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Side by Side Diff: discovery/googleapis/genomics__v1.json

Issue 3003493002: Api-Roll 53: 2017-08-21 (Closed)
Patch Set: Created 3 years, 4 months ago
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1 { 1 {
2 "auth": { 2 "auth": {
3 "oauth2": { 3 "oauth2": {
4 "scopes": { 4 "scopes": {
5 "https://www.googleapis.com/auth/genomics.readonly": {
6 "description": "View Genomics data"
7 },
8 "https://www.googleapis.com/auth/cloud-platform": {
9 "description": "View and manage your data across Google Clou d Platform services"
10 },
5 "https://www.googleapis.com/auth/genomics": { 11 "https://www.googleapis.com/auth/genomics": {
6 "description": "View and manage Genomics data" 12 "description": "View and manage Genomics data"
7 }, 13 },
8 "https://www.googleapis.com/auth/devstorage.read_write": { 14 "https://www.googleapis.com/auth/devstorage.read_write": {
9 "description": "Manage your data in Google Cloud Storage" 15 "description": "Manage your data in Google Cloud Storage"
10 }, 16 },
11 "https://www.googleapis.com/auth/bigquery": { 17 "https://www.googleapis.com/auth/bigquery": {
12 "description": "View and manage your data in Google BigQuery " 18 "description": "View and manage your data in Google BigQuery "
13 },
14 "https://www.googleapis.com/auth/genomics.readonly": {
15 "description": "View Genomics data"
16 },
17 "https://www.googleapis.com/auth/cloud-platform": {
18 "description": "View and manage your data across Google Clou d Platform services"
19 } 19 }
20 } 20 }
21 } 21 }
22 }, 22 },
23 "basePath": "", 23 "basePath": "",
24 "baseUrl": "https://genomics.googleapis.com/", 24 "baseUrl": "https://genomics.googleapis.com/",
25 "batchPath": "batch", 25 "batchPath": "batch",
26 "description": "Upload, process, query, and search Genomics data in the clou d.", 26 "description": "Upload, process, query, and search Genomics data in the clou d.",
27 "discoveryVersion": "v1", 27 "discoveryVersion": "v1",
28 "documentationLink": "https://cloud.google.com/genomics", 28 "documentationLink": "https://cloud.google.com/genomics",
29 "icons": { 29 "icons": {
30 "x16": "http://www.google.com/images/icons/product/search-16.gif", 30 "x16": "http://www.google.com/images/icons/product/search-16.gif",
31 "x32": "http://www.google.com/images/icons/product/search-32.gif" 31 "x32": "http://www.google.com/images/icons/product/search-32.gif"
32 }, 32 },
33 "id": "genomics:v1", 33 "id": "genomics:v1",
34 "kind": "discovery#restDescription", 34 "kind": "discovery#restDescription",
35 "name": "genomics", 35 "name": "genomics",
36 "ownerDomain": "google.com", 36 "ownerDomain": "google.com",
37 "ownerName": "Google", 37 "ownerName": "Google",
38 "parameters": { 38 "parameters": {
39 "$.xgafv": { 39 "access_token": {
40 "description": "V1 error format.", 40 "description": "OAuth access token.",
41 "enum": [
42 "1",
43 "2"
44 ],
45 "enumDescriptions": [
46 "v1 error format",
47 "v2 error format"
48 ],
49 "location": "query", 41 "location": "query",
50 "type": "string" 42 "type": "string"
51 }, 43 },
52 "callback": {
53 "description": "JSONP",
54 "location": "query",
55 "type": "string"
56 },
57 "alt": {
58 "default": "json",
59 "description": "Data format for response.",
60 "enum": [
61 "json",
62 "media",
63 "proto"
64 ],
65 "enumDescriptions": [
66 "Responses with Content-Type of application/json",
67 "Media download with context-dependent Content-Type",
68 "Responses with Content-Type of application/x-protobuf"
69 ],
70 "location": "query",
71 "type": "string"
72 },
73 "key": { 44 "key": {
74 "description": "API key. Your API key identifies your project and pr ovides you with API access, quota, and reports. Required unless you provide an O Auth 2.0 token.", 45 "description": "API key. Your API key identifies your project and pr ovides you with API access, quota, and reports. Required unless you provide an O Auth 2.0 token.",
75 "location": "query", 46 "location": "query",
76 "type": "string" 47 "type": "string"
77 }, 48 },
78 "access_token": {
79 "description": "OAuth access token.",
80 "location": "query",
81 "type": "string"
82 },
83 "quotaUser": { 49 "quotaUser": {
84 "description": "Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exc eed 40 characters.", 50 "description": "Available to use for quota purposes for server-side applications. Can be any arbitrary string assigned to a user, but should not exc eed 40 characters.",
85 "location": "query", 51 "location": "query",
86 "type": "string" 52 "type": "string"
87 }, 53 },
88 "pp": { 54 "pp": {
89 "default": "true", 55 "default": "true",
90 "description": "Pretty-print response.", 56 "description": "Pretty-print response.",
91 "location": "query", 57 "location": "query",
92 "type": "boolean" 58 "type": "boolean"
93 }, 59 },
60 "bearer_token": {
61 "description": "OAuth bearer token.",
62 "location": "query",
63 "type": "string"
64 },
94 "oauth_token": { 65 "oauth_token": {
95 "description": "OAuth 2.0 token for the current user.", 66 "description": "OAuth 2.0 token for the current user.",
96 "location": "query", 67 "location": "query",
97 "type": "string" 68 "type": "string"
98 }, 69 },
99 "bearer_token": {
100 "description": "OAuth bearer token.",
101 "location": "query",
102 "type": "string"
103 },
104 "upload_protocol": { 70 "upload_protocol": {
105 "description": "Upload protocol for media (e.g. \"raw\", \"multipart \").", 71 "description": "Upload protocol for media (e.g. \"raw\", \"multipart \").",
106 "location": "query", 72 "location": "query",
107 "type": "string" 73 "type": "string"
108 }, 74 },
109 "prettyPrint": { 75 "prettyPrint": {
110 "default": "true", 76 "default": "true",
111 "description": "Returns response with indentations and line breaks." , 77 "description": "Returns response with indentations and line breaks." ,
112 "location": "query", 78 "location": "query",
113 "type": "boolean" 79 "type": "boolean"
114 }, 80 },
81 "uploadType": {
82 "description": "Legacy upload protocol for media (e.g. \"media\", \" multipart\").",
83 "location": "query",
84 "type": "string"
85 },
115 "fields": { 86 "fields": {
116 "description": "Selector specifying which fields to include in a par tial response.", 87 "description": "Selector specifying which fields to include in a par tial response.",
117 "location": "query", 88 "location": "query",
118 "type": "string" 89 "type": "string"
119 }, 90 },
120 "uploadType": { 91 "$.xgafv": {
121 "description": "Legacy upload protocol for media (e.g. \"media\", \" multipart\").", 92 "description": "V1 error format.",
93 "enum": [
94 "1",
95 "2"
96 ],
97 "enumDescriptions": [
98 "v1 error format",
99 "v2 error format"
100 ],
101 "location": "query",
102 "type": "string"
103 },
104 "callback": {
105 "description": "JSONP",
106 "location": "query",
107 "type": "string"
108 },
109 "alt": {
110 "default": "json",
111 "description": "Data format for response.",
112 "enum": [
113 "json",
114 "media",
115 "proto"
116 ],
117 "enumDescriptions": [
118 "Responses with Content-Type of application/json",
119 "Media download with context-dependent Content-Type",
120 "Responses with Content-Type of application/x-protobuf"
121 ],
122 "location": "query", 122 "location": "query",
123 "type": "string" 123 "type": "string"
124 } 124 }
125 }, 125 },
126 "protocol": "rest", 126 "protocol": "rest",
127 "resources": { 127 "resources": {
128 "variantsets": { 128 "annotationsets": {
129 "methods": { 129 "methods": {
130 "create": { 130 "delete": {
131 "description": "Creates a new variant set.\n\nFor the defini tions of variant sets and other genomics resources, see\n[Fundamentals of Google \nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n \nThe provided variant set must have a valid `datasetId` set - all other\nfields are optional. Note that the `id` field will be ignored, as this is\nassigned by the server.", 131 "description": "Deletes an annotation set. Caller must have WRITE permission\nfor the associated annotation set.",
132 "httpMethod": "POST", 132 "httpMethod": "DELETE",
133 "id": "genomics.variantsets.create", 133 "id": "genomics.annotationsets.delete",
134 "parameterOrder": [], 134 "parameterOrder": [
135 "parameters": {}, 135 "annotationSetId"
136 "path": "v1/variantsets", 136 ],
137 "request": { 137 "parameters": {
138 "$ref": "VariantSet" 138 "annotationSetId": {
139 "description": "The ID of the annotation set to be d eleted.",
140 "location": "path",
141 "required": true,
142 "type": "string"
143 }
139 }, 144 },
145 "path": "v1/annotationsets/{annotationSetId}",
140 "response": { 146 "response": {
141 "$ref": "VariantSet" 147 "$ref": "Empty"
142 }, 148 },
143 "scopes": [ 149 "scopes": [
144 "https://www.googleapis.com/auth/cloud-platform", 150 "https://www.googleapis.com/auth/cloud-platform",
145 "https://www.googleapis.com/auth/genomics" 151 "https://www.googleapis.com/auth/genomics"
146 ] 152 ]
147 }, 153 },
148 "export": { 154 "search": {
149 "description": "Exports variant set data to an external dest ination.\n\nFor the definitions of variant sets and other genomics resources, se e\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamen tals-of-google-genomics)", 155 "description": "Searches for annotation sets that match the given criteria. Annotation sets\nare returned in an unspecified order. This orde r is consistent, such that\ntwo queries for the same content (regardless of page size) yield annotation\nsets in the same order across their respective streams of paginated\nresponses. Caller must have READ permission for the queried datase ts.",
150 "httpMethod": "POST", 156 "httpMethod": "POST",
151 "id": "genomics.variantsets.export", 157 "id": "genomics.annotationsets.search",
152 "parameterOrder": [ 158 "parameterOrder": [],
153 "variantSetId" 159 "parameters": {},
154 ], 160 "path": "v1/annotationsets/search",
155 "parameters": {
156 "variantSetId": {
157 "description": "Required. The ID of the variant set that contains variant data which\nshould be exported. The caller must have READ access to this variant set.",
158 "location": "path",
159 "required": true,
160 "type": "string"
161 }
162 },
163 "path": "v1/variantsets/{variantSetId}:export",
164 "request": { 161 "request": {
165 "$ref": "ExportVariantSetRequest" 162 "$ref": "SearchAnnotationSetsRequest"
166 }, 163 },
167 "response": { 164 "response": {
168 "$ref": "Operation" 165 "$ref": "SearchAnnotationSetsResponse"
169 },
170 "scopes": [
171 "https://www.googleapis.com/auth/bigquery",
172 "https://www.googleapis.com/auth/cloud-platform",
173 "https://www.googleapis.com/auth/genomics"
174 ]
175 },
176 "search": {
177 "description": "Returns a list of all variant sets matching search criteria.\n\nFor the definitions of variant sets and other genomics resou rces, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/ fundamentals-of-google-genomics)\n\nImplements\n[GlobalAllianceApi.searchVariant Sets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/varia ntmethods.avdl#L49).",
178 "httpMethod": "POST",
179 "id": "genomics.variantsets.search",
180 "parameterOrder": [],
181 "parameters": {},
182 "path": "v1/variantsets/search",
183 "request": {
184 "$ref": "SearchVariantSetsRequest"
185 },
186 "response": {
187 "$ref": "SearchVariantSetsResponse"
188 }, 166 },
189 "scopes": [ 167 "scopes": [
190 "https://www.googleapis.com/auth/cloud-platform", 168 "https://www.googleapis.com/auth/cloud-platform",
191 "https://www.googleapis.com/auth/genomics", 169 "https://www.googleapis.com/auth/genomics",
192 "https://www.googleapis.com/auth/genomics.readonly" 170 "https://www.googleapis.com/auth/genomics.readonly"
193 ] 171 ]
194 }, 172 },
195 "get": { 173 "get": {
196 "description": "Gets a variant set by ID.\n\nFor the definit ions of variant sets and other genomics resources, see\n[Fundamentals of Google\ nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)", 174 "description": "Gets an annotation set. Caller must have REA D permission for\nthe associated dataset.",
197 "httpMethod": "GET", 175 "httpMethod": "GET",
198 "id": "genomics.variantsets.get", 176 "id": "genomics.annotationsets.get",
199 "parameterOrder": [ 177 "parameterOrder": [
200 "variantSetId" 178 "annotationSetId"
201 ], 179 ],
202 "parameters": { 180 "parameters": {
203 "variantSetId": { 181 "annotationSetId": {
204 "description": "Required. The ID of the variant set. ", 182 "description": "The ID of the annotation set to be r etrieved.",
205 "location": "path", 183 "location": "path",
206 "required": true, 184 "required": true,
207 "type": "string" 185 "type": "string"
208 } 186 }
209 }, 187 },
210 "path": "v1/variantsets/{variantSetId}", 188 "path": "v1/annotationsets/{annotationSetId}",
211 "response": { 189 "response": {
212 "$ref": "VariantSet" 190 "$ref": "AnnotationSet"
213 }, 191 },
214 "scopes": [ 192 "scopes": [
215 "https://www.googleapis.com/auth/cloud-platform", 193 "https://www.googleapis.com/auth/cloud-platform",
216 "https://www.googleapis.com/auth/genomics", 194 "https://www.googleapis.com/auth/genomics",
217 "https://www.googleapis.com/auth/genomics.readonly" 195 "https://www.googleapis.com/auth/genomics.readonly"
218 ] 196 ]
219 }, 197 },
220 "patch": { 198 "update": {
221 "description": "Updates a variant set using patch semantics. \n\nFor the definitions of variant sets and other genomics resources, see\n[Fund amentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of- google-genomics)", 199 "description": "Updates an annotation set. The update must r espect all mutability\nrestrictions and other invariants described on the annota tion set resource.\nCaller must have WRITE permission for the associated dataset .",
222 "httpMethod": "PATCH", 200 "httpMethod": "PUT",
223 "id": "genomics.variantsets.patch", 201 "id": "genomics.annotationsets.update",
224 "parameterOrder": [ 202 "parameterOrder": [
225 "variantSetId" 203 "annotationSetId"
226 ], 204 ],
227 "parameters": { 205 "parameters": {
228 "updateMask": { 206 "updateMask": {
229 "description": "An optional mask specifying which fi elds to update. Supported fields:\n\n* metadata.\n* name.\n* description.\n\nLea ving `updateMask` unset is equivalent to specifying all mutable\nfields.", 207 "description": "An optional mask specifying which fi elds to update. Mutable fields are\nname,\nsource_uri, and\ninfo. If unspecified , all\nmutable fields will be updated.",
230 "format": "google-fieldmask", 208 "format": "google-fieldmask",
231 "location": "query", 209 "location": "query",
232 "type": "string" 210 "type": "string"
233 }, 211 },
234 "variantSetId": { 212 "annotationSetId": {
235 "description": "The ID of the variant to be updated (must already exist).", 213 "description": "The ID of the annotation set to be u pdated.",
236 "location": "path", 214 "location": "path",
237 "required": true, 215 "required": true,
238 "type": "string" 216 "type": "string"
239 } 217 }
240 }, 218 },
241 "path": "v1/variantsets/{variantSetId}", 219 "path": "v1/annotationsets/{annotationSetId}",
242 "request": { 220 "request": {
243 "$ref": "VariantSet" 221 "$ref": "AnnotationSet"
244 }, 222 },
245 "response": { 223 "response": {
246 "$ref": "VariantSet" 224 "$ref": "AnnotationSet"
247 }, 225 },
248 "scopes": [ 226 "scopes": [
249 "https://www.googleapis.com/auth/cloud-platform", 227 "https://www.googleapis.com/auth/cloud-platform",
250 "https://www.googleapis.com/auth/genomics" 228 "https://www.googleapis.com/auth/genomics"
251 ] 229 ]
252 }, 230 },
253 "delete": { 231 "create": {
254 "description": "Deletes a variant set including all variants , call sets, and calls within.\nThis is not reversible.\n\nFor the definitions o f variant sets and other genomics resources, see\n[Fundamentals of Google\nGenom ics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)", 232 "description": "Creates a new annotation set. Caller must ha ve WRITE permission for the\nassociated dataset.\n\nThe following fields are req uired:\n\n * datasetId\n * referenceSetId\n\nAll other fields may be optionall y specified, unless documented as being\nserver-generated (for example, the `id` field).",
255 "httpMethod": "DELETE", 233 "httpMethod": "POST",
256 "id": "genomics.variantsets.delete", 234 "id": "genomics.annotationsets.create",
257 "parameterOrder": [ 235 "parameterOrder": [],
258 "variantSetId" 236 "parameters": {},
259 ], 237 "path": "v1/annotationsets",
260 "parameters": { 238 "request": {
261 "variantSetId": { 239 "$ref": "AnnotationSet"
262 "description": "The ID of the variant set to be dele ted.",
263 "location": "path",
264 "required": true,
265 "type": "string"
266 }
267 }, 240 },
268 "path": "v1/variantsets/{variantSetId}",
269 "response": { 241 "response": {
270 "$ref": "Empty" 242 "$ref": "AnnotationSet"
271 }, 243 },
272 "scopes": [ 244 "scopes": [
273 "https://www.googleapis.com/auth/cloud-platform", 245 "https://www.googleapis.com/auth/cloud-platform",
274 "https://www.googleapis.com/auth/genomics" 246 "https://www.googleapis.com/auth/genomics"
275 ] 247 ]
276 } 248 }
277 } 249 }
278 }, 250 },
279 "annotations": { 251 "variants": {
280 "methods": { 252 "methods": {
281 "delete": {
282 "description": "Deletes an annotation. Caller must have WRIT E permission for\nthe associated annotation set.",
283 "httpMethod": "DELETE",
284 "id": "genomics.annotations.delete",
285 "parameterOrder": [
286 "annotationId"
287 ],
288 "parameters": {
289 "annotationId": {
290 "description": "The ID of the annotation to be delet ed.",
291 "location": "path",
292 "required": true,
293 "type": "string"
294 }
295 },
296 "path": "v1/annotations/{annotationId}",
297 "response": {
298 "$ref": "Empty"
299 },
300 "scopes": [
301 "https://www.googleapis.com/auth/cloud-platform",
302 "https://www.googleapis.com/auth/genomics"
303 ]
304 },
305 "create": { 253 "create": {
306 "description": "Creates a new annotation. Caller must have W RITE permission\nfor the associated annotation set.\n\nThe following fields are required:\n\n* annotationSetId\n* referenceName or\n referenceId\n\n### Transcr ipts\n\nFor annotations of type TRANSCRIPT, the following fields of\ntranscript must be provided:\n\n* exons.start\n* exons.end\n\nAll other fields may be optio nally specified, unless documented as being\nserver-generated (for example, the `id` field). The annotated\nrange must be no longer than 100Mbp (mega base pairs ). See the\nAnnotation resource\nfor additional restrictions on each field.", 254 "description": "Creates a new variant.\n\nFor the definition s of variants and other genomics resources, see\n[Fundamentals of Google\nGenomi cs](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
307 "httpMethod": "POST", 255 "httpMethod": "POST",
308 "id": "genomics.annotations.create", 256 "id": "genomics.variants.create",
309 "parameterOrder": [], 257 "parameterOrder": [],
310 "parameters": {}, 258 "parameters": {},
311 "path": "v1/annotations", 259 "path": "v1/variants",
312 "request": { 260 "request": {
313 "$ref": "Annotation" 261 "$ref": "Variant"
314 }, 262 },
315 "response": { 263 "response": {
316 "$ref": "Annotation" 264 "$ref": "Variant"
317 },
318 "scopes": [
319 "https://www.googleapis.com/auth/cloud-platform",
320 "https://www.googleapis.com/auth/genomics"
321 ]
322 },
323 "batchCreate": {
324 "description": "Creates one or more new annotations atomical ly. All annotations must\nbelong to the same annotation set. Caller must have WR ITE\npermission for this annotation set. For optimal performance, batch\npositio nally adjacent annotations together.\n\nIf the request has a systemic issue, suc h as an attempt to write to\nan inaccessible annotation set, the entire RPC will fail accordingly. For\nlesser data issues, when possible an error will be isola ted to the\ncorresponding batch entry in the response; the remaining well formed \nannotations will be created normally.\n\nFor details on the requirements for e ach individual annotation resource,\nsee\nCreateAnnotation.",
325 "httpMethod": "POST",
326 "id": "genomics.annotations.batchCreate",
327 "parameterOrder": [],
328 "parameters": {},
329 "path": "v1/annotations:batchCreate",
330 "request": {
331 "$ref": "BatchCreateAnnotationsRequest"
332 },
333 "response": {
334 "$ref": "BatchCreateAnnotationsResponse"
335 }, 265 },
336 "scopes": [ 266 "scopes": [
337 "https://www.googleapis.com/auth/cloud-platform", 267 "https://www.googleapis.com/auth/cloud-platform",
338 "https://www.googleapis.com/auth/genomics" 268 "https://www.googleapis.com/auth/genomics"
339 ] 269 ]
340 }, 270 },
341 "search": { 271 "search": {
342 "description": "Searches for annotations that match the give n criteria. Results are\nordered by genomic coordinate (by reference sequence, t hen position).\nAnnotations with equivalent genomic coordinates are returned in an\nunspecified order. This order is consistent, such that two queries for the\n same content (regardless of page size) yield annotations in the same order\nacro ss their respective streams of paginated responses. Caller must have\nREAD permi ssion for the queried annotation sets.", 272 "description": "Gets a list of variants matching the criteri a.\n\nFor the definitions of variants and other genomics resources, see\n[Fundam entals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-go ogle-genomics)\n\nImplements\n[GlobalAllianceApi.searchVariants](https://github. com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L126). ",
343 "httpMethod": "POST", 273 "httpMethod": "POST",
344 "id": "genomics.annotations.search", 274 "id": "genomics.variants.search",
345 "parameterOrder": [], 275 "parameterOrder": [],
346 "parameters": {}, 276 "parameters": {},
347 "path": "v1/annotations/search", 277 "path": "v1/variants/search",
348 "request": { 278 "request": {
349 "$ref": "SearchAnnotationsRequest" 279 "$ref": "SearchVariantsRequest"
350 }, 280 },
351 "response": { 281 "response": {
352 "$ref": "SearchAnnotationsResponse" 282 "$ref": "SearchVariantsResponse"
353 }, 283 },
354 "scopes": [ 284 "scopes": [
355 "https://www.googleapis.com/auth/cloud-platform", 285 "https://www.googleapis.com/auth/cloud-platform",
356 "https://www.googleapis.com/auth/genomics", 286 "https://www.googleapis.com/auth/genomics",
357 "https://www.googleapis.com/auth/genomics.readonly" 287 "https://www.googleapis.com/auth/genomics.readonly"
358 ] 288 ]
359 }, 289 },
360 "get": { 290 "get": {
361 "description": "Gets an annotation. Caller must have READ pe rmission\nfor the associated annotation set.", 291 "description": "Gets a variant by ID.\n\nFor the definitions of variants and other genomics resources, see\n[Fundamentals of Google\nGenomic s](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
362 "httpMethod": "GET", 292 "httpMethod": "GET",
363 "id": "genomics.annotations.get", 293 "id": "genomics.variants.get",
364 "parameterOrder": [ 294 "parameterOrder": [
365 "annotationId" 295 "variantId"
366 ], 296 ],
367 "parameters": { 297 "parameters": {
368 "annotationId": { 298 "variantId": {
369 "description": "The ID of the annotation to be retri eved.", 299 "description": "The ID of the variant.",
370 "location": "path", 300 "location": "path",
371 "required": true, 301 "required": true,
372 "type": "string" 302 "type": "string"
373 } 303 }
374 }, 304 },
375 "path": "v1/annotations/{annotationId}", 305 "path": "v1/variants/{variantId}",
376 "response": { 306 "response": {
377 "$ref": "Annotation" 307 "$ref": "Variant"
378 }, 308 },
379 "scopes": [ 309 "scopes": [
380 "https://www.googleapis.com/auth/cloud-platform", 310 "https://www.googleapis.com/auth/cloud-platform",
381 "https://www.googleapis.com/auth/genomics", 311 "https://www.googleapis.com/auth/genomics",
382 "https://www.googleapis.com/auth/genomics.readonly" 312 "https://www.googleapis.com/auth/genomics.readonly"
383 ] 313 ]
384 }, 314 },
385 "update": { 315 "patch": {
386 "description": "Updates an annotation. Caller must have\nWRI TE permission for the associated dataset.", 316 "description": "Updates a variant.\n\nFor the definitions of variants and other genomics resources, see\n[Fundamentals of Google\nGenomics]( https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nThis metho d supports patch semantics. Returns the modified variant without\nits calls.",
387 "httpMethod": "PUT", 317 "httpMethod": "PATCH",
388 "id": "genomics.annotations.update", 318 "id": "genomics.variants.patch",
389 "parameterOrder": [ 319 "parameterOrder": [
390 "annotationId" 320 "variantId"
391 ], 321 ],
392 "parameters": { 322 "parameters": {
393 "updateMask": { 323 "updateMask": {
394 "description": "An optional mask specifying which fi elds to update. Mutable fields are\nname,\nvariant,\ntranscript, and\ninfo. If u nspecified, all mutable\nfields will be updated.", 324 "description": "An optional mask specifying which fi elds to update. At this time, mutable\nfields are names and\ninfo. Acceptable va lues are \"names\" and\n\"info\". If unspecified, all mutable fields will be upd ated.",
395 "format": "google-fieldmask", 325 "format": "google-fieldmask",
396 "location": "query", 326 "location": "query",
397 "type": "string" 327 "type": "string"
398 }, 328 },
399 "annotationId": { 329 "variantId": {
400 "description": "The ID of the annotation to be updat ed.", 330 "description": "The ID of the variant to be updated. ",
401 "location": "path", 331 "location": "path",
402 "required": true, 332 "required": true,
403 "type": "string" 333 "type": "string"
404 } 334 }
405 }, 335 },
406 "path": "v1/annotations/{annotationId}", 336 "path": "v1/variants/{variantId}",
407 "request": { 337 "request": {
408 "$ref": "Annotation" 338 "$ref": "Variant"
409 }, 339 },
410 "response": { 340 "response": {
411 "$ref": "Annotation" 341 "$ref": "Variant"
412 }, 342 },
413 "scopes": [ 343 "scopes": [
414 "https://www.googleapis.com/auth/cloud-platform", 344 "https://www.googleapis.com/auth/cloud-platform",
415 "https://www.googleapis.com/auth/genomics" 345 "https://www.googleapis.com/auth/genomics"
416 ] 346 ]
417 } 347 },
418 } 348 "merge": {
419 }, 349 "description": "Merges the given variants with existing vari ants.\n\nFor the definitions of variants and other genomics resources, see\n[Fun damentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of -google-genomics)\n\nEach variant will be\nmerged with an existing variant that matches its reference sequence,\nstart, end, reference bases, and alternative ba ses. If no such variant\nexists, a new one will be created.\n\nWhen variants are merged, the call information from the new variant\nis added to the existing var iant. Variant info fields are merged as\nspecified in the\ninfoMergeConfig\nfiel d of the MergeVariantsRequest.\n\nPlease exercise caution when using this method ! It is easy to introduce\nmistakes in existing variants and difficult to back out of them. For\nexample,\nsuppose you were trying to merge a new variant with an existing one and\nboth\nvariants contain calls that belong to callsets with the same callset ID.\n\n // Existing variant - irrelevant fields trimmed for clarity\n {\n \"variantSetId\": \"10473108253681171589\",\n \"r eferenceName\": \"1\",\n \"start\": \"10582\",\n \"referenceBases\ ": \"G\",\n \"alternateBases\": [\n \"A\"\n ],\n \"calls\": [\n {\n \"callSetId\": \"10473108253681171 589-0\",\n \"callSetName\": \"CALLSET0\",\n \"geno type\": [\n 0,\n 1\n ],\n }\n ]\n }\n\n // New variant with conflicting call inform ation\n {\n \"variantSetId\": \"10473108253681171589\",\n \"ref erenceName\": \"1\",\n \"start\": \"10582\",\n \"referenceBases\": \"G\",\n \"alternateBases\": [\n \"A\"\n ],\n \ "calls\": [\n {\n \"callSetId\": \"1047310825368117158 9-0\",\n \"callSetName\": \"CALLSET0\",\n \"genoty pe\": [\n 1,\n 1\n ],\n }\n ]\n }\n\nThe resulting merged variant would overwrite the existing calls with those\nfrom the new variant:\n\n {\n \"variantSetI d\": \"10473108253681171589\",\n \"referenceName\": \"1\",\n \"sta rt\": \"10582\",\n \"referenceBases\": \"G\",\n \"alternateBases\" : [\n \"A\"\n ],\n \"calls\": [\n {\n \"callSetId\": \"10473108253681171589-0\",\n \"callSetNa me\": \"CALLSET0\",\n \"genotype\": [\n 1,\n 1\n ],\n }\n ]\n }\n\nThis may be the desired outcome, but it is up to the user to determine if\nif that i s indeed the case.",
420 "operations": {
421 "methods": {
422 "cancel": {
423 "description": "Starts asynchronous cancellation on a long-r unning operation. The server makes a best effort to cancel the operation, but su ccess is not guaranteed. Clients may use Operations.GetOperation or Operations.L istOperations to check whether the cancellation succeeded or the operation compl eted despite cancellation.",
424 "httpMethod": "POST", 350 "httpMethod": "POST",
425 "id": "genomics.operations.cancel", 351 "id": "genomics.variants.merge",
426 "parameterOrder": [ 352 "parameterOrder": [],
427 "name" 353 "parameters": {},
428 ], 354 "path": "v1/variants:merge",
429 "parameters": {
430 "name": {
431 "description": "The name of the operation resource t o be cancelled.",
432 "location": "path",
433 "pattern": "^operations/.+$",
434 "required": true,
435 "type": "string"
436 }
437 },
438 "path": "v1/{+name}:cancel",
439 "request": { 355 "request": {
440 "$ref": "CancelOperationRequest" 356 "$ref": "MergeVariantsRequest"
441 }, 357 },
442 "response": { 358 "response": {
443 "$ref": "Empty" 359 "$ref": "Empty"
444 }, 360 },
445 "scopes": [ 361 "scopes": [
446 "https://www.googleapis.com/auth/cloud-platform", 362 "https://www.googleapis.com/auth/cloud-platform",
447 "https://www.googleapis.com/auth/genomics" 363 "https://www.googleapis.com/auth/genomics"
448 ] 364 ]
449 }, 365 },
450 "get": { 366 "import": {
451 "description": "Gets the latest state of a long-running oper ation. Clients can use this\nmethod to poll the operation result at intervals a s recommended by the API\nservice.", 367 "description": "Creates variant data by asynchronously impor ting the provided information.\n\nFor the definitions of variant sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google .com/genomics/fundamentals-of-google-genomics)\n\nThe variants for import will b e merged with any existing variant that\nmatches its reference sequence, start, end, reference bases, and\nalternative bases. If no such variant exists, a new o ne will be created.\n\nWhen variants are merged, the call information from the n ew variant\nis added to the existing variant, and Variant info fields are merged \nas specified in\ninfoMergeConfig.\nAs a special case, for single-sample VCF fi les, QUAL and FILTER fields will\nbe moved to the call level; these are sometime s interpreted in a\ncall-specific context.\nImported VCF headers are appended to the metadata already in a variant set.",
452 "httpMethod": "GET", 368 "httpMethod": "POST",
453 "id": "genomics.operations.get", 369 "id": "genomics.variants.import",
454 "parameterOrder": [ 370 "parameterOrder": [],
455 "name" 371 "parameters": {},
456 ], 372 "path": "v1/variants:import",
457 "parameters": { 373 "request": {
458 "name": { 374 "$ref": "ImportVariantsRequest"
459 "description": "The name of the operation resource." ,
460 "location": "path",
461 "pattern": "^operations/.+$",
462 "required": true,
463 "type": "string"
464 }
465 }, 375 },
466 "path": "v1/{+name}",
467 "response": { 376 "response": {
468 "$ref": "Operation" 377 "$ref": "Operation"
469 }, 378 },
470 "scopes": [ 379 "scopes": [
471 "https://www.googleapis.com/auth/cloud-platform", 380 "https://www.googleapis.com/auth/cloud-platform",
381 "https://www.googleapis.com/auth/devstorage.read_write",
472 "https://www.googleapis.com/auth/genomics" 382 "https://www.googleapis.com/auth/genomics"
473 ] 383 ]
474 }, 384 },
475 "list": { 385 "delete": {
476 "description": "Lists operations that match the specified fi lter in the request.", 386 "description": "Deletes a variant.\n\nFor the definitions of variants and other genomics resources, see\n[Fundamentals of Google\nGenomics]( https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
477 "httpMethod": "GET", 387 "httpMethod": "DELETE",
478 "id": "genomics.operations.list", 388 "id": "genomics.variants.delete",
479 "parameterOrder": [ 389 "parameterOrder": [
480 "name" 390 "variantId"
481 ], 391 ],
482 "parameters": { 392 "parameters": {
483 "filter": { 393 "variantId": {
484 "description": "A string for filtering Operations.\n The following filter fields are supported&#58;\n\n* projectId&#58; Required. Cor responds to\n OperationMetadata.projectId.\n* createTime&#58; The time this job was created, in seconds from the\n [epoch](http://en.wikipedia.org/wiki/Unix_t ime). Can use `>=` and/or `<=`\n operators.\n* status&#58; Can be `RUNNING`, `S UCCESS`, `FAILURE`, or `CANCELED`. Only\n one status may be specified.\n* label s.key where key is a label key.\n\nExamples&#58;\n\n* `projectId = my-project AN D createTime >= 1432140000`\n* `projectId = my-project AND createTime >= 1432140 000 AND createTime <= 1432150000 AND status = RUNNING`\n* `projectId = my-projec t AND labels.color = *`\n* `projectId = my-project AND labels.color = red`", 394 "description": "The ID of the variant to be deleted. ",
485 "location": "query",
486 "type": "string"
487 },
488 "pageToken": {
489 "description": "The standard list page token.",
490 "location": "query",
491 "type": "string"
492 },
493 "name": {
494 "description": "The name of the operation's parent r esource.",
495 "location": "path", 395 "location": "path",
496 "pattern": "^operations$",
497 "required": true, 396 "required": true,
498 "type": "string" 397 "type": "string"
499 },
500 "pageSize": {
501 "description": "The maximum number of results to ret urn. If unspecified, defaults to\n256. The maximum value is 2048.",
502 "format": "int32",
503 "location": "query",
504 "type": "integer"
505 } 398 }
506 }, 399 },
507 "path": "v1/{+name}", 400 "path": "v1/variants/{variantId}",
508 "response": { 401 "response": {
509 "$ref": "ListOperationsResponse" 402 "$ref": "Empty"
510 }, 403 },
511 "scopes": [ 404 "scopes": [
512 "https://www.googleapis.com/auth/cloud-platform", 405 "https://www.googleapis.com/auth/cloud-platform",
513 "https://www.googleapis.com/auth/genomics" 406 "https://www.googleapis.com/auth/genomics"
514 ] 407 ]
515 } 408 }
516 } 409 }
517 }, 410 },
518 "referencesets": { 411 "references": {
519 "methods": { 412 "methods": {
520 "search": { 413 "search": {
521 "description": "Searches for reference sets which match the given criteria.\n\nFor the definitions of references and other genomics resource s, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fun damentals-of-google-genomics)\n\nImplements\n[GlobalAllianceApi.searchReferenceS ets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/refere ncemethods.avdl#L71)", 414 "description": "Searches for references which match the give n criteria.\n\nFor the definitions of references and other genomics resources, s ee\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundame ntals-of-google-genomics)\n\nImplements\n[GlobalAllianceApi.searchReferences](ht tps://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemeth ods.avdl#L146).",
522 "httpMethod": "POST", 415 "httpMethod": "POST",
523 "id": "genomics.referencesets.search", 416 "id": "genomics.references.search",
524 "parameterOrder": [], 417 "parameterOrder": [],
525 "parameters": {}, 418 "parameters": {},
526 "path": "v1/referencesets/search", 419 "path": "v1/references/search",
527 "request": { 420 "request": {
528 "$ref": "SearchReferenceSetsRequest" 421 "$ref": "SearchReferencesRequest"
529 }, 422 },
530 "response": { 423 "response": {
531 "$ref": "SearchReferenceSetsResponse" 424 "$ref": "SearchReferencesResponse"
532 }, 425 },
533 "scopes": [ 426 "scopes": [
534 "https://www.googleapis.com/auth/cloud-platform", 427 "https://www.googleapis.com/auth/cloud-platform",
535 "https://www.googleapis.com/auth/genomics", 428 "https://www.googleapis.com/auth/genomics",
536 "https://www.googleapis.com/auth/genomics.readonly" 429 "https://www.googleapis.com/auth/genomics.readonly"
537 ] 430 ]
538 }, 431 },
539 "get": { 432 "get": {
540 "description": "Gets a reference set.\n\nFor the definitions of references and other genomics resources, see\n[Fundamentals of Google\nGenom ics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nImple ments\n[GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob /v0.5.1/src/main/resources/avro/referencemethods.avdl#L83).", 433 "description": "Gets a reference.\n\nFor the definitions of references and other genomics resources, see\n[Fundamentals of Google\nGenomics] (https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nImplement s\n[GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob/v0.5.1 /src/main/resources/avro/referencemethods.avdl#L158).",
541 "httpMethod": "GET", 434 "httpMethod": "GET",
542 "id": "genomics.referencesets.get", 435 "id": "genomics.references.get",
543 "parameterOrder": [ 436 "parameterOrder": [
544 "referenceSetId" 437 "referenceId"
545 ], 438 ],
546 "parameters": { 439 "parameters": {
547 "referenceSetId": { 440 "referenceId": {
548 "description": "The ID of the reference set.", 441 "description": "The ID of the reference.",
549 "location": "path", 442 "location": "path",
550 "required": true, 443 "required": true,
551 "type": "string" 444 "type": "string"
552 } 445 }
553 }, 446 },
554 "path": "v1/referencesets/{referenceSetId}", 447 "path": "v1/references/{referenceId}",
555 "response": { 448 "response": {
556 "$ref": "ReferenceSet" 449 "$ref": "Reference"
557 }, 450 },
558 "scopes": [ 451 "scopes": [
559 "https://www.googleapis.com/auth/cloud-platform", 452 "https://www.googleapis.com/auth/cloud-platform",
560 "https://www.googleapis.com/auth/genomics", 453 "https://www.googleapis.com/auth/genomics",
561 "https://www.googleapis.com/auth/genomics.readonly" 454 "https://www.googleapis.com/auth/genomics.readonly"
562 ] 455 ]
563 } 456 }
457 },
458 "resources": {
459 "bases": {
460 "methods": {
461 "list": {
462 "description": "Lists the bases in a reference, opti onally restricted to a range.\n\nFor the definitions of references and other gen omics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.co m/genomics/fundamentals-of-google-genomics)\n\nImplements\n[GlobalAllianceApi.ge tReferenceBases](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources /avro/referencemethods.avdl#L221).",
463 "httpMethod": "GET",
464 "id": "genomics.references.bases.list",
465 "parameterOrder": [
466 "referenceId"
467 ],
468 "parameters": {
469 "pageSize": {
470 "description": "The maximum number of bases to return in a single page. If unspecified,\ndefaults to 200Kbp (kilo base pairs ). The maximum value is 10Mbp (mega base\npairs).",
471 "format": "int32",
472 "location": "query",
473 "type": "integer"
474 },
475 "start": {
476 "description": "The start position (0-based) of this query. Defaults to 0.",
477 "format": "int64",
478 "location": "query",
479 "type": "string"
480 },
481 "referenceId": {
482 "description": "The ID of the reference.",
483 "location": "path",
484 "required": true,
485 "type": "string"
486 },
487 "end": {
488 "description": "The end position (0-based, e xclusive) of this query. Defaults to the length\nof this reference.",
489 "format": "int64",
490 "location": "query",
491 "type": "string"
492 },
493 "pageToken": {
494 "description": "The continuation token, whic h is used to page through large result sets.\nTo get the next page of results, s et this parameter to the value of\n`nextPageToken` from the previous response.",
495 "location": "query",
496 "type": "string"
497 }
498 },
499 "path": "v1/references/{referenceId}/bases",
500 "response": {
501 "$ref": "ListBasesResponse"
502 },
503 "scopes": [
504 "https://www.googleapis.com/auth/cloud-platform" ,
505 "https://www.googleapis.com/auth/genomics",
506 "https://www.googleapis.com/auth/genomics.readon ly"
507 ]
508 }
509 }
510 }
564 } 511 }
565 }, 512 },
566 "callsets": { 513 "datasets": {
567 "methods": { 514 "methods": {
568 "delete": { 515 "patch": {
569 "description": "Deletes a call set.\n\nFor the definitions o f call sets and other genomics resources, see\n[Fundamentals of Google\nGenomics ](https://cloud.google.com/genomics/fundamentals-of-google-genomics)", 516 "description": "Updates a dataset.\n\nFor the definitions of datasets and other genomics resources, see\n[Fundamentals of Google\nGenomics]( https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nThis metho d supports patch semantics.",
570 "httpMethod": "DELETE", 517 "httpMethod": "PATCH",
571 "id": "genomics.callsets.delete", 518 "id": "genomics.datasets.patch",
572 "parameterOrder": [ 519 "parameterOrder": [
573 "callSetId" 520 "datasetId"
574 ], 521 ],
575 "parameters": { 522 "parameters": {
576 "callSetId": { 523 "datasetId": {
577 "description": "The ID of the call set to be deleted .", 524 "description": "The ID of the dataset to be updated. ",
578 "location": "path", 525 "location": "path",
579 "required": true, 526 "required": true,
580 "type": "string" 527 "type": "string"
528 },
529 "updateMask": {
530 "description": "An optional mask specifying which fi elds to update. At this time, the only\nmutable field is name. The only\naccepta ble value is \"name\". If unspecified, all mutable fields will be\nupdated.",
531 "format": "google-fieldmask",
532 "location": "query",
533 "type": "string"
581 } 534 }
582 }, 535 },
583 "path": "v1/callsets/{callSetId}", 536 "path": "v1/datasets/{datasetId}",
537 "request": {
538 "$ref": "Dataset"
539 },
584 "response": { 540 "response": {
585 "$ref": "Empty" 541 "$ref": "Dataset"
586 }, 542 },
587 "scopes": [ 543 "scopes": [
588 "https://www.googleapis.com/auth/cloud-platform", 544 "https://www.googleapis.com/auth/cloud-platform",
589 "https://www.googleapis.com/auth/genomics" 545 "https://www.googleapis.com/auth/genomics"
590 ] 546 ]
591 }, 547 },
592 "search": {
593 "description": "Gets a list of call sets matching the criter ia.\n\nFor the definitions of call sets and other genomics resources, see\n[Fund amentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of- google-genomics)\n\nImplements\n[GlobalAllianceApi.searchCallSets](https://githu b.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L178 ).",
594 "httpMethod": "POST",
595 "id": "genomics.callsets.search",
596 "parameterOrder": [],
597 "parameters": {},
598 "path": "v1/callsets/search",
599 "request": {
600 "$ref": "SearchCallSetsRequest"
601 },
602 "response": {
603 "$ref": "SearchCallSetsResponse"
604 },
605 "scopes": [
606 "https://www.googleapis.com/auth/cloud-platform",
607 "https://www.googleapis.com/auth/genomics",
608 "https://www.googleapis.com/auth/genomics.readonly"
609 ]
610 },
611 "get": { 548 "get": {
612 "description": "Gets a call set by ID.\n\nFor the definition s of call sets and other genomics resources, see\n[Fundamentals of Google\nGenom ics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)", 549 "description": "Gets a dataset by ID.\n\nFor the definitions of datasets and other genomics resources, see\n[Fundamentals of Google\nGenomic s](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
613 "httpMethod": "GET", 550 "httpMethod": "GET",
614 "id": "genomics.callsets.get", 551 "id": "genomics.datasets.get",
615 "parameterOrder": [ 552 "parameterOrder": [
616 "callSetId" 553 "datasetId"
617 ], 554 ],
618 "parameters": { 555 "parameters": {
619 "callSetId": { 556 "datasetId": {
620 "description": "The ID of the call set.", 557 "description": "The ID of the dataset.",
621 "location": "path", 558 "location": "path",
622 "required": true, 559 "required": true,
623 "type": "string" 560 "type": "string"
624 } 561 }
625 }, 562 },
626 "path": "v1/callsets/{callSetId}", 563 "path": "v1/datasets/{datasetId}",
627 "response": { 564 "response": {
628 "$ref": "CallSet" 565 "$ref": "Dataset"
629 }, 566 },
630 "scopes": [ 567 "scopes": [
631 "https://www.googleapis.com/auth/cloud-platform", 568 "https://www.googleapis.com/auth/cloud-platform",
632 "https://www.googleapis.com/auth/genomics", 569 "https://www.googleapis.com/auth/genomics",
633 "https://www.googleapis.com/auth/genomics.readonly" 570 "https://www.googleapis.com/auth/genomics.readonly"
634 ] 571 ]
635 }, 572 },
636 "patch": { 573 "undelete": {
637 "description": "Updates a call set.\n\nFor the definitions o f call sets and other genomics resources, see\n[Fundamentals of Google\nGenomics ](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nThis met hod supports patch semantics.", 574 "description": "Undeletes a dataset by restoring a dataset w hich was deleted via this API.\n\nFor the definitions of datasets and other geno mics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com /genomics/fundamentals-of-google-genomics)\n\nThis operation is only possible fo r a week after the deletion occurred.",
638 "httpMethod": "PATCH", 575 "httpMethod": "POST",
639 "id": "genomics.callsets.patch", 576 "id": "genomics.datasets.undelete",
640 "parameterOrder": [ 577 "parameterOrder": [
641 "callSetId" 578 "datasetId"
642 ], 579 ],
643 "parameters": { 580 "parameters": {
644 "updateMask": { 581 "datasetId": {
645 "description": "An optional mask specifying which fi elds to update. At this time, the only\nmutable field is name. The only\naccepta ble value is \"name\". If unspecified, all mutable fields will be\nupdated.", 582 "description": "The ID of the dataset to be undelete d.",
646 "format": "google-fieldmask",
647 "location": "query",
648 "type": "string"
649 },
650 "callSetId": {
651 "description": "The ID of the call set to be updated .",
652 "location": "path", 583 "location": "path",
653 "required": true, 584 "required": true,
654 "type": "string" 585 "type": "string"
655 } 586 }
656 }, 587 },
657 "path": "v1/callsets/{callSetId}", 588 "path": "v1/datasets/{datasetId}:undelete",
658 "request": { 589 "request": {
659 "$ref": "CallSet" 590 "$ref": "UndeleteDatasetRequest"
660 }, 591 },
661 "response": { 592 "response": {
662 "$ref": "CallSet" 593 "$ref": "Dataset"
663 }, 594 },
664 "scopes": [ 595 "scopes": [
665 "https://www.googleapis.com/auth/cloud-platform", 596 "https://www.googleapis.com/auth/cloud-platform",
666 "https://www.googleapis.com/auth/genomics" 597 "https://www.googleapis.com/auth/genomics"
667 ] 598 ]
668 }, 599 },
669 "create": { 600 "testIamPermissions": {
670 "description": "Creates a new call set.\n\nFor the definitio ns of call sets and other genomics resources, see\n[Fundamentals of Google\nGeno mics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)", 601 "description": "Returns permissions that a caller has on the specified resource.\nSee <a href=\"/iam/docs/managing-policies#testing_permissi ons\">Testing\nPermissions</a> for more information.\n\nFor the definitions of d atasets and other genomics resources, see\n[Fundamentals of Google\nGenomics](ht tps://cloud.google.com/genomics/fundamentals-of-google-genomics)",
671 "httpMethod": "POST", 602 "httpMethod": "POST",
672 "id": "genomics.callsets.create", 603 "id": "genomics.datasets.testIamPermissions",
673 "parameterOrder": [], 604 "parameterOrder": [
674 "parameters": {}, 605 "resource"
675 "path": "v1/callsets", 606 ],
607 "parameters": {
608 "resource": {
609 "description": "REQUIRED: The resource for which pol icy is being specified. Format is\n`datasets/<dataset ID>`.",
610 "location": "path",
611 "pattern": "^datasets/[^/]+$",
612 "required": true,
613 "type": "string"
614 }
615 },
616 "path": "v1/{+resource}:testIamPermissions",
676 "request": { 617 "request": {
677 "$ref": "CallSet" 618 "$ref": "TestIamPermissionsRequest"
678 }, 619 },
679 "response": { 620 "response": {
680 "$ref": "CallSet" 621 "$ref": "TestIamPermissionsResponse"
681 }, 622 },
682 "scopes": [ 623 "scopes": [
683 "https://www.googleapis.com/auth/cloud-platform", 624 "https://www.googleapis.com/auth/cloud-platform",
684 "https://www.googleapis.com/auth/genomics" 625 "https://www.googleapis.com/auth/genomics"
685 ] 626 ]
686 } 627 },
687 }
688 },
689 "reads": {
690 "methods": {
691 "search": {
692 "description": "Gets a list of reads for one or more read gr oup sets.\n\nFor the definitions of read group sets and other genomics resources , see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fund amentals-of-google-genomics)\n\nReads search operates over a genomic coordinate space of reference sequence\n& position defined over the reference sequences to which the requested\nread group sets are aligned.\n\nIf a target positional rang e is specified, search returns all reads whose\nalignment to the reference genom e overlap the range. A query which\nspecifies only read group set IDs yields all reads in those read group\nsets, including unmapped reads.\n\nAll reads returne d (including reads on subsequent pages) are ordered by\ngenomic coordinate (by r eference sequence, then position). Reads with\nequivalent genomic coordinates ar e returned in an unspecified order. This\norder is consistent, such that two que ries for the same content (regardless\nof page size) yield reads in the same ord er across their respective streams\nof paginated responses.\n\nImplements\n[Glob alAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main /resources/avro/readmethods.avdl#L85).",
693 "httpMethod": "POST",
694 "id": "genomics.reads.search",
695 "parameterOrder": [],
696 "parameters": {},
697 "path": "v1/reads/search",
698 "request": {
699 "$ref": "SearchReadsRequest"
700 },
701 "response": {
702 "$ref": "SearchReadsResponse"
703 },
704 "scopes": [
705 "https://www.googleapis.com/auth/cloud-platform",
706 "https://www.googleapis.com/auth/genomics",
707 "https://www.googleapis.com/auth/genomics.readonly"
708 ]
709 }
710 }
711 },
712 "readgroupsets": {
713 "methods": {
714 "delete": { 628 "delete": {
715 "description": "Deletes a read group set.\n\nFor the definit ions of read group sets and other genomics resources, see\n[Fundamentals of Goog le\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) ", 629 "description": "Deletes a dataset and all of its contents (a ll read group sets,\nreference sets, variant sets, call sets, annotation sets, e tc.)\nThis is reversible (up to one week after the deletion) via\nthe\ndatasets. undelete\noperation.\n\nFor the definitions of datasets and other genomics resou rces, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/ fundamentals-of-google-genomics)",
716 "httpMethod": "DELETE", 630 "httpMethod": "DELETE",
717 "id": "genomics.readgroupsets.delete", 631 "id": "genomics.datasets.delete",
718 "parameterOrder": [ 632 "parameterOrder": [
719 "readGroupSetId" 633 "datasetId"
720 ], 634 ],
721 "parameters": { 635 "parameters": {
722 "readGroupSetId": { 636 "datasetId": {
723 "description": "The ID of the read group set to be d eleted. The caller must have WRITE\npermissions to the dataset associated with t his read group set.", 637 "description": "The ID of the dataset to be deleted. ",
724 "location": "path", 638 "location": "path",
725 "required": true, 639 "required": true,
726 "type": "string" 640 "type": "string"
727 } 641 }
728 }, 642 },
729 "path": "v1/readgroupsets/{readGroupSetId}", 643 "path": "v1/datasets/{datasetId}",
730 "response": { 644 "response": {
731 "$ref": "Empty" 645 "$ref": "Empty"
732 }, 646 },
733 "scopes": [ 647 "scopes": [
734 "https://www.googleapis.com/auth/cloud-platform", 648 "https://www.googleapis.com/auth/cloud-platform",
735 "https://www.googleapis.com/auth/genomics" 649 "https://www.googleapis.com/auth/genomics"
736 ] 650 ]
737 }, 651 },
738 "import": { 652 "list": {
739 "description": "Creates read group sets by asynchronously im porting the provided\ninformation.\n\nFor the definitions of read group sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud .google.com/genomics/fundamentals-of-google-genomics)\n\nThe caller must have WR ITE permissions to the dataset.\n\n## Notes on [BAM](https://samtools.github.io/ hts-specs/SAMv1.pdf) import\n\n- Tags will be converted to strings - tag types a re not preserved\n- Comments (`@CO`) in the input file header will not be preser ved\n- Original header order of references (`@SQ`) will not be preserved\n- Any reverse stranded unmapped reads will be reverse complemented, and\ntheir qualiti es (also the \"BQ\" and \"OQ\" tags, if any) will be reversed\n- Unmapped reads will be stripped of positional information (reference name\nand position)", 653 "description": "Lists datasets within a project.\n\nFor the definitions of datasets and other genomics resources, see\n[Fundamentals of Goog le\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) ",
740 "httpMethod": "POST", 654 "httpMethod": "GET",
741 "id": "genomics.readgroupsets.import", 655 "id": "genomics.datasets.list",
742 "parameterOrder": [], 656 "parameterOrder": [],
743 "parameters": {},
744 "path": "v1/readgroupsets:import",
745 "request": {
746 "$ref": "ImportReadGroupSetsRequest"
747 },
748 "response": {
749 "$ref": "Operation"
750 },
751 "scopes": [
752 "https://www.googleapis.com/auth/cloud-platform",
753 "https://www.googleapis.com/auth/devstorage.read_write",
754 "https://www.googleapis.com/auth/genomics"
755 ]
756 },
757 "export": {
758 "description": "Exports a read group set to a BAM file in Go ogle Cloud Storage.\n\nFor the definitions of read group sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/gen omics/fundamentals-of-google-genomics)\n\nNote that currently there may be some differences between exported BAM\nfiles and the original BAM file at the time of import. See\nImportReadGroupSets\nfor caveats.",
759 "httpMethod": "POST",
760 "id": "genomics.readgroupsets.export",
761 "parameterOrder": [
762 "readGroupSetId"
763 ],
764 "parameters": { 657 "parameters": {
765 "readGroupSetId": { 658 "projectId": {
766 "description": "Required. The ID of the read group s et to export. The caller must have\nREAD access to this read group set.", 659 "description": "Required. The Google Cloud project I D to list datasets for.",
767 "location": "path", 660 "location": "query",
768 "required": true,
769 "type": "string" 661 "type": "string"
662 },
663 "pageToken": {
664 "description": "The continuation token, which is use d to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`nextPageToken` from the previous response.",
665 "location": "query",
666 "type": "string"
667 },
668 "pageSize": {
669 "description": "The maximum number of results to ret urn in a single page. If unspecified,\ndefaults to 50. The maximum value is 1024 .",
670 "format": "int32",
671 "location": "query",
672 "type": "integer"
770 } 673 }
771 }, 674 },
772 "path": "v1/readgroupsets/{readGroupSetId}:export", 675 "path": "v1/datasets",
773 "request": {
774 "$ref": "ExportReadGroupSetRequest"
775 },
776 "response": { 676 "response": {
777 "$ref": "Operation" 677 "$ref": "ListDatasetsResponse"
778 },
779 "scopes": [
780 "https://www.googleapis.com/auth/cloud-platform",
781 "https://www.googleapis.com/auth/devstorage.read_write",
782 "https://www.googleapis.com/auth/genomics"
783 ]
784 },
785 "search": {
786 "description": "Searches for read group sets matching the cr iteria.\n\nFor the definitions of read group sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundam entals-of-google-genomics)\n\nImplements\n[GlobalAllianceApi.searchReadGroupSets ](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmetho ds.avdl#L135).",
787 "httpMethod": "POST",
788 "id": "genomics.readgroupsets.search",
789 "parameterOrder": [],
790 "parameters": {},
791 "path": "v1/readgroupsets/search",
792 "request": {
793 "$ref": "SearchReadGroupSetsRequest"
794 },
795 "response": {
796 "$ref": "SearchReadGroupSetsResponse"
797 }, 678 },
798 "scopes": [ 679 "scopes": [
799 "https://www.googleapis.com/auth/cloud-platform", 680 "https://www.googleapis.com/auth/cloud-platform",
800 "https://www.googleapis.com/auth/genomics", 681 "https://www.googleapis.com/auth/genomics",
801 "https://www.googleapis.com/auth/genomics.readonly" 682 "https://www.googleapis.com/auth/genomics.readonly"
802 ] 683 ]
803 }, 684 },
804 "patch": { 685 "create": {
805 "description": "Updates a read group set.\n\nFor the definit ions of read group sets and other genomics resources, see\n[Fundamentals of Goog le\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) \n\nThis method supports patch semantics.", 686 "description": "Creates a new dataset.\n\nFor the definition s of datasets and other genomics resources, see\n[Fundamentals of Google\nGenomi cs](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
806 "httpMethod": "PATCH", 687 "httpMethod": "POST",
807 "id": "genomics.readgroupsets.patch", 688 "id": "genomics.datasets.create",
808 "parameterOrder": [ 689 "parameterOrder": [],
809 "readGroupSetId" 690 "parameters": {},
810 ], 691 "path": "v1/datasets",
811 "parameters": {
812 "readGroupSetId": {
813 "description": "The ID of the read group set to be u pdated. The caller must have WRITE\npermissions to the dataset associated with t his read group set.",
814 "location": "path",
815 "required": true,
816 "type": "string"
817 },
818 "updateMask": {
819 "description": "An optional mask specifying which fi elds to update. Supported fields:\n\n* name.\n* referenceSetId.\n\nLeaving `upda teMask` unset is equivalent to specifying all mutable\nfields.",
820 "format": "google-fieldmask",
821 "location": "query",
822 "type": "string"
823 }
824 },
825 "path": "v1/readgroupsets/{readGroupSetId}",
826 "request": { 692 "request": {
827 "$ref": "ReadGroupSet" 693 "$ref": "Dataset"
828 }, 694 },
829 "response": { 695 "response": {
830 "$ref": "ReadGroupSet" 696 "$ref": "Dataset"
831 }, 697 },
832 "scopes": [ 698 "scopes": [
833 "https://www.googleapis.com/auth/cloud-platform", 699 "https://www.googleapis.com/auth/cloud-platform",
834 "https://www.googleapis.com/auth/genomics" 700 "https://www.googleapis.com/auth/genomics"
835 ] 701 ]
836 }, 702 },
837 "get": { 703 "setIamPolicy": {
838 "description": "Gets a read group set by ID.\n\nFor the defi nitions of read group sets and other genomics resources, see\n[Fundamentals of G oogle\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomi cs)", 704 "description": "Sets the access control policy on the specif ied dataset. Replaces any\nexisting policy.\n\nFor the definitions of datasets a nd other genomics resources, see\n[Fundamentals of Google\nGenomics](https://clo ud.google.com/genomics/fundamentals-of-google-genomics)\n\nSee <a href=\"/iam/do cs/managing-policies#setting_a_policy\">Setting a\nPolicy</a> for more informati on.",
839 "httpMethod": "GET", 705 "httpMethod": "POST",
840 "id": "genomics.readgroupsets.get", 706 "id": "genomics.datasets.setIamPolicy",
841 "parameterOrder": [ 707 "parameterOrder": [
842 "readGroupSetId" 708 "resource"
843 ], 709 ],
844 "parameters": { 710 "parameters": {
845 "readGroupSetId": { 711 "resource": {
846 "description": "The ID of the read group set.", 712 "description": "REQUIRED: The resource for which pol icy is being specified. Format is\n`datasets/<dataset ID>`.",
847 "location": "path", 713 "location": "path",
714 "pattern": "^datasets/[^/]+$",
848 "required": true, 715 "required": true,
849 "type": "string" 716 "type": "string"
850 } 717 }
851 }, 718 },
852 "path": "v1/readgroupsets/{readGroupSetId}", 719 "path": "v1/{+resource}:setIamPolicy",
720 "request": {
721 "$ref": "SetIamPolicyRequest"
722 },
853 "response": { 723 "response": {
854 "$ref": "ReadGroupSet" 724 "$ref": "Policy"
855 }, 725 },
856 "scopes": [ 726 "scopes": [
857 "https://www.googleapis.com/auth/cloud-platform", 727 "https://www.googleapis.com/auth/cloud-platform",
858 "https://www.googleapis.com/auth/genomics", 728 "https://www.googleapis.com/auth/genomics"
859 "https://www.googleapis.com/auth/genomics.readonly"
860 ] 729 ]
861 } 730 },
862 }, 731 "getIamPolicy": {
863 "resources": { 732 "description": "Gets the access control policy for the datas et. This is empty if the\npolicy or resource does not exist.\n\nSee <a href=\"/i am/docs/managing-policies#getting_a_policy\">Getting a\nPolicy</a> for more info rmation.\n\nFor the definitions of datasets and other genomics resources, see\n[ Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals -of-google-genomics)",
864 "coveragebuckets": { 733 "httpMethod": "POST",
865 "methods": { 734 "id": "genomics.datasets.getIamPolicy",
866 "list": { 735 "parameterOrder": [
867 "description": "Lists fixed width coverage buckets f or a read group set, each of which\ncorrespond to a range of a reference sequenc e. Each bucket summarizes\ncoverage information across its corresponding genomic range.\n\nFor the definitions of read group sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundam entals-of-google-genomics)\n\nCoverage is defined as the number of reads which a re aligned to a given\nbase in the reference sequence. Coverage buckets are avai lable at several\nprecomputed bucket widths, enabling retrieval of various cover age 'zoom\nlevels'. The caller must have READ permissions for the target read gr oup\nset.", 736 "resource"
868 "httpMethod": "GET", 737 ],
869 "id": "genomics.readgroupsets.coveragebuckets.list", 738 "parameters": {
870 "parameterOrder": [ 739 "resource": {
871 "readGroupSetId" 740 "description": "REQUIRED: The resource for which pol icy is being specified. Format is\n`datasets/<dataset ID>`.",
872 ], 741 "location": "path",
873 "parameters": { 742 "pattern": "^datasets/[^/]+$",
874 "readGroupSetId": { 743 "required": true,
875 "description": "Required. The ID of the read group set over which coverage is requested.", 744 "type": "string"
876 "location": "path",
877 "required": true,
878 "type": "string"
879 },
880 "targetBucketWidth": {
881 "description": "The desired width of each re ported coverage bucket in base pairs. This\nwill be rounded down to the nearest precomputed bucket width; the value\nof which is returned as `bucketWidth` in th e response. Defaults\nto infinity (each bucket spans an entire reference sequenc e) or the length\nof the target range, if specified. The smallest precomputed\n` bucketWidth` is currently 2048 base pairs; this is subject to\nchange.",
882 "format": "int64",
883 "location": "query",
884 "type": "string"
885 },
886 "referenceName": {
887 "description": "The name of the reference to query, within the reference set associated\nwith this query. Optional.",
888 "location": "query",
889 "type": "string"
890 },
891 "end": {
892 "description": "The end position of the rang e on the reference, 0-based exclusive. If\nspecified, `referenceName` must also be specified. If unset or 0, defaults\nto the length of the reference.",
893 "format": "int64",
894 "location": "query",
895 "type": "string"
896 },
897 "pageToken": {
898 "description": "The continuation token, whic h is used to page through large result sets.\nTo get the next page of results, s et this parameter to the value of\n`nextPageToken` from the previous response.",
899 "location": "query",
900 "type": "string"
901 },
902 "pageSize": {
903 "description": "The maximum number of result s to return in a single page. If unspecified,\ndefaults to 1024. The maximum val ue is 2048.",
904 "format": "int32",
905 "location": "query",
906 "type": "integer"
907 },
908 "start": {
909 "description": "The start position of the ra nge on the reference, 0-based inclusive. If\nspecified, `referenceName` must als o be specified. Defaults to 0.",
910 "format": "int64",
911 "location": "query",
912 "type": "string"
913 }
914 },
915 "path": "v1/readgroupsets/{readGroupSetId}/coverageb uckets",
916 "response": {
917 "$ref": "ListCoverageBucketsResponse"
918 },
919 "scopes": [
920 "https://www.googleapis.com/auth/cloud-platform" ,
921 "https://www.googleapis.com/auth/genomics",
922 "https://www.googleapis.com/auth/genomics.readon ly"
923 ]
924 } 745 }
925 } 746 },
747 "path": "v1/{+resource}:getIamPolicy",
748 "request": {
749 "$ref": "GetIamPolicyRequest"
750 },
751 "response": {
752 "$ref": "Policy"
753 },
754 "scopes": [
755 "https://www.googleapis.com/auth/cloud-platform",
756 "https://www.googleapis.com/auth/genomics"
757 ]
926 } 758 }
927 } 759 }
928 }, 760 },
929 "variants": { 761 "annotations": {
930 "methods": { 762 "methods": {
931 "create": { 763 "create": {
932 "description": "Creates a new variant.\n\nFor the definition s of variants and other genomics resources, see\n[Fundamentals of Google\nGenomi cs](https://cloud.google.com/genomics/fundamentals-of-google-genomics)", 764 "description": "Creates a new annotation. Caller must have W RITE permission\nfor the associated annotation set.\n\nThe following fields are required:\n\n* annotationSetId\n* referenceName or\n referenceId\n\n### Transcr ipts\n\nFor annotations of type TRANSCRIPT, the following fields of\ntranscript must be provided:\n\n* exons.start\n* exons.end\n\nAll other fields may be optio nally specified, unless documented as being\nserver-generated (for example, the `id` field). The annotated\nrange must be no longer than 100Mbp (mega base pairs ). See the\nAnnotation resource\nfor additional restrictions on each field.",
933 "httpMethod": "POST", 765 "httpMethod": "POST",
934 "id": "genomics.variants.create", 766 "id": "genomics.annotations.create",
935 "parameterOrder": [], 767 "parameterOrder": [],
936 "parameters": {}, 768 "parameters": {},
937 "path": "v1/variants", 769 "path": "v1/annotations",
938 "request": { 770 "request": {
939 "$ref": "Variant" 771 "$ref": "Annotation"
940 }, 772 },
941 "response": { 773 "response": {
942 "$ref": "Variant" 774 "$ref": "Annotation"
943 }, 775 },
944 "scopes": [ 776 "scopes": [
945 "https://www.googleapis.com/auth/cloud-platform", 777 "https://www.googleapis.com/auth/cloud-platform",
778 "https://www.googleapis.com/auth/genomics"
779 ]
780 },
781 "batchCreate": {
782 "description": "Creates one or more new annotations atomical ly. All annotations must\nbelong to the same annotation set. Caller must have WR ITE\npermission for this annotation set. For optimal performance, batch\npositio nally adjacent annotations together.\n\nIf the request has a systemic issue, suc h as an attempt to write to\nan inaccessible annotation set, the entire RPC will fail accordingly. For\nlesser data issues, when possible an error will be isola ted to the\ncorresponding batch entry in the response; the remaining well formed \nannotations will be created normally.\n\nFor details on the requirements for e ach individual annotation resource,\nsee\nCreateAnnotation.",
783 "httpMethod": "POST",
784 "id": "genomics.annotations.batchCreate",
785 "parameterOrder": [],
786 "parameters": {},
787 "path": "v1/annotations:batchCreate",
788 "request": {
789 "$ref": "BatchCreateAnnotationsRequest"
790 },
791 "response": {
792 "$ref": "BatchCreateAnnotationsResponse"
793 },
794 "scopes": [
795 "https://www.googleapis.com/auth/cloud-platform",
946 "https://www.googleapis.com/auth/genomics" 796 "https://www.googleapis.com/auth/genomics"
947 ] 797 ]
948 }, 798 },
949 "search": { 799 "search": {
950 "description": "Gets a list of variants matching the criteri a.\n\nFor the definitions of variants and other genomics resources, see\n[Fundam entals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-go ogle-genomics)\n\nImplements\n[GlobalAllianceApi.searchVariants](https://github. com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L126). ", 800 "description": "Searches for annotations that match the give n criteria. Results are\nordered by genomic coordinate (by reference sequence, t hen position).\nAnnotations with equivalent genomic coordinates are returned in an\nunspecified order. This order is consistent, such that two queries for the\n same content (regardless of page size) yield annotations in the same order\nacro ss their respective streams of paginated responses. Caller must have\nREAD permi ssion for the queried annotation sets.",
951 "httpMethod": "POST", 801 "httpMethod": "POST",
952 "id": "genomics.variants.search", 802 "id": "genomics.annotations.search",
953 "parameterOrder": [], 803 "parameterOrder": [],
954 "parameters": {}, 804 "parameters": {},
955 "path": "v1/variants/search", 805 "path": "v1/annotations/search",
956 "request": { 806 "request": {
957 "$ref": "SearchVariantsRequest" 807 "$ref": "SearchAnnotationsRequest"
958 }, 808 },
959 "response": { 809 "response": {
960 "$ref": "SearchVariantsResponse" 810 "$ref": "SearchAnnotationsResponse"
961 }, 811 },
962 "scopes": [ 812 "scopes": [
963 "https://www.googleapis.com/auth/cloud-platform", 813 "https://www.googleapis.com/auth/cloud-platform",
964 "https://www.googleapis.com/auth/genomics", 814 "https://www.googleapis.com/auth/genomics",
965 "https://www.googleapis.com/auth/genomics.readonly" 815 "https://www.googleapis.com/auth/genomics.readonly"
966 ] 816 ]
967 }, 817 },
968 "get": { 818 "get": {
969 "description": "Gets a variant by ID.\n\nFor the definitions of variants and other genomics resources, see\n[Fundamentals of Google\nGenomic s](https://cloud.google.com/genomics/fundamentals-of-google-genomics)", 819 "description": "Gets an annotation. Caller must have READ pe rmission\nfor the associated annotation set.",
970 "httpMethod": "GET", 820 "httpMethod": "GET",
971 "id": "genomics.variants.get", 821 "id": "genomics.annotations.get",
972 "parameterOrder": [ 822 "parameterOrder": [
973 "variantId" 823 "annotationId"
974 ], 824 ],
975 "parameters": { 825 "parameters": {
976 "variantId": { 826 "annotationId": {
977 "description": "The ID of the variant.", 827 "description": "The ID of the annotation to be retri eved.",
978 "location": "path", 828 "location": "path",
979 "required": true, 829 "required": true,
980 "type": "string" 830 "type": "string"
981 } 831 }
982 }, 832 },
983 "path": "v1/variants/{variantId}", 833 "path": "v1/annotations/{annotationId}",
984 "response": { 834 "response": {
985 "$ref": "Variant" 835 "$ref": "Annotation"
986 }, 836 },
987 "scopes": [ 837 "scopes": [
988 "https://www.googleapis.com/auth/cloud-platform", 838 "https://www.googleapis.com/auth/cloud-platform",
989 "https://www.googleapis.com/auth/genomics", 839 "https://www.googleapis.com/auth/genomics",
990 "https://www.googleapis.com/auth/genomics.readonly" 840 "https://www.googleapis.com/auth/genomics.readonly"
991 ] 841 ]
992 }, 842 },
993 "patch": { 843 "update": {
994 "description": "Updates a variant.\n\nFor the definitions of variants and other genomics resources, see\n[Fundamentals of Google\nGenomics]( https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nThis metho d supports patch semantics. Returns the modified variant without\nits calls.", 844 "description": "Updates an annotation. Caller must have\nWRI TE permission for the associated dataset.",
995 "httpMethod": "PATCH", 845 "httpMethod": "PUT",
996 "id": "genomics.variants.patch", 846 "id": "genomics.annotations.update",
997 "parameterOrder": [ 847 "parameterOrder": [
998 "variantId" 848 "annotationId"
999 ], 849 ],
1000 "parameters": { 850 "parameters": {
1001 "updateMask": { 851 "updateMask": {
1002 "description": "An optional mask specifying which fi elds to update. At this time, mutable\nfields are names and\ninfo. Acceptable va lues are \"names\" and\n\"info\". If unspecified, all mutable fields will be upd ated.", 852 "description": "An optional mask specifying which fi elds to update. Mutable fields are\nname,\nvariant,\ntranscript, and\ninfo. If u nspecified, all mutable\nfields will be updated.",
1003 "format": "google-fieldmask", 853 "format": "google-fieldmask",
1004 "location": "query", 854 "location": "query",
1005 "type": "string" 855 "type": "string"
1006 }, 856 },
1007 "variantId": { 857 "annotationId": {
1008 "description": "The ID of the variant to be updated. ", 858 "description": "The ID of the annotation to be updat ed.",
1009 "location": "path", 859 "location": "path",
1010 "required": true, 860 "required": true,
1011 "type": "string" 861 "type": "string"
1012 } 862 }
1013 }, 863 },
1014 "path": "v1/variants/{variantId}", 864 "path": "v1/annotations/{annotationId}",
1015 "request": { 865 "request": {
1016 "$ref": "Variant" 866 "$ref": "Annotation"
1017 }, 867 },
1018 "response": { 868 "response": {
1019 "$ref": "Variant" 869 "$ref": "Annotation"
1020 }, 870 },
1021 "scopes": [ 871 "scopes": [
1022 "https://www.googleapis.com/auth/cloud-platform", 872 "https://www.googleapis.com/auth/cloud-platform",
1023 "https://www.googleapis.com/auth/genomics"
1024 ]
1025 },
1026 "import": {
1027 "description": "Creates variant data by asynchronously impor ting the provided information.\n\nFor the definitions of variant sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google .com/genomics/fundamentals-of-google-genomics)\n\nThe variants for import will b e merged with any existing variant that\nmatches its reference sequence, start, end, reference bases, and\nalternative bases. If no such variant exists, a new o ne will be created.\n\nWhen variants are merged, the call information from the n ew variant\nis added to the existing variant, and Variant info fields are merged \nas specified in\ninfoMergeConfig.\nAs a special case, for single-sample VCF fi les, QUAL and FILTER fields will\nbe moved to the call level; these are sometime s interpreted in a\ncall-specific context.\nImported VCF headers are appended to the metadata already in a variant set.",
1028 "httpMethod": "POST",
1029 "id": "genomics.variants.import",
1030 "parameterOrder": [],
1031 "parameters": {},
1032 "path": "v1/variants:import",
1033 "request": {
1034 "$ref": "ImportVariantsRequest"
1035 },
1036 "response": {
1037 "$ref": "Operation"
1038 },
1039 "scopes": [
1040 "https://www.googleapis.com/auth/cloud-platform",
1041 "https://www.googleapis.com/auth/devstorage.read_write",
1042 "https://www.googleapis.com/auth/genomics"
1043 ]
1044 },
1045 "merge": {
1046 "description": "Merges the given variants with existing vari ants.\n\nFor the definitions of variants and other genomics resources, see\n[Fun damentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of -google-genomics)\n\nEach variant will be\nmerged with an existing variant that matches its reference sequence,\nstart, end, reference bases, and alternative ba ses. If no such variant\nexists, a new one will be created.\n\nWhen variants are merged, the call information from the new variant\nis added to the existing var iant. Variant info fields are merged as\nspecified in the\ninfoMergeConfig\nfiel d of the MergeVariantsRequest.\n\nPlease exercise caution when using this method ! It is easy to introduce\nmistakes in existing variants and difficult to back out of them. For\nexample,\nsuppose you were trying to merge a new variant with an existing one and\nboth\nvariants contain calls that belong to callsets with the same callset ID.\n\n // Existing variant - irrelevant fields trimmed for clarity\n {\n \"variantSetId\": \"10473108253681171589\",\n \"r eferenceName\": \"1\",\n \"start\": \"10582\",\n \"referenceBases\ ": \"G\",\n \"alternateBases\": [\n \"A\"\n ],\n \"calls\": [\n {\n \"callSetId\": \"10473108253681171 589-0\",\n \"callSetName\": \"CALLSET0\",\n \"geno type\": [\n 0,\n 1\n ],\n }\n ]\n }\n\n // New variant with conflicting call inform ation\n {\n \"variantSetId\": \"10473108253681171589\",\n \"ref erenceName\": \"1\",\n \"start\": \"10582\",\n \"referenceBases\": \"G\",\n \"alternateBases\": [\n \"A\"\n ],\n \ "calls\": [\n {\n \"callSetId\": \"1047310825368117158 9-0\",\n \"callSetName\": \"CALLSET0\",\n \"genoty pe\": [\n 1,\n 1\n ],\n }\n ]\n }\n\nThe resulting merged variant would overwrite the existing calls with those\nfrom the new variant:\n\n {\n \"variantSetI d\": \"10473108253681171589\",\n \"referenceName\": \"1\",\n \"sta rt\": \"10582\",\n \"referenceBases\": \"G\",\n \"alternateBases\" : [\n \"A\"\n ],\n \"calls\": [\n {\n \"callSetId\": \"10473108253681171589-0\",\n \"callSetNa me\": \"CALLSET0\",\n \"genotype\": [\n 1,\n 1\n ],\n }\n ]\n }\n\nThis may be the desired outcome, but it is up to the user to determine if\nif that i s indeed the case.",
1047 "httpMethod": "POST",
1048 "id": "genomics.variants.merge",
1049 "parameterOrder": [],
1050 "parameters": {},
1051 "path": "v1/variants:merge",
1052 "request": {
1053 "$ref": "MergeVariantsRequest"
1054 },
1055 "response": {
1056 "$ref": "Empty"
1057 },
1058 "scopes": [
1059 "https://www.googleapis.com/auth/cloud-platform",
1060 "https://www.googleapis.com/auth/genomics" 873 "https://www.googleapis.com/auth/genomics"
1061 ] 874 ]
1062 }, 875 },
1063 "delete": { 876 "delete": {
1064 "description": "Deletes a variant.\n\nFor the definitions of variants and other genomics resources, see\n[Fundamentals of Google\nGenomics]( https://cloud.google.com/genomics/fundamentals-of-google-genomics)", 877 "description": "Deletes an annotation. Caller must have WRIT E permission for\nthe associated annotation set.",
1065 "httpMethod": "DELETE", 878 "httpMethod": "DELETE",
1066 "id": "genomics.variants.delete", 879 "id": "genomics.annotations.delete",
1067 "parameterOrder": [ 880 "parameterOrder": [
1068 "variantId" 881 "annotationId"
1069 ], 882 ],
1070 "parameters": { 883 "parameters": {
1071 "variantId": { 884 "annotationId": {
1072 "description": "The ID of the variant to be deleted. ", 885 "description": "The ID of the annotation to be delet ed.",
1073 "location": "path", 886 "location": "path",
1074 "required": true, 887 "required": true,
1075 "type": "string" 888 "type": "string"
1076 } 889 }
1077 }, 890 },
1078 "path": "v1/variants/{variantId}", 891 "path": "v1/annotations/{annotationId}",
1079 "response": { 892 "response": {
1080 "$ref": "Empty" 893 "$ref": "Empty"
1081 }, 894 },
1082 "scopes": [ 895 "scopes": [
1083 "https://www.googleapis.com/auth/cloud-platform", 896 "https://www.googleapis.com/auth/cloud-platform",
1084 "https://www.googleapis.com/auth/genomics" 897 "https://www.googleapis.com/auth/genomics"
1085 ] 898 ]
1086 } 899 }
1087 } 900 }
1088 }, 901 },
1089 "annotationsets": { 902 "variantsets": {
1090 "methods": { 903 "methods": {
1091 "delete": { 904 "create": {
1092 "description": "Deletes an annotation set. Caller must have WRITE permission\nfor the associated annotation set.", 905 "description": "Creates a new variant set.\n\nFor the defini tions of variant sets and other genomics resources, see\n[Fundamentals of Google \nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n \nThe provided variant set must have a valid `datasetId` set - all other\nfields are optional. Note that the `id` field will be ignored, as this is\nassigned by the server.",
1093 "httpMethod": "DELETE", 906 "httpMethod": "POST",
1094 "id": "genomics.annotationsets.delete", 907 "id": "genomics.variantsets.create",
1095 "parameterOrder": [ 908 "parameterOrder": [],
1096 "annotationSetId" 909 "parameters": {},
1097 ], 910 "path": "v1/variantsets",
1098 "parameters": { 911 "request": {
1099 "annotationSetId": { 912 "$ref": "VariantSet"
1100 "description": "The ID of the annotation set to be d eleted.",
1101 "location": "path",
1102 "required": true,
1103 "type": "string"
1104 }
1105 }, 913 },
1106 "path": "v1/annotationsets/{annotationSetId}",
1107 "response": { 914 "response": {
1108 "$ref": "Empty" 915 "$ref": "VariantSet"
1109 }, 916 },
1110 "scopes": [ 917 "scopes": [
1111 "https://www.googleapis.com/auth/cloud-platform", 918 "https://www.googleapis.com/auth/cloud-platform",
1112 "https://www.googleapis.com/auth/genomics" 919 "https://www.googleapis.com/auth/genomics"
1113 ] 920 ]
1114 }, 921 },
922 "export": {
923 "description": "Exports variant set data to an external dest ination.\n\nFor the definitions of variant sets and other genomics resources, se e\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamen tals-of-google-genomics)",
924 "httpMethod": "POST",
925 "id": "genomics.variantsets.export",
926 "parameterOrder": [
927 "variantSetId"
928 ],
929 "parameters": {
930 "variantSetId": {
931 "description": "Required. The ID of the variant set that contains variant data which\nshould be exported. The caller must have READ access to this variant set.",
932 "location": "path",
933 "required": true,
934 "type": "string"
935 }
936 },
937 "path": "v1/variantsets/{variantSetId}:export",
938 "request": {
939 "$ref": "ExportVariantSetRequest"
940 },
941 "response": {
942 "$ref": "Operation"
943 },
944 "scopes": [
945 "https://www.googleapis.com/auth/bigquery",
946 "https://www.googleapis.com/auth/cloud-platform",
947 "https://www.googleapis.com/auth/genomics"
948 ]
949 },
1115 "search": { 950 "search": {
1116 "description": "Searches for annotation sets that match the given criteria. Annotation sets\nare returned in an unspecified order. This orde r is consistent, such that\ntwo queries for the same content (regardless of page size) yield annotation\nsets in the same order across their respective streams of paginated\nresponses. Caller must have READ permission for the queried datase ts.", 951 "description": "Returns a list of all variant sets matching search criteria.\n\nFor the definitions of variant sets and other genomics resou rces, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/ fundamentals-of-google-genomics)\n\nImplements\n[GlobalAllianceApi.searchVariant Sets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/varia ntmethods.avdl#L49).",
1117 "httpMethod": "POST", 952 "httpMethod": "POST",
1118 "id": "genomics.annotationsets.search", 953 "id": "genomics.variantsets.search",
1119 "parameterOrder": [], 954 "parameterOrder": [],
1120 "parameters": {}, 955 "parameters": {},
1121 "path": "v1/annotationsets/search", 956 "path": "v1/variantsets/search",
1122 "request": { 957 "request": {
1123 "$ref": "SearchAnnotationSetsRequest" 958 "$ref": "SearchVariantSetsRequest"
1124 }, 959 },
1125 "response": { 960 "response": {
1126 "$ref": "SearchAnnotationSetsResponse" 961 "$ref": "SearchVariantSetsResponse"
1127 }, 962 },
1128 "scopes": [ 963 "scopes": [
1129 "https://www.googleapis.com/auth/cloud-platform", 964 "https://www.googleapis.com/auth/cloud-platform",
1130 "https://www.googleapis.com/auth/genomics", 965 "https://www.googleapis.com/auth/genomics",
1131 "https://www.googleapis.com/auth/genomics.readonly" 966 "https://www.googleapis.com/auth/genomics.readonly"
1132 ] 967 ]
1133 }, 968 },
1134 "get": { 969 "get": {
1135 "description": "Gets an annotation set. Caller must have REA D permission for\nthe associated dataset.", 970 "description": "Gets a variant set by ID.\n\nFor the definit ions of variant sets and other genomics resources, see\n[Fundamentals of Google\ nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
1136 "httpMethod": "GET", 971 "httpMethod": "GET",
1137 "id": "genomics.annotationsets.get", 972 "id": "genomics.variantsets.get",
1138 "parameterOrder": [ 973 "parameterOrder": [
1139 "annotationSetId" 974 "variantSetId"
1140 ], 975 ],
1141 "parameters": { 976 "parameters": {
1142 "annotationSetId": { 977 "variantSetId": {
1143 "description": "The ID of the annotation set to be r etrieved.", 978 "description": "Required. The ID of the variant set. ",
1144 "location": "path", 979 "location": "path",
1145 "required": true, 980 "required": true,
1146 "type": "string" 981 "type": "string"
1147 } 982 }
1148 }, 983 },
1149 "path": "v1/annotationsets/{annotationSetId}", 984 "path": "v1/variantsets/{variantSetId}",
1150 "response": { 985 "response": {
1151 "$ref": "AnnotationSet" 986 "$ref": "VariantSet"
1152 }, 987 },
1153 "scopes": [ 988 "scopes": [
1154 "https://www.googleapis.com/auth/cloud-platform", 989 "https://www.googleapis.com/auth/cloud-platform",
1155 "https://www.googleapis.com/auth/genomics", 990 "https://www.googleapis.com/auth/genomics",
1156 "https://www.googleapis.com/auth/genomics.readonly" 991 "https://www.googleapis.com/auth/genomics.readonly"
1157 ] 992 ]
1158 }, 993 },
1159 "update": { 994 "patch": {
1160 "description": "Updates an annotation set. The update must r espect all mutability\nrestrictions and other invariants described on the annota tion set resource.\nCaller must have WRITE permission for the associated dataset .", 995 "description": "Updates a variant set using patch semantics. \n\nFor the definitions of variant sets and other genomics resources, see\n[Fund amentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of- google-genomics)",
1161 "httpMethod": "PUT", 996 "httpMethod": "PATCH",
1162 "id": "genomics.annotationsets.update", 997 "id": "genomics.variantsets.patch",
1163 "parameterOrder": [ 998 "parameterOrder": [
1164 "annotationSetId" 999 "variantSetId"
1165 ], 1000 ],
1166 "parameters": { 1001 "parameters": {
1167 "updateMask": { 1002 "updateMask": {
1168 "description": "An optional mask specifying which fi elds to update. Mutable fields are\nname,\nsource_uri, and\ninfo. If unspecified , all\nmutable fields will be updated.", 1003 "description": "An optional mask specifying which fi elds to update. Supported fields:\n\n* metadata.\n* name.\n* description.\n\nLea ving `updateMask` unset is equivalent to specifying all mutable\nfields.",
1169 "format": "google-fieldmask", 1004 "format": "google-fieldmask",
1170 "location": "query", 1005 "location": "query",
1171 "type": "string" 1006 "type": "string"
1172 }, 1007 },
1173 "annotationSetId": { 1008 "variantSetId": {
1174 "description": "The ID of the annotation set to be u pdated.", 1009 "description": "The ID of the variant to be updated (must already exist).",
1175 "location": "path", 1010 "location": "path",
1176 "required": true, 1011 "required": true,
1177 "type": "string" 1012 "type": "string"
1178 } 1013 }
1179 }, 1014 },
1180 "path": "v1/annotationsets/{annotationSetId}", 1015 "path": "v1/variantsets/{variantSetId}",
1181 "request": { 1016 "request": {
1182 "$ref": "AnnotationSet" 1017 "$ref": "VariantSet"
1183 }, 1018 },
1184 "response": { 1019 "response": {
1185 "$ref": "AnnotationSet" 1020 "$ref": "VariantSet"
1186 }, 1021 },
1187 "scopes": [ 1022 "scopes": [
1188 "https://www.googleapis.com/auth/cloud-platform", 1023 "https://www.googleapis.com/auth/cloud-platform",
1189 "https://www.googleapis.com/auth/genomics" 1024 "https://www.googleapis.com/auth/genomics"
1190 ] 1025 ]
1191 }, 1026 },
1192 "create": { 1027 "delete": {
1193 "description": "Creates a new annotation set. Caller must ha ve WRITE permission for the\nassociated dataset.\n\nThe following fields are req uired:\n\n * datasetId\n * referenceSetId\n\nAll other fields may be optionall y specified, unless documented as being\nserver-generated (for example, the `id` field).", 1028 "description": "Deletes a variant set including all variants , call sets, and calls within.\nThis is not reversible.\n\nFor the definitions o f variant sets and other genomics resources, see\n[Fundamentals of Google\nGenom ics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
1194 "httpMethod": "POST", 1029 "httpMethod": "DELETE",
1195 "id": "genomics.annotationsets.create", 1030 "id": "genomics.variantsets.delete",
1196 "parameterOrder": [], 1031 "parameterOrder": [
1197 "parameters": {}, 1032 "variantSetId"
1198 "path": "v1/annotationsets", 1033 ],
1199 "request": { 1034 "parameters": {
1200 "$ref": "AnnotationSet" 1035 "variantSetId": {
1036 "description": "The ID of the variant set to be dele ted.",
1037 "location": "path",
1038 "required": true,
1039 "type": "string"
1040 }
1201 }, 1041 },
1042 "path": "v1/variantsets/{variantSetId}",
1202 "response": { 1043 "response": {
1203 "$ref": "AnnotationSet" 1044 "$ref": "Empty"
1204 }, 1045 },
1205 "scopes": [ 1046 "scopes": [
1206 "https://www.googleapis.com/auth/cloud-platform", 1047 "https://www.googleapis.com/auth/cloud-platform",
1207 "https://www.googleapis.com/auth/genomics" 1048 "https://www.googleapis.com/auth/genomics"
1208 ] 1049 ]
1209 } 1050 }
1210 } 1051 }
1211 }, 1052 },
1212 "references": { 1053 "operations": {
1213 "methods": { 1054 "methods": {
1214 "search": { 1055 "cancel": {
1215 "description": "Searches for references which match the give n criteria.\n\nFor the definitions of references and other genomics resources, s ee\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundame ntals-of-google-genomics)\n\nImplements\n[GlobalAllianceApi.searchReferences](ht tps://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemeth ods.avdl#L146).", 1056 "description": "Starts asynchronous cancellation on a long-r unning operation. The server makes a best effort to cancel the operation, but su ccess is not guaranteed. Clients may use Operations.GetOperation or Operations.L istOperations to check whether the cancellation succeeded or the operation compl eted despite cancellation.",
1216 "httpMethod": "POST", 1057 "httpMethod": "POST",
1217 "id": "genomics.references.search", 1058 "id": "genomics.operations.cancel",
1218 "parameterOrder": [], 1059 "parameterOrder": [
1219 "parameters": {}, 1060 "name"
1220 "path": "v1/references/search", 1061 ],
1221 "request": { 1062 "parameters": {
1222 "$ref": "SearchReferencesRequest" 1063 "name": {
1223 }, 1064 "description": "The name of the operation resource t o be cancelled.",
1224 "response": { 1065 "location": "path",
1225 "$ref": "SearchReferencesResponse" 1066 "pattern": "^operations/.+$",
1226 }, 1067 "required": true,
1227 "scopes": [ 1068 "type": "string"
1228 "https://www.googleapis.com/auth/cloud-platform", 1069 }
1229 "https://www.googleapis.com/auth/genomics", 1070 },
1230 "https://www.googleapis.com/auth/genomics.readonly" 1071 "path": "v1/{+name}:cancel",
1072 "request": {
1073 "$ref": "CancelOperationRequest"
1074 },
1075 "response": {
1076 "$ref": "Empty"
1077 },
1078 "scopes": [
1079 "https://www.googleapis.com/auth/cloud-platform",
1080 "https://www.googleapis.com/auth/genomics"
1231 ] 1081 ]
1232 }, 1082 },
1233 "get": { 1083 "get": {
1234 "description": "Gets a reference.\n\nFor the definitions of references and other genomics resources, see\n[Fundamentals of Google\nGenomics] (https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nImplement s\n[GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob/v0.5.1 /src/main/resources/avro/referencemethods.avdl#L158).", 1084 "description": "Gets the latest state of a long-running oper ation. Clients can use this\nmethod to poll the operation result at intervals a s recommended by the API\nservice.",
1235 "httpMethod": "GET", 1085 "httpMethod": "GET",
1236 "id": "genomics.references.get", 1086 "id": "genomics.operations.get",
1237 "parameterOrder": [ 1087 "parameterOrder": [
1238 "referenceId" 1088 "name"
1239 ], 1089 ],
1240 "parameters": { 1090 "parameters": {
1241 "referenceId": { 1091 "name": {
1242 "description": "The ID of the reference.", 1092 "description": "The name of the operation resource." ,
1243 "location": "path", 1093 "location": "path",
1244 "required": true, 1094 "pattern": "^operations/.+$",
1245 "type": "string" 1095 "required": true,
1246 } 1096 "type": "string"
1247 }, 1097 }
1248 "path": "v1/references/{referenceId}", 1098 },
1249 "response": { 1099 "path": "v1/{+name}",
1250 "$ref": "Reference" 1100 "response": {
1251 }, 1101 "$ref": "Operation"
1252 "scopes": [ 1102 },
1253 "https://www.googleapis.com/auth/cloud-platform", 1103 "scopes": [
1254 "https://www.googleapis.com/auth/genomics", 1104 "https://www.googleapis.com/auth/cloud-platform",
1255 "https://www.googleapis.com/auth/genomics.readonly" 1105 "https://www.googleapis.com/auth/genomics"
1256 ] 1106 ]
1257 } 1107 },
1258 }, 1108 "list": {
1259 "resources": { 1109 "description": "Lists operations that match the specified fi lter in the request.",
1260 "bases": { 1110 "httpMethod": "GET",
1261 "methods": { 1111 "id": "genomics.operations.list",
1262 "list": { 1112 "parameterOrder": [
1263 "description": "Lists the bases in a reference, opti onally restricted to a range.\n\nFor the definitions of references and other gen omics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.co m/genomics/fundamentals-of-google-genomics)\n\nImplements\n[GlobalAllianceApi.ge tReferenceBases](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources /avro/referencemethods.avdl#L221).", 1113 "name"
1264 "httpMethod": "GET", 1114 ],
1265 "id": "genomics.references.bases.list", 1115 "parameters": {
1266 "parameterOrder": [ 1116 "pageToken": {
1267 "referenceId" 1117 "description": "The standard list page token.",
1268 ], 1118 "location": "query",
1269 "parameters": { 1119 "type": "string"
1270 "referenceId": { 1120 },
1271 "description": "The ID of the reference.", 1121 "name": {
1272 "location": "path", 1122 "description": "The name of the operation's parent r esource.",
1273 "required": true, 1123 "location": "path",
1274 "type": "string" 1124 "pattern": "^operations$",
1275 }, 1125 "required": true,
1276 "end": { 1126 "type": "string"
1277 "description": "The end position (0-based, e xclusive) of this query. Defaults to the length\nof this reference.", 1127 },
1278 "format": "int64", 1128 "pageSize": {
1279 "location": "query", 1129 "description": "The maximum number of results to ret urn. If unspecified, defaults to\n256. The maximum value is 2048.",
1280 "type": "string" 1130 "format": "int32",
1281 }, 1131 "location": "query",
1282 "pageToken": { 1132 "type": "integer"
1283 "description": "The continuation token, whic h is used to page through large result sets.\nTo get the next page of results, s et this parameter to the value of\n`nextPageToken` from the previous response.", 1133 },
1284 "location": "query", 1134 "filter": {
1285 "type": "string" 1135 "description": "A string for filtering Operations.\n The following filter fields are supported&#58;\n\n* projectId&#58; Required. Cor responds to\n OperationMetadata.projectId.\n* createTime&#58; The time this job was created, in seconds from the\n [epoch](http://en.wikipedia.org/wiki/Unix_t ime). Can use `>=` and/or `<=`\n operators.\n* status&#58; Can be `RUNNING`, `S UCCESS`, `FAILURE`, or `CANCELED`. Only\n one status may be specified.\n* label s.key where key is a label key.\n\nExamples&#58;\n\n* `projectId = my-project AN D createTime >= 1432140000`\n* `projectId = my-project AND createTime >= 1432140 000 AND createTime <= 1432150000 AND status = RUNNING`\n* `projectId = my-projec t AND labels.color = *`\n* `projectId = my-project AND labels.color = red`",
1286 }, 1136 "location": "query",
1287 "pageSize": { 1137 "type": "string"
1288 "description": "The maximum number of bases to return in a single page. If unspecified,\ndefaults to 200Kbp (kilo base pairs ). The maximum value is 10Mbp (mega base\npairs).", 1138 }
1289 "format": "int32", 1139 },
1290 "location": "query", 1140 "path": "v1/{+name}",
1291 "type": "integer" 1141 "response": {
1292 }, 1142 "$ref": "ListOperationsResponse"
1293 "start": { 1143 },
1294 "description": "The start position (0-based) of this query. Defaults to 0.", 1144 "scopes": [
1295 "format": "int64", 1145 "https://www.googleapis.com/auth/cloud-platform",
1296 "location": "query", 1146 "https://www.googleapis.com/auth/genomics"
1297 "type": "string" 1147 ]
1298 }
1299 },
1300 "path": "v1/references/{referenceId}/bases",
1301 "response": {
1302 "$ref": "ListBasesResponse"
1303 },
1304 "scopes": [
1305 "https://www.googleapis.com/auth/cloud-platform" ,
1306 "https://www.googleapis.com/auth/genomics",
1307 "https://www.googleapis.com/auth/genomics.readon ly"
1308 ]
1309 }
1310 }
1311 } 1148 }
1312 } 1149 }
1313 }, 1150 },
1314 "datasets": { 1151 "referencesets": {
1315 "methods": { 1152 "methods": {
1316 "setIamPolicy": { 1153 "search": {
1317 "description": "Sets the access control policy on the specif ied dataset. Replaces any\nexisting policy.\n\nFor the definitions of datasets a nd other genomics resources, see\n[Fundamentals of Google\nGenomics](https://clo ud.google.com/genomics/fundamentals-of-google-genomics)\n\nSee <a href=\"/iam/do cs/managing-policies#setting_a_policy\">Setting a\nPolicy</a> for more informati on.", 1154 "description": "Searches for reference sets which match the given criteria.\n\nFor the definitions of references and other genomics resource s, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fun damentals-of-google-genomics)\n\nImplements\n[GlobalAllianceApi.searchReferenceS ets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/refere ncemethods.avdl#L71)",
1318 "httpMethod": "POST", 1155 "httpMethod": "POST",
1319 "id": "genomics.datasets.setIamPolicy", 1156 "id": "genomics.referencesets.search",
1320 "parameterOrder": [
1321 "resource"
1322 ],
1323 "parameters": {
1324 "resource": {
1325 "description": "REQUIRED: The resource for which pol icy is being specified. Format is\n`datasets/<dataset ID>`.",
1326 "location": "path",
1327 "pattern": "^datasets/[^/]+$",
1328 "required": true,
1329 "type": "string"
1330 }
1331 },
1332 "path": "v1/{+resource}:setIamPolicy",
1333 "request": {
1334 "$ref": "SetIamPolicyRequest"
1335 },
1336 "response": {
1337 "$ref": "Policy"
1338 },
1339 "scopes": [
1340 "https://www.googleapis.com/auth/cloud-platform",
1341 "https://www.googleapis.com/auth/genomics"
1342 ]
1343 },
1344 "create": {
1345 "description": "Creates a new dataset.\n\nFor the definition s of datasets and other genomics resources, see\n[Fundamentals of Google\nGenomi cs](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
1346 "httpMethod": "POST",
1347 "id": "genomics.datasets.create",
1348 "parameterOrder": [], 1157 "parameterOrder": [],
1349 "parameters": {}, 1158 "parameters": {},
1350 "path": "v1/datasets", 1159 "path": "v1/referencesets/search",
1351 "request": { 1160 "request": {
1352 "$ref": "Dataset" 1161 "$ref": "SearchReferenceSetsRequest"
1353 }, 1162 },
1354 "response": { 1163 "response": {
1355 "$ref": "Dataset" 1164 "$ref": "SearchReferenceSetsResponse"
1356 }, 1165 },
1357 "scopes": [ 1166 "scopes": [
1358 "https://www.googleapis.com/auth/cloud-platform", 1167 "https://www.googleapis.com/auth/cloud-platform",
1359 "https://www.googleapis.com/auth/genomics" 1168 "https://www.googleapis.com/auth/genomics",
1360 ] 1169 "https://www.googleapis.com/auth/genomics.readonly"
1361 },
1362 "getIamPolicy": {
1363 "description": "Gets the access control policy for the datas et. This is empty if the\npolicy or resource does not exist.\n\nSee <a href=\"/i am/docs/managing-policies#getting_a_policy\">Getting a\nPolicy</a> for more info rmation.\n\nFor the definitions of datasets and other genomics resources, see\n[ Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals -of-google-genomics)",
1364 "httpMethod": "POST",
1365 "id": "genomics.datasets.getIamPolicy",
1366 "parameterOrder": [
1367 "resource"
1368 ],
1369 "parameters": {
1370 "resource": {
1371 "description": "REQUIRED: The resource for which pol icy is being specified. Format is\n`datasets/<dataset ID>`.",
1372 "location": "path",
1373 "pattern": "^datasets/[^/]+$",
1374 "required": true,
1375 "type": "string"
1376 }
1377 },
1378 "path": "v1/{+resource}:getIamPolicy",
1379 "request": {
1380 "$ref": "GetIamPolicyRequest"
1381 },
1382 "response": {
1383 "$ref": "Policy"
1384 },
1385 "scopes": [
1386 "https://www.googleapis.com/auth/cloud-platform",
1387 "https://www.googleapis.com/auth/genomics"
1388 ]
1389 },
1390 "undelete": {
1391 "description": "Undeletes a dataset by restoring a dataset w hich was deleted via this API.\n\nFor the definitions of datasets and other geno mics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com /genomics/fundamentals-of-google-genomics)\n\nThis operation is only possible fo r a week after the deletion occurred.",
1392 "httpMethod": "POST",
1393 "id": "genomics.datasets.undelete",
1394 "parameterOrder": [
1395 "datasetId"
1396 ],
1397 "parameters": {
1398 "datasetId": {
1399 "description": "The ID of the dataset to be undelete d.",
1400 "location": "path",
1401 "required": true,
1402 "type": "string"
1403 }
1404 },
1405 "path": "v1/datasets/{datasetId}:undelete",
1406 "request": {
1407 "$ref": "UndeleteDatasetRequest"
1408 },
1409 "response": {
1410 "$ref": "Dataset"
1411 },
1412 "scopes": [
1413 "https://www.googleapis.com/auth/cloud-platform",
1414 "https://www.googleapis.com/auth/genomics"
1415 ] 1170 ]
1416 }, 1171 },
1417 "get": { 1172 "get": {
1418 "description": "Gets a dataset by ID.\n\nFor the definitions of datasets and other genomics resources, see\n[Fundamentals of Google\nGenomic s](https://cloud.google.com/genomics/fundamentals-of-google-genomics)", 1173 "description": "Gets a reference set.\n\nFor the definitions of references and other genomics resources, see\n[Fundamentals of Google\nGenom ics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nImple ments\n[GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob /v0.5.1/src/main/resources/avro/referencemethods.avdl#L83).",
1419 "httpMethod": "GET", 1174 "httpMethod": "GET",
1420 "id": "genomics.datasets.get", 1175 "id": "genomics.referencesets.get",
1421 "parameterOrder": [ 1176 "parameterOrder": [
1422 "datasetId" 1177 "referenceSetId"
1423 ], 1178 ],
1424 "parameters": { 1179 "parameters": {
1425 "datasetId": { 1180 "referenceSetId": {
1426 "description": "The ID of the dataset.", 1181 "description": "The ID of the reference set.",
1427 "location": "path", 1182 "location": "path",
1428 "required": true, 1183 "required": true,
1429 "type": "string" 1184 "type": "string"
1430 } 1185 }
1431 }, 1186 },
1432 "path": "v1/datasets/{datasetId}", 1187 "path": "v1/referencesets/{referenceSetId}",
1433 "response": { 1188 "response": {
1434 "$ref": "Dataset" 1189 "$ref": "ReferenceSet"
1435 }, 1190 },
1436 "scopes": [ 1191 "scopes": [
1437 "https://www.googleapis.com/auth/cloud-platform", 1192 "https://www.googleapis.com/auth/cloud-platform",
1193 "https://www.googleapis.com/auth/genomics",
1194 "https://www.googleapis.com/auth/genomics.readonly"
1195 ]
1196 }
1197 }
1198 },
1199 "readgroupsets": {
1200 "methods": {
1201 "import": {
1202 "description": "Creates read group sets by asynchronously im porting the provided\ninformation.\n\nFor the definitions of read group sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud .google.com/genomics/fundamentals-of-google-genomics)\n\nThe caller must have WR ITE permissions to the dataset.\n\n## Notes on [BAM](https://samtools.github.io/ hts-specs/SAMv1.pdf) import\n\n- Tags will be converted to strings - tag types a re not preserved\n- Comments (`@CO`) in the input file header will not be preser ved\n- Original header order of references (`@SQ`) will not be preserved\n- Any reverse stranded unmapped reads will be reverse complemented, and\ntheir qualiti es (also the \"BQ\" and \"OQ\" tags, if any) will be reversed\n- Unmapped reads will be stripped of positional information (reference name\nand position)",
1203 "httpMethod": "POST",
1204 "id": "genomics.readgroupsets.import",
1205 "parameterOrder": [],
1206 "parameters": {},
1207 "path": "v1/readgroupsets:import",
1208 "request": {
1209 "$ref": "ImportReadGroupSetsRequest"
1210 },
1211 "response": {
1212 "$ref": "Operation"
1213 },
1214 "scopes": [
1215 "https://www.googleapis.com/auth/cloud-platform",
1216 "https://www.googleapis.com/auth/devstorage.read_write",
1217 "https://www.googleapis.com/auth/genomics"
1218 ]
1219 },
1220 "delete": {
1221 "description": "Deletes a read group set.\n\nFor the definit ions of read group sets and other genomics resources, see\n[Fundamentals of Goog le\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) ",
1222 "httpMethod": "DELETE",
1223 "id": "genomics.readgroupsets.delete",
1224 "parameterOrder": [
1225 "readGroupSetId"
1226 ],
1227 "parameters": {
1228 "readGroupSetId": {
1229 "description": "The ID of the read group set to be d eleted. The caller must have WRITE\npermissions to the dataset associated with t his read group set.",
1230 "location": "path",
1231 "required": true,
1232 "type": "string"
1233 }
1234 },
1235 "path": "v1/readgroupsets/{readGroupSetId}",
1236 "response": {
1237 "$ref": "Empty"
1238 },
1239 "scopes": [
1240 "https://www.googleapis.com/auth/cloud-platform",
1241 "https://www.googleapis.com/auth/genomics"
1242 ]
1243 },
1244 "export": {
1245 "description": "Exports a read group set to a BAM file in Go ogle Cloud Storage.\n\nFor the definitions of read group sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/gen omics/fundamentals-of-google-genomics)\n\nNote that currently there may be some differences between exported BAM\nfiles and the original BAM file at the time of import. See\nImportReadGroupSets\nfor caveats.",
1246 "httpMethod": "POST",
1247 "id": "genomics.readgroupsets.export",
1248 "parameterOrder": [
1249 "readGroupSetId"
1250 ],
1251 "parameters": {
1252 "readGroupSetId": {
1253 "description": "Required. The ID of the read group s et to export. The caller must have\nREAD access to this read group set.",
1254 "location": "path",
1255 "required": true,
1256 "type": "string"
1257 }
1258 },
1259 "path": "v1/readgroupsets/{readGroupSetId}:export",
1260 "request": {
1261 "$ref": "ExportReadGroupSetRequest"
1262 },
1263 "response": {
1264 "$ref": "Operation"
1265 },
1266 "scopes": [
1267 "https://www.googleapis.com/auth/cloud-platform",
1268 "https://www.googleapis.com/auth/devstorage.read_write",
1269 "https://www.googleapis.com/auth/genomics"
1270 ]
1271 },
1272 "search": {
1273 "description": "Searches for read group sets matching the cr iteria.\n\nFor the definitions of read group sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundam entals-of-google-genomics)\n\nImplements\n[GlobalAllianceApi.searchReadGroupSets ](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmetho ds.avdl#L135).",
1274 "httpMethod": "POST",
1275 "id": "genomics.readgroupsets.search",
1276 "parameterOrder": [],
1277 "parameters": {},
1278 "path": "v1/readgroupsets/search",
1279 "request": {
1280 "$ref": "SearchReadGroupSetsRequest"
1281 },
1282 "response": {
1283 "$ref": "SearchReadGroupSetsResponse"
1284 },
1285 "scopes": [
1286 "https://www.googleapis.com/auth/cloud-platform",
1287 "https://www.googleapis.com/auth/genomics",
1288 "https://www.googleapis.com/auth/genomics.readonly"
1289 ]
1290 },
1291 "get": {
1292 "description": "Gets a read group set by ID.\n\nFor the defi nitions of read group sets and other genomics resources, see\n[Fundamentals of G oogle\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomi cs)",
1293 "httpMethod": "GET",
1294 "id": "genomics.readgroupsets.get",
1295 "parameterOrder": [
1296 "readGroupSetId"
1297 ],
1298 "parameters": {
1299 "readGroupSetId": {
1300 "description": "The ID of the read group set.",
1301 "location": "path",
1302 "required": true,
1303 "type": "string"
1304 }
1305 },
1306 "path": "v1/readgroupsets/{readGroupSetId}",
1307 "response": {
1308 "$ref": "ReadGroupSet"
1309 },
1310 "scopes": [
1311 "https://www.googleapis.com/auth/cloud-platform",
1438 "https://www.googleapis.com/auth/genomics", 1312 "https://www.googleapis.com/auth/genomics",
1439 "https://www.googleapis.com/auth/genomics.readonly" 1313 "https://www.googleapis.com/auth/genomics.readonly"
1440 ] 1314 ]
1441 }, 1315 },
1442 "patch": { 1316 "patch": {
1443 "description": "Updates a dataset.\n\nFor the definitions of datasets and other genomics resources, see\n[Fundamentals of Google\nGenomics]( https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nThis metho d supports patch semantics.", 1317 "description": "Updates a read group set.\n\nFor the definit ions of read group sets and other genomics resources, see\n[Fundamentals of Goog le\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) \n\nThis method supports patch semantics.",
1444 "httpMethod": "PATCH", 1318 "httpMethod": "PATCH",
1445 "id": "genomics.datasets.patch", 1319 "id": "genomics.readgroupsets.patch",
1446 "parameterOrder": [ 1320 "parameterOrder": [
1447 "datasetId" 1321 "readGroupSetId"
1448 ], 1322 ],
1449 "parameters": { 1323 "parameters": {
1450 "datasetId": { 1324 "readGroupSetId": {
1451 "description": "The ID of the dataset to be updated. ", 1325 "description": "The ID of the read group set to be u pdated. The caller must have WRITE\npermissions to the dataset associated with t his read group set.",
1452 "location": "path", 1326 "location": "path",
1453 "required": true, 1327 "required": true,
1454 "type": "string" 1328 "type": "string"
1455 }, 1329 },
1456 "updateMask": { 1330 "updateMask": {
1457 "description": "An optional mask specifying which fi elds to update. At this time, the only\nmutable field is name. The only\naccepta ble value is \"name\". If unspecified, all mutable fields will be\nupdated.", 1331 "description": "An optional mask specifying which fi elds to update. Supported fields:\n\n* name.\n* referenceSetId.\n\nLeaving `upda teMask` unset is equivalent to specifying all mutable\nfields.",
1458 "format": "google-fieldmask", 1332 "format": "google-fieldmask",
1459 "location": "query", 1333 "location": "query",
1460 "type": "string" 1334 "type": "string"
1461 } 1335 }
1462 }, 1336 },
1463 "path": "v1/datasets/{datasetId}", 1337 "path": "v1/readgroupsets/{readGroupSetId}",
1464 "request": { 1338 "request": {
1465 "$ref": "Dataset" 1339 "$ref": "ReadGroupSet"
1466 }, 1340 },
1467 "response": { 1341 "response": {
1468 "$ref": "Dataset" 1342 "$ref": "ReadGroupSet"
1469 }, 1343 },
1470 "scopes": [ 1344 "scopes": [
1471 "https://www.googleapis.com/auth/cloud-platform", 1345 "https://www.googleapis.com/auth/cloud-platform",
1472 "https://www.googleapis.com/auth/genomics" 1346 "https://www.googleapis.com/auth/genomics"
1473 ] 1347 ]
1474 }, 1348 }
1475 "testIamPermissions": { 1349 },
1476 "description": "Returns permissions that a caller has on the specified resource.\nSee <a href=\"/iam/docs/managing-policies#testing_permissi ons\">Testing\nPermissions</a> for more information.\n\nFor the definitions of d atasets and other genomics resources, see\n[Fundamentals of Google\nGenomics](ht tps://cloud.google.com/genomics/fundamentals-of-google-genomics)", 1350 "resources": {
1351 "coveragebuckets": {
1352 "methods": {
1353 "list": {
1354 "description": "Lists fixed width coverage buckets f or a read group set, each of which\ncorrespond to a range of a reference sequenc e. Each bucket summarizes\ncoverage information across its corresponding genomic range.\n\nFor the definitions of read group sets and other genomics resources, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fundam entals-of-google-genomics)\n\nCoverage is defined as the number of reads which a re aligned to a given\nbase in the reference sequence. Coverage buckets are avai lable at several\nprecomputed bucket widths, enabling retrieval of various cover age 'zoom\nlevels'. The caller must have READ permissions for the target read gr oup\nset.",
1355 "httpMethod": "GET",
1356 "id": "genomics.readgroupsets.coveragebuckets.list",
1357 "parameterOrder": [
1358 "readGroupSetId"
1359 ],
1360 "parameters": {
1361 "end": {
1362 "description": "The end position of the rang e on the reference, 0-based exclusive. If\nspecified, `referenceName` must also be specified. If unset or 0, defaults\nto the length of the reference.",
1363 "format": "int64",
1364 "location": "query",
1365 "type": "string"
1366 },
1367 "pageToken": {
1368 "description": "The continuation token, whic h is used to page through large result sets.\nTo get the next page of results, s et this parameter to the value of\n`nextPageToken` from the previous response.",
1369 "location": "query",
1370 "type": "string"
1371 },
1372 "pageSize": {
1373 "description": "The maximum number of result s to return in a single page. If unspecified,\ndefaults to 1024. The maximum val ue is 2048.",
1374 "format": "int32",
1375 "location": "query",
1376 "type": "integer"
1377 },
1378 "start": {
1379 "description": "The start position of the ra nge on the reference, 0-based inclusive. If\nspecified, `referenceName` must als o be specified. Defaults to 0.",
1380 "format": "int64",
1381 "location": "query",
1382 "type": "string"
1383 },
1384 "readGroupSetId": {
1385 "description": "Required. The ID of the read group set over which coverage is requested.",
1386 "location": "path",
1387 "required": true,
1388 "type": "string"
1389 },
1390 "targetBucketWidth": {
1391 "description": "The desired width of each re ported coverage bucket in base pairs. This\nwill be rounded down to the nearest precomputed bucket width; the value\nof which is returned as `bucketWidth` in th e response. Defaults\nto infinity (each bucket spans an entire reference sequenc e) or the length\nof the target range, if specified. The smallest precomputed\n` bucketWidth` is currently 2048 base pairs; this is subject to\nchange.",
1392 "format": "int64",
1393 "location": "query",
1394 "type": "string"
1395 },
1396 "referenceName": {
1397 "description": "The name of the reference to query, within the reference set associated\nwith this query. Optional.",
1398 "location": "query",
1399 "type": "string"
1400 }
1401 },
1402 "path": "v1/readgroupsets/{readGroupSetId}/coverageb uckets",
1403 "response": {
1404 "$ref": "ListCoverageBucketsResponse"
1405 },
1406 "scopes": [
1407 "https://www.googleapis.com/auth/cloud-platform" ,
1408 "https://www.googleapis.com/auth/genomics",
1409 "https://www.googleapis.com/auth/genomics.readon ly"
1410 ]
1411 }
1412 }
1413 }
1414 }
1415 },
1416 "reads": {
1417 "methods": {
1418 "search": {
1419 "description": "Gets a list of reads for one or more read gr oup sets.\n\nFor the definitions of read group sets and other genomics resources , see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/fund amentals-of-google-genomics)\n\nReads search operates over a genomic coordinate space of reference sequence\n& position defined over the reference sequences to which the requested\nread group sets are aligned.\n\nIf a target positional rang e is specified, search returns all reads whose\nalignment to the reference genom e overlap the range. A query which\nspecifies only read group set IDs yields all reads in those read group\nsets, including unmapped reads.\n\nAll reads returne d (including reads on subsequent pages) are ordered by\ngenomic coordinate (by r eference sequence, then position). Reads with\nequivalent genomic coordinates ar e returned in an unspecified order. This\norder is consistent, such that two que ries for the same content (regardless\nof page size) yield reads in the same ord er across their respective streams\nof paginated responses.\n\nImplements\n[Glob alAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main /resources/avro/readmethods.avdl#L85).",
1477 "httpMethod": "POST", 1420 "httpMethod": "POST",
1478 "id": "genomics.datasets.testIamPermissions", 1421 "id": "genomics.reads.search",
1479 "parameterOrder": [ 1422 "parameterOrder": [],
1480 "resource" 1423 "parameters": {},
1481 ], 1424 "path": "v1/reads/search",
1482 "parameters": {
1483 "resource": {
1484 "description": "REQUIRED: The resource for which pol icy is being specified. Format is\n`datasets/<dataset ID>`.",
1485 "location": "path",
1486 "pattern": "^datasets/[^/]+$",
1487 "required": true,
1488 "type": "string"
1489 }
1490 },
1491 "path": "v1/{+resource}:testIamPermissions",
1492 "request": { 1425 "request": {
1493 "$ref": "TestIamPermissionsRequest" 1426 "$ref": "SearchReadsRequest"
1494 }, 1427 },
1495 "response": { 1428 "response": {
1496 "$ref": "TestIamPermissionsResponse" 1429 "$ref": "SearchReadsResponse"
1497 }, 1430 },
1498 "scopes": [ 1431 "scopes": [
1499 "https://www.googleapis.com/auth/cloud-platform", 1432 "https://www.googleapis.com/auth/cloud-platform",
1500 "https://www.googleapis.com/auth/genomics" 1433 "https://www.googleapis.com/auth/genomics",
1434 "https://www.googleapis.com/auth/genomics.readonly"
1501 ] 1435 ]
1502 }, 1436 }
1437 }
1438 },
1439 "callsets": {
1440 "methods": {
1503 "delete": { 1441 "delete": {
1504 "description": "Deletes a dataset and all of its contents (a ll read group sets,\nreference sets, variant sets, call sets, annotation sets, e tc.)\nThis is reversible (up to one week after the deletion) via\nthe\ndatasets. undelete\noperation.\n\nFor the definitions of datasets and other genomics resou rces, see\n[Fundamentals of Google\nGenomics](https://cloud.google.com/genomics/ fundamentals-of-google-genomics)", 1442 "description": "Deletes a call set.\n\nFor the definitions o f call sets and other genomics resources, see\n[Fundamentals of Google\nGenomics ](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
1505 "httpMethod": "DELETE", 1443 "httpMethod": "DELETE",
1506 "id": "genomics.datasets.delete", 1444 "id": "genomics.callsets.delete",
1507 "parameterOrder": [ 1445 "parameterOrder": [
1508 "datasetId" 1446 "callSetId"
1509 ], 1447 ],
1510 "parameters": { 1448 "parameters": {
1511 "datasetId": { 1449 "callSetId": {
1512 "description": "The ID of the dataset to be deleted. ", 1450 "description": "The ID of the call set to be deleted .",
1513 "location": "path", 1451 "location": "path",
1514 "required": true, 1452 "required": true,
1515 "type": "string" 1453 "type": "string"
1516 } 1454 }
1517 }, 1455 },
1518 "path": "v1/datasets/{datasetId}", 1456 "path": "v1/callsets/{callSetId}",
1519 "response": { 1457 "response": {
1520 "$ref": "Empty" 1458 "$ref": "Empty"
1521 }, 1459 },
1522 "scopes": [ 1460 "scopes": [
1523 "https://www.googleapis.com/auth/cloud-platform", 1461 "https://www.googleapis.com/auth/cloud-platform",
1524 "https://www.googleapis.com/auth/genomics" 1462 "https://www.googleapis.com/auth/genomics"
1525 ] 1463 ]
1526 }, 1464 },
1527 "list": { 1465 "search": {
1528 "description": "Lists datasets within a project.\n\nFor the definitions of datasets and other genomics resources, see\n[Fundamentals of Goog le\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) ", 1466 "description": "Gets a list of call sets matching the criter ia.\n\nFor the definitions of call sets and other genomics resources, see\n[Fund amentals of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of- google-genomics)\n\nImplements\n[GlobalAllianceApi.searchCallSets](https://githu b.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L178 ).",
1467 "httpMethod": "POST",
1468 "id": "genomics.callsets.search",
1469 "parameterOrder": [],
1470 "parameters": {},
1471 "path": "v1/callsets/search",
1472 "request": {
1473 "$ref": "SearchCallSetsRequest"
1474 },
1475 "response": {
1476 "$ref": "SearchCallSetsResponse"
1477 },
1478 "scopes": [
1479 "https://www.googleapis.com/auth/cloud-platform",
1480 "https://www.googleapis.com/auth/genomics",
1481 "https://www.googleapis.com/auth/genomics.readonly"
1482 ]
1483 },
1484 "get": {
1485 "description": "Gets a call set by ID.\n\nFor the definition s of call sets and other genomics resources, see\n[Fundamentals of Google\nGenom ics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
1529 "httpMethod": "GET", 1486 "httpMethod": "GET",
1530 "id": "genomics.datasets.list", 1487 "id": "genomics.callsets.get",
1531 "parameterOrder": [], 1488 "parameterOrder": [
1489 "callSetId"
1490 ],
1532 "parameters": { 1491 "parameters": {
1533 "pageToken": { 1492 "callSetId": {
1534 "description": "The continuation token, which is use d to page through large result sets.\nTo get the next page of results, set this parameter to the value of\n`nextPageToken` from the previous response.", 1493 "description": "The ID of the call set.",
1535 "location": "query", 1494 "location": "path",
1495 "required": true,
1496 "type": "string"
1497 }
1498 },
1499 "path": "v1/callsets/{callSetId}",
1500 "response": {
1501 "$ref": "CallSet"
1502 },
1503 "scopes": [
1504 "https://www.googleapis.com/auth/cloud-platform",
1505 "https://www.googleapis.com/auth/genomics",
1506 "https://www.googleapis.com/auth/genomics.readonly"
1507 ]
1508 },
1509 "patch": {
1510 "description": "Updates a call set.\n\nFor the definitions o f call sets and other genomics resources, see\n[Fundamentals of Google\nGenomics ](https://cloud.google.com/genomics/fundamentals-of-google-genomics)\n\nThis met hod supports patch semantics.",
1511 "httpMethod": "PATCH",
1512 "id": "genomics.callsets.patch",
1513 "parameterOrder": [
1514 "callSetId"
1515 ],
1516 "parameters": {
1517 "callSetId": {
1518 "description": "The ID of the call set to be updated .",
1519 "location": "path",
1520 "required": true,
1536 "type": "string" 1521 "type": "string"
1537 }, 1522 },
1538 "pageSize": { 1523 "updateMask": {
1539 "description": "The maximum number of results to ret urn in a single page. If unspecified,\ndefaults to 50. The maximum value is 1024 .", 1524 "description": "An optional mask specifying which fi elds to update. At this time, the only\nmutable field is name. The only\naccepta ble value is \"name\". If unspecified, all mutable fields will be\nupdated.",
1540 "format": "int32", 1525 "format": "google-fieldmask",
1541 "location": "query",
1542 "type": "integer"
1543 },
1544 "projectId": {
1545 "description": "Required. The Google Cloud project I D to list datasets for.",
1546 "location": "query", 1526 "location": "query",
1547 "type": "string" 1527 "type": "string"
1548 } 1528 }
1549 }, 1529 },
1550 "path": "v1/datasets", 1530 "path": "v1/callsets/{callSetId}",
1551 "response": { 1531 "request": {
1552 "$ref": "ListDatasetsResponse" 1532 "$ref": "CallSet"
1553 }, 1533 },
1554 "scopes": [ 1534 "response": {
1555 "https://www.googleapis.com/auth/cloud-platform", 1535 "$ref": "CallSet"
1556 "https://www.googleapis.com/auth/genomics", 1536 },
1557 "https://www.googleapis.com/auth/genomics.readonly" 1537 "scopes": [
1538 "https://www.googleapis.com/auth/cloud-platform",
1539 "https://www.googleapis.com/auth/genomics"
1540 ]
1541 },
1542 "create": {
1543 "description": "Creates a new call set.\n\nFor the definitio ns of call sets and other genomics resources, see\n[Fundamentals of Google\nGeno mics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)",
1544 "httpMethod": "POST",
1545 "id": "genomics.callsets.create",
1546 "parameterOrder": [],
1547 "parameters": {},
1548 "path": "v1/callsets",
1549 "request": {
1550 "$ref": "CallSet"
1551 },
1552 "response": {
1553 "$ref": "CallSet"
1554 },
1555 "scopes": [
1556 "https://www.googleapis.com/auth/cloud-platform",
1557 "https://www.googleapis.com/auth/genomics"
1558 ] 1558 ]
1559 } 1559 }
1560 } 1560 }
1561 } 1561 }
1562 }, 1562 },
1563 "revision": "20170727", 1563 "revision": "20170817",
1564 "rootUrl": "https://genomics.googleapis.com/", 1564 "rootUrl": "https://genomics.googleapis.com/",
1565 "schemas": { 1565 "schemas": {
1566 "SearchReferencesRequest": { 1566 "Range": {
1567 "id": "SearchReferencesRequest", 1567 "description": "A 0-based half-open genomic coordinate range for sea rch requests.",
1568 "properties": { 1568 "id": "Range",
1569 "pageToken": { 1569 "properties": {
1570 "description": "The continuation token, which is used to pag e through large result sets.\nTo get the next page of results, set this paramete r to the value of\n`nextPageToken` from the previous response.", 1570 "referenceName": {
1571 "type": "string" 1571 "description": "The reference sequence name, for example `ch r1`,\n`1`, or `chrX`.",
1572 }, 1572 "type": "string"
1573 "accessions": { 1573 },
1574 "description": "If present, return references for which a pr efix of any of\nsourceAccessions match\nany of these strings. Accession numbers typically have a main number and a\nversion, for example `GCF_000001405.26`.", 1574 "start": {
1575 "items": { 1575 "description": "The start position of the range on the refer ence, 0-based inclusive.",
1576 "type": "string" 1576 "format": "int64",
1577 }, 1577 "type": "string"
1578 "type": "array" 1578 },
1579 }, 1579 "end": {
1580 "pageSize": { 1580 "description": "The end position of the range on the referen ce, 0-based exclusive.",
1581 "description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 1024. The maximum value is 4096.", 1581 "format": "int64",
1582 "format": "int32", 1582 "type": "string"
1583 "type": "integer" 1583 }
1584 },
1585 "type": "object"
1586 },
1587 "VariantSet": {
1588 "description": "A variant set is a collection of call sets and varia nts. It contains summary\nstatistics of those contents. A variant set belongs to a dataset.\n\nFor more genomics resource definitions, see [Fundamentals of Goog le\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) ",
1589 "id": "VariantSet",
1590 "properties": {
1591 "description": {
1592 "description": "A textual description of this variant set.",
1593 "type": "string"
1594 },
1595 "datasetId": {
1596 "description": "The dataset to which this variant set belong s.",
1597 "type": "string"
1598 },
1599 "name": {
1600 "description": "User-specified, mutable name.",
1601 "type": "string"
1584 }, 1602 },
1585 "referenceSetId": { 1603 "referenceSetId": {
1586 "description": "If present, return only references which bel ong to this reference set.", 1604 "description": "The reference set to which the variant set i s mapped. The reference set\ndescribes the alignment provenance of the variant s et, while the\n`referenceBounds` describe the shape of the actual variant data. The\nreference set's reference names are a superset of those found in the\n`refe renceBounds`.\n\nFor example, given a variant set that is mapped to the GRCh38 r eference set\nand contains a single variant on reference 'X', `referenceBounds` would\ncontain only an entry for 'X', while the associated reference set\nenumer ates all possible references: '1', '2', 'X', 'Y', 'MT', etc.",
1587 "type": "string" 1605 "type": "string"
1588 }, 1606 },
1589 "md5checksums": { 1607 "metadata": {
1590 "description": "If present, return references for which the\ nmd5checksum matches exactly.", 1608 "description": "The metadata associated with this variant se t.",
1591 "items": { 1609 "items": {
1592 "type": "string" 1610 "$ref": "VariantSetMetadata"
1593 }, 1611 },
1594 "type": "array" 1612 "type": "array"
1595 } 1613 },
1596 }, 1614 "referenceBounds": {
1597 "type": "object" 1615 "description": "A list of all references used by the variant s in a variant set\nwith associated coordinate upper bounds for each one.",
1598 }, 1616 "items": {
1599 "LinearAlignment": { 1617 "$ref": "ReferenceBound"
1600 "description": "A linear alignment can be represented by one CIGAR s tring. Describes the\nmapped position and local alignment of the read to the ref erence.", 1618 },
1601 "id": "LinearAlignment", 1619 "type": "array"
1602 "properties": {
1603 "cigar": {
1604 "description": "Represents the local alignment of this seque nce (alignment matches, indels,\netc) against the reference.",
1605 "items": {
1606 "$ref": "CigarUnit"
1607 },
1608 "type": "array"
1609 },
1610 "position": {
1611 "$ref": "Position",
1612 "description": "The position of this alignment."
1613 },
1614 "mappingQuality": {
1615 "description": "The mapping quality of this alignment. Repre sents how likely\nthe read maps to this position as opposed to other locations.\ n\nSpecifically, this is -10 log10 Pr(mapping position is wrong), rounded to\nth e nearest integer.",
1616 "format": "int32",
1617 "type": "integer"
1618 }
1619 },
1620 "type": "object"
1621 },
1622 "Dataset": {
1623 "description": "A Dataset is a collection of genomic data.\n\nFor mo re genomics resource definitions, see [Fundamentals of Google\nGenomics](https:/ /cloud.google.com/genomics/fundamentals-of-google-genomics)",
1624 "id": "Dataset",
1625 "properties": {
1626 "name": {
1627 "description": "The dataset name.",
1628 "type": "string"
1629 },
1630 "projectId": {
1631 "description": "The Google Cloud project ID that this datase t belongs to.",
1632 "type": "string"
1633 }, 1620 },
1634 "id": { 1621 "id": {
1635 "description": "The server-generated dataset ID, unique acro ss all datasets.", 1622 "description": "The server-generated variant set ID, unique across all variant sets.",
1636 "type": "string" 1623 "type": "string"
1637 }, 1624 }
1638 "createTime": { 1625 },
1639 "description": "The time this dataset was created, in second s from the epoch.", 1626 "type": "object"
1640 "format": "google-datetime", 1627 },
1641 "type": "string" 1628 "ReferenceBound": {
1642 } 1629 "description": "ReferenceBound records an upper bound for the starti ng coordinate of\nvariants in a particular reference.",
1643 }, 1630 "id": "ReferenceBound",
1644 "type": "object" 1631 "properties": {
1645 }, 1632 "referenceName": {
1646 "ImportVariantsResponse": { 1633 "description": "The name of the reference associated with th is reference bound.",
1647 "description": "The variant data import response.", 1634 "type": "string"
1648 "id": "ImportVariantsResponse", 1635 },
1649 "properties": { 1636 "upperBound": {
1650 "callSetIds": { 1637 "description": "An upper bound (inclusive) on the starting c oordinate of any\nvariant in the reference sequence.",
1651 "description": "IDs of the call sets created during the impo rt.", 1638 "format": "int64",
1652 "items": { 1639 "type": "string"
1653 "type": "string" 1640 }
1654 }, 1641 },
1655 "type": "array" 1642 "type": "object"
1656 } 1643 },
1657 }, 1644 "BatchCreateAnnotationsResponse": {
1658 "type": "object" 1645 "id": "BatchCreateAnnotationsResponse",
1659 }, 1646 "properties": {
1660 "ReadGroup": { 1647 "entries": {
1661 "description": "A read group is all the data that's processed the sa me way by the sequencer.", 1648 "description": "The resulting per-annotation entries, ordere d consistently with the\noriginal request.",
1662 "id": "ReadGroup", 1649 "items": {
1663 "properties": { 1650 "$ref": "Entry"
1664 "description": { 1651 },
1665 "description": "A free-form text description of this read gr oup.", 1652 "type": "array"
1666 "type": "string" 1653 }
1667 }, 1654 },
1668 "sampleId": { 1655 "type": "object"
1669 "description": "A client-supplied sample identifier for the reads in this read group.", 1656 },
1670 "type": "string" 1657 "SearchCallSetsResponse": {
1671 }, 1658 "description": "The call set search response.",
1672 "datasetId": { 1659 "id": "SearchCallSetsResponse",
1673 "description": "The dataset to which this read group belongs .", 1660 "properties": {
1674 "type": "string" 1661 "nextPageToken": {
1675 }, 1662 "description": "The continuation token, which is used to pag e through large result sets.\nProvide this value in a subsequent request to retu rn the next page of\nresults. This field will be empty if there aren't any addit ional results.",
1676 "experiment": { 1663 "type": "string"
1677 "$ref": "Experiment", 1664 },
1678 "description": "The experiment used to generate this read gr oup." 1665 "callSets": {
1679 }, 1666 "description": "The list of matching call sets.",
1680 "name": { 1667 "items": {
1681 "description": "The read group name. This corresponds to the @RG ID field in the SAM spec.", 1668 "$ref": "CallSet"
1682 "type": "string" 1669 },
1683 }, 1670 "type": "array"
1684 "referenceSetId": { 1671 }
1685 "description": "The reference set the reads in this read gro up are aligned to.", 1672 },
1673 "type": "object"
1674 },
1675 "Variant": {
1676 "description": "A variant represents a change in DNA sequence relati ve to a reference\nsequence. For example, a variant could represent a SNP or an insertion.\nVariants belong to a variant set.\n\nFor more genomics resource defi nitions, see [Fundamentals of Google\nGenomics](https://cloud.google.com/genomic s/fundamentals-of-google-genomics)\n\nEach of the calls on a variant represent a determination of genotype with\nrespect to that variant. For example, a call mi ght assign probability of 0.32\nto the occurrence of a SNP named rs1234 in a sam ple named NA12345. A call\nbelongs to a call set, which contains related calls t ypically from one\nsample.",
1677 "id": "Variant",
1678 "properties": {
1679 "id": {
1680 "description": "The server-generated variant ID, unique acro ss all variants.",
1681 "type": "string"
1682 },
1683 "variantSetId": {
1684 "description": "The ID of the variant set this variant belon gs to.",
1685 "type": "string"
1686 },
1687 "referenceName": {
1688 "description": "The reference on which this variant occurs.\ n(such as `chr20` or `X`)",
1686 "type": "string" 1689 "type": "string"
1687 }, 1690 },
1688 "info": { 1691 "info": {
1689 "additionalProperties": { 1692 "additionalProperties": {
1690 "items": { 1693 "items": {
1691 "type": "any" 1694 "type": "any"
1692 }, 1695 },
1693 "type": "array" 1696 "type": "array"
1694 }, 1697 },
1695 "description": "A map of additional read group information. This must be of the form\nmap<string, string[]> (string key mapping to a list of string values).", 1698 "description": "A map of additional variant information. Thi s must be of the form\nmap<string, string[]> (string key mapping to a list of st ring values).",
1696 "type": "object" 1699 "type": "object"
1697 }, 1700 },
1698 "id": { 1701 "referenceBases": {
1699 "description": "The server-generated read group ID, unique f or all read groups.\nNote: This is different than the @RG ID field in the SAM sp ec. For that\nvalue, see name.", 1702 "description": "The reference bases for this variant. They s tart at the given\nposition.",
1700 "type": "string" 1703 "type": "string"
1701 }, 1704 },
1702 "programs": { 1705 "names": {
1703 "description": "The programs used to generate this read grou p. Programs are always\nidentical for all read groups within a read group set. F or this reason,\nonly the first read group in a returned set will have this fiel d\npopulated.", 1706 "description": "Names for the variant, for example a RefSNP ID.",
1704 "items": { 1707 "items": {
1705 "$ref": "Program" 1708 "type": "string"
1706 }, 1709 },
1707 "type": "array" 1710 "type": "array"
1708 }, 1711 },
1709 "predictedInsertSize": { 1712 "alternateBases": {
1710 "description": "The predicted insert size of this read group . The insert size is the length\nthe sequenced DNA fragment from end-to-end, not including the adapters.", 1713 "description": "The bases that appear instead of the referen ce bases.",
1714 "items": {
1715 "type": "string"
1716 },
1717 "type": "array"
1718 },
1719 "end": {
1720 "description": "The end position (0-based) of this variant. This corresponds to the first\nbase after the last base in the reference allele. So, the length of\nthe reference allele is (end - start). This is useful for va riants\nthat don't explicitly give alternate bases, for example large deletions. ",
1721 "format": "int64",
1722 "type": "string"
1723 },
1724 "filter": {
1725 "description": "A list of filters (normally quality filters) this variant has failed.\n`PASS` indicates this variant has passed all filters. ",
1726 "items": {
1727 "type": "string"
1728 },
1729 "type": "array"
1730 },
1731 "calls": {
1732 "description": "The variant calls for this particular varian t. Each one represents the\ndetermination of genotype with respect to this varia nt.",
1733 "items": {
1734 "$ref": "VariantCall"
1735 },
1736 "type": "array"
1737 },
1738 "created": {
1739 "description": "The date this variant was created, in millis econds from the epoch.",
1740 "format": "int64",
1741 "type": "string"
1742 },
1743 "start": {
1744 "description": "The position at which this variant occurs (0 -based).\nThis corresponds to the first base of the string of reference bases.",
1745 "format": "int64",
1746 "type": "string"
1747 },
1748 "quality": {
1749 "description": "A measure of how likely this variant is to b e real.\nA higher value is better.",
1750 "format": "double",
1751 "type": "number"
1752 }
1753 },
1754 "type": "object"
1755 },
1756 "ListOperationsResponse": {
1757 "description": "The response message for Operations.ListOperations." ,
1758 "id": "ListOperationsResponse",
1759 "properties": {
1760 "nextPageToken": {
1761 "description": "The standard List next-page token.",
1762 "type": "string"
1763 },
1764 "operations": {
1765 "description": "A list of operations that matches the specif ied filter in the request.",
1766 "items": {
1767 "$ref": "Operation"
1768 },
1769 "type": "array"
1770 }
1771 },
1772 "type": "object"
1773 },
1774 "OperationMetadata": {
1775 "description": "Metadata describing an Operation.",
1776 "id": "OperationMetadata",
1777 "properties": {
1778 "startTime": {
1779 "description": "The time at which the job began to run.",
1780 "format": "google-datetime",
1781 "type": "string"
1782 },
1783 "request": {
1784 "additionalProperties": {
1785 "description": "Properties of the object. Contains field @type with type URL.",
1786 "type": "any"
1787 },
1788 "description": "The original request that started the operat ion. Note that this will be in\ncurrent version of the API. If the operation was started with v1beta2 API\nand a GetOperation is performed on v1 API, a v1 reque st will be returned.",
1789 "type": "object"
1790 },
1791 "runtimeMetadata": {
1792 "additionalProperties": {
1793 "description": "Properties of the object. Contains field @type with type URL.",
1794 "type": "any"
1795 },
1796 "description": "Runtime metadata on this Operation.",
1797 "type": "object"
1798 },
1799 "createTime": {
1800 "description": "The time at which the job was submitted to t he Genomics service.",
1801 "format": "google-datetime",
1802 "type": "string"
1803 },
1804 "labels": {
1805 "additionalProperties": {
1806 "type": "string"
1807 },
1808 "description": "Optionally provided by the caller when submi tting the request that creates\nthe operation.",
1809 "type": "object"
1810 },
1811 "projectId": {
1812 "description": "The Google Cloud Project in which the job is scoped.",
1813 "type": "string"
1814 },
1815 "clientId": {
1816 "description": "This field is deprecated. Use `labels` inste ad. Optionally provided by the\ncaller when submitting the request that creates the operation.",
1817 "type": "string"
1818 },
1819 "endTime": {
1820 "description": "The time at which the job stopped running.",
1821 "format": "google-datetime",
1822 "type": "string"
1823 },
1824 "events": {
1825 "description": "Optional event messages that were generated during the job's execution.\nThis also contains any warnings that were generated during import\nor export.",
1826 "items": {
1827 "$ref": "OperationEvent"
1828 },
1829 "type": "array"
1830 }
1831 },
1832 "type": "object"
1833 },
1834 "SearchVariantsRequest": {
1835 "description": "The variant search request.",
1836 "id": "SearchVariantsRequest",
1837 "properties": {
1838 "maxCalls": {
1839 "description": "The maximum number of calls to return in a s ingle page. Note that this\nlimit may be exceeded in the event that a matching v ariant contains more\ncalls than the requested maximum. If unspecified, defaults to 5000. The\nmaximum value is 10000.",
1711 "format": "int32", 1840 "format": "int32",
1712 "type": "integer" 1841 "type": "integer"
1713 } 1842 },
1714 }, 1843 "pageToken": {
1715 "type": "object" 1844 "description": "The continuation token, which is used to pag e through large result sets.\nTo get the next page of results, set this paramete r to the value of\n`nextPageToken` from the previous response.",
1716 }, 1845 "type": "string"
1717 "ReadGroupSet": { 1846 },
1718 "description": "A read group set is a logical collection of read gro ups, which are\ncollections of reads produced by a sequencer. A read group set t ypically\nmodels reads corresponding to one sample, sequenced one way, and align ed one\nway.\n\n* A read group set belongs to one dataset.\n* A read group belon gs to one read group set.\n* A read belongs to one read group.\n\nFor more genom ics resource definitions, see [Fundamentals of Google\nGenomics](https://cloud.g oogle.com/genomics/fundamentals-of-google-genomics)", 1847 "pageSize": {
1719 "id": "ReadGroupSet", 1848 "description": "The maximum number of variants to return in a single page. If unspecified,\ndefaults to 5000. The maximum value is 10000.",
1720 "properties": { 1849 "format": "int32",
1721 "datasetId": { 1850 "type": "integer"
1722 "description": "The dataset to which this read group set bel ongs.", 1851 },
1723 "type": "string" 1852 "callSetIds": {
1724 }, 1853 "description": "Only return variant calls which belong to ca ll sets with these ids.\nLeaving this blank returns all variant calls. If a vari ant has no\ncalls belonging to any of these call sets, it won't be returned at a ll.",
1725 "readGroups": { 1854 "items": {
1726 "description": "The read groups in this set. There are typic ally 1-10 read groups in a read\ngroup set.", 1855 "type": "string"
1727 "items": { 1856 },
1728 "$ref": "ReadGroup" 1857 "type": "array"
1729 }, 1858 },
1730 "type": "array" 1859 "variantName": {
1731 }, 1860 "description": "Only return variants which have exactly this name.",
1732 "filename": { 1861 "type": "string"
1733 "description": "The filename of the original source file for this read group set, if any.", 1862 },
1863 "start": {
1864 "description": "The beginning of the window (0-based, inclus ive) for which\noverlapping variants should be returned. If unspecified, default s to 0.",
1865 "format": "int64",
1866 "type": "string"
1867 },
1868 "referenceName": {
1869 "description": "Required. Only return variants in this refer ence sequence.",
1870 "type": "string"
1871 },
1872 "variantSetIds": {
1873 "description": "At most one variant set ID must be provided. Only variants from this\nvariant set will be returned. If omitted, a call set i d must be included in\nthe request.",
1874 "items": {
1875 "type": "string"
1876 },
1877 "type": "array"
1878 },
1879 "end": {
1880 "description": "The end of the window, 0-based exclusive. If unspecified or 0, defaults to\nthe length of the reference.",
1881 "format": "int64",
1882 "type": "string"
1883 }
1884 },
1885 "type": "object"
1886 },
1887 "SearchReadGroupSetsRequest": {
1888 "description": "The read group set search request.",
1889 "id": "SearchReadGroupSetsRequest",
1890 "properties": {
1891 "datasetIds": {
1892 "description": "Restricts this query to read group sets with in the given datasets. At least\none ID must be provided.",
1893 "items": {
1894 "type": "string"
1895 },
1896 "type": "array"
1897 },
1898 "pageToken": {
1899 "description": "The continuation token, which is used to pag e through large result sets.\nTo get the next page of results, set this paramete r to the value of\n`nextPageToken` from the previous response.",
1734 "type": "string" 1900 "type": "string"
1735 }, 1901 },
1736 "name": { 1902 "name": {
1737 "description": "The read group set name. By default this wil l be initialized to the sample\nname of the sequenced data contained in this set .", 1903 "description": "Only return read group sets for which a subs tring of the name matches this\nstring.",
1738 "type": "string" 1904 "type": "string"
1739 }, 1905 },
1740 "referenceSetId": { 1906 "pageSize": {
1741 "description": "The reference set to which the reads in this read group set are aligned.", 1907 "description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 256. The maximum value is 1024.",
1742 "type": "string" 1908 "format": "int32",
1743 }, 1909 "type": "integer"
1744 "info": { 1910 }
1745 "additionalProperties": { 1911 },
1746 "items": { 1912 "type": "object"
1747 "type": "any" 1913 },
1748 }, 1914 "SearchAnnotationsResponse": {
1749 "type": "array" 1915 "id": "SearchAnnotationsResponse",
1750 }, 1916 "properties": {
1751 "description": "A map of additional read group set informati on.",
1752 "type": "object"
1753 },
1754 "id": {
1755 "description": "The server-generated read group set ID, uniq ue for all read group sets.",
1756 "type": "string"
1757 }
1758 },
1759 "type": "object"
1760 },
1761 "SearchVariantSetsResponse": {
1762 "description": "The search variant sets response.",
1763 "id": "SearchVariantSetsResponse",
1764 "properties": {
1765 "variantSets": {
1766 "description": "The variant sets belonging to the requested dataset.",
1767 "items": {
1768 "$ref": "VariantSet"
1769 },
1770 "type": "array"
1771 },
1772 "nextPageToken": { 1917 "nextPageToken": {
1773 "description": "The continuation token, which is used to pag e through large result sets.\nProvide this value in a subsequent request to retu rn the next page of\nresults. This field will be empty if there aren't any addit ional results.", 1918 "description": "The continuation token, which is used to pag e through large result sets.\nProvide this value in a subsequent request to retu rn the next page of\nresults. This field will be empty if there aren't any addit ional results.",
1774 "type": "string" 1919 "type": "string"
1775 } 1920 },
1776 }, 1921 "annotations": {
1777 "type": "object" 1922 "description": "The matching annotations.",
1778 }, 1923 "items": {
1779 "Empty": { 1924 "$ref": "Annotation"
1780 "description": "A generic empty message that you can re-use to avoid defining duplicated\nempty messages in your APIs. A typical example is to use i t as the request\nor the response type of an API method. For instance:\n\n se rvice Foo {\n rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty );\n }\n\nThe JSON representation for `Empty` is empty JSON object `{}`.", 1925 },
1781 "id": "Empty", 1926 "type": "array"
1782 "properties": {}, 1927 }
1783 "type": "object" 1928 },
1784 }, 1929 "type": "object"
1785 "Entry": { 1930 },
1786 "id": "Entry", 1931 "ClinicalCondition": {
1787 "properties": { 1932 "id": "ClinicalCondition",
1788 "annotation": { 1933 "properties": {
1789 "$ref": "Annotation", 1934 "names": {
1790 "description": "The created annotation, if creation was succ essful." 1935 "description": "A set of names for the condition.",
1791 }, 1936 "items": {
1792 "status": { 1937 "type": "string"
1793 "$ref": "Status", 1938 },
1794 "description": "The creation status." 1939 "type": "array"
1795 } 1940 },
1796 }, 1941 "omimId": {
1797 "type": "object" 1942 "description": "The OMIM id for this condition.\nSearch for these IDs at http://omim.org/",
1798 }, 1943 "type": "string"
1799 "Position": { 1944 },
1800 "description": "An abstraction for referring to a genomic position, in relation to some\nalready known reference. For now, represents a genomic posi tion as a\nreference name, a base number on that reference (0-based), and a\ndet ermination of forward or reverse strand.", 1945 "externalIds": {
1801 "id": "Position", 1946 "description": "The set of external IDs for this condition." ,
1802 "properties": { 1947 "items": {
1803 "reverseStrand": { 1948 "$ref": "ExternalId"
1804 "description": "Whether this position is on the reverse stra nd, as opposed to the forward\nstrand.", 1949 },
1805 "type": "boolean" 1950 "type": "array"
1806 }, 1951 },
1807 "position": { 1952 "conceptId": {
1808 "description": "The 0-based offset from the start of the for ward strand for that reference.", 1953 "description": "The MedGen concept id associated with this g ene.\nSearch for these IDs at http://www.ncbi.nlm.nih.gov/medgen/",
1809 "format": "int64", 1954 "type": "string"
1810 "type": "string" 1955 }
1811 }, 1956 },
1812 "referenceName": { 1957 "type": "object"
1813 "description": "The name of the reference in whatever refere nce set is being used.", 1958 },
1814 "type": "string" 1959 "SearchReadsResponse": {
1815 } 1960 "description": "The read search response.",
1816 }, 1961 "id": "SearchReadsResponse",
1817 "type": "object" 1962 "properties": {
1818 },
1819 "SearchReferenceSetsResponse": {
1820 "id": "SearchReferenceSetsResponse",
1821 "properties": {
1822 "referenceSets": {
1823 "description": "The matching references sets.",
1824 "items": {
1825 "$ref": "ReferenceSet"
1826 },
1827 "type": "array"
1828 },
1829 "nextPageToken": { 1963 "nextPageToken": {
1830 "description": "The continuation token, which is used to pag e through large result sets.\nProvide this value in a subsequent request to retu rn the next page of\nresults. This field will be empty if there aren't any addit ional results.", 1964 "description": "The continuation token, which is used to pag e through large result sets.\nProvide this value in a subsequent request to retu rn the next page of\nresults. This field will be empty if there aren't any addit ional results.",
1831 "type": "string" 1965 "type": "string"
1832 } 1966 },
1833 }, 1967 "alignments": {
1834 "type": "object" 1968 "description": "The list of matching alignments sorted by ma pped genomic coordinate,\nif any, ascending in position within the same referenc e. Unmapped reads,\nwhich have no position, are returned contiguously and are so rted in\nascending lexicographic order by fragment name.",
1835 }, 1969 "items": {
1836 "SearchCallSetsRequest": { 1970 "$ref": "Read"
1837 "description": "The call set search request.", 1971 },
1838 "id": "SearchCallSetsRequest", 1972 "type": "array"
1973 }
1974 },
1975 "type": "object"
1976 },
1977 "Program": {
1978 "id": "Program",
1979 "properties": {
1980 "name": {
1981 "description": "The display name of the program. This is typ ically the colloquial name of\nthe tool used, for example 'bwa' or 'picard'.",
1982 "type": "string"
1983 },
1984 "prevProgramId": {
1985 "description": "The ID of the program run before this one.",
1986 "type": "string"
1987 },
1988 "commandLine": {
1989 "description": "The command line used to run this program.",
1990 "type": "string"
1991 },
1992 "version": {
1993 "description": "The version of the program run.",
1994 "type": "string"
1995 },
1996 "id": {
1997 "description": "The user specified locally unique ID of the program. Used along with\n`prevProgramId` to define an ordering between programs .",
1998 "type": "string"
1999 }
2000 },
2001 "type": "object"
2002 },
2003 "ComputeEngine": {
2004 "description": "Describes a Compute Engine resource that is being ma naged by a running\npipeline.",
2005 "id": "ComputeEngine",
2006 "properties": {
2007 "diskNames": {
2008 "description": "The names of the disks that were created for this pipeline.",
2009 "items": {
2010 "type": "string"
2011 },
2012 "type": "array"
2013 },
2014 "machineType": {
2015 "description": "The machine type of the instance.",
2016 "type": "string"
2017 },
2018 "instanceName": {
2019 "description": "The instance on which the operation is runni ng.",
2020 "type": "string"
2021 },
2022 "zone": {
2023 "description": "The availability zone in which the instance resides.",
2024 "type": "string"
2025 }
2026 },
2027 "type": "object"
2028 },
2029 "CoverageBucket": {
2030 "description": "A bucket over which read coverage has been precomput ed. A bucket corresponds\nto a specific range of the reference sequence.",
2031 "id": "CoverageBucket",
2032 "properties": {
2033 "range": {
2034 "$ref": "Range",
2035 "description": "The genomic coordinate range spanned by this bucket."
2036 },
2037 "meanCoverage": {
2038 "description": "The average number of reads which are aligne d to each individual\nreference base in this bucket.",
2039 "format": "float",
2040 "type": "number"
2041 }
2042 },
2043 "type": "object"
2044 },
2045 "ExternalId": {
2046 "id": "ExternalId",
2047 "properties": {
2048 "id": {
2049 "description": "The id used by the source of this data.",
2050 "type": "string"
2051 },
2052 "sourceName": {
2053 "description": "The name of the source of this data.",
2054 "type": "string"
2055 }
2056 },
2057 "type": "object"
2058 },
2059 "SearchVariantSetsRequest": {
2060 "description": "The search variant sets request.",
2061 "id": "SearchVariantSetsRequest",
1839 "properties": { 2062 "properties": {
1840 "pageToken": { 2063 "pageToken": {
1841 "description": "The continuation token, which is used to pag e through large result sets.\nTo get the next page of results, set this paramete r to the value of\n`nextPageToken` from the previous response.", 2064 "description": "The continuation token, which is used to pag e through large result sets.\nTo get the next page of results, set this paramete r to the value of\n`nextPageToken` from the previous response.",
1842 "type": "string" 2065 "type": "string"
1843 }, 2066 },
1844 "name": {
1845 "description": "Only return call sets for which a substring of the name matches this\nstring.",
1846 "type": "string"
1847 },
1848 "pageSize": { 2067 "pageSize": {
1849 "description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 1024.", 2068 "description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 1024.",
1850 "format": "int32", 2069 "format": "int32",
1851 "type": "integer" 2070 "type": "integer"
1852 }, 2071 },
1853 "variantSetIds": { 2072 "datasetIds": {
1854 "description": "Restrict the query to call sets within the g iven variant sets. At least one\nID must be provided.", 2073 "description": "Exactly one dataset ID must be provided here . Only variant sets which\nbelong to this dataset will be returned.",
1855 "items": { 2074 "items": {
1856 "type": "string" 2075 "type": "string"
1857 }, 2076 },
1858 "type": "array"
1859 }
1860 },
1861 "type": "object"
1862 },
1863 "ImportReadGroupSetsRequest": {
1864 "description": "The read group set import request.",
1865 "id": "ImportReadGroupSetsRequest",
1866 "properties": {
1867 "referenceSetId": {
1868 "description": "The reference set to which the imported read group sets are aligned to, if\nany. The reference names of this reference set m ust be a superset of those\nfound in the imported file headers. If no reference set id is provided, a\nbest effort is made to associate with a matching referenc e set.",
1869 "type": "string"
1870 },
1871 "partitionStrategy": {
1872 "description": "The partition strategy describes how read gr oups are partitioned into read\ngroup sets.",
1873 "enum": [
1874 "PARTITION_STRATEGY_UNSPECIFIED",
1875 "PER_FILE_PER_SAMPLE",
1876 "MERGE_ALL"
1877 ],
1878 "enumDescriptions": [
1879 "",
1880 "In most cases, this strategy yields one read group set per file. This is\nthe default behavior.\n\nAllocate one read group set per file per sample. For BAM files, read\ngroups are considered to share a sample if the y have identical sample\nnames. Furthermore, all reads for each file which do no t belong to a read\ngroup, if any, will be grouped into a single read group set per-file.",
1881 "Includes all read groups in all imported files into a s ingle read group\nset. Requires that the headers for all imported files are equi valent. All\nreads which do not belong to a read group, if any, will be grouped into a\nseparate read group set."
1882 ],
1883 "type": "string"
1884 },
1885 "datasetId": {
1886 "description": "Required. The ID of the dataset these read g roup sets will belong to. The\ncaller must have WRITE permissions to this datase t.",
1887 "type": "string"
1888 },
1889 "sourceUris": {
1890 "description": "A list of URIs pointing at [BAM\nfiles](http s://samtools.github.io/hts-specs/SAMv1.pdf)\nin Google Cloud Storage.\nThose URI s can include wildcards (*), but do not add or remove\nmatching files before imp ort has completed.\n\nNote that Google Cloud Storage object listing is only even tually\nconsistent: files added may be not be immediately visible to\neveryone. Thus, if using a wildcard it is preferable not to start\nthe import immediately after the files are created.",
1891 "items": {
1892 "type": "string"
1893 },
1894 "type": "array"
1895 }
1896 },
1897 "type": "object"
1898 },
1899 "Policy": {
1900 "description": "Defines an Identity and Access Management (IAM) poli cy. It is used to\nspecify access control policies for Cloud Platform resources. \n\n\nA `Policy` consists of a list of `bindings`. A `Binding` binds a list of\n `members` to a `role`, where the members can be user accounts, Google groups,\nG oogle domains, and service accounts. A `role` is a named list of permissions\nde fined by IAM.\n\n**Example**\n\n {\n \"bindings\": [\n {\n \"role\": \"roles/owner\",\n \"members\": [\n \"user:mike @example.com\",\n \"group:admins@example.com\",\n \"domain :google.com\",\n \"serviceAccount:my-other-app@appspot.gserviceaccoun t.com\",\n ]\n },\n {\n \"role\": \"roles/viewer \",\n \"members\": [\"user:sean@example.com\"]\n }\n ]\n }\n\nFor a description of IAM and its features, see the\n[IAM developer's guide ](https://cloud.google.com/iam).",
1901 "id": "Policy",
1902 "properties": {
1903 "etag": {
1904 "description": "`etag` is used for optimistic concurrency co ntrol as a way to help\nprevent simultaneous updates of a policy from overwritin g each other.\nIt is strongly suggested that systems make use of the `etag` in t he\nread-modify-write cycle to perform policy updates in order to avoid race\nco nditions: An `etag` is returned in the response to `getIamPolicy`, and\nsystems are expected to put that etag in the request to `setIamPolicy` to\nensure that t heir change will be applied to the same version of the policy.\n\nIf no `etag` i s provided in the call to `setIamPolicy`, then the existing\npolicy is overwritt en blindly.",
1905 "format": "byte",
1906 "type": "string"
1907 },
1908 "version": {
1909 "description": "Version of the `Policy`. The default version is 0.",
1910 "format": "int32",
1911 "type": "integer"
1912 },
1913 "bindings": {
1914 "description": "Associates a list of `members` to a `role`.\ n`bindings` with no members will result in an error.",
1915 "items": {
1916 "$ref": "Binding"
1917 },
1918 "type": "array"
1919 }
1920 },
1921 "type": "object"
1922 },
1923 "Annotation": {
1924 "description": "An annotation describes a region of reference genome . The value of an\nannotation may be one of several canonical types, supplemente d by arbitrary\ninfo tags. An annotation is not inherently associated with a spe cific\nsample or individual (though a client could choose to use annotations in\ nthis way). Example canonical annotation types are `GENE` and\n`VARIANT`.",
1925 "id": "Annotation",
1926 "properties": {
1927 "name": {
1928 "description": "The display name of this annotation.",
1929 "type": "string"
1930 },
1931 "variant": {
1932 "$ref": "VariantAnnotation",
1933 "description": "A variant annotation, which describes the ef fect of a variant on the\ngenome, the coding sequence, and/or higher level conse quences at the\norganism level e.g. pathogenicity. This field is only set for an notations\nof type `VARIANT`."
1934 },
1935 "id": {
1936 "description": "The server-generated annotation ID, unique a cross all annotations.",
1937 "type": "string"
1938 },
1939 "referenceId": {
1940 "description": "The ID of the Google Genomics reference asso ciated with this range.",
1941 "type": "string"
1942 },
1943 "reverseStrand": {
1944 "description": "Whether this range refers to the reverse str and, as opposed to the forward\nstrand. Note that regardless of this field, the start/end position of the\nrange always refer to the forward strand.",
1945 "type": "boolean"
1946 },
1947 "referenceName": {
1948 "description": "The display name corresponding to the refere nce specified by\n`referenceId`, for example `chr1`, `1`, or `chrX`.",
1949 "type": "string"
1950 },
1951 "info": {
1952 "additionalProperties": {
1953 "items": {
1954 "type": "any"
1955 },
1956 "type": "array"
1957 },
1958 "description": "A map of additional read alignment informati on. This must be of the form\nmap<string, string[]> (string key mapping to a lis t of string values).",
1959 "type": "object"
1960 },
1961 "type": {
1962 "description": "The data type for this annotation. Must matc h the containing annotation\nset's type.",
1963 "enum": [
1964 "ANNOTATION_TYPE_UNSPECIFIED",
1965 "GENERIC",
1966 "VARIANT",
1967 "GENE",
1968 "TRANSCRIPT"
1969 ],
1970 "enumDescriptions": [
1971 "",
1972 "A `GENERIC` annotation type should be used when no othe r annotation\ntype will suffice. This represents an untyped annotation of the re ference\ngenome.",
1973 "A `VARIANT` annotation type.",
1974 "A `GENE` annotation type represents the existence of a gene at the\nassociated reference coordinates. The start coordinate is typically the\ngene's transcription start site and the end is typically the end of the\ng ene's last exon.",
1975 "A `TRANSCRIPT` annotation type represents the assertion that a\nparticular region of the reference genome may be transcribed as RNA."
1976 ],
1977 "type": "string"
1978 },
1979 "end": {
1980 "description": "The end position of the range on the referen ce, 0-based exclusive.",
1981 "format": "int64",
1982 "type": "string"
1983 },
1984 "transcript": {
1985 "$ref": "Transcript",
1986 "description": "A transcript value represents the assertion that a particular region of\nthe reference genome may be transcribed as RNA. An alternative splicing\npattern would be represented as a separate transcript obje ct. This field\nis only set for annotations of type `TRANSCRIPT`."
1987 },
1988 "start": {
1989 "description": "The start position of the range on the refer ence, 0-based inclusive.",
1990 "format": "int64",
1991 "type": "string"
1992 },
1993 "annotationSetId": {
1994 "description": "The annotation set to which this annotation belongs.",
1995 "type": "string"
1996 }
1997 },
1998 "type": "object"
1999 },
2000 "CancelOperationRequest": {
2001 "description": "The request message for Operations.CancelOperation." ,
2002 "id": "CancelOperationRequest",
2003 "properties": {},
2004 "type": "object"
2005 },
2006 "SearchReadsRequest": {
2007 "description": "The read search request.",
2008 "id": "SearchReadsRequest",
2009 "properties": {
2010 "readGroupSetIds": {
2011 "description": "The IDs of the read groups sets within which to search for reads. All\nspecified read group sets must be aligned against a c ommon set of reference\nsequences; this defines the genomic coordinates for the query. Must specify\none of `readGroupSetIds` or `readGroupIds`.",
2012 "items": {
2013 "type": "string"
2014 },
2015 "type": "array"
2016 },
2017 "readGroupIds": {
2018 "description": "The IDs of the read groups within which to s earch for reads. All specified\nread groups must belong to the same read group s ets. Must specify one of\n`readGroupSetIds` or `readGroupIds`.",
2019 "items": {
2020 "type": "string"
2021 },
2022 "type": "array"
2023 },
2024 "end": {
2025 "description": "The end position of the range on the referen ce, 0-based exclusive. If\nspecified, `referenceName` must also be specified.",
2026 "format": "int64",
2027 "type": "string"
2028 },
2029 "pageToken": {
2030 "description": "The continuation token, which is used to pag e through large result sets.\nTo get the next page of results, set this paramete r to the value of\n`nextPageToken` from the previous response.",
2031 "type": "string"
2032 },
2033 "pageSize": {
2034 "description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 256. The maximum value is 2048.",
2035 "format": "int32",
2036 "type": "integer"
2037 },
2038 "start": {
2039 "description": "The start position of the range on the refer ence, 0-based inclusive. If\nspecified, `referenceName` must also be specified." ,
2040 "format": "int64",
2041 "type": "string"
2042 },
2043 "referenceName": {
2044 "description": "The reference sequence name, for example `ch r1`, `1`, or `chrX`. If set to\n`*`, only unmapped reads are returned. If unspec ified, all reads (mapped\nand unmapped) are returned.",
2045 "type": "string"
2046 }
2047 },
2048 "type": "object"
2049 },
2050 "Operation": {
2051 "description": "This resource represents a long-running operation th at is the result of a\nnetwork API call.",
2052 "id": "Operation",
2053 "properties": {
2054 "name": {
2055 "description": "The server-assigned name, which is only uniq ue within the same service that originally returns it. For example&#58; `operati ons/CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw`",
2056 "type": "string"
2057 },
2058 "error": {
2059 "$ref": "Status",
2060 "description": "The error result of the operation in case of failure or cancellation."
2061 },
2062 "metadata": {
2063 "additionalProperties": {
2064 "description": "Properties of the object. Contains field @type with type URL.",
2065 "type": "any"
2066 },
2067 "description": "An OperationMetadata object. This will alway s be returned with the Operation.",
2068 "type": "object"
2069 },
2070 "done": {
2071 "description": "If the value is `false`, it means the operat ion is still in progress.\nIf true, the operation is completed, and either `erro r` or `response` is\navailable.",
2072 "type": "boolean"
2073 },
2074 "response": {
2075 "additionalProperties": {
2076 "description": "Properties of the object. Contains field @type with type URL.",
2077 "type": "any"
2078 },
2079 "description": "If importing ReadGroupSets, an ImportReadGro upSetsResponse is returned. If importing Variants, an ImportVariantsResponse is returned. For pipelines and exports, an empty response is returned.",
2080 "type": "object"
2081 }
2082 },
2083 "type": "object"
2084 },
2085 "RuntimeMetadata": {
2086 "description": "Runtime metadata that will be populated in the\nrunt imeMetadata\nfield of the Operation associated with a RunPipeline execution.",
2087 "id": "RuntimeMetadata",
2088 "properties": {
2089 "computeEngine": {
2090 "$ref": "ComputeEngine",
2091 "description": "Execution information specific to Google Com pute Engine."
2092 }
2093 },
2094 "type": "object"
2095 },
2096 "ImportReadGroupSetsResponse": {
2097 "description": "The read group set import response.",
2098 "id": "ImportReadGroupSetsResponse",
2099 "properties": {
2100 "readGroupSetIds": {
2101 "description": "IDs of the read group sets that were created .",
2102 "items": {
2103 "type": "string"
2104 },
2105 "type": "array" 2077 "type": "array"
2106 } 2078 }
2107 }, 2079 },
2108 "type": "object" 2080 "type": "object"
2109 }, 2081 },
2110 "VariantCall": { 2082 "VariantSetMetadata": {
2111 "description": "A call represents the determination of genotype with respect to a particular\nvariant. It may include associated information such as quality and phasing.\nFor example, a call might assign a probability of 0.32 to the occurrence of\na SNP named rs1234 in a call set with the name NA12345.", 2083 "description": "Metadata describes a single piece of variant call me tadata.\nThese data include a top level key and either a single value string (va lue)\nor a list of key-value pairs (info.)\nValue and info are mutually exclusiv e.",
2112 "id": "VariantCall", 2084 "id": "VariantSetMetadata",
2113 "properties": { 2085 "properties": {
2114 "genotype": { 2086 "type": {
2115 "description": "The genotype of this variant call. Each valu e represents either the value\nof the `referenceBases` field or a 1-based index into\n`alternateBases`. If a variant had a `referenceBases`\nvalue of `T` and an `alternateBases`\nvalue of `[\"A\", \"C\"]`, and the `genotype` was\n`[2, 1]`, that would mean the call\nrepresented the heterozygous value `CA` for this varia nt.\nIf the `genotype` was instead `[0, 1]`, the\nrepresented value would be `TA `. Ordering of the\ngenotype values is important if the `phaseset` is present.\n If a genotype is not called (that is, a `.` is present in the\nGT string) -1 is returned.", 2087 "description": "The type of data. Possible types include: In teger, Float,\nFlag, Character, and String.",
2116 "items": { 2088 "enum": [
2117 "format": "int32", 2089 "TYPE_UNSPECIFIED",
2118 "type": "integer" 2090 "INTEGER",
2119 }, 2091 "FLOAT",
2120 "type": "array" 2092 "FLAG",
2121 }, 2093 "CHARACTER",
2122 "phaseset": { 2094 "STRING"
2123 "description": "If this field is present, this variant call' s genotype ordering implies\nthe phase of the bases and is consistent with any o ther variant calls in\nthe same reference sequence which have the same phaseset value.\nWhen importing data from VCF, if the genotype data was phased but no\nph ase set was specified this field will be set to `*`.", 2095 ],
2096 "enumDescriptions": [
2097 "",
2098 "",
2099 "",
2100 "",
2101 "",
2102 ""
2103 ],
2124 "type": "string" 2104 "type": "string"
2125 }, 2105 },
2126 "info": { 2106 "info": {
2127 "additionalProperties": { 2107 "additionalProperties": {
2128 "items": { 2108 "items": {
2129 "type": "any" 2109 "type": "any"
2130 }, 2110 },
2131 "type": "array" 2111 "type": "array"
2132 }, 2112 },
2133 "description": "A map of additional variant call information . This must be of the form\nmap<string, string[]> (string key mapping to a list of string values).", 2113 "description": "Remaining structured metadata key-value pair s. This must be of the form\nmap<string, string[]> (string key mapping to a list of string values).",
2134 "type": "object" 2114 "type": "object"
2135 }, 2115 },
2136 "callSetName": { 2116 "value": {
2137 "description": "The name of the call set this variant call b elongs to.", 2117 "description": "The value field for simple metadata",
2138 "type": "string" 2118 "type": "string"
2139 }, 2119 },
2140 "genotypeLikelihood": { 2120 "id": {
2141 "description": "The genotype likelihoods for this variant ca ll. Each array entry\nrepresents how likely a specific genotype is for this call . The value\nordering is defined by the GL tag in the VCF spec.\nIf Phred-scaled genotype likelihood scores (PL) are available and\nlog10(P) genotype likelihood scores (GL) are not, PL scores are converted\nto GL scores. If both are availa ble, PL scores are stored in `info`.", 2121 "description": "User-provided ID field, not enforced by this API.\nTwo or more pieces of structured metadata with identical\nid and key fiel ds are considered equivalent.",
2142 "items": { 2122 "type": "string"
2143 "format": "double", 2123 },
2144 "type": "number" 2124 "number": {
2145 }, 2125 "description": "The number of values that can be included in a field described by this\nmetadata.",
2146 "type": "array" 2126 "type": "string"
2147 }, 2127 },
2148 "callSetId": { 2128 "key": {
2149 "description": "The ID of the call set this variant call bel ongs to.", 2129 "description": "The top-level key.",
2150 "type": "string" 2130 "type": "string"
2151 } 2131 },
2152 }, 2132 "description": {
2153 "type": "object" 2133 "description": "A textual description of this metadata.",
2154 }, 2134 "type": "string"
2155 "SearchVariantsResponse": { 2135 }
2156 "description": "The variant search response.", 2136 },
2157 "id": "SearchVariantsResponse", 2137 "type": "object"
2138 },
2139 "Reference": {
2140 "description": "A reference is a canonical assembled DNA sequence, i ntended to act as a\nreference coordinate space for other genomic annotations. A single reference\nmight represent the human chromosome 1 or mitochandrial DNA, for instance. A\nreference belongs to one or more reference sets.\n\nFor more ge nomics resource definitions, see [Fundamentals of Google\nGenomics](https://clou d.google.com/genomics/fundamentals-of-google-genomics)",
2141 "id": "Reference",
2142 "properties": {
2143 "sourceAccessions": {
2144 "description": "All known corresponding accession IDs in INS DC (GenBank/ENA/DDBJ) ideally\nwith a version number, for example `GCF_000001405 .26`.",
2145 "items": {
2146 "type": "string"
2147 },
2148 "type": "array"
2149 },
2150 "ncbiTaxonId": {
2151 "description": "ID from http://www.ncbi.nlm.nih.gov/taxonomy . For example, 9606 for human.",
2152 "format": "int32",
2153 "type": "integer"
2154 },
2155 "sourceUri": {
2156 "description": "The URI from which the sequence was obtained . Typically specifies a FASTA\nformat file.",
2157 "type": "string"
2158 },
2159 "name": {
2160 "description": "The name of this reference, for example `22` .",
2161 "type": "string"
2162 },
2163 "md5checksum": {
2164 "description": "MD5 of the upper-case sequence excluding all whitespace characters (this\nis equivalent to SQ:M5 in SAM). This value is repr esented in lower case\nhexadecimal format.",
2165 "type": "string"
2166 },
2167 "id": {
2168 "description": "The server-generated reference ID, unique ac ross all references.",
2169 "type": "string"
2170 },
2171 "length": {
2172 "description": "The length of this reference's sequence.",
2173 "format": "int64",
2174 "type": "string"
2175 }
2176 },
2177 "type": "object"
2178 },
2179 "SearchReferenceSetsRequest": {
2180 "id": "SearchReferenceSetsRequest",
2181 "properties": {
2182 "pageToken": {
2183 "description": "The continuation token, which is used to pag e through large result sets.\nTo get the next page of results, set this paramete r to the value of\n`nextPageToken` from the previous response.",
2184 "type": "string"
2185 },
2186 "accessions": {
2187 "description": "If present, return reference sets for which a prefix of any of\nsourceAccessions\nmatch any of these strings. Accession numb ers typically have a main number\nand a version, for example `NC_000001.11`.",
2188 "items": {
2189 "type": "string"
2190 },
2191 "type": "array"
2192 },
2193 "pageSize": {
2194 "description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 1024. The maximum value is 4096.",
2195 "format": "int32",
2196 "type": "integer"
2197 },
2198 "assemblyId": {
2199 "description": "If present, return reference sets for which a substring of their\n`assemblyId` matches this string (case insensitive).",
2200 "type": "string"
2201 },
2202 "md5checksums": {
2203 "description": "If present, return reference sets for which the\nmd5checksum matches exactly.",
2204 "items": {
2205 "type": "string"
2206 },
2207 "type": "array"
2208 }
2209 },
2210 "type": "object"
2211 },
2212 "SetIamPolicyRequest": {
2213 "description": "Request message for `SetIamPolicy` method.",
2214 "id": "SetIamPolicyRequest",
2215 "properties": {
2216 "policy": {
2217 "$ref": "Policy",
2218 "description": "REQUIRED: The complete policy to be applied to the `resource`. The size of\nthe policy is limited to a few 10s of KB. An emp ty policy is a\nvalid policy but certain Cloud Platform services (such as Projec ts)\nmight reject them."
2219 }
2220 },
2221 "type": "object"
2222 },
2223 "MergeVariantsRequest": {
2224 "id": "MergeVariantsRequest",
2158 "properties": { 2225 "properties": {
2159 "variants": { 2226 "variants": {
2160 "description": "The list of matching Variants.", 2227 "description": "The variants to be merged with existing vari ants.",
2161 "items": { 2228 "items": {
2162 "$ref": "Variant" 2229 "$ref": "Variant"
2163 }, 2230 },
2164 "type": "array" 2231 "type": "array"
2165 }, 2232 },
2166 "nextPageToken": { 2233 "infoMergeConfig": {
2167 "description": "The continuation token, which is used to pag e through large result sets.\nProvide this value in a subsequent request to retu rn the next page of\nresults. This field will be empty if there aren't any addit ional results.", 2234 "additionalProperties": {
2168 "type": "string" 2235 "enum": [
2169 } 2236 "INFO_MERGE_OPERATION_UNSPECIFIED",
2170 }, 2237 "IGNORE_NEW",
2171 "type": "object" 2238 "MOVE_TO_CALLS"
2172 }, 2239 ],
2173 "ListBasesResponse": { 2240 "type": "string"
2174 "id": "ListBasesResponse", 2241 },
2175 "properties": { 2242 "description": "A mapping between info field keys and the In foMergeOperations to\nbe performed on them.",
2176 "offset": { 2243 "type": "object"
2177 "description": "The offset position (0-based) of the given ` sequence` from the\nstart of this `Reference`. This value will differ for each p age\nin a paginated request.", 2244 },
2178 "format": "int64", 2245 "variantSetId": {
2179 "type": "string" 2246 "description": "The destination variant set.",
2180 }, 2247 "type": "string"
2181 "nextPageToken": { 2248 }
2182 "description": "The continuation token, which is used to pag e through large result sets.\nProvide this value in a subsequent request to retu rn the next page of\nresults. This field will be empty if there aren't any addit ional results.", 2249 },
2183 "type": "string" 2250 "type": "object"
2184 }, 2251 },
2185 "sequence": { 2252 "BatchCreateAnnotationsRequest": {
2186 "description": "A substring of the bases that make up this r eference.", 2253 "id": "BatchCreateAnnotationsRequest",
2187 "type": "string" 2254 "properties": {
2188 } 2255 "annotations": {
2189 }, 2256 "description": "The annotations to be created. At most 4096 can be specified in a single\nrequest.",
2190 "type": "object" 2257 "items": {
2191 }, 2258 "$ref": "Annotation"
2192 "Status": { 2259 },
2193 "description": "The `Status` type defines a logical error model that is suitable for different\nprogramming environments, including REST APIs and RP C APIs. It is used by\n[gRPC](https://github.com/grpc). The error model is desig ned to be:\n\n- Simple to use and understand for most users\n- Flexible enough t o meet unexpected needs\n\n# Overview\n\nThe `Status` message contains three pie ces of data: error code, error message,\nand error details. The error code shoul d be an enum value of\ngoogle.rpc.Code, but it may accept additional error codes if needed. The\nerror message should be a developer-facing English message tha t helps\ndevelopers *understand* and *resolve* the error. If a localized user-fa cing\nerror message is needed, put the localized message in the error details or \nlocalize it in the client. The optional error details may contain arbitrary\ni nformation about the error. There is a predefined set of error detail types\nin the package `google.rpc` that can be used for common error conditions.\n\n# Lang uage mapping\n\nThe `Status` message is the logical representation of the error model, but it\nis not necessarily the actual wire format. When the `Status` mess age is\nexposed in different client libraries and different wire protocols, it c an be\nmapped differently. For example, it will likely be mapped to some excepti ons\nin Java, but more likely mapped to some error codes in C.\n\n# Other uses\n \nThe error model and the `Status` message can be used in a variety of\nenvironm ents, either with or without APIs, to provide a\nconsistent developer experience across different environments.\n\nExample uses of this error model include:\n\n - Partial errors. If a service needs to return partial errors to the client,\n it may embed the `Status` in the normal response to indicate the partial\n errors.\n\n- Workflow errors. A typical workflow has multiple steps. Each step m ay\n have a `Status` message for error reporting.\n\n- Batch operations. If a client uses batch request and batch response, the\n `Status` message should be used directly inside batch response, one for\n each error sub-response.\n\ n- Asynchronous operations. If an API call embeds asynchronous operation\n re sults in its response, the status of those operations should be\n represented directly using the `Status` message.\n\n- Logging. If some API errors are store d in logs, the message `Status` could\n be used directly after any stripping needed for security/privacy reasons.", 2260 "type": "array"
2194 "id": "Status", 2261 },
2195 "properties": { 2262 "requestId": {
2196 "message": { 2263 "description": "A unique request ID which enables the server to detect duplicated requests.\nIf provided, duplicated requests will result in the same response; if not\nprovided, duplicated requests may result in duplicat ed data. For a given\nannotation set, callers should not reuse `request_id`s whe n writing\ndifferent batches of annotations - behavior in this case is undefined .\nA common approach is to use a UUID. For batch jobs where worker crashes are\n a possibility, consider using some unique variant of a worker or run ID.",
2197 "description": "A developer-facing error message, which shou ld be in English. Any\nuser-facing error message should be localized and sent in the\ngoogle.rpc.Status.details field, or localized by the client.", 2264 "type": "string"
2198 "type": "string" 2265 }
2199 }, 2266 },
2200 "details": { 2267 "type": "object"
2201 "description": "A list of messages that carry the error deta ils. There is a common set of\nmessage types for APIs to use.", 2268 },
2202 "items": { 2269 "Read": {
2203 "additionalProperties": { 2270 "description": "A read alignment describes a linear alignment of a s tring of DNA to a\nreference sequence, in addition to metadata\nabout the fragme nt (the molecule of DNA sequenced) and the read (the bases\nwhich were read by t he sequencer). A read is equivalent to a line in a SAM\nfile. A read belongs to exactly one read group and exactly one\nread group set.\n\nFor more genomics res ource definitions, see [Fundamentals of Google\nGenomics](https://cloud.google.c om/genomics/fundamentals-of-google-genomics)\n\n### Reverse-stranded reads\n\nMa pped reads (reads having a non-null `alignment`) can be aligned to either\nthe f orward or the reverse strand of their associated reference. Strandedness\nof a m apped read is encoded by `alignment.position.reverseStrand`.\n\nIf we consider t he reference to be a forward-stranded coordinate space of\n`[0, reference.length )` with `0` as the left-most position and\n`reference.length` as the right-most position, reads are always aligned left\nto right. That is, `alignment.position. position` always refers to the\nleft-most reference coordinate and `alignment.ci gar` describes the alignment\nof this read to the reference from left to right. All per-base fields such as\n`alignedSequence` and `alignedQuality` share this s ame left-to-right\norientation; this is true of reads which are aligned to eithe r strand. For\nreverse-stranded reads, this means that `alignedSequence` is the reverse\ncomplement of the bases that were originally reported by the sequencing \nmachine.\n\n### Generating a reference-aligned sequence string\n\nWhen interac ting with mapped reads, it's often useful to produce a string\nrepresenting the local alignment of the read to reference. The following\npseudocode demonstrates one way of doing this:\n\n out = \"\"\n offset = 0\n for c in read.ali gnment.cigar {\n switch c.operation {\n case \"ALIGNMENT_MATCH\", \"SE QUENCE_MATCH\", \"SEQUENCE_MISMATCH\":\n out += read.alignedSequence[offs et:offset+c.operationLength]\n offset += c.operationLength\n break \n case \"CLIP_SOFT\", \"INSERT\":\n offset += c.operationLength\n break\n case \"PAD\":\n out += repeat(\"*\", c.operationLength )\n break\n case \"DELETE\":\n out += repeat(\"-\", c.operati onLength)\n break\n case \"SKIP\":\n out += repeat(\" \", c.o perationLength)\n break\n case \"CLIP_HARD\":\n break\n }\n }\n return out\n\n### Converting to SAM's CIGAR string\n\nThe followin g pseudocode generates a SAM CIGAR string from the\n`cigar` field. Note that thi s is a lossy conversion\n(`cigar.referenceSequence` is lost).\n\n cigarMap = {\n \"ALIGNMENT_MATCH\": \"M\",\n \"INSERT\": \"I\",\n \"DELETE\" : \"D\",\n \"SKIP\": \"N\",\n \"CLIP_SOFT\": \"S\",\n \"CLIP_HARD \": \"H\",\n \"PAD\": \"P\",\n \"SEQUENCE_MATCH\": \"=\",\n \"SEQ UENCE_MISMATCH\": \"X\",\n }\n cigarStr = \"\"\n for c in read.alignmen t.cigar {\n cigarStr += c.operationLength + cigarMap[c.operation]\n }\n return cigarStr",
2204 "description": "Properties of the object. Contains f ield @type with type URL.", 2271 "id": "Read",
2205 "type": "any" 2272 "properties": {
2206 }, 2273 "failedVendorQualityChecks": {
2207 "type": "object" 2274 "description": "Whether this read did not pass filters, such as platform or vendor quality\ncontrols (SAM flag 0x200).",
2208 }, 2275 "type": "boolean"
2209 "type": "array" 2276 },
2210 }, 2277 "alignedQuality": {
2211 "code": { 2278 "description": "The quality of the read sequence contained i n this alignment record\n(equivalent to QUAL in SAM).\n`alignedSequence` and `al ignedQuality` may be shorter than the full read\nsequence and quality. This will occur if the alignment is part of a\nchimeric alignment, or if the read was tri mmed. When this occurs, the CIGAR\nfor this read will begin/end with a hard clip operator that will indicate\nthe length of the excised sequence.",
2212 "description": "The status code, which should be an enum val ue of google.rpc.Code.", 2279 "items": {
2213 "format": "int32", 2280 "format": "int32",
2214 "type": "integer" 2281 "type": "integer"
2215 } 2282 },
2216 }, 2283 "type": "array"
2217 "type": "object" 2284 },
2218 }, 2285 "alignment": {
2219 "UndeleteDatasetRequest": { 2286 "$ref": "LinearAlignment",
2220 "id": "UndeleteDatasetRequest", 2287 "description": "The linear alignment for this alignment reco rd. This field is null for\nunmapped reads."
2221 "properties": {}, 2288 },
2222 "type": "object"
2223 },
2224 "Binding": {
2225 "description": "Associates `members` with a `role`.",
2226 "id": "Binding",
2227 "properties": {
2228 "members": {
2229 "description": "Specifies the identities requesting access f or a Cloud Platform resource.\n`members` can have the following values:\n\n* `al lUsers`: A special identifier that represents anyone who is\n on the internet; with or without a Google account.\n\n* `allAuthenticatedUsers`: A special ident ifier that represents anyone\n who is authenticated with a Google account or a service account.\n\n* `user:{emailid}`: An email address that represents a spec ific Google\n account. For example, `alice@gmail.com` or `joe@example.com`.\n\ n\n* `serviceAccount:{emailid}`: An email address that represents a service\n account. For example, `my-other-app@appspot.gserviceaccount.com`.\n\n* `group:{e mailid}`: An email address that represents a Google group.\n For example, `adm ins@example.com`.\n\n\n* `domain:{domain}`: A Google Apps domain name that repre sents all the\n users of that domain. For example, `google.com` or `example.co m`.\n\n",
2230 "items": {
2231 "type": "string"
2232 },
2233 "type": "array"
2234 },
2235 "role": {
2236 "description": "Role that is assigned to `members`.\nFor exa mple, `roles/viewer`, `roles/editor`, or `roles/owner`.\nRequired",
2237 "type": "string"
2238 }
2239 },
2240 "type": "object"
2241 },
2242 "Range": {
2243 "description": "A 0-based half-open genomic coordinate range for sea rch requests.",
2244 "id": "Range",
2245 "properties": {
2246 "end": {
2247 "description": "The end position of the range on the referen ce, 0-based exclusive.",
2248 "format": "int64",
2249 "type": "string"
2250 },
2251 "referenceName": {
2252 "description": "The reference sequence name, for example `ch r1`,\n`1`, or `chrX`.",
2253 "type": "string"
2254 },
2255 "start": {
2256 "description": "The start position of the range on the refer ence, 0-based inclusive.",
2257 "format": "int64",
2258 "type": "string"
2259 }
2260 },
2261 "type": "object"
2262 },
2263 "VariantSet": {
2264 "description": "A variant set is a collection of call sets and varia nts. It contains summary\nstatistics of those contents. A variant set belongs to a dataset.\n\nFor more genomics resource definitions, see [Fundamentals of Goog le\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) ",
2265 "id": "VariantSet",
2266 "properties": {
2267 "id": { 2289 "id": {
2268 "description": "The server-generated variant set ID, unique across all variant sets.", 2290 "description": "The server-generated read ID, unique across all reads. This is different\nfrom the `fragmentName`.",
2269 "type": "string" 2291 "type": "string"
2270 }, 2292 },
2271 "description": { 2293 "numberReads": {
2272 "description": "A textual description of this variant set.", 2294 "description": "The number of reads in the fragment (extensi on to SAM flag 0x1).",
2273 "type": "string" 2295 "format": "int32",
2274 }, 2296 "type": "integer"
2275 "datasetId": { 2297 },
2276 "description": "The dataset to which this variant set belong s.", 2298 "secondaryAlignment": {
2277 "type": "string" 2299 "description": "Whether this alignment is secondary. Equival ent to SAM flag 0x100.\nA secondary alignment represents an alternative to the p rimary alignment\nfor this read. Aligners may return secondary alignments if a r ead can map\nambiguously to multiple coordinates in the genome. By convention, e ach read\nhas one and only one alignment where both `secondaryAlignment`\nand `s upplementaryAlignment` are false.",
2278 }, 2300 "type": "boolean"
2279 "name": { 2301 },
2280 "description": "User-specified, mutable name.", 2302 "fragmentName": {
2281 "type": "string" 2303 "description": "The fragment name. Equivalent to QNAME (quer y template name) in SAM.",
2282 }, 2304 "type": "string"
2283 "referenceSetId": { 2305 },
2284 "description": "The reference set to which the variant set i s mapped. The reference set\ndescribes the alignment provenance of the variant s et, while the\n`referenceBounds` describe the shape of the actual variant data. The\nreference set's reference names are a superset of those found in the\n`refe renceBounds`.\n\nFor example, given a variant set that is mapped to the GRCh38 r eference set\nand contains a single variant on reference 'X', `referenceBounds` would\ncontain only an entry for 'X', while the associated reference set\nenumer ates all possible references: '1', '2', 'X', 'Y', 'MT', etc.", 2306 "readGroupSetId": {
2285 "type": "string" 2307 "description": "The ID of the read group set this read belon gs to. A read belongs to\nexactly one read group set.",
2286 }, 2308 "type": "string"
2287 "metadata": { 2309 },
2288 "description": "The metadata associated with this variant se t.", 2310 "duplicateFragment": {
2289 "items": { 2311 "description": "The fragment is a PCR or optical duplicate ( SAM flag 0x400).",
2290 "$ref": "VariantSetMetadata" 2312 "type": "boolean"
2291 }, 2313 },
2292 "type": "array" 2314 "readNumber": {
2293 }, 2315 "description": "The read number in sequencing. 0-based and l ess than numberReads. This\nfield replaces SAM flag 0x40 and 0x80.",
2294 "referenceBounds": { 2316 "format": "int32",
2295 "description": "A list of all references used by the variant s in a variant set\nwith associated coordinate upper bounds for each one.", 2317 "type": "integer"
2296 "items": { 2318 },
2297 "$ref": "ReferenceBound" 2319 "alignedSequence": {
2298 }, 2320 "description": "The bases of the read sequence contained in this alignment record,\n**without CIGAR operations applied** (equivalent to SEQ in SAM).\n`alignedSequence` and `alignedQuality` may be\nshorter than the full r ead sequence and quality. This will occur if the\nalignment is part of a chimeri c alignment, or if the read was trimmed. When\nthis occurs, the CIGAR for this r ead will begin/end with a hard clip\noperator that will indicate the length of t he excised sequence.",
2299 "type": "array" 2321 "type": "string"
2300 } 2322 },
2301 }, 2323 "readGroupId": {
2302 "type": "object" 2324 "description": "The ID of the read group this read belongs t o. A read belongs to exactly\none read group. This is a server-generated ID whic h is distinct from SAM's\nRG tag (for that value, see\nReadGroup.name).",
2303 }, 2325 "type": "string"
2304 "BatchCreateAnnotationsResponse": { 2326 },
2305 "id": "BatchCreateAnnotationsResponse", 2327 "nextMatePosition": {
2306 "properties": { 2328 "$ref": "Position",
2307 "entries": { 2329 "description": "The mapping of the primary alignment of the\ n`(readNumber+1)%numberReads` read in the fragment. It replaces\nmate position a nd mate strand in SAM."
2308 "description": "The resulting per-annotation entries, ordere d consistently with the\noriginal request.",
2309 "items": {
2310 "$ref": "Entry"
2311 },
2312 "type": "array"
2313 }
2314 },
2315 "type": "object"
2316 },
2317 "ReferenceBound": {
2318 "description": "ReferenceBound records an upper bound for the starti ng coordinate of\nvariants in a particular reference.",
2319 "id": "ReferenceBound",
2320 "properties": {
2321 "upperBound": {
2322 "description": "An upper bound (inclusive) on the starting c oordinate of any\nvariant in the reference sequence.",
2323 "format": "int64",
2324 "type": "string"
2325 },
2326 "referenceName": {
2327 "description": "The name of the reference associated with th is reference bound.",
2328 "type": "string"
2329 }
2330 },
2331 "type": "object"
2332 },
2333 "ListOperationsResponse": {
2334 "description": "The response message for Operations.ListOperations." ,
2335 "id": "ListOperationsResponse",
2336 "properties": {
2337 "nextPageToken": {
2338 "description": "The standard List next-page token.",
2339 "type": "string"
2340 },
2341 "operations": {
2342 "description": "A list of operations that matches the specif ied filter in the request.",
2343 "items": {
2344 "$ref": "Operation"
2345 },
2346 "type": "array"
2347 }
2348 },
2349 "type": "object"
2350 },
2351 "Variant": {
2352 "description": "A variant represents a change in DNA sequence relati ve to a reference\nsequence. For example, a variant could represent a SNP or an insertion.\nVariants belong to a variant set.\n\nFor more genomics resource defi nitions, see [Fundamentals of Google\nGenomics](https://cloud.google.com/genomic s/fundamentals-of-google-genomics)\n\nEach of the calls on a variant represent a determination of genotype with\nrespect to that variant. For example, a call mi ght assign probability of 0.32\nto the occurrence of a SNP named rs1234 in a sam ple named NA12345. A call\nbelongs to a call set, which contains related calls t ypically from one\nsample.",
2353 "id": "Variant",
2354 "properties": {
2355 "quality": {
2356 "description": "A measure of how likely this variant is to b e real.\nA higher value is better.",
2357 "format": "double",
2358 "type": "number"
2359 },
2360 "id": {
2361 "description": "The server-generated variant ID, unique acro ss all variants.",
2362 "type": "string"
2363 },
2364 "variantSetId": {
2365 "description": "The ID of the variant set this variant belon gs to.",
2366 "type": "string"
2367 },
2368 "referenceName": {
2369 "description": "The reference on which this variant occurs.\ n(such as `chr20` or `X`)",
2370 "type": "string"
2371 }, 2330 },
2372 "info": { 2331 "info": {
2373 "additionalProperties": { 2332 "additionalProperties": {
2374 "items": { 2333 "items": {
2375 "type": "any" 2334 "type": "any"
2376 }, 2335 },
2377 "type": "array" 2336 "type": "array"
2378 }, 2337 },
2379 "description": "A map of additional variant information. Thi s must be of the form\nmap<string, string[]> (string key mapping to a list of st ring values).", 2338 "description": "A map of additional read alignment informati on. This must be of the form\nmap<string, string[]> (string key mapping to a lis t of string values).",
2380 "type": "object" 2339 "type": "object"
2381 }, 2340 },
2382 "referenceBases": {
2383 "description": "The reference bases for this variant. They s tart at the given\nposition.",
2384 "type": "string"
2385 },
2386 "alternateBases": {
2387 "description": "The bases that appear instead of the referen ce bases.",
2388 "items": {
2389 "type": "string"
2390 },
2391 "type": "array"
2392 },
2393 "names": {
2394 "description": "Names for the variant, for example a RefSNP ID.",
2395 "items": {
2396 "type": "string"
2397 },
2398 "type": "array"
2399 },
2400 "end": {
2401 "description": "The end position (0-based) of this variant. This corresponds to the first\nbase after the last base in the reference allele. So, the length of\nthe reference allele is (end - start). This is useful for va riants\nthat don't explicitly give alternate bases, for example large deletions. ",
2402 "format": "int64",
2403 "type": "string"
2404 },
2405 "filter": {
2406 "description": "A list of filters (normally quality filters) this variant has failed.\n`PASS` indicates this variant has passed all filters. ",
2407 "items": {
2408 "type": "string"
2409 },
2410 "type": "array"
2411 },
2412 "calls": {
2413 "description": "The variant calls for this particular varian t. Each one represents the\ndetermination of genotype with respect to this varia nt.",
2414 "items": {
2415 "$ref": "VariantCall"
2416 },
2417 "type": "array"
2418 },
2419 "created": {
2420 "description": "The date this variant was created, in millis econds from the epoch.",
2421 "format": "int64",
2422 "type": "string"
2423 },
2424 "start": {
2425 "description": "The position at which this variant occurs (0 -based).\nThis corresponds to the first base of the string of reference bases.",
2426 "format": "int64",
2427 "type": "string"
2428 }
2429 },
2430 "type": "object"
2431 },
2432 "SearchCallSetsResponse": {
2433 "description": "The call set search response.",
2434 "id": "SearchCallSetsResponse",
2435 "properties": {
2436 "callSets": {
2437 "description": "The list of matching call sets.",
2438 "items": {
2439 "$ref": "CallSet"
2440 },
2441 "type": "array"
2442 },
2443 "nextPageToken": {
2444 "description": "The continuation token, which is used to pag e through large result sets.\nProvide this value in a subsequent request to retu rn the next page of\nresults. This field will be empty if there aren't any addit ional results.",
2445 "type": "string"
2446 }
2447 },
2448 "type": "object"
2449 },
2450 "SearchVariantsRequest": {
2451 "description": "The variant search request.",
2452 "id": "SearchVariantsRequest",
2453 "properties": {
2454 "end": {
2455 "description": "The end of the window, 0-based exclusive. If unspecified or 0, defaults to\nthe length of the reference.",
2456 "format": "int64",
2457 "type": "string"
2458 },
2459 "pageToken": {
2460 "description": "The continuation token, which is used to pag e through large result sets.\nTo get the next page of results, set this paramete r to the value of\n`nextPageToken` from the previous response.",
2461 "type": "string"
2462 },
2463 "maxCalls": {
2464 "description": "The maximum number of calls to return in a s ingle page. Note that this\nlimit may be exceeded in the event that a matching v ariant contains more\ncalls than the requested maximum. If unspecified, defaults to 5000. The\nmaximum value is 10000.",
2465 "format": "int32",
2466 "type": "integer"
2467 },
2468 "pageSize": {
2469 "description": "The maximum number of variants to return in a single page. If unspecified,\ndefaults to 5000. The maximum value is 10000.",
2470 "format": "int32",
2471 "type": "integer"
2472 },
2473 "callSetIds": {
2474 "description": "Only return variant calls which belong to ca ll sets with these ids.\nLeaving this blank returns all variant calls. If a vari ant has no\ncalls belonging to any of these call sets, it won't be returned at a ll.",
2475 "items": {
2476 "type": "string"
2477 },
2478 "type": "array"
2479 },
2480 "start": {
2481 "description": "The beginning of the window (0-based, inclus ive) for which\noverlapping variants should be returned. If unspecified, default s to 0.",
2482 "format": "int64",
2483 "type": "string"
2484 },
2485 "variantName": {
2486 "description": "Only return variants which have exactly this name.",
2487 "type": "string"
2488 },
2489 "referenceName": {
2490 "description": "Required. Only return variants in this refer ence sequence.",
2491 "type": "string"
2492 },
2493 "variantSetIds": {
2494 "description": "At most one variant set ID must be provided. Only variants from this\nvariant set will be returned. If omitted, a call set i d must be included in\nthe request.",
2495 "items": {
2496 "type": "string"
2497 },
2498 "type": "array"
2499 }
2500 },
2501 "type": "object"
2502 },
2503 "OperationMetadata": {
2504 "description": "Metadata describing an Operation.",
2505 "id": "OperationMetadata",
2506 "properties": {
2507 "clientId": {
2508 "description": "This field is deprecated. Use `labels` inste ad. Optionally provided by the\ncaller when submitting the request that creates the operation.",
2509 "type": "string"
2510 },
2511 "endTime": {
2512 "description": "The time at which the job stopped running.",
2513 "format": "google-datetime",
2514 "type": "string"
2515 },
2516 "events": {
2517 "description": "Optional event messages that were generated during the job's execution.\nThis also contains any warnings that were generated during import\nor export.",
2518 "items": {
2519 "$ref": "OperationEvent"
2520 },
2521 "type": "array"
2522 },
2523 "startTime": {
2524 "description": "The time at which the job began to run.",
2525 "format": "google-datetime",
2526 "type": "string"
2527 },
2528 "request": {
2529 "additionalProperties": {
2530 "description": "Properties of the object. Contains field @type with type URL.",
2531 "type": "any"
2532 },
2533 "description": "The original request that started the operat ion. Note that this will be in\ncurrent version of the API. If the operation was started with v1beta2 API\nand a GetOperation is performed on v1 API, a v1 reque st will be returned.",
2534 "type": "object"
2535 },
2536 "runtimeMetadata": {
2537 "additionalProperties": {
2538 "description": "Properties of the object. Contains field @type with type URL.",
2539 "type": "any"
2540 },
2541 "description": "Runtime metadata on this Operation.",
2542 "type": "object"
2543 },
2544 "createTime": {
2545 "description": "The time at which the job was submitted to t he Genomics service.",
2546 "format": "google-datetime",
2547 "type": "string"
2548 },
2549 "labels": {
2550 "additionalProperties": {
2551 "type": "string"
2552 },
2553 "description": "Optionally provided by the caller when submi tting the request that creates\nthe operation.",
2554 "type": "object"
2555 },
2556 "projectId": {
2557 "description": "The Google Cloud Project in which the job is scoped.",
2558 "type": "string"
2559 }
2560 },
2561 "type": "object"
2562 },
2563 "SearchReadGroupSetsRequest": {
2564 "description": "The read group set search request.",
2565 "id": "SearchReadGroupSetsRequest",
2566 "properties": {
2567 "pageToken": {
2568 "description": "The continuation token, which is used to pag e through large result sets.\nTo get the next page of results, set this paramete r to the value of\n`nextPageToken` from the previous response.",
2569 "type": "string"
2570 },
2571 "name": {
2572 "description": "Only return read group sets for which a subs tring of the name matches this\nstring.",
2573 "type": "string"
2574 },
2575 "pageSize": {
2576 "description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 256. The maximum value is 1024.",
2577 "format": "int32",
2578 "type": "integer"
2579 },
2580 "datasetIds": {
2581 "description": "Restricts this query to read group sets with in the given datasets. At least\none ID must be provided.",
2582 "items": {
2583 "type": "string"
2584 },
2585 "type": "array"
2586 }
2587 },
2588 "type": "object"
2589 },
2590 "SearchAnnotationsResponse": {
2591 "id": "SearchAnnotationsResponse",
2592 "properties": {
2593 "annotations": {
2594 "description": "The matching annotations.",
2595 "items": {
2596 "$ref": "Annotation"
2597 },
2598 "type": "array"
2599 },
2600 "nextPageToken": {
2601 "description": "The continuation token, which is used to pag e through large result sets.\nProvide this value in a subsequent request to retu rn the next page of\nresults. This field will be empty if there aren't any addit ional results.",
2602 "type": "string"
2603 }
2604 },
2605 "type": "object"
2606 },
2607 "ClinicalCondition": {
2608 "id": "ClinicalCondition",
2609 "properties": {
2610 "names": {
2611 "description": "A set of names for the condition.",
2612 "items": {
2613 "type": "string"
2614 },
2615 "type": "array"
2616 },
2617 "omimId": {
2618 "description": "The OMIM id for this condition.\nSearch for these IDs at http://omim.org/",
2619 "type": "string"
2620 },
2621 "externalIds": {
2622 "description": "The set of external IDs for this condition." ,
2623 "items": {
2624 "$ref": "ExternalId"
2625 },
2626 "type": "array"
2627 },
2628 "conceptId": {
2629 "description": "The MedGen concept id associated with this g ene.\nSearch for these IDs at http://www.ncbi.nlm.nih.gov/medgen/",
2630 "type": "string"
2631 }
2632 },
2633 "type": "object"
2634 },
2635 "SearchReadsResponse": {
2636 "description": "The read search response.",
2637 "id": "SearchReadsResponse",
2638 "properties": {
2639 "nextPageToken": {
2640 "description": "The continuation token, which is used to pag e through large result sets.\nProvide this value in a subsequent request to retu rn the next page of\nresults. This field will be empty if there aren't any addit ional results.",
2641 "type": "string"
2642 },
2643 "alignments": {
2644 "description": "The list of matching alignments sorted by ma pped genomic coordinate,\nif any, ascending in position within the same referenc e. Unmapped reads,\nwhich have no position, are returned contiguously and are so rted in\nascending lexicographic order by fragment name.",
2645 "items": {
2646 "$ref": "Read"
2647 },
2648 "type": "array"
2649 }
2650 },
2651 "type": "object"
2652 },
2653 "Program": {
2654 "id": "Program",
2655 "properties": {
2656 "version": {
2657 "description": "The version of the program run.",
2658 "type": "string"
2659 },
2660 "id": {
2661 "description": "The user specified locally unique ID of the program. Used along with\n`prevProgramId` to define an ordering between programs .",
2662 "type": "string"
2663 },
2664 "name": {
2665 "description": "The display name of the program. This is typ ically the colloquial name of\nthe tool used, for example 'bwa' or 'picard'.",
2666 "type": "string"
2667 },
2668 "prevProgramId": {
2669 "description": "The ID of the program run before this one.",
2670 "type": "string"
2671 },
2672 "commandLine": {
2673 "description": "The command line used to run this program.",
2674 "type": "string"
2675 }
2676 },
2677 "type": "object"
2678 },
2679 "ComputeEngine": {
2680 "description": "Describes a Compute Engine resource that is being ma naged by a running\npipeline.",
2681 "id": "ComputeEngine",
2682 "properties": {
2683 "instanceName": {
2684 "description": "The instance on which the operation is runni ng.",
2685 "type": "string"
2686 },
2687 "zone": {
2688 "description": "The availability zone in which the instance resides.",
2689 "type": "string"
2690 },
2691 "diskNames": {
2692 "description": "The names of the disks that were created for this pipeline.",
2693 "items": {
2694 "type": "string"
2695 },
2696 "type": "array"
2697 },
2698 "machineType": {
2699 "description": "The machine type of the instance.",
2700 "type": "string"
2701 }
2702 },
2703 "type": "object"
2704 },
2705 "CoverageBucket": {
2706 "description": "A bucket over which read coverage has been precomput ed. A bucket corresponds\nto a specific range of the reference sequence.",
2707 "id": "CoverageBucket",
2708 "properties": {
2709 "meanCoverage": {
2710 "description": "The average number of reads which are aligne d to each individual\nreference base in this bucket.",
2711 "format": "float",
2712 "type": "number"
2713 },
2714 "range": {
2715 "$ref": "Range",
2716 "description": "The genomic coordinate range spanned by this bucket."
2717 }
2718 },
2719 "type": "object"
2720 },
2721 "ExternalId": {
2722 "id": "ExternalId",
2723 "properties": {
2724 "sourceName": {
2725 "description": "The name of the source of this data.",
2726 "type": "string"
2727 },
2728 "id": {
2729 "description": "The id used by the source of this data.",
2730 "type": "string"
2731 }
2732 },
2733 "type": "object"
2734 },
2735 "SearchVariantSetsRequest": {
2736 "description": "The search variant sets request.",
2737 "id": "SearchVariantSetsRequest",
2738 "properties": {
2739 "datasetIds": {
2740 "description": "Exactly one dataset ID must be provided here . Only variant sets which\nbelong to this dataset will be returned.",
2741 "items": {
2742 "type": "string"
2743 },
2744 "type": "array"
2745 },
2746 "pageToken": {
2747 "description": "The continuation token, which is used to pag e through large result sets.\nTo get the next page of results, set this paramete r to the value of\n`nextPageToken` from the previous response.",
2748 "type": "string"
2749 },
2750 "pageSize": {
2751 "description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 1024.",
2752 "format": "int32",
2753 "type": "integer"
2754 }
2755 },
2756 "type": "object"
2757 },
2758 "VariantSetMetadata": {
2759 "description": "Metadata describes a single piece of variant call me tadata.\nThese data include a top level key and either a single value string (va lue)\nor a list of key-value pairs (info.)\nValue and info are mutually exclusiv e.",
2760 "id": "VariantSetMetadata",
2761 "properties": {
2762 "info": {
2763 "additionalProperties": {
2764 "items": {
2765 "type": "any"
2766 },
2767 "type": "array"
2768 },
2769 "description": "Remaining structured metadata key-value pair s. This must be of the form\nmap<string, string[]> (string key mapping to a list of string values).",
2770 "type": "object"
2771 },
2772 "type": {
2773 "description": "The type of data. Possible types include: In teger, Float,\nFlag, Character, and String.",
2774 "enum": [
2775 "TYPE_UNSPECIFIED",
2776 "INTEGER",
2777 "FLOAT",
2778 "FLAG",
2779 "CHARACTER",
2780 "STRING"
2781 ],
2782 "enumDescriptions": [
2783 "",
2784 "",
2785 "",
2786 "",
2787 "",
2788 ""
2789 ],
2790 "type": "string"
2791 },
2792 "value": {
2793 "description": "The value field for simple metadata",
2794 "type": "string"
2795 },
2796 "id": {
2797 "description": "User-provided ID field, not enforced by this API.\nTwo or more pieces of structured metadata with identical\nid and key fiel ds are considered equivalent.",
2798 "type": "string"
2799 },
2800 "number": {
2801 "description": "The number of values that can be included in a field described by this\nmetadata.",
2802 "type": "string"
2803 },
2804 "key": {
2805 "description": "The top-level key.",
2806 "type": "string"
2807 },
2808 "description": {
2809 "description": "A textual description of this metadata.",
2810 "type": "string"
2811 }
2812 },
2813 "type": "object"
2814 },
2815 "Reference": {
2816 "description": "A reference is a canonical assembled DNA sequence, i ntended to act as a\nreference coordinate space for other genomic annotations. A single reference\nmight represent the human chromosome 1 or mitochandrial DNA, for instance. A\nreference belongs to one or more reference sets.\n\nFor more ge nomics resource definitions, see [Fundamentals of Google\nGenomics](https://clou d.google.com/genomics/fundamentals-of-google-genomics)",
2817 "id": "Reference",
2818 "properties": {
2819 "id": {
2820 "description": "The server-generated reference ID, unique ac ross all references.",
2821 "type": "string"
2822 },
2823 "length": {
2824 "description": "The length of this reference's sequence.",
2825 "format": "int64",
2826 "type": "string"
2827 },
2828 "sourceAccessions": {
2829 "description": "All known corresponding accession IDs in INS DC (GenBank/ENA/DDBJ) ideally\nwith a version number, for example `GCF_000001405 .26`.",
2830 "items": {
2831 "type": "string"
2832 },
2833 "type": "array"
2834 },
2835 "sourceUri": {
2836 "description": "The URI from which the sequence was obtained . Typically specifies a FASTA\nformat file.",
2837 "type": "string"
2838 },
2839 "ncbiTaxonId": {
2840 "description": "ID from http://www.ncbi.nlm.nih.gov/taxonomy . For example, 9606 for human.",
2841 "format": "int32",
2842 "type": "integer"
2843 },
2844 "name": {
2845 "description": "The name of this reference, for example `22` .",
2846 "type": "string"
2847 },
2848 "md5checksum": {
2849 "description": "MD5 of the upper-case sequence excluding all whitespace characters (this\nis equivalent to SQ:M5 in SAM). This value is repr esented in lower case\nhexadecimal format.",
2850 "type": "string"
2851 }
2852 },
2853 "type": "object"
2854 },
2855 "SearchReferenceSetsRequest": {
2856 "id": "SearchReferenceSetsRequest",
2857 "properties": {
2858 "md5checksums": {
2859 "description": "If present, return reference sets for which the\nmd5checksum matches exactly.",
2860 "items": {
2861 "type": "string"
2862 },
2863 "type": "array"
2864 },
2865 "pageToken": {
2866 "description": "The continuation token, which is used to pag e through large result sets.\nTo get the next page of results, set this paramete r to the value of\n`nextPageToken` from the previous response.",
2867 "type": "string"
2868 },
2869 "accessions": {
2870 "description": "If present, return reference sets for which a prefix of any of\nsourceAccessions\nmatch any of these strings. Accession numb ers typically have a main number\nand a version, for example `NC_000001.11`.",
2871 "items": {
2872 "type": "string"
2873 },
2874 "type": "array"
2875 },
2876 "pageSize": {
2877 "description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 1024. The maximum value is 4096.",
2878 "format": "int32",
2879 "type": "integer"
2880 },
2881 "assemblyId": {
2882 "description": "If present, return reference sets for which a substring of their\n`assemblyId` matches this string (case insensitive).",
2883 "type": "string"
2884 }
2885 },
2886 "type": "object"
2887 },
2888 "SetIamPolicyRequest": {
2889 "description": "Request message for `SetIamPolicy` method.",
2890 "id": "SetIamPolicyRequest",
2891 "properties": {
2892 "policy": {
2893 "$ref": "Policy",
2894 "description": "REQUIRED: The complete policy to be applied to the `resource`. The size of\nthe policy is limited to a few 10s of KB. An emp ty policy is a\nvalid policy but certain Cloud Platform services (such as Projec ts)\nmight reject them."
2895 }
2896 },
2897 "type": "object"
2898 },
2899 "MergeVariantsRequest": {
2900 "id": "MergeVariantsRequest",
2901 "properties": {
2902 "variants": {
2903 "description": "The variants to be merged with existing vari ants.",
2904 "items": {
2905 "$ref": "Variant"
2906 },
2907 "type": "array"
2908 },
2909 "infoMergeConfig": {
2910 "additionalProperties": {
2911 "enum": [
2912 "INFO_MERGE_OPERATION_UNSPECIFIED",
2913 "IGNORE_NEW",
2914 "MOVE_TO_CALLS"
2915 ],
2916 "type": "string"
2917 },
2918 "description": "A mapping between info field keys and the In foMergeOperations to\nbe performed on them.",
2919 "type": "object"
2920 },
2921 "variantSetId": {
2922 "description": "The destination variant set.",
2923 "type": "string"
2924 }
2925 },
2926 "type": "object"
2927 },
2928 "Read": {
2929 "description": "A read alignment describes a linear alignment of a s tring of DNA to a\nreference sequence, in addition to metadata\nabout the fragme nt (the molecule of DNA sequenced) and the read (the bases\nwhich were read by t he sequencer). A read is equivalent to a line in a SAM\nfile. A read belongs to exactly one read group and exactly one\nread group set.\n\nFor more genomics res ource definitions, see [Fundamentals of Google\nGenomics](https://cloud.google.c om/genomics/fundamentals-of-google-genomics)\n\n### Reverse-stranded reads\n\nMa pped reads (reads having a non-null `alignment`) can be aligned to either\nthe f orward or the reverse strand of their associated reference. Strandedness\nof a m apped read is encoded by `alignment.position.reverseStrand`.\n\nIf we consider t he reference to be a forward-stranded coordinate space of\n`[0, reference.length )` with `0` as the left-most position and\n`reference.length` as the right-most position, reads are always aligned left\nto right. That is, `alignment.position. position` always refers to the\nleft-most reference coordinate and `alignment.ci gar` describes the alignment\nof this read to the reference from left to right. All per-base fields such as\n`alignedSequence` and `alignedQuality` share this s ame left-to-right\norientation; this is true of reads which are aligned to eithe r strand. For\nreverse-stranded reads, this means that `alignedSequence` is the reverse\ncomplement of the bases that were originally reported by the sequencing \nmachine.\n\n### Generating a reference-aligned sequence string\n\nWhen interac ting with mapped reads, it's often useful to produce a string\nrepresenting the local alignment of the read to reference. The following\npseudocode demonstrates one way of doing this:\n\n out = \"\"\n offset = 0\n for c in read.ali gnment.cigar {\n switch c.operation {\n case \"ALIGNMENT_MATCH\", \"SE QUENCE_MATCH\", \"SEQUENCE_MISMATCH\":\n out += read.alignedSequence[offs et:offset+c.operationLength]\n offset += c.operationLength\n break \n case \"CLIP_SOFT\", \"INSERT\":\n offset += c.operationLength\n break\n case \"PAD\":\n out += repeat(\"*\", c.operationLength )\n break\n case \"DELETE\":\n out += repeat(\"-\", c.operati onLength)\n break\n case \"SKIP\":\n out += repeat(\" \", c.o perationLength)\n break\n case \"CLIP_HARD\":\n break\n }\n }\n return out\n\n### Converting to SAM's CIGAR string\n\nThe followin g pseudocode generates a SAM CIGAR string from the\n`cigar` field. Note that thi s is a lossy conversion\n(`cigar.referenceSequence` is lost).\n\n cigarMap = {\n \"ALIGNMENT_MATCH\": \"M\",\n \"INSERT\": \"I\",\n \"DELETE\" : \"D\",\n \"SKIP\": \"N\",\n \"CLIP_SOFT\": \"S\",\n \"CLIP_HARD \": \"H\",\n \"PAD\": \"P\",\n \"SEQUENCE_MATCH\": \"=\",\n \"SEQ UENCE_MISMATCH\": \"X\",\n }\n cigarStr = \"\"\n for c in read.alignmen t.cigar {\n cigarStr += c.operationLength + cigarMap[c.operation]\n }\n return cigarStr",
2930 "id": "Read",
2931 "properties": {
2932 "supplementaryAlignment": { 2341 "supplementaryAlignment": {
2933 "description": "Whether this alignment is supplementary. Equ ivalent to SAM flag 0x800.\nSupplementary alignments are used in the representat ion of a chimeric\nalignment. In a chimeric alignment, a read is split into mult iple\nlinear alignments that map to different reference contigs. The first\nline ar alignment in the read will be designated as the representative\nalignment; th e remaining linear alignments will be designated as\nsupplementary alignments. T hese alignments may have different mapping\nquality scores. In each linear align ment in a chimeric alignment, the read\nwill be hard clipped. The `alignedSequen ce` and\n`alignedQuality` fields in the alignment record will only\nrepresent th e bases for its respective linear alignment.", 2342 "description": "Whether this alignment is supplementary. Equ ivalent to SAM flag 0x800.\nSupplementary alignments are used in the representat ion of a chimeric\nalignment. In a chimeric alignment, a read is split into mult iple\nlinear alignments that map to different reference contigs. The first\nline ar alignment in the read will be designated as the representative\nalignment; th e remaining linear alignments will be designated as\nsupplementary alignments. T hese alignments may have different mapping\nquality scores. In each linear align ment in a chimeric alignment, the read\nwill be hard clipped. The `alignedSequen ce` and\n`alignedQuality` fields in the alignment record will only\nrepresent th e bases for its respective linear alignment.",
2934 "type": "boolean" 2343 "type": "boolean"
2935 }, 2344 },
2936 "properPlacement": { 2345 "properPlacement": {
2937 "description": "The orientation and the distance between rea ds from the fragment are\nconsistent with the sequencing protocol (SAM flag 0x2) .", 2346 "description": "The orientation and the distance between rea ds from the fragment are\nconsistent with the sequencing protocol (SAM flag 0x2) .",
2938 "type": "boolean" 2347 "type": "boolean"
2939 }, 2348 },
2940 "fragmentLength": { 2349 "fragmentLength": {
2941 "description": "The observed length of the fragment, equival ent to TLEN in SAM.", 2350 "description": "The observed length of the fragment, equival ent to TLEN in SAM.",
2942 "format": "int32", 2351 "format": "int32",
2943 "type": "integer" 2352 "type": "integer"
2944 }, 2353 }
2945 "failedVendorQualityChecks": { 2354 },
2946 "description": "Whether this read did not pass filters, such as platform or vendor quality\ncontrols (SAM flag 0x200).", 2355 "type": "object"
2947 "type": "boolean" 2356 },
2948 }, 2357 "ReferenceSet": {
2949 "alignedQuality": { 2358 "description": "A reference set is a set of references which typical ly comprise a reference\nassembly for a species, such as `GRCh38` which is repre sentative\nof the human genome. A reference set defines a common coordinate spac e for\ncomparing reference-aligned experimental data. A reference set contains 1 or\nmore references.\n\nFor more genomics resource definitions, see [Fundamenta ls of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google -genomics)",
2950 "description": "The quality of the read sequence contained i n this alignment record\n(equivalent to QUAL in SAM).\n`alignedSequence` and `al ignedQuality` may be shorter than the full read\nsequence and quality. This will occur if the alignment is part of a\nchimeric alignment, or if the read was tri mmed. When this occurs, the CIGAR\nfor this read will begin/end with a hard clip operator that will indicate\nthe length of the excised sequence.", 2359 "id": "ReferenceSet",
2951 "items": { 2360 "properties": {
2952 "format": "int32", 2361 "sourceAccessions": {
2953 "type": "integer" 2362 "description": "All known corresponding accession IDs in INS DC (GenBank/ENA/DDBJ) ideally\nwith a version number, for example `NC_000001.11` .",
2954 }, 2363 "items": {
2955 "type": "array" 2364 "type": "string"
2956 }, 2365 },
2957 "alignment": { 2366 "type": "array"
2958 "$ref": "LinearAlignment", 2367 },
2959 "description": "The linear alignment for this alignment reco rd. This field is null for\nunmapped reads." 2368 "description": {
2960 }, 2369 "description": "Free text description of this reference set. ",
2961 "id": { 2370 "type": "string"
2962 "description": "The server-generated read ID, unique across all reads. This is different\nfrom the `fragmentName`.", 2371 },
2963 "type": "string" 2372 "sourceUri": {
2964 }, 2373 "description": "The URI from which the references were obtai ned.",
2965 "numberReads": { 2374 "type": "string"
2966 "description": "The number of reads in the fragment (extensi on to SAM flag 0x1).", 2375 },
2376 "ncbiTaxonId": {
2377 "description": "ID from http://www.ncbi.nlm.nih.gov/taxonomy (for example, 9606 for human)\nindicating the species which this reference set is intended to model. Note\nthat contained references may specify a different `n cbiTaxonId`, as\nassemblies may contain reference sequences which do not belong to the\nmodeled species, for example EBV in a human reference genome.",
2967 "format": "int32", 2378 "format": "int32",
2968 "type": "integer" 2379 "type": "integer"
2969 }, 2380 },
2970 "secondaryAlignment": { 2381 "referenceIds": {
2971 "description": "Whether this alignment is secondary. Equival ent to SAM flag 0x100.\nA secondary alignment represents an alternative to the p rimary alignment\nfor this read. Aligners may return secondary alignments if a r ead can map\nambiguously to multiple coordinates in the genome. By convention, e ach read\nhas one and only one alignment where both `secondaryAlignment`\nand `s upplementaryAlignment` are false.", 2382 "description": "The IDs of the reference objects that are pa rt of this set.\n`Reference.md5checksum` must be unique within this set.",
2972 "type": "boolean" 2383 "items": {
2973 }, 2384 "type": "string"
2974 "fragmentName": { 2385 },
2975 "description": "The fragment name. Equivalent to QNAME (quer y template name) in SAM.", 2386 "type": "array"
2976 "type": "string" 2387 },
2977 }, 2388 "assemblyId": {
2978 "readGroupSetId": { 2389 "description": "Public id of this reference set, such as `GR Ch37`.",
2979 "description": "The ID of the read group set this read belon gs to. A read belongs to\nexactly one read group set.", 2390 "type": "string"
2980 "type": "string" 2391 },
2981 }, 2392 "md5checksum": {
2982 "duplicateFragment": { 2393 "description": "Order-independent MD5 checksum which identif ies this reference set. The\nchecksum is computed by sorting all lower case hexi decimal string\n`reference.md5checksum` (for all reference in this set) in\nasce nding lexicographic order, concatenating, and taking the MD5 of that\nvalue. The resulting value is represented in lower case hexadecimal format.",
2983 "description": "The fragment is a PCR or optical duplicate ( SAM flag 0x400).", 2394 "type": "string"
2984 "type": "boolean" 2395 },
2985 }, 2396 "id": {
2986 "readNumber": { 2397 "description": "The server-generated reference set ID, uniqu e across all reference sets.",
2987 "description": "The read number in sequencing. 0-based and l ess than numberReads. This\nfield replaces SAM flag 0x40 and 0x80.",
2988 "format": "int32",
2989 "type": "integer"
2990 },
2991 "alignedSequence": {
2992 "description": "The bases of the read sequence contained in this alignment record,\n**without CIGAR operations applied** (equivalent to SEQ in SAM).\n`alignedSequence` and `alignedQuality` may be\nshorter than the full r ead sequence and quality. This will occur if the\nalignment is part of a chimeri c alignment, or if the read was trimmed. When\nthis occurs, the CIGAR for this r ead will begin/end with a hard clip\noperator that will indicate the length of t he excised sequence.",
2993 "type": "string"
2994 },
2995 "readGroupId": {
2996 "description": "The ID of the read group this read belongs t o. A read belongs to exactly\none read group. This is a server-generated ID whic h is distinct from SAM's\nRG tag (for that value, see\nReadGroup.name).",
2997 "type": "string"
2998 },
2999 "info": {
3000 "additionalProperties": {
3001 "items": {
3002 "type": "any"
3003 },
3004 "type": "array"
3005 },
3006 "description": "A map of additional read alignment informati on. This must be of the form\nmap<string, string[]> (string key mapping to a lis t of string values).",
3007 "type": "object"
3008 },
3009 "nextMatePosition": {
3010 "$ref": "Position",
3011 "description": "The mapping of the primary alignment of the\ n`(readNumber+1)%numberReads` read in the fragment. It replaces\nmate position a nd mate strand in SAM."
3012 }
3013 },
3014 "type": "object"
3015 },
3016 "BatchCreateAnnotationsRequest": {
3017 "id": "BatchCreateAnnotationsRequest",
3018 "properties": {
3019 "annotations": {
3020 "description": "The annotations to be created. At most 4096 can be specified in a single\nrequest.",
3021 "items": {
3022 "$ref": "Annotation"
3023 },
3024 "type": "array"
3025 },
3026 "requestId": {
3027 "description": "A unique request ID which enables the server to detect duplicated requests.\nIf provided, duplicated requests will result in the same response; if not\nprovided, duplicated requests may result in duplicat ed data. For a given\nannotation set, callers should not reuse `request_id`s whe n writing\ndifferent batches of annotations - behavior in this case is undefined .\nA common approach is to use a UUID. For batch jobs where worker crashes are\n a possibility, consider using some unique variant of a worker or run ID.",
3028 "type": "string" 2398 "type": "string"
3029 } 2399 }
3030 }, 2400 },
3031 "type": "object" 2401 "type": "object"
3032 }, 2402 },
3033 "CigarUnit": { 2403 "CigarUnit": {
3034 "description": "A single CIGAR operation.", 2404 "description": "A single CIGAR operation.",
3035 "id": "CigarUnit", 2405 "id": "CigarUnit",
3036 "properties": { 2406 "properties": {
3037 "operationLength": { 2407 "operationLength": {
(...skipping 28 matching lines...) Expand all
3066 ], 2436 ],
3067 "type": "string" 2437 "type": "string"
3068 }, 2438 },
3069 "referenceSequence": { 2439 "referenceSequence": {
3070 "description": "`referenceSequence` is only used at mismatch es\n(`SEQUENCE_MISMATCH`) and deletions (`DELETE`).\nFilling this field replaces SAM's MD tag. If the relevant information is\nnot available, this field is unse t.", 2440 "description": "`referenceSequence` is only used at mismatch es\n(`SEQUENCE_MISMATCH`) and deletions (`DELETE`).\nFilling this field replaces SAM's MD tag. If the relevant information is\nnot available, this field is unse t.",
3071 "type": "string" 2441 "type": "string"
3072 } 2442 }
3073 }, 2443 },
3074 "type": "object" 2444 "type": "object"
3075 }, 2445 },
3076 "ReferenceSet": {
3077 "description": "A reference set is a set of references which typical ly comprise a reference\nassembly for a species, such as `GRCh38` which is repre sentative\nof the human genome. A reference set defines a common coordinate spac e for\ncomparing reference-aligned experimental data. A reference set contains 1 or\nmore references.\n\nFor more genomics resource definitions, see [Fundamenta ls of Google\nGenomics](https://cloud.google.com/genomics/fundamentals-of-google -genomics)",
3078 "id": "ReferenceSet",
3079 "properties": {
3080 "id": {
3081 "description": "The server-generated reference set ID, uniqu e across all reference sets.",
3082 "type": "string"
3083 },
3084 "sourceAccessions": {
3085 "description": "All known corresponding accession IDs in INS DC (GenBank/ENA/DDBJ) ideally\nwith a version number, for example `NC_000001.11` .",
3086 "items": {
3087 "type": "string"
3088 },
3089 "type": "array"
3090 },
3091 "description": {
3092 "description": "Free text description of this reference set. ",
3093 "type": "string"
3094 },
3095 "sourceUri": {
3096 "description": "The URI from which the references were obtai ned.",
3097 "type": "string"
3098 },
3099 "ncbiTaxonId": {
3100 "description": "ID from http://www.ncbi.nlm.nih.gov/taxonomy (for example, 9606 for human)\nindicating the species which this reference set is intended to model. Note\nthat contained references may specify a different `n cbiTaxonId`, as\nassemblies may contain reference sequences which do not belong to the\nmodeled species, for example EBV in a human reference genome.",
3101 "format": "int32",
3102 "type": "integer"
3103 },
3104 "referenceIds": {
3105 "description": "The IDs of the reference objects that are pa rt of this set.\n`Reference.md5checksum` must be unique within this set.",
3106 "items": {
3107 "type": "string"
3108 },
3109 "type": "array"
3110 },
3111 "assemblyId": {
3112 "description": "Public id of this reference set, such as `GR Ch37`.",
3113 "type": "string"
3114 },
3115 "md5checksum": {
3116 "description": "Order-independent MD5 checksum which identif ies this reference set. The\nchecksum is computed by sorting all lower case hexi decimal string\n`reference.md5checksum` (for all reference in this set) in\nasce nding lexicographic order, concatenating, and taking the MD5 of that\nvalue. The resulting value is represented in lower case hexadecimal format.",
3117 "type": "string"
3118 }
3119 },
3120 "type": "object"
3121 },
3122 "Transcript": {
3123 "description": "A transcript represents the assertion that a particu lar region of the\nreference genome may be transcribed as RNA.",
3124 "id": "Transcript",
3125 "properties": {
3126 "exons": {
3127 "description": "The <a href=\"http://en.wikipedia.org/wiki/E xon\">exons</a> that compose\nthis transcript. This field should be unset for ge nomes where transcript\nsplicing does not occur, for example prokaryotes.\n\nInt rons are regions of the transcript that are not included in the\nspliced RNA pro duct. Though not explicitly modeled here, intron ranges can\nbe deduced; all reg ions of this transcript that are not exons are introns.\n\nExonic sequences do n ot necessarily code for a translational product\n(amino acids). Only the regions of exons bounded by the\ncodingSequence correspond\nto coding DNA sequence.\n\n Exons are ordered by start position and may not overlap.",
3128 "items": {
3129 "$ref": "Exon"
3130 },
3131 "type": "array"
3132 },
3133 "codingSequence": {
3134 "$ref": "CodingSequence",
3135 "description": "The range of the coding sequence for this tr anscript, if any. To determine\nthe exact ranges of coding sequence, intersect t his range with those of the\nexons, if any. If there are any\nexons, the\ncoding Sequence must start\nand end within them.\n\nNote that in some cases, the refere nce genome will not exactly match the\nobserved mRNA transcript e.g. due to vari ance in the source genome from\nreference. In these cases,\nexon.frame will not necessarily\nmatch the expected reference reading frame and coding exon referenc e bases\ncannot necessarily be concatenated to produce the original transcript m RNA."
3136 },
3137 "geneId": {
3138 "description": "The annotation ID of the gene from which thi s transcript is transcribed.",
3139 "type": "string"
3140 }
3141 },
3142 "type": "object"
3143 },
3144 "AnnotationSet": { 2446 "AnnotationSet": {
3145 "description": "An annotation set is a logical grouping of annotatio ns that share consistent\ntype information and provenance. Examples of annotatio n sets include 'all\ngenes from refseq', and 'all variant annotations from ClinV ar'.", 2447 "description": "An annotation set is a logical grouping of annotatio ns that share consistent\ntype information and provenance. Examples of annotatio n sets include 'all\ngenes from refseq', and 'all variant annotations from ClinV ar'.",
3146 "id": "AnnotationSet", 2448 "id": "AnnotationSet",
3147 "properties": { 2449 "properties": {
3148 "sourceUri": {
3149 "description": "The source URI describing the file from whic h this annotation set was\ngenerated, if any.",
3150 "type": "string"
3151 },
3152 "datasetId": {
3153 "description": "The dataset to which this annotation set bel ongs.",
3154 "type": "string"
3155 },
3156 "name": { 2450 "name": {
3157 "description": "The display name for this annotation set.", 2451 "description": "The display name for this annotation set.",
3158 "type": "string" 2452 "type": "string"
3159 }, 2453 },
3160 "referenceSetId": { 2454 "referenceSetId": {
3161 "description": "The ID of the reference set that defines the coordinate space for this\nset's annotations.", 2455 "description": "The ID of the reference set that defines the coordinate space for this\nset's annotations.",
3162 "type": "string" 2456 "type": "string"
3163 }, 2457 },
3164 "type": { 2458 "type": {
3165 "description": "The type of annotations contained within thi s set.", 2459 "description": "The type of annotations contained within thi s set.",
3166 "enum": [ 2460 "enum": [
3167 "ANNOTATION_TYPE_UNSPECIFIED", 2461 "ANNOTATION_TYPE_UNSPECIFIED",
3168 "GENERIC", 2462 "GENERIC",
3169 "VARIANT", 2463 "VARIANT",
3170 "GENE", 2464 "GENE",
3171 "TRANSCRIPT" 2465 "TRANSCRIPT"
3172 ], 2466 ],
3173 "enumDescriptions": [ 2467 "enumDescriptions": [
3174 "", 2468 "",
3175 "A `GENERIC` annotation type should be used when no othe r annotation\ntype will suffice. This represents an untyped annotation of the re ference\ngenome.", 2469 "A `GENERIC` annotation type should be used when no othe r annotation\ntype will suffice. This represents an untyped annotation of the re ference\ngenome.",
3176 "A `VARIANT` annotation type.", 2470 "A `VARIANT` annotation type.",
3177 "A `GENE` annotation type represents the existence of a gene at the\nassociated reference coordinates. The start coordinate is typically the\ngene's transcription start site and the end is typically the end of the\ng ene's last exon.", 2471 "A `GENE` annotation type represents the existence of a gene at the\nassociated reference coordinates. The start coordinate is typically the\ngene's transcription start site and the end is typically the end of the\ng ene's last exon.",
3178 "A `TRANSCRIPT` annotation type represents the assertion that a\nparticular region of the reference genome may be transcribed as RNA." 2472 "A `TRANSCRIPT` annotation type represents the assertion that a\nparticular region of the reference genome may be transcribed as RNA."
3179 ], 2473 ],
3180 "type": "string" 2474 "type": "string"
3181 }, 2475 },
3182 "info": { 2476 "info": {
2477 "additionalProperties": {
2478 "items": {
2479 "type": "any"
2480 },
2481 "type": "array"
2482 },
2483 "description": "A map of additional read alignment informati on. This must be of the form\nmap<string, string[]> (string key mapping to a lis t of string values).",
2484 "type": "object"
2485 },
2486 "id": {
2487 "description": "The server-generated annotation set ID, uniq ue across all annotation sets.",
2488 "type": "string"
2489 },
2490 "datasetId": {
2491 "description": "The dataset to which this annotation set bel ongs.",
2492 "type": "string"
2493 },
2494 "sourceUri": {
2495 "description": "The source URI describing the file from whic h this annotation set was\ngenerated, if any.",
2496 "type": "string"
2497 }
2498 },
2499 "type": "object"
2500 },
2501 "Transcript": {
2502 "description": "A transcript represents the assertion that a particu lar region of the\nreference genome may be transcribed as RNA.",
2503 "id": "Transcript",
2504 "properties": {
2505 "exons": {
2506 "description": "The <a href=\"http://en.wikipedia.org/wiki/E xon\">exons</a> that compose\nthis transcript. This field should be unset for ge nomes where transcript\nsplicing does not occur, for example prokaryotes.\n\nInt rons are regions of the transcript that are not included in the\nspliced RNA pro duct. Though not explicitly modeled here, intron ranges can\nbe deduced; all reg ions of this transcript that are not exons are introns.\n\nExonic sequences do n ot necessarily code for a translational product\n(amino acids). Only the regions of exons bounded by the\ncodingSequence correspond\nto coding DNA sequence.\n\n Exons are ordered by start position and may not overlap.",
2507 "items": {
2508 "$ref": "Exon"
2509 },
2510 "type": "array"
2511 },
2512 "codingSequence": {
2513 "$ref": "CodingSequence",
2514 "description": "The range of the coding sequence for this tr anscript, if any. To determine\nthe exact ranges of coding sequence, intersect t his range with those of the\nexons, if any. If there are any\nexons, the\ncoding Sequence must start\nand end within them.\n\nNote that in some cases, the refere nce genome will not exactly match the\nobserved mRNA transcript e.g. due to vari ance in the source genome from\nreference. In these cases,\nexon.frame will not necessarily\nmatch the expected reference reading frame and coding exon referenc e bases\ncannot necessarily be concatenated to produce the original transcript m RNA."
2515 },
2516 "geneId": {
2517 "description": "The annotation ID of the gene from which thi s transcript is transcribed.",
2518 "type": "string"
2519 }
2520 },
2521 "type": "object"
2522 },
2523 "Experiment": {
2524 "id": "Experiment",
2525 "properties": {
2526 "platformUnit": {
2527 "description": "The platform unit used as part of this exper iment, for example\nflowcell-barcode.lane for Illumina or slide for SOLiD. Corre sponds to the\n@RG PU field in the SAM spec.",
2528 "type": "string"
2529 },
2530 "instrumentModel": {
2531 "description": "The instrument model used as part of this ex periment. This maps to\nsequencing technology in the SAM spec.",
2532 "type": "string"
2533 },
2534 "libraryId": {
2535 "description": "A client-supplied library identifier; a libr ary is a collection of DNA\nfragments which have been prepared for sequencing fr om a sample. This\nfield is important for quality control as error or bias can b e introduced\nduring sample preparation.",
2536 "type": "string"
2537 },
2538 "sequencingCenter": {
2539 "description": "The sequencing center used as part of this e xperiment.",
2540 "type": "string"
2541 }
2542 },
2543 "type": "object"
2544 },
2545 "ListDatasetsResponse": {
2546 "description": "The dataset list response.",
2547 "id": "ListDatasetsResponse",
2548 "properties": {
2549 "nextPageToken": {
2550 "description": "The continuation token, which is used to pag e through large result sets.\nProvide this value in a subsequent request to retu rn the next page of\nresults. This field will be empty if there aren't any addit ional results.",
2551 "type": "string"
2552 },
2553 "datasets": {
2554 "description": "The list of matching Datasets.",
2555 "items": {
2556 "$ref": "Dataset"
2557 },
2558 "type": "array"
2559 }
2560 },
2561 "type": "object"
2562 },
2563 "TestIamPermissionsRequest": {
2564 "description": "Request message for `TestIamPermissions` method.",
2565 "id": "TestIamPermissionsRequest",
2566 "properties": {
2567 "permissions": {
2568 "description": "REQUIRED: The set of permissions to check fo r the 'resource'.\nPermissions with wildcards (such as '*' or 'storage.*') are n ot allowed.\nAllowed permissions are&#58;\n\n* `genomics.datasets.create`\n* `ge nomics.datasets.delete`\n* `genomics.datasets.get`\n* `genomics.datasets.list`\n * `genomics.datasets.update`\n* `genomics.datasets.getIamPolicy`\n* `genomics.da tasets.setIamPolicy`",
2569 "items": {
2570 "type": "string"
2571 },
2572 "type": "array"
2573 }
2574 },
2575 "type": "object"
2576 },
2577 "ExportReadGroupSetRequest": {
2578 "description": "The read group set export request.",
2579 "id": "ExportReadGroupSetRequest",
2580 "properties": {
2581 "referenceNames": {
2582 "description": "The reference names to export. If this is no t specified, all reference\nsequences, including unmapped reads, are exported.\n Use `*` to export only unmapped reads.",
2583 "items": {
2584 "type": "string"
2585 },
2586 "type": "array"
2587 },
2588 "exportUri": {
2589 "description": "Required. A Google Cloud Storage URI for the exported BAM file.\nThe currently authenticated user must have write access to the new file.\nAn error will be returned if the URI already contains data.",
2590 "type": "string"
2591 },
2592 "projectId": {
2593 "description": "Required. The Google Cloud project ID that o wns this\nexport. The caller must have WRITE access to this project.",
2594 "type": "string"
2595 }
2596 },
2597 "type": "object"
2598 },
2599 "Exon": {
2600 "id": "Exon",
2601 "properties": {
2602 "start": {
2603 "description": "The start position of the exon on this annot ation's reference sequence,\n0-based inclusive. Note that this is relative to th e reference start, and\n**not** the containing annotation start.",
2604 "format": "int64",
2605 "type": "string"
2606 },
2607 "frame": {
2608 "description": "The frame of this exon. Contains a value of 0, 1, or 2, which indicates\nthe offset of the first coding base of the exon wit hin the reading frame\nof the coding DNA sequence, if any. This field is depende nt on the\nstrandedness of this annotation (see\nAnnotation.reverse_strand).\nFo r forward stranded annotations, this offset is relative to the\nexon.start. For reverse\nstrand annotations, this offset is relative to the\nexon.end `- 1`.\n\n Unset if this exon does not intersect the coding sequence. Upon creation\nof a t ranscript, the frame must be populated for all or none of the\ncoding exons.",
2609 "format": "int32",
2610 "type": "integer"
2611 },
2612 "end": {
2613 "description": "The end position of the exon on this annotat ion's reference sequence,\n0-based exclusive. Note that this is relative to the reference start, and\n*not* the containing annotation start.",
2614 "format": "int64",
2615 "type": "string"
2616 }
2617 },
2618 "type": "object"
2619 },
2620 "CallSet": {
2621 "description": "A call set is a collection of variant calls, typical ly for one sample. It\nbelongs to a variant set.\n\nFor more genomics resource d efinitions, see [Fundamentals of Google\nGenomics](https://cloud.google.com/geno mics/fundamentals-of-google-genomics)",
2622 "id": "CallSet",
2623 "properties": {
2624 "created": {
2625 "description": "The date this call set was created in millis econds from the epoch.",
2626 "format": "int64",
2627 "type": "string"
2628 },
2629 "sampleId": {
2630 "description": "The sample ID this call set corresponds to." ,
2631 "type": "string"
2632 },
2633 "name": {
2634 "description": "The call set name.",
2635 "type": "string"
2636 },
2637 "info": {
2638 "additionalProperties": {
2639 "items": {
2640 "type": "any"
2641 },
2642 "type": "array"
2643 },
2644 "description": "A map of additional call set information. Th is must be of the form\nmap<string, string[]> (string key mapping to a list of s tring values).",
2645 "type": "object"
2646 },
2647 "variantSetIds": {
2648 "description": "The IDs of the variant sets this call set be longs to. This field must\nhave exactly length one, as a call set belongs to a s ingle variant set.\nThis field is repeated for compatibility with the\n[GA4GH 0. 5.1\nAPI](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/v ariants.avdl#L76).",
2649 "items": {
2650 "type": "string"
2651 },
2652 "type": "array"
2653 },
2654 "id": {
2655 "description": "The server-generated call set ID, unique acr oss all call sets.",
2656 "type": "string"
2657 }
2658 },
2659 "type": "object"
2660 },
2661 "SearchAnnotationSetsResponse": {
2662 "id": "SearchAnnotationSetsResponse",
2663 "properties": {
2664 "nextPageToken": {
2665 "description": "The continuation token, which is used to pag e through large result sets.\nProvide this value in a subsequent request to retu rn the next page of\nresults. This field will be empty if there aren't any addit ional results.",
2666 "type": "string"
2667 },
2668 "annotationSets": {
2669 "description": "The matching annotation sets.",
2670 "items": {
2671 "$ref": "AnnotationSet"
2672 },
2673 "type": "array"
2674 }
2675 },
2676 "type": "object"
2677 },
2678 "ImportVariantsRequest": {
2679 "description": "The variant data import request.",
2680 "id": "ImportVariantsRequest",
2681 "properties": {
2682 "infoMergeConfig": {
2683 "additionalProperties": {
2684 "enum": [
2685 "INFO_MERGE_OPERATION_UNSPECIFIED",
2686 "IGNORE_NEW",
2687 "MOVE_TO_CALLS"
2688 ],
2689 "type": "string"
2690 },
2691 "description": "A mapping between info field keys and the In foMergeOperations to\nbe performed on them. This is plumbed down to the MergeVar iantRequests\ngenerated by the resulting import job.",
2692 "type": "object"
2693 },
2694 "sourceUris": {
2695 "description": "A list of URIs referencing variant files in Google Cloud Storage. URIs can\ninclude wildcards [as described\nhere](https://c loud.google.com/storage/docs/gsutil/addlhelp/WildcardNames).\nNote that recursiv e wildcards ('**') are not supported.",
2696 "items": {
2697 "type": "string"
2698 },
2699 "type": "array"
2700 },
2701 "variantSetId": {
2702 "description": "Required. The variant set to which variant d ata should be imported.",
2703 "type": "string"
2704 },
2705 "normalizeReferenceNames": {
2706 "description": "Convert reference names to the canonical rep resentation.\nhg19 haploytypes (those reference names containing \"_hap\")\nare not modified in any way.\nAll other reference names are modified according to th e following rules:\nThe reference name is capitalized.\nThe \"chr\" prefix is dr opped for all autosomes and sex chromsomes.\nFor example \"chr17\" becomes \"17\ " and \"chrX\" becomes \"X\".\nAll mitochondrial chromosomes (\"chrM\", \"chrMT\ ", etc) become \"MT\".",
2707 "type": "boolean"
2708 },
2709 "format": {
2710 "description": "The format of the variant data being importe d. If unspecified, defaults to\nto `VCF`.",
2711 "enum": [
2712 "FORMAT_UNSPECIFIED",
2713 "FORMAT_VCF",
2714 "FORMAT_COMPLETE_GENOMICS"
2715 ],
2716 "enumDescriptions": [
2717 "",
2718 "VCF (Variant Call Format). The VCF files may be gzip co mpressed. gVCF is\nalso supported. Disclaimer: gzip VCF imports are currently mu ch slower\nthan equivalent uncompressed VCF imports. For this reason, uncompress ed\nVCF is currently recommended for imports with more than 1GB combined\nuncomp ressed size, or for time sensitive imports.",
2719 "Complete Genomics masterVarBeta format. The masterVarBe ta files may\nbe bzip2 compressed."
2720 ],
2721 "type": "string"
2722 }
2723 },
2724 "type": "object"
2725 },
2726 "VariantAnnotation": {
2727 "id": "VariantAnnotation",
2728 "properties": {
2729 "effect": {
2730 "description": "Effect of the variant on the coding sequence .",
2731 "enum": [
2732 "EFFECT_UNSPECIFIED",
2733 "EFFECT_OTHER",
2734 "FRAMESHIFT",
2735 "FRAME_PRESERVING_INDEL",
2736 "SYNONYMOUS_SNP",
2737 "NONSYNONYMOUS_SNP",
2738 "STOP_GAIN",
2739 "STOP_LOSS",
2740 "SPLICE_SITE_DISRUPTION"
2741 ],
2742 "enumDescriptions": [
2743 "",
2744 "`EFFECT_OTHER` should be used when no other Effect\nwil l suffice.",
2745 "`FRAMESHIFT` indicates a mutation in which the insertio n or\ndeletion of nucleotides resulted in a frameshift change.",
2746 "`FRAME_PRESERVING_INDEL` indicates a mutation in which a\nmultiple of three nucleotides has been inserted or deleted, resulting\nin no change to the reading frame of the coding sequence.",
2747 "`SYNONYMOUS_SNP` indicates a single nucleotide polymorp hism\nmutation that results in no amino acid change.",
2748 "`NONSYNONYMOUS_SNP` indicates a single nucleotide\npoly morphism mutation that results in an amino acid change.",
2749 "`STOP_GAIN` indicates a mutation that leads to the crea tion\nof a stop codon at the variant site. Frameshift mutations creating\ndownst ream stop codons do not count as `STOP_GAIN`.",
2750 "`STOP_LOSS` indicates a mutation that eliminates a\nsto p codon at the variant site.",
2751 "`SPLICE_SITE_DISRUPTION` indicates that this variant is \nfound in a splice site for the associated transcript, and alters the\nnormal s plicing pattern."
2752 ],
2753 "type": "string"
2754 },
2755 "transcriptIds": {
2756 "description": "Google annotation IDs of the transcripts aff ected by this variant. These\nshould be provided when the variant is created.",
2757 "items": {
2758 "type": "string"
2759 },
2760 "type": "array"
2761 },
2762 "type": {
2763 "description": "Type has been adapted from ClinVar's list of variant types.",
2764 "enum": [
2765 "TYPE_UNSPECIFIED",
2766 "TYPE_OTHER",
2767 "INSERTION",
2768 "DELETION",
2769 "SUBSTITUTION",
2770 "SNP",
2771 "STRUCTURAL",
2772 "CNV"
2773 ],
2774 "enumDescriptions": [
2775 "",
2776 "`TYPE_OTHER` should be used when no other Type will suf fice.\nFurther explanation of the variant type may be included in the\ninfo fiel d.",
2777 "`INSERTION` indicates an insertion.",
2778 "`DELETION` indicates a deletion.",
2779 "`SUBSTITUTION` indicates a block substitution of\ntwo o r more nucleotides.",
2780 "`SNP` indicates a single nucleotide polymorphism.",
2781 "`STRUCTURAL` indicates a large structural variant,\ninc luding chromosomal fusions, inversions, etc.",
2782 "`CNV` indicates a variation in copy number."
2783 ],
2784 "type": "string"
2785 },
2786 "alternateBases": {
2787 "description": "The alternate allele for this variant. If mu ltiple alternate alleles\nexist at this location, create a separate variant for each one, as they\nmay represent distinct conditions.",
2788 "type": "string"
2789 },
2790 "geneId": {
2791 "description": "Google annotation ID of the gene affected by this variant. This should\nbe provided when the variant is created.",
2792 "type": "string"
2793 },
2794 "clinicalSignificance": {
2795 "description": "Describes the clinical significance of a var iant.\nIt is adapted from the ClinVar controlled vocabulary for clinical\nsignif icance described at:\nhttp://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/",
2796 "enum": [
2797 "CLINICAL_SIGNIFICANCE_UNSPECIFIED",
2798 "CLINICAL_SIGNIFICANCE_OTHER",
2799 "UNCERTAIN",
2800 "BENIGN",
2801 "LIKELY_BENIGN",
2802 "LIKELY_PATHOGENIC",
2803 "PATHOGENIC",
2804 "DRUG_RESPONSE",
2805 "HISTOCOMPATIBILITY",
2806 "CONFERS_SENSITIVITY",
2807 "RISK_FACTOR",
2808 "ASSOCIATION",
2809 "PROTECTIVE",
2810 "MULTIPLE_REPORTED"
2811 ],
2812 "enumDescriptions": [
2813 "",
2814 "`OTHER` should be used when no other clinical significa nce\nvalue will suffice.",
2815 "",
2816 "",
2817 "",
2818 "",
2819 "",
2820 "",
2821 "",
2822 "",
2823 "",
2824 "",
2825 "",
2826 "`MULTIPLE_REPORTED` should be used when multiple clinic al\nsignficances are reported for a variant. The original clinical\nsignificance values may be provided in the `info` field."
2827 ],
2828 "type": "string"
2829 },
2830 "conditions": {
2831 "description": "The set of conditions associated with this v ariant.\nA condition describes the way a variant influences human health.",
2832 "items": {
2833 "$ref": "ClinicalCondition"
2834 },
2835 "type": "array"
2836 }
2837 },
2838 "type": "object"
2839 },
2840 "ListCoverageBucketsResponse": {
2841 "id": "ListCoverageBucketsResponse",
2842 "properties": {
2843 "coverageBuckets": {
2844 "description": "The coverage buckets. The list of buckets is sparse; a bucket with 0\noverlapping reads is not returned. A bucket never cros ses more than one\nreference sequence. Each bucket has width `bucketWidth`, unle ss\nits end is the end of the reference sequence.",
2845 "items": {
2846 "$ref": "CoverageBucket"
2847 },
2848 "type": "array"
2849 },
2850 "nextPageToken": {
2851 "description": "The continuation token, which is used to pag e through large result sets.\nProvide this value in a subsequent request to retu rn the next page of\nresults. This field will be empty if there aren't any addit ional results.",
2852 "type": "string"
2853 },
2854 "bucketWidth": {
2855 "description": "The length of each coverage bucket in base p airs. Note that buckets at the\nend of a reference sequence may be shorter. This value is omitted if the\nbucket width is infinity (the default behaviour, with no range or\n`targetBucketWidth`).",
2856 "format": "int64",
2857 "type": "string"
2858 }
2859 },
2860 "type": "object"
2861 },
2862 "ExportVariantSetRequest": {
2863 "description": "The variant data export request.",
2864 "id": "ExportVariantSetRequest",
2865 "properties": {
2866 "bigqueryTable": {
2867 "description": "Required. The BigQuery table to export data to.\nIf the table doesn't exist, it will be created. If it already exists, it\nw ill be overwritten.",
2868 "type": "string"
2869 },
2870 "bigqueryDataset": {
2871 "description": "Required. The BigQuery dataset to export dat a to. This dataset must already\nexist. Note that this is distinct from the Geno mics concept of \"dataset\".",
2872 "type": "string"
2873 },
2874 "format": {
2875 "description": "The format for the exported data.",
2876 "enum": [
2877 "FORMAT_UNSPECIFIED",
2878 "FORMAT_BIGQUERY"
2879 ],
2880 "enumDescriptions": [
2881 "",
2882 "Export the data to Google BigQuery."
2883 ],
2884 "type": "string"
2885 },
2886 "projectId": {
2887 "description": "Required. The Google Cloud project ID that o wns the destination\nBigQuery dataset. The caller must have WRITE access to this project. This\nproject will also own the resulting export job.",
2888 "type": "string"
2889 },
2890 "callSetIds": {
2891 "description": "If provided, only variant call information f rom the specified call sets\nwill be exported. By default all variant calls are exported.",
2892 "items": {
2893 "type": "string"
2894 },
2895 "type": "array"
2896 }
2897 },
2898 "type": "object"
2899 },
2900 "SearchAnnotationsRequest": {
2901 "id": "SearchAnnotationsRequest",
2902 "properties": {
2903 "pageToken": {
2904 "description": "The continuation token, which is used to pag e through large result sets.\nTo get the next page of results, set this paramete r to the value of\n`nextPageToken` from the previous response.",
2905 "type": "string"
2906 },
2907 "pageSize": {
2908 "description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 256. The maximum value is 2048.",
2909 "format": "int32",
2910 "type": "integer"
2911 },
2912 "start": {
2913 "description": "The start position of the range on the refer ence, 0-based inclusive. If\nspecified,\nreferenceId or\nreferenceName\nmust be specified. Defaults to 0.",
2914 "format": "int64",
2915 "type": "string"
2916 },
2917 "annotationSetIds": {
2918 "description": "Required. The annotation sets to search with in. The caller must have\n`READ` access to these annotation sets.\nAll queried a nnotation sets must have the same type.",
2919 "items": {
2920 "type": "string"
2921 },
2922 "type": "array"
2923 },
2924 "referenceName": {
2925 "description": "The name of the reference to query, within t he reference set associated\nwith this query.",
2926 "type": "string"
2927 },
2928 "referenceId": {
2929 "description": "The ID of the reference to query.",
2930 "type": "string"
2931 },
2932 "end": {
2933 "description": "The end position of the range on the referen ce, 0-based exclusive. If\nreferenceId or\nreferenceName\nmust be specified, Def aults to the length of the reference.",
2934 "format": "int64",
2935 "type": "string"
2936 }
2937 },
2938 "type": "object"
2939 },
2940 "OperationEvent": {
2941 "description": "An event that occurred during an Operation.",
2942 "id": "OperationEvent",
2943 "properties": {
2944 "description": {
2945 "description": "Required description of event.",
2946 "type": "string"
2947 },
2948 "endTime": {
2949 "description": "Optional time of when event finished. An eve nt can have a start time and no\nfinish time. If an event has a finish time, the re must be a start time.",
2950 "format": "google-datetime",
2951 "type": "string"
2952 },
2953 "startTime": {
2954 "description": "Optional time of when event started.",
2955 "format": "google-datetime",
2956 "type": "string"
2957 }
2958 },
2959 "type": "object"
2960 },
2961 "CodingSequence": {
2962 "id": "CodingSequence",
2963 "properties": {
2964 "end": {
2965 "description": "The end of the coding sequence on this annot ation's reference sequence,\n0-based exclusive. Note that this position is relat ive to the reference\nstart, and *not* the containing annotation start.",
2966 "format": "int64",
2967 "type": "string"
2968 },
2969 "start": {
2970 "description": "The start of the coding sequence on this ann otation's reference sequence,\n0-based inclusive. Note that this position is rel ative to the reference\nstart, and *not* the containing annotation start.",
2971 "format": "int64",
2972 "type": "string"
2973 }
2974 },
2975 "type": "object"
2976 },
2977 "SearchReferencesResponse": {
2978 "id": "SearchReferencesResponse",
2979 "properties": {
2980 "references": {
2981 "description": "The matching references.",
2982 "items": {
2983 "$ref": "Reference"
2984 },
2985 "type": "array"
2986 },
2987 "nextPageToken": {
2988 "description": "The continuation token, which is used to pag e through large result sets.\nProvide this value in a subsequent request to retu rn the next page of\nresults. This field will be empty if there aren't any addit ional results.",
2989 "type": "string"
2990 }
2991 },
2992 "type": "object"
2993 },
2994 "GetIamPolicyRequest": {
2995 "description": "Request message for `GetIamPolicy` method.",
2996 "id": "GetIamPolicyRequest",
2997 "properties": {},
2998 "type": "object"
2999 },
3000 "TestIamPermissionsResponse": {
3001 "description": "Response message for `TestIamPermissions` method.",
3002 "id": "TestIamPermissionsResponse",
3003 "properties": {
3004 "permissions": {
3005 "description": "A subset of `TestPermissionsRequest.permissi ons` that the caller is\nallowed.",
3006 "items": {
3007 "type": "string"
3008 },
3009 "type": "array"
3010 }
3011 },
3012 "type": "object"
3013 },
3014 "SearchAnnotationSetsRequest": {
3015 "id": "SearchAnnotationSetsRequest",
3016 "properties": {
3017 "pageToken": {
3018 "description": "The continuation token, which is used to pag e through large result sets.\nTo get the next page of results, set this paramete r to the value of\n`nextPageToken` from the previous response.",
3019 "type": "string"
3020 },
3021 "pageSize": {
3022 "description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 128. The maximum value is 1024.",
3023 "format": "int32",
3024 "type": "integer"
3025 },
3026 "datasetIds": {
3027 "description": "Required. The dataset IDs to search within. Caller must have `READ` access\nto these datasets.",
3028 "items": {
3029 "type": "string"
3030 },
3031 "type": "array"
3032 },
3033 "types": {
3034 "description": "If specified, only annotation sets that have any of these types are\nreturned.",
3035 "enumDescriptions": [
3036 "",
3037 "A `GENERIC` annotation type should be used when no othe r annotation\ntype will suffice. This represents an untyped annotation of the re ference\ngenome.",
3038 "A `VARIANT` annotation type.",
3039 "A `GENE` annotation type represents the existence of a gene at the\nassociated reference coordinates. The start coordinate is typically the\ngene's transcription start site and the end is typically the end of the\ng ene's last exon.",
3040 "A `TRANSCRIPT` annotation type represents the assertion that a\nparticular region of the reference genome may be transcribed as RNA."
3041 ],
3042 "items": {
3043 "enum": [
3044 "ANNOTATION_TYPE_UNSPECIFIED",
3045 "GENERIC",
3046 "VARIANT",
3047 "GENE",
3048 "TRANSCRIPT"
3049 ],
3050 "type": "string"
3051 },
3052 "type": "array"
3053 },
3054 "name": {
3055 "description": "Only return annotations sets for which a sub string of the name matches this\nstring (case insensitive).",
3056 "type": "string"
3057 },
3058 "referenceSetId": {
3059 "description": "If specified, only annotation sets associate d with the given reference set\nare returned.",
3060 "type": "string"
3061 }
3062 },
3063 "type": "object"
3064 },
3065 "SearchReadGroupSetsResponse": {
3066 "description": "The read group set search response.",
3067 "id": "SearchReadGroupSetsResponse",
3068 "properties": {
3069 "readGroupSets": {
3070 "description": "The list of matching read group sets.",
3071 "items": {
3072 "$ref": "ReadGroupSet"
3073 },
3074 "type": "array"
3075 },
3076 "nextPageToken": {
3077 "description": "The continuation token, which is used to pag e through large result sets.\nProvide this value in a subsequent request to retu rn the next page of\nresults. This field will be empty if there aren't any addit ional results.",
3078 "type": "string"
3079 }
3080 },
3081 "type": "object"
3082 },
3083 "SearchReferencesRequest": {
3084 "id": "SearchReferencesRequest",
3085 "properties": {
3086 "pageToken": {
3087 "description": "The continuation token, which is used to pag e through large result sets.\nTo get the next page of results, set this paramete r to the value of\n`nextPageToken` from the previous response.",
3088 "type": "string"
3089 },
3090 "accessions": {
3091 "description": "If present, return references for which a pr efix of any of\nsourceAccessions match\nany of these strings. Accession numbers typically have a main number and a\nversion, for example `GCF_000001405.26`.",
3092 "items": {
3093 "type": "string"
3094 },
3095 "type": "array"
3096 },
3097 "pageSize": {
3098 "description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 1024. The maximum value is 4096.",
3099 "format": "int32",
3100 "type": "integer"
3101 },
3102 "referenceSetId": {
3103 "description": "If present, return only references which bel ong to this reference set.",
3104 "type": "string"
3105 },
3106 "md5checksums": {
3107 "description": "If present, return references for which the\ nmd5checksum matches exactly.",
3108 "items": {
3109 "type": "string"
3110 },
3111 "type": "array"
3112 }
3113 },
3114 "type": "object"
3115 },
3116 "LinearAlignment": {
3117 "description": "A linear alignment can be represented by one CIGAR s tring. Describes the\nmapped position and local alignment of the read to the ref erence.",
3118 "id": "LinearAlignment",
3119 "properties": {
3120 "mappingQuality": {
3121 "description": "The mapping quality of this alignment. Repre sents how likely\nthe read maps to this position as opposed to other locations.\ n\nSpecifically, this is -10 log10 Pr(mapping position is wrong), rounded to\nth e nearest integer.",
3122 "format": "int32",
3123 "type": "integer"
3124 },
3125 "cigar": {
3126 "description": "Represents the local alignment of this seque nce (alignment matches, indels,\netc) against the reference.",
3127 "items": {
3128 "$ref": "CigarUnit"
3129 },
3130 "type": "array"
3131 },
3132 "position": {
3133 "$ref": "Position",
3134 "description": "The position of this alignment."
3135 }
3136 },
3137 "type": "object"
3138 },
3139 "Dataset": {
3140 "description": "A Dataset is a collection of genomic data.\n\nFor mo re genomics resource definitions, see [Fundamentals of Google\nGenomics](https:/ /cloud.google.com/genomics/fundamentals-of-google-genomics)",
3141 "id": "Dataset",
3142 "properties": {
3143 "name": {
3144 "description": "The dataset name.",
3145 "type": "string"
3146 },
3147 "projectId": {
3148 "description": "The Google Cloud project ID that this datase t belongs to.",
3149 "type": "string"
3150 },
3151 "id": {
3152 "description": "The server-generated dataset ID, unique acro ss all datasets.",
3153 "type": "string"
3154 },
3155 "createTime": {
3156 "description": "The time this dataset was created, in second s from the epoch.",
3157 "format": "google-datetime",
3158 "type": "string"
3159 }
3160 },
3161 "type": "object"
3162 },
3163 "ImportVariantsResponse": {
3164 "description": "The variant data import response.",
3165 "id": "ImportVariantsResponse",
3166 "properties": {
3167 "callSetIds": {
3168 "description": "IDs of the call sets created during the impo rt.",
3169 "items": {
3170 "type": "string"
3171 },
3172 "type": "array"
3173 }
3174 },
3175 "type": "object"
3176 },
3177 "ReadGroup": {
3178 "description": "A read group is all the data that's processed the sa me way by the sequencer.",
3179 "id": "ReadGroup",
3180 "properties": {
3181 "info": {
3182 "additionalProperties": {
3183 "items": {
3184 "type": "any"
3185 },
3186 "type": "array"
3187 },
3188 "description": "A map of additional read group information. This must be of the form\nmap<string, string[]> (string key mapping to a list of string values).",
3189 "type": "object"
3190 },
3191 "id": {
3192 "description": "The server-generated read group ID, unique f or all read groups.\nNote: This is different than the @RG ID field in the SAM sp ec. For that\nvalue, see name.",
3193 "type": "string"
3194 },
3195 "programs": {
3196 "description": "The programs used to generate this read grou p. Programs are always\nidentical for all read groups within a read group set. F or this reason,\nonly the first read group in a returned set will have this fiel d\npopulated.",
3197 "items": {
3198 "$ref": "Program"
3199 },
3200 "type": "array"
3201 },
3202 "predictedInsertSize": {
3203 "description": "The predicted insert size of this read group . The insert size is the length\nthe sequenced DNA fragment from end-to-end, not including the adapters.",
3204 "format": "int32",
3205 "type": "integer"
3206 },
3207 "description": {
3208 "description": "A free-form text description of this read gr oup.",
3209 "type": "string"
3210 },
3211 "sampleId": {
3212 "description": "A client-supplied sample identifier for the reads in this read group.",
3213 "type": "string"
3214 },
3215 "datasetId": {
3216 "description": "The dataset to which this read group belongs .",
3217 "type": "string"
3218 },
3219 "experiment": {
3220 "$ref": "Experiment",
3221 "description": "The experiment used to generate this read gr oup."
3222 },
3223 "name": {
3224 "description": "The read group name. This corresponds to the @RG ID field in the SAM spec.",
3225 "type": "string"
3226 },
3227 "referenceSetId": {
3228 "description": "The reference set the reads in this read gro up are aligned to.",
3229 "type": "string"
3230 }
3231 },
3232 "type": "object"
3233 },
3234 "ReadGroupSet": {
3235 "description": "A read group set is a logical collection of read gro ups, which are\ncollections of reads produced by a sequencer. A read group set t ypically\nmodels reads corresponding to one sample, sequenced one way, and align ed one\nway.\n\n* A read group set belongs to one dataset.\n* A read group belon gs to one read group set.\n* A read belongs to one read group.\n\nFor more genom ics resource definitions, see [Fundamentals of Google\nGenomics](https://cloud.g oogle.com/genomics/fundamentals-of-google-genomics)",
3236 "id": "ReadGroupSet",
3237 "properties": {
3238 "datasetId": {
3239 "description": "The dataset to which this read group set bel ongs.",
3240 "type": "string"
3241 },
3242 "readGroups": {
3243 "description": "The read groups in this set. There are typic ally 1-10 read groups in a read\ngroup set.",
3244 "items": {
3245 "$ref": "ReadGroup"
3246 },
3247 "type": "array"
3248 },
3249 "filename": {
3250 "description": "The filename of the original source file for this read group set, if any.",
3251 "type": "string"
3252 },
3253 "name": {
3254 "description": "The read group set name. By default this wil l be initialized to the sample\nname of the sequenced data contained in this set .",
3255 "type": "string"
3256 },
3257 "referenceSetId": {
3258 "description": "The reference set to which the reads in this read group set are aligned.",
3259 "type": "string"
3260 },
3261 "info": {
3183 "additionalProperties": { 3262 "additionalProperties": {
3184 "items": { 3263 "items": {
3185 "type": "any" 3264 "type": "any"
3186 }, 3265 },
3187 "type": "array" 3266 "type": "array"
3188 }, 3267 },
3189 "description": "A map of additional read alignment informati on. This must be of the form\nmap<string, string[]> (string key mapping to a lis t of string values).", 3268 "description": "A map of additional read group set informati on.",
3190 "type": "object" 3269 "type": "object"
3191 }, 3270 },
3192 "id": { 3271 "id": {
3193 "description": "The server-generated annotation set ID, uniq ue across all annotation sets.", 3272 "description": "The server-generated read group set ID, uniq ue for all read group sets.",
3194 "type": "string" 3273 "type": "string"
3195 } 3274 }
3196 }, 3275 },
3197 "type": "object" 3276 "type": "object"
3198 }, 3277 },
3199 "Experiment": { 3278 "SearchVariantSetsResponse": {
3200 "id": "Experiment", 3279 "description": "The search variant sets response.",
3201 "properties": { 3280 "id": "SearchVariantSetsResponse",
3202 "sequencingCenter": { 3281 "properties": {
3203 "description": "The sequencing center used as part of this e xperiment.", 3282 "variantSets": {
3204 "type": "string" 3283 "description": "The variant sets belonging to the requested dataset.",
3205 }, 3284 "items": {
3206 "platformUnit": { 3285 "$ref": "VariantSet"
3207 "description": "The platform unit used as part of this exper iment, for example\nflowcell-barcode.lane for Illumina or slide for SOLiD. Corre sponds to the\n@RG PU field in the SAM spec.", 3286 },
3208 "type": "string" 3287 "type": "array"
3209 }, 3288 },
3210 "instrumentModel": {
3211 "description": "The instrument model used as part of this ex periment. This maps to\nsequencing technology in the SAM spec.",
3212 "type": "string"
3213 },
3214 "libraryId": {
3215 "description": "A client-supplied library identifier; a libr ary is a collection of DNA\nfragments which have been prepared for sequencing fr om a sample. This\nfield is important for quality control as error or bias can b e introduced\nduring sample preparation.",
3216 "type": "string"
3217 }
3218 },
3219 "type": "object"
3220 },
3221 "ListDatasetsResponse": {
3222 "description": "The dataset list response.",
3223 "id": "ListDatasetsResponse",
3224 "properties": {
3225 "nextPageToken": { 3289 "nextPageToken": {
3226 "description": "The continuation token, which is used to pag e through large result sets.\nProvide this value in a subsequent request to retu rn the next page of\nresults. This field will be empty if there aren't any addit ional results.", 3290 "description": "The continuation token, which is used to pag e through large result sets.\nProvide this value in a subsequent request to retu rn the next page of\nresults. This field will be empty if there aren't any addit ional results.",
3227 "type": "string" 3291 "type": "string"
3228 }, 3292 }
3229 "datasets": { 3293 },
3230 "description": "The list of matching Datasets.", 3294 "type": "object"
3231 "items": { 3295 },
3232 "$ref": "Dataset" 3296 "Empty": {
3233 }, 3297 "description": "A generic empty message that you can re-use to avoid defining duplicated\nempty messages in your APIs. A typical example is to use i t as the request\nor the response type of an API method. For instance:\n\n se rvice Foo {\n rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty );\n }\n\nThe JSON representation for `Empty` is empty JSON object `{}`.",
3234 "type": "array" 3298 "id": "Empty",
3235 } 3299 "properties": {},
3236 }, 3300 "type": "object"
3237 "type": "object" 3301 },
3238 }, 3302 "Entry": {
3239 "TestIamPermissionsRequest": { 3303 "id": "Entry",
3240 "description": "Request message for `TestIamPermissions` method.", 3304 "properties": {
3241 "id": "TestIamPermissionsRequest", 3305 "annotation": {
3242 "properties": { 3306 "$ref": "Annotation",
3243 "permissions": { 3307 "description": "The created annotation, if creation was succ essful."
3244 "description": "REQUIRED: The set of permissions to check fo r the 'resource'.\nPermissions with wildcards (such as '*' or 'storage.*') are n ot allowed.\nAllowed permissions are&#58;\n\n* `genomics.datasets.create`\n* `ge nomics.datasets.delete`\n* `genomics.datasets.get`\n* `genomics.datasets.list`\n * `genomics.datasets.update`\n* `genomics.datasets.getIamPolicy`\n* `genomics.da tasets.setIamPolicy`", 3308 },
3245 "items": { 3309 "status": {
3246 "type": "string" 3310 "$ref": "Status",
3247 }, 3311 "description": "The creation status."
3248 "type": "array" 3312 }
3249 } 3313 },
3250 }, 3314 "type": "object"
3251 "type": "object" 3315 },
3252 }, 3316 "Position": {
3253 "ExportReadGroupSetRequest": { 3317 "description": "An abstraction for referring to a genomic position, in relation to some\nalready known reference. For now, represents a genomic posi tion as a\nreference name, a base number on that reference (0-based), and a\ndet ermination of forward or reverse strand.",
3254 "description": "The read group set export request.", 3318 "id": "Position",
3255 "id": "ExportReadGroupSetRequest", 3319 "properties": {
3256 "properties": { 3320 "reverseStrand": {
3257 "referenceNames": { 3321 "description": "Whether this position is on the reverse stra nd, as opposed to the forward\nstrand.",
3258 "description": "The reference names to export. If this is no t specified, all reference\nsequences, including unmapped reads, are exported.\n Use `*` to export only unmapped reads.", 3322 "type": "boolean"
3259 "items": { 3323 },
3260 "type": "string" 3324 "position": {
3261 }, 3325 "description": "The 0-based offset from the start of the for ward strand for that reference.",
3262 "type": "array" 3326 "format": "int64",
3263 }, 3327 "type": "string"
3264 "exportUri": { 3328 },
3265 "description": "Required. A Google Cloud Storage URI for the exported BAM file.\nThe currently authenticated user must have write access to the new file.\nAn error will be returned if the URI already contains data.", 3329 "referenceName": {
3266 "type": "string" 3330 "description": "The name of the reference in whatever refere nce set is being used.",
3267 }, 3331 "type": "string"
3268 "projectId": { 3332 }
3269 "description": "Required. The Google Cloud project ID that o wns this\nexport. The caller must have WRITE access to this project.", 3333 },
3270 "type": "string" 3334 "type": "object"
3271 } 3335 },
3272 }, 3336 "SearchReferenceSetsResponse": {
3273 "type": "object" 3337 "id": "SearchReferenceSetsResponse",
3274 }, 3338 "properties": {
3275 "Exon": { 3339 "referenceSets": {
3276 "id": "Exon", 3340 "description": "The matching references sets.",
3277 "properties": { 3341 "items": {
3278 "start": { 3342 "$ref": "ReferenceSet"
3279 "description": "The start position of the exon on this annot ation's reference sequence,\n0-based inclusive. Note that this is relative to th e reference start, and\n**not** the containing annotation start.", 3343 },
3280 "format": "int64", 3344 "type": "array"
3281 "type": "string" 3345 },
3282 }, 3346 "nextPageToken": {
3283 "frame": { 3347 "description": "The continuation token, which is used to pag e through large result sets.\nProvide this value in a subsequent request to retu rn the next page of\nresults. This field will be empty if there aren't any addit ional results.",
3284 "description": "The frame of this exon. Contains a value of 0, 1, or 2, which indicates\nthe offset of the first coding base of the exon wit hin the reading frame\nof the coding DNA sequence, if any. This field is depende nt on the\nstrandedness of this annotation (see\nAnnotation.reverse_strand).\nFo r forward stranded annotations, this offset is relative to the\nexon.start. For reverse\nstrand annotations, this offset is relative to the\nexon.end `- 1`.\n\n Unset if this exon does not intersect the coding sequence. Upon creation\nof a t ranscript, the frame must be populated for all or none of the\ncoding exons.", 3348 "type": "string"
3349 }
3350 },
3351 "type": "object"
3352 },
3353 "SearchCallSetsRequest": {
3354 "description": "The call set search request.",
3355 "id": "SearchCallSetsRequest",
3356 "properties": {
3357 "pageToken": {
3358 "description": "The continuation token, which is used to pag e through large result sets.\nTo get the next page of results, set this paramete r to the value of\n`nextPageToken` from the previous response.",
3359 "type": "string"
3360 },
3361 "name": {
3362 "description": "Only return call sets for which a substring of the name matches this\nstring.",
3363 "type": "string"
3364 },
3365 "pageSize": {
3366 "description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 1024.",
3285 "format": "int32", 3367 "format": "int32",
3286 "type": "integer" 3368 "type": "integer"
3287 }, 3369 },
3370 "variantSetIds": {
3371 "description": "Restrict the query to call sets within the g iven variant sets. At least one\nID must be provided.",
3372 "items": {
3373 "type": "string"
3374 },
3375 "type": "array"
3376 }
3377 },
3378 "type": "object"
3379 },
3380 "ImportReadGroupSetsRequest": {
3381 "description": "The read group set import request.",
3382 "id": "ImportReadGroupSetsRequest",
3383 "properties": {
3384 "sourceUris": {
3385 "description": "A list of URIs pointing at [BAM\nfiles](http s://samtools.github.io/hts-specs/SAMv1.pdf)\nin Google Cloud Storage.\nThose URI s can include wildcards (*), but do not add or remove\nmatching files before imp ort has completed.\n\nNote that Google Cloud Storage object listing is only even tually\nconsistent: files added may be not be immediately visible to\neveryone. Thus, if using a wildcard it is preferable not to start\nthe import immediately after the files are created.",
3386 "items": {
3387 "type": "string"
3388 },
3389 "type": "array"
3390 },
3391 "referenceSetId": {
3392 "description": "The reference set to which the imported read group sets are aligned to, if\nany. The reference names of this reference set m ust be a superset of those\nfound in the imported file headers. If no reference set id is provided, a\nbest effort is made to associate with a matching referenc e set.",
3393 "type": "string"
3394 },
3395 "partitionStrategy": {
3396 "description": "The partition strategy describes how read gr oups are partitioned into read\ngroup sets.",
3397 "enum": [
3398 "PARTITION_STRATEGY_UNSPECIFIED",
3399 "PER_FILE_PER_SAMPLE",
3400 "MERGE_ALL"
3401 ],
3402 "enumDescriptions": [
3403 "",
3404 "In most cases, this strategy yields one read group set per file. This is\nthe default behavior.\n\nAllocate one read group set per file per sample. For BAM files, read\ngroups are considered to share a sample if the y have identical sample\nnames. Furthermore, all reads for each file which do no t belong to a read\ngroup, if any, will be grouped into a single read group set per-file.",
3405 "Includes all read groups in all imported files into a s ingle read group\nset. Requires that the headers for all imported files are equi valent. All\nreads which do not belong to a read group, if any, will be grouped into a\nseparate read group set."
3406 ],
3407 "type": "string"
3408 },
3409 "datasetId": {
3410 "description": "Required. The ID of the dataset these read g roup sets will belong to. The\ncaller must have WRITE permissions to this datase t.",
3411 "type": "string"
3412 }
3413 },
3414 "type": "object"
3415 },
3416 "Policy": {
3417 "description": "Defines an Identity and Access Management (IAM) poli cy. It is used to\nspecify access control policies for Cloud Platform resources. \n\n\nA `Policy` consists of a list of `bindings`. A `Binding` binds a list of\n `members` to a `role`, where the members can be user accounts, Google groups,\nG oogle domains, and service accounts. A `role` is a named list of permissions\nde fined by IAM.\n\n**Example**\n\n {\n \"bindings\": [\n {\n \"role\": \"roles/owner\",\n \"members\": [\n \"user:mike @example.com\",\n \"group:admins@example.com\",\n \"domain :google.com\",\n \"serviceAccount:my-other-app@appspot.gserviceaccoun t.com\",\n ]\n },\n {\n \"role\": \"roles/viewer \",\n \"members\": [\"user:sean@example.com\"]\n }\n ]\n }\n\nFor a description of IAM and its features, see the\n[IAM developer's guide ](https://cloud.google.com/iam).",
3418 "id": "Policy",
3419 "properties": {
3420 "etag": {
3421 "description": "`etag` is used for optimistic concurrency co ntrol as a way to help\nprevent simultaneous updates of a policy from overwritin g each other.\nIt is strongly suggested that systems make use of the `etag` in t he\nread-modify-write cycle to perform policy updates in order to avoid race\nco nditions: An `etag` is returned in the response to `getIamPolicy`, and\nsystems are expected to put that etag in the request to `setIamPolicy` to\nensure that t heir change will be applied to the same version of the policy.\n\nIf no `etag` i s provided in the call to `setIamPolicy`, then the existing\npolicy is overwritt en blindly.",
3422 "format": "byte",
3423 "type": "string"
3424 },
3425 "version": {
3426 "description": "Version of the `Policy`. The default version is 0.",
3427 "format": "int32",
3428 "type": "integer"
3429 },
3430 "bindings": {
3431 "description": "Associates a list of `members` to a `role`.\ n`bindings` with no members will result in an error.",
3432 "items": {
3433 "$ref": "Binding"
3434 },
3435 "type": "array"
3436 }
3437 },
3438 "type": "object"
3439 },
3440 "Annotation": {
3441 "description": "An annotation describes a region of reference genome . The value of an\nannotation may be one of several canonical types, supplemente d by arbitrary\ninfo tags. An annotation is not inherently associated with a spe cific\nsample or individual (though a client could choose to use annotations in\ nthis way). Example canonical annotation types are `GENE` and\n`VARIANT`.",
3442 "id": "Annotation",
3443 "properties": {
3288 "end": { 3444 "end": {
3289 "description": "The end position of the exon on this annotat ion's reference sequence,\n0-based exclusive. Note that this is relative to the reference start, and\n*not* the containing annotation start.", 3445 "description": "The end position of the range on the referen ce, 0-based exclusive.",
3290 "format": "int64", 3446 "format": "int64",
3291 "type": "string" 3447 "type": "string"
3292 } 3448 },
3293 }, 3449 "transcript": {
3294 "type": "object" 3450 "$ref": "Transcript",
3295 }, 3451 "description": "A transcript value represents the assertion that a particular region of\nthe reference genome may be transcribed as RNA. An alternative splicing\npattern would be represented as a separate transcript obje ct. This field\nis only set for annotations of type `TRANSCRIPT`."
3296 "CallSet": { 3452 },
3297 "description": "A call set is a collection of variant calls, typical ly for one sample. It\nbelongs to a variant set.\n\nFor more genomics resource d efinitions, see [Fundamentals of Google\nGenomics](https://cloud.google.com/geno mics/fundamentals-of-google-genomics)", 3453 "start": {
3298 "id": "CallSet", 3454 "description": "The start position of the range on the refer ence, 0-based inclusive.",
3299 "properties": { 3455 "format": "int64",
3456 "type": "string"
3457 },
3458 "annotationSetId": {
3459 "description": "The annotation set to which this annotation belongs.",
3460 "type": "string"
3461 },
3300 "name": { 3462 "name": {
3301 "description": "The call set name.", 3463 "description": "The display name of this annotation.",
3464 "type": "string"
3465 },
3466 "variant": {
3467 "$ref": "VariantAnnotation",
3468 "description": "A variant annotation, which describes the ef fect of a variant on the\ngenome, the coding sequence, and/or higher level conse quences at the\norganism level e.g. pathogenicity. This field is only set for an notations\nof type `VARIANT`."
3469 },
3470 "id": {
3471 "description": "The server-generated annotation ID, unique a cross all annotations.",
3472 "type": "string"
3473 },
3474 "referenceId": {
3475 "description": "The ID of the Google Genomics reference asso ciated with this range.",
3476 "type": "string"
3477 },
3478 "reverseStrand": {
3479 "description": "Whether this range refers to the reverse str and, as opposed to the forward\nstrand. Note that regardless of this field, the start/end position of the\nrange always refer to the forward strand.",
3480 "type": "boolean"
3481 },
3482 "referenceName": {
3483 "description": "The display name corresponding to the refere nce specified by\n`referenceId`, for example `chr1`, `1`, or `chrX`.",
3484 "type": "string"
3485 },
3486 "type": {
3487 "description": "The data type for this annotation. Must matc h the containing annotation\nset's type.",
3488 "enum": [
3489 "ANNOTATION_TYPE_UNSPECIFIED",
3490 "GENERIC",
3491 "VARIANT",
3492 "GENE",
3493 "TRANSCRIPT"
3494 ],
3495 "enumDescriptions": [
3496 "",
3497 "A `GENERIC` annotation type should be used when no othe r annotation\ntype will suffice. This represents an untyped annotation of the re ference\ngenome.",
3498 "A `VARIANT` annotation type.",
3499 "A `GENE` annotation type represents the existence of a gene at the\nassociated reference coordinates. The start coordinate is typically the\ngene's transcription start site and the end is typically the end of the\ng ene's last exon.",
3500 "A `TRANSCRIPT` annotation type represents the assertion that a\nparticular region of the reference genome may be transcribed as RNA."
3501 ],
3302 "type": "string" 3502 "type": "string"
3303 }, 3503 },
3304 "info": { 3504 "info": {
3305 "additionalProperties": { 3505 "additionalProperties": {
3306 "items": { 3506 "items": {
3307 "type": "any" 3507 "type": "any"
3308 }, 3508 },
3309 "type": "array" 3509 "type": "array"
3310 }, 3510 },
3311 "description": "A map of additional call set information. Th is must be of the form\nmap<string, string[]> (string key mapping to a list of s tring values).", 3511 "description": "A map of additional read alignment informati on. This must be of the form\nmap<string, string[]> (string key mapping to a lis t of string values).",
3312 "type": "object" 3512 "type": "object"
3313 }, 3513 }
3314 "variantSetIds": { 3514 },
3315 "description": "The IDs of the variant sets this call set be longs to. This field must\nhave exactly length one, as a call set belongs to a s ingle variant set.\nThis field is repeated for compatibility with the\n[GA4GH 0. 5.1\nAPI](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/v ariants.avdl#L76).", 3515 "type": "object"
3316 "items": { 3516 },
3317 "type": "string" 3517 "CancelOperationRequest": {
3318 }, 3518 "description": "The request message for Operations.CancelOperation." ,
3319 "type": "array" 3519 "id": "CancelOperationRequest",
3320 }, 3520 "properties": {},
3321 "id": { 3521 "type": "object"
3322 "description": "The server-generated call set ID, unique acr oss all call sets.", 3522 },
3323 "type": "string" 3523 "SearchReadsRequest": {
3324 }, 3524 "description": "The read search request.",
3325 "created": { 3525 "id": "SearchReadsRequest",
3326 "description": "The date this call set was created in millis econds from the epoch.", 3526 "properties": {
3327 "format": "int64",
3328 "type": "string"
3329 },
3330 "sampleId": {
3331 "description": "The sample ID this call set corresponds to." ,
3332 "type": "string"
3333 }
3334 },
3335 "type": "object"
3336 },
3337 "SearchAnnotationSetsResponse": {
3338 "id": "SearchAnnotationSetsResponse",
3339 "properties": {
3340 "annotationSets": {
3341 "description": "The matching annotation sets.",
3342 "items": {
3343 "$ref": "AnnotationSet"
3344 },
3345 "type": "array"
3346 },
3347 "nextPageToken": {
3348 "description": "The continuation token, which is used to pag e through large result sets.\nProvide this value in a subsequent request to retu rn the next page of\nresults. This field will be empty if there aren't any addit ional results.",
3349 "type": "string"
3350 }
3351 },
3352 "type": "object"
3353 },
3354 "ImportVariantsRequest": {
3355 "description": "The variant data import request.",
3356 "id": "ImportVariantsRequest",
3357 "properties": {
3358 "format": {
3359 "description": "The format of the variant data being importe d. If unspecified, defaults to\nto `VCF`.",
3360 "enum": [
3361 "FORMAT_UNSPECIFIED",
3362 "FORMAT_VCF",
3363 "FORMAT_COMPLETE_GENOMICS"
3364 ],
3365 "enumDescriptions": [
3366 "",
3367 "VCF (Variant Call Format). The VCF files may be gzip co mpressed. gVCF is\nalso supported. Disclaimer: gzip VCF imports are currently mu ch slower\nthan equivalent uncompressed VCF imports. For this reason, uncompress ed\nVCF is currently recommended for imports with more than 1GB combined\nuncomp ressed size, or for time sensitive imports.",
3368 "Complete Genomics masterVarBeta format. The masterVarBe ta files may\nbe bzip2 compressed."
3369 ],
3370 "type": "string"
3371 },
3372 "infoMergeConfig": {
3373 "additionalProperties": {
3374 "enum": [
3375 "INFO_MERGE_OPERATION_UNSPECIFIED",
3376 "IGNORE_NEW",
3377 "MOVE_TO_CALLS"
3378 ],
3379 "type": "string"
3380 },
3381 "description": "A mapping between info field keys and the In foMergeOperations to\nbe performed on them. This is plumbed down to the MergeVar iantRequests\ngenerated by the resulting import job.",
3382 "type": "object"
3383 },
3384 "sourceUris": {
3385 "description": "A list of URIs referencing variant files in Google Cloud Storage. URIs can\ninclude wildcards [as described\nhere](https://c loud.google.com/storage/docs/gsutil/addlhelp/WildcardNames).\nNote that recursiv e wildcards ('**') are not supported.",
3386 "items": {
3387 "type": "string"
3388 },
3389 "type": "array"
3390 },
3391 "variantSetId": {
3392 "description": "Required. The variant set to which variant d ata should be imported.",
3393 "type": "string"
3394 },
3395 "normalizeReferenceNames": {
3396 "description": "Convert reference names to the canonical rep resentation.\nhg19 haploytypes (those reference names containing \"_hap\")\nare not modified in any way.\nAll other reference names are modified according to th e following rules:\nThe reference name is capitalized.\nThe \"chr\" prefix is dr opped for all autosomes and sex chromsomes.\nFor example \"chr17\" becomes \"17\ " and \"chrX\" becomes \"X\".\nAll mitochondrial chromosomes (\"chrM\", \"chrMT\ ", etc) become \"MT\".",
3397 "type": "boolean"
3398 }
3399 },
3400 "type": "object"
3401 },
3402 "VariantAnnotation": {
3403 "id": "VariantAnnotation",
3404 "properties": {
3405 "effect": {
3406 "description": "Effect of the variant on the coding sequence .",
3407 "enum": [
3408 "EFFECT_UNSPECIFIED",
3409 "EFFECT_OTHER",
3410 "FRAMESHIFT",
3411 "FRAME_PRESERVING_INDEL",
3412 "SYNONYMOUS_SNP",
3413 "NONSYNONYMOUS_SNP",
3414 "STOP_GAIN",
3415 "STOP_LOSS",
3416 "SPLICE_SITE_DISRUPTION"
3417 ],
3418 "enumDescriptions": [
3419 "",
3420 "`EFFECT_OTHER` should be used when no other Effect\nwil l suffice.",
3421 "`FRAMESHIFT` indicates a mutation in which the insertio n or\ndeletion of nucleotides resulted in a frameshift change.",
3422 "`FRAME_PRESERVING_INDEL` indicates a mutation in which a\nmultiple of three nucleotides has been inserted or deleted, resulting\nin no change to the reading frame of the coding sequence.",
3423 "`SYNONYMOUS_SNP` indicates a single nucleotide polymorp hism\nmutation that results in no amino acid change.",
3424 "`NONSYNONYMOUS_SNP` indicates a single nucleotide\npoly morphism mutation that results in an amino acid change.",
3425 "`STOP_GAIN` indicates a mutation that leads to the crea tion\nof a stop codon at the variant site. Frameshift mutations creating\ndownst ream stop codons do not count as `STOP_GAIN`.",
3426 "`STOP_LOSS` indicates a mutation that eliminates a\nsto p codon at the variant site.",
3427 "`SPLICE_SITE_DISRUPTION` indicates that this variant is \nfound in a splice site for the associated transcript, and alters the\nnormal s plicing pattern."
3428 ],
3429 "type": "string"
3430 },
3431 "transcriptIds": {
3432 "description": "Google annotation IDs of the transcripts aff ected by this variant. These\nshould be provided when the variant is created.",
3433 "items": {
3434 "type": "string"
3435 },
3436 "type": "array"
3437 },
3438 "type": {
3439 "description": "Type has been adapted from ClinVar's list of variant types.",
3440 "enum": [
3441 "TYPE_UNSPECIFIED",
3442 "TYPE_OTHER",
3443 "INSERTION",
3444 "DELETION",
3445 "SUBSTITUTION",
3446 "SNP",
3447 "STRUCTURAL",
3448 "CNV"
3449 ],
3450 "enumDescriptions": [
3451 "",
3452 "`TYPE_OTHER` should be used when no other Type will suf fice.\nFurther explanation of the variant type may be included in the\ninfo fiel d.",
3453 "`INSERTION` indicates an insertion.",
3454 "`DELETION` indicates a deletion.",
3455 "`SUBSTITUTION` indicates a block substitution of\ntwo o r more nucleotides.",
3456 "`SNP` indicates a single nucleotide polymorphism.",
3457 "`STRUCTURAL` indicates a large structural variant,\ninc luding chromosomal fusions, inversions, etc.",
3458 "`CNV` indicates a variation in copy number."
3459 ],
3460 "type": "string"
3461 },
3462 "alternateBases": {
3463 "description": "The alternate allele for this variant. If mu ltiple alternate alleles\nexist at this location, create a separate variant for each one, as they\nmay represent distinct conditions.",
3464 "type": "string"
3465 },
3466 "geneId": {
3467 "description": "Google annotation ID of the gene affected by this variant. This should\nbe provided when the variant is created.",
3468 "type": "string"
3469 },
3470 "clinicalSignificance": {
3471 "description": "Describes the clinical significance of a var iant.\nIt is adapted from the ClinVar controlled vocabulary for clinical\nsignif icance described at:\nhttp://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/",
3472 "enum": [
3473 "CLINICAL_SIGNIFICANCE_UNSPECIFIED",
3474 "CLINICAL_SIGNIFICANCE_OTHER",
3475 "UNCERTAIN",
3476 "BENIGN",
3477 "LIKELY_BENIGN",
3478 "LIKELY_PATHOGENIC",
3479 "PATHOGENIC",
3480 "DRUG_RESPONSE",
3481 "HISTOCOMPATIBILITY",
3482 "CONFERS_SENSITIVITY",
3483 "RISK_FACTOR",
3484 "ASSOCIATION",
3485 "PROTECTIVE",
3486 "MULTIPLE_REPORTED"
3487 ],
3488 "enumDescriptions": [
3489 "",
3490 "`OTHER` should be used when no other clinical significa nce\nvalue will suffice.",
3491 "",
3492 "",
3493 "",
3494 "",
3495 "",
3496 "",
3497 "",
3498 "",
3499 "",
3500 "",
3501 "",
3502 "`MULTIPLE_REPORTED` should be used when multiple clinic al\nsignficances are reported for a variant. The original clinical\nsignificance values may be provided in the `info` field."
3503 ],
3504 "type": "string"
3505 },
3506 "conditions": {
3507 "description": "The set of conditions associated with this v ariant.\nA condition describes the way a variant influences human health.",
3508 "items": {
3509 "$ref": "ClinicalCondition"
3510 },
3511 "type": "array"
3512 }
3513 },
3514 "type": "object"
3515 },
3516 "ListCoverageBucketsResponse": {
3517 "id": "ListCoverageBucketsResponse",
3518 "properties": {
3519 "bucketWidth": {
3520 "description": "The length of each coverage bucket in base p airs. Note that buckets at the\nend of a reference sequence may be shorter. This value is omitted if the\nbucket width is infinity (the default behaviour, with no range or\n`targetBucketWidth`).",
3521 "format": "int64",
3522 "type": "string"
3523 },
3524 "coverageBuckets": {
3525 "description": "The coverage buckets. The list of buckets is sparse; a bucket with 0\noverlapping reads is not returned. A bucket never cros ses more than one\nreference sequence. Each bucket has width `bucketWidth`, unle ss\nits end is the end of the reference sequence.",
3526 "items": {
3527 "$ref": "CoverageBucket"
3528 },
3529 "type": "array"
3530 },
3531 "nextPageToken": {
3532 "description": "The continuation token, which is used to pag e through large result sets.\nProvide this value in a subsequent request to retu rn the next page of\nresults. This field will be empty if there aren't any addit ional results.",
3533 "type": "string"
3534 }
3535 },
3536 "type": "object"
3537 },
3538 "ExportVariantSetRequest": {
3539 "description": "The variant data export request.",
3540 "id": "ExportVariantSetRequest",
3541 "properties": {
3542 "bigqueryTable": {
3543 "description": "Required. The BigQuery table to export data to.\nIf the table doesn't exist, it will be created. If it already exists, it\nw ill be overwritten.",
3544 "type": "string"
3545 },
3546 "bigqueryDataset": {
3547 "description": "Required. The BigQuery dataset to export dat a to. This dataset must already\nexist. Note that this is distinct from the Geno mics concept of \"dataset\".",
3548 "type": "string"
3549 },
3550 "format": {
3551 "description": "The format for the exported data.",
3552 "enum": [
3553 "FORMAT_UNSPECIFIED",
3554 "FORMAT_BIGQUERY"
3555 ],
3556 "enumDescriptions": [
3557 "",
3558 "Export the data to Google BigQuery."
3559 ],
3560 "type": "string"
3561 },
3562 "projectId": {
3563 "description": "Required. The Google Cloud project ID that o wns the destination\nBigQuery dataset. The caller must have WRITE access to this project. This\nproject will also own the resulting export job.",
3564 "type": "string"
3565 },
3566 "callSetIds": {
3567 "description": "If provided, only variant call information f rom the specified call sets\nwill be exported. By default all variant calls are exported.",
3568 "items": {
3569 "type": "string"
3570 },
3571 "type": "array"
3572 }
3573 },
3574 "type": "object"
3575 },
3576 "SearchAnnotationsRequest": {
3577 "id": "SearchAnnotationsRequest",
3578 "properties": {
3579 "annotationSetIds": {
3580 "description": "Required. The annotation sets to search with in. The caller must have\n`READ` access to these annotation sets.\nAll queried a nnotation sets must have the same type.",
3581 "items": {
3582 "type": "string"
3583 },
3584 "type": "array"
3585 },
3586 "referenceName": {
3587 "description": "The name of the reference to query, within t he reference set associated\nwith this query.",
3588 "type": "string"
3589 },
3590 "referenceId": {
3591 "description": "The ID of the reference to query.",
3592 "type": "string"
3593 },
3594 "end": { 3527 "end": {
3595 "description": "The end position of the range on the referen ce, 0-based exclusive. If\nreferenceId or\nreferenceName\nmust be specified, Def aults to the length of the reference.", 3528 "description": "The end position of the range on the referen ce, 0-based exclusive. If\nspecified, `referenceName` must also be specified.",
3596 "format": "int64", 3529 "format": "int64",
3597 "type": "string" 3530 "type": "string"
3598 }, 3531 },
3599 "pageToken": { 3532 "pageToken": {
3600 "description": "The continuation token, which is used to pag e through large result sets.\nTo get the next page of results, set this paramete r to the value of\n`nextPageToken` from the previous response.", 3533 "description": "The continuation token, which is used to pag e through large result sets.\nTo get the next page of results, set this paramete r to the value of\n`nextPageToken` from the previous response.",
3601 "type": "string" 3534 "type": "string"
3602 }, 3535 },
3603 "pageSize": { 3536 "pageSize": {
3604 "description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 256. The maximum value is 2048.", 3537 "description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 256. The maximum value is 2048.",
3605 "format": "int32", 3538 "format": "int32",
3606 "type": "integer" 3539 "type": "integer"
3607 }, 3540 },
3608 "start": { 3541 "start": {
3609 "description": "The start position of the range on the refer ence, 0-based inclusive. If\nspecified,\nreferenceId or\nreferenceName\nmust be specified. Defaults to 0.", 3542 "description": "The start position of the range on the refer ence, 0-based inclusive. If\nspecified, `referenceName` must also be specified." ,
3610 "format": "int64", 3543 "format": "int64",
3611 "type": "string" 3544 "type": "string"
3545 },
3546 "referenceName": {
3547 "description": "The reference sequence name, for example `ch r1`, `1`, or `chrX`. If set to\n`*`, only unmapped reads are returned. If unspec ified, all reads (mapped\nand unmapped) are returned.",
3548 "type": "string"
3549 },
3550 "readGroupSetIds": {
3551 "description": "The IDs of the read groups sets within which to search for reads. All\nspecified read group sets must be aligned against a c ommon set of reference\nsequences; this defines the genomic coordinates for the query. Must specify\none of `readGroupSetIds` or `readGroupIds`.",
3552 "items": {
3553 "type": "string"
3554 },
3555 "type": "array"
3556 },
3557 "readGroupIds": {
3558 "description": "The IDs of the read groups within which to s earch for reads. All specified\nread groups must belong to the same read group s ets. Must specify one of\n`readGroupSetIds` or `readGroupIds`.",
3559 "items": {
3560 "type": "string"
3561 },
3562 "type": "array"
3612 } 3563 }
3613 }, 3564 },
3614 "type": "object" 3565 "type": "object"
3615 }, 3566 },
3616 "OperationEvent": { 3567 "RuntimeMetadata": {
3617 "description": "An event that occurred during an Operation.", 3568 "description": "Runtime metadata that will be populated in the\nrunt imeMetadata\nfield of the Operation associated with a RunPipeline execution.",
3618 "id": "OperationEvent", 3569 "id": "RuntimeMetadata",
3619 "properties": { 3570 "properties": {
3620 "startTime": { 3571 "computeEngine": {
3621 "description": "Optional time of when event started.", 3572 "$ref": "ComputeEngine",
3622 "format": "google-datetime", 3573 "description": "Execution information specific to Google Com pute Engine."
3623 "type": "string"
3624 },
3625 "description": {
3626 "description": "Required description of event.",
3627 "type": "string"
3628 },
3629 "endTime": {
3630 "description": "Optional time of when event finished. An eve nt can have a start time and no\nfinish time. If an event has a finish time, the re must be a start time.",
3631 "format": "google-datetime",
3632 "type": "string"
3633 } 3574 }
3634 }, 3575 },
3635 "type": "object" 3576 "type": "object"
3636 }, 3577 },
3637 "CodingSequence": { 3578 "Operation": {
3638 "id": "CodingSequence", 3579 "description": "This resource represents a long-running operation th at is the result of a\nnetwork API call.",
3580 "id": "Operation",
3639 "properties": { 3581 "properties": {
3640 "end": { 3582 "done": {
3641 "description": "The end of the coding sequence on this annot ation's reference sequence,\n0-based exclusive. Note that this position is relat ive to the reference\nstart, and *not* the containing annotation start.", 3583 "description": "If the value is `false`, it means the operat ion is still in progress.\nIf true, the operation is completed, and either `erro r` or `response` is\navailable.",
3642 "format": "int64", 3584 "type": "boolean"
3585 },
3586 "response": {
3587 "additionalProperties": {
3588 "description": "Properties of the object. Contains field @type with type URL.",
3589 "type": "any"
3590 },
3591 "description": "If importing ReadGroupSets, an ImportReadGro upSetsResponse is returned. If importing Variants, an ImportVariantsResponse is returned. For pipelines and exports, an empty response is returned.",
3592 "type": "object"
3593 },
3594 "name": {
3595 "description": "The server-assigned name, which is only uniq ue within the same service that originally returns it. For example&#58; `operati ons/CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw`",
3643 "type": "string" 3596 "type": "string"
3644 }, 3597 },
3645 "start": { 3598 "error": {
3646 "description": "The start of the coding sequence on this ann otation's reference sequence,\n0-based inclusive. Note that this position is rel ative to the reference\nstart, and *not* the containing annotation start.", 3599 "$ref": "Status",
3647 "format": "int64", 3600 "description": "The error result of the operation in case of failure or cancellation."
3648 "type": "string" 3601 },
3602 "metadata": {
3603 "additionalProperties": {
3604 "description": "Properties of the object. Contains field @type with type URL.",
3605 "type": "any"
3606 },
3607 "description": "An OperationMetadata object. This will alway s be returned with the Operation.",
3608 "type": "object"
3649 } 3609 }
3650 }, 3610 },
3651 "type": "object" 3611 "type": "object"
3652 }, 3612 },
3653 "SearchReferencesResponse": { 3613 "ImportReadGroupSetsResponse": {
3654 "id": "SearchReferencesResponse", 3614 "description": "The read group set import response.",
3615 "id": "ImportReadGroupSetsResponse",
3655 "properties": { 3616 "properties": {
3656 "references": { 3617 "readGroupSetIds": {
3657 "description": "The matching references.", 3618 "description": "IDs of the read group sets that were created .",
3658 "items": {
3659 "$ref": "Reference"
3660 },
3661 "type": "array"
3662 },
3663 "nextPageToken": {
3664 "description": "The continuation token, which is used to pag e through large result sets.\nProvide this value in a subsequent request to retu rn the next page of\nresults. This field will be empty if there aren't any addit ional results.",
3665 "type": "string"
3666 }
3667 },
3668 "type": "object"
3669 },
3670 "GetIamPolicyRequest": {
3671 "description": "Request message for `GetIamPolicy` method.",
3672 "id": "GetIamPolicyRequest",
3673 "properties": {},
3674 "type": "object"
3675 },
3676 "TestIamPermissionsResponse": {
3677 "description": "Response message for `TestIamPermissions` method.",
3678 "id": "TestIamPermissionsResponse",
3679 "properties": {
3680 "permissions": {
3681 "description": "A subset of `TestPermissionsRequest.permissi ons` that the caller is\nallowed.",
3682 "items": { 3619 "items": {
3683 "type": "string" 3620 "type": "string"
3684 }, 3621 },
3685 "type": "array" 3622 "type": "array"
3686 } 3623 }
3687 }, 3624 },
3688 "type": "object" 3625 "type": "object"
3689 }, 3626 },
3690 "SearchAnnotationSetsRequest": { 3627 "VariantCall": {
3691 "id": "SearchAnnotationSetsRequest", 3628 "description": "A call represents the determination of genotype with respect to a particular\nvariant. It may include associated information such as quality and phasing.\nFor example, a call might assign a probability of 0.32 to the occurrence of\na SNP named rs1234 in a call set with the name NA12345.",
3629 "id": "VariantCall",
3692 "properties": { 3630 "properties": {
3693 "datasetIds": { 3631 "genotypeLikelihood": {
3694 "description": "Required. The dataset IDs to search within. Caller must have `READ` access\nto these datasets.", 3632 "description": "The genotype likelihoods for this variant ca ll. Each array entry\nrepresents how likely a specific genotype is for this call . The value\nordering is defined by the GL tag in the VCF spec.\nIf Phred-scaled genotype likelihood scores (PL) are available and\nlog10(P) genotype likelihood scores (GL) are not, PL scores are converted\nto GL scores. If both are availa ble, PL scores are stored in `info`.",
3633 "items": {
3634 "format": "double",
3635 "type": "number"
3636 },
3637 "type": "array"
3638 },
3639 "callSetId": {
3640 "description": "The ID of the call set this variant call bel ongs to.",
3641 "type": "string"
3642 },
3643 "genotype": {
3644 "description": "The genotype of this variant call. Each valu e represents either the value\nof the `referenceBases` field or a 1-based index into\n`alternateBases`. If a variant had a `referenceBases`\nvalue of `T` and an `alternateBases`\nvalue of `[\"A\", \"C\"]`, and the `genotype` was\n`[2, 1]`, that would mean the call\nrepresented the heterozygous value `CA` for this varia nt.\nIf the `genotype` was instead `[0, 1]`, the\nrepresented value would be `TA `. Ordering of the\ngenotype values is important if the `phaseset` is present.\n If a genotype is not called (that is, a `.` is present in the\nGT string) -1 is returned.",
3645 "items": {
3646 "format": "int32",
3647 "type": "integer"
3648 },
3649 "type": "array"
3650 },
3651 "phaseset": {
3652 "description": "If this field is present, this variant call' s genotype ordering implies\nthe phase of the bases and is consistent with any o ther variant calls in\nthe same reference sequence which have the same phaseset value.\nWhen importing data from VCF, if the genotype data was phased but no\nph ase set was specified this field will be set to `*`.",
3653 "type": "string"
3654 },
3655 "info": {
3656 "additionalProperties": {
3657 "items": {
3658 "type": "any"
3659 },
3660 "type": "array"
3661 },
3662 "description": "A map of additional variant call information . This must be of the form\nmap<string, string[]> (string key mapping to a list of string values).",
3663 "type": "object"
3664 },
3665 "callSetName": {
3666 "description": "The name of the call set this variant call b elongs to.",
3667 "type": "string"
3668 }
3669 },
3670 "type": "object"
3671 },
3672 "SearchVariantsResponse": {
3673 "description": "The variant search response.",
3674 "id": "SearchVariantsResponse",
3675 "properties": {
3676 "variants": {
3677 "description": "The list of matching Variants.",
3678 "items": {
3679 "$ref": "Variant"
3680 },
3681 "type": "array"
3682 },
3683 "nextPageToken": {
3684 "description": "The continuation token, which is used to pag e through large result sets.\nProvide this value in a subsequent request to retu rn the next page of\nresults. This field will be empty if there aren't any addit ional results.",
3685 "type": "string"
3686 }
3687 },
3688 "type": "object"
3689 },
3690 "ListBasesResponse": {
3691 "id": "ListBasesResponse",
3692 "properties": {
3693 "sequence": {
3694 "description": "A substring of the bases that make up this r eference.",
3695 "type": "string"
3696 },
3697 "offset": {
3698 "description": "The offset position (0-based) of the given ` sequence` from the\nstart of this `Reference`. This value will differ for each p age\nin a paginated request.",
3699 "format": "int64",
3700 "type": "string"
3701 },
3702 "nextPageToken": {
3703 "description": "The continuation token, which is used to pag e through large result sets.\nProvide this value in a subsequent request to retu rn the next page of\nresults. This field will be empty if there aren't any addit ional results.",
3704 "type": "string"
3705 }
3706 },
3707 "type": "object"
3708 },
3709 "Status": {
3710 "description": "The `Status` type defines a logical error model that is suitable for different\nprogramming environments, including REST APIs and RP C APIs. It is used by\n[gRPC](https://github.com/grpc). The error model is desig ned to be:\n\n- Simple to use and understand for most users\n- Flexible enough t o meet unexpected needs\n\n# Overview\n\nThe `Status` message contains three pie ces of data: error code, error message,\nand error details. The error code shoul d be an enum value of\ngoogle.rpc.Code, but it may accept additional error codes if needed. The\nerror message should be a developer-facing English message tha t helps\ndevelopers *understand* and *resolve* the error. If a localized user-fa cing\nerror message is needed, put the localized message in the error details or \nlocalize it in the client. The optional error details may contain arbitrary\ni nformation about the error. There is a predefined set of error detail types\nin the package `google.rpc` that can be used for common error conditions.\n\n# Lang uage mapping\n\nThe `Status` message is the logical representation of the error model, but it\nis not necessarily the actual wire format. When the `Status` mess age is\nexposed in different client libraries and different wire protocols, it c an be\nmapped differently. For example, it will likely be mapped to some excepti ons\nin Java, but more likely mapped to some error codes in C.\n\n# Other uses\n \nThe error model and the `Status` message can be used in a variety of\nenvironm ents, either with or without APIs, to provide a\nconsistent developer experience across different environments.\n\nExample uses of this error model include:\n\n - Partial errors. If a service needs to return partial errors to the client,\n it may embed the `Status` in the normal response to indicate the partial\n errors.\n\n- Workflow errors. A typical workflow has multiple steps. Each step m ay\n have a `Status` message for error reporting.\n\n- Batch operations. If a client uses batch request and batch response, the\n `Status` message should be used directly inside batch response, one for\n each error sub-response.\n\ n- Asynchronous operations. If an API call embeds asynchronous operation\n re sults in its response, the status of those operations should be\n represented directly using the `Status` message.\n\n- Logging. If some API errors are store d in logs, the message `Status` could\n be used directly after any stripping needed for security/privacy reasons.",
3711 "id": "Status",
3712 "properties": {
3713 "code": {
3714 "description": "The status code, which should be an enum val ue of google.rpc.Code.",
3715 "format": "int32",
3716 "type": "integer"
3717 },
3718 "message": {
3719 "description": "A developer-facing error message, which shou ld be in English. Any\nuser-facing error message should be localized and sent in the\ngoogle.rpc.Status.details field, or localized by the client.",
3720 "type": "string"
3721 },
3722 "details": {
3723 "description": "A list of messages that carry the error deta ils. There is a common set of\nmessage types for APIs to use.",
3724 "items": {
3725 "additionalProperties": {
3726 "description": "Properties of the object. Contains f ield @type with type URL.",
3727 "type": "any"
3728 },
3729 "type": "object"
3730 },
3731 "type": "array"
3732 }
3733 },
3734 "type": "object"
3735 },
3736 "Binding": {
3737 "description": "Associates `members` with a `role`.",
3738 "id": "Binding",
3739 "properties": {
3740 "members": {
3741 "description": "Specifies the identities requesting access f or a Cloud Platform resource.\n`members` can have the following values:\n\n* `al lUsers`: A special identifier that represents anyone who is\n on the internet; with or without a Google account.\n\n* `allAuthenticatedUsers`: A special ident ifier that represents anyone\n who is authenticated with a Google account or a service account.\n\n* `user:{emailid}`: An email address that represents a spec ific Google\n account. For example, `alice@gmail.com` or `joe@example.com`.\n\ n\n* `serviceAccount:{emailid}`: An email address that represents a service\n account. For example, `my-other-app@appspot.gserviceaccount.com`.\n\n* `group:{e mailid}`: An email address that represents a Google group.\n For example, `adm ins@example.com`.\n\n\n* `domain:{domain}`: A Google Apps domain name that repre sents all the\n users of that domain. For example, `google.com` or `example.co m`.\n\n",
3695 "items": { 3742 "items": {
3696 "type": "string" 3743 "type": "string"
3697 }, 3744 },
3698 "type": "array" 3745 "type": "array"
3699 }, 3746 },
3700 "types": { 3747 "role": {
3701 "description": "If specified, only annotation sets that have any of these types are\nreturned.", 3748 "description": "Role that is assigned to `members`.\nFor exa mple, `roles/viewer`, `roles/editor`, or `roles/owner`.\nRequired",
3702 "enumDescriptions": [
3703 "",
3704 "A `GENERIC` annotation type should be used when no othe r annotation\ntype will suffice. This represents an untyped annotation of the re ference\ngenome.",
3705 "A `VARIANT` annotation type.",
3706 "A `GENE` annotation type represents the existence of a gene at the\nassociated reference coordinates. The start coordinate is typically the\ngene's transcription start site and the end is typically the end of the\ng ene's last exon.",
3707 "A `TRANSCRIPT` annotation type represents the assertion that a\nparticular region of the reference genome may be transcribed as RNA."
3708 ],
3709 "items": {
3710 "enum": [
3711 "ANNOTATION_TYPE_UNSPECIFIED",
3712 "GENERIC",
3713 "VARIANT",
3714 "GENE",
3715 "TRANSCRIPT"
3716 ],
3717 "type": "string"
3718 },
3719 "type": "array"
3720 },
3721 "name": {
3722 "description": "Only return annotations sets for which a sub string of the name matches this\nstring (case insensitive).",
3723 "type": "string" 3749 "type": "string"
3724 },
3725 "referenceSetId": {
3726 "description": "If specified, only annotation sets associate d with the given reference set\nare returned.",
3727 "type": "string"
3728 },
3729 "pageToken": {
3730 "description": "The continuation token, which is used to pag e through large result sets.\nTo get the next page of results, set this paramete r to the value of\n`nextPageToken` from the previous response.",
3731 "type": "string"
3732 },
3733 "pageSize": {
3734 "description": "The maximum number of results to return in a single page. If unspecified,\ndefaults to 128. The maximum value is 1024.",
3735 "format": "int32",
3736 "type": "integer"
3737 } 3750 }
3738 }, 3751 },
3739 "type": "object" 3752 "type": "object"
3740 }, 3753 },
3741 "SearchReadGroupSetsResponse": { 3754 "UndeleteDatasetRequest": {
3742 "description": "The read group set search response.", 3755 "id": "UndeleteDatasetRequest",
3743 "id": "SearchReadGroupSetsResponse", 3756 "properties": {},
3744 "properties": {
3745 "nextPageToken": {
3746 "description": "The continuation token, which is used to pag e through large result sets.\nProvide this value in a subsequent request to retu rn the next page of\nresults. This field will be empty if there aren't any addit ional results.",
3747 "type": "string"
3748 },
3749 "readGroupSets": {
3750 "description": "The list of matching read group sets.",
3751 "items": {
3752 "$ref": "ReadGroupSet"
3753 },
3754 "type": "array"
3755 }
3756 },
3757 "type": "object" 3757 "type": "object"
3758 } 3758 }
3759 }, 3759 },
3760 "servicePath": "", 3760 "servicePath": "",
3761 "title": "Genomics API", 3761 "title": "Genomics API",
3762 "version": "v1" 3762 "version": "v1"
3763 } 3763 }
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