } 4461 }
4571 if (_json.containsKey("variants")) { 4462 if (_json.containsKey("variants")) {
4572 variants = _json["variants"].map((value) => new Variant.fromJson(value)).t oList(); 4463 variants = _json["variants"]
4464 .map((value) => new Variant.fromJson(value))
4465 .toList();
4573 } 4466 }
4574 } 4467 }
4575 4468
4576 core.Map<core.String, core.Object> toJson() { 4469 core.Map<core.String, core.Object> toJson() {
4577 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 4470 final core.Map<core.String, core.Object> _json =
4471 new core.Map<core.String, core.Object>();
4578 if (infoMergeConfig != null) { 4472 if (infoMergeConfig != null) {
4579 _json["infoMergeConfig"] = infoMergeConfig; 4473 _json["infoMergeConfig"] = infoMergeConfig;
4580 } 4474 }
4581 if (variantSetId != null) { 4475 if (variantSetId != null) {
4582 _json["variantSetId"] = variantSetId; 4476 _json["variantSetId"] = variantSetId;
4583 } 4477 }
4584 if (variants != null) { 4478 if (variants != null) {
4585 _json["variants"] = variants.map((value) => (value).toJson()).toList(); 4479 _json["variants"] = variants.map((value) => (value).toJson()).toList();
4586 } 4480 }
4587 return _json; 4481 return _json;
4588 } 4482 }
4589 } 4483 }
4590 4484
4591 /** 4485 /// This resource represents a long-running operation that is the result of a
4592 * This resource represents a long-running operation that is the result of a 4486 /// network API call.
4593 * network API call.
4594 */
4595 class Operation { 4487 class Operation {
4596 /** 4488 /// If the value is `false`, it means the operation is still in progress.
4597 * If the value is `false`, it means the operation is still in progress. 4489 /// If `true`, the operation is completed, and either `error` or `response`
4598 * If true, the operation is completed, and either `error` or `response` is 4490 /// is
4599 * available. 4491 /// available.
4600 */
4601 core.bool done; 4492 core.bool done;
4602 /** The error result of the operation in case of failure or cancellation. */ 4493
4494 /// The error result of the operation in case of failure or cancellation.
4603 Status error; 4495 Status error;
4604 /** 4496
4605 * An OperationMetadata object. This will always be returned with the 4497 /// An OperationMetadata object. This will always be returned with the
4606 * Operation. 4498 /// Operation.
4607 * 4499 ///
4608 * The values for Object must be JSON objects. It can consist of `num`, 4500 /// The values for Object must be JSON objects. It can consist of `num`,
4609 * `String`, `bool` and `null` as well as `Map` and `List` values. 4501 /// `String`, `bool` and `null` as well as `Map` and `List` values.
4610 */
4611 core.Map<core.String, core.Object> metadata; 4502 core.Map<core.String, core.Object> metadata;
4612 /** 4503
4613 * The server-assigned name, which is only unique within the same service that 4504 /// The server-assigned name, which is only unique within the same service
4614 * originally returns it. For example&#58; 4505 /// that originally returns it. For example&#58;
4615 * `operations/CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw` 4506 /// `operations/CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw`
4616 */
4617 core.String name; 4507 core.String name;
4618 /** 4508
4619 * If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If 4509 /// If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned.
4620 * importing Variants, an ImportVariantsResponse is returned. For pipelines 4510 /// If importing Variants, an ImportVariantsResponse is returned. For
4621 * and exports, an empty response is returned. 4511 /// pipelines and exports, an empty response is returned.
4622 * 4512 ///
4623 * The values for Object must be JSON objects. It can consist of `num`, 4513 /// The values for Object must be JSON objects. It can consist of `num`,
4624 * `String`, `bool` and `null` as well as `Map` and `List` values. 4514 /// `String`, `bool` and `null` as well as `Map` and `List` values.
4625 */
4626 core.Map<core.String, core.Object> response; 4515 core.Map<core.String, core.Object> response;
4627 4516
4628 Operation(); 4517 Operation();
4629 4518
4630 Operation.fromJson(core.Map _json) { 4519 Operation.fromJson(core.Map _json) {
4631 if (_json.containsKey("done")) { 4520 if (_json.containsKey("done")) {
4632 done = _json["done"]; 4521 done = _json["done"];
4633 } 4522 }
4634 if (_json.containsKey("error")) { 4523 if (_json.containsKey("error")) {
4635 error = new Status.fromJson(_json["error"]); 4524 error = new Status.fromJson(_json["error"]);
4636 } 4525 }
4637 if (_json.containsKey("metadata")) { 4526 if (_json.containsKey("metadata")) {
4638 metadata = _json["metadata"]; 4527 metadata = _json["metadata"];
4639 } 4528 }
4640 if (_json.containsKey("name")) { 4529 if (_json.containsKey("name")) {
4641 name = _json["name"]; 4530 name = _json["name"];
4642 } 4531 }
4643 if (_json.containsKey("response")) { 4532 if (_json.containsKey("response")) {
4644 response = _json["response"]; 4533 response = _json["response"];
4645 } 4534 }
4646 } 4535 }
4647 4536
4648 core.Map<core.String, core.Object> toJson() { 4537 core.Map<core.String, core.Object> toJson() {
4649 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 4538 final core.Map<core.String, core.Object> _json =
4539 new core.Map<core.String, core.Object>();
4650 if (done != null) { 4540 if (done != null) {
4651 _json["done"] = done; 4541 _json["done"] = done;
4652 } 4542 }
4653 if (error != null) { 4543 if (error != null) {
4654 _json["error"] = (error).toJson(); 4544 _json["error"] = (error).toJson();
4655 } 4545 }
4656 if (metadata != null) { 4546 if (metadata != null) {
4657 _json["metadata"] = metadata; 4547 _json["metadata"] = metadata;
4658 } 4548 }
4659 if (name != null) { 4549 if (name != null) {
4660 _json["name"] = name; 4550 _json["name"] = name;
4661 } 4551 }
4662 if (response != null) { 4552 if (response != null) {
4663 _json["response"] = response; 4553 _json["response"] = response;
4664 } 4554 }
4665 return _json; 4555 return _json;
4666 } 4556 }
4667 } 4557 }
4668 4558
4669 /** An event that occurred during an Operation. */ 4559 /// An event that occurred during an Operation.
4670 class OperationEvent { 4560 class OperationEvent {
4671 /** Required description of event. */ 4561 /// Required description of event.
4672 core.String description; 4562 core.String description;
4673 /** 4563
4674 * Optional time of when event finished. An event can have a start time and no 4564 /// Optional time of when event finished. An event can have a start time and
4675 * finish time. If an event has a finish time, there must be a start time. 4565 /// no
4676 */ 4566 /// finish time. If an event has a finish time, there must be a start time.
4677 core.String endTime; 4567 core.String endTime;
4678 /** Optional time of when event started. */ 4568
4569 /// Optional time of when event started.
4679 core.String startTime; 4570 core.String startTime;
4680 4571
4681 OperationEvent(); 4572 OperationEvent();
4682 4573
4683 OperationEvent.fromJson(core.Map _json) { 4574 OperationEvent.fromJson(core.Map _json) {
4684 if (_json.containsKey("description")) { 4575 if (_json.containsKey("description")) {
4685 description = _json["description"]; 4576 description = _json["description"];
4686 } 4577 }
4687 if (_json.containsKey("endTime")) { 4578 if (_json.containsKey("endTime")) {
4688 endTime = _json["endTime"]; 4579 endTime = _json["endTime"];
4689 } 4580 }
4690 if (_json.containsKey("startTime")) { 4581 if (_json.containsKey("startTime")) {
4691 startTime = _json["startTime"]; 4582 startTime = _json["startTime"];
4692 } 4583 }
4693 } 4584 }
4694 4585
4695 core.Map<core.String, core.Object> toJson() { 4586 core.Map<core.String, core.Object> toJson() {
4696 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 4587 final core.Map<core.String, core.Object> _json =
4588 new core.Map<core.String, core.Object>();
4697 if (description != null) { 4589 if (description != null) {
4698 _json["description"] = description; 4590 _json["description"] = description;
4699 } 4591 }
4700 if (endTime != null) { 4592 if (endTime != null) {
4701 _json["endTime"] = endTime; 4593 _json["endTime"] = endTime;
4702 } 4594 }
4703 if (startTime != null) { 4595 if (startTime != null) {
4704 _json["startTime"] = startTime; 4596 _json["startTime"] = startTime;
4705 } 4597 }
4706 return _json; 4598 return _json;
4707 } 4599 }
4708 } 4600 }
4709 4601
4710 /** Metadata describing an Operation. */ 4602 /// Metadata describing an Operation.
4711 class OperationMetadata { 4603 class OperationMetadata {
4712 /** 4604 /// This field is deprecated. Use `labels` instead. Optionally provided by
4713 * This field is deprecated. Use `labels` instead. Optionally provided by the 4605 /// the
4714 * caller when submitting the request that creates the operation. 4606 /// caller when submitting the request that creates the operation.
4715 */
4716 core.String clientId; 4607 core.String clientId;
4717 /** The time at which the job was submitted to the Genomics service. */ 4608
4609 /// The time at which the job was submitted to the Genomics service.
4718 core.String createTime; 4610 core.String createTime;
4719 /** The time at which the job stopped running. */ 4611
4612 /// The time at which the job stopped running.
4720 core.String endTime; 4613 core.String endTime;
4721 /** 4614
4722 * Optional event messages that were generated during the job's execution. 4615 /// Optional event messages that were generated during the job's execution.
4723 * This also contains any warnings that were generated during import 4616 /// This also contains any warnings that were generated during import
4724 * or export. 4617 /// or export.
4725 */
4726 core.List<OperationEvent> events; 4618 core.List<OperationEvent> events;
4727 /** 4619
4728 * Optionally provided by the caller when submitting the request that creates 4620 /// Optionally provided by the caller when submitting the request that
4729 * the operation. 4621 /// creates
4730 */ 4622 /// the operation.
4731 core.Map<core.String, core.String> labels; 4623 core.Map<core.String, core.String> labels;
4732 /** The Google Cloud Project in which the job is scoped. */ 4624
4625 /// The Google Cloud Project in which the job is scoped.
4733 core.String projectId; 4626 core.String projectId;
4734 /** 4627
4735 * The original request that started the operation. Note that this will be in 4628 /// The original request that started the operation. Note that this will be
4736 * current version of the API. If the operation was started with v1beta2 API 4629 /// in
4737 * and a GetOperation is performed on v1 API, a v1 request will be returned. 4630 /// current version of the API. If the operation was started with v1beta2 API
4738 * 4631 /// and a GetOperation is performed on v1 API, a v1 request will be returned.
4739 * The values for Object must be JSON objects. It can consist of `num`, 4632 ///
4740 * `String`, `bool` and `null` as well as `Map` and `List` values. 4633 /// The values for Object must be JSON objects. It can consist of `num`,
4741 */ 4634 /// `String`, `bool` and `null` as well as `Map` and `List` values.
4742 core.Map<core.String, core.Object> request; 4635 core.Map<core.String, core.Object> request;
4743 /** 4636
4744 * Runtime metadata on this Operation. 4637 /// Runtime metadata on this Operation.
4745 * 4638 ///
4746 * The values for Object must be JSON objects. It can consist of `num`, 4639 /// The values for Object must be JSON objects. It can consist of `num`,
4747 * `String`, `bool` and `null` as well as `Map` and `List` values. 4640 /// `String`, `bool` and `null` as well as `Map` and `List` values.
4748 */
4749 core.Map<core.String, core.Object> runtimeMetadata; 4641 core.Map<core.String, core.Object> runtimeMetadata;
4750 /** The time at which the job began to run. */ 4642
4643 /// The time at which the job began to run.
4751 core.String startTime; 4644 core.String startTime;
4752 4645
4753 OperationMetadata(); 4646 OperationMetadata();
4754 4647
4755 OperationMetadata.fromJson(core.Map _json) { 4648 OperationMetadata.fromJson(core.Map _json) {
4756 if (_json.containsKey("clientId")) { 4649 if (_json.containsKey("clientId")) {
4757 clientId = _json["clientId"]; 4650 clientId = _json["clientId"];
4758 } 4651 }
4759 if (_json.containsKey("createTime")) { 4652 if (_json.containsKey("createTime")) {
4760 createTime = _json["createTime"]; 4653 createTime = _json["createTime"];
4761 } 4654 }
4762 if (_json.containsKey("endTime")) { 4655 if (_json.containsKey("endTime")) {
4763 endTime = _json["endTime"]; 4656 endTime = _json["endTime"];
4764 } 4657 }
4765 if (_json.containsKey("events")) { 4658 if (_json.containsKey("events")) {
4766 events = _json["events"].map((value) => new OperationEvent.fromJson(value) ).toList(); 4659 events = _json["events"]
4660 .map((value) => new OperationEvent.fromJson(value))
4661 .toList();
4767 } 4662 }
4768 if (_json.containsKey("labels")) { 4663 if (_json.containsKey("labels")) {
4769 labels = _json["labels"]; 4664 labels = _json["labels"];
4770 } 4665 }
4771 if (_json.containsKey("projectId")) { 4666 if (_json.containsKey("projectId")) {
4772 projectId = _json["projectId"]; 4667 projectId = _json["projectId"];
4773 } 4668 }
4774 if (_json.containsKey("request")) { 4669 if (_json.containsKey("request")) {
4775 request = _json["request"]; 4670 request = _json["request"];
4776 } 4671 }
4777 if (_json.containsKey("runtimeMetadata")) { 4672 if (_json.containsKey("runtimeMetadata")) {
4778 runtimeMetadata = _json["runtimeMetadata"]; 4673 runtimeMetadata = _json["runtimeMetadata"];
4779 } 4674 }
4780 if (_json.containsKey("startTime")) { 4675 if (_json.containsKey("startTime")) {
4781 startTime = _json["startTime"]; 4676 startTime = _json["startTime"];
4782 } 4677 }
4783 } 4678 }
4784 4679
4785 core.Map<core.String, core.Object> toJson() { 4680 core.Map<core.String, core.Object> toJson() {
4786 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 4681 final core.Map<core.String, core.Object> _json =
4682 new core.Map<core.String, core.Object>();
4787 if (clientId != null) { 4683 if (clientId != null) {
4788 _json["clientId"] = clientId; 4684 _json["clientId"] = clientId;
4789 } 4685 }
4790 if (createTime != null) { 4686 if (createTime != null) {
4791 _json["createTime"] = createTime; 4687 _json["createTime"] = createTime;
4792 } 4688 }
4793 if (endTime != null) { 4689 if (endTime != null) {
4794 _json["endTime"] = endTime; 4690 _json["endTime"] = endTime;
4795 } 4691 }
4796 if (events != null) { 4692 if (events != null) {
(...skipping 11 matching lines...) Expand all
4808 if (runtimeMetadata != null) { 4704 if (runtimeMetadata != null) {
4809 _json["runtimeMetadata"] = runtimeMetadata; 4705 _json["runtimeMetadata"] = runtimeMetadata;
4810 } 4706 }
4811 if (startTime != null) { 4707 if (startTime != null) {
4812 _json["startTime"] = startTime; 4708 _json["startTime"] = startTime;
4813 } 4709 }
4814 return _json; 4710 return _json;
4815 } 4711 }
4816 } 4712 }
4817 4713
4818 /** 4714 /// Defines an Identity and Access Management (IAM) policy. It is used to
4819 * Defines an Identity and Access Management (IAM) policy. It is used to 4715 /// specify access control policies for Cloud Platform resources.
4820 * specify access control policies for Cloud Platform resources. 4716 ///
4821 * 4717 ///
4822 * 4718 /// A `Policy` consists of a list of `bindings`. A `Binding` binds a list of
4823 * A `Policy` consists of a list of `bindings`. A `Binding` binds a list of 4719 /// `members` to a `role`, where the members can be user accounts, Google
4824 * `members` to a `role`, where the members can be user accounts, Google groups, 4720 /// groups,
4825 * Google domains, and service accounts. A `role` is a named list of permissions 4721 /// Google domains, and service accounts. A `role` is a named list of
4826 * defined by IAM. 4722 /// permissions
4827 * 4723 /// defined by IAM.
4828 * **Example** 4724 ///
4829 * 4725 /// **Example**
4830 * { 4726 ///
4831 * "bindings": [ 4727 /// {
4832 * { 4728 /// "bindings": [
4833 * "role": "roles/owner", 4729 /// {
4834 * "members": [ 4730 /// "role": "roles/owner",
4835 * "user:mike@example.com", 4731 /// "members": [
4836 * "group:admins@example.com", 4732 /// "user:mike@example.com",
4837 * "domain:google.com", 4733 /// "group:admins@example.com",
4838 * "serviceAccount:my-other-app@appspot.gserviceaccount.com", 4734 /// "domain:google.com",
4839 * ] 4735 /// "serviceAccount:my-other-app@appspot.gserviceaccount.com",
4840 * }, 4736 /// ]
4841 * { 4737 /// },
4842 * "role": "roles/viewer", 4738 /// {
4843 * "members": ["user:sean@example.com"] 4739 /// "role": "roles/viewer",
4844 * } 4740 /// "members": ["user:sean@example.com"]
4845 * ] 4741 /// }
4846 * } 4742 /// ]
4847 * 4743 /// }
4848 * For a description of IAM and its features, see the 4744 ///
4849 * [IAM developer's guide](https://cloud.google.com/iam). 4745 /// For a description of IAM and its features, see the
4850 */ 4746 /// [IAM developer's guide](https://cloud.google.com/iam).
4851 class Policy { 4747 class Policy {
4852 /** 4748 /// Associates a list of `members` to a `role`.
4853 * Associates a list of `members` to a `role`. 4749 /// `bindings` with no members will result in an error.
4854 * `bindings` with no members will result in an error.
4855 */
4856 core.List<Binding> bindings; 4750 core.List<Binding> bindings;
4857 /** 4751
4858 * `etag` is used for optimistic concurrency control as a way to help 4752 /// `etag` is used for optimistic concurrency control as a way to help
4859 * prevent simultaneous updates of a policy from overwriting each other. 4753 /// prevent simultaneous updates of a policy from overwriting each other.
4860 * It is strongly suggested that systems make use of the `etag` in the 4754 /// It is strongly suggested that systems make use of the `etag` in the
4861 * read-modify-write cycle to perform policy updates in order to avoid race 4755 /// read-modify-write cycle to perform policy updates in order to avoid race
4862 * conditions: An `etag` is returned in the response to `getIamPolicy`, and 4756 /// conditions: An `etag` is returned in the response to `getIamPolicy`, and
4863 * systems are expected to put that etag in the request to `setIamPolicy` to 4757 /// systems are expected to put that etag in the request to `setIamPolicy` to
4864 * ensure that their change will be applied to the same version of the policy. 4758 /// ensure that their change will be applied to the same version of the
4865 * 4759 /// policy.
4866 * If no `etag` is provided in the call to `setIamPolicy`, then the existing 4760 ///
4867 * policy is overwritten blindly. 4761 /// If no `etag` is provided in the call to `setIamPolicy`, then the existing
4868 */ 4762 /// policy is overwritten blindly.
4869 core.String etag; 4763 core.String etag;
4870 core.List<core.int> get etagAsBytes { 4764 core.List<core.int> get etagAsBytes {
4871 return convert.BASE64.decode(etag); 4765 return convert.BASE64.decode(etag);
4872 } 4766 }
4873 4767
4874 void set etagAsBytes(core.List<core.int> _bytes) { 4768 void set etagAsBytes(core.List<core.int> _bytes) {
4875 etag = convert.BASE64.encode(_bytes).replaceAll("/", "_").replaceAll("+", "- "); 4769 etag =
4770 convert.BASE64.encode(_bytes).replaceAll("/", "_").replaceAll("+", "-");
4876 } 4771 }
4877 /** Version of the `Policy`. The default version is 0. */ 4772
4773 /// Version of the `Policy`. The default version is 0.
4878 core.int version; 4774 core.int version;
4879 4775
4880 Policy(); 4776 Policy();
4881 4777
4882 Policy.fromJson(core.Map _json) { 4778 Policy.fromJson(core.Map _json) {
4883 if (_json.containsKey("bindings")) { 4779 if (_json.containsKey("bindings")) {
4884 bindings = _json["bindings"].map((value) => new Binding.fromJson(value)).t oList(); 4780 bindings = _json["bindings"]
4781 .map((value) => new Binding.fromJson(value))
4782 .toList();
4885 } 4783 }
4886 if (_json.containsKey("etag")) { 4784 if (_json.containsKey("etag")) {
4887 etag = _json["etag"]; 4785 etag = _json["etag"];
4888 } 4786 }
4889 if (_json.containsKey("version")) { 4787 if (_json.containsKey("version")) {
4890 version = _json["version"]; 4788 version = _json["version"];
4891 } 4789 }
4892 } 4790 }
4893 4791
4894 core.Map<core.String, core.Object> toJson() { 4792 core.Map<core.String, core.Object> toJson() {
4895 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 4793 final core.Map<core.String, core.Object> _json =
4794 new core.Map<core.String, core.Object>();
4896 if (bindings != null) { 4795 if (bindings != null) {
4897 _json["bindings"] = bindings.map((value) => (value).toJson()).toList(); 4796 _json["bindings"] = bindings.map((value) => (value).toJson()).toList();
4898 } 4797 }
4899 if (etag != null) { 4798 if (etag != null) {
4900 _json["etag"] = etag; 4799 _json["etag"] = etag;
4901 } 4800 }
4902 if (version != null) { 4801 if (version != null) {
4903 _json["version"] = version; 4802 _json["version"] = version;
4904 } 4803 }
4905 return _json; 4804 return _json;
4906 } 4805 }
4907 } 4806 }
4908 4807
4909 /** 4808 /// An abstraction for referring to a genomic position, in relation to some
4910 * An abstraction for referring to a genomic position, in relation to some 4809 /// already known reference. For now, represents a genomic position as a
4911 * already known reference. For now, represents a genomic position as a 4810 /// reference name, a base number on that reference (0-based), and a
4912 * reference name, a base number on that reference (0-based), and a 4811 /// determination of forward or reverse strand.
4913 * determination of forward or reverse strand.
4914 */
4915 class Position { 4812 class Position {
4916 /** 4813 /// The 0-based offset from the start of the forward strand for that
4917 * The 0-based offset from the start of the forward strand for that reference. 4814 /// reference.
4918 */
4919 core.String position; 4815 core.String position;
4920 /** The name of the reference in whatever reference set is being used. */ 4816
4817 /// The name of the reference in whatever reference set is being used.
4921 core.String referenceName; 4818 core.String referenceName;
4922 /** 4819
4923 * Whether this position is on the reverse strand, as opposed to the forward 4820 /// Whether this position is on the reverse strand, as opposed to the forward
4924 * strand. 4821 /// strand.
4925 */
4926 core.bool reverseStrand; 4822 core.bool reverseStrand;
4927 4823
4928 Position(); 4824 Position();
4929 4825
4930 Position.fromJson(core.Map _json) { 4826 Position.fromJson(core.Map _json) {
4931 if (_json.containsKey("position")) { 4827 if (_json.containsKey("position")) {
4932 position = _json["position"]; 4828 position = _json["position"];
4933 } 4829 }
4934 if (_json.containsKey("referenceName")) { 4830 if (_json.containsKey("referenceName")) {
4935 referenceName = _json["referenceName"]; 4831 referenceName = _json["referenceName"];
4936 } 4832 }
4937 if (_json.containsKey("reverseStrand")) { 4833 if (_json.containsKey("reverseStrand")) {
4938 reverseStrand = _json["reverseStrand"]; 4834 reverseStrand = _json["reverseStrand"];
4939 } 4835 }
4940 } 4836 }
4941 4837
4942 core.Map<core.String, core.Object> toJson() { 4838 core.Map<core.String, core.Object> toJson() {
4943 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 4839 final core.Map<core.String, core.Object> _json =
4840 new core.Map<core.String, core.Object>();
4944 if (position != null) { 4841 if (position != null) {
4945 _json["position"] = position; 4842 _json["position"] = position;
4946 } 4843 }
4947 if (referenceName != null) { 4844 if (referenceName != null) {
4948 _json["referenceName"] = referenceName; 4845 _json["referenceName"] = referenceName;
4949 } 4846 }
4950 if (reverseStrand != null) { 4847 if (reverseStrand != null) {
4951 _json["reverseStrand"] = reverseStrand; 4848 _json["reverseStrand"] = reverseStrand;
4952 } 4849 }
4953 return _json; 4850 return _json;
4954 } 4851 }
4955 } 4852 }
4956 4853
4957 class Program { 4854 class Program {
4958 /** The command line used to run this program. */ 4855 /// The command line used to run this program.
4959 core.String commandLine; 4856 core.String commandLine;
4960 /** 4857
4961 * The user specified locally unique ID of the program. Used along with 4858 /// The user specified locally unique ID of the program. Used along with
4962 * `prevProgramId` to define an ordering between programs. 4859 /// `prevProgramId` to define an ordering between programs.
4963 */
4964 core.String id; 4860 core.String id;
4965 /** 4861
4966 * The display name of the program. This is typically the colloquial name of 4862 /// The display name of the program. This is typically the colloquial name of
4967 * the tool used, for example 'bwa' or 'picard'. 4863 /// the tool used, for example 'bwa' or 'picard'.
4968 */
4969 core.String name; 4864 core.String name;
4970 /** The ID of the program run before this one. */ 4865
4866 /// The ID of the program run before this one.
4971 core.String prevProgramId; 4867 core.String prevProgramId;
4972 /** The version of the program run. */ 4868
4869 /// The version of the program run.
4973 core.String version; 4870 core.String version;
4974 4871
4975 Program(); 4872 Program();
4976 4873
4977 Program.fromJson(core.Map _json) { 4874 Program.fromJson(core.Map _json) {
4978 if (_json.containsKey("commandLine")) { 4875 if (_json.containsKey("commandLine")) {
4979 commandLine = _json["commandLine"]; 4876 commandLine = _json["commandLine"];
4980 } 4877 }
4981 if (_json.containsKey("id")) { 4878 if (_json.containsKey("id")) {
4982 id = _json["id"]; 4879 id = _json["id"];
4983 } 4880 }
4984 if (_json.containsKey("name")) { 4881 if (_json.containsKey("name")) {
4985 name = _json["name"]; 4882 name = _json["name"];
4986 } 4883 }
4987 if (_json.containsKey("prevProgramId")) { 4884 if (_json.containsKey("prevProgramId")) {
4988 prevProgramId = _json["prevProgramId"]; 4885 prevProgramId = _json["prevProgramId"];
4989 } 4886 }
4990 if (_json.containsKey("version")) { 4887 if (_json.containsKey("version")) {
4991 version = _json["version"]; 4888 version = _json["version"];
4992 } 4889 }
4993 } 4890 }
4994 4891
4995 core.Map<core.String, core.Object> toJson() { 4892 core.Map<core.String, core.Object> toJson() {
4996 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 4893 final core.Map<core.String, core.Object> _json =
4894 new core.Map<core.String, core.Object>();
4997 if (commandLine != null) { 4895 if (commandLine != null) {
4998 _json["commandLine"] = commandLine; 4896 _json["commandLine"] = commandLine;
4999 } 4897 }
5000 if (id != null) { 4898 if (id != null) {
5001 _json["id"] = id; 4899 _json["id"] = id;
5002 } 4900 }
5003 if (name != null) { 4901 if (name != null) {
5004 _json["name"] = name; 4902 _json["name"] = name;
5005 } 4903 }
5006 if (prevProgramId != null) { 4904 if (prevProgramId != null) {
5007 _json["prevProgramId"] = prevProgramId; 4905 _json["prevProgramId"] = prevProgramId;
5008 } 4906 }
5009 if (version != null) { 4907 if (version != null) {
5010 _json["version"] = version; 4908 _json["version"] = version;
5011 } 4909 }
5012 return _json; 4910 return _json;
5013 } 4911 }
5014 } 4912 }
5015 4913
5016 /** A 0-based half-open genomic coordinate range for search requests. */ 4914 /// A 0-based half-open genomic coordinate range for search requests.
5017 class Range { 4915 class Range {
5018 /** The end position of the range on the reference, 0-based exclusive. */ 4916 /// The end position of the range on the reference, 0-based exclusive.
5019 core.String end; 4917 core.String end;
5020 /** 4918
5021 * The reference sequence name, for example `chr1`, 4919 /// The reference sequence name, for example `chr1`,
5022 * `1`, or `chrX`. 4920 /// `1`, or `chrX`.
5023 */
5024 core.String referenceName; 4921 core.String referenceName;
5025 /** The start position of the range on the reference, 0-based inclusive. */ 4922
4923 /// The start position of the range on the reference, 0-based inclusive.
5026 core.String start; 4924 core.String start;
5027 4925
5028 Range(); 4926 Range();
5029 4927
5030 Range.fromJson(core.Map _json) { 4928 Range.fromJson(core.Map _json) {
5031 if (_json.containsKey("end")) { 4929 if (_json.containsKey("end")) {
5032 end = _json["end"]; 4930 end = _json["end"];
5033 } 4931 }
5034 if (_json.containsKey("referenceName")) { 4932 if (_json.containsKey("referenceName")) {
5035 referenceName = _json["referenceName"]; 4933 referenceName = _json["referenceName"];
5036 } 4934 }
5037 if (_json.containsKey("start")) { 4935 if (_json.containsKey("start")) {
5038 start = _json["start"]; 4936 start = _json["start"];
5039 } 4937 }
5040 } 4938 }
5041 4939
5042 core.Map<core.String, core.Object> toJson() { 4940 core.Map<core.String, core.Object> toJson() {
5043 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 4941 final core.Map<core.String, core.Object> _json =
4942 new core.Map<core.String, core.Object>();
5044 if (end != null) { 4943 if (end != null) {
5045 _json["end"] = end; 4944 _json["end"] = end;
5046 } 4945 }
5047 if (referenceName != null) { 4946 if (referenceName != null) {
5048 _json["referenceName"] = referenceName; 4947 _json["referenceName"] = referenceName;
5049 } 4948 }
5050 if (start != null) { 4949 if (start != null) {
5051 _json["start"] = start; 4950 _json["start"] = start;
5052 } 4951 }
5053 return _json; 4952 return _json;
5054 } 4953 }
5055 } 4954 }
5056 4955
5057 /** 4956 /// A read alignment describes a linear alignment of a string of DNA to a
5058 * A read alignment describes a linear alignment of a string of DNA to a 4957 /// reference sequence, in addition to metadata
5059 * reference sequence, in addition to metadata 4958 /// about the fragment (the molecule of DNA sequenced) and the read (the bases
5060 * about the fragment (the molecule of DNA sequenced) and the read (the bases 4959 /// which were read by the sequencer). A read is equivalent to a line in a SAM
5061 * which were read by the sequencer). A read is equivalent to a line in a SAM 4960 /// file. A read belongs to exactly one read group and exactly one
5062 * file. A read belongs to exactly one read group and exactly one 4961 /// read group set.
5063 * read group set. 4962 ///
5064 * 4963 /// For more genomics resource definitions, see [Fundamentals of Google
5065 * For more genomics resource definitions, see [Fundamentals of Google 4964 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
5066 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 4965 ///
5067 * 4966 /// ### Reverse-stranded reads
5068 * ### Reverse-stranded reads 4967 ///
5069 * 4968 /// Mapped reads (reads having a non-null `alignment`) can be aligned to either
5070 * Mapped reads (reads having a non-null `alignment`) can be aligned to either 4969 /// the forward or the reverse strand of their associated reference.
5071 * the forward or the reverse strand of their associated reference. Strandedness 4970 /// Strandedness
5072 * of a mapped read is encoded by `alignment.position.reverseStrand`. 4971 /// of a mapped read is encoded by `alignment.position.reverseStrand`.
5073 * 4972 ///
5074 * If we consider the reference to be a forward-stranded coordinate space of 4973 /// If we consider the reference to be a forward-stranded coordinate space of
5075 * `[0, reference.length)` with `0` as the left-most position and 4974 /// `[0, reference.length)` with `0` as the left-most position and
5076 * `reference.length` as the right-most position, reads are always aligned left 4975 /// `reference.length` as the right-most position, reads are always aligned
5077 * to right. That is, `alignment.position.position` always refers to the 4976 /// left
5078 * left-most reference coordinate and `alignment.cigar` describes the alignment 4977 /// to right. That is, `alignment.position.position` always refers to the
5079 * of this read to the reference from left to right. All per-base fields such as 4978 /// left-most reference coordinate and `alignment.cigar` describes the
5080 * `alignedSequence` and `alignedQuality` share this same left-to-right 4979 /// alignment
5081 * orientation; this is true of reads which are aligned to either strand. For 4980 /// of this read to the reference from left to right. All per-base fields such
5082 * reverse-stranded reads, this means that `alignedSequence` is the reverse 4981 /// as
5083 * complement of the bases that were originally reported by the sequencing 4982 /// `alignedSequence` and `alignedQuality` share this same left-to-right
5084 * machine. 4983 /// orientation; this is true of reads which are aligned to either strand. For
5085 * 4984 /// reverse-stranded reads, this means that `alignedSequence` is the reverse
5086 * ### Generating a reference-aligned sequence string 4985 /// complement of the bases that were originally reported by the sequencing
5087 * 4986 /// machine.
5088 * When interacting with mapped reads, it's often useful to produce a string 4987 ///
5089 * representing the local alignment of the read to reference. The following 4988 /// ### Generating a reference-aligned sequence string
5090 * pseudocode demonstrates one way of doing this: 4989 ///
5091 * 4990 /// When interacting with mapped reads, it's often useful to produce a string
5092 * out = "" 4991 /// representing the local alignment of the read to reference. The following
5093 * offset = 0 4992 /// pseudocode demonstrates one way of doing this:
5094 * for c in read.alignment.cigar { 4993 ///
5095 * switch c.operation { 4994 /// out = ""
5096 * case "ALIGNMENT_MATCH", "SEQUENCE_MATCH", "SEQUENCE_MISMATCH": 4995 /// offset = 0
5097 * out += read.alignedSequence[offset:offset+c.operationLength] 4996 /// for c in read.alignment.cigar {
5098 * offset += c.operationLength 4997 /// switch c.operation {
5099 * break 4998 /// case "ALIGNMENT_MATCH", "SEQUENCE_MATCH", "SEQUENCE_MISMATCH":
5100 * case "CLIP_SOFT", "INSERT": 4999 /// out += read.alignedSequence[offset:offset+c.operationLength]
5101 * offset += c.operationLength 5000 /// offset += c.operationLength
5102 * break 5001 /// break
5103 * case "PAD": 5002 /// case "CLIP_SOFT", "INSERT":
5104 * out += repeat("*", c.operationLength) 5003 /// offset += c.operationLength
5105 * break 5004 /// break
5106 * case "DELETE": 5005 /// case "PAD":
5107 * out += repeat("-", c.operationLength) 5006 /// out += repeat("*", c.operationLength)
5108 * break 5007 /// break
5109 * case "SKIP": 5008 /// case "DELETE":
5110 * out += repeat(" ", c.operationLength) 5009 /// out += repeat("-", c.operationLength)
5111 * break 5010 /// break
5112 * case "CLIP_HARD": 5011 /// case "SKIP":
5113 * break 5012 /// out += repeat(" ", c.operationLength)
5114 * } 5013 /// break
5115 * } 5014 /// case "CLIP_HARD":
5116 * return out 5015 /// break
5117 * 5016 /// }
5118 * ### Converting to SAM's CIGAR string 5017 /// }
5119 * 5018 /// return out
5120 * The following pseudocode generates a SAM CIGAR string from the 5019 ///
5121 * `cigar` field. Note that this is a lossy conversion 5020 /// ### Converting to SAM's CIGAR string
5122 * (`cigar.referenceSequence` is lost). 5021 ///
5123 * 5022 /// The following pseudocode generates a SAM CIGAR string from the
5124 * cigarMap = { 5023 /// `cigar` field. Note that this is a lossy conversion
5125 * "ALIGNMENT_MATCH": "M", 5024 /// (`cigar.referenceSequence` is lost).
5126 * "INSERT": "I", 5025 ///
5127 * "DELETE": "D", 5026 /// cigarMap = {
5128 * "SKIP": "N", 5027 /// "ALIGNMENT_MATCH": "M",
5129 * "CLIP_SOFT": "S", 5028 /// "INSERT": "I",
5130 * "CLIP_HARD": "H", 5029 /// "DELETE": "D",
5131 * "PAD": "P", 5030 /// "SKIP": "N",
5132 * "SEQUENCE_MATCH": "=", 5031 /// "CLIP_SOFT": "S",
5133 * "SEQUENCE_MISMATCH": "X", 5032 /// "CLIP_HARD": "H",
5134 * } 5033 /// "PAD": "P",
5135 * cigarStr = "" 5034 /// "SEQUENCE_MATCH": "=",
5136 * for c in read.alignment.cigar { 5035 /// "SEQUENCE_MISMATCH": "X",
5137 * cigarStr += c.operationLength + cigarMap[c.operation] 5036 /// }
5138 * } 5037 /// cigarStr = ""
5139 * return cigarStr 5038 /// for c in read.alignment.cigar {
5140 */ 5039 /// cigarStr += c.operationLength + cigarMap[c.operation]
5040 /// }
5041 /// return cigarStr
5141 class Read { 5042 class Read {
5142 /** 5043 /// The quality of the read sequence contained in this alignment record
5143 * The quality of the read sequence contained in this alignment record 5044 /// (equivalent to QUAL in SAM).
5144 * (equivalent to QUAL in SAM). 5045 /// `alignedSequence` and `alignedQuality` may be shorter than the full read
5145 * `alignedSequence` and `alignedQuality` may be shorter than the full read 5046 /// sequence and quality. This will occur if the alignment is part of a
5146 * sequence and quality. This will occur if the alignment is part of a 5047 /// chimeric alignment, or if the read was trimmed. When this occurs, the
5147 * chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR 5048 /// CIGAR
5148 * for this read will begin/end with a hard clip operator that will indicate 5049 /// for this read will begin/end with a hard clip operator that will indicate
5149 * the length of the excised sequence. 5050 /// the length of the excised sequence.
5150 */
5151 core.List<core.int> alignedQuality; 5051 core.List<core.int> alignedQuality;
5152 /** 5052
5153 * The bases of the read sequence contained in this alignment record, 5053 /// The bases of the read sequence contained in this alignment record,
5154 * **without CIGAR operations applied** (equivalent to SEQ in SAM). 5054 /// **without CIGAR operations applied** (equivalent to SEQ in SAM).
5155 * `alignedSequence` and `alignedQuality` may be 5055 /// `alignedSequence` and `alignedQuality` may be
5156 * shorter than the full read sequence and quality. This will occur if the 5056 /// shorter than the full read sequence and quality. This will occur if the
5157 * alignment is part of a chimeric alignment, or if the read was trimmed. When 5057 /// alignment is part of a chimeric alignment, or if the read was trimmed.
5158 * this occurs, the CIGAR for this read will begin/end with a hard clip 5058 /// When
5159 * operator that will indicate the length of the excised sequence. 5059 /// this occurs, the CIGAR for this read will begin/end with a hard clip
5160 */ 5060 /// operator that will indicate the length of the excised sequence.
5161 core.String alignedSequence; 5061 core.String alignedSequence;
5162 /** 5062
5163 * The linear alignment for this alignment record. This field is null for 5063 /// The linear alignment for this alignment record. This field is null for
5164 * unmapped reads. 5064 /// unmapped reads.
5165 */
5166 LinearAlignment alignment; 5065 LinearAlignment alignment;
5167 /** The fragment is a PCR or optical duplicate (SAM flag 0x400). */ 5066
5067 /// The fragment is a PCR or optical duplicate (SAM flag 0x400).
5168 core.bool duplicateFragment; 5068 core.bool duplicateFragment;
5169 /** 5069
5170 * Whether this read did not pass filters, such as platform or vendor quality 5070 /// Whether this read did not pass filters, such as platform or vendor
5171 * controls (SAM flag 0x200). 5071 /// quality
5172 */ 5072 /// controls (SAM flag 0x200).
5173 core.bool failedVendorQualityChecks; 5073 core.bool failedVendorQualityChecks;
5174 /** The observed length of the fragment, equivalent to TLEN in SAM. */ 5074
5075 /// The observed length of the fragment, equivalent to TLEN in SAM.
5175 core.int fragmentLength; 5076 core.int fragmentLength;
5176 /** The fragment name. Equivalent to QNAME (query template name) in SAM. */ 5077
5078 /// The fragment name. Equivalent to QNAME (query template name) in SAM.
5177 core.String fragmentName; 5079 core.String fragmentName;
5178 /** 5080
5179 * The server-generated read ID, unique across all reads. This is different 5081 /// The server-generated read ID, unique across all reads. This is different
5180 * from the `fragmentName`. 5082 /// from the `fragmentName`.
5181 */
5182 core.String id; 5083 core.String id;
5183 /** 5084
5184 * A map of additional read alignment information. This must be of the form 5085 /// A map of additional read alignment information. This must be of the form
5185 * map<string, string[]> (string key mapping to a list of string values). 5086 /// map<string, string[]> (string key mapping to a list of string values).
5186 * 5087 ///
5187 * The values for Object must be JSON objects. It can consist of `num`, 5088 /// The values for Object must be JSON objects. It can consist of `num`,
5188 * `String`, `bool` and `null` as well as `Map` and `List` values. 5089 /// `String`, `bool` and `null` as well as `Map` and `List` values.
5189 */
5190 core.Map<core.String, core.List<core.Object>> info; 5090 core.Map<core.String, core.List<core.Object>> info;
5191 /** 5091
5192 * The mapping of the primary alignment of the 5092 /// The mapping of the primary alignment of the
5193 * `(readNumber+1)%numberReads` read in the fragment. It replaces 5093 /// `(readNumber+1)%numberReads` read in the fragment. It replaces
5194 * mate position and mate strand in SAM. 5094 /// mate position and mate strand in SAM.
5195 */
5196 Position nextMatePosition; 5095 Position nextMatePosition;
5197 /** The number of reads in the fragment (extension to SAM flag 0x1). */ 5096
5097 /// The number of reads in the fragment (extension to SAM flag 0x1).
5198 core.int numberReads; 5098 core.int numberReads;
5199 /** 5099
5200 * The orientation and the distance between reads from the fragment are 5100 /// The orientation and the distance between reads from the fragment are
5201 * consistent with the sequencing protocol (SAM flag 0x2). 5101 /// consistent with the sequencing protocol (SAM flag 0x2).
5202 */
5203 core.bool properPlacement; 5102 core.bool properPlacement;
5204 /** 5103
5205 * The ID of the read group this read belongs to. A read belongs to exactly 5104 /// The ID of the read group this read belongs to. A read belongs to exactly
5206 * one read group. This is a server-generated ID which is distinct from SAM's 5105 /// one read group. This is a server-generated ID which is distinct from
5207 * RG tag (for that value, see 5106 /// SAM's
5208 * ReadGroup.name). 5107 /// RG tag (for that value, see
5209 */ 5108 /// ReadGroup.name).
5210 core.String readGroupId; 5109 core.String readGroupId;
5211 /** 5110
5212 * The ID of the read group set this read belongs to. A read belongs to 5111 /// The ID of the read group set this read belongs to. A read belongs to
5213 * exactly one read group set. 5112 /// exactly one read group set.
5214 */
5215 core.String readGroupSetId; 5113 core.String readGroupSetId;
5216 /** 5114
5217 * The read number in sequencing. 0-based and less than numberReads. This 5115 /// The read number in sequencing. 0-based and less than numberReads. This
5218 * field replaces SAM flag 0x40 and 0x80. 5116 /// field replaces SAM flag 0x40 and 0x80.
5219 */
5220 core.int readNumber; 5117 core.int readNumber;
5221 /** 5118
5222 * Whether this alignment is secondary. Equivalent to SAM flag 0x100. 5119 /// Whether this alignment is secondary. Equivalent to SAM flag 0x100.
5223 * A secondary alignment represents an alternative to the primary alignment 5120 /// A secondary alignment represents an alternative to the primary alignment
5224 * for this read. Aligners may return secondary alignments if a read can map 5121 /// for this read. Aligners may return secondary alignments if a read can map
5225 * ambiguously to multiple coordinates in the genome. By convention, each read 5122 /// ambiguously to multiple coordinates in the genome. By convention, each
5226 * has one and only one alignment where both `secondaryAlignment` 5123 /// read
5227 * and `supplementaryAlignment` are false. 5124 /// has one and only one alignment where both `secondaryAlignment`
5228 */ 5125 /// and `supplementaryAlignment` are false.
5229 core.bool secondaryAlignment; 5126 core.bool secondaryAlignment;
5230 /** 5127
5231 * Whether this alignment is supplementary. Equivalent to SAM flag 0x800. 5128 /// Whether this alignment is supplementary. Equivalent to SAM flag 0x800.
5232 * Supplementary alignments are used in the representation of a chimeric 5129 /// Supplementary alignments are used in the representation of a chimeric
5233 * alignment. In a chimeric alignment, a read is split into multiple 5130 /// alignment. In a chimeric alignment, a read is split into multiple
5234 * linear alignments that map to different reference contigs. The first 5131 /// linear alignments that map to different reference contigs. The first
5235 * linear alignment in the read will be designated as the representative 5132 /// linear alignment in the read will be designated as the representative
5236 * alignment; the remaining linear alignments will be designated as 5133 /// alignment; the remaining linear alignments will be designated as
5237 * supplementary alignments. These alignments may have different mapping 5134 /// supplementary alignments. These alignments may have different mapping
5238 * quality scores. In each linear alignment in a chimeric alignment, the read 5135 /// quality scores. In each linear alignment in a chimeric alignment, the
5239 * will be hard clipped. The `alignedSequence` and 5136 /// read
5240 * `alignedQuality` fields in the alignment record will only 5137 /// will be hard clipped. The `alignedSequence` and
5241 * represent the bases for its respective linear alignment. 5138 /// `alignedQuality` fields in the alignment record will only
5242 */ 5139 /// represent the bases for its respective linear alignment.
5243 core.bool supplementaryAlignment; 5140 core.bool supplementaryAlignment;
5244 5141
5245 Read(); 5142 Read();
5246 5143
5247 Read.fromJson(core.Map _json) { 5144 Read.fromJson(core.Map _json) {
5248 if (_json.containsKey("alignedQuality")) { 5145 if (_json.containsKey("alignedQuality")) {
5249 alignedQuality = _json["alignedQuality"]; 5146 alignedQuality = _json["alignedQuality"];
5250 } 5147 }
5251 if (_json.containsKey("alignedSequence")) { 5148 if (_json.containsKey("alignedSequence")) {
5252 alignedSequence = _json["alignedSequence"]; 5149 alignedSequence = _json["alignedSequence"];
(...skipping 39 matching lines...) Expand 10 before | Expand all | Expand 10 after
5292 } 5189 }
5293 if (_json.containsKey("secondaryAlignment")) { 5190 if (_json.containsKey("secondaryAlignment")) {
5294 secondaryAlignment = _json["secondaryAlignment"]; 5191 secondaryAlignment = _json["secondaryAlignment"];
5295 } 5192 }
5296 if (_json.containsKey("supplementaryAlignment")) { 5193 if (_json.containsKey("supplementaryAlignment")) {
5297 supplementaryAlignment = _json["supplementaryAlignment"]; 5194 supplementaryAlignment = _json["supplementaryAlignment"];
5298 } 5195 }
5299 } 5196 }
5300 5197
5301 core.Map<core.String, core.Object> toJson() { 5198 core.Map<core.String, core.Object> toJson() {
5302 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 5199 final core.Map<core.String, core.Object> _json =
5200 new core.Map<core.String, core.Object>();
5303 if (alignedQuality != null) { 5201 if (alignedQuality != null) {
5304 _json["alignedQuality"] = alignedQuality; 5202 _json["alignedQuality"] = alignedQuality;
5305 } 5203 }
5306 if (alignedSequence != null) { 5204 if (alignedSequence != null) {
5307 _json["alignedSequence"] = alignedSequence; 5205 _json["alignedSequence"] = alignedSequence;
5308 } 5206 }
5309 if (alignment != null) { 5207 if (alignment != null) {
5310 _json["alignment"] = (alignment).toJson(); 5208 _json["alignment"] = (alignment).toJson();
5311 } 5209 }
5312 if (duplicateFragment != null) { 5210 if (duplicateFragment != null) {
(...skipping 35 matching lines...) Expand 10 before | Expand all | Expand 10 after
5348 if (secondaryAlignment != null) { 5246 if (secondaryAlignment != null) {
5349 _json["secondaryAlignment"] = secondaryAlignment; 5247 _json["secondaryAlignment"] = secondaryAlignment;
5350 } 5248 }
5351 if (supplementaryAlignment != null) { 5249 if (supplementaryAlignment != null) {
5352 _json["supplementaryAlignment"] = supplementaryAlignment; 5250 _json["supplementaryAlignment"] = supplementaryAlignment;
5353 } 5251 }
5354 return _json; 5252 return _json;
5355 } 5253 }
5356 } 5254 }
5357 5255
5358 /** 5256 /// A read group is all the data that's processed the same way by the
5359 * A read group is all the data that's processed the same way by the sequencer. 5257 /// sequencer.
5360 */
5361 class ReadGroup { 5258 class ReadGroup {
5362 /** The dataset to which this read group belongs. */ 5259 /// The dataset to which this read group belongs.
5363 core.String datasetId; 5260 core.String datasetId;
5364 /** A free-form text description of this read group. */ 5261
5262 /// A free-form text description of this read group.
5365 core.String description; 5263 core.String description;
5366 /** The experiment used to generate this read group. */ 5264
5265 /// The experiment used to generate this read group.
5367 Experiment experiment; 5266 Experiment experiment;
5368 /** 5267
5369 * The server-generated read group ID, unique for all read groups. 5268 /// The server-generated read group ID, unique for all read groups.
5370 * Note: This is different than the @RG ID field in the SAM spec. For that 5269 /// Note: This is different than the @RG ID field in the SAM spec. For that
5371 * value, see name. 5270 /// value, see name.
5372 */
5373 core.String id; 5271 core.String id;
5374 /** 5272
5375 * A map of additional read group information. This must be of the form 5273 /// A map of additional read group information. This must be of the form
5376 * map<string, string[]> (string key mapping to a list of string values). 5274 /// map<string, string[]> (string key mapping to a list of string values).
5377 * 5275 ///
5378 * The values for Object must be JSON objects. It can consist of `num`, 5276 /// The values for Object must be JSON objects. It can consist of `num`,
5379 * `String`, `bool` and `null` as well as `Map` and `List` values. 5277 /// `String`, `bool` and `null` as well as `Map` and `List` values.
5380 */
5381 core.Map<core.String, core.List<core.Object>> info; 5278 core.Map<core.String, core.List<core.Object>> info;
5382 /** 5279
5383 * The read group name. This corresponds to the @RG ID field in the SAM spec. 5280 /// The read group name. This corresponds to the @RG ID field in the SAM
5384 */ 5281 /// spec.
5385 core.String name; 5282 core.String name;
5386 /** 5283
5387 * The predicted insert size of this read group. The insert size is the length 5284 /// The predicted insert size of this read group. The insert size is the
5388 * the sequenced DNA fragment from end-to-end, not including the adapters. 5285 /// length
5389 */ 5286 /// the sequenced DNA fragment from end-to-end, not including the adapters.
5390 core.int predictedInsertSize; 5287 core.int predictedInsertSize;
5391 /** 5288
5392 * The programs used to generate this read group. Programs are always 5289 /// The programs used to generate this read group. Programs are always
5393 * identical for all read groups within a read group set. For this reason, 5290 /// identical for all read groups within a read group set. For this reason,
5394 * only the first read group in a returned set will have this field 5291 /// only the first read group in a returned set will have this field
5395 * populated. 5292 /// populated.
5396 */
5397 core.List<Program> programs; 5293 core.List<Program> programs;
5398 /** The reference set the reads in this read group are aligned to. */ 5294
5295 /// The reference set the reads in this read group are aligned to.
5399 core.String referenceSetId; 5296 core.String referenceSetId;
5400 /** A client-supplied sample identifier for the reads in this read group. */ 5297
5298 /// A client-supplied sample identifier for the reads in this read group.
5401 core.String sampleId; 5299 core.String sampleId;
5402 5300
5403 ReadGroup(); 5301 ReadGroup();
5404 5302
5405 ReadGroup.fromJson(core.Map _json) { 5303 ReadGroup.fromJson(core.Map _json) {
5406 if (_json.containsKey("datasetId")) { 5304 if (_json.containsKey("datasetId")) {
5407 datasetId = _json["datasetId"]; 5305 datasetId = _json["datasetId"];
5408 } 5306 }
5409 if (_json.containsKey("description")) { 5307 if (_json.containsKey("description")) {
5410 description = _json["description"]; 5308 description = _json["description"];
5411 } 5309 }
5412 if (_json.containsKey("experiment")) { 5310 if (_json.containsKey("experiment")) {
5413 experiment = new Experiment.fromJson(_json["experiment"]); 5311 experiment = new Experiment.fromJson(_json["experiment"]);
5414 } 5312 }
5415 if (_json.containsKey("id")) { 5313 if (_json.containsKey("id")) {
5416 id = _json["id"]; 5314 id = _json["id"];
5417 } 5315 }
5418 if (_json.containsKey("info")) { 5316 if (_json.containsKey("info")) {
5419 info = _json["info"]; 5317 info = _json["info"];
5420 } 5318 }
5421 if (_json.containsKey("name")) { 5319 if (_json.containsKey("name")) {
5422 name = _json["name"]; 5320 name = _json["name"];
5423 } 5321 }
5424 if (_json.containsKey("predictedInsertSize")) { 5322 if (_json.containsKey("predictedInsertSize")) {
5425 predictedInsertSize = _json["predictedInsertSize"]; 5323 predictedInsertSize = _json["predictedInsertSize"];
5426 } 5324 }
5427 if (_json.containsKey("programs")) { 5325 if (_json.containsKey("programs")) {
5428 programs = _json["programs"].map((value) => new Program.fromJson(value)).t oList(); 5326 programs = _json["programs"]
5327 .map((value) => new Program.fromJson(value))
5328 .toList();
5429 } 5329 }
5430 if (_json.containsKey("referenceSetId")) { 5330 if (_json.containsKey("referenceSetId")) {
5431 referenceSetId = _json["referenceSetId"]; 5331 referenceSetId = _json["referenceSetId"];
5432 } 5332 }
5433 if (_json.containsKey("sampleId")) { 5333 if (_json.containsKey("sampleId")) {
5434 sampleId = _json["sampleId"]; 5334 sampleId = _json["sampleId"];
5435 } 5335 }
5436 } 5336 }
5437 5337
5438 core.Map<core.String, core.Object> toJson() { 5338 core.Map<core.String, core.Object> toJson() {
5439 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 5339 final core.Map<core.String, core.Object> _json =
5340 new core.Map<core.String, core.Object>();
5440 if (datasetId != null) { 5341 if (datasetId != null) {
5441 _json["datasetId"] = datasetId; 5342 _json["datasetId"] = datasetId;
5442 } 5343 }
5443 if (description != null) { 5344 if (description != null) {
5444 _json["description"] = description; 5345 _json["description"] = description;
5445 } 5346 }
5446 if (experiment != null) { 5347 if (experiment != null) {
5447 _json["experiment"] = (experiment).toJson(); 5348 _json["experiment"] = (experiment).toJson();
5448 } 5349 }
5449 if (id != null) { 5350 if (id != null) {
(...skipping 14 matching lines...) Expand all
5464 if (referenceSetId != null) { 5365 if (referenceSetId != null) {
5465 _json["referenceSetId"] = referenceSetId; 5366 _json["referenceSetId"] = referenceSetId;
5466 } 5367 }
5467 if (sampleId != null) { 5368 if (sampleId != null) {
5468 _json["sampleId"] = sampleId; 5369 _json["sampleId"] = sampleId;
5469 } 5370 }
5470 return _json; 5371 return _json;
5471 } 5372 }
5472 } 5373 }
5473 5374
5474 /** 5375 /// A read group set is a logical collection of read groups, which are
5475 * A read group set is a logical collection of read groups, which are 5376 /// collections of reads produced by a sequencer. A read group set typically
5476 * collections of reads produced by a sequencer. A read group set typically 5377 /// models reads corresponding to one sample, sequenced one way, and aligned
5477 * models reads corresponding to one sample, sequenced one way, and aligned one 5378 /// one
5478 * way. 5379 /// way.
5479 * 5380 ///
5480 * * A read group set belongs to one dataset. 5381 /// * A read group set belongs to one dataset.
5481 * * A read group belongs to one read group set. 5382 /// * A read group belongs to one read group set.
5482 * * A read belongs to one read group. 5383 /// * A read belongs to one read group.
5483 * 5384 ///
5484 * For more genomics resource definitions, see [Fundamentals of Google 5385 /// For more genomics resource definitions, see [Fundamentals of Google
5485 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 5386 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
5486 */
5487 class ReadGroupSet { 5387 class ReadGroupSet {
5488 /** The dataset to which this read group set belongs. */ 5388 /// The dataset to which this read group set belongs.
5489 core.String datasetId; 5389 core.String datasetId;
5490 /** 5390
5491 * The filename of the original source file for this read group set, if any. 5391 /// The filename of the original source file for this read group set, if any.
5492 */
5493 core.String filename; 5392 core.String filename;
5494 /** 5393
5495 * The server-generated read group set ID, unique for all read group sets. 5394 /// The server-generated read group set ID, unique for all read group sets.
5496 */
5497 core.String id; 5395 core.String id;
5498 /** 5396
5499 * A map of additional read group set information. 5397 /// A map of additional read group set information.
5500 * 5398 ///
5501 * The values for Object must be JSON objects. It can consist of `num`, 5399 /// The values for Object must be JSON objects. It can consist of `num`,
5502 * `String`, `bool` and `null` as well as `Map` and `List` values. 5400 /// `String`, `bool` and `null` as well as `Map` and `List` values.
5503 */
5504 core.Map<core.String, core.List<core.Object>> info; 5401 core.Map<core.String, core.List<core.Object>> info;
5505 /** 5402
5506 * The read group set name. By default this will be initialized to the sample 5403 /// The read group set name. By default this will be initialized to the
5507 * name of the sequenced data contained in this set. 5404 /// sample
5508 */ 5405 /// name of the sequenced data contained in this set.
5509 core.String name; 5406 core.String name;
5510 /** 5407
5511 * The read groups in this set. There are typically 1-10 read groups in a read 5408 /// The read groups in this set. There are typically 1-10 read groups in a
5512 * group set. 5409 /// read
5513 */ 5410 /// group set.
5514 core.List<ReadGroup> readGroups; 5411 core.List<ReadGroup> readGroups;
5515 /** 5412
5516 * The reference set to which the reads in this read group set are aligned. 5413 /// The reference set to which the reads in this read group set are aligned.
5517 */
5518 core.String referenceSetId; 5414 core.String referenceSetId;
5519 5415
5520 ReadGroupSet(); 5416 ReadGroupSet();
5521 5417
5522 ReadGroupSet.fromJson(core.Map _json) { 5418 ReadGroupSet.fromJson(core.Map _json) {
5523 if (_json.containsKey("datasetId")) { 5419 if (_json.containsKey("datasetId")) {
5524 datasetId = _json["datasetId"]; 5420 datasetId = _json["datasetId"];
5525 } 5421 }
5526 if (_json.containsKey("filename")) { 5422 if (_json.containsKey("filename")) {
5527 filename = _json["filename"]; 5423 filename = _json["filename"];
5528 } 5424 }
5529 if (_json.containsKey("id")) { 5425 if (_json.containsKey("id")) {
5530 id = _json["id"]; 5426 id = _json["id"];
5531 } 5427 }
5532 if (_json.containsKey("info")) { 5428 if (_json.containsKey("info")) {
5533 info = _json["info"]; 5429 info = _json["info"];
5534 } 5430 }
5535 if (_json.containsKey("name")) { 5431 if (_json.containsKey("name")) {
5536 name = _json["name"]; 5432 name = _json["name"];
5537 } 5433 }
5538 if (_json.containsKey("readGroups")) { 5434 if (_json.containsKey("readGroups")) {
5539 readGroups = _json["readGroups"].map((value) => new ReadGroup.fromJson(val ue)).toList(); 5435 readGroups = _json["readGroups"]
5436 .map((value) => new ReadGroup.fromJson(value))
5437 .toList();
5540 } 5438 }
5541 if (_json.containsKey("referenceSetId")) { 5439 if (_json.containsKey("referenceSetId")) {
5542 referenceSetId = _json["referenceSetId"]; 5440 referenceSetId = _json["referenceSetId"];
5543 } 5441 }
5544 } 5442 }
5545 5443
5546 core.Map<core.String, core.Object> toJson() { 5444 core.Map<core.String, core.Object> toJson() {
5547 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 5445 final core.Map<core.String, core.Object> _json =
5446 new core.Map<core.String, core.Object>();
5548 if (datasetId != null) { 5447 if (datasetId != null) {
5549 _json["datasetId"] = datasetId; 5448 _json["datasetId"] = datasetId;
5550 } 5449 }
5551 if (filename != null) { 5450 if (filename != null) {
5552 _json["filename"] = filename; 5451 _json["filename"] = filename;
5553 } 5452 }
5554 if (id != null) { 5453 if (id != null) {
5555 _json["id"] = id; 5454 _json["id"] = id;
5556 } 5455 }
5557 if (info != null) { 5456 if (info != null) {
5558 _json["info"] = info; 5457 _json["info"] = info;
5559 } 5458 }
5560 if (name != null) { 5459 if (name != null) {
5561 _json["name"] = name; 5460 _json["name"] = name;
5562 } 5461 }
5563 if (readGroups != null) { 5462 if (readGroups != null) {
5564 _json["readGroups"] = readGroups.map((value) => (value).toJson()).toList() ; 5463 _json["readGroups"] =
5464 readGroups.map((value) => (value).toJson()).toList();
5565 } 5465 }
5566 if (referenceSetId != null) { 5466 if (referenceSetId != null) {
5567 _json["referenceSetId"] = referenceSetId; 5467 _json["referenceSetId"] = referenceSetId;
5568 } 5468 }
5569 return _json; 5469 return _json;
5570 } 5470 }
5571 } 5471 }
5572 5472
5573 /** 5473 /// A reference is a canonical assembled DNA sequence, intended to act as a
5574 * A reference is a canonical assembled DNA sequence, intended to act as a 5474 /// reference coordinate space for other genomic annotations. A single
5575 * reference coordinate space for other genomic annotations. A single reference 5475 /// reference
5576 * might represent the human chromosome 1 or mitochandrial DNA, for instance. A 5476 /// might represent the human chromosome 1 or mitochandrial DNA, for instance.
5577 * reference belongs to one or more reference sets. 5477 /// A
5578 * 5478 /// reference belongs to one or more reference sets.
5579 * For more genomics resource definitions, see [Fundamentals of Google 5479 ///
5580 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 5480 /// For more genomics resource definitions, see [Fundamentals of Google
5581 */ 5481 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
5582 class Reference { 5482 class Reference {
5583 /** The server-generated reference ID, unique across all references. */ 5483 /// The server-generated reference ID, unique across all references.
5584 core.String id; 5484 core.String id;
5585 /** The length of this reference's sequence. */ 5485
5486 /// The length of this reference's sequence.
5586 core.String length; 5487 core.String length;
5587 /** 5488
5588 * MD5 of the upper-case sequence excluding all whitespace characters (this 5489 /// MD5 of the upper-case sequence excluding all whitespace characters (this
5589 * is equivalent to SQ:M5 in SAM). This value is represented in lower case 5490 /// is equivalent to SQ:M5 in SAM). This value is represented in lower case
5590 * hexadecimal format. 5491 /// hexadecimal format.
5591 */
5592 core.String md5checksum; 5492 core.String md5checksum;
5593 /** The name of this reference, for example `22`. */ 5493
5494 /// The name of this reference, for example `22`.
5594 core.String name; 5495 core.String name;
5595 /** 5496
5596 * ID from http://www.ncbi.nlm.nih.gov/taxonomy. For example, 9606 for human. 5497 /// ID from http://www.ncbi.nlm.nih.gov/taxonomy. For example, 9606 for
5597 */ 5498 /// human.
5598 core.int ncbiTaxonId; 5499 core.int ncbiTaxonId;
5599 /** 5500
5600 * All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally 5501 /// All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
5601 * with a version number, for example `GCF_000001405.26`. 5502 /// with a version number, for example `GCF_000001405.26`.
5602 */
5603 core.List<core.String> sourceAccessions; 5503 core.List<core.String> sourceAccessions;
5604 /** 5504
5605 * The URI from which the sequence was obtained. Typically specifies a FASTA 5505 /// The URI from which the sequence was obtained. Typically specifies a FASTA
5606 * format file. 5506 /// format file.
5607 */
5608 core.String sourceUri; 5507 core.String sourceUri;
5609 5508
5610 Reference(); 5509 Reference();
5611 5510
5612 Reference.fromJson(core.Map _json) { 5511 Reference.fromJson(core.Map _json) {
5613 if (_json.containsKey("id")) { 5512 if (_json.containsKey("id")) {
5614 id = _json["id"]; 5513 id = _json["id"];
5615 } 5514 }
5616 if (_json.containsKey("length")) { 5515 if (_json.containsKey("length")) {
5617 length = _json["length"]; 5516 length = _json["length"];
5618 } 5517 }
5619 if (_json.containsKey("md5checksum")) { 5518 if (_json.containsKey("md5checksum")) {
5620 md5checksum = _json["md5checksum"]; 5519 md5checksum = _json["md5checksum"];
5621 } 5520 }
5622 if (_json.containsKey("name")) { 5521 if (_json.containsKey("name")) {
5623 name = _json["name"]; 5522 name = _json["name"];
5624 } 5523 }
5625 if (_json.containsKey("ncbiTaxonId")) { 5524 if (_json.containsKey("ncbiTaxonId")) {
5626 ncbiTaxonId = _json["ncbiTaxonId"]; 5525 ncbiTaxonId = _json["ncbiTaxonId"];
5627 } 5526 }
5628 if (_json.containsKey("sourceAccessions")) { 5527 if (_json.containsKey("sourceAccessions")) {
5629 sourceAccessions = _json["sourceAccessions"]; 5528 sourceAccessions = _json["sourceAccessions"];
5630 } 5529 }
5631 if (_json.containsKey("sourceUri")) { 5530 if (_json.containsKey("sourceUri")) {
5632 sourceUri = _json["sourceUri"]; 5531 sourceUri = _json["sourceUri"];
5633 } 5532 }
5634 } 5533 }
5635 5534
5636 core.Map<core.String, core.Object> toJson() { 5535 core.Map<core.String, core.Object> toJson() {
5637 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 5536 final core.Map<core.String, core.Object> _json =
5537 new core.Map<core.String, core.Object>();
5638 if (id != null) { 5538 if (id != null) {
5639 _json["id"] = id; 5539 _json["id"] = id;
5640 } 5540 }
5641 if (length != null) { 5541 if (length != null) {
5642 _json["length"] = length; 5542 _json["length"] = length;
5643 } 5543 }
5644 if (md5checksum != null) { 5544 if (md5checksum != null) {
5645 _json["md5checksum"] = md5checksum; 5545 _json["md5checksum"] = md5checksum;
5646 } 5546 }
5647 if (name != null) { 5547 if (name != null) {
5648 _json["name"] = name; 5548 _json["name"] = name;
5649 } 5549 }
5650 if (ncbiTaxonId != null) { 5550 if (ncbiTaxonId != null) {
5651 _json["ncbiTaxonId"] = ncbiTaxonId; 5551 _json["ncbiTaxonId"] = ncbiTaxonId;
5652 } 5552 }
5653 if (sourceAccessions != null) { 5553 if (sourceAccessions != null) {
5654 _json["sourceAccessions"] = sourceAccessions; 5554 _json["sourceAccessions"] = sourceAccessions;
5655 } 5555 }
5656 if (sourceUri != null) { 5556 if (sourceUri != null) {
5657 _json["sourceUri"] = sourceUri; 5557 _json["sourceUri"] = sourceUri;
5658 } 5558 }
5659 return _json; 5559 return _json;
5660 } 5560 }
5661 } 5561 }
5662 5562
5663 /** 5563 /// ReferenceBound records an upper bound for the starting coordinate of
5664 * ReferenceBound records an upper bound for the starting coordinate of 5564 /// variants in a particular reference.
5665 * variants in a particular reference.
5666 */
5667 class ReferenceBound { 5565 class ReferenceBound {
5668 /** The name of the reference associated with this reference bound. */ 5566 /// The name of the reference associated with this reference bound.
5669 core.String referenceName; 5567 core.String referenceName;
5670 /** 5568
5671 * An upper bound (inclusive) on the starting coordinate of any 5569 /// An upper bound (inclusive) on the starting coordinate of any
5672 * variant in the reference sequence. 5570 /// variant in the reference sequence.
5673 */
5674 core.String upperBound; 5571 core.String upperBound;
5675 5572
5676 ReferenceBound(); 5573 ReferenceBound();
5677 5574
5678 ReferenceBound.fromJson(core.Map _json) { 5575 ReferenceBound.fromJson(core.Map _json) {
5679 if (_json.containsKey("referenceName")) { 5576 if (_json.containsKey("referenceName")) {
5680 referenceName = _json["referenceName"]; 5577 referenceName = _json["referenceName"];
5681 } 5578 }
5682 if (_json.containsKey("upperBound")) { 5579 if (_json.containsKey("upperBound")) {
5683 upperBound = _json["upperBound"]; 5580 upperBound = _json["upperBound"];
5684 } 5581 }
5685 } 5582 }
5686 5583
5687 core.Map<core.String, core.Object> toJson() { 5584 core.Map<core.String, core.Object> toJson() {
5688 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 5585 final core.Map<core.String, core.Object> _json =
5586 new core.Map<core.String, core.Object>();
5689 if (referenceName != null) { 5587 if (referenceName != null) {
5690 _json["referenceName"] = referenceName; 5588 _json["referenceName"] = referenceName;
5691 } 5589 }
5692 if (upperBound != null) { 5590 if (upperBound != null) {
5693 _json["upperBound"] = upperBound; 5591 _json["upperBound"] = upperBound;
5694 } 5592 }
5695 return _json; 5593 return _json;
5696 } 5594 }
5697 } 5595 }
5698 5596
5699 /** 5597 /// A reference set is a set of references which typically comprise a reference
5700 * A reference set is a set of references which typically comprise a reference 5598 /// assembly for a species, such as `GRCh38` which is representative
5701 * assembly for a species, such as `GRCh38` which is representative 5599 /// of the human genome. A reference set defines a common coordinate space for
5702 * of the human genome. A reference set defines a common coordinate space for 5600 /// comparing reference-aligned experimental data. A reference set contains 1
5703 * comparing reference-aligned experimental data. A reference set contains 1 or 5601 /// or
5704 * more references. 5602 /// more references.
5705 * 5603 ///
5706 * For more genomics resource definitions, see [Fundamentals of Google 5604 /// For more genomics resource definitions, see [Fundamentals of Google
5707 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 5605 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
5708 */
5709 class ReferenceSet { 5606 class ReferenceSet {
5710 /** Public id of this reference set, such as `GRCh37`. */ 5607 /// Public id of this reference set, such as `GRCh37`.
5711 core.String assemblyId; 5608 core.String assemblyId;
5712 /** Free text description of this reference set. */ 5609
5610 /// Free text description of this reference set.
5713 core.String description; 5611 core.String description;
5714 /** 5612
5715 * The server-generated reference set ID, unique across all reference sets. 5613 /// The server-generated reference set ID, unique across all reference sets.
5716 */
5717 core.String id; 5614 core.String id;
5718 /** 5615
5719 * Order-independent MD5 checksum which identifies this reference set. The 5616 /// Order-independent MD5 checksum which identifies this reference set. The
5720 * checksum is computed by sorting all lower case hexidecimal string 5617 /// checksum is computed by sorting all lower case hexidecimal string
5721 * `reference.md5checksum` (for all reference in this set) in 5618 /// `reference.md5checksum` (for all reference in this set) in
5722 * ascending lexicographic order, concatenating, and taking the MD5 of that 5619 /// ascending lexicographic order, concatenating, and taking the MD5 of that
5723 * value. The resulting value is represented in lower case hexadecimal format. 5620 /// value. The resulting value is represented in lower case hexadecimal
5724 */ 5621 /// format.
5725 core.String md5checksum; 5622 core.String md5checksum;
5726 /** 5623
5727 * ID from http://www.ncbi.nlm.nih.gov/taxonomy (for example, 9606 for human) 5624 /// ID from http://www.ncbi.nlm.nih.gov/taxonomy (for example, 9606 for
5728 * indicating the species which this reference set is intended to model. Note 5625 /// human)
5729 * that contained references may specify a different `ncbiTaxonId`, as 5626 /// indicating the species which this reference set is intended to model.
5730 * assemblies may contain reference sequences which do not belong to the 5627 /// Note
5731 * modeled species, for example EBV in a human reference genome. 5628 /// that contained references may specify a different `ncbiTaxonId`, as
5732 */ 5629 /// assemblies may contain reference sequences which do not belong to the
5630 /// modeled species, for example EBV in a human reference genome.
5733 core.int ncbiTaxonId; 5631 core.int ncbiTaxonId;
5734 /** 5632
5735 * The IDs of the reference objects that are part of this set. 5633 /// The IDs of the reference objects that are part of this set.
5736 * `Reference.md5checksum` must be unique within this set. 5634 /// `Reference.md5checksum` must be unique within this set.
5737 */
5738 core.List<core.String> referenceIds; 5635 core.List<core.String> referenceIds;
5739 /** 5636
5740 * All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally 5637 /// All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
5741 * with a version number, for example `NC_000001.11`. 5638 /// with a version number, for example `NC_000001.11`.
5742 */
5743 core.List<core.String> sourceAccessions; 5639 core.List<core.String> sourceAccessions;
5744 /** The URI from which the references were obtained. */ 5640
5641 /// The URI from which the references were obtained.
5745 core.String sourceUri; 5642 core.String sourceUri;
5746 5643
5747 ReferenceSet(); 5644 ReferenceSet();
5748 5645
5749 ReferenceSet.fromJson(core.Map _json) { 5646 ReferenceSet.fromJson(core.Map _json) {
5750 if (_json.containsKey("assemblyId")) { 5647 if (_json.containsKey("assemblyId")) {
5751 assemblyId = _json["assemblyId"]; 5648 assemblyId = _json["assemblyId"];
5752 } 5649 }
5753 if (_json.containsKey("description")) { 5650 if (_json.containsKey("description")) {
5754 description = _json["description"]; 5651 description = _json["description"];
(...skipping 12 matching lines...) Expand all
5767 } 5664 }
5768 if (_json.containsKey("sourceAccessions")) { 5665 if (_json.containsKey("sourceAccessions")) {
5769 sourceAccessions = _json["sourceAccessions"]; 5666 sourceAccessions = _json["sourceAccessions"];
5770 } 5667 }
5771 if (_json.containsKey("sourceUri")) { 5668 if (_json.containsKey("sourceUri")) {
5772 sourceUri = _json["sourceUri"]; 5669 sourceUri = _json["sourceUri"];
5773 } 5670 }
5774 } 5671 }
5775 5672
5776 core.Map<core.String, core.Object> toJson() { 5673 core.Map<core.String, core.Object> toJson() {
5777 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 5674 final core.Map<core.String, core.Object> _json =
5675 new core.Map<core.String, core.Object>();
5778 if (assemblyId != null) { 5676 if (assemblyId != null) {
5779 _json["assemblyId"] = assemblyId; 5677 _json["assemblyId"] = assemblyId;
5780 } 5678 }
5781 if (description != null) { 5679 if (description != null) {
5782 _json["description"] = description; 5680 _json["description"] = description;
5783 } 5681 }
5784 if (id != null) { 5682 if (id != null) {
5785 _json["id"] = id; 5683 _json["id"] = id;
5786 } 5684 }
5787 if (md5checksum != null) { 5685 if (md5checksum != null) {
5788 _json["md5checksum"] = md5checksum; 5686 _json["md5checksum"] = md5checksum;
5789 } 5687 }
5790 if (ncbiTaxonId != null) { 5688 if (ncbiTaxonId != null) {
5791 _json["ncbiTaxonId"] = ncbiTaxonId; 5689 _json["ncbiTaxonId"] = ncbiTaxonId;
5792 } 5690 }
5793 if (referenceIds != null) { 5691 if (referenceIds != null) {
5794 _json["referenceIds"] = referenceIds; 5692 _json["referenceIds"] = referenceIds;
5795 } 5693 }
5796 if (sourceAccessions != null) { 5694 if (sourceAccessions != null) {
5797 _json["sourceAccessions"] = sourceAccessions; 5695 _json["sourceAccessions"] = sourceAccessions;
5798 } 5696 }
5799 if (sourceUri != null) { 5697 if (sourceUri != null) {
5800 _json["sourceUri"] = sourceUri; 5698 _json["sourceUri"] = sourceUri;
5801 } 5699 }
5802 return _json; 5700 return _json;
5803 } 5701 }
5804 } 5702 }
5805 5703
5806 /** 5704 /// Runtime metadata that will be populated in the
5807 * Runtime metadata that will be populated in the 5705 /// runtimeMetadata
5808 * runtimeMetadata 5706 /// field of the Operation associated with a RunPipeline execution.
5809 * field of the Operation associated with a RunPipeline execution.
5810 */
5811 class RuntimeMetadata { 5707 class RuntimeMetadata {
5812 /** Execution information specific to Google Compute Engine. */ 5708 /// Execution information specific to Google Compute Engine.
5813 ComputeEngine computeEngine; 5709 ComputeEngine computeEngine;
5814 5710
5815 RuntimeMetadata(); 5711 RuntimeMetadata();
5816 5712
5817 RuntimeMetadata.fromJson(core.Map _json) { 5713 RuntimeMetadata.fromJson(core.Map _json) {
5818 if (_json.containsKey("computeEngine")) { 5714 if (_json.containsKey("computeEngine")) {
5819 computeEngine = new ComputeEngine.fromJson(_json["computeEngine"]); 5715 computeEngine = new ComputeEngine.fromJson(_json["computeEngine"]);
5820 } 5716 }
5821 } 5717 }
5822 5718
5823 core.Map<core.String, core.Object> toJson() { 5719 core.Map<core.String, core.Object> toJson() {
5824 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 5720 final core.Map<core.String, core.Object> _json =
5721 new core.Map<core.String, core.Object>();
5825 if (computeEngine != null) { 5722 if (computeEngine != null) {
5826 _json["computeEngine"] = (computeEngine).toJson(); 5723 _json["computeEngine"] = (computeEngine).toJson();
5827 } 5724 }
5828 return _json; 5725 return _json;
5829 } 5726 }
5830 } 5727 }
5831 5728
5832 class SearchAnnotationSetsRequest { 5729 class SearchAnnotationSetsRequest {
5833 /** 5730 /// Required. The dataset IDs to search within. Caller must have `READ`
5834 * Required. The dataset IDs to search within. Caller must have `READ` access 5731 /// access
5835 * to these datasets. 5732 /// to these datasets.
5836 */
5837 core.List<core.String> datasetIds; 5733 core.List<core.String> datasetIds;
5838 /** 5734
5839 * Only return annotations sets for which a substring of the name matches this 5735 /// Only return annotations sets for which a substring of the name matches
5840 * string (case insensitive). 5736 /// this
5841 */ 5737 /// string (case insensitive).
5842 core.String name; 5738 core.String name;
5843 /** 5739
5844 * The maximum number of results to return in a single page. If unspecified, 5740 /// The maximum number of results to return in a single page. If unspecified,
5845 * defaults to 128. The maximum value is 1024. 5741 /// defaults to 128. The maximum value is 1024.
5846 */
5847 core.int pageSize; 5742 core.int pageSize;
5848 /** 5743
5849 * The continuation token, which is used to page through large result sets. 5744 /// The continuation token, which is used to page through large result sets.
5850 * To get the next page of results, set this parameter to the value of 5745 /// To get the next page of results, set this parameter to the value of
5851 * `nextPageToken` from the previous response. 5746 /// `nextPageToken` from the previous response.
5852 */
5853 core.String pageToken; 5747 core.String pageToken;
5854 /** 5748
5855 * If specified, only annotation sets associated with the given reference set 5749 /// If specified, only annotation sets associated with the given reference
5856 * are returned. 5750 /// set
5857 */ 5751 /// are returned.
5858 core.String referenceSetId; 5752 core.String referenceSetId;
5859 /** 5753
5860 * If specified, only annotation sets that have any of these types are 5754 /// If specified, only annotation sets that have any of these types are
5861 * returned. 5755 /// returned.
5862 */
5863 core.List<core.String> types; 5756 core.List<core.String> types;
5864 5757
5865 SearchAnnotationSetsRequest(); 5758 SearchAnnotationSetsRequest();
5866 5759
5867 SearchAnnotationSetsRequest.fromJson(core.Map _json) { 5760 SearchAnnotationSetsRequest.fromJson(core.Map _json) {
5868 if (_json.containsKey("datasetIds")) { 5761 if (_json.containsKey("datasetIds")) {
5869 datasetIds = _json["datasetIds"]; 5762 datasetIds = _json["datasetIds"];
5870 } 5763 }
5871 if (_json.containsKey("name")) { 5764 if (_json.containsKey("name")) {
5872 name = _json["name"]; 5765 name = _json["name"];
5873 } 5766 }
5874 if (_json.containsKey("pageSize")) { 5767 if (_json.containsKey("pageSize")) {
5875 pageSize = _json["pageSize"]; 5768 pageSize = _json["pageSize"];
5876 } 5769 }
5877 if (_json.containsKey("pageToken")) { 5770 if (_json.containsKey("pageToken")) {
5878 pageToken = _json["pageToken"]; 5771 pageToken = _json["pageToken"];
5879 } 5772 }
5880 if (_json.containsKey("referenceSetId")) { 5773 if (_json.containsKey("referenceSetId")) {
5881 referenceSetId = _json["referenceSetId"]; 5774 referenceSetId = _json["referenceSetId"];
5882 } 5775 }
5883 if (_json.containsKey("types")) { 5776 if (_json.containsKey("types")) {
5884 types = _json["types"]; 5777 types = _json["types"];
5885 } 5778 }
5886 } 5779 }
5887 5780
5888 core.Map<core.String, core.Object> toJson() { 5781 core.Map<core.String, core.Object> toJson() {
5889 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 5782 final core.Map<core.String, core.Object> _json =
5783 new core.Map<core.String, core.Object>();
5890 if (datasetIds != null) { 5784 if (datasetIds != null) {
5891 _json["datasetIds"] = datasetIds; 5785 _json["datasetIds"] = datasetIds;
5892 } 5786 }
5893 if (name != null) { 5787 if (name != null) {
5894 _json["name"] = name; 5788 _json["name"] = name;
5895 } 5789 }
5896 if (pageSize != null) { 5790 if (pageSize != null) {
5897 _json["pageSize"] = pageSize; 5791 _json["pageSize"] = pageSize;
5898 } 5792 }
5899 if (pageToken != null) { 5793 if (pageToken != null) {
5900 _json["pageToken"] = pageToken; 5794 _json["pageToken"] = pageToken;
5901 } 5795 }
5902 if (referenceSetId != null) { 5796 if (referenceSetId != null) {
5903 _json["referenceSetId"] = referenceSetId; 5797 _json["referenceSetId"] = referenceSetId;
5904 } 5798 }
5905 if (types != null) { 5799 if (types != null) {
5906 _json["types"] = types; 5800 _json["types"] = types;
5907 } 5801 }
5908 return _json; 5802 return _json;
5909 } 5803 }
5910 } 5804 }
5911 5805
5912 class SearchAnnotationSetsResponse { 5806 class SearchAnnotationSetsResponse {
5913 /** The matching annotation sets. */ 5807 /// The matching annotation sets.
5914 core.List<AnnotationSet> annotationSets; 5808 core.List<AnnotationSet> annotationSets;
5915 /** 5809
5916 * The continuation token, which is used to page through large result sets. 5810 /// The continuation token, which is used to page through large result sets.
5917 * Provide this value in a subsequent request to return the next page of 5811 /// Provide this value in a subsequent request to return the next page of
5918 * results. This field will be empty if there aren't any additional results. 5812 /// results. This field will be empty if there aren't any additional results.
5919 */
5920 core.String nextPageToken; 5813 core.String nextPageToken;
5921 5814
5922 SearchAnnotationSetsResponse(); 5815 SearchAnnotationSetsResponse();
5923 5816
5924 SearchAnnotationSetsResponse.fromJson(core.Map _json) { 5817 SearchAnnotationSetsResponse.fromJson(core.Map _json) {
5925 if (_json.containsKey("annotationSets")) { 5818 if (_json.containsKey("annotationSets")) {
5926 annotationSets = _json["annotationSets"].map((value) => new AnnotationSet. fromJson(value)).toList(); 5819 annotationSets = _json["annotationSets"]
5820 .map((value) => new AnnotationSet.fromJson(value))
5821 .toList();
5927 } 5822 }
5928 if (_json.containsKey("nextPageToken")) { 5823 if (_json.containsKey("nextPageToken")) {
5929 nextPageToken = _json["nextPageToken"]; 5824 nextPageToken = _json["nextPageToken"];
5930 } 5825 }
5931 } 5826 }
5932 5827
5933 core.Map<core.String, core.Object> toJson() { 5828 core.Map<core.String, core.Object> toJson() {
5934 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 5829 final core.Map<core.String, core.Object> _json =
5830 new core.Map<core.String, core.Object>();
5935 if (annotationSets != null) { 5831 if (annotationSets != null) {
5936 _json["annotationSets"] = annotationSets.map((value) => (value).toJson()). toList(); 5832 _json["annotationSets"] =
5833 annotationSets.map((value) => (value).toJson()).toList();
5937 } 5834 }
5938 if (nextPageToken != null) { 5835 if (nextPageToken != null) {
5939 _json["nextPageToken"] = nextPageToken; 5836 _json["nextPageToken"] = nextPageToken;
5940 } 5837 }
5941 return _json; 5838 return _json;
5942 } 5839 }
5943 } 5840 }
5944 5841
5945 class SearchAnnotationsRequest { 5842 class SearchAnnotationsRequest {
5946 /** 5843 /// Required. The annotation sets to search within. The caller must have
5947 * Required. The annotation sets to search within. The caller must have 5844 /// `READ` access to these annotation sets.
5948 * `READ` access to these annotation sets. 5845 /// All queried annotation sets must have the same type.
5949 * All queried annotation sets must have the same type.
5950 */
5951 core.List<core.String> annotationSetIds; 5846 core.List<core.String> annotationSetIds;
5952 /** 5847
5953 * The end position of the range on the reference, 0-based exclusive. If 5848 /// The end position of the range on the reference, 0-based exclusive. If
5954 * referenceId or 5849 /// referenceId or
5955 * referenceName 5850 /// referenceName
5956 * must be specified, Defaults to the length of the reference. 5851 /// must be specified, Defaults to the length of the reference.
5957 */
5958 core.String end; 5852 core.String end;
5959 /** 5853
5960 * The maximum number of results to return in a single page. If unspecified, 5854 /// The maximum number of results to return in a single page. If unspecified,
5961 * defaults to 256. The maximum value is 2048. 5855 /// defaults to 256. The maximum value is 2048.
5962 */
5963 core.int pageSize; 5856 core.int pageSize;
5964 /** 5857
5965 * The continuation token, which is used to page through large result sets. 5858 /// The continuation token, which is used to page through large result sets.
5966 * To get the next page of results, set this parameter to the value of 5859 /// To get the next page of results, set this parameter to the value of
5967 * `nextPageToken` from the previous response. 5860 /// `nextPageToken` from the previous response.
5968 */
5969 core.String pageToken; 5861 core.String pageToken;
5970 /** The ID of the reference to query. */ 5862
5863 /// The ID of the reference to query.
5971 core.String referenceId; 5864 core.String referenceId;
5972 /** 5865
5973 * The name of the reference to query, within the reference set associated 5866 /// The name of the reference to query, within the reference set associated
5974 * with this query. 5867 /// with this query.
5975 */
5976 core.String referenceName; 5868 core.String referenceName;
5977 /** 5869
5978 * The start position of the range on the reference, 0-based inclusive. If 5870 /// The start position of the range on the reference, 0-based inclusive. If
5979 * specified, 5871 /// specified,
5980 * referenceId or 5872 /// referenceId or
5981 * referenceName 5873 /// referenceName
5982 * must be specified. Defaults to 0. 5874 /// must be specified. Defaults to 0.
5983 */
5984 core.String start; 5875 core.String start;
5985 5876
5986 SearchAnnotationsRequest(); 5877 SearchAnnotationsRequest();
5987 5878
5988 SearchAnnotationsRequest.fromJson(core.Map _json) { 5879 SearchAnnotationsRequest.fromJson(core.Map _json) {
5989 if (_json.containsKey("annotationSetIds")) { 5880 if (_json.containsKey("annotationSetIds")) {
5990 annotationSetIds = _json["annotationSetIds"]; 5881 annotationSetIds = _json["annotationSetIds"];
5991 } 5882 }
5992 if (_json.containsKey("end")) { 5883 if (_json.containsKey("end")) {
5993 end = _json["end"]; 5884 end = _json["end"];
5994 } 5885 }
5995 if (_json.containsKey("pageSize")) { 5886 if (_json.containsKey("pageSize")) {
5996 pageSize = _json["pageSize"]; 5887 pageSize = _json["pageSize"];
5997 } 5888 }
5998 if (_json.containsKey("pageToken")) { 5889 if (_json.containsKey("pageToken")) {
5999 pageToken = _json["pageToken"]; 5890 pageToken = _json["pageToken"];
6000 } 5891 }
6001 if (_json.containsKey("referenceId")) { 5892 if (_json.containsKey("referenceId")) {
6002 referenceId = _json["referenceId"]; 5893 referenceId = _json["referenceId"];
6003 } 5894 }
6004 if (_json.containsKey("referenceName")) { 5895 if (_json.containsKey("referenceName")) {
6005 referenceName = _json["referenceName"]; 5896 referenceName = _json["referenceName"];
6006 } 5897 }
6007 if (_json.containsKey("start")) { 5898 if (_json.containsKey("start")) {
6008 start = _json["start"]; 5899 start = _json["start"];
6009 } 5900 }
6010 } 5901 }
6011 5902
6012 core.Map<core.String, core.Object> toJson() { 5903 core.Map<core.String, core.Object> toJson() {
6013 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 5904 final core.Map<core.String, core.Object> _json =
5905 new core.Map<core.String, core.Object>();
6014 if (annotationSetIds != null) { 5906 if (annotationSetIds != null) {
6015 _json["annotationSetIds"] = annotationSetIds; 5907 _json["annotationSetIds"] = annotationSetIds;
6016 } 5908 }
6017 if (end != null) { 5909 if (end != null) {
6018 _json["end"] = end; 5910 _json["end"] = end;
6019 } 5911 }
6020 if (pageSize != null) { 5912 if (pageSize != null) {
6021 _json["pageSize"] = pageSize; 5913 _json["pageSize"] = pageSize;
6022 } 5914 }
6023 if (pageToken != null) { 5915 if (pageToken != null) {
6024 _json["pageToken"] = pageToken; 5916 _json["pageToken"] = pageToken;
6025 } 5917 }
6026 if (referenceId != null) { 5918 if (referenceId != null) {
6027 _json["referenceId"] = referenceId; 5919 _json["referenceId"] = referenceId;
6028 } 5920 }
6029 if (referenceName != null) { 5921 if (referenceName != null) {
6030 _json["referenceName"] = referenceName; 5922 _json["referenceName"] = referenceName;
6031 } 5923 }
6032 if (start != null) { 5924 if (start != null) {
6033 _json["start"] = start; 5925 _json["start"] = start;
6034 } 5926 }
6035 return _json; 5927 return _json;
6036 } 5928 }
6037 } 5929 }
6038 5930
6039 class SearchAnnotationsResponse { 5931 class SearchAnnotationsResponse {
6040 /** The matching annotations. */ 5932 /// The matching annotations.
6041 core.List<Annotation> annotations; 5933 core.List<Annotation> annotations;
6042 /** 5934
6043 * The continuation token, which is used to page through large result sets. 5935 /// The continuation token, which is used to page through large result sets.
6044 * Provide this value in a subsequent request to return the next page of 5936 /// Provide this value in a subsequent request to return the next page of
6045 * results. This field will be empty if there aren't any additional results. 5937 /// results. This field will be empty if there aren't any additional results.
6046 */
6047 core.String nextPageToken; 5938 core.String nextPageToken;
6048 5939
6049 SearchAnnotationsResponse(); 5940 SearchAnnotationsResponse();
6050 5941
6051 SearchAnnotationsResponse.fromJson(core.Map _json) { 5942 SearchAnnotationsResponse.fromJson(core.Map _json) {
6052 if (_json.containsKey("annotations")) { 5943 if (_json.containsKey("annotations")) {
6053 annotations = _json["annotations"].map((value) => new Annotation.fromJson( value)).toList(); 5944 annotations = _json["annotations"]
5945 .map((value) => new Annotation.fromJson(value))
5946 .toList();
6054 } 5947 }
6055 if (_json.containsKey("nextPageToken")) { 5948 if (_json.containsKey("nextPageToken")) {
6056 nextPageToken = _json["nextPageToken"]; 5949 nextPageToken = _json["nextPageToken"];
6057 } 5950 }
6058 } 5951 }
6059 5952
6060 core.Map<core.String, core.Object> toJson() { 5953 core.Map<core.String, core.Object> toJson() {
6061 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 5954 final core.Map<core.String, core.Object> _json =
5955 new core.Map<core.String, core.Object>();
6062 if (annotations != null) { 5956 if (annotations != null) {
6063 _json["annotations"] = annotations.map((value) => (value).toJson()).toList (); 5957 _json["annotations"] =
5958 annotations.map((value) => (value).toJson()).toList();
6064 } 5959 }
6065 if (nextPageToken != null) { 5960 if (nextPageToken != null) {
6066 _json["nextPageToken"] = nextPageToken; 5961 _json["nextPageToken"] = nextPageToken;
6067 } 5962 }
6068 return _json; 5963 return _json;
6069 } 5964 }
6070 } 5965 }
6071 5966
6072 /** The call set search request. */ 5967 /// The call set search request.
6073 class SearchCallSetsRequest { 5968 class SearchCallSetsRequest {
6074 /** 5969 /// Only return call sets for which a substring of the name matches this
6075 * Only return call sets for which a substring of the name matches this 5970 /// string.
6076 * string.
6077 */
6078 core.String name; 5971 core.String name;
6079 /** 5972
6080 * The maximum number of results to return in a single page. If unspecified, 5973 /// The maximum number of results to return in a single page. If unspecified,
6081 * defaults to 1024. 5974 /// defaults to 1024.
6082 */
6083 core.int pageSize; 5975 core.int pageSize;
6084 /** 5976
6085 * The continuation token, which is used to page through large result sets. 5977 /// The continuation token, which is used to page through large result sets.
6086 * To get the next page of results, set this parameter to the value of 5978 /// To get the next page of results, set this parameter to the value of
6087 * `nextPageToken` from the previous response. 5979 /// `nextPageToken` from the previous response.
6088 */
6089 core.String pageToken; 5980 core.String pageToken;
6090 /** 5981
6091 * Restrict the query to call sets within the given variant sets. At least one 5982 /// Restrict the query to call sets within the given variant sets. At least
6092 * ID must be provided. 5983 /// one
6093 */ 5984 /// ID must be provided.
6094 core.List<core.String> variantSetIds; 5985 core.List<core.String> variantSetIds;
6095 5986
6096 SearchCallSetsRequest(); 5987 SearchCallSetsRequest();
6097 5988
6098 SearchCallSetsRequest.fromJson(core.Map _json) { 5989 SearchCallSetsRequest.fromJson(core.Map _json) {
6099 if (_json.containsKey("name")) { 5990 if (_json.containsKey("name")) {
6100 name = _json["name"]; 5991 name = _json["name"];
6101 } 5992 }
6102 if (_json.containsKey("pageSize")) { 5993 if (_json.containsKey("pageSize")) {
6103 pageSize = _json["pageSize"]; 5994 pageSize = _json["pageSize"];
6104 } 5995 }
6105 if (_json.containsKey("pageToken")) { 5996 if (_json.containsKey("pageToken")) {
6106 pageToken = _json["pageToken"]; 5997 pageToken = _json["pageToken"];
6107 } 5998 }
6108 if (_json.containsKey("variantSetIds")) { 5999 if (_json.containsKey("variantSetIds")) {
6109 variantSetIds = _json["variantSetIds"]; 6000 variantSetIds = _json["variantSetIds"];
6110 } 6001 }
6111 } 6002 }
6112 6003
6113 core.Map<core.String, core.Object> toJson() { 6004 core.Map<core.String, core.Object> toJson() {
6114 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 6005 final core.Map<core.String, core.Object> _json =
6006 new core.Map<core.String, core.Object>();
6115 if (name != null) { 6007 if (name != null) {
6116 _json["name"] = name; 6008 _json["name"] = name;
6117 } 6009 }
6118 if (pageSize != null) { 6010 if (pageSize != null) {
6119 _json["pageSize"] = pageSize; 6011 _json["pageSize"] = pageSize;
6120 } 6012 }
6121 if (pageToken != null) { 6013 if (pageToken != null) {
6122 _json["pageToken"] = pageToken; 6014 _json["pageToken"] = pageToken;
6123 } 6015 }
6124 if (variantSetIds != null) { 6016 if (variantSetIds != null) {
6125 _json["variantSetIds"] = variantSetIds; 6017 _json["variantSetIds"] = variantSetIds;
6126 } 6018 }
6127 return _json; 6019 return _json;
6128 } 6020 }
6129 } 6021 }
6130 6022
6131 /** The call set search response. */ 6023 /// The call set search response.
6132 class SearchCallSetsResponse { 6024 class SearchCallSetsResponse {
6133 /** The list of matching call sets. */ 6025 /// The list of matching call sets.
6134 core.List<CallSet> callSets; 6026 core.List<CallSet> callSets;
6135 /** 6027
6136 * The continuation token, which is used to page through large result sets. 6028 /// The continuation token, which is used to page through large result sets.
6137 * Provide this value in a subsequent request to return the next page of 6029 /// Provide this value in a subsequent request to return the next page of
6138 * results. This field will be empty if there aren't any additional results. 6030 /// results. This field will be empty if there aren't any additional results.
6139 */
6140 core.String nextPageToken; 6031 core.String nextPageToken;
6141 6032
6142 SearchCallSetsResponse(); 6033 SearchCallSetsResponse();
6143 6034
6144 SearchCallSetsResponse.fromJson(core.Map _json) { 6035 SearchCallSetsResponse.fromJson(core.Map _json) {
6145 if (_json.containsKey("callSets")) { 6036 if (_json.containsKey("callSets")) {
6146 callSets = _json["callSets"].map((value) => new CallSet.fromJson(value)).t oList(); 6037 callSets = _json["callSets"]
6038 .map((value) => new CallSet.fromJson(value))
6039 .toList();
6147 } 6040 }
6148 if (_json.containsKey("nextPageToken")) { 6041 if (_json.containsKey("nextPageToken")) {
6149 nextPageToken = _json["nextPageToken"]; 6042 nextPageToken = _json["nextPageToken"];
6150 } 6043 }
6151 } 6044 }
6152 6045
6153 core.Map<core.String, core.Object> toJson() { 6046 core.Map<core.String, core.Object> toJson() {
6154 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 6047 final core.Map<core.String, core.Object> _json =
6048 new core.Map<core.String, core.Object>();
6155 if (callSets != null) { 6049 if (callSets != null) {
6156 _json["callSets"] = callSets.map((value) => (value).toJson()).toList(); 6050 _json["callSets"] = callSets.map((value) => (value).toJson()).toList();
6157 } 6051 }
6158 if (nextPageToken != null) { 6052 if (nextPageToken != null) {
6159 _json["nextPageToken"] = nextPageToken; 6053 _json["nextPageToken"] = nextPageToken;
6160 } 6054 }
6161 return _json; 6055 return _json;
6162 } 6056 }
6163 } 6057 }
6164 6058
6165 /** The read group set search request. */ 6059 /// The read group set search request.
6166 class SearchReadGroupSetsRequest { 6060 class SearchReadGroupSetsRequest {
6167 /** 6061 /// Restricts this query to read group sets within the given datasets. At
6168 * Restricts this query to read group sets within the given datasets. At least 6062 /// least
6169 * one ID must be provided. 6063 /// one ID must be provided.
6170 */
6171 core.List<core.String> datasetIds; 6064 core.List<core.String> datasetIds;
6172 /** 6065
6173 * Only return read group sets for which a substring of the name matches this 6066 /// Only return read group sets for which a substring of the name matches
6174 * string. 6067 /// this
6175 */ 6068 /// string.
6176 core.String name; 6069 core.String name;
6177 /** 6070
6178 * The maximum number of results to return in a single page. If unspecified, 6071 /// The maximum number of results to return in a single page. If unspecified,
6179 * defaults to 256. The maximum value is 1024. 6072 /// defaults to 256. The maximum value is 1024.
6180 */
6181 core.int pageSize; 6073 core.int pageSize;
6182 /** 6074
6183 * The continuation token, which is used to page through large result sets. 6075 /// The continuation token, which is used to page through large result sets.
6184 * To get the next page of results, set this parameter to the value of 6076 /// To get the next page of results, set this parameter to the value of
6185 * `nextPageToken` from the previous response. 6077 /// `nextPageToken` from the previous response.
6186 */
6187 core.String pageToken; 6078 core.String pageToken;
6188 6079
6189 SearchReadGroupSetsRequest(); 6080 SearchReadGroupSetsRequest();
6190 6081
6191 SearchReadGroupSetsRequest.fromJson(core.Map _json) { 6082 SearchReadGroupSetsRequest.fromJson(core.Map _json) {
6192 if (_json.containsKey("datasetIds")) { 6083 if (_json.containsKey("datasetIds")) {
6193 datasetIds = _json["datasetIds"]; 6084 datasetIds = _json["datasetIds"];
6194 } 6085 }
6195 if (_json.containsKey("name")) { 6086 if (_json.containsKey("name")) {
6196 name = _json["name"]; 6087 name = _json["name"];
6197 } 6088 }
6198 if (_json.containsKey("pageSize")) { 6089 if (_json.containsKey("pageSize")) {
6199 pageSize = _json["pageSize"]; 6090 pageSize = _json["pageSize"];
6200 } 6091 }
6201 if (_json.containsKey("pageToken")) { 6092 if (_json.containsKey("pageToken")) {
6202 pageToken = _json["pageToken"]; 6093 pageToken = _json["pageToken"];
6203 } 6094 }
6204 } 6095 }
6205 6096
6206 core.Map<core.String, core.Object> toJson() { 6097 core.Map<core.String, core.Object> toJson() {
6207 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 6098 final core.Map<core.String, core.Object> _json =
6099 new core.Map<core.String, core.Object>();
6208 if (datasetIds != null) { 6100 if (datasetIds != null) {
6209 _json["datasetIds"] = datasetIds; 6101 _json["datasetIds"] = datasetIds;
6210 } 6102 }
6211 if (name != null) { 6103 if (name != null) {
6212 _json["name"] = name; 6104 _json["name"] = name;
6213 } 6105 }
6214 if (pageSize != null) { 6106 if (pageSize != null) {
6215 _json["pageSize"] = pageSize; 6107 _json["pageSize"] = pageSize;
6216 } 6108 }
6217 if (pageToken != null) { 6109 if (pageToken != null) {
6218 _json["pageToken"] = pageToken; 6110 _json["pageToken"] = pageToken;
6219 } 6111 }
6220 return _json; 6112 return _json;
6221 } 6113 }
6222 } 6114 }
6223 6115
6224 /** The read group set search response. */ 6116 /// The read group set search response.
6225 class SearchReadGroupSetsResponse { 6117 class SearchReadGroupSetsResponse {
6226 /** 6118 /// The continuation token, which is used to page through large result sets.
6227 * The continuation token, which is used to page through large result sets. 6119 /// Provide this value in a subsequent request to return the next page of
6228 * Provide this value in a subsequent request to return the next page of 6120 /// results. This field will be empty if there aren't any additional results.
6229 * results. This field will be empty if there aren't any additional results.
6230 */
6231 core.String nextPageToken; 6121 core.String nextPageToken;
6232 /** The list of matching read group sets. */ 6122
6123 /// The list of matching read group sets.
6233 core.List<ReadGroupSet> readGroupSets; 6124 core.List<ReadGroupSet> readGroupSets;
6234 6125
6235 SearchReadGroupSetsResponse(); 6126 SearchReadGroupSetsResponse();
6236 6127
6237 SearchReadGroupSetsResponse.fromJson(core.Map _json) { 6128 SearchReadGroupSetsResponse.fromJson(core.Map _json) {
6238 if (_json.containsKey("nextPageToken")) { 6129 if (_json.containsKey("nextPageToken")) {
6239 nextPageToken = _json["nextPageToken"]; 6130 nextPageToken = _json["nextPageToken"];
6240 } 6131 }
6241 if (_json.containsKey("readGroupSets")) { 6132 if (_json.containsKey("readGroupSets")) {
6242 readGroupSets = _json["readGroupSets"].map((value) => new ReadGroupSet.fro mJson(value)).toList(); 6133 readGroupSets = _json["readGroupSets"]
6134 .map((value) => new ReadGroupSet.fromJson(value))
6135 .toList();
6243 } 6136 }
6244 } 6137 }
6245 6138
6246 core.Map<core.String, core.Object> toJson() { 6139 core.Map<core.String, core.Object> toJson() {
6247 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 6140 final core.Map<core.String, core.Object> _json =
6141 new core.Map<core.String, core.Object>();
6248 if (nextPageToken != null) { 6142 if (nextPageToken != null) {
6249 _json["nextPageToken"] = nextPageToken; 6143 _json["nextPageToken"] = nextPageToken;
6250 } 6144 }
6251 if (readGroupSets != null) { 6145 if (readGroupSets != null) {
6252 _json["readGroupSets"] = readGroupSets.map((value) => (value).toJson()).to List(); 6146 _json["readGroupSets"] =
6147 readGroupSets.map((value) => (value).toJson()).toList();
6253 } 6148 }
6254 return _json; 6149 return _json;
6255 } 6150 }
6256 } 6151 }
6257 6152
6258 /** The read search request. */ 6153 /// The read search request.
6259 class SearchReadsRequest { 6154 class SearchReadsRequest {
6260 /** 6155 /// The end position of the range on the reference, 0-based exclusive. If
6261 * The end position of the range on the reference, 0-based exclusive. If 6156 /// specified, `referenceName` must also be specified.
6262 * specified, `referenceName` must also be specified.
6263 */
6264 core.String end; 6157 core.String end;
6265 /** 6158
6266 * The maximum number of results to return in a single page. If unspecified, 6159 /// The maximum number of results to return in a single page. If unspecified,
6267 * defaults to 256. The maximum value is 2048. 6160 /// defaults to 256. The maximum value is 2048.
6268 */
6269 core.int pageSize; 6161 core.int pageSize;
6270 /** 6162
6271 * The continuation token, which is used to page through large result sets. 6163 /// The continuation token, which is used to page through large result sets.
6272 * To get the next page of results, set this parameter to the value of 6164 /// To get the next page of results, set this parameter to the value of
6273 * `nextPageToken` from the previous response. 6165 /// `nextPageToken` from the previous response.
6274 */
6275 core.String pageToken; 6166 core.String pageToken;
6276 /** 6167
6277 * The IDs of the read groups within which to search for reads. All specified 6168 /// The IDs of the read groups within which to search for reads. All
6278 * read groups must belong to the same read group sets. Must specify one of 6169 /// specified
6279 * `readGroupSetIds` or `readGroupIds`. 6170 /// read groups must belong to the same read group sets. Must specify one of
6280 */ 6171 /// `readGroupSetIds` or `readGroupIds`.
6281 core.List<core.String> readGroupIds; 6172 core.List<core.String> readGroupIds;
6282 /** 6173
6283 * The IDs of the read groups sets within which to search for reads. All 6174 /// The IDs of the read groups sets within which to search for reads. All
6284 * specified read group sets must be aligned against a common set of reference 6175 /// specified read group sets must be aligned against a common set of
6285 * sequences; this defines the genomic coordinates for the query. Must specify 6176 /// reference
6286 * one of `readGroupSetIds` or `readGroupIds`. 6177 /// sequences; this defines the genomic coordinates for the query. Must
6287 */ 6178 /// specify
6179 /// one of `readGroupSetIds` or `readGroupIds`.
6288 core.List<core.String> readGroupSetIds; 6180 core.List<core.String> readGroupSetIds;
6289 /** 6181
6290 * The reference sequence name, for example `chr1`, `1`, or `chrX`. If set to 6182 /// The reference sequence name, for example `chr1`, `1`, or `chrX`. If set
6291 * `*`, only unmapped reads are returned. If unspecified, all reads (mapped 6183 /// to
6292 * and unmapped) are returned. 6184 /// `*`, only unmapped reads are returned. If unspecified, all reads (mapped
6293 */ 6185 /// and unmapped) are returned.
6294 core.String referenceName; 6186 core.String referenceName;
6295 /** 6187
6296 * The start position of the range on the reference, 0-based inclusive. If 6188 /// The start position of the range on the reference, 0-based inclusive. If
6297 * specified, `referenceName` must also be specified. 6189 /// specified, `referenceName` must also be specified.
6298 */
6299 core.String start; 6190 core.String start;
6300 6191
6301 SearchReadsRequest(); 6192 SearchReadsRequest();
6302 6193
6303 SearchReadsRequest.fromJson(core.Map _json) { 6194 SearchReadsRequest.fromJson(core.Map _json) {
6304 if (_json.containsKey("end")) { 6195 if (_json.containsKey("end")) {
6305 end = _json["end"]; 6196 end = _json["end"];
6306 } 6197 }
6307 if (_json.containsKey("pageSize")) { 6198 if (_json.containsKey("pageSize")) {
6308 pageSize = _json["pageSize"]; 6199 pageSize = _json["pageSize"];
6309 } 6200 }
6310 if (_json.containsKey("pageToken")) { 6201 if (_json.containsKey("pageToken")) {
6311 pageToken = _json["pageToken"]; 6202 pageToken = _json["pageToken"];
6312 } 6203 }
6313 if (_json.containsKey("readGroupIds")) { 6204 if (_json.containsKey("readGroupIds")) {
6314 readGroupIds = _json["readGroupIds"]; 6205 readGroupIds = _json["readGroupIds"];
6315 } 6206 }
6316 if (_json.containsKey("readGroupSetIds")) { 6207 if (_json.containsKey("readGroupSetIds")) {
6317 readGroupSetIds = _json["readGroupSetIds"]; 6208 readGroupSetIds = _json["readGroupSetIds"];
6318 } 6209 }
6319 if (_json.containsKey("referenceName")) { 6210 if (_json.containsKey("referenceName")) {
6320 referenceName = _json["referenceName"]; 6211 referenceName = _json["referenceName"];
6321 } 6212 }
6322 if (_json.containsKey("start")) { 6213 if (_json.containsKey("start")) {
6323 start = _json["start"]; 6214 start = _json["start"];
6324 } 6215 }
6325 } 6216 }
6326 6217
6327 core.Map<core.String, core.Object> toJson() { 6218 core.Map<core.String, core.Object> toJson() {
6328 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 6219 final core.Map<core.String, core.Object> _json =
6220 new core.Map<core.String, core.Object>();
6329 if (end != null) { 6221 if (end != null) {
6330 _json["end"] = end; 6222 _json["end"] = end;
6331 } 6223 }
6332 if (pageSize != null) { 6224 if (pageSize != null) {
6333 _json["pageSize"] = pageSize; 6225 _json["pageSize"] = pageSize;
6334 } 6226 }
6335 if (pageToken != null) { 6227 if (pageToken != null) {
6336 _json["pageToken"] = pageToken; 6228 _json["pageToken"] = pageToken;
6337 } 6229 }
6338 if (readGroupIds != null) { 6230 if (readGroupIds != null) {
6339 _json["readGroupIds"] = readGroupIds; 6231 _json["readGroupIds"] = readGroupIds;
6340 } 6232 }
6341 if (readGroupSetIds != null) { 6233 if (readGroupSetIds != null) {
6342 _json["readGroupSetIds"] = readGroupSetIds; 6234 _json["readGroupSetIds"] = readGroupSetIds;
6343 } 6235 }
6344 if (referenceName != null) { 6236 if (referenceName != null) {
6345 _json["referenceName"] = referenceName; 6237 _json["referenceName"] = referenceName;
6346 } 6238 }
6347 if (start != null) { 6239 if (start != null) {
6348 _json["start"] = start; 6240 _json["start"] = start;
6349 } 6241 }
6350 return _json; 6242 return _json;
6351 } 6243 }
6352 } 6244 }
6353 6245
6354 /** The read search response. */ 6246 /// The read search response.
6355 class SearchReadsResponse { 6247 class SearchReadsResponse {
6356 /** 6248 /// The list of matching alignments sorted by mapped genomic coordinate,
6357 * The list of matching alignments sorted by mapped genomic coordinate, 6249 /// if any, ascending in position within the same reference. Unmapped reads,
6358 * if any, ascending in position within the same reference. Unmapped reads, 6250 /// which have no position, are returned contiguously and are sorted in
6359 * which have no position, are returned contiguously and are sorted in 6251 /// ascending lexicographic order by fragment name.
6360 * ascending lexicographic order by fragment name.
6361 */
6362 core.List<Read> alignments; 6252 core.List<Read> alignments;
6363 /** 6253
6364 * The continuation token, which is used to page through large result sets. 6254 /// The continuation token, which is used to page through large result sets.
6365 * Provide this value in a subsequent request to return the next page of 6255 /// Provide this value in a subsequent request to return the next page of
6366 * results. This field will be empty if there aren't any additional results. 6256 /// results. This field will be empty if there aren't any additional results.
6367 */
6368 core.String nextPageToken; 6257 core.String nextPageToken;
6369 6258
6370 SearchReadsResponse(); 6259 SearchReadsResponse();
6371 6260
6372 SearchReadsResponse.fromJson(core.Map _json) { 6261 SearchReadsResponse.fromJson(core.Map _json) {
6373 if (_json.containsKey("alignments")) { 6262 if (_json.containsKey("alignments")) {
6374 alignments = _json["alignments"].map((value) => new Read.fromJson(value)). toList(); 6263 alignments =
6264 _json["alignments"].map((value) => new Read.fromJson(value)).toList();
6375 } 6265 }
6376 if (_json.containsKey("nextPageToken")) { 6266 if (_json.containsKey("nextPageToken")) {
6377 nextPageToken = _json["nextPageToken"]; 6267 nextPageToken = _json["nextPageToken"];
6378 } 6268 }
6379 } 6269 }
6380 6270
6381 core.Map<core.String, core.Object> toJson() { 6271 core.Map<core.String, core.Object> toJson() {
6382 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 6272 final core.Map<core.String, core.Object> _json =
6273 new core.Map<core.String, core.Object>();
6383 if (alignments != null) { 6274 if (alignments != null) {
6384 _json["alignments"] = alignments.map((value) => (value).toJson()).toList() ; 6275 _json["alignments"] =
6276 alignments.map((value) => (value).toJson()).toList();
6385 } 6277 }
6386 if (nextPageToken != null) { 6278 if (nextPageToken != null) {
6387 _json["nextPageToken"] = nextPageToken; 6279 _json["nextPageToken"] = nextPageToken;
6388 } 6280 }
6389 return _json; 6281 return _json;
6390 } 6282 }
6391 } 6283 }
6392 6284
6393 class SearchReferenceSetsRequest { 6285 class SearchReferenceSetsRequest {
6394 /** 6286 /// If present, return reference sets for which a prefix of any of
6395 * If present, return reference sets for which a prefix of any of 6287 /// sourceAccessions
6396 * sourceAccessions 6288 /// match any of these strings. Accession numbers typically have a main
6397 * match any of these strings. Accession numbers typically have a main number 6289 /// number
6398 * and a version, for example `NC_000001.11`. 6290 /// and a version, for example `NC_000001.11`.
6399 */
6400 core.List<core.String> accessions; 6291 core.List<core.String> accessions;
6401 /** 6292
6402 * If present, return reference sets for which a substring of their 6293 /// If present, return reference sets for which a substring of their
6403 * `assemblyId` matches this string (case insensitive). 6294 /// `assemblyId` matches this string (case insensitive).
6404 */
6405 core.String assemblyId; 6295 core.String assemblyId;
6406 /** 6296
6407 * If present, return reference sets for which the 6297 /// If present, return reference sets for which the
6408 * md5checksum matches exactly. 6298 /// md5checksum matches exactly.
6409 */
6410 core.List<core.String> md5checksums; 6299 core.List<core.String> md5checksums;
6411 /** 6300
6412 * The maximum number of results to return in a single page. If unspecified, 6301 /// The maximum number of results to return in a single page. If unspecified,
6413 * defaults to 1024. The maximum value is 4096. 6302 /// defaults to 1024. The maximum value is 4096.
6414 */
6415 core.int pageSize; 6303 core.int pageSize;
6416 /** 6304
6417 * The continuation token, which is used to page through large result sets. 6305 /// The continuation token, which is used to page through large result sets.
6418 * To get the next page of results, set this parameter to the value of 6306 /// To get the next page of results, set this parameter to the value of
6419 * `nextPageToken` from the previous response. 6307 /// `nextPageToken` from the previous response.
6420 */
6421 core.String pageToken; 6308 core.String pageToken;
6422 6309
6423 SearchReferenceSetsRequest(); 6310 SearchReferenceSetsRequest();
6424 6311
6425 SearchReferenceSetsRequest.fromJson(core.Map _json) { 6312 SearchReferenceSetsRequest.fromJson(core.Map _json) {
6426 if (_json.containsKey("accessions")) { 6313 if (_json.containsKey("accessions")) {
6427 accessions = _json["accessions"]; 6314 accessions = _json["accessions"];
6428 } 6315 }
6429 if (_json.containsKey("assemblyId")) { 6316 if (_json.containsKey("assemblyId")) {
6430 assemblyId = _json["assemblyId"]; 6317 assemblyId = _json["assemblyId"];
6431 } 6318 }
6432 if (_json.containsKey("md5checksums")) { 6319 if (_json.containsKey("md5checksums")) {
6433 md5checksums = _json["md5checksums"]; 6320 md5checksums = _json["md5checksums"];
6434 } 6321 }
6435 if (_json.containsKey("pageSize")) { 6322 if (_json.containsKey("pageSize")) {
6436 pageSize = _json["pageSize"]; 6323 pageSize = _json["pageSize"];
6437 } 6324 }
6438 if (_json.containsKey("pageToken")) { 6325 if (_json.containsKey("pageToken")) {
6439 pageToken = _json["pageToken"]; 6326 pageToken = _json["pageToken"];
6440 } 6327 }
6441 } 6328 }
6442 6329
6443 core.Map<core.String, core.Object> toJson() { 6330 core.Map<core.String, core.Object> toJson() {
6444 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 6331 final core.Map<core.String, core.Object> _json =
6332 new core.Map<core.String, core.Object>();
6445 if (accessions != null) { 6333 if (accessions != null) {
6446 _json["accessions"] = accessions; 6334 _json["accessions"] = accessions;
6447 } 6335 }
6448 if (assemblyId != null) { 6336 if (assemblyId != null) {
6449 _json["assemblyId"] = assemblyId; 6337 _json["assemblyId"] = assemblyId;
6450 } 6338 }
6451 if (md5checksums != null) { 6339 if (md5checksums != null) {
6452 _json["md5checksums"] = md5checksums; 6340 _json["md5checksums"] = md5checksums;
6453 } 6341 }
6454 if (pageSize != null) { 6342 if (pageSize != null) {
6455 _json["pageSize"] = pageSize; 6343 _json["pageSize"] = pageSize;
6456 } 6344 }
6457 if (pageToken != null) { 6345 if (pageToken != null) {
6458 _json["pageToken"] = pageToken; 6346 _json["pageToken"] = pageToken;
6459 } 6347 }
6460 return _json; 6348 return _json;
6461 } 6349 }
6462 } 6350 }
6463 6351
6464 class SearchReferenceSetsResponse { 6352 class SearchReferenceSetsResponse {
6465 /** 6353 /// The continuation token, which is used to page through large result sets.
6466 * The continuation token, which is used to page through large result sets. 6354 /// Provide this value in a subsequent request to return the next page of
6467 * Provide this value in a subsequent request to return the next page of 6355 /// results. This field will be empty if there aren't any additional results.
6468 * results. This field will be empty if there aren't any additional results.
6469 */
6470 core.String nextPageToken; 6356 core.String nextPageToken;
6471 /** The matching references sets. */ 6357
6358 /// The matching references sets.
6472 core.List<ReferenceSet> referenceSets; 6359 core.List<ReferenceSet> referenceSets;
6473 6360
6474 SearchReferenceSetsResponse(); 6361 SearchReferenceSetsResponse();
6475 6362
6476 SearchReferenceSetsResponse.fromJson(core.Map _json) { 6363 SearchReferenceSetsResponse.fromJson(core.Map _json) {
6477 if (_json.containsKey("nextPageToken")) { 6364 if (_json.containsKey("nextPageToken")) {
6478 nextPageToken = _json["nextPageToken"]; 6365 nextPageToken = _json["nextPageToken"];
6479 } 6366 }
6480 if (_json.containsKey("referenceSets")) { 6367 if (_json.containsKey("referenceSets")) {
6481 referenceSets = _json["referenceSets"].map((value) => new ReferenceSet.fro mJson(value)).toList(); 6368 referenceSets = _json["referenceSets"]
6369 .map((value) => new ReferenceSet.fromJson(value))
6370 .toList();
6482 } 6371 }
6483 } 6372 }
6484 6373
6485 core.Map<core.String, core.Object> toJson() { 6374 core.Map<core.String, core.Object> toJson() {
6486 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 6375 final core.Map<core.String, core.Object> _json =
6376 new core.Map<core.String, core.Object>();
6487 if (nextPageToken != null) { 6377 if (nextPageToken != null) {
6488 _json["nextPageToken"] = nextPageToken; 6378 _json["nextPageToken"] = nextPageToken;
6489 } 6379 }
6490 if (referenceSets != null) { 6380 if (referenceSets != null) {
6491 _json["referenceSets"] = referenceSets.map((value) => (value).toJson()).to List(); 6381 _json["referenceSets"] =
6382 referenceSets.map((value) => (value).toJson()).toList();
6492 } 6383 }
6493 return _json; 6384 return _json;
6494 } 6385 }
6495 } 6386 }
6496 6387
6497 class SearchReferencesRequest { 6388 class SearchReferencesRequest {
6498 /** 6389 /// If present, return references for which a prefix of any of
6499 * If present, return references for which a prefix of any of 6390 /// sourceAccessions match
6500 * sourceAccessions match 6391 /// any of these strings. Accession numbers typically have a main number and
6501 * any of these strings. Accession numbers typically have a main number and a 6392 /// a
6502 * version, for example `GCF_000001405.26`. 6393 /// version, for example `GCF_000001405.26`.
6503 */
6504 core.List<core.String> accessions; 6394 core.List<core.String> accessions;
6505 /** 6395
6506 * If present, return references for which the 6396 /// If present, return references for which the
6507 * md5checksum matches exactly. 6397 /// md5checksum matches exactly.
6508 */
6509 core.List<core.String> md5checksums; 6398 core.List<core.String> md5checksums;
6510 /** 6399
6511 * The maximum number of results to return in a single page. If unspecified, 6400 /// The maximum number of results to return in a single page. If unspecified,
6512 * defaults to 1024. The maximum value is 4096. 6401 /// defaults to 1024. The maximum value is 4096.
6513 */
6514 core.int pageSize; 6402 core.int pageSize;
6515 /** 6403
6516 * The continuation token, which is used to page through large result sets. 6404 /// The continuation token, which is used to page through large result sets.
6517 * To get the next page of results, set this parameter to the value of 6405 /// To get the next page of results, set this parameter to the value of
6518 * `nextPageToken` from the previous response. 6406 /// `nextPageToken` from the previous response.
6519 */
6520 core.String pageToken; 6407 core.String pageToken;
6521 /** If present, return only references which belong to this reference set. */ 6408
6409 /// If present, return only references which belong to this reference set.
6522 core.String referenceSetId; 6410 core.String referenceSetId;
6523 6411
6524 SearchReferencesRequest(); 6412 SearchReferencesRequest();
6525 6413
6526 SearchReferencesRequest.fromJson(core.Map _json) { 6414 SearchReferencesRequest.fromJson(core.Map _json) {
6527 if (_json.containsKey("accessions")) { 6415 if (_json.containsKey("accessions")) {
6528 accessions = _json["accessions"]; 6416 accessions = _json["accessions"];
6529 } 6417 }
6530 if (_json.containsKey("md5checksums")) { 6418 if (_json.containsKey("md5checksums")) {
6531 md5checksums = _json["md5checksums"]; 6419 md5checksums = _json["md5checksums"];
6532 } 6420 }
6533 if (_json.containsKey("pageSize")) { 6421 if (_json.containsKey("pageSize")) {
6534 pageSize = _json["pageSize"]; 6422 pageSize = _json["pageSize"];
6535 } 6423 }
6536 if (_json.containsKey("pageToken")) { 6424 if (_json.containsKey("pageToken")) {
6537 pageToken = _json["pageToken"]; 6425 pageToken = _json["pageToken"];
6538 } 6426 }
6539 if (_json.containsKey("referenceSetId")) { 6427 if (_json.containsKey("referenceSetId")) {
6540 referenceSetId = _json["referenceSetId"]; 6428 referenceSetId = _json["referenceSetId"];
6541 } 6429 }
6542 } 6430 }
6543 6431
6544 core.Map<core.String, core.Object> toJson() { 6432 core.Map<core.String, core.Object> toJson() {
6545 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 6433 final core.Map<core.String, core.Object> _json =
6434 new core.Map<core.String, core.Object>();
6546 if (accessions != null) { 6435 if (accessions != null) {
6547 _json["accessions"] = accessions; 6436 _json["accessions"] = accessions;
6548 } 6437 }
6549 if (md5checksums != null) { 6438 if (md5checksums != null) {
6550 _json["md5checksums"] = md5checksums; 6439 _json["md5checksums"] = md5checksums;
6551 } 6440 }
6552 if (pageSize != null) { 6441 if (pageSize != null) {
6553 _json["pageSize"] = pageSize; 6442 _json["pageSize"] = pageSize;
6554 } 6443 }
6555 if (pageToken != null) { 6444 if (pageToken != null) {
6556 _json["pageToken"] = pageToken; 6445 _json["pageToken"] = pageToken;
6557 } 6446 }
6558 if (referenceSetId != null) { 6447 if (referenceSetId != null) {
6559 _json["referenceSetId"] = referenceSetId; 6448 _json["referenceSetId"] = referenceSetId;
6560 } 6449 }
6561 return _json; 6450 return _json;
6562 } 6451 }
6563 } 6452 }
6564 6453
6565 class SearchReferencesResponse { 6454 class SearchReferencesResponse {
6566 /** 6455 /// The continuation token, which is used to page through large result sets.
6567 * The continuation token, which is used to page through large result sets. 6456 /// Provide this value in a subsequent request to return the next page of
6568 * Provide this value in a subsequent request to return the next page of 6457 /// results. This field will be empty if there aren't any additional results.
6569 * results. This field will be empty if there aren't any additional results.
6570 */
6571 core.String nextPageToken; 6458 core.String nextPageToken;
6572 /** The matching references. */ 6459
6460 /// The matching references.
6573 core.List<Reference> references; 6461 core.List<Reference> references;
6574 6462
6575 SearchReferencesResponse(); 6463 SearchReferencesResponse();
6576 6464
6577 SearchReferencesResponse.fromJson(core.Map _json) { 6465 SearchReferencesResponse.fromJson(core.Map _json) {
6578 if (_json.containsKey("nextPageToken")) { 6466 if (_json.containsKey("nextPageToken")) {
6579 nextPageToken = _json["nextPageToken"]; 6467 nextPageToken = _json["nextPageToken"];
6580 } 6468 }
6581 if (_json.containsKey("references")) { 6469 if (_json.containsKey("references")) {
6582 references = _json["references"].map((value) => new Reference.fromJson(val ue)).toList(); 6470 references = _json["references"]
6471 .map((value) => new Reference.fromJson(value))
6472 .toList();
6583 } 6473 }
6584 } 6474 }
6585 6475
6586 core.Map<core.String, core.Object> toJson() { 6476 core.Map<core.String, core.Object> toJson() {
6587 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 6477 final core.Map<core.String, core.Object> _json =
6478 new core.Map<core.String, core.Object>();
6588 if (nextPageToken != null) { 6479 if (nextPageToken != null) {
6589 _json["nextPageToken"] = nextPageToken; 6480 _json["nextPageToken"] = nextPageToken;
6590 } 6481 }
6591 if (references != null) { 6482 if (references != null) {
6592 _json["references"] = references.map((value) => (value).toJson()).toList() ; 6483 _json["references"] =
6484 references.map((value) => (value).toJson()).toList();
6593 } 6485 }
6594 return _json; 6486 return _json;
6595 } 6487 }
6596 } 6488 }
6597 6489
6598 /** The search variant sets request. */ 6490 /// The search variant sets request.
6599 class SearchVariantSetsRequest { 6491 class SearchVariantSetsRequest {
6600 /** 6492 /// Exactly one dataset ID must be provided here. Only variant sets which
6601 * Exactly one dataset ID must be provided here. Only variant sets which 6493 /// belong to this dataset will be returned.
6602 * belong to this dataset will be returned.
6603 */
6604 core.List<core.String> datasetIds; 6494 core.List<core.String> datasetIds;
6605 /** 6495
6606 * The maximum number of results to return in a single page. If unspecified, 6496 /// The maximum number of results to return in a single page. If unspecified,
6607 * defaults to 1024. 6497 /// defaults to 1024.
6608 */
6609 core.int pageSize; 6498 core.int pageSize;
6610 /** 6499
6611 * The continuation token, which is used to page through large result sets. 6500 /// The continuation token, which is used to page through large result sets.
6612 * To get the next page of results, set this parameter to the value of 6501 /// To get the next page of results, set this parameter to the value of
6613 * `nextPageToken` from the previous response. 6502 /// `nextPageToken` from the previous response.
6614 */
6615 core.String pageToken; 6503 core.String pageToken;
6616 6504
6617 SearchVariantSetsRequest(); 6505 SearchVariantSetsRequest();
6618 6506
6619 SearchVariantSetsRequest.fromJson(core.Map _json) { 6507 SearchVariantSetsRequest.fromJson(core.Map _json) {
6620 if (_json.containsKey("datasetIds")) { 6508 if (_json.containsKey("datasetIds")) {
6621 datasetIds = _json["datasetIds"]; 6509 datasetIds = _json["datasetIds"];
6622 } 6510 }
6623 if (_json.containsKey("pageSize")) { 6511 if (_json.containsKey("pageSize")) {
6624 pageSize = _json["pageSize"]; 6512 pageSize = _json["pageSize"];
6625 } 6513 }
6626 if (_json.containsKey("pageToken")) { 6514 if (_json.containsKey("pageToken")) {
6627 pageToken = _json["pageToken"]; 6515 pageToken = _json["pageToken"];
6628 } 6516 }
6629 } 6517 }
6630 6518
6631 core.Map<core.String, core.Object> toJson() { 6519 core.Map<core.String, core.Object> toJson() {
6632 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 6520 final core.Map<core.String, core.Object> _json =
6521 new core.Map<core.String, core.Object>();
6633 if (datasetIds != null) { 6522 if (datasetIds != null) {
6634 _json["datasetIds"] = datasetIds; 6523 _json["datasetIds"] = datasetIds;
6635 } 6524 }
6636 if (pageSize != null) { 6525 if (pageSize != null) {
6637 _json["pageSize"] = pageSize; 6526 _json["pageSize"] = pageSize;
6638 } 6527 }
6639 if (pageToken != null) { 6528 if (pageToken != null) {
6640 _json["pageToken"] = pageToken; 6529 _json["pageToken"] = pageToken;
6641 } 6530 }
6642 return _json; 6531 return _json;
6643 } 6532 }
6644 } 6533 }
6645 6534
6646 /** The search variant sets response. */ 6535 /// The search variant sets response.
6647 class SearchVariantSetsResponse { 6536 class SearchVariantSetsResponse {
6648 /** 6537 /// The continuation token, which is used to page through large result sets.
6649 * The continuation token, which is used to page through large result sets. 6538 /// Provide this value in a subsequent request to return the next page of
6650 * Provide this value in a subsequent request to return the next page of 6539 /// results. This field will be empty if there aren't any additional results.
6651 * results. This field will be empty if there aren't any additional results.
6652 */
6653 core.String nextPageToken; 6540 core.String nextPageToken;
6654 /** The variant sets belonging to the requested dataset. */ 6541
6542 /// The variant sets belonging to the requested dataset.
6655 core.List<VariantSet> variantSets; 6543 core.List<VariantSet> variantSets;
6656 6544
6657 SearchVariantSetsResponse(); 6545 SearchVariantSetsResponse();
6658 6546
6659 SearchVariantSetsResponse.fromJson(core.Map _json) { 6547 SearchVariantSetsResponse.fromJson(core.Map _json) {
6660 if (_json.containsKey("nextPageToken")) { 6548 if (_json.containsKey("nextPageToken")) {
6661 nextPageToken = _json["nextPageToken"]; 6549 nextPageToken = _json["nextPageToken"];
6662 } 6550 }
6663 if (_json.containsKey("variantSets")) { 6551 if (_json.containsKey("variantSets")) {
6664 variantSets = _json["variantSets"].map((value) => new VariantSet.fromJson( value)).toList(); 6552 variantSets = _json["variantSets"]
6553 .map((value) => new VariantSet.fromJson(value))
6554 .toList();
6665 } 6555 }
6666 } 6556 }
6667 6557
6668 core.Map<core.String, core.Object> toJson() { 6558 core.Map<core.String, core.Object> toJson() {
6669 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 6559 final core.Map<core.String, core.Object> _json =
6560 new core.Map<core.String, core.Object>();
6670 if (nextPageToken != null) { 6561 if (nextPageToken != null) {
6671 _json["nextPageToken"] = nextPageToken; 6562 _json["nextPageToken"] = nextPageToken;
6672 } 6563 }
6673 if (variantSets != null) { 6564 if (variantSets != null) {
6674 _json["variantSets"] = variantSets.map((value) => (value).toJson()).toList (); 6565 _json["variantSets"] =
6566 variantSets.map((value) => (value).toJson()).toList();
6675 } 6567 }
6676 return _json; 6568 return _json;
6677 } 6569 }
6678 } 6570 }
6679 6571
6680 /** The variant search request. */ 6572 /// The variant search request.
6681 class SearchVariantsRequest { 6573 class SearchVariantsRequest {
6682 /** 6574 /// Only return variant calls which belong to call sets with these ids.
6683 * Only return variant calls which belong to call sets with these ids. 6575 /// Leaving this blank returns all variant calls. If a variant has no
6684 * Leaving this blank returns all variant calls. If a variant has no 6576 /// calls belonging to any of these call sets, it won't be returned at all.
6685 * calls belonging to any of these call sets, it won't be returned at all.
6686 */
6687 core.List<core.String> callSetIds; 6577 core.List<core.String> callSetIds;
6688 /** 6578
6689 * The end of the window, 0-based exclusive. If unspecified or 0, defaults to 6579 /// The end of the window, 0-based exclusive. If unspecified or 0, defaults
6690 * the length of the reference. 6580 /// to
6691 */ 6581 /// the length of the reference.
6692 core.String end; 6582 core.String end;
6693 /** 6583
6694 * The maximum number of calls to return in a single page. Note that this 6584 /// The maximum number of calls to return in a single page. Note that this
6695 * limit may be exceeded in the event that a matching variant contains more 6585 /// limit may be exceeded in the event that a matching variant contains more
6696 * calls than the requested maximum. If unspecified, defaults to 5000. The 6586 /// calls than the requested maximum. If unspecified, defaults to 5000. The
6697 * maximum value is 10000. 6587 /// maximum value is 10000.
6698 */
6699 core.int maxCalls; 6588 core.int maxCalls;
6700 /** 6589
6701 * The maximum number of variants to return in a single page. If unspecified, 6590 /// The maximum number of variants to return in a single page. If
6702 * defaults to 5000. The maximum value is 10000. 6591 /// unspecified,
6703 */ 6592 /// defaults to 5000. The maximum value is 10000.
6704 core.int pageSize; 6593 core.int pageSize;
6705 /** 6594
6706 * The continuation token, which is used to page through large result sets. 6595 /// The continuation token, which is used to page through large result sets.
6707 * To get the next page of results, set this parameter to the value of 6596 /// To get the next page of results, set this parameter to the value of
6708 * `nextPageToken` from the previous response. 6597 /// `nextPageToken` from the previous response.
6709 */
6710 core.String pageToken; 6598 core.String pageToken;
6711 /** Required. Only return variants in this reference sequence. */ 6599
6600 /// Required. Only return variants in this reference sequence.
6712 core.String referenceName; 6601 core.String referenceName;
6713 /** 6602
6714 * The beginning of the window (0-based, inclusive) for which 6603 /// The beginning of the window (0-based, inclusive) for which
6715 * overlapping variants should be returned. If unspecified, defaults to 0. 6604 /// overlapping variants should be returned. If unspecified, defaults to 0.
6716 */
6717 core.String start; 6605 core.String start;
6718 /** Only return variants which have exactly this name. */ 6606
6607 /// Only return variants which have exactly this name.
6719 core.String variantName; 6608 core.String variantName;
6720 /** 6609
6721 * At most one variant set ID must be provided. Only variants from this 6610 /// At most one variant set ID must be provided. Only variants from this
6722 * variant set will be returned. If omitted, a call set id must be included in 6611 /// variant set will be returned. If omitted, a call set id must be included
6723 * the request. 6612 /// in
6724 */ 6613 /// the request.
6725 core.List<core.String> variantSetIds; 6614 core.List<core.String> variantSetIds;
6726 6615
6727 SearchVariantsRequest(); 6616 SearchVariantsRequest();
6728 6617
6729 SearchVariantsRequest.fromJson(core.Map _json) { 6618 SearchVariantsRequest.fromJson(core.Map _json) {
6730 if (_json.containsKey("callSetIds")) { 6619 if (_json.containsKey("callSetIds")) {
6731 callSetIds = _json["callSetIds"]; 6620 callSetIds = _json["callSetIds"];
6732 } 6621 }
6733 if (_json.containsKey("end")) { 6622 if (_json.containsKey("end")) {
6734 end = _json["end"]; 6623 end = _json["end"];
(...skipping 15 matching lines...) Expand all
6750 } 6639 }
6751 if (_json.containsKey("variantName")) { 6640 if (_json.containsKey("variantName")) {
6752 variantName = _json["variantName"]; 6641 variantName = _json["variantName"];
6753 } 6642 }
6754 if (_json.containsKey("variantSetIds")) { 6643 if (_json.containsKey("variantSetIds")) {
6755 variantSetIds = _json["variantSetIds"]; 6644 variantSetIds = _json["variantSetIds"];
6756 } 6645 }
6757 } 6646 }
6758 6647
6759 core.Map<core.String, core.Object> toJson() { 6648 core.Map<core.String, core.Object> toJson() {
6760 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 6649 final core.Map<core.String, core.Object> _json =
6650 new core.Map<core.String, core.Object>();
6761 if (callSetIds != null) { 6651 if (callSetIds != null) {
6762 _json["callSetIds"] = callSetIds; 6652 _json["callSetIds"] = callSetIds;
6763 } 6653 }
6764 if (end != null) { 6654 if (end != null) {
6765 _json["end"] = end; 6655 _json["end"] = end;
6766 } 6656 }
6767 if (maxCalls != null) { 6657 if (maxCalls != null) {
6768 _json["maxCalls"] = maxCalls; 6658 _json["maxCalls"] = maxCalls;
6769 } 6659 }
6770 if (pageSize != null) { 6660 if (pageSize != null) {
(...skipping 11 matching lines...) Expand all
6782 if (variantName != null) { 6672 if (variantName != null) {
6783 _json["variantName"] = variantName; 6673 _json["variantName"] = variantName;
6784 } 6674 }
6785 if (variantSetIds != null) { 6675 if (variantSetIds != null) {
6786 _json["variantSetIds"] = variantSetIds; 6676 _json["variantSetIds"] = variantSetIds;
6787 } 6677 }
6788 return _json; 6678 return _json;
6789 } 6679 }
6790 } 6680 }
6791 6681
6792 /** The variant search response. */ 6682 /// The variant search response.
6793 class SearchVariantsResponse { 6683 class SearchVariantsResponse {
6794 /** 6684 /// The continuation token, which is used to page through large result sets.
6795 * The continuation token, which is used to page through large result sets. 6685 /// Provide this value in a subsequent request to return the next page of
6796 * Provide this value in a subsequent request to return the next page of 6686 /// results. This field will be empty if there aren't any additional results.
6797 * results. This field will be empty if there aren't any additional results.
6798 */
6799 core.String nextPageToken; 6687 core.String nextPageToken;
6800 /** The list of matching Variants. */ 6688
6689 /// The list of matching Variants.
6801 core.List<Variant> variants; 6690 core.List<Variant> variants;
6802 6691
6803 SearchVariantsResponse(); 6692 SearchVariantsResponse();
6804 6693
6805 SearchVariantsResponse.fromJson(core.Map _json) { 6694 SearchVariantsResponse.fromJson(core.Map _json) {
6806 if (_json.containsKey("nextPageToken")) { 6695 if (_json.containsKey("nextPageToken")) {
6807 nextPageToken = _json["nextPageToken"]; 6696 nextPageToken = _json["nextPageToken"];
6808 } 6697 }
6809 if (_json.containsKey("variants")) { 6698 if (_json.containsKey("variants")) {
6810 variants = _json["variants"].map((value) => new Variant.fromJson(value)).t oList(); 6699 variants = _json["variants"]
6700 .map((value) => new Variant.fromJson(value))
6701 .toList();
6811 } 6702 }
6812 } 6703 }
6813 6704
6814 core.Map<core.String, core.Object> toJson() { 6705 core.Map<core.String, core.Object> toJson() {
6815 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 6706 final core.Map<core.String, core.Object> _json =
6707 new core.Map<core.String, core.Object>();
6816 if (nextPageToken != null) { 6708 if (nextPageToken != null) {
6817 _json["nextPageToken"] = nextPageToken; 6709 _json["nextPageToken"] = nextPageToken;
6818 } 6710 }
6819 if (variants != null) { 6711 if (variants != null) {
6820 _json["variants"] = variants.map((value) => (value).toJson()).toList(); 6712 _json["variants"] = variants.map((value) => (value).toJson()).toList();
6821 } 6713 }
6822 return _json; 6714 return _json;
6823 } 6715 }
6824 } 6716 }
6825 6717
6826 /** Request message for `SetIamPolicy` method. */ 6718 /// Request message for `SetIamPolicy` method.
6827 class SetIamPolicyRequest { 6719 class SetIamPolicyRequest {
6828 /** 6720 /// REQUIRED: The complete policy to be applied to the `resource`. The size
6829 * REQUIRED: The complete policy to be applied to the `resource`. The size of 6721 /// of
6830 * the policy is limited to a few 10s of KB. An empty policy is a 6722 /// the policy is limited to a few 10s of KB. An empty policy is a
6831 * valid policy but certain Cloud Platform services (such as Projects) 6723 /// valid policy but certain Cloud Platform services (such as Projects)
6832 * might reject them. 6724 /// might reject them.
6833 */
6834 Policy policy; 6725 Policy policy;
6835 6726
6836 SetIamPolicyRequest(); 6727 SetIamPolicyRequest();
6837 6728
6838 SetIamPolicyRequest.fromJson(core.Map _json) { 6729 SetIamPolicyRequest.fromJson(core.Map _json) {
6839 if (_json.containsKey("policy")) { 6730 if (_json.containsKey("policy")) {
6840 policy = new Policy.fromJson(_json["policy"]); 6731 policy = new Policy.fromJson(_json["policy"]);
6841 } 6732 }
6842 } 6733 }
6843 6734
6844 core.Map<core.String, core.Object> toJson() { 6735 core.Map<core.String, core.Object> toJson() {
6845 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 6736 final core.Map<core.String, core.Object> _json =
6737 new core.Map<core.String, core.Object>();
6846 if (policy != null) { 6738 if (policy != null) {
6847 _json["policy"] = (policy).toJson(); 6739 _json["policy"] = (policy).toJson();
6848 } 6740 }
6849 return _json; 6741 return _json;
6850 } 6742 }
6851 } 6743 }
6852 6744
6853 /** 6745 /// The `Status` type defines a logical error model that is suitable for
6854 * The `Status` type defines a logical error model that is suitable for 6746 /// different
6855 * different 6747 /// programming environments, including REST APIs and RPC APIs. It is used by
6856 * programming environments, including REST APIs and RPC APIs. It is used by 6748 /// [gRPC](https://github.com/grpc). The error model is designed to be:
6857 * [gRPC](https://github.com/grpc). The error model is designed to be: 6749 ///
6858 * 6750 /// - Simple to use and understand for most users
6859 * - Simple to use and understand for most users 6751 /// - Flexible enough to meet unexpected needs
6860 * - Flexible enough to meet unexpected needs 6752 ///
6861 * 6753 /// # Overview
6862 * # Overview 6754 ///
6863 * 6755 /// The `Status` message contains three pieces of data: error code, error
6864 * The `Status` message contains three pieces of data: error code, error 6756 /// message,
6865 * message, 6757 /// and error details. The error code should be an enum value of
6866 * and error details. The error code should be an enum value of 6758 /// google.rpc.Code, but it may accept additional error codes if needed. The
6867 * google.rpc.Code, but it may accept additional error codes if needed. The 6759 /// error message should be a developer-facing English message that helps
6868 * error message should be a developer-facing English message that helps 6760 /// developers *understand* and *resolve* the error. If a localized user-facing
6869 * developers *understand* and *resolve* the error. If a localized user-facing 6761 /// error message is needed, put the localized message in the error details or
6870 * error message is needed, put the localized message in the error details or 6762 /// localize it in the client. The optional error details may contain arbitrary
6871 * localize it in the client. The optional error details may contain arbitrary 6763 /// information about the error. There is a predefined set of error detail
6872 * information about the error. There is a predefined set of error detail types 6764 /// types
6873 * in the package `google.rpc` that can be used for common error conditions. 6765 /// in the package `google.rpc` that can be used for common error conditions.
6874 * 6766 ///
6875 * # Language mapping 6767 /// # Language mapping
6876 * 6768 ///
6877 * The `Status` message is the logical representation of the error model, but it 6769 /// The `Status` message is the logical representation of the error model, but
6878 * is not necessarily the actual wire format. When the `Status` message is 6770 /// it
6879 * exposed in different client libraries and different wire protocols, it can be 6771 /// is not necessarily the actual wire format. When the `Status` message is
6880 * mapped differently. For example, it will likely be mapped to some exceptions 6772 /// exposed in different client libraries and different wire protocols, it can
6881 * in Java, but more likely mapped to some error codes in C. 6773 /// be
6882 * 6774 /// mapped differently. For example, it will likely be mapped to some
6883 * # Other uses 6775 /// exceptions
6884 * 6776 /// in Java, but more likely mapped to some error codes in C.
6885 * The error model and the `Status` message can be used in a variety of 6777 ///
6886 * environments, either with or without APIs, to provide a 6778 /// # Other uses
6887 * consistent developer experience across different environments. 6779 ///
6888 * 6780 /// The error model and the `Status` message can be used in a variety of
6889 * Example uses of this error model include: 6781 /// environments, either with or without APIs, to provide a
6890 * 6782 /// consistent developer experience across different environments.
6891 * - Partial errors. If a service needs to return partial errors to the client, 6783 ///
6892 * it may embed the `Status` in the normal response to indicate the partial 6784 /// Example uses of this error model include:
6893 * errors. 6785 ///
6894 * 6786 /// - Partial errors. If a service needs to return partial errors to the
6895 * - Workflow errors. A typical workflow has multiple steps. Each step may 6787 /// client,
6896 * have a `Status` message for error reporting. 6788 /// it may embed the `Status` in the normal response to indicate the partial
6897 * 6789 /// errors.
6898 * - Batch operations. If a client uses batch request and batch response, the 6790 ///
6899 * `Status` message should be used directly inside batch response, one for 6791 /// - Workflow errors. A typical workflow has multiple steps. Each step may
6900 * each error sub-response. 6792 /// have a `Status` message for error reporting.
6901 * 6793 ///
6902 * - Asynchronous operations. If an API call embeds asynchronous operation 6794 /// - Batch operations. If a client uses batch request and batch response, the
6903 * results in its response, the status of those operations should be 6795 /// `Status` message should be used directly inside batch response, one for
6904 * represented directly using the `Status` message. 6796 /// each error sub-response.
6905 * 6797 ///
6906 * - Logging. If some API errors are stored in logs, the message `Status` could 6798 /// - Asynchronous operations. If an API call embeds asynchronous operation
6907 * be used directly after any stripping needed for security/privacy reasons. 6799 /// results in its response, the status of those operations should be
6908 */ 6800 /// represented directly using the `Status` message.
6801 ///
6802 /// - Logging. If some API errors are stored in logs, the message `Status`
6803 /// could
6804 /// be used directly after any stripping needed for security/privacy reasons.
6909 class Status { 6805 class Status {
6910 /** The status code, which should be an enum value of google.rpc.Code. */ 6806 /// The status code, which should be an enum value of google.rpc.Code.
6911 core.int code; 6807 core.int code;
6912 /** 6808
6913 * A list of messages that carry the error details. There is a common set of 6809 /// A list of messages that carry the error details. There is a common set
6914 * message types for APIs to use. 6810 /// of
6915 * 6811 /// message types for APIs to use.
6916 * The values for Object must be JSON objects. It can consist of `num`, 6812 ///
6917 * `String`, `bool` and `null` as well as `Map` and `List` values. 6813 /// The values for Object must be JSON objects. It can consist of `num`,
6918 */ 6814 /// `String`, `bool` and `null` as well as `Map` and `List` values.
6919 core.List<core.Map<core.String, core.Object>> details; 6815 core.List<core.Map<core.String, core.Object>> details;
6920 /** 6816
6921 * A developer-facing error message, which should be in English. Any 6817 /// A developer-facing error message, which should be in English. Any
6922 * user-facing error message should be localized and sent in the 6818 /// user-facing error message should be localized and sent in the
6923 * google.rpc.Status.details field, or localized by the client. 6819 /// google.rpc.Status.details field, or localized by the client.
6924 */
6925 core.String message; 6820 core.String message;
6926 6821
6927 Status(); 6822 Status();
6928 6823
6929 Status.fromJson(core.Map _json) { 6824 Status.fromJson(core.Map _json) {
6930 if (_json.containsKey("code")) { 6825 if (_json.containsKey("code")) {
6931 code = _json["code"]; 6826 code = _json["code"];
6932 } 6827 }
6933 if (_json.containsKey("details")) { 6828 if (_json.containsKey("details")) {
6934 details = _json["details"]; 6829 details = _json["details"];
6935 } 6830 }
6936 if (_json.containsKey("message")) { 6831 if (_json.containsKey("message")) {
6937 message = _json["message"]; 6832 message = _json["message"];
6938 } 6833 }
6939 } 6834 }
6940 6835
6941 core.Map<core.String, core.Object> toJson() { 6836 core.Map<core.String, core.Object> toJson() {
6942 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 6837 final core.Map<core.String, core.Object> _json =
6838 new core.Map<core.String, core.Object>();
6943 if (code != null) { 6839 if (code != null) {
6944 _json["code"] = code; 6840 _json["code"] = code;
6945 } 6841 }
6946 if (details != null) { 6842 if (details != null) {
6947 _json["details"] = details; 6843 _json["details"] = details;
6948 } 6844 }
6949 if (message != null) { 6845 if (message != null) {
6950 _json["message"] = message; 6846 _json["message"] = message;
6951 } 6847 }
6952 return _json; 6848 return _json;
6953 } 6849 }
6954 } 6850 }
6955 6851
6956 /** Request message for `TestIamPermissions` method. */ 6852 /// Request message for `TestIamPermissions` method.
6957 class TestIamPermissionsRequest { 6853 class TestIamPermissionsRequest {
6958 /** 6854 /// REQUIRED: The set of permissions to check for the 'resource'.
6959 * REQUIRED: The set of permissions to check for the 'resource'. 6855 /// Permissions with wildcards (such as '*' or 'storage.*') are not allowed.
6960 * Permissions with wildcards (such as '*' or 'storage.*') are not allowed. 6856 /// Allowed permissions are&#58;
6961 * Allowed permissions are&#58; 6857 ///
6962 * 6858 /// * `genomics.datasets.create`
6963 * * `genomics.datasets.create` 6859 /// * `genomics.datasets.delete`
6964 * * `genomics.datasets.delete` 6860 /// * `genomics.datasets.get`
6965 * * `genomics.datasets.get` 6861 /// * `genomics.datasets.list`
6966 * * `genomics.datasets.list` 6862 /// * `genomics.datasets.update`
6967 * * `genomics.datasets.update` 6863 /// * `genomics.datasets.getIamPolicy`
6968 * * `genomics.datasets.getIamPolicy` 6864 /// * `genomics.datasets.setIamPolicy`
6969 * * `genomics.datasets.setIamPolicy`
6970 */
6971 core.List<core.String> permissions; 6865 core.List<core.String> permissions;
6972 6866
6973 TestIamPermissionsRequest(); 6867 TestIamPermissionsRequest();
6974 6868
6975 TestIamPermissionsRequest.fromJson(core.Map _json) { 6869 TestIamPermissionsRequest.fromJson(core.Map _json) {
6976 if (_json.containsKey("permissions")) { 6870 if (_json.containsKey("permissions")) {
6977 permissions = _json["permissions"]; 6871 permissions = _json["permissions"];
6978 } 6872 }
6979 } 6873 }
6980 6874
6981 core.Map<core.String, core.Object> toJson() { 6875 core.Map<core.String, core.Object> toJson() {
6982 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 6876 final core.Map<core.String, core.Object> _json =
6877 new core.Map<core.String, core.Object>();
6983 if (permissions != null) { 6878 if (permissions != null) {
6984 _json["permissions"] = permissions; 6879 _json["permissions"] = permissions;
6985 } 6880 }
6986 return _json; 6881 return _json;
6987 } 6882 }
6988 } 6883 }
6989 6884
6990 /** Response message for `TestIamPermissions` method. */ 6885 /// Response message for `TestIamPermissions` method.
6991 class TestIamPermissionsResponse { 6886 class TestIamPermissionsResponse {
6992 /** 6887 /// A subset of `TestPermissionsRequest.permissions` that the caller is
6993 * A subset of `TestPermissionsRequest.permissions` that the caller is 6888 /// allowed.
6994 * allowed.
6995 */
6996 core.List<core.String> permissions; 6889 core.List<core.String> permissions;
6997 6890
6998 TestIamPermissionsResponse(); 6891 TestIamPermissionsResponse();
6999 6892
7000 TestIamPermissionsResponse.fromJson(core.Map _json) { 6893 TestIamPermissionsResponse.fromJson(core.Map _json) {
7001 if (_json.containsKey("permissions")) { 6894 if (_json.containsKey("permissions")) {
7002 permissions = _json["permissions"]; 6895 permissions = _json["permissions"];
7003 } 6896 }
7004 } 6897 }
7005 6898
7006 core.Map<core.String, core.Object> toJson() { 6899 core.Map<core.String, core.Object> toJson() {
7007 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 6900 final core.Map<core.String, core.Object> _json =
6901 new core.Map<core.String, core.Object>();
7008 if (permissions != null) { 6902 if (permissions != null) {
7009 _json["permissions"] = permissions; 6903 _json["permissions"] = permissions;
7010 } 6904 }
7011 return _json; 6905 return _json;
7012 } 6906 }
7013 } 6907 }
7014 6908
7015 /** 6909 /// A transcript represents the assertion that a particular region of the
7016 * A transcript represents the assertion that a particular region of the 6910 /// reference genome may be transcribed as RNA.
7017 * reference genome may be transcribed as RNA.
7018 */
7019 class Transcript { 6911 class Transcript {
7020 /** 6912 /// The range of the coding sequence for this transcript, if any. To
7021 * The range of the coding sequence for this transcript, if any. To determine 6913 /// determine
7022 * the exact ranges of coding sequence, intersect this range with those of the 6914 /// the exact ranges of coding sequence, intersect this range with those of
7023 * exons, if any. If there are any 6915 /// the
7024 * exons, the 6916 /// exons, if any. If there are any
7025 * codingSequence must start 6917 /// exons, the
7026 * and end within them. 6918 /// codingSequence must start
7027 * 6919 /// and end within them.
7028 * Note that in some cases, the reference genome will not exactly match the 6920 ///
7029 * observed mRNA transcript e.g. due to variance in the source genome from 6921 /// Note that in some cases, the reference genome will not exactly match the
7030 * reference. In these cases, 6922 /// observed mRNA transcript e.g. due to variance in the source genome from
7031 * exon.frame will not necessarily 6923 /// reference. In these cases,
7032 * match the expected reference reading frame and coding exon reference bases 6924 /// exon.frame will not necessarily
7033 * cannot necessarily be concatenated to produce the original transcript mRNA. 6925 /// match the expected reference reading frame and coding exon reference
7034 */ 6926 /// bases
6927 /// cannot necessarily be concatenated to produce the original transcript
6928 /// mRNA.
7035 CodingSequence codingSequence; 6929 CodingSequence codingSequence;
7036 /** 6930
7037 * The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose 6931 /// The <a href="http://en.wikipedia.org/wiki/Exon">exons</a> that compose
7038 * this transcript. This field should be unset for genomes where transcript 6932 /// this transcript. This field should be unset for genomes where transcript
7039 * splicing does not occur, for example prokaryotes. 6933 /// splicing does not occur, for example prokaryotes.
7040 * 6934 ///
7041 * Introns are regions of the transcript that are not included in the 6935 /// Introns are regions of the transcript that are not included in the
7042 * spliced RNA product. Though not explicitly modeled here, intron ranges can 6936 /// spliced RNA product. Though not explicitly modeled here, intron ranges
7043 * be deduced; all regions of this transcript that are not exons are introns. 6937 /// can
7044 * 6938 /// be deduced; all regions of this transcript that are not exons are
7045 * Exonic sequences do not necessarily code for a translational product 6939 /// introns.
7046 * (amino acids). Only the regions of exons bounded by the 6940 ///
7047 * codingSequence correspond 6941 /// Exonic sequences do not necessarily code for a translational product
7048 * to coding DNA sequence. 6942 /// (amino acids). Only the regions of exons bounded by the
7049 * 6943 /// codingSequence correspond
7050 * Exons are ordered by start position and may not overlap. 6944 /// to coding DNA sequence.
7051 */ 6945 ///
6946 /// Exons are ordered by start position and may not overlap.
7052 core.List<Exon> exons; 6947 core.List<Exon> exons;
7053 /** 6948
7054 * The annotation ID of the gene from which this transcript is transcribed. 6949 /// The annotation ID of the gene from which this transcript is transcribed.
7055 */
7056 core.String geneId; 6950 core.String geneId;
7057 6951
7058 Transcript(); 6952 Transcript();
7059 6953
7060 Transcript.fromJson(core.Map _json) { 6954 Transcript.fromJson(core.Map _json) {
7061 if (_json.containsKey("codingSequence")) { 6955 if (_json.containsKey("codingSequence")) {
7062 codingSequence = new CodingSequence.fromJson(_json["codingSequence"]); 6956 codingSequence = new CodingSequence.fromJson(_json["codingSequence"]);
7063 } 6957 }
7064 if (_json.containsKey("exons")) { 6958 if (_json.containsKey("exons")) {
7065 exons = _json["exons"].map((value) => new Exon.fromJson(value)).toList(); 6959 exons = _json["exons"].map((value) => new Exon.fromJson(value)).toList();
7066 } 6960 }
7067 if (_json.containsKey("geneId")) { 6961 if (_json.containsKey("geneId")) {
7068 geneId = _json["geneId"]; 6962 geneId = _json["geneId"];
7069 } 6963 }
7070 } 6964 }
7071 6965
7072 core.Map<core.String, core.Object> toJson() { 6966 core.Map<core.String, core.Object> toJson() {
7073 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 6967 final core.Map<core.String, core.Object> _json =
6968 new core.Map<core.String, core.Object>();
7074 if (codingSequence != null) { 6969 if (codingSequence != null) {
7075 _json["codingSequence"] = (codingSequence).toJson(); 6970 _json["codingSequence"] = (codingSequence).toJson();
7076 } 6971 }
7077 if (exons != null) { 6972 if (exons != null) {
7078 _json["exons"] = exons.map((value) => (value).toJson()).toList(); 6973 _json["exons"] = exons.map((value) => (value).toJson()).toList();
7079 } 6974 }
7080 if (geneId != null) { 6975 if (geneId != null) {
7081 _json["geneId"] = geneId; 6976 _json["geneId"] = geneId;
7082 } 6977 }
7083 return _json; 6978 return _json;
7084 } 6979 }
7085 } 6980 }
7086 6981
7087 class UndeleteDatasetRequest { 6982 class UndeleteDatasetRequest {
7088
7089 UndeleteDatasetRequest(); 6983 UndeleteDatasetRequest();
7090 6984
7091 UndeleteDatasetRequest.fromJson(core.Map _json) { 6985 UndeleteDatasetRequest.fromJson(core.Map _json) {}
7092 }
7093 6986
7094 core.Map<core.String, core.Object> toJson() { 6987 core.Map<core.String, core.Object> toJson() {
7095 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 6988 final core.Map<core.String, core.Object> _json =
6989 new core.Map<core.String, core.Object>();
7096 return _json; 6990 return _json;
7097 } 6991 }
7098 } 6992 }
7099 6993
7100 /** 6994 /// A variant represents a change in DNA sequence relative to a reference
7101 * A variant represents a change in DNA sequence relative to a reference 6995 /// sequence. For example, a variant could represent a SNP or an insertion.
7102 * sequence. For example, a variant could represent a SNP or an insertion. 6996 /// Variants belong to a variant set.
7103 * Variants belong to a variant set. 6997 ///
7104 * 6998 /// For more genomics resource definitions, see [Fundamentals of Google
7105 * For more genomics resource definitions, see [Fundamentals of Google 6999 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
7106 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 7000 ///
7107 * 7001 /// Each of the calls on a variant represent a determination of genotype with
7108 * Each of the calls on a variant represent a determination of genotype with 7002 /// respect to that variant. For example, a call might assign probability of
7109 * respect to that variant. For example, a call might assign probability of 0.32 7003 /// 0.32
7110 * to the occurrence of a SNP named rs1234 in a sample named NA12345. A call 7004 /// to the occurrence of a SNP named rs1234 in a sample named NA12345. A call
7111 * belongs to a call set, which contains related calls typically from one 7005 /// belongs to a call set, which contains related calls typically from one
7112 * sample. 7006 /// sample.
7113 */
7114 class Variant { 7007 class Variant {
7115 /** The bases that appear instead of the reference bases. */ 7008 /// The bases that appear instead of the reference bases.
7116 core.List<core.String> alternateBases; 7009 core.List<core.String> alternateBases;
7117 /** 7010
7118 * The variant calls for this particular variant. Each one represents the 7011 /// The variant calls for this particular variant. Each one represents the
7119 * determination of genotype with respect to this variant. 7012 /// determination of genotype with respect to this variant.
7120 */
7121 core.List<VariantCall> calls; 7013 core.List<VariantCall> calls;
7122 /** The date this variant was created, in milliseconds from the epoch. */ 7014
7015 /// The date this variant was created, in milliseconds from the epoch.
7123 core.String created; 7016 core.String created;
7124 /** 7017
7125 * The end position (0-based) of this variant. This corresponds to the first 7018 /// The end position (0-based) of this variant. This corresponds to the first
7126 * base after the last base in the reference allele. So, the length of 7019 /// base after the last base in the reference allele. So, the length of
7127 * the reference allele is (end - start). This is useful for variants 7020 /// the reference allele is (end - start). This is useful for variants
7128 * that don't explicitly give alternate bases, for example large deletions. 7021 /// that don't explicitly give alternate bases, for example large deletions.
7129 */
7130 core.String end; 7022 core.String end;
7131 /** 7023
7132 * A list of filters (normally quality filters) this variant has failed. 7024 /// A list of filters (normally quality filters) this variant has failed.
7133 * `PASS` indicates this variant has passed all filters. 7025 /// `PASS` indicates this variant has passed all filters.
7134 */
7135 core.List<core.String> filter; 7026 core.List<core.String> filter;
7136 /** The server-generated variant ID, unique across all variants. */ 7027
7028 /// The server-generated variant ID, unique across all variants.
7137 core.String id; 7029 core.String id;
7138 /** 7030
7139 * A map of additional variant information. This must be of the form 7031 /// A map of additional variant information. This must be of the form
7140 * map<string, string[]> (string key mapping to a list of string values). 7032 /// map<string, string[]> (string key mapping to a list of string values).
7141 * 7033 ///
7142 * The values for Object must be JSON objects. It can consist of `num`, 7034 /// The values for Object must be JSON objects. It can consist of `num`,
7143 * `String`, `bool` and `null` as well as `Map` and `List` values. 7035 /// `String`, `bool` and `null` as well as `Map` and `List` values.
7144 */
7145 core.Map<core.String, core.List<core.Object>> info; 7036 core.Map<core.String, core.List<core.Object>> info;
7146 /** Names for the variant, for example a RefSNP ID. */ 7037
7038 /// Names for the variant, for example a RefSNP ID.
7147 core.List<core.String> names; 7039 core.List<core.String> names;
7148 /** 7040
7149 * A measure of how likely this variant is to be real. 7041 /// A measure of how likely this variant is to be real.
7150 * A higher value is better. 7042 /// A higher value is better.
7151 */
7152 core.double quality; 7043 core.double quality;
7153 /** 7044
7154 * The reference bases for this variant. They start at the given 7045 /// The reference bases for this variant. They start at the given
7155 * position. 7046 /// position.
7156 */
7157 core.String referenceBases; 7047 core.String referenceBases;
7158 /** 7048
7159 * The reference on which this variant occurs. 7049 /// The reference on which this variant occurs.
7160 * (such as `chr20` or `X`) 7050 /// (such as `chr20` or `X`)
7161 */
7162 core.String referenceName; 7051 core.String referenceName;
7163 /** 7052
7164 * The position at which this variant occurs (0-based). 7053 /// The position at which this variant occurs (0-based).
7165 * This corresponds to the first base of the string of reference bases. 7054 /// This corresponds to the first base of the string of reference bases.
7166 */
7167 core.String start; 7055 core.String start;
7168 /** The ID of the variant set this variant belongs to. */ 7056
7057 /// The ID of the variant set this variant belongs to.
7169 core.String variantSetId; 7058 core.String variantSetId;
7170 7059
7171 Variant(); 7060 Variant();
7172 7061
7173 Variant.fromJson(core.Map _json) { 7062 Variant.fromJson(core.Map _json) {
7174 if (_json.containsKey("alternateBases")) { 7063 if (_json.containsKey("alternateBases")) {
7175 alternateBases = _json["alternateBases"]; 7064 alternateBases = _json["alternateBases"];
7176 } 7065 }
7177 if (_json.containsKey("calls")) { 7066 if (_json.containsKey("calls")) {
7178 calls = _json["calls"].map((value) => new VariantCall.fromJson(value)).toL ist(); 7067 calls = _json["calls"]
7068 .map((value) => new VariantCall.fromJson(value))
7069 .toList();
7179 } 7070 }
7180 if (_json.containsKey("created")) { 7071 if (_json.containsKey("created")) {
7181 created = _json["created"]; 7072 created = _json["created"];
7182 } 7073 }
7183 if (_json.containsKey("end")) { 7074 if (_json.containsKey("end")) {
7184 end = _json["end"]; 7075 end = _json["end"];
7185 } 7076 }
7186 if (_json.containsKey("filter")) { 7077 if (_json.containsKey("filter")) {
7187 filter = _json["filter"]; 7078 filter = _json["filter"];
7188 } 7079 }
(...skipping 17 matching lines...) Expand all
7206 } 7097 }
7207 if (_json.containsKey("start")) { 7098 if (_json.containsKey("start")) {
7208 start = _json["start"]; 7099 start = _json["start"];
7209 } 7100 }
7210 if (_json.containsKey("variantSetId")) { 7101 if (_json.containsKey("variantSetId")) {
7211 variantSetId = _json["variantSetId"]; 7102 variantSetId = _json["variantSetId"];
7212 } 7103 }
7213 } 7104 }
7214 7105
7215 core.Map<core.String, core.Object> toJson() { 7106 core.Map<core.String, core.Object> toJson() {
7216 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 7107 final core.Map<core.String, core.Object> _json =
7108 new core.Map<core.String, core.Object>();
7217 if (alternateBases != null) { 7109 if (alternateBases != null) {
7218 _json["alternateBases"] = alternateBases; 7110 _json["alternateBases"] = alternateBases;
7219 } 7111 }
7220 if (calls != null) { 7112 if (calls != null) {
7221 _json["calls"] = calls.map((value) => (value).toJson()).toList(); 7113 _json["calls"] = calls.map((value) => (value).toJson()).toList();
7222 } 7114 }
7223 if (created != null) { 7115 if (created != null) {
7224 _json["created"] = created; 7116 _json["created"] = created;
7225 } 7117 }
7226 if (end != null) { 7118 if (end != null) {
(...skipping 24 matching lines...) Expand all
7251 _json["start"] = start; 7143 _json["start"] = start;
7252 } 7144 }
7253 if (variantSetId != null) { 7145 if (variantSetId != null) {
7254 _json["variantSetId"] = variantSetId; 7146 _json["variantSetId"] = variantSetId;
7255 } 7147 }
7256 return _json; 7148 return _json;
7257 } 7149 }
7258 } 7150 }
7259 7151
7260 class VariantAnnotation { 7152 class VariantAnnotation {
7261 /** 7153 /// The alternate allele for this variant. If multiple alternate alleles
7262 * The alternate allele for this variant. If multiple alternate alleles 7154 /// exist at this location, create a separate variant for each one, as they
7263 * exist at this location, create a separate variant for each one, as they 7155 /// may represent distinct conditions.
7264 * may represent distinct conditions.
7265 */
7266 core.String alternateBases; 7156 core.String alternateBases;
7267 /** 7157
7268 * Describes the clinical significance of a variant. 7158 /// Describes the clinical significance of a variant.
7269 * It is adapted from the ClinVar controlled vocabulary for clinical 7159 /// It is adapted from the ClinVar controlled vocabulary for clinical
7270 * significance described at: 7160 /// significance described at:
7271 * http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/ 7161 /// http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
7272 * Possible string values are: 7162 /// Possible string values are:
7273 * - "CLINICAL_SIGNIFICANCE_UNSPECIFIED" 7163 /// - "CLINICAL_SIGNIFICANCE_UNSPECIFIED"
7274 * - "CLINICAL_SIGNIFICANCE_OTHER" : `OTHER` should be used when no other 7164 /// - "CLINICAL_SIGNIFICANCE_OTHER" : `OTHER` should be used when no other
7275 * clinical significance 7165 /// clinical significance
7276 * value will suffice. 7166 /// value will suffice.
7277 * - "UNCERTAIN" 7167 /// - "UNCERTAIN"
7278 * - "BENIGN" 7168 /// - "BENIGN"
7279 * - "LIKELY_BENIGN" 7169 /// - "LIKELY_BENIGN"
7280 * - "LIKELY_PATHOGENIC" 7170 /// - "LIKELY_PATHOGENIC"
7281 * - "PATHOGENIC" 7171 /// - "PATHOGENIC"
7282 * - "DRUG_RESPONSE" 7172 /// - "DRUG_RESPONSE"
7283 * - "HISTOCOMPATIBILITY" 7173 /// - "HISTOCOMPATIBILITY"
7284 * - "CONFERS_SENSITIVITY" 7174 /// - "CONFERS_SENSITIVITY"
7285 * - "RISK_FACTOR" 7175 /// - "RISK_FACTOR"
7286 * - "ASSOCIATION" 7176 /// - "ASSOCIATION"
7287 * - "PROTECTIVE" 7177 /// - "PROTECTIVE"
7288 * - "MULTIPLE_REPORTED" : `MULTIPLE_REPORTED` should be used when multiple 7178 /// - "MULTIPLE_REPORTED" : `MULTIPLE_REPORTED` should be used when multiple
7289 * clinical 7179 /// clinical
7290 * signficances are reported for a variant. The original clinical 7180 /// signficances are reported for a variant. The original clinical
7291 * significance values may be provided in the `info` field. 7181 /// significance values may be provided in the `info` field.
7292 */
7293 core.String clinicalSignificance; 7182 core.String clinicalSignificance;
7294 /** 7183
7295 * The set of conditions associated with this variant. 7184 /// The set of conditions associated with this variant.
7296 * A condition describes the way a variant influences human health. 7185 /// A condition describes the way a variant influences human health.
7297 */
7298 core.List<ClinicalCondition> conditions; 7186 core.List<ClinicalCondition> conditions;
7299 /** 7187
7300 * Effect of the variant on the coding sequence. 7188 /// Effect of the variant on the coding sequence.
7301 * Possible string values are: 7189 /// Possible string values are:
7302 * - "EFFECT_UNSPECIFIED" 7190 /// - "EFFECT_UNSPECIFIED"
7303 * - "EFFECT_OTHER" : `EFFECT_OTHER` should be used when no other Effect 7191 /// - "EFFECT_OTHER" : `EFFECT_OTHER` should be used when no other Effect
7304 * will suffice. 7192 /// will suffice.
7305 * - "FRAMESHIFT" : `FRAMESHIFT` indicates a mutation in which the insertion 7193 /// - "FRAMESHIFT" : `FRAMESHIFT` indicates a mutation in which the insertion
7306 * or 7194 /// or
7307 * deletion of nucleotides resulted in a frameshift change. 7195 /// deletion of nucleotides resulted in a frameshift change.
7308 * - "FRAME_PRESERVING_INDEL" : `FRAME_PRESERVING_INDEL` indicates a mutation 7196 /// - "FRAME_PRESERVING_INDEL" : `FRAME_PRESERVING_INDEL` indicates a
7309 * in which a 7197 /// mutation in which a
7310 * multiple of three nucleotides has been inserted or deleted, resulting 7198 /// multiple of three nucleotides has been inserted or deleted, resulting
7311 * in no change to the reading frame of the coding sequence. 7199 /// in no change to the reading frame of the coding sequence.
7312 * - "SYNONYMOUS_SNP" : `SYNONYMOUS_SNP` indicates a single nucleotide 7200 /// - "SYNONYMOUS_SNP" : `SYNONYMOUS_SNP` indicates a single nucleotide
7313 * polymorphism 7201 /// polymorphism
7314 * mutation that results in no amino acid change. 7202 /// mutation that results in no amino acid change.
7315 * - "NONSYNONYMOUS_SNP" : `NONSYNONYMOUS_SNP` indicates a single nucleotide 7203 /// - "NONSYNONYMOUS_SNP" : `NONSYNONYMOUS_SNP` indicates a single nucleotide
7316 * polymorphism mutation that results in an amino acid change. 7204 /// polymorphism mutation that results in an amino acid change.
7317 * - "STOP_GAIN" : `STOP_GAIN` indicates a mutation that leads to the creation 7205 /// - "STOP_GAIN" : `STOP_GAIN` indicates a mutation that leads to the
7318 * of a stop codon at the variant site. Frameshift mutations creating 7206 /// creation
7319 * downstream stop codons do not count as `STOP_GAIN`. 7207 /// of a stop codon at the variant site. Frameshift mutations creating
7320 * - "STOP_LOSS" : `STOP_LOSS` indicates a mutation that eliminates a 7208 /// downstream stop codons do not count as `STOP_GAIN`.
7321 * stop codon at the variant site. 7209 /// - "STOP_LOSS" : `STOP_LOSS` indicates a mutation that eliminates a
7322 * - "SPLICE_SITE_DISRUPTION" : `SPLICE_SITE_DISRUPTION` indicates that this 7210 /// stop codon at the variant site.
7323 * variant is 7211 /// - "SPLICE_SITE_DISRUPTION" : `SPLICE_SITE_DISRUPTION` indicates that this
7324 * found in a splice site for the associated transcript, and alters the 7212 /// variant is
7325 * normal splicing pattern. 7213 /// found in a splice site for the associated transcript, and alters the
7326 */ 7214 /// normal splicing pattern.
7327 core.String effect; 7215 core.String effect;
7328 /** 7216
7329 * Google annotation ID of the gene affected by this variant. This should 7217 /// Google annotation ID of the gene affected by this variant. This should
7330 * be provided when the variant is created. 7218 /// be provided when the variant is created.
7331 */
7332 core.String geneId; 7219 core.String geneId;
7333 /** 7220
7334 * Google annotation IDs of the transcripts affected by this variant. These 7221 /// Google annotation IDs of the transcripts affected by this variant. These
7335 * should be provided when the variant is created. 7222 /// should be provided when the variant is created.
7336 */
7337 core.List<core.String> transcriptIds; 7223 core.List<core.String> transcriptIds;
7338 /** 7224
7339 * Type has been adapted from ClinVar's list of variant types. 7225 /// Type has been adapted from ClinVar's list of variant types.
7340 * Possible string values are: 7226 /// Possible string values are:
7341 * - "TYPE_UNSPECIFIED" 7227 /// - "TYPE_UNSPECIFIED"
7342 * - "TYPE_OTHER" : `TYPE_OTHER` should be used when no other Type will 7228 /// - "TYPE_OTHER" : `TYPE_OTHER` should be used when no other Type will
7343 * suffice. 7229 /// suffice.
7344 * Further explanation of the variant type may be included in the 7230 /// Further explanation of the variant type may be included in the
7345 * info field. 7231 /// info field.
7346 * - "INSERTION" : `INSERTION` indicates an insertion. 7232 /// - "INSERTION" : `INSERTION` indicates an insertion.
7347 * - "DELETION" : `DELETION` indicates a deletion. 7233 /// - "DELETION" : `DELETION` indicates a deletion.
7348 * - "SUBSTITUTION" : `SUBSTITUTION` indicates a block substitution of 7234 /// - "SUBSTITUTION" : `SUBSTITUTION` indicates a block substitution of
7349 * two or more nucleotides. 7235 /// two or more nucleotides.
7350 * - "SNP" : `SNP` indicates a single nucleotide polymorphism. 7236 /// - "SNP" : `SNP` indicates a single nucleotide polymorphism.
7351 * - "STRUCTURAL" : `STRUCTURAL` indicates a large structural variant, 7237 /// - "STRUCTURAL" : `STRUCTURAL` indicates a large structural variant,
7352 * including chromosomal fusions, inversions, etc. 7238 /// including chromosomal fusions, inversions, etc.
7353 * - "CNV" : `CNV` indicates a variation in copy number. 7239 /// - "CNV" : `CNV` indicates a variation in copy number.
7354 */
7355 core.String type; 7240 core.String type;
7356 7241
7357 VariantAnnotation(); 7242 VariantAnnotation();
7358 7243
7359 VariantAnnotation.fromJson(core.Map _json) { 7244 VariantAnnotation.fromJson(core.Map _json) {
7360 if (_json.containsKey("alternateBases")) { 7245 if (_json.containsKey("alternateBases")) {
7361 alternateBases = _json["alternateBases"]; 7246 alternateBases = _json["alternateBases"];
7362 } 7247 }
7363 if (_json.containsKey("clinicalSignificance")) { 7248 if (_json.containsKey("clinicalSignificance")) {
7364 clinicalSignificance = _json["clinicalSignificance"]; 7249 clinicalSignificance = _json["clinicalSignificance"];
7365 } 7250 }
7366 if (_json.containsKey("conditions")) { 7251 if (_json.containsKey("conditions")) {
7367 conditions = _json["conditions"].map((value) => new ClinicalCondition.from Json(value)).toList(); 7252 conditions = _json["conditions"]
7253 .map((value) => new ClinicalCondition.fromJson(value))
7254 .toList();
7368 } 7255 }
7369 if (_json.containsKey("effect")) { 7256 if (_json.containsKey("effect")) {
7370 effect = _json["effect"]; 7257 effect = _json["effect"];
7371 } 7258 }
7372 if (_json.containsKey("geneId")) { 7259 if (_json.containsKey("geneId")) {
7373 geneId = _json["geneId"]; 7260 geneId = _json["geneId"];
7374 } 7261 }
7375 if (_json.containsKey("transcriptIds")) { 7262 if (_json.containsKey("transcriptIds")) {
7376 transcriptIds = _json["transcriptIds"]; 7263 transcriptIds = _json["transcriptIds"];
7377 } 7264 }
7378 if (_json.containsKey("type")) { 7265 if (_json.containsKey("type")) {
7379 type = _json["type"]; 7266 type = _json["type"];
7380 } 7267 }
7381 } 7268 }
7382 7269
7383 core.Map<core.String, core.Object> toJson() { 7270 core.Map<core.String, core.Object> toJson() {
7384 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 7271 final core.Map<core.String, core.Object> _json =
7272 new core.Map<core.String, core.Object>();
7385 if (alternateBases != null) { 7273 if (alternateBases != null) {
7386 _json["alternateBases"] = alternateBases; 7274 _json["alternateBases"] = alternateBases;
7387 } 7275 }
7388 if (clinicalSignificance != null) { 7276 if (clinicalSignificance != null) {
7389 _json["clinicalSignificance"] = clinicalSignificance; 7277 _json["clinicalSignificance"] = clinicalSignificance;
7390 } 7278 }
7391 if (conditions != null) { 7279 if (conditions != null) {
7392 _json["conditions"] = conditions.map((value) => (value).toJson()).toList() ; 7280 _json["conditions"] =
7281 conditions.map((value) => (value).toJson()).toList();
7393 } 7282 }
7394 if (effect != null) { 7283 if (effect != null) {
7395 _json["effect"] = effect; 7284 _json["effect"] = effect;
7396 } 7285 }
7397 if (geneId != null) { 7286 if (geneId != null) {
7398 _json["geneId"] = geneId; 7287 _json["geneId"] = geneId;
7399 } 7288 }
7400 if (transcriptIds != null) { 7289 if (transcriptIds != null) {
7401 _json["transcriptIds"] = transcriptIds; 7290 _json["transcriptIds"] = transcriptIds;
7402 } 7291 }
7403 if (type != null) { 7292 if (type != null) {
7404 _json["type"] = type; 7293 _json["type"] = type;
7405 } 7294 }
7406 return _json; 7295 return _json;
7407 } 7296 }
7408 } 7297 }
7409 7298
7410 /** 7299 /// A call represents the determination of genotype with respect to a
7411 * A call represents the determination of genotype with respect to a particular 7300 /// particular
7412 * variant. It may include associated information such as quality and phasing. 7301 /// variant. It may include associated information such as quality and phasing.
7413 * For example, a call might assign a probability of 0.32 to the occurrence of 7302 /// For example, a call might assign a probability of 0.32 to the occurrence of
7414 * a SNP named rs1234 in a call set with the name NA12345. 7303 /// a SNP named rs1234 in a call set with the name NA12345.
7415 */
7416 class VariantCall { 7304 class VariantCall {
7417 /** The ID of the call set this variant call belongs to. */ 7305 /// The ID of the call set this variant call belongs to.
7418 core.String callSetId; 7306 core.String callSetId;
7419 /** The name of the call set this variant call belongs to. */ 7307
7308 /// The name of the call set this variant call belongs to.
7420 core.String callSetName; 7309 core.String callSetName;
7421 /** 7310
7422 * The genotype of this variant call. Each value represents either the value 7311 /// The genotype of this variant call. Each value represents either the value
7423 * of the `referenceBases` field or a 1-based index into 7312 /// of the `referenceBases` field or a 1-based index into
7424 * `alternateBases`. If a variant had a `referenceBases` 7313 /// `alternateBases`. If a variant had a `referenceBases`
7425 * value of `T` and an `alternateBases` 7314 /// value of `T` and an `alternateBases`
7426 * value of `["A", "C"]`, and the `genotype` was 7315 /// value of `["A", "C"]`, and the `genotype` was
7427 * `[2, 1]`, that would mean the call 7316 /// `[2, 1]`, that would mean the call
7428 * represented the heterozygous value `CA` for this variant. 7317 /// represented the heterozygous value `CA` for this variant.
7429 * If the `genotype` was instead `[0, 1]`, the 7318 /// If the `genotype` was instead `[0, 1]`, the
7430 * represented value would be `TA`. Ordering of the 7319 /// represented value would be `TA`. Ordering of the
7431 * genotype values is important if the `phaseset` is present. 7320 /// genotype values is important if the `phaseset` is present.
7432 * If a genotype is not called (that is, a `.` is present in the 7321 /// If a genotype is not called (that is, a `.` is present in the
7433 * GT string) -1 is returned. 7322 /// GT string) -1 is returned.
7434 */
7435 core.List<core.int> genotype; 7323 core.List<core.int> genotype;
7436 /** 7324
7437 * The genotype likelihoods for this variant call. Each array entry 7325 /// The genotype likelihoods for this variant call. Each array entry
7438 * represents how likely a specific genotype is for this call. The value 7326 /// represents how likely a specific genotype is for this call. The value
7439 * ordering is defined by the GL tag in the VCF spec. 7327 /// ordering is defined by the GL tag in the VCF spec.
7440 * If Phred-scaled genotype likelihood scores (PL) are available and 7328 /// If Phred-scaled genotype likelihood scores (PL) are available and
7441 * log10(P) genotype likelihood scores (GL) are not, PL scores are converted 7329 /// log10(P) genotype likelihood scores (GL) are not, PL scores are converted
7442 * to GL scores. If both are available, PL scores are stored in `info`. 7330 /// to GL scores. If both are available, PL scores are stored in `info`.
7443 */
7444 core.List<core.double> genotypeLikelihood; 7331 core.List<core.double> genotypeLikelihood;
7445 /** 7332
7446 * A map of additional variant call information. This must be of the form 7333 /// A map of additional variant call information. This must be of the form
7447 * map<string, string[]> (string key mapping to a list of string values). 7334 /// map<string, string[]> (string key mapping to a list of string values).
7448 * 7335 ///
7449 * The values for Object must be JSON objects. It can consist of `num`, 7336 /// The values for Object must be JSON objects. It can consist of `num`,
7450 * `String`, `bool` and `null` as well as `Map` and `List` values. 7337 /// `String`, `bool` and `null` as well as `Map` and `List` values.
7451 */
7452 core.Map<core.String, core.List<core.Object>> info; 7338 core.Map<core.String, core.List<core.Object>> info;
7453 /** 7339
7454 * If this field is present, this variant call's genotype ordering implies 7340 /// If this field is present, this variant call's genotype ordering implies
7455 * the phase of the bases and is consistent with any other variant calls in 7341 /// the phase of the bases and is consistent with any other variant calls in
7456 * the same reference sequence which have the same phaseset value. 7342 /// the same reference sequence which have the same phaseset value.
7457 * When importing data from VCF, if the genotype data was phased but no 7343 /// When importing data from VCF, if the genotype data was phased but no
7458 * phase set was specified this field will be set to `*`. 7344 /// phase set was specified this field will be set to `*`.
7459 */
7460 core.String phaseset; 7345 core.String phaseset;
7461 7346
7462 VariantCall(); 7347 VariantCall();
7463 7348
7464 VariantCall.fromJson(core.Map _json) { 7349 VariantCall.fromJson(core.Map _json) {
7465 if (_json.containsKey("callSetId")) { 7350 if (_json.containsKey("callSetId")) {
7466 callSetId = _json["callSetId"]; 7351 callSetId = _json["callSetId"];
7467 } 7352 }
7468 if (_json.containsKey("callSetName")) { 7353 if (_json.containsKey("callSetName")) {
7469 callSetName = _json["callSetName"]; 7354 callSetName = _json["callSetName"];
7470 } 7355 }
7471 if (_json.containsKey("genotype")) { 7356 if (_json.containsKey("genotype")) {
7472 genotype = _json["genotype"]; 7357 genotype = _json["genotype"];
7473 } 7358 }
7474 if (_json.containsKey("genotypeLikelihood")) { 7359 if (_json.containsKey("genotypeLikelihood")) {
7475 genotypeLikelihood = _json["genotypeLikelihood"]; 7360 genotypeLikelihood = _json["genotypeLikelihood"];
7476 } 7361 }
7477 if (_json.containsKey("info")) { 7362 if (_json.containsKey("info")) {
7478 info = _json["info"]; 7363 info = _json["info"];
7479 } 7364 }
7480 if (_json.containsKey("phaseset")) { 7365 if (_json.containsKey("phaseset")) {
7481 phaseset = _json["phaseset"]; 7366 phaseset = _json["phaseset"];
7482 } 7367 }
7483 } 7368 }
7484 7369
7485 core.Map<core.String, core.Object> toJson() { 7370 core.Map<core.String, core.Object> toJson() {
7486 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 7371 final core.Map<core.String, core.Object> _json =
7372 new core.Map<core.String, core.Object>();
7487 if (callSetId != null) { 7373 if (callSetId != null) {
7488 _json["callSetId"] = callSetId; 7374 _json["callSetId"] = callSetId;
7489 } 7375 }
7490 if (callSetName != null) { 7376 if (callSetName != null) {
7491 _json["callSetName"] = callSetName; 7377 _json["callSetName"] = callSetName;
7492 } 7378 }
7493 if (genotype != null) { 7379 if (genotype != null) {
7494 _json["genotype"] = genotype; 7380 _json["genotype"] = genotype;
7495 } 7381 }
7496 if (genotypeLikelihood != null) { 7382 if (genotypeLikelihood != null) {
7497 _json["genotypeLikelihood"] = genotypeLikelihood; 7383 _json["genotypeLikelihood"] = genotypeLikelihood;
7498 } 7384 }
7499 if (info != null) { 7385 if (info != null) {
7500 _json["info"] = info; 7386 _json["info"] = info;
7501 } 7387 }
7502 if (phaseset != null) { 7388 if (phaseset != null) {
7503 _json["phaseset"] = phaseset; 7389 _json["phaseset"] = phaseset;
7504 } 7390 }
7505 return _json; 7391 return _json;
7506 } 7392 }
7507 } 7393 }
7508 7394
7509 /** 7395 /// A variant set is a collection of call sets and variants. It contains
7510 * A variant set is a collection of call sets and variants. It contains summary 7396 /// summary
7511 * statistics of those contents. A variant set belongs to a dataset. 7397 /// statistics of those contents. A variant set belongs to a dataset.
7512 * 7398 ///
7513 * For more genomics resource definitions, see [Fundamentals of Google 7399 /// For more genomics resource definitions, see [Fundamentals of Google
7514 * Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 7400 /// Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
7515 */
7516 class VariantSet { 7401 class VariantSet {
7517 /** The dataset to which this variant set belongs. */ 7402 /// The dataset to which this variant set belongs.
7518 core.String datasetId; 7403 core.String datasetId;
7519 /** A textual description of this variant set. */ 7404
7405 /// A textual description of this variant set.
7520 core.String description; 7406 core.String description;
7521 /** The server-generated variant set ID, unique across all variant sets. */ 7407
7408 /// The server-generated variant set ID, unique across all variant sets.
7522 core.String id; 7409 core.String id;
7523 /** The metadata associated with this variant set. */ 7410
7411 /// The metadata associated with this variant set.
7524 core.List<VariantSetMetadata> metadata; 7412 core.List<VariantSetMetadata> metadata;
7525 /** User-specified, mutable name. */ 7413
7414 /// User-specified, mutable name.
7526 core.String name; 7415 core.String name;
7527 /** 7416
7528 * A list of all references used by the variants in a variant set 7417 /// A list of all references used by the variants in a variant set
7529 * with associated coordinate upper bounds for each one. 7418 /// with associated coordinate upper bounds for each one.
7530 */
7531 core.List<ReferenceBound> referenceBounds; 7419 core.List<ReferenceBound> referenceBounds;
7532 /** 7420
7533 * The reference set to which the variant set is mapped. The reference set 7421 /// The reference set to which the variant set is mapped. The reference set
7534 * describes the alignment provenance of the variant set, while the 7422 /// describes the alignment provenance of the variant set, while the
7535 * `referenceBounds` describe the shape of the actual variant data. The 7423 /// `referenceBounds` describe the shape of the actual variant data. The
7536 * reference set's reference names are a superset of those found in the 7424 /// reference set's reference names are a superset of those found in the
7537 * `referenceBounds`. 7425 /// `referenceBounds`.
7538 * 7426 ///
7539 * For example, given a variant set that is mapped to the GRCh38 reference set 7427 /// For example, given a variant set that is mapped to the GRCh38 reference
7540 * and contains a single variant on reference 'X', `referenceBounds` would 7428 /// set
7541 * contain only an entry for 'X', while the associated reference set 7429 /// and contains a single variant on reference 'X', `referenceBounds` would
7542 * enumerates all possible references: '1', '2', 'X', 'Y', 'MT', etc. 7430 /// contain only an entry for 'X', while the associated reference set
7543 */ 7431 /// enumerates all possible references: '1', '2', 'X', 'Y', 'MT', etc.
7544 core.String referenceSetId; 7432 core.String referenceSetId;
7545 7433
7546 VariantSet(); 7434 VariantSet();
7547 7435
7548 VariantSet.fromJson(core.Map _json) { 7436 VariantSet.fromJson(core.Map _json) {
7549 if (_json.containsKey("datasetId")) { 7437 if (_json.containsKey("datasetId")) {
7550 datasetId = _json["datasetId"]; 7438 datasetId = _json["datasetId"];
7551 } 7439 }
7552 if (_json.containsKey("description")) { 7440 if (_json.containsKey("description")) {
7553 description = _json["description"]; 7441 description = _json["description"];
7554 } 7442 }
7555 if (_json.containsKey("id")) { 7443 if (_json.containsKey("id")) {
7556 id = _json["id"]; 7444 id = _json["id"];
7557 } 7445 }
7558 if (_json.containsKey("metadata")) { 7446 if (_json.containsKey("metadata")) {
7559 metadata = _json["metadata"].map((value) => new VariantSetMetadata.fromJso n(value)).toList(); 7447 metadata = _json["metadata"]
7448 .map((value) => new VariantSetMetadata.fromJson(value))
7449 .toList();
7560 } 7450 }
7561 if (_json.containsKey("name")) { 7451 if (_json.containsKey("name")) {
7562 name = _json["name"]; 7452 name = _json["name"];
7563 } 7453 }
7564 if (_json.containsKey("referenceBounds")) { 7454 if (_json.containsKey("referenceBounds")) {
7565 referenceBounds = _json["referenceBounds"].map((value) => new ReferenceBou nd.fromJson(value)).toList(); 7455 referenceBounds = _json["referenceBounds"]
7456 .map((value) => new ReferenceBound.fromJson(value))
7457 .toList();
7566 } 7458 }
7567 if (_json.containsKey("referenceSetId")) { 7459 if (_json.containsKey("referenceSetId")) {
7568 referenceSetId = _json["referenceSetId"]; 7460 referenceSetId = _json["referenceSetId"];
7569 } 7461 }
7570 } 7462 }
7571 7463
7572 core.Map<core.String, core.Object> toJson() { 7464 core.Map<core.String, core.Object> toJson() {
7573 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 7465 final core.Map<core.String, core.Object> _json =
7466 new core.Map<core.String, core.Object>();
7574 if (datasetId != null) { 7467 if (datasetId != null) {
7575 _json["datasetId"] = datasetId; 7468 _json["datasetId"] = datasetId;
7576 } 7469 }
7577 if (description != null) { 7470 if (description != null) {
7578 _json["description"] = description; 7471 _json["description"] = description;
7579 } 7472 }
7580 if (id != null) { 7473 if (id != null) {
7581 _json["id"] = id; 7474 _json["id"] = id;
7582 } 7475 }
7583 if (metadata != null) { 7476 if (metadata != null) {
7584 _json["metadata"] = metadata.map((value) => (value).toJson()).toList(); 7477 _json["metadata"] = metadata.map((value) => (value).toJson()).toList();
7585 } 7478 }
7586 if (name != null) { 7479 if (name != null) {
7587 _json["name"] = name; 7480 _json["name"] = name;
7588 } 7481 }
7589 if (referenceBounds != null) { 7482 if (referenceBounds != null) {
7590 _json["referenceBounds"] = referenceBounds.map((value) => (value).toJson() ).toList(); 7483 _json["referenceBounds"] =
7484 referenceBounds.map((value) => (value).toJson()).toList();
7591 } 7485 }
7592 if (referenceSetId != null) { 7486 if (referenceSetId != null) {
7593 _json["referenceSetId"] = referenceSetId; 7487 _json["referenceSetId"] = referenceSetId;
7594 } 7488 }
7595 return _json; 7489 return _json;
7596 } 7490 }
7597 } 7491 }
7598 7492
7599 /** 7493 /// Metadata describes a single piece of variant call metadata.
7600 * Metadata describes a single piece of variant call metadata. 7494 /// These data include a top level key and either a single value string (value)
7601 * These data include a top level key and either a single value string (value) 7495 /// or a list of key-value pairs (info.)
7602 * or a list of key-value pairs (info.) 7496 /// Value and info are mutually exclusive.
7603 * Value and info are mutually exclusive.
7604 */
7605 class VariantSetMetadata { 7497 class VariantSetMetadata {
7606 /** A textual description of this metadata. */ 7498 /// A textual description of this metadata.
7607 core.String description; 7499 core.String description;
7608 /** 7500
7609 * User-provided ID field, not enforced by this API. 7501 /// User-provided ID field, not enforced by this API.
7610 * Two or more pieces of structured metadata with identical 7502 /// Two or more pieces of structured metadata with identical
7611 * id and key fields are considered equivalent. 7503 /// id and key fields are considered equivalent.
7612 */
7613 core.String id; 7504 core.String id;
7614 /** 7505
7615 * Remaining structured metadata key-value pairs. This must be of the form 7506 /// Remaining structured metadata key-value pairs. This must be of the form
7616 * map<string, string[]> (string key mapping to a list of string values). 7507 /// map<string, string[]> (string key mapping to a list of string values).
7617 * 7508 ///
7618 * The values for Object must be JSON objects. It can consist of `num`, 7509 /// The values for Object must be JSON objects. It can consist of `num`,
7619 * `String`, `bool` and `null` as well as `Map` and `List` values. 7510 /// `String`, `bool` and `null` as well as `Map` and `List` values.
7620 */
7621 core.Map<core.String, core.List<core.Object>> info; 7511 core.Map<core.String, core.List<core.Object>> info;
7622 /** The top-level key. */ 7512
7513 /// The top-level key.
7623 core.String key; 7514 core.String key;
7624 /** 7515
7625 * The number of values that can be included in a field described by this 7516 /// The number of values that can be included in a field described by this
7626 * metadata. 7517 /// metadata.
7627 */
7628 core.String number; 7518 core.String number;
7629 /** 7519
7630 * The type of data. Possible types include: Integer, Float, 7520 /// The type of data. Possible types include: Integer, Float,
7631 * Flag, Character, and String. 7521 /// Flag, Character, and String.
7632 * Possible string values are: 7522 /// Possible string values are:
7633 * - "TYPE_UNSPECIFIED" 7523 /// - "TYPE_UNSPECIFIED"
7634 * - "INTEGER" 7524 /// - "INTEGER"
7635 * - "FLOAT" 7525 /// - "FLOAT"
7636 * - "FLAG" 7526 /// - "FLAG"
7637 * - "CHARACTER" 7527 /// - "CHARACTER"
7638 * - "STRING" 7528 /// - "STRING"
7639 */
7640 core.String type; 7529 core.String type;
7641 /** The value field for simple metadata */ 7530
7531 /// The value field for simple metadata
7642 core.String value; 7532 core.String value;
7643 7533
7644 VariantSetMetadata(); 7534 VariantSetMetadata();
7645 7535
7646 VariantSetMetadata.fromJson(core.Map _json) { 7536 VariantSetMetadata.fromJson(core.Map _json) {
7647 if (_json.containsKey("description")) { 7537 if (_json.containsKey("description")) {
7648 description = _json["description"]; 7538 description = _json["description"];
7649 } 7539 }
7650 if (_json.containsKey("id")) { 7540 if (_json.containsKey("id")) {
7651 id = _json["id"]; 7541 id = _json["id"];
7652 } 7542 }
7653 if (_json.containsKey("info")) { 7543 if (_json.containsKey("info")) {
7654 info = _json["info"]; 7544 info = _json["info"];
7655 } 7545 }
7656 if (_json.containsKey("key")) { 7546 if (_json.containsKey("key")) {
7657 key = _json["key"]; 7547 key = _json["key"];
7658 } 7548 }
7659 if (_json.containsKey("number")) { 7549 if (_json.containsKey("number")) {
7660 number = _json["number"]; 7550 number = _json["number"];
7661 } 7551 }
7662 if (_json.containsKey("type")) { 7552 if (_json.containsKey("type")) {
7663 type = _json["type"]; 7553 type = _json["type"];
7664 } 7554 }
7665 if (_json.containsKey("value")) { 7555 if (_json.containsKey("value")) {
7666 value = _json["value"]; 7556 value = _json["value"];
7667 } 7557 }
7668 } 7558 }
7669 7559
7670 core.Map<core.String, core.Object> toJson() { 7560 core.Map<core.String, core.Object> toJson() {
7671 final core.Map<core.String, core.Object> _json = new core.Map<core.String, c ore.Object>(); 7561 final core.Map<core.String, core.Object> _json =
7562 new core.Map<core.String, core.Object>();
7672 if (description != null) { 7563 if (description != null) {
7673 _json["description"] = description; 7564 _json["description"] = description;
7674 } 7565 }
7675 if (id != null) { 7566 if (id != null) {
7676 _json["id"] = id; 7567 _json["id"] = id;
7677 } 7568 }
7678 if (info != null) { 7569 if (info != null) {
7679 _json["info"] = info; 7570 _json["info"] = info;
7680 } 7571 }
7681 if (key != null) { 7572 if (key != null) {
7682 _json["key"] = key; 7573 _json["key"] = key;
7683 } 7574 }
7684 if (number != null) { 7575 if (number != null) {
7685 _json["number"] = number; 7576 _json["number"] = number;
7686 } 7577 }
7687 if (type != null) { 7578 if (type != null) {
7688 _json["type"] = type; 7579 _json["type"] = type;
7689 } 7580 }
7690 if (value != null) { 7581 if (value != null) {
7691 _json["value"] = value; 7582 _json["value"] = value;
7692 } 7583 }
7693 return _json; 7584 return _json;
7694 } 7585 }
7695 } 7586 }
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