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| 1 library googleapis_beta.genomics.v1beta; |
| 2 |
| 3 import "dart:core" as core; |
| 4 import "dart:collection" as collection; |
| 5 import "dart:async" as async; |
| 6 import "dart:convert" as convert; |
| 7 |
| 8 import "package:crypto/crypto.dart" as crypto; |
| 9 import 'package:http/http.dart' as http; |
| 10 import '../src/common_internal.dart' as common_internal; |
| 11 import '../common/common.dart' as common; |
| 12 |
| 13 export '../common/common.dart' show ApiRequestError; |
| 14 export '../common/common.dart' show DetailedApiRequestError; |
| 15 |
| 16 /** Provides access to Genomics data. */ |
| 17 class GenomicsApi { |
| 18 /** View and manage your data in Google BigQuery */ |
| 19 static const BigqueryScope = "https://www.googleapis.com/auth/bigquery"; |
| 20 |
| 21 /** Manage your data in Google Cloud Storage */ |
| 22 static const DevstorageReadWriteScope = "https://www.googleapis.com/auth/devst
orage.read_write"; |
| 23 |
| 24 /** View and manage Genomics data */ |
| 25 static const GenomicsScope = "https://www.googleapis.com/auth/genomics"; |
| 26 |
| 27 /** View Genomics data */ |
| 28 static const GenomicsReadonlyScope = "https://www.googleapis.com/auth/genomics
.readonly"; |
| 29 |
| 30 |
| 31 final common_internal.ApiRequester _requester; |
| 32 |
| 33 BeaconsResourceApi get beacons => new BeaconsResourceApi(_requester); |
| 34 CallsetsResourceApi get callsets => new CallsetsResourceApi(_requester); |
| 35 DatasetsResourceApi get datasets => new DatasetsResourceApi(_requester); |
| 36 ExperimentalResourceApi get experimental => new ExperimentalResourceApi(_reque
ster); |
| 37 JobsResourceApi get jobs => new JobsResourceApi(_requester); |
| 38 ReadsResourceApi get reads => new ReadsResourceApi(_requester); |
| 39 ReadsetsResourceApi get readsets => new ReadsetsResourceApi(_requester); |
| 40 VariantsResourceApi get variants => new VariantsResourceApi(_requester); |
| 41 |
| 42 GenomicsApi(http.Client client) : |
| 43 _requester = new common_internal.ApiRequester(client, "https://www.googlea
pis.com/", "/genomics/v1beta/"); |
| 44 } |
| 45 |
| 46 |
| 47 /** Not documented yet. */ |
| 48 class BeaconsResourceApi { |
| 49 final common_internal.ApiRequester _requester; |
| 50 |
| 51 BeaconsResourceApi(common_internal.ApiRequester client) : |
| 52 _requester = client; |
| 53 |
| 54 /** |
| 55 * This is an experimental API that provides a Global Alliance for Genomics |
| 56 * and Health Beacon. It may change at any time. |
| 57 * |
| 58 * Request parameters: |
| 59 * |
| 60 * [variantsetId] - The ID of the variantset to query over. It must be public. |
| 61 * Private variantsets will return an unauthorized exception. |
| 62 * |
| 63 * [allele] - Required. The allele to look for ('A', 'C', 'G' or 'T'). |
| 64 * |
| 65 * [contig] - Required. The contig to query over. |
| 66 * |
| 67 * [position] - Required. The 0-based position to query. |
| 68 * |
| 69 * Completes with a [Beacon]. |
| 70 * |
| 71 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 72 * error. |
| 73 * |
| 74 * If the used [http.Client] completes with an error when making a REST call, |
| 75 * this method will complete with the same error. |
| 76 */ |
| 77 async.Future<Beacon> get(core.String variantsetId, {core.String allele, core.S
tring contig, core.String position}) { |
| 78 var _url = null; |
| 79 var _queryParams = new core.Map(); |
| 80 var _uploadMedia = null; |
| 81 var _uploadOptions = null; |
| 82 var _downloadOptions = common.DownloadOptions.Metadata; |
| 83 var _body = null; |
| 84 |
| 85 if (variantsetId == null) { |
| 86 throw new core.ArgumentError("Parameter variantsetId is required."); |
| 87 } |
| 88 if (allele != null) { |
| 89 _queryParams["allele"] = [allele]; |
| 90 } |
| 91 if (contig != null) { |
| 92 _queryParams["contig"] = [contig]; |
| 93 } |
| 94 if (position != null) { |
| 95 _queryParams["position"] = [position]; |
| 96 } |
| 97 |
| 98 |
| 99 _url = 'beacons/' + common_internal.Escaper.ecapeVariable('$variantsetId'); |
| 100 |
| 101 var _response = _requester.request(_url, |
| 102 "GET", |
| 103 body: _body, |
| 104 queryParams: _queryParams, |
| 105 uploadOptions: _uploadOptions, |
| 106 uploadMedia: _uploadMedia, |
| 107 downloadOptions: _downloadOptions); |
| 108 return _response.then((data) => new Beacon.fromJson(data)); |
| 109 } |
| 110 |
| 111 } |
| 112 |
| 113 |
| 114 /** Not documented yet. */ |
| 115 class CallsetsResourceApi { |
| 116 final common_internal.ApiRequester _requester; |
| 117 |
| 118 CallsetsResourceApi(common_internal.ApiRequester client) : |
| 119 _requester = client; |
| 120 |
| 121 /** |
| 122 * Creates a new callset. |
| 123 * |
| 124 * [request] - The metadata request object. |
| 125 * |
| 126 * Request parameters: |
| 127 * |
| 128 * Completes with a [Callset]. |
| 129 * |
| 130 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 131 * error. |
| 132 * |
| 133 * If the used [http.Client] completes with an error when making a REST call, |
| 134 * this method will complete with the same error. |
| 135 */ |
| 136 async.Future<Callset> create(Callset request) { |
| 137 var _url = null; |
| 138 var _queryParams = new core.Map(); |
| 139 var _uploadMedia = null; |
| 140 var _uploadOptions = null; |
| 141 var _downloadOptions = common.DownloadOptions.Metadata; |
| 142 var _body = null; |
| 143 |
| 144 if (request != null) { |
| 145 _body = convert.JSON.encode((request).toJson()); |
| 146 } |
| 147 |
| 148 |
| 149 _url = 'callsets'; |
| 150 |
| 151 var _response = _requester.request(_url, |
| 152 "POST", |
| 153 body: _body, |
| 154 queryParams: _queryParams, |
| 155 uploadOptions: _uploadOptions, |
| 156 uploadMedia: _uploadMedia, |
| 157 downloadOptions: _downloadOptions); |
| 158 return _response.then((data) => new Callset.fromJson(data)); |
| 159 } |
| 160 |
| 161 /** |
| 162 * Deletes a callset. |
| 163 * |
| 164 * Request parameters: |
| 165 * |
| 166 * [callsetId] - The ID of the callset to be deleted. |
| 167 * |
| 168 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 169 * error. |
| 170 * |
| 171 * If the used [http.Client] completes with an error when making a REST call, |
| 172 * this method will complete with the same error. |
| 173 */ |
| 174 async.Future delete(core.String callsetId) { |
| 175 var _url = null; |
| 176 var _queryParams = new core.Map(); |
| 177 var _uploadMedia = null; |
| 178 var _uploadOptions = null; |
| 179 var _downloadOptions = common.DownloadOptions.Metadata; |
| 180 var _body = null; |
| 181 |
| 182 if (callsetId == null) { |
| 183 throw new core.ArgumentError("Parameter callsetId is required."); |
| 184 } |
| 185 |
| 186 _downloadOptions = null; |
| 187 |
| 188 _url = 'callsets/' + common_internal.Escaper.ecapeVariable('$callsetId'); |
| 189 |
| 190 var _response = _requester.request(_url, |
| 191 "DELETE", |
| 192 body: _body, |
| 193 queryParams: _queryParams, |
| 194 uploadOptions: _uploadOptions, |
| 195 uploadMedia: _uploadMedia, |
| 196 downloadOptions: _downloadOptions); |
| 197 return _response.then((data) => null); |
| 198 } |
| 199 |
| 200 /** |
| 201 * Gets a callset by ID. |
| 202 * |
| 203 * Request parameters: |
| 204 * |
| 205 * [callsetId] - The ID of the callset. |
| 206 * |
| 207 * Completes with a [Callset]. |
| 208 * |
| 209 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 210 * error. |
| 211 * |
| 212 * If the used [http.Client] completes with an error when making a REST call, |
| 213 * this method will complete with the same error. |
| 214 */ |
| 215 async.Future<Callset> get(core.String callsetId) { |
| 216 var _url = null; |
| 217 var _queryParams = new core.Map(); |
| 218 var _uploadMedia = null; |
| 219 var _uploadOptions = null; |
| 220 var _downloadOptions = common.DownloadOptions.Metadata; |
| 221 var _body = null; |
| 222 |
| 223 if (callsetId == null) { |
| 224 throw new core.ArgumentError("Parameter callsetId is required."); |
| 225 } |
| 226 |
| 227 |
| 228 _url = 'callsets/' + common_internal.Escaper.ecapeVariable('$callsetId'); |
| 229 |
| 230 var _response = _requester.request(_url, |
| 231 "GET", |
| 232 body: _body, |
| 233 queryParams: _queryParams, |
| 234 uploadOptions: _uploadOptions, |
| 235 uploadMedia: _uploadMedia, |
| 236 downloadOptions: _downloadOptions); |
| 237 return _response.then((data) => new Callset.fromJson(data)); |
| 238 } |
| 239 |
| 240 /** |
| 241 * Updates a callset. This method supports patch semantics. |
| 242 * |
| 243 * [request] - The metadata request object. |
| 244 * |
| 245 * Request parameters: |
| 246 * |
| 247 * [callsetId] - The ID of the callset to be updated. |
| 248 * |
| 249 * Completes with a [Callset]. |
| 250 * |
| 251 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 252 * error. |
| 253 * |
| 254 * If the used [http.Client] completes with an error when making a REST call, |
| 255 * this method will complete with the same error. |
| 256 */ |
| 257 async.Future<Callset> patch(Callset request, core.String callsetId) { |
| 258 var _url = null; |
| 259 var _queryParams = new core.Map(); |
| 260 var _uploadMedia = null; |
| 261 var _uploadOptions = null; |
| 262 var _downloadOptions = common.DownloadOptions.Metadata; |
| 263 var _body = null; |
| 264 |
| 265 if (request != null) { |
| 266 _body = convert.JSON.encode((request).toJson()); |
| 267 } |
| 268 if (callsetId == null) { |
| 269 throw new core.ArgumentError("Parameter callsetId is required."); |
| 270 } |
| 271 |
| 272 |
| 273 _url = 'callsets/' + common_internal.Escaper.ecapeVariable('$callsetId'); |
| 274 |
| 275 var _response = _requester.request(_url, |
| 276 "PATCH", |
| 277 body: _body, |
| 278 queryParams: _queryParams, |
| 279 uploadOptions: _uploadOptions, |
| 280 uploadMedia: _uploadMedia, |
| 281 downloadOptions: _downloadOptions); |
| 282 return _response.then((data) => new Callset.fromJson(data)); |
| 283 } |
| 284 |
| 285 /** |
| 286 * Gets a list of callsets matching the criteria. |
| 287 * |
| 288 * [request] - The metadata request object. |
| 289 * |
| 290 * Request parameters: |
| 291 * |
| 292 * Completes with a [SearchCallsetsResponse]. |
| 293 * |
| 294 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 295 * error. |
| 296 * |
| 297 * If the used [http.Client] completes with an error when making a REST call, |
| 298 * this method will complete with the same error. |
| 299 */ |
| 300 async.Future<SearchCallsetsResponse> search(SearchCallsetsRequest request) { |
| 301 var _url = null; |
| 302 var _queryParams = new core.Map(); |
| 303 var _uploadMedia = null; |
| 304 var _uploadOptions = null; |
| 305 var _downloadOptions = common.DownloadOptions.Metadata; |
| 306 var _body = null; |
| 307 |
| 308 if (request != null) { |
| 309 _body = convert.JSON.encode((request).toJson()); |
| 310 } |
| 311 |
| 312 |
| 313 _url = 'callsets/search'; |
| 314 |
| 315 var _response = _requester.request(_url, |
| 316 "POST", |
| 317 body: _body, |
| 318 queryParams: _queryParams, |
| 319 uploadOptions: _uploadOptions, |
| 320 uploadMedia: _uploadMedia, |
| 321 downloadOptions: _downloadOptions); |
| 322 return _response.then((data) => new SearchCallsetsResponse.fromJson(data)); |
| 323 } |
| 324 |
| 325 /** |
| 326 * Updates a callset. |
| 327 * |
| 328 * [request] - The metadata request object. |
| 329 * |
| 330 * Request parameters: |
| 331 * |
| 332 * [callsetId] - The ID of the callset to be updated. |
| 333 * |
| 334 * Completes with a [Callset]. |
| 335 * |
| 336 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 337 * error. |
| 338 * |
| 339 * If the used [http.Client] completes with an error when making a REST call, |
| 340 * this method will complete with the same error. |
| 341 */ |
| 342 async.Future<Callset> update(Callset request, core.String callsetId) { |
| 343 var _url = null; |
| 344 var _queryParams = new core.Map(); |
| 345 var _uploadMedia = null; |
| 346 var _uploadOptions = null; |
| 347 var _downloadOptions = common.DownloadOptions.Metadata; |
| 348 var _body = null; |
| 349 |
| 350 if (request != null) { |
| 351 _body = convert.JSON.encode((request).toJson()); |
| 352 } |
| 353 if (callsetId == null) { |
| 354 throw new core.ArgumentError("Parameter callsetId is required."); |
| 355 } |
| 356 |
| 357 |
| 358 _url = 'callsets/' + common_internal.Escaper.ecapeVariable('$callsetId'); |
| 359 |
| 360 var _response = _requester.request(_url, |
| 361 "PUT", |
| 362 body: _body, |
| 363 queryParams: _queryParams, |
| 364 uploadOptions: _uploadOptions, |
| 365 uploadMedia: _uploadMedia, |
| 366 downloadOptions: _downloadOptions); |
| 367 return _response.then((data) => new Callset.fromJson(data)); |
| 368 } |
| 369 |
| 370 } |
| 371 |
| 372 |
| 373 /** Not documented yet. */ |
| 374 class DatasetsResourceApi { |
| 375 final common_internal.ApiRequester _requester; |
| 376 |
| 377 DatasetsResourceApi(common_internal.ApiRequester client) : |
| 378 _requester = client; |
| 379 |
| 380 /** |
| 381 * Creates a new dataset. |
| 382 * |
| 383 * [request] - The metadata request object. |
| 384 * |
| 385 * Request parameters: |
| 386 * |
| 387 * Completes with a [Dataset]. |
| 388 * |
| 389 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 390 * error. |
| 391 * |
| 392 * If the used [http.Client] completes with an error when making a REST call, |
| 393 * this method will complete with the same error. |
| 394 */ |
| 395 async.Future<Dataset> create(Dataset request) { |
| 396 var _url = null; |
| 397 var _queryParams = new core.Map(); |
| 398 var _uploadMedia = null; |
| 399 var _uploadOptions = null; |
| 400 var _downloadOptions = common.DownloadOptions.Metadata; |
| 401 var _body = null; |
| 402 |
| 403 if (request != null) { |
| 404 _body = convert.JSON.encode((request).toJson()); |
| 405 } |
| 406 |
| 407 |
| 408 _url = 'datasets'; |
| 409 |
| 410 var _response = _requester.request(_url, |
| 411 "POST", |
| 412 body: _body, |
| 413 queryParams: _queryParams, |
| 414 uploadOptions: _uploadOptions, |
| 415 uploadMedia: _uploadMedia, |
| 416 downloadOptions: _downloadOptions); |
| 417 return _response.then((data) => new Dataset.fromJson(data)); |
| 418 } |
| 419 |
| 420 /** |
| 421 * Deletes a dataset. |
| 422 * |
| 423 * Request parameters: |
| 424 * |
| 425 * [datasetId] - The ID of the dataset to be deleted. |
| 426 * |
| 427 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 428 * error. |
| 429 * |
| 430 * If the used [http.Client] completes with an error when making a REST call, |
| 431 * this method will complete with the same error. |
| 432 */ |
| 433 async.Future delete(core.String datasetId) { |
| 434 var _url = null; |
| 435 var _queryParams = new core.Map(); |
| 436 var _uploadMedia = null; |
| 437 var _uploadOptions = null; |
| 438 var _downloadOptions = common.DownloadOptions.Metadata; |
| 439 var _body = null; |
| 440 |
| 441 if (datasetId == null) { |
| 442 throw new core.ArgumentError("Parameter datasetId is required."); |
| 443 } |
| 444 |
| 445 _downloadOptions = null; |
| 446 |
| 447 _url = 'datasets/' + common_internal.Escaper.ecapeVariable('$datasetId'); |
| 448 |
| 449 var _response = _requester.request(_url, |
| 450 "DELETE", |
| 451 body: _body, |
| 452 queryParams: _queryParams, |
| 453 uploadOptions: _uploadOptions, |
| 454 uploadMedia: _uploadMedia, |
| 455 downloadOptions: _downloadOptions); |
| 456 return _response.then((data) => null); |
| 457 } |
| 458 |
| 459 /** |
| 460 * Gets a dataset by ID. |
| 461 * |
| 462 * Request parameters: |
| 463 * |
| 464 * [datasetId] - The ID of the dataset. |
| 465 * |
| 466 * Completes with a [Dataset]. |
| 467 * |
| 468 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 469 * error. |
| 470 * |
| 471 * If the used [http.Client] completes with an error when making a REST call, |
| 472 * this method will complete with the same error. |
| 473 */ |
| 474 async.Future<Dataset> get(core.String datasetId) { |
| 475 var _url = null; |
| 476 var _queryParams = new core.Map(); |
| 477 var _uploadMedia = null; |
| 478 var _uploadOptions = null; |
| 479 var _downloadOptions = common.DownloadOptions.Metadata; |
| 480 var _body = null; |
| 481 |
| 482 if (datasetId == null) { |
| 483 throw new core.ArgumentError("Parameter datasetId is required."); |
| 484 } |
| 485 |
| 486 |
| 487 _url = 'datasets/' + common_internal.Escaper.ecapeVariable('$datasetId'); |
| 488 |
| 489 var _response = _requester.request(_url, |
| 490 "GET", |
| 491 body: _body, |
| 492 queryParams: _queryParams, |
| 493 uploadOptions: _uploadOptions, |
| 494 uploadMedia: _uploadMedia, |
| 495 downloadOptions: _downloadOptions); |
| 496 return _response.then((data) => new Dataset.fromJson(data)); |
| 497 } |
| 498 |
| 499 /** |
| 500 * Lists all datasets. |
| 501 * |
| 502 * Request parameters: |
| 503 * |
| 504 * [maxResults] - The maximum number of results returned by this request. |
| 505 * |
| 506 * [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 * value of "nextPageToken" from the previous response. |
| 509 * |
| 510 * [projectId] - Only return datasets which belong to this Google Developers |
| 511 * Console project. Only accepts project numbers. |
| 512 * |
| 513 * Completes with a [ListDatasetsResponse]. |
| 514 * |
| 515 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 516 * error. |
| 517 * |
| 518 * If the used [http.Client] completes with an error when making a REST call, |
| 519 * this method will complete with the same error. |
| 520 */ |
| 521 async.Future<ListDatasetsResponse> list({core.String maxResults, core.String p
ageToken, core.String projectId}) { |
| 522 var _url = null; |
| 523 var _queryParams = new core.Map(); |
| 524 var _uploadMedia = null; |
| 525 var _uploadOptions = null; |
| 526 var _downloadOptions = common.DownloadOptions.Metadata; |
| 527 var _body = null; |
| 528 |
| 529 if (maxResults != null) { |
| 530 _queryParams["maxResults"] = [maxResults]; |
| 531 } |
| 532 if (pageToken != null) { |
| 533 _queryParams["pageToken"] = [pageToken]; |
| 534 } |
| 535 if (projectId != null) { |
| 536 _queryParams["projectId"] = [projectId]; |
| 537 } |
| 538 |
| 539 |
| 540 _url = 'datasets'; |
| 541 |
| 542 var _response = _requester.request(_url, |
| 543 "GET", |
| 544 body: _body, |
| 545 queryParams: _queryParams, |
| 546 uploadOptions: _uploadOptions, |
| 547 uploadMedia: _uploadMedia, |
| 548 downloadOptions: _downloadOptions); |
| 549 return _response.then((data) => new ListDatasetsResponse.fromJson(data)); |
| 550 } |
| 551 |
| 552 /** |
| 553 * Updates a dataset. This method supports patch semantics. |
| 554 * |
| 555 * [request] - The metadata request object. |
| 556 * |
| 557 * Request parameters: |
| 558 * |
| 559 * [datasetId] - The ID of the dataset to be updated. |
| 560 * |
| 561 * Completes with a [Dataset]. |
| 562 * |
| 563 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 564 * error. |
| 565 * |
| 566 * If the used [http.Client] completes with an error when making a REST call, |
| 567 * this method will complete with the same error. |
| 568 */ |
| 569 async.Future<Dataset> patch(Dataset request, core.String datasetId) { |
| 570 var _url = null; |
| 571 var _queryParams = new core.Map(); |
| 572 var _uploadMedia = null; |
| 573 var _uploadOptions = null; |
| 574 var _downloadOptions = common.DownloadOptions.Metadata; |
| 575 var _body = null; |
| 576 |
| 577 if (request != null) { |
| 578 _body = convert.JSON.encode((request).toJson()); |
| 579 } |
| 580 if (datasetId == null) { |
| 581 throw new core.ArgumentError("Parameter datasetId is required."); |
| 582 } |
| 583 |
| 584 |
| 585 _url = 'datasets/' + common_internal.Escaper.ecapeVariable('$datasetId'); |
| 586 |
| 587 var _response = _requester.request(_url, |
| 588 "PATCH", |
| 589 body: _body, |
| 590 queryParams: _queryParams, |
| 591 uploadOptions: _uploadOptions, |
| 592 uploadMedia: _uploadMedia, |
| 593 downloadOptions: _downloadOptions); |
| 594 return _response.then((data) => new Dataset.fromJson(data)); |
| 595 } |
| 596 |
| 597 /** |
| 598 * Undeletes a dataset by restoring a dataset which was deleted via this API. |
| 599 * This operation is only possible for a week after the deletion occurred. |
| 600 * |
| 601 * Request parameters: |
| 602 * |
| 603 * [datasetId] - The ID of the dataset to be undeleted. |
| 604 * |
| 605 * Completes with a [Dataset]. |
| 606 * |
| 607 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 608 * error. |
| 609 * |
| 610 * If the used [http.Client] completes with an error when making a REST call, |
| 611 * this method will complete with the same error. |
| 612 */ |
| 613 async.Future<Dataset> undelete(core.String datasetId) { |
| 614 var _url = null; |
| 615 var _queryParams = new core.Map(); |
| 616 var _uploadMedia = null; |
| 617 var _uploadOptions = null; |
| 618 var _downloadOptions = common.DownloadOptions.Metadata; |
| 619 var _body = null; |
| 620 |
| 621 if (datasetId == null) { |
| 622 throw new core.ArgumentError("Parameter datasetId is required."); |
| 623 } |
| 624 |
| 625 |
| 626 _url = 'datasets/' + common_internal.Escaper.ecapeVariable('$datasetId') + '
/undelete'; |
| 627 |
| 628 var _response = _requester.request(_url, |
| 629 "POST", |
| 630 body: _body, |
| 631 queryParams: _queryParams, |
| 632 uploadOptions: _uploadOptions, |
| 633 uploadMedia: _uploadMedia, |
| 634 downloadOptions: _downloadOptions); |
| 635 return _response.then((data) => new Dataset.fromJson(data)); |
| 636 } |
| 637 |
| 638 /** |
| 639 * Updates a dataset. |
| 640 * |
| 641 * [request] - The metadata request object. |
| 642 * |
| 643 * Request parameters: |
| 644 * |
| 645 * [datasetId] - The ID of the dataset to be updated. |
| 646 * |
| 647 * Completes with a [Dataset]. |
| 648 * |
| 649 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 650 * error. |
| 651 * |
| 652 * If the used [http.Client] completes with an error when making a REST call, |
| 653 * this method will complete with the same error. |
| 654 */ |
| 655 async.Future<Dataset> update(Dataset request, core.String datasetId) { |
| 656 var _url = null; |
| 657 var _queryParams = new core.Map(); |
| 658 var _uploadMedia = null; |
| 659 var _uploadOptions = null; |
| 660 var _downloadOptions = common.DownloadOptions.Metadata; |
| 661 var _body = null; |
| 662 |
| 663 if (request != null) { |
| 664 _body = convert.JSON.encode((request).toJson()); |
| 665 } |
| 666 if (datasetId == null) { |
| 667 throw new core.ArgumentError("Parameter datasetId is required."); |
| 668 } |
| 669 |
| 670 |
| 671 _url = 'datasets/' + common_internal.Escaper.ecapeVariable('$datasetId'); |
| 672 |
| 673 var _response = _requester.request(_url, |
| 674 "PUT", |
| 675 body: _body, |
| 676 queryParams: _queryParams, |
| 677 uploadOptions: _uploadOptions, |
| 678 uploadMedia: _uploadMedia, |
| 679 downloadOptions: _downloadOptions); |
| 680 return _response.then((data) => new Dataset.fromJson(data)); |
| 681 } |
| 682 |
| 683 } |
| 684 |
| 685 |
| 686 /** Not documented yet. */ |
| 687 class ExperimentalResourceApi { |
| 688 final common_internal.ApiRequester _requester; |
| 689 |
| 690 ExperimentalJobsResourceApi get jobs => new ExperimentalJobsResourceApi(_reque
ster); |
| 691 |
| 692 ExperimentalResourceApi(common_internal.ApiRequester client) : |
| 693 _requester = client; |
| 694 } |
| 695 |
| 696 |
| 697 /** Not documented yet. */ |
| 698 class ExperimentalJobsResourceApi { |
| 699 final common_internal.ApiRequester _requester; |
| 700 |
| 701 ExperimentalJobsResourceApi(common_internal.ApiRequester client) : |
| 702 _requester = client; |
| 703 |
| 704 /** |
| 705 * Creates and asynchronously runs an ad-hoc job. This is an experimental call |
| 706 * and may be removed or changed at any time. |
| 707 * |
| 708 * [request] - The metadata request object. |
| 709 * |
| 710 * Request parameters: |
| 711 * |
| 712 * Completes with a [ExperimentalCreateJobResponse]. |
| 713 * |
| 714 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 715 * error. |
| 716 * |
| 717 * If the used [http.Client] completes with an error when making a REST call, |
| 718 * this method will complete with the same error. |
| 719 */ |
| 720 async.Future<ExperimentalCreateJobResponse> create(ExperimentalCreateJobReques
t request) { |
| 721 var _url = null; |
| 722 var _queryParams = new core.Map(); |
| 723 var _uploadMedia = null; |
| 724 var _uploadOptions = null; |
| 725 var _downloadOptions = common.DownloadOptions.Metadata; |
| 726 var _body = null; |
| 727 |
| 728 if (request != null) { |
| 729 _body = convert.JSON.encode((request).toJson()); |
| 730 } |
| 731 |
| 732 |
| 733 _url = 'experimental/jobs/create'; |
| 734 |
| 735 var _response = _requester.request(_url, |
| 736 "POST", |
| 737 body: _body, |
| 738 queryParams: _queryParams, |
| 739 uploadOptions: _uploadOptions, |
| 740 uploadMedia: _uploadMedia, |
| 741 downloadOptions: _downloadOptions); |
| 742 return _response.then((data) => new ExperimentalCreateJobResponse.fromJson(d
ata)); |
| 743 } |
| 744 |
| 745 } |
| 746 |
| 747 |
| 748 /** Not documented yet. */ |
| 749 class JobsResourceApi { |
| 750 final common_internal.ApiRequester _requester; |
| 751 |
| 752 JobsResourceApi(common_internal.ApiRequester client) : |
| 753 _requester = client; |
| 754 |
| 755 /** |
| 756 * Cancels a job by ID. Note that it is possible for partial results to be |
| 757 * generated and stored for cancelled jobs. |
| 758 * |
| 759 * Request parameters: |
| 760 * |
| 761 * [jobId] - Required. The ID of the job. |
| 762 * |
| 763 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 764 * error. |
| 765 * |
| 766 * If the used [http.Client] completes with an error when making a REST call, |
| 767 * this method will complete with the same error. |
| 768 */ |
| 769 async.Future cancel(core.String jobId) { |
| 770 var _url = null; |
| 771 var _queryParams = new core.Map(); |
| 772 var _uploadMedia = null; |
| 773 var _uploadOptions = null; |
| 774 var _downloadOptions = common.DownloadOptions.Metadata; |
| 775 var _body = null; |
| 776 |
| 777 if (jobId == null) { |
| 778 throw new core.ArgumentError("Parameter jobId is required."); |
| 779 } |
| 780 |
| 781 _downloadOptions = null; |
| 782 |
| 783 _url = 'jobs/' + common_internal.Escaper.ecapeVariable('$jobId') + '/cancel'
; |
| 784 |
| 785 var _response = _requester.request(_url, |
| 786 "POST", |
| 787 body: _body, |
| 788 queryParams: _queryParams, |
| 789 uploadOptions: _uploadOptions, |
| 790 uploadMedia: _uploadMedia, |
| 791 downloadOptions: _downloadOptions); |
| 792 return _response.then((data) => null); |
| 793 } |
| 794 |
| 795 /** |
| 796 * Gets a job by ID. |
| 797 * |
| 798 * Request parameters: |
| 799 * |
| 800 * [jobId] - Required. The ID of the job. |
| 801 * |
| 802 * Completes with a [Job]. |
| 803 * |
| 804 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 805 * error. |
| 806 * |
| 807 * If the used [http.Client] completes with an error when making a REST call, |
| 808 * this method will complete with the same error. |
| 809 */ |
| 810 async.Future<Job> get(core.String jobId) { |
| 811 var _url = null; |
| 812 var _queryParams = new core.Map(); |
| 813 var _uploadMedia = null; |
| 814 var _uploadOptions = null; |
| 815 var _downloadOptions = common.DownloadOptions.Metadata; |
| 816 var _body = null; |
| 817 |
| 818 if (jobId == null) { |
| 819 throw new core.ArgumentError("Parameter jobId is required."); |
| 820 } |
| 821 |
| 822 |
| 823 _url = 'jobs/' + common_internal.Escaper.ecapeVariable('$jobId'); |
| 824 |
| 825 var _response = _requester.request(_url, |
| 826 "GET", |
| 827 body: _body, |
| 828 queryParams: _queryParams, |
| 829 uploadOptions: _uploadOptions, |
| 830 uploadMedia: _uploadMedia, |
| 831 downloadOptions: _downloadOptions); |
| 832 return _response.then((data) => new Job.fromJson(data)); |
| 833 } |
| 834 |
| 835 /** |
| 836 * Gets a list of jobs matching the criteria. |
| 837 * |
| 838 * [request] - The metadata request object. |
| 839 * |
| 840 * Request parameters: |
| 841 * |
| 842 * Completes with a [SearchJobsResponse]. |
| 843 * |
| 844 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 845 * error. |
| 846 * |
| 847 * If the used [http.Client] completes with an error when making a REST call, |
| 848 * this method will complete with the same error. |
| 849 */ |
| 850 async.Future<SearchJobsResponse> search(SearchJobsRequest request) { |
| 851 var _url = null; |
| 852 var _queryParams = new core.Map(); |
| 853 var _uploadMedia = null; |
| 854 var _uploadOptions = null; |
| 855 var _downloadOptions = common.DownloadOptions.Metadata; |
| 856 var _body = null; |
| 857 |
| 858 if (request != null) { |
| 859 _body = convert.JSON.encode((request).toJson()); |
| 860 } |
| 861 |
| 862 |
| 863 _url = 'jobs/search'; |
| 864 |
| 865 var _response = _requester.request(_url, |
| 866 "POST", |
| 867 body: _body, |
| 868 queryParams: _queryParams, |
| 869 uploadOptions: _uploadOptions, |
| 870 uploadMedia: _uploadMedia, |
| 871 downloadOptions: _downloadOptions); |
| 872 return _response.then((data) => new SearchJobsResponse.fromJson(data)); |
| 873 } |
| 874 |
| 875 } |
| 876 |
| 877 |
| 878 /** Not documented yet. */ |
| 879 class ReadsResourceApi { |
| 880 final common_internal.ApiRequester _requester; |
| 881 |
| 882 ReadsResourceApi(common_internal.ApiRequester client) : |
| 883 _requester = client; |
| 884 |
| 885 /** |
| 886 * Gets a list of reads for one or more readsets. Reads search operates over a |
| 887 * genomic coordinate space of reference sequence & position defined over the |
| 888 * reference sequences to which the requested readsets are aligned. If a |
| 889 * target positional range is specified, search returns all reads whose |
| 890 * alignment to the reference genome overlap the range. A query which |
| 891 * specifies only readset IDs yields all reads in those readsets, including |
| 892 * unmapped reads. All reads returned (including reads on subsequent pages) |
| 893 * are ordered by genomic coordinate (reference sequence & position). Reads |
| 894 * with equivalent genomic coordinates are returned in a deterministic order. |
| 895 * |
| 896 * [request] - The metadata request object. |
| 897 * |
| 898 * Request parameters: |
| 899 * |
| 900 * Completes with a [SearchReadsResponse]. |
| 901 * |
| 902 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 903 * error. |
| 904 * |
| 905 * If the used [http.Client] completes with an error when making a REST call, |
| 906 * this method will complete with the same error. |
| 907 */ |
| 908 async.Future<SearchReadsResponse> search(SearchReadsRequest request) { |
| 909 var _url = null; |
| 910 var _queryParams = new core.Map(); |
| 911 var _uploadMedia = null; |
| 912 var _uploadOptions = null; |
| 913 var _downloadOptions = common.DownloadOptions.Metadata; |
| 914 var _body = null; |
| 915 |
| 916 if (request != null) { |
| 917 _body = convert.JSON.encode((request).toJson()); |
| 918 } |
| 919 |
| 920 |
| 921 _url = 'reads/search'; |
| 922 |
| 923 var _response = _requester.request(_url, |
| 924 "POST", |
| 925 body: _body, |
| 926 queryParams: _queryParams, |
| 927 uploadOptions: _uploadOptions, |
| 928 uploadMedia: _uploadMedia, |
| 929 downloadOptions: _downloadOptions); |
| 930 return _response.then((data) => new SearchReadsResponse.fromJson(data)); |
| 931 } |
| 932 |
| 933 } |
| 934 |
| 935 |
| 936 /** Not documented yet. */ |
| 937 class ReadsetsResourceApi { |
| 938 final common_internal.ApiRequester _requester; |
| 939 |
| 940 ReadsetsCoveragebucketsResourceApi get coveragebuckets => new ReadsetsCoverage
bucketsResourceApi(_requester); |
| 941 |
| 942 ReadsetsResourceApi(common_internal.ApiRequester client) : |
| 943 _requester = client; |
| 944 |
| 945 /** |
| 946 * Deletes a readset. |
| 947 * |
| 948 * Request parameters: |
| 949 * |
| 950 * [readsetId] - The ID of the readset to be deleted. The caller must have |
| 951 * WRITE permissions to the dataset associated with this readset. |
| 952 * |
| 953 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 954 * error. |
| 955 * |
| 956 * If the used [http.Client] completes with an error when making a REST call, |
| 957 * this method will complete with the same error. |
| 958 */ |
| 959 async.Future delete(core.String readsetId) { |
| 960 var _url = null; |
| 961 var _queryParams = new core.Map(); |
| 962 var _uploadMedia = null; |
| 963 var _uploadOptions = null; |
| 964 var _downloadOptions = common.DownloadOptions.Metadata; |
| 965 var _body = null; |
| 966 |
| 967 if (readsetId == null) { |
| 968 throw new core.ArgumentError("Parameter readsetId is required."); |
| 969 } |
| 970 |
| 971 _downloadOptions = null; |
| 972 |
| 973 _url = 'readsets/' + common_internal.Escaper.ecapeVariable('$readsetId'); |
| 974 |
| 975 var _response = _requester.request(_url, |
| 976 "DELETE", |
| 977 body: _body, |
| 978 queryParams: _queryParams, |
| 979 uploadOptions: _uploadOptions, |
| 980 uploadMedia: _uploadMedia, |
| 981 downloadOptions: _downloadOptions); |
| 982 return _response.then((data) => null); |
| 983 } |
| 984 |
| 985 /** |
| 986 * Exports readsets to a BAM file in Google Cloud Storage. Note that currently |
| 987 * there may be some differences between exported BAM files and the original |
| 988 * BAM file at the time of import. In particular, comments in the input file |
| 989 * header will not be preserved, and some custom tags will be converted to |
| 990 * strings. |
| 991 * |
| 992 * [request] - The metadata request object. |
| 993 * |
| 994 * Request parameters: |
| 995 * |
| 996 * Completes with a [ExportReadsetsResponse]. |
| 997 * |
| 998 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 999 * error. |
| 1000 * |
| 1001 * If the used [http.Client] completes with an error when making a REST call, |
| 1002 * this method will complete with the same error. |
| 1003 */ |
| 1004 async.Future<ExportReadsetsResponse> export(ExportReadsetsRequest request) { |
| 1005 var _url = null; |
| 1006 var _queryParams = new core.Map(); |
| 1007 var _uploadMedia = null; |
| 1008 var _uploadOptions = null; |
| 1009 var _downloadOptions = common.DownloadOptions.Metadata; |
| 1010 var _body = null; |
| 1011 |
| 1012 if (request != null) { |
| 1013 _body = convert.JSON.encode((request).toJson()); |
| 1014 } |
| 1015 |
| 1016 |
| 1017 _url = 'readsets/export'; |
| 1018 |
| 1019 var _response = _requester.request(_url, |
| 1020 "POST", |
| 1021 body: _body, |
| 1022 queryParams: _queryParams, |
| 1023 uploadOptions: _uploadOptions, |
| 1024 uploadMedia: _uploadMedia, |
| 1025 downloadOptions: _downloadOptions); |
| 1026 return _response.then((data) => new ExportReadsetsResponse.fromJson(data)); |
| 1027 } |
| 1028 |
| 1029 /** |
| 1030 * Gets a readset by ID. |
| 1031 * |
| 1032 * Request parameters: |
| 1033 * |
| 1034 * [readsetId] - The ID of the readset. |
| 1035 * |
| 1036 * Completes with a [Readset]. |
| 1037 * |
| 1038 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 1039 * error. |
| 1040 * |
| 1041 * If the used [http.Client] completes with an error when making a REST call, |
| 1042 * this method will complete with the same error. |
| 1043 */ |
| 1044 async.Future<Readset> get(core.String readsetId) { |
| 1045 var _url = null; |
| 1046 var _queryParams = new core.Map(); |
| 1047 var _uploadMedia = null; |
| 1048 var _uploadOptions = null; |
| 1049 var _downloadOptions = common.DownloadOptions.Metadata; |
| 1050 var _body = null; |
| 1051 |
| 1052 if (readsetId == null) { |
| 1053 throw new core.ArgumentError("Parameter readsetId is required."); |
| 1054 } |
| 1055 |
| 1056 |
| 1057 _url = 'readsets/' + common_internal.Escaper.ecapeVariable('$readsetId'); |
| 1058 |
| 1059 var _response = _requester.request(_url, |
| 1060 "GET", |
| 1061 body: _body, |
| 1062 queryParams: _queryParams, |
| 1063 uploadOptions: _uploadOptions, |
| 1064 uploadMedia: _uploadMedia, |
| 1065 downloadOptions: _downloadOptions); |
| 1066 return _response.then((data) => new Readset.fromJson(data)); |
| 1067 } |
| 1068 |
| 1069 /** |
| 1070 * Creates readsets by asynchronously importing the provided information. Note |
| 1071 * that currently comments in the input file header are not imported and some |
| 1072 * custom tags will be converted to strings, rather than preserving tag types. |
| 1073 * The caller must have WRITE permissions to the dataset. |
| 1074 * |
| 1075 * [request] - The metadata request object. |
| 1076 * |
| 1077 * Request parameters: |
| 1078 * |
| 1079 * Completes with a [ImportReadsetsResponse]. |
| 1080 * |
| 1081 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 1082 * error. |
| 1083 * |
| 1084 * If the used [http.Client] completes with an error when making a REST call, |
| 1085 * this method will complete with the same error. |
| 1086 */ |
| 1087 async.Future<ImportReadsetsResponse> import(ImportReadsetsRequest request) { |
| 1088 var _url = null; |
| 1089 var _queryParams = new core.Map(); |
| 1090 var _uploadMedia = null; |
| 1091 var _uploadOptions = null; |
| 1092 var _downloadOptions = common.DownloadOptions.Metadata; |
| 1093 var _body = null; |
| 1094 |
| 1095 if (request != null) { |
| 1096 _body = convert.JSON.encode((request).toJson()); |
| 1097 } |
| 1098 |
| 1099 |
| 1100 _url = 'readsets/import'; |
| 1101 |
| 1102 var _response = _requester.request(_url, |
| 1103 "POST", |
| 1104 body: _body, |
| 1105 queryParams: _queryParams, |
| 1106 uploadOptions: _uploadOptions, |
| 1107 uploadMedia: _uploadMedia, |
| 1108 downloadOptions: _downloadOptions); |
| 1109 return _response.then((data) => new ImportReadsetsResponse.fromJson(data)); |
| 1110 } |
| 1111 |
| 1112 /** |
| 1113 * Updates a readset. This method supports patch semantics. |
| 1114 * |
| 1115 * [request] - The metadata request object. |
| 1116 * |
| 1117 * Request parameters: |
| 1118 * |
| 1119 * [readsetId] - The ID of the readset to be updated. The caller must have |
| 1120 * WRITE permissions to the dataset associated with this readset. |
| 1121 * |
| 1122 * Completes with a [Readset]. |
| 1123 * |
| 1124 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 1125 * error. |
| 1126 * |
| 1127 * If the used [http.Client] completes with an error when making a REST call, |
| 1128 * this method will complete with the same error. |
| 1129 */ |
| 1130 async.Future<Readset> patch(Readset request, core.String readsetId) { |
| 1131 var _url = null; |
| 1132 var _queryParams = new core.Map(); |
| 1133 var _uploadMedia = null; |
| 1134 var _uploadOptions = null; |
| 1135 var _downloadOptions = common.DownloadOptions.Metadata; |
| 1136 var _body = null; |
| 1137 |
| 1138 if (request != null) { |
| 1139 _body = convert.JSON.encode((request).toJson()); |
| 1140 } |
| 1141 if (readsetId == null) { |
| 1142 throw new core.ArgumentError("Parameter readsetId is required."); |
| 1143 } |
| 1144 |
| 1145 |
| 1146 _url = 'readsets/' + common_internal.Escaper.ecapeVariable('$readsetId'); |
| 1147 |
| 1148 var _response = _requester.request(_url, |
| 1149 "PATCH", |
| 1150 body: _body, |
| 1151 queryParams: _queryParams, |
| 1152 uploadOptions: _uploadOptions, |
| 1153 uploadMedia: _uploadMedia, |
| 1154 downloadOptions: _downloadOptions); |
| 1155 return _response.then((data) => new Readset.fromJson(data)); |
| 1156 } |
| 1157 |
| 1158 /** |
| 1159 * Gets a list of readsets matching the criteria. |
| 1160 * |
| 1161 * [request] - The metadata request object. |
| 1162 * |
| 1163 * Request parameters: |
| 1164 * |
| 1165 * Completes with a [SearchReadsetsResponse]. |
| 1166 * |
| 1167 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 1168 * error. |
| 1169 * |
| 1170 * If the used [http.Client] completes with an error when making a REST call, |
| 1171 * this method will complete with the same error. |
| 1172 */ |
| 1173 async.Future<SearchReadsetsResponse> search(SearchReadsetsRequest request) { |
| 1174 var _url = null; |
| 1175 var _queryParams = new core.Map(); |
| 1176 var _uploadMedia = null; |
| 1177 var _uploadOptions = null; |
| 1178 var _downloadOptions = common.DownloadOptions.Metadata; |
| 1179 var _body = null; |
| 1180 |
| 1181 if (request != null) { |
| 1182 _body = convert.JSON.encode((request).toJson()); |
| 1183 } |
| 1184 |
| 1185 |
| 1186 _url = 'readsets/search'; |
| 1187 |
| 1188 var _response = _requester.request(_url, |
| 1189 "POST", |
| 1190 body: _body, |
| 1191 queryParams: _queryParams, |
| 1192 uploadOptions: _uploadOptions, |
| 1193 uploadMedia: _uploadMedia, |
| 1194 downloadOptions: _downloadOptions); |
| 1195 return _response.then((data) => new SearchReadsetsResponse.fromJson(data)); |
| 1196 } |
| 1197 |
| 1198 /** |
| 1199 * Updates a readset. |
| 1200 * |
| 1201 * [request] - The metadata request object. |
| 1202 * |
| 1203 * Request parameters: |
| 1204 * |
| 1205 * [readsetId] - The ID of the readset to be updated. The caller must have |
| 1206 * WRITE permissions to the dataset associated with this readset. |
| 1207 * |
| 1208 * Completes with a [Readset]. |
| 1209 * |
| 1210 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 1211 * error. |
| 1212 * |
| 1213 * If the used [http.Client] completes with an error when making a REST call, |
| 1214 * this method will complete with the same error. |
| 1215 */ |
| 1216 async.Future<Readset> update(Readset request, core.String readsetId) { |
| 1217 var _url = null; |
| 1218 var _queryParams = new core.Map(); |
| 1219 var _uploadMedia = null; |
| 1220 var _uploadOptions = null; |
| 1221 var _downloadOptions = common.DownloadOptions.Metadata; |
| 1222 var _body = null; |
| 1223 |
| 1224 if (request != null) { |
| 1225 _body = convert.JSON.encode((request).toJson()); |
| 1226 } |
| 1227 if (readsetId == null) { |
| 1228 throw new core.ArgumentError("Parameter readsetId is required."); |
| 1229 } |
| 1230 |
| 1231 |
| 1232 _url = 'readsets/' + common_internal.Escaper.ecapeVariable('$readsetId'); |
| 1233 |
| 1234 var _response = _requester.request(_url, |
| 1235 "PUT", |
| 1236 body: _body, |
| 1237 queryParams: _queryParams, |
| 1238 uploadOptions: _uploadOptions, |
| 1239 uploadMedia: _uploadMedia, |
| 1240 downloadOptions: _downloadOptions); |
| 1241 return _response.then((data) => new Readset.fromJson(data)); |
| 1242 } |
| 1243 |
| 1244 } |
| 1245 |
| 1246 |
| 1247 /** Not documented yet. */ |
| 1248 class ReadsetsCoveragebucketsResourceApi { |
| 1249 final common_internal.ApiRequester _requester; |
| 1250 |
| 1251 ReadsetsCoveragebucketsResourceApi(common_internal.ApiRequester client) : |
| 1252 _requester = client; |
| 1253 |
| 1254 /** |
| 1255 * Lists fixed width coverage buckets for a readset, each of which correspond |
| 1256 * to a range of a reference sequence. Each bucket summarizes coverage |
| 1257 * information across its corresponding genomic range. Coverage is defined as |
| 1258 * the number of reads which are aligned to a given base in the reference |
| 1259 * sequence. Coverage buckets are available at various bucket widths, enabling |
| 1260 * various coverage "zoom levels". The caller must have READ permissions for |
| 1261 * the target readset. |
| 1262 * |
| 1263 * Request parameters: |
| 1264 * |
| 1265 * [readsetId] - Required. The ID of the readset over which coverage is |
| 1266 * requested. |
| 1267 * |
| 1268 * [maxResults] - The maximum number of results to return in a single page. If |
| 1269 * unspecified, defaults to 1024. The maximum value is 2048. |
| 1270 * |
| 1271 * [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 * value of "nextPageToken" from the previous response. |
| 1274 * |
| 1275 * [range_sequenceEnd] - The end position of the range on the reference, |
| 1276 * 1-based exclusive. If specified, sequenceName must also be specified. |
| 1277 * |
| 1278 * [range_sequenceName] - The reference sequence name, for example "chr1", |
| 1279 * "1", or "chrX". |
| 1280 * |
| 1281 * [range_sequenceStart] - The start position of the range on the reference, |
| 1282 * 1-based inclusive. If specified, sequenceName must also be specified. |
| 1283 * |
| 1284 * [targetBucketWidth] - The desired width of each reported coverage bucket in |
| 1285 * 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 * Defaults to infinity (each bucket spans an entire reference sequence) or |
| 1288 * 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 * |
| 1291 * Completes with a [ListCoverageBucketsResponse]. |
| 1292 * |
| 1293 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 1294 * error. |
| 1295 * |
| 1296 * If the used [http.Client] completes with an error when making a REST call, |
| 1297 * this method will complete with the same error. |
| 1298 */ |
| 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 var _url = null; |
| 1301 var _queryParams = new core.Map(); |
| 1302 var _uploadMedia = null; |
| 1303 var _uploadOptions = null; |
| 1304 var _downloadOptions = common.DownloadOptions.Metadata; |
| 1305 var _body = null; |
| 1306 |
| 1307 if (readsetId == null) { |
| 1308 throw new core.ArgumentError("Parameter readsetId is required."); |
| 1309 } |
| 1310 if (maxResults != null) { |
| 1311 _queryParams["maxResults"] = [maxResults]; |
| 1312 } |
| 1313 if (pageToken != null) { |
| 1314 _queryParams["pageToken"] = [pageToken]; |
| 1315 } |
| 1316 if (range_sequenceEnd != null) { |
| 1317 _queryParams["range.sequenceEnd"] = [range_sequenceEnd]; |
| 1318 } |
| 1319 if (range_sequenceName != null) { |
| 1320 _queryParams["range.sequenceName"] = [range_sequenceName]; |
| 1321 } |
| 1322 if (range_sequenceStart != null) { |
| 1323 _queryParams["range.sequenceStart"] = [range_sequenceStart]; |
| 1324 } |
| 1325 if (targetBucketWidth != null) { |
| 1326 _queryParams["targetBucketWidth"] = [targetBucketWidth]; |
| 1327 } |
| 1328 |
| 1329 |
| 1330 _url = 'readsets/' + common_internal.Escaper.ecapeVariable('$readsetId') + '
/coveragebuckets'; |
| 1331 |
| 1332 var _response = _requester.request(_url, |
| 1333 "GET", |
| 1334 body: _body, |
| 1335 queryParams: _queryParams, |
| 1336 uploadOptions: _uploadOptions, |
| 1337 uploadMedia: _uploadMedia, |
| 1338 downloadOptions: _downloadOptions); |
| 1339 return _response.then((data) => new ListCoverageBucketsResponse.fromJson(dat
a)); |
| 1340 } |
| 1341 |
| 1342 } |
| 1343 |
| 1344 |
| 1345 /** Not documented yet. */ |
| 1346 class VariantsResourceApi { |
| 1347 final common_internal.ApiRequester _requester; |
| 1348 |
| 1349 VariantsResourceApi(common_internal.ApiRequester client) : |
| 1350 _requester = client; |
| 1351 |
| 1352 /** |
| 1353 * Creates a new variant. |
| 1354 * |
| 1355 * [request] - The metadata request object. |
| 1356 * |
| 1357 * Request parameters: |
| 1358 * |
| 1359 * Completes with a [Variant]. |
| 1360 * |
| 1361 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 1362 * error. |
| 1363 * |
| 1364 * If the used [http.Client] completes with an error when making a REST call, |
| 1365 * this method will complete with the same error. |
| 1366 */ |
| 1367 async.Future<Variant> create(Variant request) { |
| 1368 var _url = null; |
| 1369 var _queryParams = new core.Map(); |
| 1370 var _uploadMedia = null; |
| 1371 var _uploadOptions = null; |
| 1372 var _downloadOptions = common.DownloadOptions.Metadata; |
| 1373 var _body = null; |
| 1374 |
| 1375 if (request != null) { |
| 1376 _body = convert.JSON.encode((request).toJson()); |
| 1377 } |
| 1378 |
| 1379 |
| 1380 _url = 'variants'; |
| 1381 |
| 1382 var _response = _requester.request(_url, |
| 1383 "POST", |
| 1384 body: _body, |
| 1385 queryParams: _queryParams, |
| 1386 uploadOptions: _uploadOptions, |
| 1387 uploadMedia: _uploadMedia, |
| 1388 downloadOptions: _downloadOptions); |
| 1389 return _response.then((data) => new Variant.fromJson(data)); |
| 1390 } |
| 1391 |
| 1392 /** |
| 1393 * Deletes a variant. |
| 1394 * |
| 1395 * Request parameters: |
| 1396 * |
| 1397 * [variantId] - The ID of the variant to be deleted. |
| 1398 * |
| 1399 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 1400 * error. |
| 1401 * |
| 1402 * If the used [http.Client] completes with an error when making a REST call, |
| 1403 * this method will complete with the same error. |
| 1404 */ |
| 1405 async.Future delete(core.String variantId) { |
| 1406 var _url = null; |
| 1407 var _queryParams = new core.Map(); |
| 1408 var _uploadMedia = null; |
| 1409 var _uploadOptions = null; |
| 1410 var _downloadOptions = common.DownloadOptions.Metadata; |
| 1411 var _body = null; |
| 1412 |
| 1413 if (variantId == null) { |
| 1414 throw new core.ArgumentError("Parameter variantId is required."); |
| 1415 } |
| 1416 |
| 1417 _downloadOptions = null; |
| 1418 |
| 1419 _url = 'variants/' + common_internal.Escaper.ecapeVariable('$variantId'); |
| 1420 |
| 1421 var _response = _requester.request(_url, |
| 1422 "DELETE", |
| 1423 body: _body, |
| 1424 queryParams: _queryParams, |
| 1425 uploadOptions: _uploadOptions, |
| 1426 uploadMedia: _uploadMedia, |
| 1427 downloadOptions: _downloadOptions); |
| 1428 return _response.then((data) => null); |
| 1429 } |
| 1430 |
| 1431 /** |
| 1432 * Exports variant data to an external destination. |
| 1433 * |
| 1434 * [request] - The metadata request object. |
| 1435 * |
| 1436 * Request parameters: |
| 1437 * |
| 1438 * Completes with a [ExportVariantsResponse]. |
| 1439 * |
| 1440 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 1441 * error. |
| 1442 * |
| 1443 * If the used [http.Client] completes with an error when making a REST call, |
| 1444 * this method will complete with the same error. |
| 1445 */ |
| 1446 async.Future<ExportVariantsResponse> export(ExportVariantsRequest request) { |
| 1447 var _url = null; |
| 1448 var _queryParams = new core.Map(); |
| 1449 var _uploadMedia = null; |
| 1450 var _uploadOptions = null; |
| 1451 var _downloadOptions = common.DownloadOptions.Metadata; |
| 1452 var _body = null; |
| 1453 |
| 1454 if (request != null) { |
| 1455 _body = convert.JSON.encode((request).toJson()); |
| 1456 } |
| 1457 |
| 1458 |
| 1459 _url = 'variants/export'; |
| 1460 |
| 1461 var _response = _requester.request(_url, |
| 1462 "POST", |
| 1463 body: _body, |
| 1464 queryParams: _queryParams, |
| 1465 uploadOptions: _uploadOptions, |
| 1466 uploadMedia: _uploadMedia, |
| 1467 downloadOptions: _downloadOptions); |
| 1468 return _response.then((data) => new ExportVariantsResponse.fromJson(data)); |
| 1469 } |
| 1470 |
| 1471 /** |
| 1472 * Gets a variant by ID. |
| 1473 * |
| 1474 * Request parameters: |
| 1475 * |
| 1476 * [variantId] - The ID of the variant. |
| 1477 * |
| 1478 * Completes with a [Variant]. |
| 1479 * |
| 1480 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 1481 * error. |
| 1482 * |
| 1483 * If the used [http.Client] completes with an error when making a REST call, |
| 1484 * this method will complete with the same error. |
| 1485 */ |
| 1486 async.Future<Variant> get(core.String variantId) { |
| 1487 var _url = null; |
| 1488 var _queryParams = new core.Map(); |
| 1489 var _uploadMedia = null; |
| 1490 var _uploadOptions = null; |
| 1491 var _downloadOptions = common.DownloadOptions.Metadata; |
| 1492 var _body = null; |
| 1493 |
| 1494 if (variantId == null) { |
| 1495 throw new core.ArgumentError("Parameter variantId is required."); |
| 1496 } |
| 1497 |
| 1498 |
| 1499 _url = 'variants/' + common_internal.Escaper.ecapeVariable('$variantId'); |
| 1500 |
| 1501 var _response = _requester.request(_url, |
| 1502 "GET", |
| 1503 body: _body, |
| 1504 queryParams: _queryParams, |
| 1505 uploadOptions: _uploadOptions, |
| 1506 uploadMedia: _uploadMedia, |
| 1507 downloadOptions: _downloadOptions); |
| 1508 return _response.then((data) => new Variant.fromJson(data)); |
| 1509 } |
| 1510 |
| 1511 /** |
| 1512 * Gets a summary of all the variant data in a variantset. |
| 1513 * |
| 1514 * Request parameters: |
| 1515 * |
| 1516 * [variantsetId] - Required. The ID of the variant set to get variant summary |
| 1517 * information for. |
| 1518 * |
| 1519 * Completes with a [GetVariantsSummaryResponse]. |
| 1520 * |
| 1521 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 1522 * error. |
| 1523 * |
| 1524 * If the used [http.Client] completes with an error when making a REST call, |
| 1525 * this method will complete with the same error. |
| 1526 */ |
| 1527 async.Future<GetVariantsSummaryResponse> getSummary({core.String variantsetId}
) { |
| 1528 var _url = null; |
| 1529 var _queryParams = new core.Map(); |
| 1530 var _uploadMedia = null; |
| 1531 var _uploadOptions = null; |
| 1532 var _downloadOptions = common.DownloadOptions.Metadata; |
| 1533 var _body = null; |
| 1534 |
| 1535 if (variantsetId != null) { |
| 1536 _queryParams["variantsetId"] = [variantsetId]; |
| 1537 } |
| 1538 |
| 1539 |
| 1540 _url = 'variants/summary'; |
| 1541 |
| 1542 var _response = _requester.request(_url, |
| 1543 "GET", |
| 1544 body: _body, |
| 1545 queryParams: _queryParams, |
| 1546 uploadOptions: _uploadOptions, |
| 1547 uploadMedia: _uploadMedia, |
| 1548 downloadOptions: _downloadOptions); |
| 1549 return _response.then((data) => new GetVariantsSummaryResponse.fromJson(data
)); |
| 1550 } |
| 1551 |
| 1552 /** |
| 1553 * Creates variant data by asynchronously importing the provided information. |
| 1554 * |
| 1555 * [request] - The metadata request object. |
| 1556 * |
| 1557 * Request parameters: |
| 1558 * |
| 1559 * Completes with a [ImportVariantsResponse]. |
| 1560 * |
| 1561 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 1562 * error. |
| 1563 * |
| 1564 * If the used [http.Client] completes with an error when making a REST call, |
| 1565 * this method will complete with the same error. |
| 1566 */ |
| 1567 async.Future<ImportVariantsResponse> import(ImportVariantsRequest request) { |
| 1568 var _url = null; |
| 1569 var _queryParams = new core.Map(); |
| 1570 var _uploadMedia = null; |
| 1571 var _uploadOptions = null; |
| 1572 var _downloadOptions = common.DownloadOptions.Metadata; |
| 1573 var _body = null; |
| 1574 |
| 1575 if (request != null) { |
| 1576 _body = convert.JSON.encode((request).toJson()); |
| 1577 } |
| 1578 |
| 1579 |
| 1580 _url = 'variants/import'; |
| 1581 |
| 1582 var _response = _requester.request(_url, |
| 1583 "POST", |
| 1584 body: _body, |
| 1585 queryParams: _queryParams, |
| 1586 uploadOptions: _uploadOptions, |
| 1587 uploadMedia: _uploadMedia, |
| 1588 downloadOptions: _downloadOptions); |
| 1589 return _response.then((data) => new ImportVariantsResponse.fromJson(data)); |
| 1590 } |
| 1591 |
| 1592 /** |
| 1593 * Updates a variant. This method supports patch semantics. |
| 1594 * |
| 1595 * [request] - The metadata request object. |
| 1596 * |
| 1597 * Request parameters: |
| 1598 * |
| 1599 * [variantId] - The ID of the variant to be updated.. |
| 1600 * |
| 1601 * Completes with a [Variant]. |
| 1602 * |
| 1603 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 1604 * error. |
| 1605 * |
| 1606 * If the used [http.Client] completes with an error when making a REST call, |
| 1607 * this method will complete with the same error. |
| 1608 */ |
| 1609 async.Future<Variant> patch(Variant request, core.String variantId) { |
| 1610 var _url = null; |
| 1611 var _queryParams = new core.Map(); |
| 1612 var _uploadMedia = null; |
| 1613 var _uploadOptions = null; |
| 1614 var _downloadOptions = common.DownloadOptions.Metadata; |
| 1615 var _body = null; |
| 1616 |
| 1617 if (request != null) { |
| 1618 _body = convert.JSON.encode((request).toJson()); |
| 1619 } |
| 1620 if (variantId == null) { |
| 1621 throw new core.ArgumentError("Parameter variantId is required."); |
| 1622 } |
| 1623 |
| 1624 |
| 1625 _url = 'variants/' + common_internal.Escaper.ecapeVariable('$variantId'); |
| 1626 |
| 1627 var _response = _requester.request(_url, |
| 1628 "PATCH", |
| 1629 body: _body, |
| 1630 queryParams: _queryParams, |
| 1631 uploadOptions: _uploadOptions, |
| 1632 uploadMedia: _uploadMedia, |
| 1633 downloadOptions: _downloadOptions); |
| 1634 return _response.then((data) => new Variant.fromJson(data)); |
| 1635 } |
| 1636 |
| 1637 /** |
| 1638 * Gets a list of variants matching the criteria. |
| 1639 * |
| 1640 * [request] - The metadata request object. |
| 1641 * |
| 1642 * Request parameters: |
| 1643 * |
| 1644 * Completes with a [SearchVariantsResponse]. |
| 1645 * |
| 1646 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 1647 * error. |
| 1648 * |
| 1649 * If the used [http.Client] completes with an error when making a REST call, |
| 1650 * this method will complete with the same error. |
| 1651 */ |
| 1652 async.Future<SearchVariantsResponse> search(SearchVariantsRequest request) { |
| 1653 var _url = null; |
| 1654 var _queryParams = new core.Map(); |
| 1655 var _uploadMedia = null; |
| 1656 var _uploadOptions = null; |
| 1657 var _downloadOptions = common.DownloadOptions.Metadata; |
| 1658 var _body = null; |
| 1659 |
| 1660 if (request != null) { |
| 1661 _body = convert.JSON.encode((request).toJson()); |
| 1662 } |
| 1663 |
| 1664 |
| 1665 _url = 'variants/search'; |
| 1666 |
| 1667 var _response = _requester.request(_url, |
| 1668 "POST", |
| 1669 body: _body, |
| 1670 queryParams: _queryParams, |
| 1671 uploadOptions: _uploadOptions, |
| 1672 uploadMedia: _uploadMedia, |
| 1673 downloadOptions: _downloadOptions); |
| 1674 return _response.then((data) => new SearchVariantsResponse.fromJson(data)); |
| 1675 } |
| 1676 |
| 1677 /** |
| 1678 * Updates a variant. |
| 1679 * |
| 1680 * [request] - The metadata request object. |
| 1681 * |
| 1682 * Request parameters: |
| 1683 * |
| 1684 * [variantId] - The ID of the variant to be updated.. |
| 1685 * |
| 1686 * Completes with a [Variant]. |
| 1687 * |
| 1688 * Completes with a [common.ApiRequestError] if the API endpoint returned an |
| 1689 * error. |
| 1690 * |
| 1691 * If the used [http.Client] completes with an error when making a REST call, |
| 1692 * this method will complete with the same error. |
| 1693 */ |
| 1694 async.Future<Variant> update(Variant request, core.String variantId) { |
| 1695 var _url = null; |
| 1696 var _queryParams = new core.Map(); |
| 1697 var _uploadMedia = null; |
| 1698 var _uploadOptions = null; |
| 1699 var _downloadOptions = common.DownloadOptions.Metadata; |
| 1700 var _body = null; |
| 1701 |
| 1702 if (request != null) { |
| 1703 _body = convert.JSON.encode((request).toJson()); |
| 1704 } |
| 1705 if (variantId == null) { |
| 1706 throw new core.ArgumentError("Parameter variantId is required."); |
| 1707 } |
| 1708 |
| 1709 |
| 1710 _url = 'variants/' + common_internal.Escaper.ecapeVariable('$variantId'); |
| 1711 |
| 1712 var _response = _requester.request(_url, |
| 1713 "PUT", |
| 1714 body: _body, |
| 1715 queryParams: _queryParams, |
| 1716 uploadOptions: _uploadOptions, |
| 1717 uploadMedia: _uploadMedia, |
| 1718 downloadOptions: _downloadOptions); |
| 1719 return _response.then((data) => new Variant.fromJson(data)); |
| 1720 } |
| 1721 |
| 1722 } |
| 1723 |
| 1724 |
| 1725 |
| 1726 /** |
| 1727 * A beacon represents whether any variant call in a variantset has a specific |
| 1728 * allele at a particular position. |
| 1729 */ |
| 1730 class Beacon { |
| 1731 /** True if the allele exists on any variant call, false otherwise. */ |
| 1732 core.bool exists; |
| 1733 |
| 1734 |
| 1735 Beacon(); |
| 1736 |
| 1737 Beacon.fromJson(core.Map _json) { |
| 1738 if (_json.containsKey("exists")) { |
| 1739 exists = _json["exists"]; |
| 1740 } |
| 1741 } |
| 1742 |
| 1743 core.Map toJson() { |
| 1744 var _json = new core.Map(); |
| 1745 if (exists != null) { |
| 1746 _json["exists"] = exists; |
| 1747 } |
| 1748 return _json; |
| 1749 } |
| 1750 } |
| 1751 |
| 1752 |
| 1753 /** |
| 1754 * A Call represents the determination of genotype with respect to a particular |
| 1755 * 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 |
| 1757 * SNP named rs1234 in a callset with the name NA12345. |
| 1758 */ |
| 1759 class Call { |
| 1760 /** The ID of the callset this variant call belongs to. */ |
| 1761 core.String callsetId; |
| 1762 |
| 1763 /** The name of the callset this variant call belongs to. */ |
| 1764 core.String callsetName; |
| 1765 |
| 1766 /** |
| 1767 * 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 |
| 1769 * variant had a referenceBases field of "T" and an alternateBases value of |
| 1770 * ["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 |
| 1772 * was instead [0, 1], the represented value would be "TA". Ordering of the |
| 1773 * genotype values is important if the phaseset field is present. If a |
| 1774 * genotype is not called (that is, a "." is present in the GT string) -1 is |
| 1775 * returned. |
| 1776 */ |
| 1777 core.List<core.int> genotype; |
| 1778 |
| 1779 /** |
| 1780 * 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 |
| 1782 * defined by the GL tag in the VCF spec. |
| 1783 */ |
| 1784 core.List<core.double> genotypeLikelihood; |
| 1785 |
| 1786 /** A map of additional variant call information. */ |
| 1787 core.Map<core.String, core.List<core.String>> info; |
| 1788 |
| 1789 /** |
| 1790 * 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 |
| 1792 * same contig which have the same phaseset value. When importing data from |
| 1793 * VCF, if the genotype data was phased but no phase set was specified this |
| 1794 * field will be set to "*". |
| 1795 */ |
| 1796 core.String phaseset; |
| 1797 |
| 1798 |
| 1799 Call(); |
| 1800 |
| 1801 Call.fromJson(core.Map _json) { |
| 1802 if (_json.containsKey("callsetId")) { |
| 1803 callsetId = _json["callsetId"]; |
| 1804 } |
| 1805 if (_json.containsKey("callsetName")) { |
| 1806 callsetName = _json["callsetName"]; |
| 1807 } |
| 1808 if (_json.containsKey("genotype")) { |
| 1809 genotype = _json["genotype"]; |
| 1810 } |
| 1811 if (_json.containsKey("genotypeLikelihood")) { |
| 1812 genotypeLikelihood = _json["genotypeLikelihood"]; |
| 1813 } |
| 1814 if (_json.containsKey("info")) { |
| 1815 info = _json["info"]; |
| 1816 } |
| 1817 if (_json.containsKey("phaseset")) { |
| 1818 phaseset = _json["phaseset"]; |
| 1819 } |
| 1820 } |
| 1821 |
| 1822 core.Map toJson() { |
| 1823 var _json = new core.Map(); |
| 1824 if (callsetId != null) { |
| 1825 _json["callsetId"] = callsetId; |
| 1826 } |
| 1827 if (callsetName != null) { |
| 1828 _json["callsetName"] = callsetName; |
| 1829 } |
| 1830 if (genotype != null) { |
| 1831 _json["genotype"] = genotype; |
| 1832 } |
| 1833 if (genotypeLikelihood != null) { |
| 1834 _json["genotypeLikelihood"] = genotypeLikelihood; |
| 1835 } |
| 1836 if (info != null) { |
| 1837 _json["info"] = info; |
| 1838 } |
| 1839 if (phaseset != null) { |
| 1840 _json["phaseset"] = phaseset; |
| 1841 } |
| 1842 return _json; |
| 1843 } |
| 1844 } |
| 1845 |
| 1846 |
| 1847 /** A Callset is a collection of Variant Calls. It belongs to a Variantset. */ |
| 1848 class Callset { |
| 1849 /** The date this callset was created in milliseconds from the epoch. */ |
| 1850 core.String created; |
| 1851 |
| 1852 /** The Google generated ID of the callset, immutable. */ |
| 1853 core.String id; |
| 1854 |
| 1855 /** A map of additional callset information. */ |
| 1856 core.Map<core.String, core.List<core.String>> info; |
| 1857 |
| 1858 /** The callset name. */ |
| 1859 core.String name; |
| 1860 |
| 1861 /** The ID of the variantset this callset belongs to. */ |
| 1862 core.String variantsetId; |
| 1863 |
| 1864 |
| 1865 Callset(); |
| 1866 |
| 1867 Callset.fromJson(core.Map _json) { |
| 1868 if (_json.containsKey("created")) { |
| 1869 created = _json["created"]; |
| 1870 } |
| 1871 if (_json.containsKey("id")) { |
| 1872 id = _json["id"]; |
| 1873 } |
| 1874 if (_json.containsKey("info")) { |
| 1875 info = _json["info"]; |
| 1876 } |
| 1877 if (_json.containsKey("name")) { |
| 1878 name = _json["name"]; |
| 1879 } |
| 1880 if (_json.containsKey("variantsetId")) { |
| 1881 variantsetId = _json["variantsetId"]; |
| 1882 } |
| 1883 } |
| 1884 |
| 1885 core.Map toJson() { |
| 1886 var _json = new core.Map(); |
| 1887 if (created != null) { |
| 1888 _json["created"] = created; |
| 1889 } |
| 1890 if (id != null) { |
| 1891 _json["id"] = id; |
| 1892 } |
| 1893 if (info != null) { |
| 1894 _json["info"] = info; |
| 1895 } |
| 1896 if (name != null) { |
| 1897 _json["name"] = name; |
| 1898 } |
| 1899 if (variantsetId != null) { |
| 1900 _json["variantsetId"] = variantsetId; |
| 1901 } |
| 1902 return _json; |
| 1903 } |
| 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 } |
| 1944 |
| 1945 |
| 1946 /** |
| 1947 * A bucket over which read coverage has been precomputed. A bucket corresponds |
| 1948 * to a specific range of the reference sequence. |
| 1949 */ |
| 1950 class CoverageBucket { |
| 1951 /** |
| 1952 * The average number of reads which are aligned to each individual reference |
| 1953 * base in this bucket. |
| 1954 */ |
| 1955 core.double meanCoverage; |
| 1956 |
| 1957 /** The genomic coordinate range spanned by this bucket. */ |
| 1958 GenomicRange range; |
| 1959 |
| 1960 |
| 1961 CoverageBucket(); |
| 1962 |
| 1963 CoverageBucket.fromJson(core.Map _json) { |
| 1964 if (_json.containsKey("meanCoverage")) { |
| 1965 meanCoverage = _json["meanCoverage"]; |
| 1966 } |
| 1967 if (_json.containsKey("range")) { |
| 1968 range = new GenomicRange.fromJson(_json["range"]); |
| 1969 } |
| 1970 } |
| 1971 |
| 1972 core.Map toJson() { |
| 1973 var _json = new core.Map(); |
| 1974 if (meanCoverage != null) { |
| 1975 _json["meanCoverage"] = meanCoverage; |
| 1976 } |
| 1977 if (range != null) { |
| 1978 _json["range"] = (range).toJson(); |
| 1979 } |
| 1980 return _json; |
| 1981 } |
| 1982 } |
| 1983 |
| 1984 |
| 1985 /** A Dataset is a collection of genomic data. */ |
| 1986 class Dataset { |
| 1987 /** The Google generated ID of the dataset, immutable. */ |
| 1988 core.String id; |
| 1989 |
| 1990 /** |
| 1991 * Flag indicating whether or not a dataset is publicly viewable. If a dataset |
| 1992 * is not public, it inherits viewing permissions from its project. |
| 1993 */ |
| 1994 core.bool isPublic; |
| 1995 |
| 1996 /** The dataset name. */ |
| 1997 core.String name; |
| 1998 |
| 1999 /** |
| 2000 * The Google Developers Console project number that this dataset belongs to. |
| 2001 */ |
| 2002 core.String projectId; |
| 2003 |
| 2004 |
| 2005 Dataset(); |
| 2006 |
| 2007 Dataset.fromJson(core.Map _json) { |
| 2008 if (_json.containsKey("id")) { |
| 2009 id = _json["id"]; |
| 2010 } |
| 2011 if (_json.containsKey("isPublic")) { |
| 2012 isPublic = _json["isPublic"]; |
| 2013 } |
| 2014 if (_json.containsKey("name")) { |
| 2015 name = _json["name"]; |
| 2016 } |
| 2017 if (_json.containsKey("projectId")) { |
| 2018 projectId = _json["projectId"]; |
| 2019 } |
| 2020 } |
| 2021 |
| 2022 core.Map toJson() { |
| 2023 var _json = new core.Map(); |
| 2024 if (id != null) { |
| 2025 _json["id"] = id; |
| 2026 } |
| 2027 if (isPublic != null) { |
| 2028 _json["isPublic"] = isPublic; |
| 2029 } |
| 2030 if (name != null) { |
| 2031 _json["name"] = name; |
| 2032 } |
| 2033 if (projectId != null) { |
| 2034 _json["projectId"] = projectId; |
| 2035 } |
| 2036 return _json; |
| 2037 } |
| 2038 } |
| 2039 |
| 2040 |
| 2041 /** The job creation request. */ |
| 2042 class ExperimentalCreateJobRequest { |
| 2043 /** |
| 2044 * Specifies whether or not to run the alignment pipeline. At least one of |
| 2045 * align or call_variants must be provided. |
| 2046 */ |
| 2047 core.bool align; |
| 2048 |
| 2049 /** |
| 2050 * 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 |
| 2052 * to the variant caller. At least one of align or call_variants must be |
| 2053 * provided. |
| 2054 */ |
| 2055 core.bool callVariants; |
| 2056 |
| 2057 /** |
| 2058 * Specifies where to copy the results of certain pipelines. This shoud be in |
| 2059 * the form of "gs://bucket/path". |
| 2060 */ |
| 2061 core.String gcsOutputPath; |
| 2062 |
| 2063 /** |
| 2064 * 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 |
| 2066 * file. The first file of each pair should be specified in "sourceUris". |
| 2067 */ |
| 2068 core.List<core.String> pairedSourceUris; |
| 2069 |
| 2070 /** |
| 2071 * Required. The Google Cloud Project ID with which to associate the request. |
| 2072 */ |
| 2073 core.String projectId; |
| 2074 |
| 2075 /** |
| 2076 * 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 |
| 2078 * .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". |
| 2080 */ |
| 2081 core.List<core.String> sourceUris; |
| 2082 |
| 2083 |
| 2084 ExperimentalCreateJobRequest(); |
| 2085 |
| 2086 ExperimentalCreateJobRequest.fromJson(core.Map _json) { |
| 2087 if (_json.containsKey("align")) { |
| 2088 align = _json["align"]; |
| 2089 } |
| 2090 if (_json.containsKey("callVariants")) { |
| 2091 callVariants = _json["callVariants"]; |
| 2092 } |
| 2093 if (_json.containsKey("gcsOutputPath")) { |
| 2094 gcsOutputPath = _json["gcsOutputPath"]; |
| 2095 } |
| 2096 if (_json.containsKey("pairedSourceUris")) { |
| 2097 pairedSourceUris = _json["pairedSourceUris"]; |
| 2098 } |
| 2099 if (_json.containsKey("projectId")) { |
| 2100 projectId = _json["projectId"]; |
| 2101 } |
| 2102 if (_json.containsKey("sourceUris")) { |
| 2103 sourceUris = _json["sourceUris"]; |
| 2104 } |
| 2105 } |
| 2106 |
| 2107 core.Map toJson() { |
| 2108 var _json = new core.Map(); |
| 2109 if (align != null) { |
| 2110 _json["align"] = align; |
| 2111 } |
| 2112 if (callVariants != null) { |
| 2113 _json["callVariants"] = callVariants; |
| 2114 } |
| 2115 if (gcsOutputPath != null) { |
| 2116 _json["gcsOutputPath"] = gcsOutputPath; |
| 2117 } |
| 2118 if (pairedSourceUris != null) { |
| 2119 _json["pairedSourceUris"] = pairedSourceUris; |
| 2120 } |
| 2121 if (projectId != null) { |
| 2122 _json["projectId"] = projectId; |
| 2123 } |
| 2124 if (sourceUris != null) { |
| 2125 _json["sourceUris"] = sourceUris; |
| 2126 } |
| 2127 return _json; |
| 2128 } |
| 2129 } |
| 2130 |
| 2131 |
| 2132 /** The job creation response. */ |
| 2133 class ExperimentalCreateJobResponse { |
| 2134 /** A job ID that can be used to get status information. */ |
| 2135 core.String jobId; |
| 2136 |
| 2137 |
| 2138 ExperimentalCreateJobResponse(); |
| 2139 |
| 2140 ExperimentalCreateJobResponse.fromJson(core.Map _json) { |
| 2141 if (_json.containsKey("jobId")) { |
| 2142 jobId = _json["jobId"]; |
| 2143 } |
| 2144 } |
| 2145 |
| 2146 core.Map toJson() { |
| 2147 var _json = new core.Map(); |
| 2148 if (jobId != null) { |
| 2149 _json["jobId"] = jobId; |
| 2150 } |
| 2151 return _json; |
| 2152 } |
| 2153 } |
| 2154 |
| 2155 |
| 2156 /** The readset export request. */ |
| 2157 class ExportReadsetsRequest { |
| 2158 /** |
| 2159 * A Google Cloud Storage URI where the exported BAM file will be created. The |
| 2160 * currently authenticated user must have write access to the new file |
| 2161 * location. An error will be returned if the URI already contains data. |
| 2162 */ |
| 2163 core.String exportUri; |
| 2164 |
| 2165 /** |
| 2166 * The Google Developers Console project number that owns this export. This is |
| 2167 * the project that will be billed. |
| 2168 */ |
| 2169 core.String projectId; |
| 2170 |
| 2171 /** The IDs of the readsets to export. */ |
| 2172 core.List<core.String> readsetIds; |
| 2173 |
| 2174 /** |
| 2175 * The reference names to export. If this is not specified, all reference |
| 2176 * sequences are exported. Use '*' to export unmapped reads. |
| 2177 */ |
| 2178 core.List<core.String> referenceNames; |
| 2179 |
| 2180 |
| 2181 ExportReadsetsRequest(); |
| 2182 |
| 2183 ExportReadsetsRequest.fromJson(core.Map _json) { |
| 2184 if (_json.containsKey("exportUri")) { |
| 2185 exportUri = _json["exportUri"]; |
| 2186 } |
| 2187 if (_json.containsKey("projectId")) { |
| 2188 projectId = _json["projectId"]; |
| 2189 } |
| 2190 if (_json.containsKey("readsetIds")) { |
| 2191 readsetIds = _json["readsetIds"]; |
| 2192 } |
| 2193 if (_json.containsKey("referenceNames")) { |
| 2194 referenceNames = _json["referenceNames"]; |
| 2195 } |
| 2196 } |
| 2197 |
| 2198 core.Map toJson() { |
| 2199 var _json = new core.Map(); |
| 2200 if (exportUri != null) { |
| 2201 _json["exportUri"] = exportUri; |
| 2202 } |
| 2203 if (projectId != null) { |
| 2204 _json["projectId"] = projectId; |
| 2205 } |
| 2206 if (readsetIds != null) { |
| 2207 _json["readsetIds"] = readsetIds; |
| 2208 } |
| 2209 if (referenceNames != null) { |
| 2210 _json["referenceNames"] = referenceNames; |
| 2211 } |
| 2212 return _json; |
| 2213 } |
| 2214 } |
| 2215 |
| 2216 |
| 2217 /** The readset export response. */ |
| 2218 class ExportReadsetsResponse { |
| 2219 /** A job ID that can be used to get status information. */ |
| 2220 core.String jobId; |
| 2221 |
| 2222 |
| 2223 ExportReadsetsResponse(); |
| 2224 |
| 2225 ExportReadsetsResponse.fromJson(core.Map _json) { |
| 2226 if (_json.containsKey("jobId")) { |
| 2227 jobId = _json["jobId"]; |
| 2228 } |
| 2229 } |
| 2230 |
| 2231 core.Map toJson() { |
| 2232 var _json = new core.Map(); |
| 2233 if (jobId != null) { |
| 2234 _json["jobId"] = jobId; |
| 2235 } |
| 2236 return _json; |
| 2237 } |
| 2238 } |
| 2239 |
| 2240 |
| 2241 /** The variant data export request. */ |
| 2242 class ExportVariantsRequest { |
| 2243 /** |
| 2244 * The BigQuery dataset to export data to. Note that this is distinct from the |
| 2245 * Genomics concept of "dataset". The caller must have WRITE access to this |
| 2246 * BigQuery dataset. |
| 2247 */ |
| 2248 core.String bigqueryDataset; |
| 2249 |
| 2250 /** |
| 2251 * The BigQuery table to export data to. The caller must have WRITE access to |
| 2252 * this BigQuery table. |
| 2253 */ |
| 2254 core.String bigqueryTable; |
| 2255 |
| 2256 /** |
| 2257 * If provided, only variant call information from the specified callsets will |
| 2258 * be exported. By default all variant calls are exported. |
| 2259 */ |
| 2260 core.List<core.String> callsetIds; |
| 2261 |
| 2262 /** |
| 2263 * The format for the exported data. |
| 2264 * Possible string values are: |
| 2265 * - "bigquery" |
| 2266 */ |
| 2267 core.String format; |
| 2268 |
| 2269 /** |
| 2270 * The Google Cloud project number that owns this export. This is the project |
| 2271 * that will be billed. |
| 2272 */ |
| 2273 core.String projectId; |
| 2274 |
| 2275 /** |
| 2276 * Required. The ID of the variantset that contains variant data which should |
| 2277 * be exported. The caller must have READ access to this variantset. |
| 2278 */ |
| 2279 core.String variantsetId; |
| 2280 |
| 2281 |
| 2282 ExportVariantsRequest(); |
| 2283 |
| 2284 ExportVariantsRequest.fromJson(core.Map _json) { |
| 2285 if (_json.containsKey("bigqueryDataset")) { |
| 2286 bigqueryDataset = _json["bigqueryDataset"]; |
| 2287 } |
| 2288 if (_json.containsKey("bigqueryTable")) { |
| 2289 bigqueryTable = _json["bigqueryTable"]; |
| 2290 } |
| 2291 if (_json.containsKey("callsetIds")) { |
| 2292 callsetIds = _json["callsetIds"]; |
| 2293 } |
| 2294 if (_json.containsKey("format")) { |
| 2295 format = _json["format"]; |
| 2296 } |
| 2297 if (_json.containsKey("projectId")) { |
| 2298 projectId = _json["projectId"]; |
| 2299 } |
| 2300 if (_json.containsKey("variantsetId")) { |
| 2301 variantsetId = _json["variantsetId"]; |
| 2302 } |
| 2303 } |
| 2304 |
| 2305 core.Map toJson() { |
| 2306 var _json = new core.Map(); |
| 2307 if (bigqueryDataset != null) { |
| 2308 _json["bigqueryDataset"] = bigqueryDataset; |
| 2309 } |
| 2310 if (bigqueryTable != null) { |
| 2311 _json["bigqueryTable"] = bigqueryTable; |
| 2312 } |
| 2313 if (callsetIds != null) { |
| 2314 _json["callsetIds"] = callsetIds; |
| 2315 } |
| 2316 if (format != null) { |
| 2317 _json["format"] = format; |
| 2318 } |
| 2319 if (projectId != null) { |
| 2320 _json["projectId"] = projectId; |
| 2321 } |
| 2322 if (variantsetId != null) { |
| 2323 _json["variantsetId"] = variantsetId; |
| 2324 } |
| 2325 return _json; |
| 2326 } |
| 2327 } |
| 2328 |
| 2329 |
| 2330 /** The variant data export response. */ |
| 2331 class ExportVariantsResponse { |
| 2332 /** A job ID that can be used to get status information. */ |
| 2333 core.String jobId; |
| 2334 |
| 2335 |
| 2336 ExportVariantsResponse(); |
| 2337 |
| 2338 ExportVariantsResponse.fromJson(core.Map _json) { |
| 2339 if (_json.containsKey("jobId")) { |
| 2340 jobId = _json["jobId"]; |
| 2341 } |
| 2342 } |
| 2343 |
| 2344 core.Map toJson() { |
| 2345 var _json = new core.Map(); |
| 2346 if (jobId != null) { |
| 2347 _json["jobId"] = jobId; |
| 2348 } |
| 2349 return _json; |
| 2350 } |
| 2351 } |
| 2352 |
| 2353 |
| 2354 /** |
| 2355 * An inclusive, exclusive genomic coordinate range over a reference sequence. |
| 2356 */ |
| 2357 class GenomicRange { |
| 2358 /** |
| 2359 * The end position of the range on the reference, 1-based exclusive. If |
| 2360 * specified, sequenceName must also be specified. |
| 2361 */ |
| 2362 core.String sequenceEnd; |
| 2363 |
| 2364 /** The reference sequence name, for example "chr1", "1", or "chrX". */ |
| 2365 core.String sequenceName; |
| 2366 |
| 2367 /** |
| 2368 * The start position of the range on the reference, 1-based inclusive. If |
| 2369 * specified, sequenceName must also be specified. |
| 2370 */ |
| 2371 core.String sequenceStart; |
| 2372 |
| 2373 |
| 2374 GenomicRange(); |
| 2375 |
| 2376 GenomicRange.fromJson(core.Map _json) { |
| 2377 if (_json.containsKey("sequenceEnd")) { |
| 2378 sequenceEnd = _json["sequenceEnd"]; |
| 2379 } |
| 2380 if (_json.containsKey("sequenceName")) { |
| 2381 sequenceName = _json["sequenceName"]; |
| 2382 } |
| 2383 if (_json.containsKey("sequenceStart")) { |
| 2384 sequenceStart = _json["sequenceStart"]; |
| 2385 } |
| 2386 } |
| 2387 |
| 2388 core.Map toJson() { |
| 2389 var _json = new core.Map(); |
| 2390 if (sequenceEnd != null) { |
| 2391 _json["sequenceEnd"] = sequenceEnd; |
| 2392 } |
| 2393 if (sequenceName != null) { |
| 2394 _json["sequenceName"] = sequenceName; |
| 2395 } |
| 2396 if (sequenceStart != null) { |
| 2397 _json["sequenceStart"] = sequenceStart; |
| 2398 } |
| 2399 return _json; |
| 2400 } |
| 2401 } |
| 2402 |
| 2403 |
| 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. */ |
| 2441 class Header { |
| 2442 /** (SO) Sorting order of alignments. */ |
| 2443 core.String sortingOrder; |
| 2444 |
| 2445 /** (VN) BAM format version. */ |
| 2446 core.String version; |
| 2447 |
| 2448 |
| 2449 Header(); |
| 2450 |
| 2451 Header.fromJson(core.Map _json) { |
| 2452 if (_json.containsKey("sortingOrder")) { |
| 2453 sortingOrder = _json["sortingOrder"]; |
| 2454 } |
| 2455 if (_json.containsKey("version")) { |
| 2456 version = _json["version"]; |
| 2457 } |
| 2458 } |
| 2459 |
| 2460 core.Map toJson() { |
| 2461 var _json = new core.Map(); |
| 2462 if (sortingOrder != null) { |
| 2463 _json["sortingOrder"] = sortingOrder; |
| 2464 } |
| 2465 if (version != null) { |
| 2466 _json["version"] = version; |
| 2467 } |
| 2468 return _json; |
| 2469 } |
| 2470 } |
| 2471 |
| 2472 |
| 2473 /** The header section of the BAM/SAM file. */ |
| 2474 class HeaderSection { |
| 2475 /** (@CO) One-line text comments. */ |
| 2476 core.List<core.String> comments; |
| 2477 |
| 2478 /** |
| 2479 * [Deprecated] This field is deprecated and will no longer be populated. |
| 2480 * Please use filename instead. |
| 2481 */ |
| 2482 core.String fileUri; |
| 2483 |
| 2484 /** The name of the file from which this data was imported. */ |
| 2485 core.String filename; |
| 2486 |
| 2487 /** (@HD) The header line. */ |
| 2488 core.List<Header> headers; |
| 2489 |
| 2490 /** (@PG) Programs. */ |
| 2491 core.List<Program> programs; |
| 2492 |
| 2493 /** (@RG) Read group. */ |
| 2494 core.List<ReadGroup> readGroups; |
| 2495 |
| 2496 /** (@SQ) Reference sequence dictionary. */ |
| 2497 core.List<ReferenceSequence> refSequences; |
| 2498 |
| 2499 |
| 2500 HeaderSection(); |
| 2501 |
| 2502 HeaderSection.fromJson(core.Map _json) { |
| 2503 if (_json.containsKey("comments")) { |
| 2504 comments = _json["comments"]; |
| 2505 } |
| 2506 if (_json.containsKey("fileUri")) { |
| 2507 fileUri = _json["fileUri"]; |
| 2508 } |
| 2509 if (_json.containsKey("filename")) { |
| 2510 filename = _json["filename"]; |
| 2511 } |
| 2512 if (_json.containsKey("headers")) { |
| 2513 headers = _json["headers"].map((value) => new Header.fromJson(value)).toLi
st(); |
| 2514 } |
| 2515 if (_json.containsKey("programs")) { |
| 2516 programs = _json["programs"].map((value) => new Program.fromJson(value)).t
oList(); |
| 2517 } |
| 2518 if (_json.containsKey("readGroups")) { |
| 2519 readGroups = _json["readGroups"].map((value) => new ReadGroup.fromJson(val
ue)).toList(); |
| 2520 } |
| 2521 if (_json.containsKey("refSequences")) { |
| 2522 refSequences = _json["refSequences"].map((value) => new ReferenceSequence.
fromJson(value)).toList(); |
| 2523 } |
| 2524 } |
| 2525 |
| 2526 core.Map toJson() { |
| 2527 var _json = new core.Map(); |
| 2528 if (comments != null) { |
| 2529 _json["comments"] = comments; |
| 2530 } |
| 2531 if (fileUri != null) { |
| 2532 _json["fileUri"] = fileUri; |
| 2533 } |
| 2534 if (filename != null) { |
| 2535 _json["filename"] = filename; |
| 2536 } |
| 2537 if (headers != null) { |
| 2538 _json["headers"] = headers.map((value) => (value).toJson()).toList(); |
| 2539 } |
| 2540 if (programs != null) { |
| 2541 _json["programs"] = programs.map((value) => (value).toJson()).toList(); |
| 2542 } |
| 2543 if (readGroups != null) { |
| 2544 _json["readGroups"] = readGroups.map((value) => (value).toJson()).toList()
; |
| 2545 } |
| 2546 if (refSequences != null) { |
| 2547 _json["refSequences"] = refSequences.map((value) => (value).toJson()).toLi
st(); |
| 2548 } |
| 2549 return _json; |
| 2550 } |
| 2551 } |
| 2552 |
| 2553 |
| 2554 /** The readset import request. */ |
| 2555 class ImportReadsetsRequest { |
| 2556 /** |
| 2557 * Required. The ID of the dataset these readsets will belong to. The caller |
| 2558 * must have WRITE permissions to this dataset. |
| 2559 */ |
| 2560 core.String datasetId; |
| 2561 |
| 2562 /** A list of URIs pointing at BAM files in Google Cloud Storage. */ |
| 2563 core.List<core.String> sourceUris; |
| 2564 |
| 2565 |
| 2566 ImportReadsetsRequest(); |
| 2567 |
| 2568 ImportReadsetsRequest.fromJson(core.Map _json) { |
| 2569 if (_json.containsKey("datasetId")) { |
| 2570 datasetId = _json["datasetId"]; |
| 2571 } |
| 2572 if (_json.containsKey("sourceUris")) { |
| 2573 sourceUris = _json["sourceUris"]; |
| 2574 } |
| 2575 } |
| 2576 |
| 2577 core.Map toJson() { |
| 2578 var _json = new core.Map(); |
| 2579 if (datasetId != null) { |
| 2580 _json["datasetId"] = datasetId; |
| 2581 } |
| 2582 if (sourceUris != null) { |
| 2583 _json["sourceUris"] = sourceUris; |
| 2584 } |
| 2585 return _json; |
| 2586 } |
| 2587 } |
| 2588 |
| 2589 |
| 2590 /** The readset import response. */ |
| 2591 class ImportReadsetsResponse { |
| 2592 /** A job ID that can be used to get status information. */ |
| 2593 core.String jobId; |
| 2594 |
| 2595 |
| 2596 ImportReadsetsResponse(); |
| 2597 |
| 2598 ImportReadsetsResponse.fromJson(core.Map _json) { |
| 2599 if (_json.containsKey("jobId")) { |
| 2600 jobId = _json["jobId"]; |
| 2601 } |
| 2602 } |
| 2603 |
| 2604 core.Map toJson() { |
| 2605 var _json = new core.Map(); |
| 2606 if (jobId != null) { |
| 2607 _json["jobId"] = jobId; |
| 2608 } |
| 2609 return _json; |
| 2610 } |
| 2611 } |
| 2612 |
| 2613 |
| 2614 /** The variant data import request. */ |
| 2615 class ImportVariantsRequest { |
| 2616 /** |
| 2617 * The format of the variant data being imported. |
| 2618 * Possible string values are: |
| 2619 * - "completeGenomics" |
| 2620 * - "vcf" |
| 2621 */ |
| 2622 core.String format; |
| 2623 |
| 2624 /** |
| 2625 * A list of URIs pointing at VCF files in Google Cloud Storage. See the VCF |
| 2626 * Specification for more details on the input format. |
| 2627 */ |
| 2628 core.List<core.String> sourceUris; |
| 2629 |
| 2630 /** Required. The variantset to which variant data should be imported. */ |
| 2631 core.String variantsetId; |
| 2632 |
| 2633 |
| 2634 ImportVariantsRequest(); |
| 2635 |
| 2636 ImportVariantsRequest.fromJson(core.Map _json) { |
| 2637 if (_json.containsKey("format")) { |
| 2638 format = _json["format"]; |
| 2639 } |
| 2640 if (_json.containsKey("sourceUris")) { |
| 2641 sourceUris = _json["sourceUris"]; |
| 2642 } |
| 2643 if (_json.containsKey("variantsetId")) { |
| 2644 variantsetId = _json["variantsetId"]; |
| 2645 } |
| 2646 } |
| 2647 |
| 2648 core.Map toJson() { |
| 2649 var _json = new core.Map(); |
| 2650 if (format != null) { |
| 2651 _json["format"] = format; |
| 2652 } |
| 2653 if (sourceUris != null) { |
| 2654 _json["sourceUris"] = sourceUris; |
| 2655 } |
| 2656 if (variantsetId != null) { |
| 2657 _json["variantsetId"] = variantsetId; |
| 2658 } |
| 2659 return _json; |
| 2660 } |
| 2661 } |
| 2662 |
| 2663 |
| 2664 /** The variant data import response. */ |
| 2665 class ImportVariantsResponse { |
| 2666 /** A job ID that can be used to get status information. */ |
| 2667 core.String jobId; |
| 2668 |
| 2669 |
| 2670 ImportVariantsResponse(); |
| 2671 |
| 2672 ImportVariantsResponse.fromJson(core.Map _json) { |
| 2673 if (_json.containsKey("jobId")) { |
| 2674 jobId = _json["jobId"]; |
| 2675 } |
| 2676 } |
| 2677 |
| 2678 core.Map toJson() { |
| 2679 var _json = new core.Map(); |
| 2680 if (jobId != null) { |
| 2681 _json["jobId"] = jobId; |
| 2682 } |
| 2683 return _json; |
| 2684 } |
| 2685 } |
| 2686 |
| 2687 |
| 2688 /** |
| 2689 * A Job represents an ongoing process that can be monitored for status |
| 2690 * information. |
| 2691 */ |
| 2692 class Job { |
| 2693 /** The date this job was created, in milliseconds from the epoch. */ |
| 2694 core.String created; |
| 2695 |
| 2696 /** A more detailed description of this job's current status. */ |
| 2697 core.String description; |
| 2698 |
| 2699 /** Any errors that occurred during processing. */ |
| 2700 core.List<core.String> errors; |
| 2701 |
| 2702 /** The job ID. */ |
| 2703 core.String id; |
| 2704 |
| 2705 /** |
| 2706 * If this Job represents an import, this field will contain the IDs of the |
| 2707 * objects that were successfully imported. |
| 2708 */ |
| 2709 core.List<core.String> importedIds; |
| 2710 |
| 2711 /** |
| 2712 * The Google Developers Console project number to which this job belongs. |
| 2713 */ |
| 2714 core.String projectId; |
| 2715 |
| 2716 /** A summarized representation of the original service request. */ |
| 2717 JobRequest request; |
| 2718 |
| 2719 /** |
| 2720 * The status of this job. |
| 2721 * Possible string values are: |
| 2722 * - "canceled" |
| 2723 * - "failure" |
| 2724 * - "new" |
| 2725 * - "pending" |
| 2726 * - "running" |
| 2727 * - "success" |
| 2728 * - "unknownStatus" |
| 2729 */ |
| 2730 core.String status; |
| 2731 |
| 2732 /** Any warnings that occurred during processing. */ |
| 2733 core.List<core.String> warnings; |
| 2734 |
| 2735 |
| 2736 Job(); |
| 2737 |
| 2738 Job.fromJson(core.Map _json) { |
| 2739 if (_json.containsKey("created")) { |
| 2740 created = _json["created"]; |
| 2741 } |
| 2742 if (_json.containsKey("description")) { |
| 2743 description = _json["description"]; |
| 2744 } |
| 2745 if (_json.containsKey("errors")) { |
| 2746 errors = _json["errors"]; |
| 2747 } |
| 2748 if (_json.containsKey("id")) { |
| 2749 id = _json["id"]; |
| 2750 } |
| 2751 if (_json.containsKey("importedIds")) { |
| 2752 importedIds = _json["importedIds"]; |
| 2753 } |
| 2754 if (_json.containsKey("projectId")) { |
| 2755 projectId = _json["projectId"]; |
| 2756 } |
| 2757 if (_json.containsKey("request")) { |
| 2758 request = new JobRequest.fromJson(_json["request"]); |
| 2759 } |
| 2760 if (_json.containsKey("status")) { |
| 2761 status = _json["status"]; |
| 2762 } |
| 2763 if (_json.containsKey("warnings")) { |
| 2764 warnings = _json["warnings"]; |
| 2765 } |
| 2766 } |
| 2767 |
| 2768 core.Map toJson() { |
| 2769 var _json = new core.Map(); |
| 2770 if (created != null) { |
| 2771 _json["created"] = created; |
| 2772 } |
| 2773 if (description != null) { |
| 2774 _json["description"] = description; |
| 2775 } |
| 2776 if (errors != null) { |
| 2777 _json["errors"] = errors; |
| 2778 } |
| 2779 if (id != null) { |
| 2780 _json["id"] = id; |
| 2781 } |
| 2782 if (importedIds != null) { |
| 2783 _json["importedIds"] = importedIds; |
| 2784 } |
| 2785 if (projectId != null) { |
| 2786 _json["projectId"] = projectId; |
| 2787 } |
| 2788 if (request != null) { |
| 2789 _json["request"] = (request).toJson(); |
| 2790 } |
| 2791 if (status != null) { |
| 2792 _json["status"] = status; |
| 2793 } |
| 2794 if (warnings != null) { |
| 2795 _json["warnings"] = warnings; |
| 2796 } |
| 2797 return _json; |
| 2798 } |
| 2799 } |
| 2800 |
| 2801 |
| 2802 /** A summary representation of the service request that spawned the job. */ |
| 2803 class JobRequest { |
| 2804 /** |
| 2805 * The data destination of the request, for example, a Google BigQuery Table |
| 2806 * or Dataset ID. |
| 2807 */ |
| 2808 core.List<core.String> destination; |
| 2809 |
| 2810 /** |
| 2811 * The data source of the request, for example, a Google Cloud Storage object |
| 2812 * path or Readset ID. |
| 2813 */ |
| 2814 core.List<core.String> source; |
| 2815 |
| 2816 /** |
| 2817 * The original request type. |
| 2818 * Possible string values are: |
| 2819 * - "experimentalCreateJob" |
| 2820 * - "exportReadsets" |
| 2821 * - "exportVariants" |
| 2822 * - "importReadsets" |
| 2823 * - "importVariants" |
| 2824 * - "unknownType" |
| 2825 */ |
| 2826 core.String type; |
| 2827 |
| 2828 |
| 2829 JobRequest(); |
| 2830 |
| 2831 JobRequest.fromJson(core.Map _json) { |
| 2832 if (_json.containsKey("destination")) { |
| 2833 destination = _json["destination"]; |
| 2834 } |
| 2835 if (_json.containsKey("source")) { |
| 2836 source = _json["source"]; |
| 2837 } |
| 2838 if (_json.containsKey("type")) { |
| 2839 type = _json["type"]; |
| 2840 } |
| 2841 } |
| 2842 |
| 2843 core.Map toJson() { |
| 2844 var _json = new core.Map(); |
| 2845 if (destination != null) { |
| 2846 _json["destination"] = destination; |
| 2847 } |
| 2848 if (source != null) { |
| 2849 _json["source"] = source; |
| 2850 } |
| 2851 if (type != null) { |
| 2852 _json["type"] = type; |
| 2853 } |
| 2854 return _json; |
| 2855 } |
| 2856 } |
| 2857 |
| 2858 |
| 2859 /** Not documented yet. */ |
| 2860 class ListCoverageBucketsResponse { |
| 2861 /** |
| 2862 * 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 |
| 2864 * bucket width is infinity (the default behaviour, with no range or |
| 2865 * target_bucket_width). |
| 2866 */ |
| 2867 core.String bucketWidth; |
| 2868 |
| 2869 /** |
| 2870 * 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 |
| 2872 * reference sequence. Each bucket has width bucket_width, unless its end is |
| 2873 * is the end of the reference sequence. |
| 2874 */ |
| 2875 core.List<CoverageBucket> coverageBuckets; |
| 2876 |
| 2877 /** |
| 2878 * 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 |
| 2880 * results. This field will be empty if there aren't any additional results. |
| 2881 */ |
| 2882 core.String nextPageToken; |
| 2883 |
| 2884 |
| 2885 ListCoverageBucketsResponse(); |
| 2886 |
| 2887 ListCoverageBucketsResponse.fromJson(core.Map _json) { |
| 2888 if (_json.containsKey("bucketWidth")) { |
| 2889 bucketWidth = _json["bucketWidth"]; |
| 2890 } |
| 2891 if (_json.containsKey("coverageBuckets")) { |
| 2892 coverageBuckets = _json["coverageBuckets"].map((value) => new CoverageBuck
et.fromJson(value)).toList(); |
| 2893 } |
| 2894 if (_json.containsKey("nextPageToken")) { |
| 2895 nextPageToken = _json["nextPageToken"]; |
| 2896 } |
| 2897 } |
| 2898 |
| 2899 core.Map toJson() { |
| 2900 var _json = new core.Map(); |
| 2901 if (bucketWidth != null) { |
| 2902 _json["bucketWidth"] = bucketWidth; |
| 2903 } |
| 2904 if (coverageBuckets != null) { |
| 2905 _json["coverageBuckets"] = coverageBuckets.map((value) => (value).toJson()
).toList(); |
| 2906 } |
| 2907 if (nextPageToken != null) { |
| 2908 _json["nextPageToken"] = nextPageToken; |
| 2909 } |
| 2910 return _json; |
| 2911 } |
| 2912 } |
| 2913 |
| 2914 |
| 2915 /** The dataset list response. */ |
| 2916 class ListDatasetsResponse { |
| 2917 /** The list of matching Datasets. */ |
| 2918 core.List<Dataset> datasets; |
| 2919 |
| 2920 /** |
| 2921 * The continuation token, which is used to page through large result sets. |
| 2922 * Provide this value in a subsequent request to return the next page of |
| 2923 * results. This field will be empty if there aren't any additional results. |
| 2924 */ |
| 2925 core.String nextPageToken; |
| 2926 |
| 2927 |
| 2928 ListDatasetsResponse(); |
| 2929 |
| 2930 ListDatasetsResponse.fromJson(core.Map _json) { |
| 2931 if (_json.containsKey("datasets")) { |
| 2932 datasets = _json["datasets"].map((value) => new Dataset.fromJson(value)).t
oList(); |
| 2933 } |
| 2934 if (_json.containsKey("nextPageToken")) { |
| 2935 nextPageToken = _json["nextPageToken"]; |
| 2936 } |
| 2937 } |
| 2938 |
| 2939 core.Map toJson() { |
| 2940 var _json = new core.Map(); |
| 2941 if (datasets != null) { |
| 2942 _json["datasets"] = datasets.map((value) => (value).toJson()).toList(); |
| 2943 } |
| 2944 if (nextPageToken != null) { |
| 2945 _json["nextPageToken"] = nextPageToken; |
| 2946 } |
| 2947 return _json; |
| 2948 } |
| 2949 } |
| 2950 |
| 2951 |
| 2952 /** |
| 2953 * Metadata describes a single piece of variant call metadata. These data |
| 2954 * include a top level key and either a single value string (value) or a list of |
| 2955 * key-value pairs (info.) Value and info are mutually exclusive. |
| 2956 */ |
| 2957 class Metadata { |
| 2958 /** A textual description of this metadata. */ |
| 2959 core.String description; |
| 2960 |
| 2961 /** |
| 2962 * User-provided ID field, not enforced by this API. Two or more pieces of |
| 2963 * structured metadata with identical id and key fields are considered |
| 2964 * equivalent. |
| 2965 */ |
| 2966 core.String id; |
| 2967 |
| 2968 /** Remaining structured metadata key-value pairs. */ |
| 2969 core.Map<core.String, core.List<core.String>> info; |
| 2970 |
| 2971 /** The top-level key. */ |
| 2972 core.String key; |
| 2973 |
| 2974 /** |
| 2975 * The number of values that can be included in a field described by this |
| 2976 * metadata. |
| 2977 */ |
| 2978 core.String number; |
| 2979 |
| 2980 /** |
| 2981 * The type of data. Possible types include: Integer, Float, Flag, Character, |
| 2982 * and String. |
| 2983 * Possible string values are: |
| 2984 * - "character" |
| 2985 * - "flag" |
| 2986 * - "float" |
| 2987 * - "integer" |
| 2988 * - "string" |
| 2989 * - "unknownType" |
| 2990 */ |
| 2991 core.String type; |
| 2992 |
| 2993 /** The value field for simple metadata */ |
| 2994 core.String value; |
| 2995 |
| 2996 |
| 2997 Metadata(); |
| 2998 |
| 2999 Metadata.fromJson(core.Map _json) { |
| 3000 if (_json.containsKey("description")) { |
| 3001 description = _json["description"]; |
| 3002 } |
| 3003 if (_json.containsKey("id")) { |
| 3004 id = _json["id"]; |
| 3005 } |
| 3006 if (_json.containsKey("info")) { |
| 3007 info = _json["info"]; |
| 3008 } |
| 3009 if (_json.containsKey("key")) { |
| 3010 key = _json["key"]; |
| 3011 } |
| 3012 if (_json.containsKey("number")) { |
| 3013 number = _json["number"]; |
| 3014 } |
| 3015 if (_json.containsKey("type")) { |
| 3016 type = _json["type"]; |
| 3017 } |
| 3018 if (_json.containsKey("value")) { |
| 3019 value = _json["value"]; |
| 3020 } |
| 3021 } |
| 3022 |
| 3023 core.Map toJson() { |
| 3024 var _json = new core.Map(); |
| 3025 if (description != null) { |
| 3026 _json["description"] = description; |
| 3027 } |
| 3028 if (id != null) { |
| 3029 _json["id"] = id; |
| 3030 } |
| 3031 if (info != null) { |
| 3032 _json["info"] = info; |
| 3033 } |
| 3034 if (key != null) { |
| 3035 _json["key"] = key; |
| 3036 } |
| 3037 if (number != null) { |
| 3038 _json["number"] = number; |
| 3039 } |
| 3040 if (type != null) { |
| 3041 _json["type"] = type; |
| 3042 } |
| 3043 if (value != null) { |
| 3044 _json["value"] = value; |
| 3045 } |
| 3046 return _json; |
| 3047 } |
| 3048 } |
| 3049 |
| 3050 |
| 3051 /** Not documented yet. */ |
| 3052 class Program { |
| 3053 /** (CL) Command line. */ |
| 3054 core.String commandLine; |
| 3055 |
| 3056 /** (ID) Program record identifier. */ |
| 3057 core.String id; |
| 3058 |
| 3059 /** (PN) Program name. */ |
| 3060 core.String name; |
| 3061 |
| 3062 /** (PP) Previous program ID. */ |
| 3063 core.String prevProgramId; |
| 3064 |
| 3065 /** (VN) Program version. */ |
| 3066 core.String version; |
| 3067 |
| 3068 |
| 3069 Program(); |
| 3070 |
| 3071 Program.fromJson(core.Map _json) { |
| 3072 if (_json.containsKey("commandLine")) { |
| 3073 commandLine = _json["commandLine"]; |
| 3074 } |
| 3075 if (_json.containsKey("id")) { |
| 3076 id = _json["id"]; |
| 3077 } |
| 3078 if (_json.containsKey("name")) { |
| 3079 name = _json["name"]; |
| 3080 } |
| 3081 if (_json.containsKey("prevProgramId")) { |
| 3082 prevProgramId = _json["prevProgramId"]; |
| 3083 } |
| 3084 if (_json.containsKey("version")) { |
| 3085 version = _json["version"]; |
| 3086 } |
| 3087 } |
| 3088 |
| 3089 core.Map toJson() { |
| 3090 var _json = new core.Map(); |
| 3091 if (commandLine != null) { |
| 3092 _json["commandLine"] = commandLine; |
| 3093 } |
| 3094 if (id != null) { |
| 3095 _json["id"] = id; |
| 3096 } |
| 3097 if (name != null) { |
| 3098 _json["name"] = name; |
| 3099 } |
| 3100 if (prevProgramId != null) { |
| 3101 _json["prevProgramId"] = prevProgramId; |
| 3102 } |
| 3103 if (version != null) { |
| 3104 _json["version"] = version; |
| 3105 } |
| 3106 return _json; |
| 3107 } |
| 3108 } |
| 3109 |
| 3110 |
| 3111 /** |
| 3112 * A Read is a group of bases that may or may not have been aligned to a |
| 3113 * reference. It contains quality information and other metadata. |
| 3114 */ |
| 3115 class Read { |
| 3116 /** |
| 3117 * The originalBases after the cigar field has been applied. Deletions are |
| 3118 * represented with '-' and insertions are omitted. |
| 3119 */ |
| 3120 core.String alignedBases; |
| 3121 |
| 3122 /** |
| 3123 * Represents the quality of each base in this read. Each character represents |
| 3124 * one base. To get the quality, take the ASCII value of the character and |
| 3125 * subtract 33. (QUAL) |
| 3126 */ |
| 3127 core.String baseQuality; |
| 3128 |
| 3129 /** |
| 3130 * A condensed representation of how this read matches up to the reference. |
| 3131 * (CIGAR) |
| 3132 */ |
| 3133 core.String cigar; |
| 3134 |
| 3135 /** |
| 3136 * Each bit of this number has a different meaning if enabled. See the full |
| 3137 * BAM spec for more details. (FLAG) |
| 3138 */ |
| 3139 core.int flags; |
| 3140 |
| 3141 /** The Google generated ID of the read, immutable. */ |
| 3142 core.String id; |
| 3143 |
| 3144 /** |
| 3145 * A score up to 255 that represents how likely this read's aligned position |
| 3146 * is to be correct. A higher value is better. (MAPQ) |
| 3147 */ |
| 3148 core.int mappingQuality; |
| 3149 |
| 3150 /** The 1-based start position of the paired read. (PNEXT) */ |
| 3151 core.int matePosition; |
| 3152 |
| 3153 /** |
| 3154 * The name of the sequence that the paired read is aligned to. This is |
| 3155 * usually the same as referenceSequenceName. (RNEXT) |
| 3156 */ |
| 3157 core.String mateReferenceSequenceName; |
| 3158 |
| 3159 /** |
| 3160 * The name of the read. When imported from a BAM file, this is the query |
| 3161 * template name. (QNAME) |
| 3162 */ |
| 3163 core.String name; |
| 3164 |
| 3165 /** The list of bases that this read represents (such as "CATCGA"). (SEQ) */ |
| 3166 core.String originalBases; |
| 3167 |
| 3168 /** |
| 3169 * The 1-based start position of the aligned read. If the first base starts at |
| 3170 * the very beginning of the reference sequence, then the position would be |
| 3171 * '1'. (POS) |
| 3172 */ |
| 3173 core.int position; |
| 3174 |
| 3175 /** The ID of the readset this read belongs to. */ |
| 3176 core.String readsetId; |
| 3177 |
| 3178 /** |
| 3179 * The name of the sequence that this read is aligned to. This would be, for |
| 3180 * example, 'X' for the X Chromosome or '20' for Chromosome 20. (RNAME) |
| 3181 */ |
| 3182 core.String referenceSequenceName; |
| 3183 |
| 3184 /** A map of additional read information. (TAG) */ |
| 3185 core.Map<core.String, core.List<core.String>> tags; |
| 3186 |
| 3187 /** |
| 3188 * Length of the original piece of DNA that produced both this read and the |
| 3189 * paired read. (TLEN) |
| 3190 */ |
| 3191 core.int templateLength; |
| 3192 |
| 3193 |
| 3194 Read(); |
| 3195 |
| 3196 Read.fromJson(core.Map _json) { |
| 3197 if (_json.containsKey("alignedBases")) { |
| 3198 alignedBases = _json["alignedBases"]; |
| 3199 } |
| 3200 if (_json.containsKey("baseQuality")) { |
| 3201 baseQuality = _json["baseQuality"]; |
| 3202 } |
| 3203 if (_json.containsKey("cigar")) { |
| 3204 cigar = _json["cigar"]; |
| 3205 } |
| 3206 if (_json.containsKey("flags")) { |
| 3207 flags = _json["flags"]; |
| 3208 } |
| 3209 if (_json.containsKey("id")) { |
| 3210 id = _json["id"]; |
| 3211 } |
| 3212 if (_json.containsKey("mappingQuality")) { |
| 3213 mappingQuality = _json["mappingQuality"]; |
| 3214 } |
| 3215 if (_json.containsKey("matePosition")) { |
| 3216 matePosition = _json["matePosition"]; |
| 3217 } |
| 3218 if (_json.containsKey("mateReferenceSequenceName")) { |
| 3219 mateReferenceSequenceName = _json["mateReferenceSequenceName"]; |
| 3220 } |
| 3221 if (_json.containsKey("name")) { |
| 3222 name = _json["name"]; |
| 3223 } |
| 3224 if (_json.containsKey("originalBases")) { |
| 3225 originalBases = _json["originalBases"]; |
| 3226 } |
| 3227 if (_json.containsKey("position")) { |
| 3228 position = _json["position"]; |
| 3229 } |
| 3230 if (_json.containsKey("readsetId")) { |
| 3231 readsetId = _json["readsetId"]; |
| 3232 } |
| 3233 if (_json.containsKey("referenceSequenceName")) { |
| 3234 referenceSequenceName = _json["referenceSequenceName"]; |
| 3235 } |
| 3236 if (_json.containsKey("tags")) { |
| 3237 tags = _json["tags"]; |
| 3238 } |
| 3239 if (_json.containsKey("templateLength")) { |
| 3240 templateLength = _json["templateLength"]; |
| 3241 } |
| 3242 } |
| 3243 |
| 3244 core.Map toJson() { |
| 3245 var _json = new core.Map(); |
| 3246 if (alignedBases != null) { |
| 3247 _json["alignedBases"] = alignedBases; |
| 3248 } |
| 3249 if (baseQuality != null) { |
| 3250 _json["baseQuality"] = baseQuality; |
| 3251 } |
| 3252 if (cigar != null) { |
| 3253 _json["cigar"] = cigar; |
| 3254 } |
| 3255 if (flags != null) { |
| 3256 _json["flags"] = flags; |
| 3257 } |
| 3258 if (id != null) { |
| 3259 _json["id"] = id; |
| 3260 } |
| 3261 if (mappingQuality != null) { |
| 3262 _json["mappingQuality"] = mappingQuality; |
| 3263 } |
| 3264 if (matePosition != null) { |
| 3265 _json["matePosition"] = matePosition; |
| 3266 } |
| 3267 if (mateReferenceSequenceName != null) { |
| 3268 _json["mateReferenceSequenceName"] = mateReferenceSequenceName; |
| 3269 } |
| 3270 if (name != null) { |
| 3271 _json["name"] = name; |
| 3272 } |
| 3273 if (originalBases != null) { |
| 3274 _json["originalBases"] = originalBases; |
| 3275 } |
| 3276 if (position != null) { |
| 3277 _json["position"] = position; |
| 3278 } |
| 3279 if (readsetId != null) { |
| 3280 _json["readsetId"] = readsetId; |
| 3281 } |
| 3282 if (referenceSequenceName != null) { |
| 3283 _json["referenceSequenceName"] = referenceSequenceName; |
| 3284 } |
| 3285 if (tags != null) { |
| 3286 _json["tags"] = tags; |
| 3287 } |
| 3288 if (templateLength != null) { |
| 3289 _json["templateLength"] = templateLength; |
| 3290 } |
| 3291 return _json; |
| 3292 } |
| 3293 } |
| 3294 |
| 3295 |
| 3296 /** Not documented yet. */ |
| 3297 class ReadGroup { |
| 3298 /** (DT) Date the run was produced (ISO8601 date or date/time). */ |
| 3299 core.String date; |
| 3300 |
| 3301 /** (DS) Description. */ |
| 3302 core.String description; |
| 3303 |
| 3304 /** |
| 3305 * (FO) Flow order. The array of nucleotide bases that correspond to the |
| 3306 * nucleotides used for each flow of each read. |
| 3307 */ |
| 3308 core.String flowOrder; |
| 3309 |
| 3310 /** (ID) Read group identifier. */ |
| 3311 core.String id; |
| 3312 |
| 3313 /** |
| 3314 * (KS) The array of nucleotide bases that correspond to the key sequence of |
| 3315 * each read. |
| 3316 */ |
| 3317 core.String keySequence; |
| 3318 |
| 3319 /** (LS) Library. */ |
| 3320 core.String library; |
| 3321 |
| 3322 /** (PU) Platform unit. */ |
| 3323 core.String platformUnit; |
| 3324 |
| 3325 /** (PI) Predicted median insert size. */ |
| 3326 core.int predictedInsertSize; |
| 3327 |
| 3328 /** (PG) Programs used for processing the read group. */ |
| 3329 core.String processingProgram; |
| 3330 |
| 3331 /** (SM) Sample. */ |
| 3332 core.String sample; |
| 3333 |
| 3334 /** (CN) Name of sequencing center producing the read. */ |
| 3335 core.String sequencingCenterName; |
| 3336 |
| 3337 /** (PL) Platform/technology used to produce the reads. */ |
| 3338 core.String sequencingTechnology; |
| 3339 |
| 3340 |
| 3341 ReadGroup(); |
| 3342 |
| 3343 ReadGroup.fromJson(core.Map _json) { |
| 3344 if (_json.containsKey("date")) { |
| 3345 date = _json["date"]; |
| 3346 } |
| 3347 if (_json.containsKey("description")) { |
| 3348 description = _json["description"]; |
| 3349 } |
| 3350 if (_json.containsKey("flowOrder")) { |
| 3351 flowOrder = _json["flowOrder"]; |
| 3352 } |
| 3353 if (_json.containsKey("id")) { |
| 3354 id = _json["id"]; |
| 3355 } |
| 3356 if (_json.containsKey("keySequence")) { |
| 3357 keySequence = _json["keySequence"]; |
| 3358 } |
| 3359 if (_json.containsKey("library")) { |
| 3360 library = _json["library"]; |
| 3361 } |
| 3362 if (_json.containsKey("platformUnit")) { |
| 3363 platformUnit = _json["platformUnit"]; |
| 3364 } |
| 3365 if (_json.containsKey("predictedInsertSize")) { |
| 3366 predictedInsertSize = _json["predictedInsertSize"]; |
| 3367 } |
| 3368 if (_json.containsKey("processingProgram")) { |
| 3369 processingProgram = _json["processingProgram"]; |
| 3370 } |
| 3371 if (_json.containsKey("sample")) { |
| 3372 sample = _json["sample"]; |
| 3373 } |
| 3374 if (_json.containsKey("sequencingCenterName")) { |
| 3375 sequencingCenterName = _json["sequencingCenterName"]; |
| 3376 } |
| 3377 if (_json.containsKey("sequencingTechnology")) { |
| 3378 sequencingTechnology = _json["sequencingTechnology"]; |
| 3379 } |
| 3380 } |
| 3381 |
| 3382 core.Map toJson() { |
| 3383 var _json = new core.Map(); |
| 3384 if (date != null) { |
| 3385 _json["date"] = date; |
| 3386 } |
| 3387 if (description != null) { |
| 3388 _json["description"] = description; |
| 3389 } |
| 3390 if (flowOrder != null) { |
| 3391 _json["flowOrder"] = flowOrder; |
| 3392 } |
| 3393 if (id != null) { |
| 3394 _json["id"] = id; |
| 3395 } |
| 3396 if (keySequence != null) { |
| 3397 _json["keySequence"] = keySequence; |
| 3398 } |
| 3399 if (library != null) { |
| 3400 _json["library"] = library; |
| 3401 } |
| 3402 if (platformUnit != null) { |
| 3403 _json["platformUnit"] = platformUnit; |
| 3404 } |
| 3405 if (predictedInsertSize != null) { |
| 3406 _json["predictedInsertSize"] = predictedInsertSize; |
| 3407 } |
| 3408 if (processingProgram != null) { |
| 3409 _json["processingProgram"] = processingProgram; |
| 3410 } |
| 3411 if (sample != null) { |
| 3412 _json["sample"] = sample; |
| 3413 } |
| 3414 if (sequencingCenterName != null) { |
| 3415 _json["sequencingCenterName"] = sequencingCenterName; |
| 3416 } |
| 3417 if (sequencingTechnology != null) { |
| 3418 _json["sequencingTechnology"] = sequencingTechnology; |
| 3419 } |
| 3420 return _json; |
| 3421 } |
| 3422 } |
| 3423 |
| 3424 |
| 3425 /** A Readset is a collection of Reads. */ |
| 3426 class Readset { |
| 3427 /** The ID of the dataset this readset belongs to. */ |
| 3428 core.String datasetId; |
| 3429 |
| 3430 /** |
| 3431 * File information from the original BAM import. See the BAM format |
| 3432 * specification for additional information on each field. |
| 3433 */ |
| 3434 core.List<HeaderSection> fileData; |
| 3435 |
| 3436 /** The Google generated ID of the readset, immutable. */ |
| 3437 core.String id; |
| 3438 |
| 3439 /** The readset name, typically this is the sample name. */ |
| 3440 core.String name; |
| 3441 |
| 3442 |
| 3443 Readset(); |
| 3444 |
| 3445 Readset.fromJson(core.Map _json) { |
| 3446 if (_json.containsKey("datasetId")) { |
| 3447 datasetId = _json["datasetId"]; |
| 3448 } |
| 3449 if (_json.containsKey("fileData")) { |
| 3450 fileData = _json["fileData"].map((value) => new HeaderSection.fromJson(val
ue)).toList(); |
| 3451 } |
| 3452 if (_json.containsKey("id")) { |
| 3453 id = _json["id"]; |
| 3454 } |
| 3455 if (_json.containsKey("name")) { |
| 3456 name = _json["name"]; |
| 3457 } |
| 3458 } |
| 3459 |
| 3460 core.Map toJson() { |
| 3461 var _json = new core.Map(); |
| 3462 if (datasetId != null) { |
| 3463 _json["datasetId"] = datasetId; |
| 3464 } |
| 3465 if (fileData != null) { |
| 3466 _json["fileData"] = fileData.map((value) => (value).toJson()).toList(); |
| 3467 } |
| 3468 if (id != null) { |
| 3469 _json["id"] = id; |
| 3470 } |
| 3471 if (name != null) { |
| 3472 _json["name"] = name; |
| 3473 } |
| 3474 return _json; |
| 3475 } |
| 3476 } |
| 3477 |
| 3478 |
| 3479 /** Not documented yet. */ |
| 3480 class ReferenceSequence { |
| 3481 /** (AS) Genome assembly identifier. */ |
| 3482 core.String assemblyId; |
| 3483 |
| 3484 /** (LN) Reference sequence length. */ |
| 3485 core.int length; |
| 3486 |
| 3487 /** |
| 3488 * (M5) MD5 checksum of the sequence in the uppercase, excluding spaces but |
| 3489 * including pads as *. |
| 3490 */ |
| 3491 core.String md5Checksum; |
| 3492 |
| 3493 /** (SN) Reference sequence name. */ |
| 3494 core.String name; |
| 3495 |
| 3496 /** (SP) Species. */ |
| 3497 core.String species; |
| 3498 |
| 3499 /** (UR) URI of the sequence. */ |
| 3500 core.String uri; |
| 3501 |
| 3502 |
| 3503 ReferenceSequence(); |
| 3504 |
| 3505 ReferenceSequence.fromJson(core.Map _json) { |
| 3506 if (_json.containsKey("assemblyId")) { |
| 3507 assemblyId = _json["assemblyId"]; |
| 3508 } |
| 3509 if (_json.containsKey("length")) { |
| 3510 length = _json["length"]; |
| 3511 } |
| 3512 if (_json.containsKey("md5Checksum")) { |
| 3513 md5Checksum = _json["md5Checksum"]; |
| 3514 } |
| 3515 if (_json.containsKey("name")) { |
| 3516 name = _json["name"]; |
| 3517 } |
| 3518 if (_json.containsKey("species")) { |
| 3519 species = _json["species"]; |
| 3520 } |
| 3521 if (_json.containsKey("uri")) { |
| 3522 uri = _json["uri"]; |
| 3523 } |
| 3524 } |
| 3525 |
| 3526 core.Map toJson() { |
| 3527 var _json = new core.Map(); |
| 3528 if (assemblyId != null) { |
| 3529 _json["assemblyId"] = assemblyId; |
| 3530 } |
| 3531 if (length != null) { |
| 3532 _json["length"] = length; |
| 3533 } |
| 3534 if (md5Checksum != null) { |
| 3535 _json["md5Checksum"] = md5Checksum; |
| 3536 } |
| 3537 if (name != null) { |
| 3538 _json["name"] = name; |
| 3539 } |
| 3540 if (species != null) { |
| 3541 _json["species"] = species; |
| 3542 } |
| 3543 if (uri != null) { |
| 3544 _json["uri"] = uri; |
| 3545 } |
| 3546 return _json; |
| 3547 } |
| 3548 } |
| 3549 |
| 3550 |
| 3551 /** The callset search request. */ |
| 3552 class SearchCallsetsRequest { |
| 3553 /** The maximum number of callsets to return. */ |
| 3554 core.String maxResults; |
| 3555 |
| 3556 /** |
| 3557 * Only return callsets for which a substring of the name matches this string. |
| 3558 */ |
| 3559 core.String name; |
| 3560 |
| 3561 /** |
| 3562 * 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 |
| 3564 * "nextPageToken" from the previous response. |
| 3565 */ |
| 3566 core.String pageToken; |
| 3567 |
| 3568 /** |
| 3569 * Restrict the query to callsets within the given variantsets. At least one |
| 3570 * ID must be provided. |
| 3571 */ |
| 3572 core.List<core.String> variantsetIds; |
| 3573 |
| 3574 |
| 3575 SearchCallsetsRequest(); |
| 3576 |
| 3577 SearchCallsetsRequest.fromJson(core.Map _json) { |
| 3578 if (_json.containsKey("maxResults")) { |
| 3579 maxResults = _json["maxResults"]; |
| 3580 } |
| 3581 if (_json.containsKey("name")) { |
| 3582 name = _json["name"]; |
| 3583 } |
| 3584 if (_json.containsKey("pageToken")) { |
| 3585 pageToken = _json["pageToken"]; |
| 3586 } |
| 3587 if (_json.containsKey("variantsetIds")) { |
| 3588 variantsetIds = _json["variantsetIds"]; |
| 3589 } |
| 3590 } |
| 3591 |
| 3592 core.Map toJson() { |
| 3593 var _json = new core.Map(); |
| 3594 if (maxResults != null) { |
| 3595 _json["maxResults"] = maxResults; |
| 3596 } |
| 3597 if (name != null) { |
| 3598 _json["name"] = name; |
| 3599 } |
| 3600 if (pageToken != null) { |
| 3601 _json["pageToken"] = pageToken; |
| 3602 } |
| 3603 if (variantsetIds != null) { |
| 3604 _json["variantsetIds"] = variantsetIds; |
| 3605 } |
| 3606 return _json; |
| 3607 } |
| 3608 } |
| 3609 |
| 3610 |
| 3611 /** The callset search response. */ |
| 3612 class SearchCallsetsResponse { |
| 3613 /** The list of matching callsets. */ |
| 3614 core.List<Callset> callsets; |
| 3615 |
| 3616 /** |
| 3617 * 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 |
| 3619 * results. This field will be empty if there aren't any additional results. |
| 3620 */ |
| 3621 core.String nextPageToken; |
| 3622 |
| 3623 |
| 3624 SearchCallsetsResponse(); |
| 3625 |
| 3626 SearchCallsetsResponse.fromJson(core.Map _json) { |
| 3627 if (_json.containsKey("callsets")) { |
| 3628 callsets = _json["callsets"].map((value) => new Callset.fromJson(value)).t
oList(); |
| 3629 } |
| 3630 if (_json.containsKey("nextPageToken")) { |
| 3631 nextPageToken = _json["nextPageToken"]; |
| 3632 } |
| 3633 } |
| 3634 |
| 3635 core.Map toJson() { |
| 3636 var _json = new core.Map(); |
| 3637 if (callsets != null) { |
| 3638 _json["callsets"] = callsets.map((value) => (value).toJson()).toList(); |
| 3639 } |
| 3640 if (nextPageToken != null) { |
| 3641 _json["nextPageToken"] = nextPageToken; |
| 3642 } |
| 3643 return _json; |
| 3644 } |
| 3645 } |
| 3646 |
| 3647 |
| 3648 /** The jobs search request. */ |
| 3649 class SearchJobsRequest { |
| 3650 /** |
| 3651 * If specified, only jobs created on or after this date, given in |
| 3652 * milliseconds since Unix epoch, will be returned. |
| 3653 */ |
| 3654 core.String createdAfter; |
| 3655 |
| 3656 /** |
| 3657 * If specified, only jobs created prior to this date, given in milliseconds |
| 3658 * since Unix epoch, will be returned. |
| 3659 */ |
| 3660 core.String createdBefore; |
| 3661 |
| 3662 /** |
| 3663 * Specifies the number of results to return in a single page. Defaults to |
| 3664 * 128. The maximum value is 256. |
| 3665 */ |
| 3666 core.String maxResults; |
| 3667 |
| 3668 /** |
| 3669 * 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 |
| 3671 * "nextPageToken" from the previous response. |
| 3672 */ |
| 3673 core.String pageToken; |
| 3674 |
| 3675 /** |
| 3676 * Required. Only return jobs which belong to this Google Developers Console |
| 3677 * project. Only accepts project numbers. |
| 3678 */ |
| 3679 core.String projectId; |
| 3680 |
| 3681 /** Only return jobs which have a matching status. */ |
| 3682 core.List<core.String> status; |
| 3683 |
| 3684 |
| 3685 SearchJobsRequest(); |
| 3686 |
| 3687 SearchJobsRequest.fromJson(core.Map _json) { |
| 3688 if (_json.containsKey("createdAfter")) { |
| 3689 createdAfter = _json["createdAfter"]; |
| 3690 } |
| 3691 if (_json.containsKey("createdBefore")) { |
| 3692 createdBefore = _json["createdBefore"]; |
| 3693 } |
| 3694 if (_json.containsKey("maxResults")) { |
| 3695 maxResults = _json["maxResults"]; |
| 3696 } |
| 3697 if (_json.containsKey("pageToken")) { |
| 3698 pageToken = _json["pageToken"]; |
| 3699 } |
| 3700 if (_json.containsKey("projectId")) { |
| 3701 projectId = _json["projectId"]; |
| 3702 } |
| 3703 if (_json.containsKey("status")) { |
| 3704 status = _json["status"]; |
| 3705 } |
| 3706 } |
| 3707 |
| 3708 core.Map toJson() { |
| 3709 var _json = new core.Map(); |
| 3710 if (createdAfter != null) { |
| 3711 _json["createdAfter"] = createdAfter; |
| 3712 } |
| 3713 if (createdBefore != null) { |
| 3714 _json["createdBefore"] = createdBefore; |
| 3715 } |
| 3716 if (maxResults != null) { |
| 3717 _json["maxResults"] = maxResults; |
| 3718 } |
| 3719 if (pageToken != null) { |
| 3720 _json["pageToken"] = pageToken; |
| 3721 } |
| 3722 if (projectId != null) { |
| 3723 _json["projectId"] = projectId; |
| 3724 } |
| 3725 if (status != null) { |
| 3726 _json["status"] = status; |
| 3727 } |
| 3728 return _json; |
| 3729 } |
| 3730 } |
| 3731 |
| 3732 |
| 3733 /** The job search response. */ |
| 3734 class SearchJobsResponse { |
| 3735 /** The list of jobs results, ordered newest to oldest. */ |
| 3736 core.List<Job> jobs; |
| 3737 |
| 3738 /** |
| 3739 * The continuation token which is used to page through large result sets. |
| 3740 * Provide this value is a subsequent request to return the next page of |
| 3741 * results. This field will be empty if there are no more results. |
| 3742 */ |
| 3743 core.String nextPageToken; |
| 3744 |
| 3745 |
| 3746 SearchJobsResponse(); |
| 3747 |
| 3748 SearchJobsResponse.fromJson(core.Map _json) { |
| 3749 if (_json.containsKey("jobs")) { |
| 3750 jobs = _json["jobs"].map((value) => new Job.fromJson(value)).toList(); |
| 3751 } |
| 3752 if (_json.containsKey("nextPageToken")) { |
| 3753 nextPageToken = _json["nextPageToken"]; |
| 3754 } |
| 3755 } |
| 3756 |
| 3757 core.Map toJson() { |
| 3758 var _json = new core.Map(); |
| 3759 if (jobs != null) { |
| 3760 _json["jobs"] = jobs.map((value) => (value).toJson()).toList(); |
| 3761 } |
| 3762 if (nextPageToken != null) { |
| 3763 _json["nextPageToken"] = nextPageToken; |
| 3764 } |
| 3765 return _json; |
| 3766 } |
| 3767 } |
| 3768 |
| 3769 |
| 3770 /** The read search request. */ |
| 3771 class SearchReadsRequest { |
| 3772 /** |
| 3773 * Specifies number of results to return in a single page. If unspecified, it |
| 3774 * will default to 256. The maximum value is 2048. |
| 3775 */ |
| 3776 core.String maxResults; |
| 3777 |
| 3778 /** |
| 3779 * 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 |
| 3781 * "nextPageToken" from the previous response. |
| 3782 */ |
| 3783 core.String pageToken; |
| 3784 |
| 3785 /** |
| 3786 * 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 |
| 3788 * reference sequences; this defines the genomic coordinates for the query. |
| 3789 */ |
| 3790 core.List<core.String> readsetIds; |
| 3791 |
| 3792 /** |
| 3793 * 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 |
| 3795 * reference sequence, if any. |
| 3796 */ |
| 3797 core.String sequenceEnd; |
| 3798 |
| 3799 /** |
| 3800 * Restricts the results to a particular reference sequence such as '1', |
| 3801 * 'chr1', or 'X'. The set of valid references sequences depends on the |
| 3802 * readsets specified. If set to "*", only unmapped Reads are returned. |
| 3803 */ |
| 3804 core.String sequenceName; |
| 3805 |
| 3806 /** |
| 3807 * 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 |
| 3809 * reference sequence, if any. |
| 3810 */ |
| 3811 core.String sequenceStart; |
| 3812 |
| 3813 |
| 3814 SearchReadsRequest(); |
| 3815 |
| 3816 SearchReadsRequest.fromJson(core.Map _json) { |
| 3817 if (_json.containsKey("maxResults")) { |
| 3818 maxResults = _json["maxResults"]; |
| 3819 } |
| 3820 if (_json.containsKey("pageToken")) { |
| 3821 pageToken = _json["pageToken"]; |
| 3822 } |
| 3823 if (_json.containsKey("readsetIds")) { |
| 3824 readsetIds = _json["readsetIds"]; |
| 3825 } |
| 3826 if (_json.containsKey("sequenceEnd")) { |
| 3827 sequenceEnd = _json["sequenceEnd"]; |
| 3828 } |
| 3829 if (_json.containsKey("sequenceName")) { |
| 3830 sequenceName = _json["sequenceName"]; |
| 3831 } |
| 3832 if (_json.containsKey("sequenceStart")) { |
| 3833 sequenceStart = _json["sequenceStart"]; |
| 3834 } |
| 3835 } |
| 3836 |
| 3837 core.Map toJson() { |
| 3838 var _json = new core.Map(); |
| 3839 if (maxResults != null) { |
| 3840 _json["maxResults"] = maxResults; |
| 3841 } |
| 3842 if (pageToken != null) { |
| 3843 _json["pageToken"] = pageToken; |
| 3844 } |
| 3845 if (readsetIds != null) { |
| 3846 _json["readsetIds"] = readsetIds; |
| 3847 } |
| 3848 if (sequenceEnd != null) { |
| 3849 _json["sequenceEnd"] = sequenceEnd; |
| 3850 } |
| 3851 if (sequenceName != null) { |
| 3852 _json["sequenceName"] = sequenceName; |
| 3853 } |
| 3854 if (sequenceStart != null) { |
| 3855 _json["sequenceStart"] = sequenceStart; |
| 3856 } |
| 3857 return _json; |
| 3858 } |
| 3859 } |
| 3860 |
| 3861 |
| 3862 /** The read search response. */ |
| 3863 class SearchReadsResponse { |
| 3864 /** |
| 3865 * The continuation token, which is used to page through large result sets. |
| 3866 * Provide this value in a subsequent request to return the next page of |
| 3867 * results. This field will be empty if there aren't any additional results. |
| 3868 */ |
| 3869 core.String nextPageToken; |
| 3870 |
| 3871 /** |
| 3872 * The list of matching Reads. The resulting Reads are sorted by position; the |
| 3873 * smallest positions are returned first. Unmapped reads, which have no |
| 3874 * position, are returned last and are further sorted alphabetically by name. |
| 3875 */ |
| 3876 core.List<Read> reads; |
| 3877 |
| 3878 |
| 3879 SearchReadsResponse(); |
| 3880 |
| 3881 SearchReadsResponse.fromJson(core.Map _json) { |
| 3882 if (_json.containsKey("nextPageToken")) { |
| 3883 nextPageToken = _json["nextPageToken"]; |
| 3884 } |
| 3885 if (_json.containsKey("reads")) { |
| 3886 reads = _json["reads"].map((value) => new Read.fromJson(value)).toList(); |
| 3887 } |
| 3888 } |
| 3889 |
| 3890 core.Map toJson() { |
| 3891 var _json = new core.Map(); |
| 3892 if (nextPageToken != null) { |
| 3893 _json["nextPageToken"] = nextPageToken; |
| 3894 } |
| 3895 if (reads != null) { |
| 3896 _json["reads"] = reads.map((value) => (value).toJson()).toList(); |
| 3897 } |
| 3898 return _json; |
| 3899 } |
| 3900 } |
| 3901 |
| 3902 |
| 3903 /** The readset search request. */ |
| 3904 class SearchReadsetsRequest { |
| 3905 /** |
| 3906 * Restricts this query to readsets within the given datasets. At least one ID |
| 3907 * must be provided. |
| 3908 */ |
| 3909 core.List<core.String> datasetIds; |
| 3910 |
| 3911 /** |
| 3912 * Specifies number of results to return in a single page. If unspecified, it |
| 3913 * will default to 128. The maximum value is 1024. |
| 3914 */ |
| 3915 core.String maxResults; |
| 3916 |
| 3917 /** |
| 3918 * Only return readsets for which a substring of the name matches this string. |
| 3919 */ |
| 3920 core.String name; |
| 3921 |
| 3922 /** |
| 3923 * 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 |
| 3925 * "nextPageToken" from the previous response. |
| 3926 */ |
| 3927 core.String pageToken; |
| 3928 |
| 3929 |
| 3930 SearchReadsetsRequest(); |
| 3931 |
| 3932 SearchReadsetsRequest.fromJson(core.Map _json) { |
| 3933 if (_json.containsKey("datasetIds")) { |
| 3934 datasetIds = _json["datasetIds"]; |
| 3935 } |
| 3936 if (_json.containsKey("maxResults")) { |
| 3937 maxResults = _json["maxResults"]; |
| 3938 } |
| 3939 if (_json.containsKey("name")) { |
| 3940 name = _json["name"]; |
| 3941 } |
| 3942 if (_json.containsKey("pageToken")) { |
| 3943 pageToken = _json["pageToken"]; |
| 3944 } |
| 3945 } |
| 3946 |
| 3947 core.Map toJson() { |
| 3948 var _json = new core.Map(); |
| 3949 if (datasetIds != null) { |
| 3950 _json["datasetIds"] = datasetIds; |
| 3951 } |
| 3952 if (maxResults != null) { |
| 3953 _json["maxResults"] = maxResults; |
| 3954 } |
| 3955 if (name != null) { |
| 3956 _json["name"] = name; |
| 3957 } |
| 3958 if (pageToken != null) { |
| 3959 _json["pageToken"] = pageToken; |
| 3960 } |
| 3961 return _json; |
| 3962 } |
| 3963 } |
| 3964 |
| 3965 |
| 3966 /** The readset search response. */ |
| 3967 class SearchReadsetsResponse { |
| 3968 /** |
| 3969 * The continuation token, which is used to page through large result sets. |
| 3970 * Provide this value in a subsequent request to return the next page of |
| 3971 * results. This field will be empty if there aren't any additional results. |
| 3972 */ |
| 3973 core.String nextPageToken; |
| 3974 |
| 3975 /** The list of matching Readsets. */ |
| 3976 core.List<Readset> readsets; |
| 3977 |
| 3978 |
| 3979 SearchReadsetsResponse(); |
| 3980 |
| 3981 SearchReadsetsResponse.fromJson(core.Map _json) { |
| 3982 if (_json.containsKey("nextPageToken")) { |
| 3983 nextPageToken = _json["nextPageToken"]; |
| 3984 } |
| 3985 if (_json.containsKey("readsets")) { |
| 3986 readsets = _json["readsets"].map((value) => new Readset.fromJson(value)).t
oList(); |
| 3987 } |
| 3988 } |
| 3989 |
| 3990 core.Map toJson() { |
| 3991 var _json = new core.Map(); |
| 3992 if (nextPageToken != null) { |
| 3993 _json["nextPageToken"] = nextPageToken; |
| 3994 } |
| 3995 if (readsets != null) { |
| 3996 _json["readsets"] = readsets.map((value) => (value).toJson()).toList(); |
| 3997 } |
| 3998 return _json; |
| 3999 } |
| 4000 } |
| 4001 |
| 4002 |
| 4003 /** The variant search request. */ |
| 4004 class SearchVariantsRequest { |
| 4005 /** |
| 4006 * Only return variant calls which belong to callsets with these ids. Leaving |
| 4007 * this blank returns all variant calls. At most one of callsetNames or |
| 4008 * callsetIds should be provided. |
| 4009 */ |
| 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 |
| 4022 /** |
| 4023 * Required. The end of the window (0-based, exclusive) for which overlapping |
| 4024 * variants should be returned. |
| 4025 */ |
| 4026 core.String endPosition; |
| 4027 |
| 4028 /** The maximum number of variants to return. */ |
| 4029 core.String maxResults; |
| 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 * Required. The beginning of the window (0-based, inclusive) for which |
| 4040 * overlapping variants should be returned. |
| 4041 */ |
| 4042 core.String startPosition; |
| 4043 |
| 4044 /** Only return variants which have exactly this name. */ |
| 4045 core.String variantName; |
| 4046 |
| 4047 /** Required. The ID of the variantset to search. */ |
| 4048 core.String variantsetId; |
| 4049 |
| 4050 |
| 4051 SearchVariantsRequest(); |
| 4052 |
| 4053 SearchVariantsRequest.fromJson(core.Map _json) { |
| 4054 if (_json.containsKey("callsetIds")) { |
| 4055 callsetIds = _json["callsetIds"]; |
| 4056 } |
| 4057 if (_json.containsKey("callsetNames")) { |
| 4058 callsetNames = _json["callsetNames"]; |
| 4059 } |
| 4060 if (_json.containsKey("contig")) { |
| 4061 contig = _json["contig"]; |
| 4062 } |
| 4063 if (_json.containsKey("endPosition")) { |
| 4064 endPosition = _json["endPosition"]; |
| 4065 } |
| 4066 if (_json.containsKey("maxResults")) { |
| 4067 maxResults = _json["maxResults"]; |
| 4068 } |
| 4069 if (_json.containsKey("pageToken")) { |
| 4070 pageToken = _json["pageToken"]; |
| 4071 } |
| 4072 if (_json.containsKey("startPosition")) { |
| 4073 startPosition = _json["startPosition"]; |
| 4074 } |
| 4075 if (_json.containsKey("variantName")) { |
| 4076 variantName = _json["variantName"]; |
| 4077 } |
| 4078 if (_json.containsKey("variantsetId")) { |
| 4079 variantsetId = _json["variantsetId"]; |
| 4080 } |
| 4081 } |
| 4082 |
| 4083 core.Map toJson() { |
| 4084 var _json = new core.Map(); |
| 4085 if (callsetIds != null) { |
| 4086 _json["callsetIds"] = callsetIds; |
| 4087 } |
| 4088 if (callsetNames != null) { |
| 4089 _json["callsetNames"] = callsetNames; |
| 4090 } |
| 4091 if (contig != null) { |
| 4092 _json["contig"] = contig; |
| 4093 } |
| 4094 if (endPosition != null) { |
| 4095 _json["endPosition"] = endPosition; |
| 4096 } |
| 4097 if (maxResults != null) { |
| 4098 _json["maxResults"] = maxResults; |
| 4099 } |
| 4100 if (pageToken != null) { |
| 4101 _json["pageToken"] = pageToken; |
| 4102 } |
| 4103 if (startPosition != null) { |
| 4104 _json["startPosition"] = startPosition; |
| 4105 } |
| 4106 if (variantName != null) { |
| 4107 _json["variantName"] = variantName; |
| 4108 } |
| 4109 if (variantsetId != null) { |
| 4110 _json["variantsetId"] = variantsetId; |
| 4111 } |
| 4112 return _json; |
| 4113 } |
| 4114 } |
| 4115 |
| 4116 |
| 4117 /** The variant search response. */ |
| 4118 class SearchVariantsResponse { |
| 4119 /** |
| 4120 * The continuation token, which is used to page through large result sets. |
| 4121 * Provide this value in a subsequent request to return the next page of |
| 4122 * results. This field will be empty if there aren't any additional results. |
| 4123 */ |
| 4124 core.String nextPageToken; |
| 4125 |
| 4126 /** The list of matching Variants. */ |
| 4127 core.List<Variant> variants; |
| 4128 |
| 4129 |
| 4130 SearchVariantsResponse(); |
| 4131 |
| 4132 SearchVariantsResponse.fromJson(core.Map _json) { |
| 4133 if (_json.containsKey("nextPageToken")) { |
| 4134 nextPageToken = _json["nextPageToken"]; |
| 4135 } |
| 4136 if (_json.containsKey("variants")) { |
| 4137 variants = _json["variants"].map((value) => new Variant.fromJson(value)).t
oList(); |
| 4138 } |
| 4139 } |
| 4140 |
| 4141 core.Map toJson() { |
| 4142 var _json = new core.Map(); |
| 4143 if (nextPageToken != null) { |
| 4144 _json["nextPageToken"] = nextPageToken; |
| 4145 } |
| 4146 if (variants != null) { |
| 4147 _json["variants"] = variants.map((value) => (value).toJson()).toList(); |
| 4148 } |
| 4149 return _json; |
| 4150 } |
| 4151 } |
| 4152 |
| 4153 |
| 4154 /** |
| 4155 * 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 |
| 4157 * a Variantset. |
| 4158 */ |
| 4159 class Variant { |
| 4160 /** The bases that appear instead of the reference bases. */ |
| 4161 core.List<core.String> alternateBases; |
| 4162 |
| 4163 /** |
| 4164 * The variant calls for this particular variant. Each one represents the |
| 4165 * determination of genotype with respect to this variant. |
| 4166 */ |
| 4167 core.List<Call> calls; |
| 4168 |
| 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. */ |
| 4173 core.String created; |
| 4174 |
| 4175 /** |
| 4176 * 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 |
| 4178 * reference allele is (end - position). This is useful for variants that |
| 4179 * don't explicitly give alternate bases, for example large deletions. |
| 4180 */ |
| 4181 core.String end; |
| 4182 |
| 4183 /** The Google generated ID of the variant, immutable. */ |
| 4184 core.String id; |
| 4185 |
| 4186 /** A map of additional variant information. */ |
| 4187 core.Map<core.String, core.List<core.String>> info; |
| 4188 |
| 4189 /** Names for the variant, for example a RefSNP ID. */ |
| 4190 core.List<core.String> names; |
| 4191 |
| 4192 /** |
| 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. |
| 4200 */ |
| 4201 core.String referenceBases; |
| 4202 |
| 4203 /** The ID of the variantset this variant belongs to. */ |
| 4204 core.String variantsetId; |
| 4205 |
| 4206 |
| 4207 Variant(); |
| 4208 |
| 4209 Variant.fromJson(core.Map _json) { |
| 4210 if (_json.containsKey("alternateBases")) { |
| 4211 alternateBases = _json["alternateBases"]; |
| 4212 } |
| 4213 if (_json.containsKey("calls")) { |
| 4214 calls = _json["calls"].map((value) => new Call.fromJson(value)).toList(); |
| 4215 } |
| 4216 if (_json.containsKey("contig")) { |
| 4217 contig = _json["contig"]; |
| 4218 } |
| 4219 if (_json.containsKey("created")) { |
| 4220 created = _json["created"]; |
| 4221 } |
| 4222 if (_json.containsKey("end")) { |
| 4223 end = _json["end"]; |
| 4224 } |
| 4225 if (_json.containsKey("id")) { |
| 4226 id = _json["id"]; |
| 4227 } |
| 4228 if (_json.containsKey("info")) { |
| 4229 info = _json["info"]; |
| 4230 } |
| 4231 if (_json.containsKey("names")) { |
| 4232 names = _json["names"]; |
| 4233 } |
| 4234 if (_json.containsKey("position")) { |
| 4235 position = _json["position"]; |
| 4236 } |
| 4237 if (_json.containsKey("referenceBases")) { |
| 4238 referenceBases = _json["referenceBases"]; |
| 4239 } |
| 4240 if (_json.containsKey("variantsetId")) { |
| 4241 variantsetId = _json["variantsetId"]; |
| 4242 } |
| 4243 } |
| 4244 |
| 4245 core.Map toJson() { |
| 4246 var _json = new core.Map(); |
| 4247 if (alternateBases != null) { |
| 4248 _json["alternateBases"] = alternateBases; |
| 4249 } |
| 4250 if (calls != null) { |
| 4251 _json["calls"] = calls.map((value) => (value).toJson()).toList(); |
| 4252 } |
| 4253 if (contig != null) { |
| 4254 _json["contig"] = contig; |
| 4255 } |
| 4256 if (created != null) { |
| 4257 _json["created"] = created; |
| 4258 } |
| 4259 if (end != null) { |
| 4260 _json["end"] = end; |
| 4261 } |
| 4262 if (id != null) { |
| 4263 _json["id"] = id; |
| 4264 } |
| 4265 if (info != null) { |
| 4266 _json["info"] = info; |
| 4267 } |
| 4268 if (names != null) { |
| 4269 _json["names"] = names; |
| 4270 } |
| 4271 if (position != null) { |
| 4272 _json["position"] = position; |
| 4273 } |
| 4274 if (referenceBases != null) { |
| 4275 _json["referenceBases"] = referenceBases; |
| 4276 } |
| 4277 if (variantsetId != null) { |
| 4278 _json["variantsetId"] = variantsetId; |
| 4279 } |
| 4280 return _json; |
| 4281 } |
| 4282 } |
| 4283 |
| 4284 |
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