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Side by Side Diff: generated/googleapis_beta/lib/genomics/v1beta.dart

Issue 595873002: Api roll 1: 2014-09-23 (Closed) Base URL: git@github.com:dart-lang/googleapis.git@master
Patch Set: Created 6 years, 2 months ago
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1 library googleapis_beta.genomics.v1beta; 1 library googleapis_beta.genomics.v1beta;
2 2
3 import "dart:core" as core; 3 import "dart:core" as core;
4 import "dart:collection" as collection; 4 import "dart:collection" as collection;
5 import "dart:async" as async; 5 import "dart:async" as async;
6 import "dart:convert" as convert; 6 import "dart:convert" as convert;
7 7
8 import "package:crypto/crypto.dart" as crypto; 8 import "package:crypto/crypto.dart" as crypto;
9 import 'package:http/http.dart' as http; 9 import 'package:http/http.dart' as http;
10 import '../src/common_internal.dart' as common_internal; 10 import '../src/common_internal.dart' as common_internal;
(...skipping 20 matching lines...) Expand all
31 final common_internal.ApiRequester _requester; 31 final common_internal.ApiRequester _requester;
32 32
33 BeaconsResourceApi get beacons => new BeaconsResourceApi(_requester); 33 BeaconsResourceApi get beacons => new BeaconsResourceApi(_requester);
34 CallsetsResourceApi get callsets => new CallsetsResourceApi(_requester); 34 CallsetsResourceApi get callsets => new CallsetsResourceApi(_requester);
35 DatasetsResourceApi get datasets => new DatasetsResourceApi(_requester); 35 DatasetsResourceApi get datasets => new DatasetsResourceApi(_requester);
36 ExperimentalResourceApi get experimental => new ExperimentalResourceApi(_reque ster); 36 ExperimentalResourceApi get experimental => new ExperimentalResourceApi(_reque ster);
37 JobsResourceApi get jobs => new JobsResourceApi(_requester); 37 JobsResourceApi get jobs => new JobsResourceApi(_requester);
38 ReadsResourceApi get reads => new ReadsResourceApi(_requester); 38 ReadsResourceApi get reads => new ReadsResourceApi(_requester);
39 ReadsetsResourceApi get readsets => new ReadsetsResourceApi(_requester); 39 ReadsetsResourceApi get readsets => new ReadsetsResourceApi(_requester);
40 VariantsResourceApi get variants => new VariantsResourceApi(_requester); 40 VariantsResourceApi get variants => new VariantsResourceApi(_requester);
41 VariantsetsResourceApi get variantsets => new VariantsetsResourceApi(_requeste r);
41 42
42 GenomicsApi(http.Client client) : 43 GenomicsApi(http.Client client) :
43 _requester = new common_internal.ApiRequester(client, "https://www.googlea pis.com/", "/genomics/v1beta/"); 44 _requester = new common_internal.ApiRequester(client, "https://www.googlea pis.com/", "genomics/v1beta/");
44 } 45 }
45 46
46 47
47 /** Not documented yet. */ 48 /** Not documented yet. */
48 class BeaconsResourceApi { 49 class BeaconsResourceApi {
49 final common_internal.ApiRequester _requester; 50 final common_internal.ApiRequester _requester;
50 51
51 BeaconsResourceApi(common_internal.ApiRequester client) : 52 BeaconsResourceApi(common_internal.ApiRequester client) :
52 _requester = client; 53 _requester = client;
53 54
54 /** 55 /**
55 * This is an experimental API that provides a Global Alliance for Genomics 56 * This is an experimental API that provides a Global Alliance for Genomics
56 * and Health Beacon. It may change at any time. 57 * and Health Beacon. It may change at any time.
57 * 58 *
58 * Request parameters: 59 * Request parameters:
59 * 60 *
60 * [variantsetId] - The ID of the variantset to query over. It must be public. 61 * [variantSetId] - The ID of the variant set to query over. It must be
61 * Private variantsets will return an unauthorized exception. 62 * public. Private variant sets will return an unauthorized exception.
62 * 63 *
63 * [allele] - Required. The allele to look for ('A', 'C', 'G' or 'T'). 64 * [allele] - Required. The allele to look for ('A', 'C', 'G' or 'T').
64 * 65 *
65 * [contig] - Required. The contig to query over. 66 * [position] - Required. The 0-based position to query.
66 * 67 *
67 * [position] - Required. The 0-based position to query. 68 * [referenceName] - Required. The reference to query over.
68 * 69 *
69 * Completes with a [Beacon]. 70 * Completes with a [Beacon].
70 * 71 *
71 * Completes with a [common.ApiRequestError] if the API endpoint returned an 72 * Completes with a [common.ApiRequestError] if the API endpoint returned an
72 * error. 73 * error.
73 * 74 *
74 * If the used [http.Client] completes with an error when making a REST call, 75 * If the used [http.Client] completes with an error when making a REST call,
75 * this method will complete with the same error. 76 * this method will complete with the same error.
76 */ 77 */
77 async.Future<Beacon> get(core.String variantsetId, {core.String allele, core.S tring contig, core.String position}) { 78 async.Future<Beacon> get(core.String variantSetId, {core.String allele, core.S tring position, core.String referenceName}) {
78 var _url = null; 79 var _url = null;
79 var _queryParams = new core.Map(); 80 var _queryParams = new core.Map();
80 var _uploadMedia = null; 81 var _uploadMedia = null;
81 var _uploadOptions = null; 82 var _uploadOptions = null;
82 var _downloadOptions = common.DownloadOptions.Metadata; 83 var _downloadOptions = common.DownloadOptions.Metadata;
83 var _body = null; 84 var _body = null;
84 85
85 if (variantsetId == null) { 86 if (variantSetId == null) {
86 throw new core.ArgumentError("Parameter variantsetId is required."); 87 throw new core.ArgumentError("Parameter variantSetId is required.");
87 } 88 }
88 if (allele != null) { 89 if (allele != null) {
89 _queryParams["allele"] = [allele]; 90 _queryParams["allele"] = [allele];
90 } 91 }
91 if (contig != null) {
92 _queryParams["contig"] = [contig];
93 }
94 if (position != null) { 92 if (position != null) {
95 _queryParams["position"] = [position]; 93 _queryParams["position"] = [position];
96 } 94 }
95 if (referenceName != null) {
96 _queryParams["referenceName"] = [referenceName];
97 }
97 98
98 99
99 _url = 'beacons/' + common_internal.Escaper.ecapeVariable('$variantsetId'); 100 _url = 'beacons/' + common_internal.Escaper.ecapeVariable('$variantSetId');
100 101
101 var _response = _requester.request(_url, 102 var _response = _requester.request(_url,
102 "GET", 103 "GET",
103 body: _body, 104 body: _body,
104 queryParams: _queryParams, 105 queryParams: _queryParams,
105 uploadOptions: _uploadOptions, 106 uploadOptions: _uploadOptions,
106 uploadMedia: _uploadMedia, 107 uploadMedia: _uploadMedia,
107 downloadOptions: _downloadOptions); 108 downloadOptions: _downloadOptions);
108 return _response.then((data) => new Beacon.fromJson(data)); 109 return _response.then((data) => new Beacon.fromJson(data));
109 } 110 }
110 111
111 } 112 }
112 113
113 114
114 /** Not documented yet. */ 115 /** Not documented yet. */
115 class CallsetsResourceApi { 116 class CallsetsResourceApi {
116 final common_internal.ApiRequester _requester; 117 final common_internal.ApiRequester _requester;
117 118
118 CallsetsResourceApi(common_internal.ApiRequester client) : 119 CallsetsResourceApi(common_internal.ApiRequester client) :
119 _requester = client; 120 _requester = client;
120 121
121 /** 122 /**
122 * Creates a new callset. 123 * Creates a new call set.
123 * 124 *
124 * [request] - The metadata request object. 125 * [request] - The metadata request object.
125 * 126 *
126 * Request parameters: 127 * Request parameters:
127 * 128 *
128 * Completes with a [Callset]. 129 * Completes with a [CallSet].
129 * 130 *
130 * Completes with a [common.ApiRequestError] if the API endpoint returned an 131 * Completes with a [common.ApiRequestError] if the API endpoint returned an
131 * error. 132 * error.
132 * 133 *
133 * If the used [http.Client] completes with an error when making a REST call, 134 * If the used [http.Client] completes with an error when making a REST call,
134 * this method will complete with the same error. 135 * this method will complete with the same error.
135 */ 136 */
136 async.Future<Callset> create(Callset request) { 137 async.Future<CallSet> create(CallSet request) {
137 var _url = null; 138 var _url = null;
138 var _queryParams = new core.Map(); 139 var _queryParams = new core.Map();
139 var _uploadMedia = null; 140 var _uploadMedia = null;
140 var _uploadOptions = null; 141 var _uploadOptions = null;
141 var _downloadOptions = common.DownloadOptions.Metadata; 142 var _downloadOptions = common.DownloadOptions.Metadata;
142 var _body = null; 143 var _body = null;
143 144
144 if (request != null) { 145 if (request != null) {
145 _body = convert.JSON.encode((request).toJson()); 146 _body = convert.JSON.encode((request).toJson());
146 } 147 }
147 148
148 149
149 _url = 'callsets'; 150 _url = 'callsets';
150 151
151 var _response = _requester.request(_url, 152 var _response = _requester.request(_url,
152 "POST", 153 "POST",
153 body: _body, 154 body: _body,
154 queryParams: _queryParams, 155 queryParams: _queryParams,
155 uploadOptions: _uploadOptions, 156 uploadOptions: _uploadOptions,
156 uploadMedia: _uploadMedia, 157 uploadMedia: _uploadMedia,
157 downloadOptions: _downloadOptions); 158 downloadOptions: _downloadOptions);
158 return _response.then((data) => new Callset.fromJson(data)); 159 return _response.then((data) => new CallSet.fromJson(data));
159 } 160 }
160 161
161 /** 162 /**
162 * Deletes a callset. 163 * Deletes a call set.
163 * 164 *
164 * Request parameters: 165 * Request parameters:
165 * 166 *
166 * [callsetId] - The ID of the callset to be deleted. 167 * [callSetId] - The ID of the callset to be deleted.
167 * 168 *
168 * Completes with a [common.ApiRequestError] if the API endpoint returned an 169 * Completes with a [common.ApiRequestError] if the API endpoint returned an
169 * error. 170 * error.
170 * 171 *
171 * If the used [http.Client] completes with an error when making a REST call, 172 * If the used [http.Client] completes with an error when making a REST call,
172 * this method will complete with the same error. 173 * this method will complete with the same error.
173 */ 174 */
174 async.Future delete(core.String callsetId) { 175 async.Future delete(core.String callSetId) {
175 var _url = null; 176 var _url = null;
176 var _queryParams = new core.Map(); 177 var _queryParams = new core.Map();
177 var _uploadMedia = null; 178 var _uploadMedia = null;
178 var _uploadOptions = null; 179 var _uploadOptions = null;
179 var _downloadOptions = common.DownloadOptions.Metadata; 180 var _downloadOptions = common.DownloadOptions.Metadata;
180 var _body = null; 181 var _body = null;
181 182
182 if (callsetId == null) { 183 if (callSetId == null) {
183 throw new core.ArgumentError("Parameter callsetId is required."); 184 throw new core.ArgumentError("Parameter callSetId is required.");
184 } 185 }
185 186
186 _downloadOptions = null; 187 _downloadOptions = null;
187 188
188 _url = 'callsets/' + common_internal.Escaper.ecapeVariable('$callsetId'); 189 _url = 'callsets/' + common_internal.Escaper.ecapeVariable('$callSetId');
189 190
190 var _response = _requester.request(_url, 191 var _response = _requester.request(_url,
191 "DELETE", 192 "DELETE",
192 body: _body, 193 body: _body,
193 queryParams: _queryParams, 194 queryParams: _queryParams,
194 uploadOptions: _uploadOptions, 195 uploadOptions: _uploadOptions,
195 uploadMedia: _uploadMedia, 196 uploadMedia: _uploadMedia,
196 downloadOptions: _downloadOptions); 197 downloadOptions: _downloadOptions);
197 return _response.then((data) => null); 198 return _response.then((data) => null);
198 } 199 }
199 200
200 /** 201 /**
201 * Gets a callset by ID. 202 * Gets a call set by ID.
202 * 203 *
203 * Request parameters: 204 * Request parameters:
204 * 205 *
205 * [callsetId] - The ID of the callset. 206 * [callSetId] - The ID of the callset.
206 * 207 *
207 * Completes with a [Callset]. 208 * Completes with a [CallSet].
208 * 209 *
209 * Completes with a [common.ApiRequestError] if the API endpoint returned an 210 * Completes with a [common.ApiRequestError] if the API endpoint returned an
210 * error. 211 * error.
211 * 212 *
212 * If the used [http.Client] completes with an error when making a REST call, 213 * If the used [http.Client] completes with an error when making a REST call,
213 * this method will complete with the same error. 214 * this method will complete with the same error.
214 */ 215 */
215 async.Future<Callset> get(core.String callsetId) { 216 async.Future<CallSet> get(core.String callSetId) {
216 var _url = null; 217 var _url = null;
217 var _queryParams = new core.Map(); 218 var _queryParams = new core.Map();
218 var _uploadMedia = null; 219 var _uploadMedia = null;
219 var _uploadOptions = null; 220 var _uploadOptions = null;
220 var _downloadOptions = common.DownloadOptions.Metadata; 221 var _downloadOptions = common.DownloadOptions.Metadata;
221 var _body = null; 222 var _body = null;
222 223
223 if (callsetId == null) { 224 if (callSetId == null) {
224 throw new core.ArgumentError("Parameter callsetId is required."); 225 throw new core.ArgumentError("Parameter callSetId is required.");
225 } 226 }
226 227
227 228
228 _url = 'callsets/' + common_internal.Escaper.ecapeVariable('$callsetId'); 229 _url = 'callsets/' + common_internal.Escaper.ecapeVariable('$callSetId');
229 230
230 var _response = _requester.request(_url, 231 var _response = _requester.request(_url,
231 "GET", 232 "GET",
232 body: _body, 233 body: _body,
233 queryParams: _queryParams, 234 queryParams: _queryParams,
234 uploadOptions: _uploadOptions, 235 uploadOptions: _uploadOptions,
235 uploadMedia: _uploadMedia, 236 uploadMedia: _uploadMedia,
236 downloadOptions: _downloadOptions); 237 downloadOptions: _downloadOptions);
237 return _response.then((data) => new Callset.fromJson(data)); 238 return _response.then((data) => new CallSet.fromJson(data));
238 } 239 }
239 240
240 /** 241 /**
241 * Updates a callset. This method supports patch semantics. 242 * Updates a call set. This method supports patch semantics.
242 * 243 *
243 * [request] - The metadata request object. 244 * [request] - The metadata request object.
244 * 245 *
245 * Request parameters: 246 * Request parameters:
246 * 247 *
247 * [callsetId] - The ID of the callset to be updated. 248 * [callSetId] - The ID of the callset to be updated.
248 * 249 *
249 * Completes with a [Callset]. 250 * Completes with a [CallSet].
250 * 251 *
251 * Completes with a [common.ApiRequestError] if the API endpoint returned an 252 * Completes with a [common.ApiRequestError] if the API endpoint returned an
252 * error. 253 * error.
253 * 254 *
254 * If the used [http.Client] completes with an error when making a REST call, 255 * If the used [http.Client] completes with an error when making a REST call,
255 * this method will complete with the same error. 256 * this method will complete with the same error.
256 */ 257 */
257 async.Future<Callset> patch(Callset request, core.String callsetId) { 258 async.Future<CallSet> patch(CallSet request, core.String callSetId) {
258 var _url = null; 259 var _url = null;
259 var _queryParams = new core.Map(); 260 var _queryParams = new core.Map();
260 var _uploadMedia = null; 261 var _uploadMedia = null;
261 var _uploadOptions = null; 262 var _uploadOptions = null;
262 var _downloadOptions = common.DownloadOptions.Metadata; 263 var _downloadOptions = common.DownloadOptions.Metadata;
263 var _body = null; 264 var _body = null;
264 265
265 if (request != null) { 266 if (request != null) {
266 _body = convert.JSON.encode((request).toJson()); 267 _body = convert.JSON.encode((request).toJson());
267 } 268 }
268 if (callsetId == null) { 269 if (callSetId == null) {
269 throw new core.ArgumentError("Parameter callsetId is required."); 270 throw new core.ArgumentError("Parameter callSetId is required.");
270 } 271 }
271 272
272 273
273 _url = 'callsets/' + common_internal.Escaper.ecapeVariable('$callsetId'); 274 _url = 'callsets/' + common_internal.Escaper.ecapeVariable('$callSetId');
274 275
275 var _response = _requester.request(_url, 276 var _response = _requester.request(_url,
276 "PATCH", 277 "PATCH",
277 body: _body, 278 body: _body,
278 queryParams: _queryParams, 279 queryParams: _queryParams,
279 uploadOptions: _uploadOptions, 280 uploadOptions: _uploadOptions,
280 uploadMedia: _uploadMedia, 281 uploadMedia: _uploadMedia,
281 downloadOptions: _downloadOptions); 282 downloadOptions: _downloadOptions);
282 return _response.then((data) => new Callset.fromJson(data)); 283 return _response.then((data) => new CallSet.fromJson(data));
283 } 284 }
284 285
285 /** 286 /**
286 * Gets a list of callsets matching the criteria. 287 * Gets a list of call sets matching the criteria.
287 * 288 *
288 * [request] - The metadata request object. 289 * [request] - The metadata request object.
289 * 290 *
290 * Request parameters: 291 * Request parameters:
291 * 292 *
292 * Completes with a [SearchCallsetsResponse]. 293 * Completes with a [SearchCallSetsResponse].
293 * 294 *
294 * Completes with a [common.ApiRequestError] if the API endpoint returned an 295 * Completes with a [common.ApiRequestError] if the API endpoint returned an
295 * error. 296 * error.
296 * 297 *
297 * If the used [http.Client] completes with an error when making a REST call, 298 * If the used [http.Client] completes with an error when making a REST call,
298 * this method will complete with the same error. 299 * this method will complete with the same error.
299 */ 300 */
300 async.Future<SearchCallsetsResponse> search(SearchCallsetsRequest request) { 301 async.Future<SearchCallSetsResponse> search(SearchCallSetsRequest request) {
301 var _url = null; 302 var _url = null;
302 var _queryParams = new core.Map(); 303 var _queryParams = new core.Map();
303 var _uploadMedia = null; 304 var _uploadMedia = null;
304 var _uploadOptions = null; 305 var _uploadOptions = null;
305 var _downloadOptions = common.DownloadOptions.Metadata; 306 var _downloadOptions = common.DownloadOptions.Metadata;
306 var _body = null; 307 var _body = null;
307 308
308 if (request != null) { 309 if (request != null) {
309 _body = convert.JSON.encode((request).toJson()); 310 _body = convert.JSON.encode((request).toJson());
310 } 311 }
311 312
312 313
313 _url = 'callsets/search'; 314 _url = 'callsets/search';
314 315
315 var _response = _requester.request(_url, 316 var _response = _requester.request(_url,
316 "POST", 317 "POST",
317 body: _body, 318 body: _body,
318 queryParams: _queryParams, 319 queryParams: _queryParams,
319 uploadOptions: _uploadOptions, 320 uploadOptions: _uploadOptions,
320 uploadMedia: _uploadMedia, 321 uploadMedia: _uploadMedia,
321 downloadOptions: _downloadOptions); 322 downloadOptions: _downloadOptions);
322 return _response.then((data) => new SearchCallsetsResponse.fromJson(data)); 323 return _response.then((data) => new SearchCallSetsResponse.fromJson(data));
323 } 324 }
324 325
325 /** 326 /**
326 * Updates a callset. 327 * Updates a call set.
327 * 328 *
328 * [request] - The metadata request object. 329 * [request] - The metadata request object.
329 * 330 *
330 * Request parameters: 331 * Request parameters:
331 * 332 *
332 * [callsetId] - The ID of the callset to be updated. 333 * [callSetId] - The ID of the callset to be updated.
333 * 334 *
334 * Completes with a [Callset]. 335 * Completes with a [CallSet].
335 * 336 *
336 * Completes with a [common.ApiRequestError] if the API endpoint returned an 337 * Completes with a [common.ApiRequestError] if the API endpoint returned an
337 * error. 338 * error.
338 * 339 *
339 * If the used [http.Client] completes with an error when making a REST call, 340 * If the used [http.Client] completes with an error when making a REST call,
340 * this method will complete with the same error. 341 * this method will complete with the same error.
341 */ 342 */
342 async.Future<Callset> update(Callset request, core.String callsetId) { 343 async.Future<CallSet> update(CallSet request, core.String callSetId) {
343 var _url = null; 344 var _url = null;
344 var _queryParams = new core.Map(); 345 var _queryParams = new core.Map();
345 var _uploadMedia = null; 346 var _uploadMedia = null;
346 var _uploadOptions = null; 347 var _uploadOptions = null;
347 var _downloadOptions = common.DownloadOptions.Metadata; 348 var _downloadOptions = common.DownloadOptions.Metadata;
348 var _body = null; 349 var _body = null;
349 350
350 if (request != null) { 351 if (request != null) {
351 _body = convert.JSON.encode((request).toJson()); 352 _body = convert.JSON.encode((request).toJson());
352 } 353 }
353 if (callsetId == null) { 354 if (callSetId == null) {
354 throw new core.ArgumentError("Parameter callsetId is required."); 355 throw new core.ArgumentError("Parameter callSetId is required.");
355 } 356 }
356 357
357 358
358 _url = 'callsets/' + common_internal.Escaper.ecapeVariable('$callsetId'); 359 _url = 'callsets/' + common_internal.Escaper.ecapeVariable('$callSetId');
359 360
360 var _response = _requester.request(_url, 361 var _response = _requester.request(_url,
361 "PUT", 362 "PUT",
362 body: _body, 363 body: _body,
363 queryParams: _queryParams, 364 queryParams: _queryParams,
364 uploadOptions: _uploadOptions, 365 uploadOptions: _uploadOptions,
365 uploadMedia: _uploadMedia, 366 uploadMedia: _uploadMedia,
366 downloadOptions: _downloadOptions); 367 downloadOptions: _downloadOptions);
367 return _response.then((data) => new Callset.fromJson(data)); 368 return _response.then((data) => new CallSet.fromJson(data));
368 } 369 }
369 370
370 } 371 }
371 372
372 373
373 /** Not documented yet. */ 374 /** Not documented yet. */
374 class DatasetsResourceApi { 375 class DatasetsResourceApi {
375 final common_internal.ApiRequester _requester; 376 final common_internal.ApiRequester _requester;
376 377
377 DatasetsResourceApi(common_internal.ApiRequester client) : 378 DatasetsResourceApi(common_internal.ApiRequester client) :
(...skipping 120 matching lines...) Expand 10 before | Expand all | Expand 10 after
498 499
499 /** 500 /**
500 * Lists all datasets. 501 * Lists all datasets.
501 * 502 *
502 * Request parameters: 503 * Request parameters:
503 * 504 *
504 * [maxResults] - The maximum number of results returned by this request. 505 * [maxResults] - The maximum number of results returned by this request.
505 * 506 *
506 * [pageToken] - The continuation token, which is used to page through large 507 * [pageToken] - The continuation token, which is used to page through large
507 * result sets. To get the next page of results, set this parameter to the 508 * result sets. To get the next page of results, set this parameter to the
508 * value of "nextPageToken" from the previous response. 509 * value of nextPageToken from the previous response.
509 * 510 *
510 * [projectId] - Only return datasets which belong to this Google Developers 511 * [projectId] - Only return datasets which belong to this Google Developers
511 * Console project. Only accepts project numbers. 512 * Console project. Only accepts project numbers.
512 * 513 *
513 * Completes with a [ListDatasetsResponse]. 514 * Completes with a [ListDatasetsResponse].
514 * 515 *
515 * Completes with a [common.ApiRequestError] if the API endpoint returned an 516 * Completes with a [common.ApiRequestError] if the API endpoint returned an
516 * error. 517 * error.
517 * 518 *
518 * If the used [http.Client] completes with an error when making a REST call, 519 * If the used [http.Client] completes with an error when making a REST call,
(...skipping 744 matching lines...) Expand 10 before | Expand all | Expand 10 after
1263 * Request parameters: 1264 * Request parameters:
1264 * 1265 *
1265 * [readsetId] - Required. The ID of the readset over which coverage is 1266 * [readsetId] - Required. The ID of the readset over which coverage is
1266 * requested. 1267 * requested.
1267 * 1268 *
1268 * [maxResults] - The maximum number of results to return in a single page. If 1269 * [maxResults] - The maximum number of results to return in a single page. If
1269 * unspecified, defaults to 1024. The maximum value is 2048. 1270 * unspecified, defaults to 1024. The maximum value is 2048.
1270 * 1271 *
1271 * [pageToken] - The continuation token, which is used to page through large 1272 * [pageToken] - The continuation token, which is used to page through large
1272 * result sets. To get the next page of results, set this parameter to the 1273 * result sets. To get the next page of results, set this parameter to the
1273 * value of "nextPageToken" from the previous response. 1274 * value of nextPageToken from the previous response.
1274 * 1275 *
1275 * [range_sequenceEnd] - The end position of the range on the reference, 1276 * [range_sequenceEnd] - The end position of the range on the reference,
1276 * 1-based exclusive. If specified, sequenceName must also be specified. 1277 * 1-based exclusive. If specified, sequenceName must also be specified.
1277 * 1278 *
1278 * [range_sequenceName] - The reference sequence name, for example "chr1", 1279 * [range_sequenceName] - The reference sequence name, for example chr1, 1, or
1279 * "1", or "chrX". 1280 * chrX.
1280 * 1281 *
1281 * [range_sequenceStart] - The start position of the range on the reference, 1282 * [range_sequenceStart] - The start position of the range on the reference,
1282 * 1-based inclusive. If specified, sequenceName must also be specified. 1283 * 1-based inclusive. If specified, sequenceName must also be specified.
1283 * 1284 *
1284 * [targetBucketWidth] - The desired width of each reported coverage bucket in 1285 * [targetBucketWidth] - The desired width of each reported coverage bucket in
1285 * base pairs. This will be rounded down to the nearest precomputed bucket 1286 * base pairs. This will be rounded down to the nearest precomputed bucket
1286 * width; the value of which is returned as bucket_width in the response. 1287 * width; the value of which is returned as bucketWidth in the response.
1287 * Defaults to infinity (each bucket spans an entire reference sequence) or 1288 * Defaults to infinity (each bucket spans an entire reference sequence) or
1288 * the length of the target range, if specified. The smallest precomputed 1289 * the length of the target range, if specified. The smallest precomputed
1289 * bucket_width is currently 2048 base pairs; this is subject to change. 1290 * bucketWidth is currently 2048 base pairs; this is subject to change.
1290 * 1291 *
1291 * Completes with a [ListCoverageBucketsResponse]. 1292 * Completes with a [ListCoverageBucketsResponse].
1292 * 1293 *
1293 * Completes with a [common.ApiRequestError] if the API endpoint returned an 1294 * Completes with a [common.ApiRequestError] if the API endpoint returned an
1294 * error. 1295 * error.
1295 * 1296 *
1296 * If the used [http.Client] completes with an error when making a REST call, 1297 * If the used [http.Client] completes with an error when making a REST call,
1297 * this method will complete with the same error. 1298 * this method will complete with the same error.
1298 */ 1299 */
1299 async.Future<ListCoverageBucketsResponse> list(core.String readsetId, {core.St ring maxResults, core.String pageToken, core.String range_sequenceEnd, core.Stri ng range_sequenceName, core.String range_sequenceStart, core.String targetBucket Width}) { 1300 async.Future<ListCoverageBucketsResponse> list(core.String readsetId, {core.St ring maxResults, core.String pageToken, core.String range_sequenceEnd, core.Stri ng range_sequenceName, core.String range_sequenceStart, core.String targetBucket Width}) {
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1502 "GET", 1503 "GET",
1503 body: _body, 1504 body: _body,
1504 queryParams: _queryParams, 1505 queryParams: _queryParams,
1505 uploadOptions: _uploadOptions, 1506 uploadOptions: _uploadOptions,
1506 uploadMedia: _uploadMedia, 1507 uploadMedia: _uploadMedia,
1507 downloadOptions: _downloadOptions); 1508 downloadOptions: _downloadOptions);
1508 return _response.then((data) => new Variant.fromJson(data)); 1509 return _response.then((data) => new Variant.fromJson(data));
1509 } 1510 }
1510 1511
1511 /** 1512 /**
1512 * Gets a summary of all the variant data in a variantset. 1513 * Creates variant data by asynchronously importing the provided information.
1514 *
1515 * [request] - The metadata request object.
1513 * 1516 *
1514 * Request parameters: 1517 * Request parameters:
1515 * 1518 *
1516 * [variantsetId] - Required. The ID of the variant set to get variant summary 1519 * Completes with a [ImportVariantsResponse].
1517 * information for.
1518 *
1519 * Completes with a [GetVariantsSummaryResponse].
1520 * 1520 *
1521 * Completes with a [common.ApiRequestError] if the API endpoint returned an 1521 * Completes with a [common.ApiRequestError] if the API endpoint returned an
1522 * error. 1522 * error.
1523 * 1523 *
1524 * If the used [http.Client] completes with an error when making a REST call, 1524 * If the used [http.Client] completes with an error when making a REST call,
1525 * this method will complete with the same error. 1525 * this method will complete with the same error.
1526 */ 1526 */
1527 async.Future<GetVariantsSummaryResponse> getSummary({core.String variantsetId} ) { 1527 async.Future<ImportVariantsResponse> import(ImportVariantsRequest request) {
1528 var _url = null; 1528 var _url = null;
1529 var _queryParams = new core.Map(); 1529 var _queryParams = new core.Map();
1530 var _uploadMedia = null; 1530 var _uploadMedia = null;
1531 var _uploadOptions = null; 1531 var _uploadOptions = null;
1532 var _downloadOptions = common.DownloadOptions.Metadata; 1532 var _downloadOptions = common.DownloadOptions.Metadata;
1533 var _body = null; 1533 var _body = null;
1534 1534
1535 if (variantsetId != null) { 1535 if (request != null) {
1536 _queryParams["variantsetId"] = [variantsetId]; 1536 _body = convert.JSON.encode((request).toJson());
1537 } 1537 }
1538 1538
1539 1539
1540 _url = 'variants/summary'; 1540 _url = 'variants/import';
1541 1541
1542 var _response = _requester.request(_url, 1542 var _response = _requester.request(_url,
1543 "GET", 1543 "POST",
1544 body: _body, 1544 body: _body,
1545 queryParams: _queryParams, 1545 queryParams: _queryParams,
1546 uploadOptions: _uploadOptions, 1546 uploadOptions: _uploadOptions,
1547 uploadMedia: _uploadMedia, 1547 uploadMedia: _uploadMedia,
1548 downloadOptions: _downloadOptions); 1548 downloadOptions: _downloadOptions);
1549 return _response.then((data) => new GetVariantsSummaryResponse.fromJson(data )); 1549 return _response.then((data) => new ImportVariantsResponse.fromJson(data));
1550 } 1550 }
1551 1551
1552 /** 1552 /**
1553 * Creates variant data by asynchronously importing the provided information. 1553 * Gets a list of variants matching the criteria.
1554 * 1554 *
1555 * [request] - The metadata request object. 1555 * [request] - The metadata request object.
1556 * 1556 *
1557 * Request parameters: 1557 * Request parameters:
1558 * 1558 *
1559 * Completes with a [ImportVariantsResponse]. 1559 * Completes with a [SearchVariantsResponse].
1560 * 1560 *
1561 * Completes with a [common.ApiRequestError] if the API endpoint returned an 1561 * Completes with a [common.ApiRequestError] if the API endpoint returned an
1562 * error. 1562 * error.
1563 * 1563 *
1564 * If the used [http.Client] completes with an error when making a REST call, 1564 * If the used [http.Client] completes with an error when making a REST call,
1565 * this method will complete with the same error. 1565 * this method will complete with the same error.
1566 */ 1566 */
1567 async.Future<ImportVariantsResponse> import(ImportVariantsRequest request) { 1567 async.Future<SearchVariantsResponse> search(SearchVariantsRequest request) {
1568 var _url = null; 1568 var _url = null;
1569 var _queryParams = new core.Map(); 1569 var _queryParams = new core.Map();
1570 var _uploadMedia = null; 1570 var _uploadMedia = null;
1571 var _uploadOptions = null; 1571 var _uploadOptions = null;
1572 var _downloadOptions = common.DownloadOptions.Metadata; 1572 var _downloadOptions = common.DownloadOptions.Metadata;
1573 var _body = null; 1573 var _body = null;
1574 1574
1575 if (request != null) { 1575 if (request != null) {
1576 _body = convert.JSON.encode((request).toJson()); 1576 _body = convert.JSON.encode((request).toJson());
1577 } 1577 }
1578 1578
1579 1579
1580 _url = 'variants/import'; 1580 _url = 'variants/search';
1581 1581
1582 var _response = _requester.request(_url, 1582 var _response = _requester.request(_url,
1583 "POST", 1583 "POST",
1584 body: _body, 1584 body: _body,
1585 queryParams: _queryParams, 1585 queryParams: _queryParams,
1586 uploadOptions: _uploadOptions, 1586 uploadOptions: _uploadOptions,
1587 uploadMedia: _uploadMedia, 1587 uploadMedia: _uploadMedia,
1588 downloadOptions: _downloadOptions); 1588 downloadOptions: _downloadOptions);
1589 return _response.then((data) => new ImportVariantsResponse.fromJson(data)); 1589 return _response.then((data) => new SearchVariantsResponse.fromJson(data));
1590 } 1590 }
1591 1591
1592 /** 1592 /**
1593 * Updates a variant. This method supports patch semantics. 1593 * Updates a variant's names and info fields. All other modifications are
1594 * silently ignored. Returns the modified variant without its calls.
1594 * 1595 *
1595 * [request] - The metadata request object. 1596 * [request] - The metadata request object.
1596 * 1597 *
1597 * Request parameters: 1598 * Request parameters:
1598 * 1599 *
1599 * [variantId] - The ID of the variant to be updated.. 1600 * [variantId] - The ID of the variant to be updated.
1600 * 1601 *
1601 * Completes with a [Variant]. 1602 * Completes with a [Variant].
1602 * 1603 *
1603 * Completes with a [common.ApiRequestError] if the API endpoint returned an 1604 * Completes with a [common.ApiRequestError] if the API endpoint returned an
1604 * error. 1605 * error.
1605 * 1606 *
1606 * If the used [http.Client] completes with an error when making a REST call, 1607 * If the used [http.Client] completes with an error when making a REST call,
1607 * this method will complete with the same error. 1608 * this method will complete with the same error.
1608 */ 1609 */
1609 async.Future<Variant> patch(Variant request, core.String variantId) { 1610 async.Future<Variant> update(Variant request, core.String variantId) {
1610 var _url = null; 1611 var _url = null;
1611 var _queryParams = new core.Map(); 1612 var _queryParams = new core.Map();
1612 var _uploadMedia = null; 1613 var _uploadMedia = null;
1613 var _uploadOptions = null; 1614 var _uploadOptions = null;
1614 var _downloadOptions = common.DownloadOptions.Metadata; 1615 var _downloadOptions = common.DownloadOptions.Metadata;
1615 var _body = null; 1616 var _body = null;
1616 1617
1617 if (request != null) { 1618 if (request != null) {
1618 _body = convert.JSON.encode((request).toJson()); 1619 _body = convert.JSON.encode((request).toJson());
1619 } 1620 }
1620 if (variantId == null) { 1621 if (variantId == null) {
1621 throw new core.ArgumentError("Parameter variantId is required."); 1622 throw new core.ArgumentError("Parameter variantId is required.");
1622 } 1623 }
1623 1624
1624 1625
1625 _url = 'variants/' + common_internal.Escaper.ecapeVariable('$variantId'); 1626 _url = 'variants/' + common_internal.Escaper.ecapeVariable('$variantId');
1626 1627
1627 var _response = _requester.request(_url, 1628 var _response = _requester.request(_url,
1628 "PATCH", 1629 "PUT",
1629 body: _body, 1630 body: _body,
1630 queryParams: _queryParams, 1631 queryParams: _queryParams,
1631 uploadOptions: _uploadOptions, 1632 uploadOptions: _uploadOptions,
1632 uploadMedia: _uploadMedia, 1633 uploadMedia: _uploadMedia,
1633 downloadOptions: _downloadOptions); 1634 downloadOptions: _downloadOptions);
1634 return _response.then((data) => new Variant.fromJson(data)); 1635 return _response.then((data) => new Variant.fromJson(data));
1635 } 1636 }
1636 1637
1638 }
1639
1640
1641 /** Not documented yet. */
1642 class VariantsetsResourceApi {
1643 final common_internal.ApiRequester _requester;
1644
1645 VariantsetsResourceApi(common_internal.ApiRequester client) :
1646 _requester = client;
1647
1637 /** 1648 /**
1638 * Gets a list of variants matching the criteria. 1649 * Deletes the contents of a variant set. The variant set object is not
1639 * 1650 * deleted.
1640 * [request] - The metadata request object.
1641 * 1651 *
1642 * Request parameters: 1652 * Request parameters:
1643 * 1653 *
1644 * Completes with a [SearchVariantsResponse]. 1654 * [variantSetId] - The ID of the variant set to be deleted.
1645 * 1655 *
1646 * Completes with a [common.ApiRequestError] if the API endpoint returned an 1656 * Completes with a [common.ApiRequestError] if the API endpoint returned an
1647 * error. 1657 * error.
1658 *
1659 * If the used [http.Client] completes with an error when making a REST call,
1660 * this method will complete with the same error.
1661 */
1662 async.Future delete(core.String variantSetId) {
1663 var _url = null;
1664 var _queryParams = new core.Map();
1665 var _uploadMedia = null;
1666 var _uploadOptions = null;
1667 var _downloadOptions = common.DownloadOptions.Metadata;
1668 var _body = null;
1669
1670 if (variantSetId == null) {
1671 throw new core.ArgumentError("Parameter variantSetId is required.");
1672 }
1673
1674 _downloadOptions = null;
1675
1676 _url = 'variantsets/' + common_internal.Escaper.ecapeVariable('$variantSetId ');
1677
1678 var _response = _requester.request(_url,
1679 "DELETE",
1680 body: _body,
1681 queryParams: _queryParams,
1682 uploadOptions: _uploadOptions,
1683 uploadMedia: _uploadMedia,
1684 downloadOptions: _downloadOptions);
1685 return _response.then((data) => null);
1686 }
1687
1688 /**
1689 * Gets a variant set by ID.
1690 *
1691 * Request parameters:
1692 *
1693 * [variantSetId] - Required. The ID of the variant set.
1694 *
1695 * Completes with a [VariantSet].
1696 *
1697 * Completes with a [common.ApiRequestError] if the API endpoint returned an
1698 * error.
1648 * 1699 *
1649 * If the used [http.Client] completes with an error when making a REST call, 1700 * If the used [http.Client] completes with an error when making a REST call,
1650 * this method will complete with the same error. 1701 * this method will complete with the same error.
1651 */ 1702 */
1652 async.Future<SearchVariantsResponse> search(SearchVariantsRequest request) { 1703 async.Future<VariantSet> get(core.String variantSetId) {
1653 var _url = null; 1704 var _url = null;
1654 var _queryParams = new core.Map(); 1705 var _queryParams = new core.Map();
1655 var _uploadMedia = null; 1706 var _uploadMedia = null;
1656 var _uploadOptions = null; 1707 var _uploadOptions = null;
1657 var _downloadOptions = common.DownloadOptions.Metadata; 1708 var _downloadOptions = common.DownloadOptions.Metadata;
1658 var _body = null; 1709 var _body = null;
1659 1710
1660 if (request != null) { 1711 if (variantSetId == null) {
1661 _body = convert.JSON.encode((request).toJson()); 1712 throw new core.ArgumentError("Parameter variantSetId is required.");
1662 } 1713 }
1663 1714
1664 1715
1665 _url = 'variants/search'; 1716 _url = 'variantsets/' + common_internal.Escaper.ecapeVariable('$variantSetId ');
1666 1717
1667 var _response = _requester.request(_url, 1718 var _response = _requester.request(_url,
1668 "POST", 1719 "GET",
1669 body: _body, 1720 body: _body,
1670 queryParams: _queryParams, 1721 queryParams: _queryParams,
1671 uploadOptions: _uploadOptions, 1722 uploadOptions: _uploadOptions,
1672 uploadMedia: _uploadMedia, 1723 uploadMedia: _uploadMedia,
1673 downloadOptions: _downloadOptions); 1724 downloadOptions: _downloadOptions);
1674 return _response.then((data) => new SearchVariantsResponse.fromJson(data)); 1725 return _response.then((data) => new VariantSet.fromJson(data));
1675 } 1726 }
1676 1727
1677 /** 1728 /**
1678 * Updates a variant. 1729 * Returns a list of all variant sets matching search criteria.
1679 * 1730 *
1680 * [request] - The metadata request object. 1731 * [request] - The metadata request object.
1681 * 1732 *
1682 * Request parameters: 1733 * Request parameters:
1683 * 1734 *
1684 * [variantId] - The ID of the variant to be updated.. 1735 * Completes with a [SearchVariantSetsResponse].
1685 *
1686 * Completes with a [Variant].
1687 * 1736 *
1688 * Completes with a [common.ApiRequestError] if the API endpoint returned an 1737 * Completes with a [common.ApiRequestError] if the API endpoint returned an
1689 * error. 1738 * error.
1690 * 1739 *
1691 * If the used [http.Client] completes with an error when making a REST call, 1740 * If the used [http.Client] completes with an error when making a REST call,
1692 * this method will complete with the same error. 1741 * this method will complete with the same error.
1693 */ 1742 */
1694 async.Future<Variant> update(Variant request, core.String variantId) { 1743 async.Future<SearchVariantSetsResponse> search(SearchVariantSetsRequest reques t) {
1695 var _url = null; 1744 var _url = null;
1696 var _queryParams = new core.Map(); 1745 var _queryParams = new core.Map();
1697 var _uploadMedia = null; 1746 var _uploadMedia = null;
1698 var _uploadOptions = null; 1747 var _uploadOptions = null;
1699 var _downloadOptions = common.DownloadOptions.Metadata; 1748 var _downloadOptions = common.DownloadOptions.Metadata;
1700 var _body = null; 1749 var _body = null;
1701 1750
1702 if (request != null) { 1751 if (request != null) {
1703 _body = convert.JSON.encode((request).toJson()); 1752 _body = convert.JSON.encode((request).toJson());
1704 } 1753 }
1705 if (variantId == null) {
1706 throw new core.ArgumentError("Parameter variantId is required.");
1707 }
1708 1754
1709 1755
1710 _url = 'variants/' + common_internal.Escaper.ecapeVariable('$variantId'); 1756 _url = 'variantsets/search';
1711 1757
1712 var _response = _requester.request(_url, 1758 var _response = _requester.request(_url,
1713 "PUT", 1759 "POST",
1714 body: _body, 1760 body: _body,
1715 queryParams: _queryParams, 1761 queryParams: _queryParams,
1716 uploadOptions: _uploadOptions, 1762 uploadOptions: _uploadOptions,
1717 uploadMedia: _uploadMedia, 1763 uploadMedia: _uploadMedia,
1718 downloadOptions: _downloadOptions); 1764 downloadOptions: _downloadOptions);
1719 return _response.then((data) => new Variant.fromJson(data)); 1765 return _response.then((data) => new SearchVariantSetsResponse.fromJson(data) );
1720 } 1766 }
1721 1767
1722 } 1768 }
1723 1769
1724 1770
1725 1771
1726 /** 1772 /**
1727 * A beacon represents whether any variant call in a variantset has a specific 1773 * A beacon represents whether any variant call in a variant set has a specific
1728 * allele at a particular position. 1774 * allele at a particular position.
1729 */ 1775 */
1730 class Beacon { 1776 class Beacon {
1731 /** True if the allele exists on any variant call, false otherwise. */ 1777 /** True if the allele exists on any variant call, false otherwise. */
1732 core.bool exists; 1778 core.bool exists;
1733 1779
1734 1780
1735 Beacon(); 1781 Beacon();
1736 1782
1737 Beacon.fromJson(core.Map _json) { 1783 Beacon.fromJson(core.Map _json) {
1738 if (_json.containsKey("exists")) { 1784 if (_json.containsKey("exists")) {
1739 exists = _json["exists"]; 1785 exists = _json["exists"];
1740 } 1786 }
1741 } 1787 }
1742 1788
1743 core.Map toJson() { 1789 core.Map toJson() {
1744 var _json = new core.Map(); 1790 var _json = new core.Map();
1745 if (exists != null) { 1791 if (exists != null) {
1746 _json["exists"] = exists; 1792 _json["exists"] = exists;
1747 } 1793 }
1748 return _json; 1794 return _json;
1749 } 1795 }
1750 } 1796 }
1751 1797
1752 1798
1753 /** 1799 /**
1754 * A Call represents the determination of genotype with respect to a particular 1800 * A Call represents the determination of genotype with respect to a particular
1755 * variant. It may include associated information such as quality and phasing. 1801 * variant. It may include associated information such as quality and phasing.
1756 * For example, a Call might assign a probability of 0.32 to the occurrence of a 1802 * For example, a Call might assign a probability of 0.32 to the occurrence of a
1757 * SNP named rs1234 in a callset with the name NA12345. 1803 * SNP named rs1234 in a call set with the name NA12345.
1758 */ 1804 */
1759 class Call { 1805 class Call {
1760 /** The ID of the callset this variant call belongs to. */ 1806 /** The ID of the call set this variant call belongs to. */
1761 core.String callsetId; 1807 core.String callSetId;
1762 1808
1763 /** The name of the callset this variant call belongs to. */ 1809 /** The name of the call set this variant call belongs to. */
1764 core.String callsetName; 1810 core.String callSetName;
1765 1811
1766 /** 1812 /**
1767 * The genotype of this variant call. Each value represents either the value 1813 * The genotype of this variant call. Each value represents either the value
1768 * of the referenceBases field or a 1-based index into alternateBases. If a 1814 * of the referenceBases field or a 1-based index into alternateBases. If a
1769 * variant had a referenceBases field of "T" and an alternateBases value of 1815 * variant had a referenceBases value of T and an alternateBases value of
1770 * ["A", "C"], and the genotype was [2, 1], that would mean the call 1816 * ["A", "C"], and the genotype was [2, 1], that would mean the call
1771 * represented the heterozygous value "CA" for this variant. If the genotype 1817 * represented the heterozygous value CA for this variant. If the genotype was
1772 * was instead [0, 1], the represented value would be "TA". Ordering of the 1818 * instead [0, 1], the represented value would be TA. Ordering of the genotype
1773 * genotype values is important if the phaseset field is present. If a 1819 * values is important if the phaseset is present. If a genotype is not called
1774 * genotype is not called (that is, a "." is present in the GT string) -1 is 1820 * (that is, a . is present in the GT string) -1 is returned.
1775 * returned.
1776 */ 1821 */
1777 core.List<core.int> genotype; 1822 core.List<core.int> genotype;
1778 1823
1779 /** 1824 /**
1780 * The genotype likelihoods for this variant call. Each array entry represents 1825 * The genotype likelihoods for this variant call. Each array entry represents
1781 * how likely a specific genotype is for this call. The value ordering is 1826 * how likely a specific genotype is for this call. The value ordering is
1782 * defined by the GL tag in the VCF spec. 1827 * defined by the GL tag in the VCF spec.
1783 */ 1828 */
1784 core.List<core.double> genotypeLikelihood; 1829 core.List<core.double> genotypeLikelihood;
1785 1830
1786 /** A map of additional variant call information. */ 1831 /** A map of additional variant call information. */
1787 core.Map<core.String, core.List<core.String>> info; 1832 core.Map<core.String, core.List<core.String>> info;
1788 1833
1789 /** 1834 /**
1790 * If this field is present, this variant call's genotype ordering implies the 1835 * If this field is present, this variant call's genotype ordering implies the
1791 * phase of the bases and is consistent with any other variant calls on the 1836 * phase of the bases and is consistent with any other variant calls in the
1792 * same contig which have the same phaseset value. When importing data from 1837 * same reference sequence which have the same phaseset value. When importing
1793 * VCF, if the genotype data was phased but no phase set was specified this 1838 * data from VCF, if the genotype data was phased but no phase set was
1794 * field will be set to "*". 1839 * specified this field will be set to *.
1795 */ 1840 */
1796 core.String phaseset; 1841 core.String phaseset;
1797 1842
1798 1843
1799 Call(); 1844 Call();
1800 1845
1801 Call.fromJson(core.Map _json) { 1846 Call.fromJson(core.Map _json) {
1802 if (_json.containsKey("callsetId")) { 1847 if (_json.containsKey("callSetId")) {
1803 callsetId = _json["callsetId"]; 1848 callSetId = _json["callSetId"];
1804 } 1849 }
1805 if (_json.containsKey("callsetName")) { 1850 if (_json.containsKey("callSetName")) {
1806 callsetName = _json["callsetName"]; 1851 callSetName = _json["callSetName"];
1807 } 1852 }
1808 if (_json.containsKey("genotype")) { 1853 if (_json.containsKey("genotype")) {
1809 genotype = _json["genotype"]; 1854 genotype = _json["genotype"];
1810 } 1855 }
1811 if (_json.containsKey("genotypeLikelihood")) { 1856 if (_json.containsKey("genotypeLikelihood")) {
1812 genotypeLikelihood = _json["genotypeLikelihood"]; 1857 genotypeLikelihood = _json["genotypeLikelihood"];
1813 } 1858 }
1814 if (_json.containsKey("info")) { 1859 if (_json.containsKey("info")) {
1815 info = _json["info"]; 1860 info = _json["info"];
1816 } 1861 }
1817 if (_json.containsKey("phaseset")) { 1862 if (_json.containsKey("phaseset")) {
1818 phaseset = _json["phaseset"]; 1863 phaseset = _json["phaseset"];
1819 } 1864 }
1820 } 1865 }
1821 1866
1822 core.Map toJson() { 1867 core.Map toJson() {
1823 var _json = new core.Map(); 1868 var _json = new core.Map();
1824 if (callsetId != null) { 1869 if (callSetId != null) {
1825 _json["callsetId"] = callsetId; 1870 _json["callSetId"] = callSetId;
1826 } 1871 }
1827 if (callsetName != null) { 1872 if (callSetName != null) {
1828 _json["callsetName"] = callsetName; 1873 _json["callSetName"] = callSetName;
1829 } 1874 }
1830 if (genotype != null) { 1875 if (genotype != null) {
1831 _json["genotype"] = genotype; 1876 _json["genotype"] = genotype;
1832 } 1877 }
1833 if (genotypeLikelihood != null) { 1878 if (genotypeLikelihood != null) {
1834 _json["genotypeLikelihood"] = genotypeLikelihood; 1879 _json["genotypeLikelihood"] = genotypeLikelihood;
1835 } 1880 }
1836 if (info != null) { 1881 if (info != null) {
1837 _json["info"] = info; 1882 _json["info"] = info;
1838 } 1883 }
1839 if (phaseset != null) { 1884 if (phaseset != null) {
1840 _json["phaseset"] = phaseset; 1885 _json["phaseset"] = phaseset;
1841 } 1886 }
1842 return _json; 1887 return _json;
1843 } 1888 }
1844 } 1889 }
1845 1890
1846 1891
1847 /** A Callset is a collection of Variant Calls. It belongs to a Variantset. */ 1892 /** A CallSet is a collection of variant calls. It belongs to a variant set. */
1848 class Callset { 1893 class CallSet {
1849 /** The date this callset was created in milliseconds from the epoch. */ 1894 /** The date this call set was created in milliseconds from the epoch. */
1850 core.String created; 1895 core.String created;
1851 1896
1852 /** The Google generated ID of the callset, immutable. */ 1897 /** The Google generated ID of the call set, immutable. */
1853 core.String id; 1898 core.String id;
1854 1899
1855 /** A map of additional callset information. */ 1900 /** A map of additional callset information. */
1856 core.Map<core.String, core.List<core.String>> info; 1901 core.Map<core.String, core.List<core.String>> info;
1857 1902
1858 /** The callset name. */ 1903 /** The callset name. */
1859 core.String name; 1904 core.String name;
1860 1905
1861 /** The ID of the variantset this callset belongs to. */ 1906 /** The sample ID this call set corresponds to. */
1862 core.String variantsetId; 1907 core.String sampleId;
1908
1909 /** The IDs of the variant sets this call set belongs to. */
1910 core.List<core.String> variantSetIds;
1863 1911
1864 1912
1865 Callset(); 1913 CallSet();
1866 1914
1867 Callset.fromJson(core.Map _json) { 1915 CallSet.fromJson(core.Map _json) {
1868 if (_json.containsKey("created")) { 1916 if (_json.containsKey("created")) {
1869 created = _json["created"]; 1917 created = _json["created"];
1870 } 1918 }
1871 if (_json.containsKey("id")) { 1919 if (_json.containsKey("id")) {
1872 id = _json["id"]; 1920 id = _json["id"];
1873 } 1921 }
1874 if (_json.containsKey("info")) { 1922 if (_json.containsKey("info")) {
1875 info = _json["info"]; 1923 info = _json["info"];
1876 } 1924 }
1877 if (_json.containsKey("name")) { 1925 if (_json.containsKey("name")) {
1878 name = _json["name"]; 1926 name = _json["name"];
1879 } 1927 }
1880 if (_json.containsKey("variantsetId")) { 1928 if (_json.containsKey("sampleId")) {
1881 variantsetId = _json["variantsetId"]; 1929 sampleId = _json["sampleId"];
1930 }
1931 if (_json.containsKey("variantSetIds")) {
1932 variantSetIds = _json["variantSetIds"];
1882 } 1933 }
1883 } 1934 }
1884 1935
1885 core.Map toJson() { 1936 core.Map toJson() {
1886 var _json = new core.Map(); 1937 var _json = new core.Map();
1887 if (created != null) { 1938 if (created != null) {
1888 _json["created"] = created; 1939 _json["created"] = created;
1889 } 1940 }
1890 if (id != null) { 1941 if (id != null) {
1891 _json["id"] = id; 1942 _json["id"] = id;
1892 } 1943 }
1893 if (info != null) { 1944 if (info != null) {
1894 _json["info"] = info; 1945 _json["info"] = info;
1895 } 1946 }
1896 if (name != null) { 1947 if (name != null) {
1897 _json["name"] = name; 1948 _json["name"] = name;
1898 } 1949 }
1899 if (variantsetId != null) { 1950 if (sampleId != null) {
1900 _json["variantsetId"] = variantsetId; 1951 _json["sampleId"] = sampleId;
1952 }
1953 if (variantSetIds != null) {
1954 _json["variantSetIds"] = variantSetIds;
1901 } 1955 }
1902 return _json; 1956 return _json;
1903 } 1957 }
1904 }
1905
1906
1907 /**
1908 * ContigBound records an upper bound for the starting coordinate of variants in
1909 * a particular contig.
1910 */
1911 class ContigBound {
1912 /** The contig the bound is associate with. */
1913 core.String contig;
1914
1915 /**
1916 * An upper bound (inclusive) on the starting coordinate of any variant in the
1917 * contig.
1918 */
1919 core.String upperBound;
1920
1921
1922 ContigBound();
1923
1924 ContigBound.fromJson(core.Map _json) {
1925 if (_json.containsKey("contig")) {
1926 contig = _json["contig"];
1927 }
1928 if (_json.containsKey("upperBound")) {
1929 upperBound = _json["upperBound"];
1930 }
1931 }
1932
1933 core.Map toJson() {
1934 var _json = new core.Map();
1935 if (contig != null) {
1936 _json["contig"] = contig;
1937 }
1938 if (upperBound != null) {
1939 _json["upperBound"] = upperBound;
1940 }
1941 return _json;
1942 }
1943 } 1958 }
1944 1959
1945 1960
1946 /** 1961 /**
1947 * A bucket over which read coverage has been precomputed. A bucket corresponds 1962 * A bucket over which read coverage has been precomputed. A bucket corresponds
1948 * to a specific range of the reference sequence. 1963 * to a specific range of the reference sequence.
1949 */ 1964 */
1950 class CoverageBucket { 1965 class CoverageBucket {
1951 /** 1966 /**
1952 * The average number of reads which are aligned to each individual reference 1967 * The average number of reads which are aligned to each individual reference
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2035 } 2050 }
2036 return _json; 2051 return _json;
2037 } 2052 }
2038 } 2053 }
2039 2054
2040 2055
2041 /** The job creation request. */ 2056 /** The job creation request. */
2042 class ExperimentalCreateJobRequest { 2057 class ExperimentalCreateJobRequest {
2043 /** 2058 /**
2044 * Specifies whether or not to run the alignment pipeline. At least one of 2059 * Specifies whether or not to run the alignment pipeline. At least one of
2045 * align or call_variants must be provided. 2060 * align or callVariants must be provided.
2046 */ 2061 */
2047 core.bool align; 2062 core.bool align;
2048 2063
2049 /** 2064 /**
2050 * Specifies whether or not to run the variant calling pipeline. If specified, 2065 * Specifies whether or not to run the variant calling pipeline. If specified,
2051 * alignment will be performed first and the aligned BAMs will passed as input 2066 * alignment will be performed first and the aligned BAMs will passed as input
2052 * to the variant caller. At least one of align or call_variants must be 2067 * to the variant caller. At least one of align or callVariants must be
2053 * provided. 2068 * provided.
2054 */ 2069 */
2055 core.bool callVariants; 2070 core.bool callVariants;
2056 2071
2057 /** 2072 /**
2058 * Specifies where to copy the results of certain pipelines. This shoud be in 2073 * Specifies where to copy the results of certain pipelines. This should be in
2059 * the form of "gs://bucket/path". 2074 * the form of gs://bucket/path.
2060 */ 2075 */
2061 core.String gcsOutputPath; 2076 core.String gcsOutputPath;
2062 2077
2063 /** 2078 /**
2064 * A list of Google Cloud Storage URIs of paired end .fastq files to operate 2079 * A list of Google Cloud Storage URIs of paired end .fastq files to operate
2065 * upon. If specified, this represents the second file of each paired .fastq 2080 * upon. If specified, this represents the second file of each paired .fastq
2066 * file. The first file of each pair should be specified in "sourceUris". 2081 * file. The first file of each pair should be specified in sourceUris.
2067 */ 2082 */
2068 core.List<core.String> pairedSourceUris; 2083 core.List<core.String> pairedSourceUris;
2069 2084
2070 /** 2085 /**
2071 * Required. The Google Cloud Project ID with which to associate the request. 2086 * Required. The Google Cloud Project ID with which to associate the request.
2072 */ 2087 */
2073 core.String projectId; 2088 core.String projectId;
2074 2089
2075 /** 2090 /**
2076 * A list of Google Cloud Storage URIs of data files to operate upon. These 2091 * A list of Google Cloud Storage URIs of data files to operate upon. These
2077 * can be .bam, interleaved .fastq, or paired .fastq. If specifying paired 2092 * can be .bam, interleaved .fastq, or paired .fastq. If specifying paired
2078 * .fastq files, the first of each pair of files should be listed here, and 2093 * .fastq files, the first of each pair of files should be listed here, and
2079 * the second of each pair should be listed in "pairedSourceUris". 2094 * the second of each pair should be listed in pairedSourceUris.
2080 */ 2095 */
2081 core.List<core.String> sourceUris; 2096 core.List<core.String> sourceUris;
2082 2097
2083 2098
2084 ExperimentalCreateJobRequest(); 2099 ExperimentalCreateJobRequest();
2085 2100
2086 ExperimentalCreateJobRequest.fromJson(core.Map _json) { 2101 ExperimentalCreateJobRequest.fromJson(core.Map _json) {
2087 if (_json.containsKey("align")) { 2102 if (_json.containsKey("align")) {
2088 align = _json["align"]; 2103 align = _json["align"];
2089 } 2104 }
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2166 * The Google Developers Console project number that owns this export. This is 2181 * The Google Developers Console project number that owns this export. This is
2167 * the project that will be billed. 2182 * the project that will be billed.
2168 */ 2183 */
2169 core.String projectId; 2184 core.String projectId;
2170 2185
2171 /** The IDs of the readsets to export. */ 2186 /** The IDs of the readsets to export. */
2172 core.List<core.String> readsetIds; 2187 core.List<core.String> readsetIds;
2173 2188
2174 /** 2189 /**
2175 * The reference names to export. If this is not specified, all reference 2190 * The reference names to export. If this is not specified, all reference
2176 * sequences are exported. Use '*' to export unmapped reads. 2191 * sequences, including unmapped reads, are exported. Use * to export only
2192 * unmapped reads.
2177 */ 2193 */
2178 core.List<core.String> referenceNames; 2194 core.List<core.String> referenceNames;
2179 2195
2180 2196
2181 ExportReadsetsRequest(); 2197 ExportReadsetsRequest();
2182 2198
2183 ExportReadsetsRequest.fromJson(core.Map _json) { 2199 ExportReadsetsRequest.fromJson(core.Map _json) {
2184 if (_json.containsKey("exportUri")) { 2200 if (_json.containsKey("exportUri")) {
2185 exportUri = _json["exportUri"]; 2201 exportUri = _json["exportUri"];
2186 } 2202 }
(...skipping 60 matching lines...) Expand 10 before | Expand all | Expand 10 after
2247 */ 2263 */
2248 core.String bigqueryDataset; 2264 core.String bigqueryDataset;
2249 2265
2250 /** 2266 /**
2251 * The BigQuery table to export data to. The caller must have WRITE access to 2267 * The BigQuery table to export data to. The caller must have WRITE access to
2252 * this BigQuery table. 2268 * this BigQuery table.
2253 */ 2269 */
2254 core.String bigqueryTable; 2270 core.String bigqueryTable;
2255 2271
2256 /** 2272 /**
2257 * If provided, only variant call information from the specified callsets will 2273 * If provided, only variant call information from the specified call sets
2258 * be exported. By default all variant calls are exported. 2274 * will be exported. By default all variant calls are exported.
2259 */ 2275 */
2260 core.List<core.String> callsetIds; 2276 core.List<core.String> callSetIds;
2261 2277
2262 /** 2278 /**
2263 * The format for the exported data. 2279 * The format for the exported data.
2264 * Possible string values are: 2280 * Possible string values are:
2265 * - "bigquery" 2281 * - "bigquery"
2266 */ 2282 */
2267 core.String format; 2283 core.String format;
2268 2284
2269 /** 2285 /**
2270 * The Google Cloud project number that owns this export. This is the project 2286 * The Google Cloud project number that owns this export. This is the project
2271 * that will be billed. 2287 * that will be billed.
2272 */ 2288 */
2273 core.String projectId; 2289 core.String projectId;
2274 2290
2275 /** 2291 /**
2276 * Required. The ID of the variantset that contains variant data which should 2292 * Required. The ID of the variant set that contains variant data which should
2277 * be exported. The caller must have READ access to this variantset. 2293 * be exported. The caller must have READ access to this variant set.
2278 */ 2294 */
2279 core.String variantsetId; 2295 core.String variantSetId;
2280 2296
2281 2297
2282 ExportVariantsRequest(); 2298 ExportVariantsRequest();
2283 2299
2284 ExportVariantsRequest.fromJson(core.Map _json) { 2300 ExportVariantsRequest.fromJson(core.Map _json) {
2285 if (_json.containsKey("bigqueryDataset")) { 2301 if (_json.containsKey("bigqueryDataset")) {
2286 bigqueryDataset = _json["bigqueryDataset"]; 2302 bigqueryDataset = _json["bigqueryDataset"];
2287 } 2303 }
2288 if (_json.containsKey("bigqueryTable")) { 2304 if (_json.containsKey("bigqueryTable")) {
2289 bigqueryTable = _json["bigqueryTable"]; 2305 bigqueryTable = _json["bigqueryTable"];
2290 } 2306 }
2291 if (_json.containsKey("callsetIds")) { 2307 if (_json.containsKey("callSetIds")) {
2292 callsetIds = _json["callsetIds"]; 2308 callSetIds = _json["callSetIds"];
2293 } 2309 }
2294 if (_json.containsKey("format")) { 2310 if (_json.containsKey("format")) {
2295 format = _json["format"]; 2311 format = _json["format"];
2296 } 2312 }
2297 if (_json.containsKey("projectId")) { 2313 if (_json.containsKey("projectId")) {
2298 projectId = _json["projectId"]; 2314 projectId = _json["projectId"];
2299 } 2315 }
2300 if (_json.containsKey("variantsetId")) { 2316 if (_json.containsKey("variantSetId")) {
2301 variantsetId = _json["variantsetId"]; 2317 variantSetId = _json["variantSetId"];
2302 } 2318 }
2303 } 2319 }
2304 2320
2305 core.Map toJson() { 2321 core.Map toJson() {
2306 var _json = new core.Map(); 2322 var _json = new core.Map();
2307 if (bigqueryDataset != null) { 2323 if (bigqueryDataset != null) {
2308 _json["bigqueryDataset"] = bigqueryDataset; 2324 _json["bigqueryDataset"] = bigqueryDataset;
2309 } 2325 }
2310 if (bigqueryTable != null) { 2326 if (bigqueryTable != null) {
2311 _json["bigqueryTable"] = bigqueryTable; 2327 _json["bigqueryTable"] = bigqueryTable;
2312 } 2328 }
2313 if (callsetIds != null) { 2329 if (callSetIds != null) {
2314 _json["callsetIds"] = callsetIds; 2330 _json["callSetIds"] = callSetIds;
2315 } 2331 }
2316 if (format != null) { 2332 if (format != null) {
2317 _json["format"] = format; 2333 _json["format"] = format;
2318 } 2334 }
2319 if (projectId != null) { 2335 if (projectId != null) {
2320 _json["projectId"] = projectId; 2336 _json["projectId"] = projectId;
2321 } 2337 }
2322 if (variantsetId != null) { 2338 if (variantSetId != null) {
2323 _json["variantsetId"] = variantsetId; 2339 _json["variantSetId"] = variantSetId;
2324 } 2340 }
2325 return _json; 2341 return _json;
2326 } 2342 }
2327 } 2343 }
2328 2344
2329 2345
2330 /** The variant data export response. */ 2346 /** The variant data export response. */
2331 class ExportVariantsResponse { 2347 class ExportVariantsResponse {
2332 /** A job ID that can be used to get status information. */ 2348 /** A job ID that can be used to get status information. */
2333 core.String jobId; 2349 core.String jobId;
(...skipping 20 matching lines...) Expand all
2354 /** 2370 /**
2355 * An inclusive, exclusive genomic coordinate range over a reference sequence. 2371 * An inclusive, exclusive genomic coordinate range over a reference sequence.
2356 */ 2372 */
2357 class GenomicRange { 2373 class GenomicRange {
2358 /** 2374 /**
2359 * The end position of the range on the reference, 1-based exclusive. If 2375 * The end position of the range on the reference, 1-based exclusive. If
2360 * specified, sequenceName must also be specified. 2376 * specified, sequenceName must also be specified.
2361 */ 2377 */
2362 core.String sequenceEnd; 2378 core.String sequenceEnd;
2363 2379
2364 /** The reference sequence name, for example "chr1", "1", or "chrX". */ 2380 /** The reference sequence name, for example chr1, 1, or chrX. */
2365 core.String sequenceName; 2381 core.String sequenceName;
2366 2382
2367 /** 2383 /**
2368 * The start position of the range on the reference, 1-based inclusive. If 2384 * The start position of the range on the reference, 1-based inclusive. If
2369 * specified, sequenceName must also be specified. 2385 * specified, sequenceName must also be specified.
2370 */ 2386 */
2371 core.String sequenceStart; 2387 core.String sequenceStart;
2372 2388
2373 2389
2374 GenomicRange(); 2390 GenomicRange();
(...skipping 19 matching lines...) Expand all
2394 _json["sequenceName"] = sequenceName; 2410 _json["sequenceName"] = sequenceName;
2395 } 2411 }
2396 if (sequenceStart != null) { 2412 if (sequenceStart != null) {
2397 _json["sequenceStart"] = sequenceStart; 2413 _json["sequenceStart"] = sequenceStart;
2398 } 2414 }
2399 return _json; 2415 return _json;
2400 } 2416 }
2401 } 2417 }
2402 2418
2403 2419
2404 /** The variants summary response. */
2405 class GetVariantsSummaryResponse {
2406 /**
2407 * A list of all contigs used by the variants in a dataset with associated
2408 * coordinate upper bounds for each one.
2409 */
2410 core.List<ContigBound> contigBounds;
2411
2412 /** The metadata associated with this dataset. */
2413 core.List<Metadata> metadata;
2414
2415
2416 GetVariantsSummaryResponse();
2417
2418 GetVariantsSummaryResponse.fromJson(core.Map _json) {
2419 if (_json.containsKey("contigBounds")) {
2420 contigBounds = _json["contigBounds"].map((value) => new ContigBound.fromJs on(value)).toList();
2421 }
2422 if (_json.containsKey("metadata")) {
2423 metadata = _json["metadata"].map((value) => new Metadata.fromJson(value)). toList();
2424 }
2425 }
2426
2427 core.Map toJson() {
2428 var _json = new core.Map();
2429 if (contigBounds != null) {
2430 _json["contigBounds"] = contigBounds.map((value) => (value).toJson()).toLi st();
2431 }
2432 if (metadata != null) {
2433 _json["metadata"] = metadata.map((value) => (value).toJson()).toList();
2434 }
2435 return _json;
2436 }
2437 }
2438
2439
2440 /** Not documented yet. */ 2420 /** Not documented yet. */
2441 class Header { 2421 class Header {
2442 /** (SO) Sorting order of alignments. */ 2422 /** (SO) Sorting order of alignments. */
2443 core.String sortingOrder; 2423 core.String sortingOrder;
2444 2424
2445 /** (VN) BAM format version. */ 2425 /** (VN) BAM format version. */
2446 core.String version; 2426 core.String version;
2447 2427
2448 2428
2449 Header(); 2429 Header();
(...skipping 170 matching lines...) Expand 10 before | Expand all | Expand 10 after
2620 * - "vcf" 2600 * - "vcf"
2621 */ 2601 */
2622 core.String format; 2602 core.String format;
2623 2603
2624 /** 2604 /**
2625 * A list of URIs pointing at VCF files in Google Cloud Storage. See the VCF 2605 * A list of URIs pointing at VCF files in Google Cloud Storage. See the VCF
2626 * Specification for more details on the input format. 2606 * Specification for more details on the input format.
2627 */ 2607 */
2628 core.List<core.String> sourceUris; 2608 core.List<core.String> sourceUris;
2629 2609
2630 /** Required. The variantset to which variant data should be imported. */ 2610 /** Required. The variant set to which variant data should be imported. */
2631 core.String variantsetId; 2611 core.String variantSetId;
2632 2612
2633 2613
2634 ImportVariantsRequest(); 2614 ImportVariantsRequest();
2635 2615
2636 ImportVariantsRequest.fromJson(core.Map _json) { 2616 ImportVariantsRequest.fromJson(core.Map _json) {
2637 if (_json.containsKey("format")) { 2617 if (_json.containsKey("format")) {
2638 format = _json["format"]; 2618 format = _json["format"];
2639 } 2619 }
2640 if (_json.containsKey("sourceUris")) { 2620 if (_json.containsKey("sourceUris")) {
2641 sourceUris = _json["sourceUris"]; 2621 sourceUris = _json["sourceUris"];
2642 } 2622 }
2643 if (_json.containsKey("variantsetId")) { 2623 if (_json.containsKey("variantSetId")) {
2644 variantsetId = _json["variantsetId"]; 2624 variantSetId = _json["variantSetId"];
2645 } 2625 }
2646 } 2626 }
2647 2627
2648 core.Map toJson() { 2628 core.Map toJson() {
2649 var _json = new core.Map(); 2629 var _json = new core.Map();
2650 if (format != null) { 2630 if (format != null) {
2651 _json["format"] = format; 2631 _json["format"] = format;
2652 } 2632 }
2653 if (sourceUris != null) { 2633 if (sourceUris != null) {
2654 _json["sourceUris"] = sourceUris; 2634 _json["sourceUris"] = sourceUris;
2655 } 2635 }
2656 if (variantsetId != null) { 2636 if (variantSetId != null) {
2657 _json["variantsetId"] = variantsetId; 2637 _json["variantSetId"] = variantSetId;
2658 } 2638 }
2659 return _json; 2639 return _json;
2660 } 2640 }
2661 } 2641 }
2662 2642
2663 2643
2664 /** The variant data import response. */ 2644 /** The variant data import response. */
2665 class ImportVariantsResponse { 2645 class ImportVariantsResponse {
2666 /** A job ID that can be used to get status information. */ 2646 /** A job ID that can be used to get status information. */
2667 core.String jobId; 2647 core.String jobId;
(...skipping 187 matching lines...) Expand 10 before | Expand all | Expand 10 after
2855 } 2835 }
2856 } 2836 }
2857 2837
2858 2838
2859 /** Not documented yet. */ 2839 /** Not documented yet. */
2860 class ListCoverageBucketsResponse { 2840 class ListCoverageBucketsResponse {
2861 /** 2841 /**
2862 * The length of each coverage bucket in base pairs. Note that buckets at the 2842 * The length of each coverage bucket in base pairs. Note that buckets at the
2863 * end of a reference sequence may be shorter. This value is omitted if the 2843 * end of a reference sequence may be shorter. This value is omitted if the
2864 * bucket width is infinity (the default behaviour, with no range or 2844 * bucket width is infinity (the default behaviour, with no range or
2865 * target_bucket_width). 2845 * targetBucketWidth).
2866 */ 2846 */
2867 core.String bucketWidth; 2847 core.String bucketWidth;
2868 2848
2869 /** 2849 /**
2870 * The coverage buckets. The list of buckets is sparse; a bucket with 0 2850 * The coverage buckets. The list of buckets is sparse; a bucket with 0
2871 * overlapping reads is not returned. A bucket never crosses more than one 2851 * overlapping reads is not returned. A bucket never crosses more than one
2872 * reference sequence. Each bucket has width bucket_width, unless its end is 2852 * reference sequence. Each bucket has width bucketWidth, unless its end is
2873 * is the end of the reference sequence. 2853 * the end of the reference sequence.
2874 */ 2854 */
2875 core.List<CoverageBucket> coverageBuckets; 2855 core.List<CoverageBucket> coverageBuckets;
2876 2856
2877 /** 2857 /**
2878 * The continuation token, which is used to page through large result sets. 2858 * The continuation token, which is used to page through large result sets.
2879 * Provide this value in a subsequent request to return the next page of 2859 * Provide this value in a subsequent request to return the next page of
2880 * results. This field will be empty if there aren't any additional results. 2860 * results. This field will be empty if there aren't any additional results.
2881 */ 2861 */
2882 core.String nextPageToken; 2862 core.String nextPageToken;
2883 2863
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3469 _json["id"] = id; 3449 _json["id"] = id;
3470 } 3450 }
3471 if (name != null) { 3451 if (name != null) {
3472 _json["name"] = name; 3452 _json["name"] = name;
3473 } 3453 }
3474 return _json; 3454 return _json;
3475 } 3455 }
3476 } 3456 }
3477 3457
3478 3458
3459 /**
3460 * ReferenceBound records an upper bound for the starting coordinate of variants
3461 * in a particular reference.
3462 */
3463 class ReferenceBound {
3464 /** The reference the bound is associate with. */
3465 core.String referenceName;
3466
3467 /**
3468 * An upper bound (inclusive) on the starting coordinate of any variant in the
3469 * reference sequence.
3470 */
3471 core.String upperBound;
3472
3473
3474 ReferenceBound();
3475
3476 ReferenceBound.fromJson(core.Map _json) {
3477 if (_json.containsKey("referenceName")) {
3478 referenceName = _json["referenceName"];
3479 }
3480 if (_json.containsKey("upperBound")) {
3481 upperBound = _json["upperBound"];
3482 }
3483 }
3484
3485 core.Map toJson() {
3486 var _json = new core.Map();
3487 if (referenceName != null) {
3488 _json["referenceName"] = referenceName;
3489 }
3490 if (upperBound != null) {
3491 _json["upperBound"] = upperBound;
3492 }
3493 return _json;
3494 }
3495 }
3496
3497
3479 /** Not documented yet. */ 3498 /** Not documented yet. */
3480 class ReferenceSequence { 3499 class ReferenceSequence {
3481 /** (AS) Genome assembly identifier. */ 3500 /** (AS) Genome assembly identifier. */
3482 core.String assemblyId; 3501 core.String assemblyId;
3483 3502
3484 /** (LN) Reference sequence length. */ 3503 /** (LN) Reference sequence length. */
3485 core.int length; 3504 core.int length;
3486 3505
3487 /** 3506 /**
3488 * (M5) MD5 checksum of the sequence in the uppercase, excluding spaces but 3507 * (M5) MD5 checksum of the sequence in the uppercase, excluding spaces but
(...skipping 52 matching lines...) Expand 10 before | Expand all | Expand 10 after
3541 _json["species"] = species; 3560 _json["species"] = species;
3542 } 3561 }
3543 if (uri != null) { 3562 if (uri != null) {
3544 _json["uri"] = uri; 3563 _json["uri"] = uri;
3545 } 3564 }
3546 return _json; 3565 return _json;
3547 } 3566 }
3548 } 3567 }
3549 3568
3550 3569
3551 /** The callset search request. */ 3570 /** The call set search request. */
3552 class SearchCallsetsRequest { 3571 class SearchCallSetsRequest {
3553 /** The maximum number of callsets to return. */
3554 core.String maxResults;
3555
3556 /** 3572 /**
3557 * Only return callsets for which a substring of the name matches this string. 3573 * Only return call sets for which a substring of the name matches this
3574 * string.
3558 */ 3575 */
3559 core.String name; 3576 core.String name;
3560 3577
3578 /** The maximum number of call sets to return. */
3579 core.int pageSize;
3580
3561 /** 3581 /**
3562 * The continuation token, which is used to page through large result sets. To 3582 * The continuation token, which is used to page through large result sets. To
3563 * get the next page of results, set this parameter to the value of 3583 * get the next page of results, set this parameter to the value of
3564 * "nextPageToken" from the previous response. 3584 * nextPageToken from the previous response.
3565 */ 3585 */
3566 core.String pageToken; 3586 core.String pageToken;
3567 3587
3568 /** 3588 /**
3569 * Restrict the query to callsets within the given variantsets. At least one 3589 * Restrict the query to call sets within the given variant sets. At least one
3570 * ID must be provided. 3590 * ID must be provided.
3571 */ 3591 */
3572 core.List<core.String> variantsetIds; 3592 core.List<core.String> variantSetIds;
3573 3593
3574 3594
3575 SearchCallsetsRequest(); 3595 SearchCallSetsRequest();
3576 3596
3577 SearchCallsetsRequest.fromJson(core.Map _json) { 3597 SearchCallSetsRequest.fromJson(core.Map _json) {
3578 if (_json.containsKey("maxResults")) {
3579 maxResults = _json["maxResults"];
3580 }
3581 if (_json.containsKey("name")) { 3598 if (_json.containsKey("name")) {
3582 name = _json["name"]; 3599 name = _json["name"];
3583 } 3600 }
3601 if (_json.containsKey("pageSize")) {
3602 pageSize = _json["pageSize"];
3603 }
3584 if (_json.containsKey("pageToken")) { 3604 if (_json.containsKey("pageToken")) {
3585 pageToken = _json["pageToken"]; 3605 pageToken = _json["pageToken"];
3586 } 3606 }
3587 if (_json.containsKey("variantsetIds")) { 3607 if (_json.containsKey("variantSetIds")) {
3588 variantsetIds = _json["variantsetIds"]; 3608 variantSetIds = _json["variantSetIds"];
3589 } 3609 }
3590 } 3610 }
3591 3611
3592 core.Map toJson() { 3612 core.Map toJson() {
3593 var _json = new core.Map(); 3613 var _json = new core.Map();
3594 if (maxResults != null) {
3595 _json["maxResults"] = maxResults;
3596 }
3597 if (name != null) { 3614 if (name != null) {
3598 _json["name"] = name; 3615 _json["name"] = name;
3599 } 3616 }
3617 if (pageSize != null) {
3618 _json["pageSize"] = pageSize;
3619 }
3600 if (pageToken != null) { 3620 if (pageToken != null) {
3601 _json["pageToken"] = pageToken; 3621 _json["pageToken"] = pageToken;
3602 } 3622 }
3603 if (variantsetIds != null) { 3623 if (variantSetIds != null) {
3604 _json["variantsetIds"] = variantsetIds; 3624 _json["variantSetIds"] = variantSetIds;
3605 } 3625 }
3606 return _json; 3626 return _json;
3607 } 3627 }
3608 } 3628 }
3609 3629
3610 3630
3611 /** The callset search response. */ 3631 /** The call set search response. */
3612 class SearchCallsetsResponse { 3632 class SearchCallSetsResponse {
3613 /** The list of matching callsets. */ 3633 /** The list of matching call sets. */
3614 core.List<Callset> callsets; 3634 core.List<CallSet> callSets;
3615 3635
3616 /** 3636 /**
3617 * The continuation token, which is used to page through large result sets. 3637 * The continuation token, which is used to page through large result sets.
3618 * Provide this value in a subsequent request to return the next page of 3638 * Provide this value in a subsequent request to return the next page of
3619 * results. This field will be empty if there aren't any additional results. 3639 * results. This field will be empty if there aren't any additional results.
3620 */ 3640 */
3621 core.String nextPageToken; 3641 core.String nextPageToken;
3622 3642
3623 3643
3624 SearchCallsetsResponse(); 3644 SearchCallSetsResponse();
3625 3645
3626 SearchCallsetsResponse.fromJson(core.Map _json) { 3646 SearchCallSetsResponse.fromJson(core.Map _json) {
3627 if (_json.containsKey("callsets")) { 3647 if (_json.containsKey("callSets")) {
3628 callsets = _json["callsets"].map((value) => new Callset.fromJson(value)).t oList(); 3648 callSets = _json["callSets"].map((value) => new CallSet.fromJson(value)).t oList();
3629 } 3649 }
3630 if (_json.containsKey("nextPageToken")) { 3650 if (_json.containsKey("nextPageToken")) {
3631 nextPageToken = _json["nextPageToken"]; 3651 nextPageToken = _json["nextPageToken"];
3632 } 3652 }
3633 } 3653 }
3634 3654
3635 core.Map toJson() { 3655 core.Map toJson() {
3636 var _json = new core.Map(); 3656 var _json = new core.Map();
3637 if (callsets != null) { 3657 if (callSets != null) {
3638 _json["callsets"] = callsets.map((value) => (value).toJson()).toList(); 3658 _json["callSets"] = callSets.map((value) => (value).toJson()).toList();
3639 } 3659 }
3640 if (nextPageToken != null) { 3660 if (nextPageToken != null) {
3641 _json["nextPageToken"] = nextPageToken; 3661 _json["nextPageToken"] = nextPageToken;
3642 } 3662 }
3643 return _json; 3663 return _json;
3644 } 3664 }
3645 } 3665 }
3646 3666
3647 3667
3648 /** The jobs search request. */ 3668 /** The jobs search request. */
(...skipping 12 matching lines...) Expand all
3661 3681
3662 /** 3682 /**
3663 * Specifies the number of results to return in a single page. Defaults to 3683 * Specifies the number of results to return in a single page. Defaults to
3664 * 128. The maximum value is 256. 3684 * 128. The maximum value is 256.
3665 */ 3685 */
3666 core.String maxResults; 3686 core.String maxResults;
3667 3687
3668 /** 3688 /**
3669 * The continuation token which is used to page through large result sets. To 3689 * The continuation token which is used to page through large result sets. To
3670 * get the next page of results, set this parameter to the value of the 3690 * get the next page of results, set this parameter to the value of the
3671 * "nextPageToken" from the previous response. 3691 * nextPageToken from the previous response.
3672 */ 3692 */
3673 core.String pageToken; 3693 core.String pageToken;
3674 3694
3675 /** 3695 /** Required. Only return jobs which belong to this Google Developers */
3676 * Required. Only return jobs which belong to this Google Developers Console
3677 * project. Only accepts project numbers.
3678 */
3679 core.String projectId; 3696 core.String projectId;
3680 3697
3681 /** Only return jobs which have a matching status. */ 3698 /** Only return jobs which have a matching status. */
3682 core.List<core.String> status; 3699 core.List<core.String> status;
3683 3700
3684 3701
3685 SearchJobsRequest(); 3702 SearchJobsRequest();
3686 3703
3687 SearchJobsRequest.fromJson(core.Map _json) { 3704 SearchJobsRequest.fromJson(core.Map _json) {
3688 if (_json.containsKey("createdAfter")) { 3705 if (_json.containsKey("createdAfter")) {
(...skipping 82 matching lines...) Expand 10 before | Expand all | Expand 10 after
3771 class SearchReadsRequest { 3788 class SearchReadsRequest {
3772 /** 3789 /**
3773 * Specifies number of results to return in a single page. If unspecified, it 3790 * Specifies number of results to return in a single page. If unspecified, it
3774 * will default to 256. The maximum value is 2048. 3791 * will default to 256. The maximum value is 2048.
3775 */ 3792 */
3776 core.String maxResults; 3793 core.String maxResults;
3777 3794
3778 /** 3795 /**
3779 * The continuation token, which is used to page through large result sets. To 3796 * The continuation token, which is used to page through large result sets. To
3780 * get the next page of results, set this parameter to the value of 3797 * get the next page of results, set this parameter to the value of
3781 * "nextPageToken" from the previous response. 3798 * nextPageToken from the previous response.
3782 */ 3799 */
3783 core.String pageToken; 3800 core.String pageToken;
3784 3801
3785 /** 3802 /**
3786 * The readsets within which to search for reads. At least one readset ID must 3803 * The readsets within which to search for reads. At least one readset ID must
3787 * be provided. All specified readsets must be aligned against a common set of 3804 * be provided. All specified readsets must be aligned against a common set of
3788 * reference sequences; this defines the genomic coordinates for the query. 3805 * reference sequences; this defines the genomic coordinates for the query.
3789 */ 3806 */
3790 core.List<core.String> readsetIds; 3807 core.List<core.String> readsetIds;
3791 3808
3792 /** 3809 /**
3793 * The end position (1-based, inclusive) of the target range. If specified, 3810 * The end position (1-based, inclusive) of the target range. If specified,
3794 * "sequenceName" must also be specified. Defaults to the end of the target 3811 * sequenceName must also be specified. Defaults to the end of the target
3795 * reference sequence, if any. 3812 * reference sequence, if any.
3796 */ 3813 */
3797 core.String sequenceEnd; 3814 core.String sequenceEnd;
3798 3815
3799 /** 3816 /**
3800 * Restricts the results to a particular reference sequence such as '1', 3817 * Restricts the results to a particular reference sequence such as 1, chr1,
3801 * 'chr1', or 'X'. The set of valid references sequences depends on the 3818 * or X. The set of valid references sequences depends on the readsets
3802 * readsets specified. If set to "*", only unmapped Reads are returned. 3819 * specified. If set to *, only unmapped Reads are returned.
3803 */ 3820 */
3804 core.String sequenceName; 3821 core.String sequenceName;
3805 3822
3806 /** 3823 /**
3807 * The start position (1-based, inclusive) of the target range. If specified, 3824 * The start position (1-based, inclusive) of the target range. If specified,
3808 * "sequenceName" must also be specified. Defaults to the start of the target 3825 * sequenceName must also be specified. Defaults to the start of the target
3809 * reference sequence, if any. 3826 * reference sequence, if any.
3810 */ 3827 */
3811 core.String sequenceStart; 3828 core.String sequenceStart;
3812 3829
3813 3830
3814 SearchReadsRequest(); 3831 SearchReadsRequest();
3815 3832
3816 SearchReadsRequest.fromJson(core.Map _json) { 3833 SearchReadsRequest.fromJson(core.Map _json) {
3817 if (_json.containsKey("maxResults")) { 3834 if (_json.containsKey("maxResults")) {
3818 maxResults = _json["maxResults"]; 3835 maxResults = _json["maxResults"];
(...skipping 96 matching lines...) Expand 10 before | Expand all | Expand 10 after
3915 core.String maxResults; 3932 core.String maxResults;
3916 3933
3917 /** 3934 /**
3918 * Only return readsets for which a substring of the name matches this string. 3935 * Only return readsets for which a substring of the name matches this string.
3919 */ 3936 */
3920 core.String name; 3937 core.String name;
3921 3938
3922 /** 3939 /**
3923 * The continuation token, which is used to page through large result sets. To 3940 * The continuation token, which is used to page through large result sets. To
3924 * get the next page of results, set this parameter to the value of 3941 * get the next page of results, set this parameter to the value of
3925 * "nextPageToken" from the previous response. 3942 * nextPageToken from the previous response.
3926 */ 3943 */
3927 core.String pageToken; 3944 core.String pageToken;
3928 3945
3929 3946
3930 SearchReadsetsRequest(); 3947 SearchReadsetsRequest();
3931 3948
3932 SearchReadsetsRequest.fromJson(core.Map _json) { 3949 SearchReadsetsRequest.fromJson(core.Map _json) {
3933 if (_json.containsKey("datasetIds")) { 3950 if (_json.containsKey("datasetIds")) {
3934 datasetIds = _json["datasetIds"]; 3951 datasetIds = _json["datasetIds"];
3935 } 3952 }
(...skipping 57 matching lines...) Expand 10 before | Expand all | Expand 10 after
3993 _json["nextPageToken"] = nextPageToken; 4010 _json["nextPageToken"] = nextPageToken;
3994 } 4011 }
3995 if (readsets != null) { 4012 if (readsets != null) {
3996 _json["readsets"] = readsets.map((value) => (value).toJson()).toList(); 4013 _json["readsets"] = readsets.map((value) => (value).toJson()).toList();
3997 } 4014 }
3998 return _json; 4015 return _json;
3999 } 4016 }
4000 } 4017 }
4001 4018
4002 4019
4020 /** The search variant sets request. */
4021 class SearchVariantSetsRequest {
4022 /**
4023 * Exactly one dataset ID must be provided here. Only variant sets which
4024 * belong to this dataset will be returned.
4025 */
4026 core.List<core.String> datasetIds;
4027
4028 /** The maximum number of variant sets to return in a request. */
4029 core.int pageSize;
4030
4031 /**
4032 * The continuation token, which is used to page through large result sets. To
4033 * get the next page of results, set this parameter to the value of
4034 * nextPageToken from the previous response.
4035 */
4036 core.String pageToken;
4037
4038
4039 SearchVariantSetsRequest();
4040
4041 SearchVariantSetsRequest.fromJson(core.Map _json) {
4042 if (_json.containsKey("datasetIds")) {
4043 datasetIds = _json["datasetIds"];
4044 }
4045 if (_json.containsKey("pageSize")) {
4046 pageSize = _json["pageSize"];
4047 }
4048 if (_json.containsKey("pageToken")) {
4049 pageToken = _json["pageToken"];
4050 }
4051 }
4052
4053 core.Map toJson() {
4054 var _json = new core.Map();
4055 if (datasetIds != null) {
4056 _json["datasetIds"] = datasetIds;
4057 }
4058 if (pageSize != null) {
4059 _json["pageSize"] = pageSize;
4060 }
4061 if (pageToken != null) {
4062 _json["pageToken"] = pageToken;
4063 }
4064 return _json;
4065 }
4066 }
4067
4068
4069 /** The search variant sets response. */
4070 class SearchVariantSetsResponse {
4071 /**
4072 * The continuation token, which is used to page through large result sets.
4073 * Provide this value in a subsequent request to return the next page of
4074 * results. This field will be empty if there aren't any additional results.
4075 */
4076 core.String nextPageToken;
4077
4078 /** The variant sets belonging to the requested dataset. */
4079 core.List<VariantSet> variantSets;
4080
4081
4082 SearchVariantSetsResponse();
4083
4084 SearchVariantSetsResponse.fromJson(core.Map _json) {
4085 if (_json.containsKey("nextPageToken")) {
4086 nextPageToken = _json["nextPageToken"];
4087 }
4088 if (_json.containsKey("variantSets")) {
4089 variantSets = _json["variantSets"].map((value) => new VariantSet.fromJson( value)).toList();
4090 }
4091 }
4092
4093 core.Map toJson() {
4094 var _json = new core.Map();
4095 if (nextPageToken != null) {
4096 _json["nextPageToken"] = nextPageToken;
4097 }
4098 if (variantSets != null) {
4099 _json["variantSets"] = variantSets.map((value) => (value).toJson()).toList ();
4100 }
4101 return _json;
4102 }
4103 }
4104
4105
4003 /** The variant search request. */ 4106 /** The variant search request. */
4004 class SearchVariantsRequest { 4107 class SearchVariantsRequest {
4005 /** 4108 /**
4006 * Only return variant calls which belong to callsets with these ids. Leaving 4109 * Only return variant calls which belong to call sets with these ids. Leaving
4007 * this blank returns all variant calls. At most one of callsetNames or 4110 * this blank returns all variant calls.
4008 * callsetIds should be provided. 4111 */
4009 */ 4112 core.List<core.String> callSetIds;
4010 core.List<core.String> callsetIds;
4011
4012 /**
4013 * Only return variant calls which belong to callsets which have exactly these
4014 * names. Leaving this blank returns all variant calls. At most one of
4015 * callsetNames or callsetIds should be provided.
4016 */
4017 core.List<core.String> callsetNames;
4018
4019 /** Required. Only return variants on this contig. */
4020 core.String contig;
4021 4113
4022 /** 4114 /**
4023 * Required. The end of the window (0-based, exclusive) for which overlapping 4115 * Required. The end of the window (0-based, exclusive) for which overlapping
4024 * variants should be returned. 4116 * variants should be returned.
4025 */ 4117 */
4026 core.String endPosition; 4118 core.String end;
4119
4120 /**
4121 * The maximum number of calls to return. However, at least one variant will
4122 * always be returned, even if it has more calls than this limit.
4123 */
4124 core.int maxCalls;
4027 4125
4028 /** The maximum number of variants to return. */ 4126 /** The maximum number of variants to return. */
4029 core.String maxResults; 4127 core.int pageSize;
4030 4128
4031 /** 4129 /**
4032 * The continuation token, which is used to page through large result sets. To 4130 * The continuation token, which is used to page through large result sets. To
4033 * get the next page of results, set this parameter to the value of 4131 * get the next page of results, set this parameter to the value of
4034 * "nextPageToken" from the previous response. 4132 * nextPageToken from the previous response.
4035 */ 4133 */
4036 core.String pageToken; 4134 core.String pageToken;
4037 4135
4136 /** Required. Only return variants in this reference sequence. */
4137 core.String referenceName;
4138
4038 /** 4139 /**
4039 * Required. The beginning of the window (0-based, inclusive) for which 4140 * Required. The beginning of the window (0-based, inclusive) for which
4040 * overlapping variants should be returned. 4141 * overlapping variants should be returned.
4041 */ 4142 */
4042 core.String startPosition; 4143 core.String start;
4043 4144
4044 /** Only return variants which have exactly this name. */ 4145 /** Only return variants which have exactly this name. */
4045 core.String variantName; 4146 core.String variantName;
4046 4147
4047 /** Required. The ID of the variantset to search. */ 4148 /**
4048 core.String variantsetId; 4149 * Exactly one variant set ID must be provided. Only variants from this
4150 * variant set will be returned.
4151 */
4152 core.List<core.String> variantSetIds;
4049 4153
4050 4154
4051 SearchVariantsRequest(); 4155 SearchVariantsRequest();
4052 4156
4053 SearchVariantsRequest.fromJson(core.Map _json) { 4157 SearchVariantsRequest.fromJson(core.Map _json) {
4054 if (_json.containsKey("callsetIds")) { 4158 if (_json.containsKey("callSetIds")) {
4055 callsetIds = _json["callsetIds"]; 4159 callSetIds = _json["callSetIds"];
4056 } 4160 }
4057 if (_json.containsKey("callsetNames")) { 4161 if (_json.containsKey("end")) {
4058 callsetNames = _json["callsetNames"]; 4162 end = _json["end"];
4059 } 4163 }
4060 if (_json.containsKey("contig")) { 4164 if (_json.containsKey("maxCalls")) {
4061 contig = _json["contig"]; 4165 maxCalls = _json["maxCalls"];
4062 } 4166 }
4063 if (_json.containsKey("endPosition")) { 4167 if (_json.containsKey("pageSize")) {
4064 endPosition = _json["endPosition"]; 4168 pageSize = _json["pageSize"];
4065 }
4066 if (_json.containsKey("maxResults")) {
4067 maxResults = _json["maxResults"];
4068 } 4169 }
4069 if (_json.containsKey("pageToken")) { 4170 if (_json.containsKey("pageToken")) {
4070 pageToken = _json["pageToken"]; 4171 pageToken = _json["pageToken"];
4071 } 4172 }
4072 if (_json.containsKey("startPosition")) { 4173 if (_json.containsKey("referenceName")) {
4073 startPosition = _json["startPosition"]; 4174 referenceName = _json["referenceName"];
4175 }
4176 if (_json.containsKey("start")) {
4177 start = _json["start"];
4074 } 4178 }
4075 if (_json.containsKey("variantName")) { 4179 if (_json.containsKey("variantName")) {
4076 variantName = _json["variantName"]; 4180 variantName = _json["variantName"];
4077 } 4181 }
4078 if (_json.containsKey("variantsetId")) { 4182 if (_json.containsKey("variantSetIds")) {
4079 variantsetId = _json["variantsetId"]; 4183 variantSetIds = _json["variantSetIds"];
4080 } 4184 }
4081 } 4185 }
4082 4186
4083 core.Map toJson() { 4187 core.Map toJson() {
4084 var _json = new core.Map(); 4188 var _json = new core.Map();
4085 if (callsetIds != null) { 4189 if (callSetIds != null) {
4086 _json["callsetIds"] = callsetIds; 4190 _json["callSetIds"] = callSetIds;
4087 } 4191 }
4088 if (callsetNames != null) { 4192 if (end != null) {
4089 _json["callsetNames"] = callsetNames; 4193 _json["end"] = end;
4090 } 4194 }
4091 if (contig != null) { 4195 if (maxCalls != null) {
4092 _json["contig"] = contig; 4196 _json["maxCalls"] = maxCalls;
4093 } 4197 }
4094 if (endPosition != null) { 4198 if (pageSize != null) {
4095 _json["endPosition"] = endPosition; 4199 _json["pageSize"] = pageSize;
4096 }
4097 if (maxResults != null) {
4098 _json["maxResults"] = maxResults;
4099 } 4200 }
4100 if (pageToken != null) { 4201 if (pageToken != null) {
4101 _json["pageToken"] = pageToken; 4202 _json["pageToken"] = pageToken;
4102 } 4203 }
4103 if (startPosition != null) { 4204 if (referenceName != null) {
4104 _json["startPosition"] = startPosition; 4205 _json["referenceName"] = referenceName;
4206 }
4207 if (start != null) {
4208 _json["start"] = start;
4105 } 4209 }
4106 if (variantName != null) { 4210 if (variantName != null) {
4107 _json["variantName"] = variantName; 4211 _json["variantName"] = variantName;
4108 } 4212 }
4109 if (variantsetId != null) { 4213 if (variantSetIds != null) {
4110 _json["variantsetId"] = variantsetId; 4214 _json["variantSetIds"] = variantSetIds;
4111 } 4215 }
4112 return _json; 4216 return _json;
4113 } 4217 }
4114 } 4218 }
4115 4219
4116 4220
4117 /** The variant search response. */ 4221 /** The variant search response. */
4118 class SearchVariantsResponse { 4222 class SearchVariantsResponse {
4119 /** 4223 /**
4120 * The continuation token, which is used to page through large result sets. 4224 * The continuation token, which is used to page through large result sets.
(...skipping 26 matching lines...) Expand all
4147 _json["variants"] = variants.map((value) => (value).toJson()).toList(); 4251 _json["variants"] = variants.map((value) => (value).toJson()).toList();
4148 } 4252 }
4149 return _json; 4253 return _json;
4150 } 4254 }
4151 } 4255 }
4152 4256
4153 4257
4154 /** 4258 /**
4155 * A Variant represents a change in DNA sequence relative to some reference. For 4259 * A Variant represents a change in DNA sequence relative to some reference. For
4156 * example, a Variant could represent a SNP or an insertion. Variants belong to 4260 * example, a Variant could represent a SNP or an insertion. Variants belong to
4157 * a Variantset. 4261 * a variant set.
4158 */ 4262 */
4159 class Variant { 4263 class Variant {
4160 /** The bases that appear instead of the reference bases. */ 4264 /** The bases that appear instead of the reference bases. */
4161 core.List<core.String> alternateBases; 4265 core.List<core.String> alternateBases;
4162 4266
4163 /** 4267 /**
4164 * The variant calls for this particular variant. Each one represents the 4268 * The variant calls for this particular variant. Each one represents the
4165 * determination of genotype with respect to this variant. 4269 * determination of genotype with respect to this variant.
4166 */ 4270 */
4167 core.List<Call> calls; 4271 core.List<Call> calls;
4168 4272
4169 /** The contig on which this variant occurs. (such as 'chr20' or 'X') */
4170 core.String contig;
4171
4172 /** The date this variant was created, in milliseconds from the epoch. */ 4273 /** The date this variant was created, in milliseconds from the epoch. */
4173 core.String created; 4274 core.String created;
4174 4275
4175 /** 4276 /**
4176 * The end position (0-based) of this variant. This corresponds to the first 4277 * The end position (0-based) of this variant. This corresponds to the first
4177 * base after the last base in the reference allele. So, the length of the 4278 * base after the last base in the reference allele. So, the length of the
4178 * reference allele is (end - position). This is useful for variants that 4279 * reference allele is (end - start). This is useful for variants that don't
4179 * don't explicitly give alternate bases, for example large deletions. 4280 * explicitly give alternate bases, for example large deletions.
4180 */ 4281 */
4181 core.String end; 4282 core.String end;
4182 4283
4183 /** The Google generated ID of the variant, immutable. */ 4284 /** The Google generated ID of the variant, immutable. */
4184 core.String id; 4285 core.String id;
4185 4286
4186 /** A map of additional variant information. */ 4287 /** A map of additional variant information. */
4187 core.Map<core.String, core.List<core.String>> info; 4288 core.Map<core.String, core.List<core.String>> info;
4188 4289
4189 /** Names for the variant, for example a RefSNP ID. */ 4290 /** Names for the variant, for example a RefSNP ID. */
4190 core.List<core.String> names; 4291 core.List<core.String> names;
4191 4292
4192 /** 4293 /**
4193 * The position at which this variant occurs (0-based). This corresponds to
4194 * the first base of the string of reference bases.
4195 */
4196 core.String position;
4197
4198 /**
4199 * The reference bases for this variant. They start at the given position. 4294 * The reference bases for this variant. They start at the given position.
4200 */ 4295 */
4201 core.String referenceBases; 4296 core.String referenceBases;
4202 4297
4203 /** The ID of the variantset this variant belongs to. */ 4298 /** The reference on which this variant occurs. (such as chr20 or X) */
4204 core.String variantsetId; 4299 core.String referenceName;
4300
4301 /**
4302 * The position at which this variant occurs (0-based). This corresponds to
4303 * the first base of the string of reference bases.
4304 */
4305 core.String start;
4306
4307 /** The ID of the variant set this variant belongs to. */
4308 core.String variantSetId;
4205 4309
4206 4310
4207 Variant(); 4311 Variant();
4208 4312
4209 Variant.fromJson(core.Map _json) { 4313 Variant.fromJson(core.Map _json) {
4210 if (_json.containsKey("alternateBases")) { 4314 if (_json.containsKey("alternateBases")) {
4211 alternateBases = _json["alternateBases"]; 4315 alternateBases = _json["alternateBases"];
4212 } 4316 }
4213 if (_json.containsKey("calls")) { 4317 if (_json.containsKey("calls")) {
4214 calls = _json["calls"].map((value) => new Call.fromJson(value)).toList(); 4318 calls = _json["calls"].map((value) => new Call.fromJson(value)).toList();
4215 } 4319 }
4216 if (_json.containsKey("contig")) {
4217 contig = _json["contig"];
4218 }
4219 if (_json.containsKey("created")) { 4320 if (_json.containsKey("created")) {
4220 created = _json["created"]; 4321 created = _json["created"];
4221 } 4322 }
4222 if (_json.containsKey("end")) { 4323 if (_json.containsKey("end")) {
4223 end = _json["end"]; 4324 end = _json["end"];
4224 } 4325 }
4225 if (_json.containsKey("id")) { 4326 if (_json.containsKey("id")) {
4226 id = _json["id"]; 4327 id = _json["id"];
4227 } 4328 }
4228 if (_json.containsKey("info")) { 4329 if (_json.containsKey("info")) {
4229 info = _json["info"]; 4330 info = _json["info"];
4230 } 4331 }
4231 if (_json.containsKey("names")) { 4332 if (_json.containsKey("names")) {
4232 names = _json["names"]; 4333 names = _json["names"];
4233 } 4334 }
4234 if (_json.containsKey("position")) {
4235 position = _json["position"];
4236 }
4237 if (_json.containsKey("referenceBases")) { 4335 if (_json.containsKey("referenceBases")) {
4238 referenceBases = _json["referenceBases"]; 4336 referenceBases = _json["referenceBases"];
4239 } 4337 }
4240 if (_json.containsKey("variantsetId")) { 4338 if (_json.containsKey("referenceName")) {
4241 variantsetId = _json["variantsetId"]; 4339 referenceName = _json["referenceName"];
4340 }
4341 if (_json.containsKey("start")) {
4342 start = _json["start"];
4343 }
4344 if (_json.containsKey("variantSetId")) {
4345 variantSetId = _json["variantSetId"];
4242 } 4346 }
4243 } 4347 }
4244 4348
4245 core.Map toJson() { 4349 core.Map toJson() {
4246 var _json = new core.Map(); 4350 var _json = new core.Map();
4247 if (alternateBases != null) { 4351 if (alternateBases != null) {
4248 _json["alternateBases"] = alternateBases; 4352 _json["alternateBases"] = alternateBases;
4249 } 4353 }
4250 if (calls != null) { 4354 if (calls != null) {
4251 _json["calls"] = calls.map((value) => (value).toJson()).toList(); 4355 _json["calls"] = calls.map((value) => (value).toJson()).toList();
4252 } 4356 }
4253 if (contig != null) {
4254 _json["contig"] = contig;
4255 }
4256 if (created != null) { 4357 if (created != null) {
4257 _json["created"] = created; 4358 _json["created"] = created;
4258 } 4359 }
4259 if (end != null) { 4360 if (end != null) {
4260 _json["end"] = end; 4361 _json["end"] = end;
4261 } 4362 }
4262 if (id != null) { 4363 if (id != null) {
4263 _json["id"] = id; 4364 _json["id"] = id;
4264 } 4365 }
4265 if (info != null) { 4366 if (info != null) {
4266 _json["info"] = info; 4367 _json["info"] = info;
4267 } 4368 }
4268 if (names != null) { 4369 if (names != null) {
4269 _json["names"] = names; 4370 _json["names"] = names;
4270 } 4371 }
4271 if (position != null) {
4272 _json["position"] = position;
4273 }
4274 if (referenceBases != null) { 4372 if (referenceBases != null) {
4275 _json["referenceBases"] = referenceBases; 4373 _json["referenceBases"] = referenceBases;
4276 } 4374 }
4277 if (variantsetId != null) { 4375 if (referenceName != null) {
4278 _json["variantsetId"] = variantsetId; 4376 _json["referenceName"] = referenceName;
4377 }
4378 if (start != null) {
4379 _json["start"] = start;
4380 }
4381 if (variantSetId != null) {
4382 _json["variantSetId"] = variantSetId;
4279 } 4383 }
4280 return _json; 4384 return _json;
4281 } 4385 }
4386 }
4387
4388
4389 /**
4390 * A VariantSet represents a collection of Variants and their summary
4391 * statistics.
4392 */
4393 class VariantSet {
4394 /** The dataset to which this variant set belongs. Immutable. */
4395 core.String datasetId;
4396
4397 /** The Google-generated ID of the variant set. Immutable. */
4398 core.String id;
4399
4400 /** The metadata associated with this variant set. */
4401 core.List<Metadata> metadata;
4402
4403 /**
4404 * A list of all references used by the variants in a variant set with
4405 * associated coordinate upper bounds for each one.
4406 */
4407 core.List<ReferenceBound> referenceBounds;
4408
4409
4410 VariantSet();
4411
4412 VariantSet.fromJson(core.Map _json) {
4413 if (_json.containsKey("datasetId")) {
4414 datasetId = _json["datasetId"];
4415 }
4416 if (_json.containsKey("id")) {
4417 id = _json["id"];
4418 }
4419 if (_json.containsKey("metadata")) {
4420 metadata = _json["metadata"].map((value) => new Metadata.fromJson(value)). toList();
4421 }
4422 if (_json.containsKey("referenceBounds")) {
4423 referenceBounds = _json["referenceBounds"].map((value) => new ReferenceBou nd.fromJson(value)).toList();
4424 }
4425 }
4426
4427 core.Map toJson() {
4428 var _json = new core.Map();
4429 if (datasetId != null) {
4430 _json["datasetId"] = datasetId;
4431 }
4432 if (id != null) {
4433 _json["id"] = id;
4434 }
4435 if (metadata != null) {
4436 _json["metadata"] = metadata.map((value) => (value).toJson()).toList();
4437 }
4438 if (referenceBounds != null) {
4439 _json["referenceBounds"] = referenceBounds.map((value) => (value).toJson() ).toList();
4440 }
4441 return _json;
4442 }
4282 } 4443 }
4283 4444
4284 4445
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