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