discovery/googleapis/genomics__v1.json - Issue 1268013003: Api-roll 21: 2015-08-04

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Issue 1268013003: Api-roll 21: 2015-08-04 (Closed) Base URL: git@github.com:dart-lang/googleapis.git@master

Patch Set: Created 5 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/bigquery": {	5 "https://www.googleapis.com/auth/bigquery": {

6 "description": "View and manage your data in Google BigQuery "	6 "description": "View and manage your data in Google BigQuery "

7 },	7 },

8 "https://www.googleapis.com/auth/cloud-platform": {	8 "https://www.googleapis.com/auth/cloud-platform": {

9 "description": "View and manage your data across Google Clou d Platform services"	9 "description": "View and manage your data across Google Clou d Platform services"

10 },	10 },

11 "https://www.googleapis.com/auth/devstorage.read_write": {	11 "https://www.googleapis.com/auth/devstorage.read_write": {

12 "description": "Manage your data in Google Cloud Storage"	12 "description": "Manage your data in Google Cloud Storage"

13 },	13 },

14 "https://www.googleapis.com/auth/genomics": {	14 "https://www.googleapis.com/auth/genomics": {

15 "description": "View and manage Genomics data"	15 "description": "View and manage Genomics data"

16 },	16 },

17 "https://www.googleapis.com/auth/genomics.readonly": {	17 "https://www.googleapis.com/auth/genomics.readonly": {

18 "description": "View Genomics data"	18 "description": "View Genomics data"

19 }	19 }

20 }	20 }

21 }	21 }

22 },	22 },

23 "basePath": "/genomics/v1beta2/",	23 "basePath": "",

24 "baseUrl": "https://www.googleapis.com/genomics/v1beta2/",	24 "baseUrl": "https://genomics.googleapis.com/",

25 "batchPath": "batch",	25 "batchPath": "batch",

26 "description": "Provides access to Genomics data.",	26 "description": "An API to store, process, explore, and share DNA sequence re ads, reference-based alignments, and variant calls.",

27 "discoveryVersion": "v1",	27 "discoveryVersion": "v1",

28 "documentationLink": "https://developers.google.com/genomics/v1beta2/referen ce",	28 "documentationLink": "",

29 "etag": "\"ye6orv2F-1npMW3u9suM3a7C5Bo/Rb7-9Pk3C2nyGTw9tsYHv2nAxPQ\"",	29 "etag": "\"ye6orv2F-1npMW3u9suM3a7C5Bo/XILvP_efgPuxb7JT-rkhdFInZts\"",

30 "icons": {	30 "icons": {

31 "x16": "http://www.google.com/images/icons/product/search-16.gif",	31 "x16": "http://www.google.com/images/icons/product/search-16.gif",

32 "x32": "http://www.google.com/images/icons/product/search-32.gif"	32 "x32": "http://www.google.com/images/icons/product/search-32.gif"

33 },	33 },

34 "id": "genomics:v1beta2",	34 "id": "genomics:v1",

35 "kind": "discovery#restDescription",	35 "kind": "discovery#restDescription",

36 "name": "genomics",	36 "name": "genomics",

37 "ownerDomain": "google.com",	37 "ownerDomain": "google.com",

38 "ownerName": "Google",	38 "ownerName": "Google",

39 "parameters": {	39 "parameters": {

	40 "access_token": {

	41 "description": "OAuth access token.",

	42 "location": "query",

	43 "type": "string"

	44 },

40 "alt": {	45 "alt": {

41 "default": "json",	46 "default": "json",

42 "description": "Data format for the response.",	47 "description": "Data format for response.",

43 "enum": [	48 "enumDescriptions": [

44 "json"	49 "Responses with Content-Type of application/json",

	50 "Media download with context-dependent Content-Type",

	51 "Responses with Content-Type of application/x-protobuf"

45 ],	52 ],

46 "enumDescriptions": [	53 "location": "query",

47 "Responses with Content-Type of application/json"	54 "type": "string"

48 ],	55 },

	56 "bearer_token": {

	57 "description": "OAuth bearer token.",

	58 "location": "query",

	59 "type": "string"

	60 },

	61 "callback": {

	62 "description": "JSONP",

49 "location": "query",	63 "location": "query",

50 "type": "string"	64 "type": "string"

51 },	65 },

52 "fields": {	66 "fields": {

53 "description": "Selector specifying which fields to include in a par tial response.",	67 "description": "Selector specifying which fields to include in a par tial response.",

54 "location": "query",	68 "location": "query",

55 "type": "string"	69 "type": "string"

56 },	70 },

57 "key": {	71 "key": {

58 "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.",	72 "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.",

59 "location": "query",	73 "location": "query",

60 "type": "string"	74 "type": "string"

61 },	75 },

62 "oauth_token": {	76 "oauth_token": {

63 "description": "OAuth 2.0 token for the current user.",	77 "description": "OAuth 2.0 token for the current user.",

64 "location": "query",	78 "location": "query",

65 "type": "string"	79 "type": "string"

66 },	80 },

	81 "pp": {

	82 "default": "true",

	83 "description": "Pretty-print response.",

	84 "location": "query",

	85 "type": "boolean"

	86 },

67 "prettyPrint": {	87 "prettyPrint": {

68 "default": "true",	88 "default": "true",

69 "description": "Returns response with indentations and line breaks." ,	89 "description": "Returns response with indentations and line breaks." ,

70 "location": "query",	90 "location": "query",

71 "type": "boolean"	91 "type": "boolean"

72 },	92 },

73 "quotaUser": {	93 "quotaUser": {

74 "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. Overrides userIp if both are provided.",	94 "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.",

75 "location": "query",	95 "location": "query",

76 "type": "string"	96 "type": "string"

77 },	97 },

78 "userIp": {	98 "upload_protocol": {

79 "description": "IP address of the site where the request originates. Use this if you want to enforce per-user limits.",	99 "description": "Upload protocol for media (e.g. \"raw\", \"multipart \").",

	100 "location": "query",

	101 "type": "string"

	102 },

	103 "uploadType": {

	104 "description": "Legacy upload protocol for media (e.g. \"media\", \" multipart\").",

	105 "location": "query",

	106 "type": "string"

	107 },

	108 "$.xgafv": {

	109 "description": "V1 error format.",

	110 "enumDescriptions": [

	111 "v1 error format",

	112 "v2 error format"

	113 ],

80 "location": "query",	114 "location": "query",

81 "type": "string"	115 "type": "string"

82 }	116 }

83 },	117 },

84 "protocol": "rest",	118 "protocol": "rest",

85 "resources": {	119 "resources": {

86 "annotationSets": {	120 "datasets": {

87 "methods": {	121 "methods": {

	122 "list": {

	123 "description": "Lists datasets within a project.",

	124 "httpMethod": "GET",

	125 "id": "genomics.datasets.list",

	126 "parameters": {

	127 "projectId": {

	128 "description": "Required. The project to list datase ts for.",

	129 "location": "query",

	130 "type": "string"

	131 },

	132 "pageSize": {

	133 "description": "The maximum number of results return ed by this request. If unspecified, defaults to 50. The maximum value is 1024.",

	134 "format": "int32",

	135 "location": "query",

	136 "type": "integer"

	137 },

	138 "pageToken": {

	139 "description": "The continuation token, which is use d to page through large result sets. To get the next page of results, set this p arameter to the value of `nextPageToken` from the previous response.",

	140 "location": "query",

	141 "type": "string"

	142 }

	143 },

	144 "path": "v1/datasets",

	145 "response": {

	146 "$ref": "ListDatasetsResponse"

	147 },

	148 "scopes": [

	149 "https://www.googleapis.com/auth/cloud-platform",

	150 "https://www.googleapis.com/auth/genomics",

	151 "https://www.googleapis.com/auth/genomics.readonly"

	152 ]

	153 },

88 "create": {	154 "create": {

89 "description": "Creates a new annotation set. Caller must ha ve WRITE permission for the associated dataset.",	155 "description": "Creates a new dataset.",

90 "httpMethod": "POST",	156 "httpMethod": "POST",

91 "id": "genomics.annotationSets.create",	157 "id": "genomics.datasets.create",

92 "path": "annotationSets",	158 "path": "v1/datasets",

93 "request": {	159 "request": {

94 "$ref": "AnnotationSet"	160 "$ref": "Dataset"

95 },	161 },

96 "response": {	162 "response": {

97 "$ref": "AnnotationSet"	163 "$ref": "Dataset"

98 },	164 },

99 "scopes": [	165 "scopes": [

100 "https://www.googleapis.com/auth/cloud-platform",	166 "https://www.googleapis.com/auth/cloud-platform",

101 "https://www.googleapis.com/auth/genomics"	167 "https://www.googleapis.com/auth/genomics"

102 ]	168 ]

103 },	169 },

104 "delete": {	170 "get": {

105 "description": "Deletes an annotation set. Caller must have WRITE permission for the associated annotation set.",	171 "description": "Gets a dataset by ID.",

106 "httpMethod": "DELETE",	172 "httpMethod": "GET",

107 "id": "genomics.annotationSets.delete",	173 "id": "genomics.datasets.get",

108 "parameterOrder": [	174 "parameterOrder": [

109 "annotationSetId"	175 "datasetId"

110 ],	176 ],

111 "parameters": {	177 "parameters": {

112 "annotationSetId": {	178 "datasetId": {

113 "description": "The ID of the annotation set to be d eleted.",	179 "description": "The ID of the dataset.",

114 "location": "path",	180 "location": "path",

115 "required": true,	181 "required": true,

116 "type": "string"	182 "type": "string"

117 }	183 }

118 },	184 },

119 "path": "annotationSets/{annotationSetId}",	185 "path": "v1/datasets/{datasetId}",

120 "scopes": [

121 "https://www.googleapis.com/auth/cloud-platform",

122 "https://www.googleapis.com/auth/genomics"

123 ]

124 },

125 "get": {

126 "description": "Gets an annotation set. Caller must have REA D permission for the associated dataset.",

127 "httpMethod": "GET",

128 "id": "genomics.annotationSets.get",

129 "parameterOrder": [

130 "annotationSetId"

131 ],

132 "parameters": {

133 "annotationSetId": {

134 "description": "The ID of the annotation set to be r etrieved.",

135 "location": "path",

136 "required": true,

137 "type": "string"

138 }

139 },

140 "path": "annotationSets/{annotationSetId}",

141 "response": {	186 "response": {

142 "$ref": "AnnotationSet"	187 "$ref": "Dataset"

143 },	188 },

144 "scopes": [	189 "scopes": [

145 "https://www.googleapis.com/auth/cloud-platform",	190 "https://www.googleapis.com/auth/cloud-platform",

146 "https://www.googleapis.com/auth/genomics",	191 "https://www.googleapis.com/auth/genomics",

147 "https://www.googleapis.com/auth/genomics.readonly"	192 "https://www.googleapis.com/auth/genomics.readonly"

148 ]	193 ]

149 },	194 },

150 "patch": {	195 "patch": {

151 "description": "Updates an annotation set. The update must r espect all mutability restrictions and other invariants described on the annotat ion set resource. Caller must have WRITE permission for the associated dataset. This method supports patch semantics.",	196 "description": "Updates a dataset. This method supports patc h semantics.",

152 "httpMethod": "PATCH",	197 "httpMethod": "PATCH",

153 "id": "genomics.annotationSets.patch",	198 "id": "genomics.datasets.patch",

154 "parameterOrder": [	199 "parameterOrder": [

155 "annotationSetId"	200 "datasetId"

156 ],	201 ],

157 "parameters": {	202 "parameters": {

158 "annotationSetId": {	203 "datasetId": {

159 "description": "The ID of the annotation set to be u pdated.",	204 "description": "The ID of the dataset to be updated. ",

160 "location": "path",	205 "location": "path",

161 "required": true,	206 "required": true,

162 "type": "string"	207 "type": "string"

	208 },

	209 "updateMask": {

	210 "description": "An optional mask specifying which fi elds to update. At this time, the only mutable field is [name][google.genomics.v 1.Dataset.name]. The only acceptable value is \"name\". If unspecified, all muta ble fields will be updated.",

	211 "location": "query",

	212 "type": "string"

163 }	213 }

164 },	214 },

165 "path": "annotationSets/{annotationSetId}",	215 "path": "v1/datasets/{datasetId}",

166 "request": {	216 "request": {

167 "$ref": "AnnotationSet"	217 "$ref": "Dataset"

168 },	218 },

169 "response": {	219 "response": {

170 "$ref": "AnnotationSet"	220 "$ref": "Dataset"

171 },	221 },

172 "scopes": [	222 "scopes": [

173 "https://www.googleapis.com/auth/cloud-platform",	223 "https://www.googleapis.com/auth/cloud-platform",

174 "https://www.googleapis.com/auth/genomics"	224 "https://www.googleapis.com/auth/genomics"

175 ]	225 ]

176 },	226 },

177 "search": {	227 "delete": {

178 "description": "Searches for annotation sets that match the given criteria. Results are returned in a deterministic order. Caller must have READ permission for the queried datasets.",	228 "description": "Deletes a dataset.",

179 "httpMethod": "POST",	229 "httpMethod": "DELETE",

180 "id": "genomics.annotationSets.search",	230 "id": "genomics.datasets.delete",

181 "path": "annotationSets/search",

182 "request": {

183 "$ref": "SearchAnnotationSetsRequest"

184 },

185 "response": {

186 "$ref": "SearchAnnotationSetsResponse"

187 },

188 "scopes": [

189 "https://www.googleapis.com/auth/cloud-platform",

190 "https://www.googleapis.com/auth/genomics",

191 "https://www.googleapis.com/auth/genomics.readonly"

192 ]

193 },

194 "update": {

195 "description": "Updates an annotation set. The update must r espect all mutability restrictions and other invariants described on the annotat ion set resource. Caller must have WRITE permission for the associated dataset." ,

196 "httpMethod": "PUT",

197 "id": "genomics.annotationSets.update",

198 "parameterOrder": [	231 "parameterOrder": [

199 "annotationSetId"	232 "datasetId"

200 ],	233 ],

201 "parameters": {	234 "parameters": {

202 "annotationSetId": {	235 "datasetId": {

203 "description": "The ID of the annotation set to be u pdated.",	236 "description": "The ID of the dataset to be deleted. ",

204 "location": "path",	237 "location": "path",

205 "required": true,	238 "required": true,

206 "type": "string"	239 "type": "string"

207 }	240 }

208 },	241 },

209 "path": "annotationSets/{annotationSetId}",	242 "path": "v1/datasets/{datasetId}",

210 "request": {

211 "$ref": "AnnotationSet"

212 },

213 "response": {	243 "response": {

214 "$ref": "AnnotationSet"	244 "$ref": "Empty"

215 },	245 },

216 "scopes": [	246 "scopes": [

217 "https://www.googleapis.com/auth/cloud-platform",	247 "https://www.googleapis.com/auth/cloud-platform",

	248 "https://www.googleapis.com/auth/genomics"

	249 ]

	250 },

	251 "undelete": {

	252 "description": "Undeletes a dataset by restoring a dataset w hich was deleted via this API. This operation is only possible for a week after the deletion occurred.",

	253 "httpMethod": "POST",

	254 "id": "genomics.datasets.undelete",

	255 "parameterOrder": [

	256 "datasetId"

	257 ],

	258 "parameters": {

	259 "datasetId": {

	260 "description": "The ID of the dataset to be undelete d.",

	261 "location": "path",

	262 "required": true,

	263 "type": "string"

	264 }

	265 },

	266 "path": "v1/datasets/{datasetId}:undelete",

	267 "request": {

	268 "$ref": "UndeleteDatasetRequest"

	269 },

	270 "response": {

	271 "$ref": "Dataset"

	272 },

	273 "scopes": [

	274 "https://www.googleapis.com/auth/cloud-platform",

218 "https://www.googleapis.com/auth/genomics"	275 "https://www.googleapis.com/auth/genomics"

219 ]	276 ]

220 }	277 }

221 }	278 }

222 },	279 },

223 "annotations": {	280 "operations": {

224 "methods": {	281 "methods": {

225 "batchCreate": {	282 "get": {

226 "description": "Creates one or more new annotations atomical ly. All annotations must belong to the same annotation set. Caller must have WRI TE permission for this annotation set. For optimal performance, batch positional ly adjacent annotations together.\n\n\nIf the request has a systemic issue, such as an attempt to write to an inaccessible annotation set, the entire RPC will f ail accordingly. For lesser data issues, when possible an error will be isolated to the corresponding batch entry in the response; the remaining well formed ann otations will be created normally.",	283 "description": "Gets the latest state of a long-running oper ation. Clients can use this method to poll the operation result at intervals as recommended by the API service.",

227 "httpMethod": "POST",	284 "httpMethod": "GET",

228 "id": "genomics.annotations.batchCreate",	285 "id": "genomics.operations.get",

229 "path": "annotations:batchCreate",	286 "parameterOrder": [

230 "request": {	287 "name"

231 "$ref": "BatchCreateAnnotationsRequest"	288 ],

	289 "parameters": {

	290 "name": {

	291 "description": "The name of the operation resource." ,

	292 "location": "path",

	293 "pattern": "^operations/.*$",

	294 "required": true,

	295 "type": "string"

	296 }

232 },	297 },

	298 "path": "v1/{+name}",

233 "response": {	299 "response": {

234 "$ref": "BatchAnnotationsResponse"	300 "$ref": "Operation"

235 },	301 },

236 "scopes": [	302 "scopes": [

237 "https://www.googleapis.com/auth/cloud-platform",	303 "https://www.googleapis.com/auth/cloud-platform",

238 "https://www.googleapis.com/auth/genomics"	304 "https://www.googleapis.com/auth/genomics"

239 ]	305 ]

240 },	306 },

241 "create": {	307 "list": {

242 "description": "Creates a new annotation. Caller must have W RITE permission for the associated annotation set.",	308 "description": "Lists operations that match the specified fi lter in the request.",

	309 "httpMethod": "GET",

	310 "id": "genomics.operations.list",

	311 "parameterOrder": [

	312 "name"

	313 ],

	314 "parameters": {

	315 "name": {

	316 "description": "The name of the operation collection .",

	317 "location": "path",

	318 "pattern": "^operations$",

	319 "required": true,

	320 "type": "string"

	321 },

	322 "filter": {

	323 "description": "A string for filtering [Operations][ google.longrunning.Operation]. The following filter fields are supported: * proj ectId: Required. Corresponds to [OperationMetadata.projectId][google.genomics.v1 .OperationMetadata.project_id]. * createTime: The time this job was created, in seconds from the [epoch](http://en.wikipedia.org/wiki/Unix_time). Can use `>=` a nd/or `= 1432140000` * `projectId = my-project AND createTime >= 1432140000 AND createTime <= 1432150000 AND status = RUNNING`",

	324 "location": "query",

	325 "type": "string"

	326 },

	327 "pageSize": {

	328 "description": "The maximum number of results to ret urn. If unspecified, defaults to 256. The maximum value is 2048.",

	329 "format": "int32",

	330 "location": "query",

	331 "type": "integer"

	332 },

	333 "pageToken": {

	334 "description": "The standard list page token.",

	335 "location": "query",

	336 "type": "string"

	337 }

	338 },

	339 "path": "v1/{+name}",

	340 "response": {

	341 "$ref": "ListOperationsResponse"

	342 },

	343 "scopes": [

	344 "https://www.googleapis.com/auth/cloud-platform",

	345 "https://www.googleapis.com/auth/genomics"

	346 ]

	347 },

	348 "cancel": {

	349 "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][google.longru nning.Operations.GetOperation] or [Operations.ListOperations][google.longrunning .Operations.ListOperations] to check whether the cancellation succeeded or the o peration completed despite cancellation.",

243 "httpMethod": "POST",	350 "httpMethod": "POST",

244 "id": "genomics.annotations.create",	351 "id": "genomics.operations.cancel",

245 "path": "annotations",	352 "parameterOrder": [

	353 "name"

	354 ],

	355 "parameters": {

	356 "name": {

	357 "description": "The name of the operation resource t o be cancelled.",

	358 "location": "path",

	359 "pattern": "^operations/.*$",

	360 "required": true,

	361 "type": "string"

	362 }

	363 },

	364 "path": "v1/{+name}:cancel",

246 "request": {	365 "request": {

247 "$ref": "Annotation"	366 "$ref": "CancelOperationRequest"

248 },	367 },

249 "response": {	368 "response": {

250 "$ref": "Annotation"	369 "$ref": "Empty"

251 },	370 },

252 "scopes": [	371 "scopes": [

253 "https://www.googleapis.com/auth/cloud-platform",	372 "https://www.googleapis.com/auth/cloud-platform",

254 "https://www.googleapis.com/auth/genomics"	373 "https://www.googleapis.com/auth/genomics"

255 ]	374 ]

256 },	375 },

257 "delete": {	376 "delete": {

258 "description": "Deletes an annotation. Caller must have WRIT E permission for the associated annotation set.",	377 "description": "This method is not implemented. To cancel an operation, please use [Operations.CancelOperation][google.longrunning.Operation s.CancelOperation].",

259 "httpMethod": "DELETE",	378 "httpMethod": "DELETE",

260 "id": "genomics.annotations.delete",	379 "id": "genomics.operations.delete",

261 "parameterOrder": [	380 "parameterOrder": [

262 "annotationId"	381 "name"

263 ],	382 ],

264 "parameters": {	383 "parameters": {

265 "annotationId": {	384 "name": {

266 "description": "The ID of the annotation set to be d eleted.",	385 "description": "The name of the operation resource t o be deleted.",

	386 "location": "path",

	387 "pattern": "^operations/.*$",

	388 "required": true,

	389 "type": "string"

	390 }

	391 },

	392 "path": "v1/{+name}",

	393 "response": {

	394 "$ref": "Empty"

	395 },

	396 "scopes": [

	397 "https://www.googleapis.com/auth/cloud-platform",

	398 "https://www.googleapis.com/auth/genomics"

	399 ]

	400 }

	401 }

	402 },

	403 "readgroupsets": {

	404 "methods": {

	405 "import": {

	406 "description": "Creates read group sets by asynchronously im porting the provided information. Note that currently comments in the input file header are not imported and some custom tags will be converted to strings, rather than preserving tag types. The caller must have WRITE permissions to the dataset.",

	407 "httpMethod": "POST",

	408 "id": "genomics.readgroupsets.import",

	409 "path": "v1/readgroupsets:import",

	410 "request": {

	411 "$ref": "ImportReadGroupSetsRequest"

	412 },

	413 "response": {

	414 "$ref": "Operation"

	415 },

	416 "scopes": [

	417 "https://www.googleapis.com/auth/cloud-platform",

	418 "https://www.googleapis.com/auth/devstorage.read_write",

	419 "https://www.googleapis.com/auth/genomics"

	420 ]

	421 },

	422 "export": {

	423 "description": "Exports a read group set to a BAM file in Go ogle Cloud Storage. Note that currently there may be some differences between ex ported BAM files and the original BAM file at the time of import. In particular, comments in the input file header will not be preserved, some custom tags will be converted to strings, and original reference sequence order is not necessaril y preserved.",

	424 "httpMethod": "POST",

	425 "id": "genomics.readgroupsets.export",

	426 "parameterOrder": [

	427 "readGroupSetId"

	428 ],

	429 "parameters": {

	430 "readGroupSetId": {

	431 "description": "Required. The ID of the read group s et to export.",

267 "location": "path",	432 "location": "path",

268 "required": true,	433 "required": true,

269 "type": "string"	434 "type": "string"

270 }	435 }

271 },	436 },

272 "path": "annotations/{annotationId}",	437 "path": "v1/readgroupsets/{readGroupSetId}:export",

273 "scopes": [	438 "request": {

274 "https://www.googleapis.com/auth/cloud-platform",	439 "$ref": "ExportReadGroupSetRequest"

275 "https://www.googleapis.com/auth/genomics"

276 ]

277 },

278 "get": {

279 "description": "Gets an annotation. Caller must have READ pe rmission for the associated annotation set.",

280 "httpMethod": "GET",

281 "id": "genomics.annotations.get",

282 "parameterOrder": [

283 "annotationId"

284 ],

285 "parameters": {

286 "annotationId": {

287 "description": "The ID of the annotation set to be r etrieved.",

288 "location": "path",

289 "required": true,

290 "type": "string"

291 }

292 },	440 },

293 "path": "annotations/{annotationId}",

294 "response": {	441 "response": {

295 "$ref": "Annotation"	442 "$ref": "Operation"

296 },	443 },

297 "scopes": [	444 "scopes": [

298 "https://www.googleapis.com/auth/cloud-platform",	445 "https://www.googleapis.com/auth/cloud-platform",

299 "https://www.googleapis.com/auth/genomics",	446 "https://www.googleapis.com/auth/devstorage.read_write",

300 "https://www.googleapis.com/auth/genomics.readonly"

301 ]

302 },

303 "patch": {

304 "description": "Updates an annotation. The update must respe ct all mutability restrictions and other invariants described on the annotation resource. Caller must have WRITE permission for the associated dataset. This met hod supports patch semantics.",

305 "httpMethod": "PATCH",

306 "id": "genomics.annotations.patch",

307 "parameterOrder": [

308 "annotationId"

309 ],

310 "parameters": {

311 "annotationId": {

312 "description": "The ID of the annotation set to be u pdated.",

313 "location": "path",

314 "required": true,

315 "type": "string"

316 }

317 },

318 "path": "annotations/{annotationId}",

319 "request": {

320 "$ref": "Annotation"

321 },

322 "response": {

323 "$ref": "Annotation"

324 },

325 "scopes": [

326 "https://www.googleapis.com/auth/cloud-platform",

327 "https://www.googleapis.com/auth/genomics"	447 "https://www.googleapis.com/auth/genomics"

328 ]	448 ]

329 },	449 },

330 "search": {	450 "search": {

331 "description": "Searches for annotations that match the give n criteria. Results are returned ordered by start position. Annotations that hav e matching start positions are ordered deterministically. Caller must have READ permission for the queried annotation sets.",	451 "description": "Searches for read group sets matching the cr iteria. Implements [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga 4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135).",

332 "httpMethod": "POST",	452 "httpMethod": "POST",

333 "id": "genomics.annotations.search",	453 "id": "genomics.readgroupsets.search",

334 "path": "annotations/search",	454 "path": "v1/readgroupsets/search",

335 "request": {	455 "request": {

336 "$ref": "SearchAnnotationsRequest"	456 "$ref": "SearchReadGroupSetsRequest"

337 },	457 },

338 "response": {	458 "response": {

339 "$ref": "SearchAnnotationsResponse"	459 "$ref": "SearchReadGroupSetsResponse"

340 },	460 },

341 "scopes": [	461 "scopes": [

342 "https://www.googleapis.com/auth/cloud-platform",	462 "https://www.googleapis.com/auth/cloud-platform",

343 "https://www.googleapis.com/auth/genomics",	463 "https://www.googleapis.com/auth/genomics",

344 "https://www.googleapis.com/auth/genomics.readonly"	464 "https://www.googleapis.com/auth/genomics.readonly"

345 ]	465 ]

346 },	466 },

347 "update": {	467 "patch": {

348 "description": "Updates an annotation. The update must respe ct all mutability restrictions and other invariants described on the annotation resource. Caller must have WRITE permission for the associated dataset.",	468 "description": "Updates a read group set. This method suppor ts patch semantics.",

349 "httpMethod": "PUT",	469 "httpMethod": "PATCH",

350 "id": "genomics.annotations.update",	470 "id": "genomics.readgroupsets.patch",

351 "parameterOrder": [	471 "parameterOrder": [

352 "annotationId"	472 "readGroupSetId"

353 ],	473 ],

354 "parameters": {	474 "parameters": {

355 "annotationId": {	475 "readGroupSetId": {

356 "description": "The ID of the annotation set to be u pdated.",	476 "description": "The ID of the read group set to be u pdated. The caller must have WRITE permissions to the dataset associated with th is read group set.",

357 "location": "path",	477 "location": "path",

358 "required": true,	478 "required": true,

359 "type": "string"	479 "type": "string"

	480 },

	481 "updateMask": {

	482 "description": "An optional mask specifying which fi elds to update. At this time, mutable fields are [referenceSetId][google.genomic s.v1.ReadGroupSet.reference_set_id] and [name][google.genomics.v1.ReadGroupSet.n ame]. Acceptable values are \"referenceSetId\" and \"name\". If unspecified, all mutable fields will be updated.",

	483 "location": "query",

	484 "type": "string"

360 }	485 }

361 },	486 },

362 "path": "annotations/{annotationId}",	487 "path": "v1/readgroupsets/{readGroupSetId}",

363 "request": {	488 "request": {

364 "$ref": "Annotation"	489 "$ref": "ReadGroupSet"

365 },	490 },

366 "response": {	491 "response": {

367 "$ref": "Annotation"	492 "$ref": "ReadGroupSet"

368 },	493 },

369 "scopes": [	494 "scopes": [

370 "https://www.googleapis.com/auth/cloud-platform",	495 "https://www.googleapis.com/auth/cloud-platform",

371 "https://www.googleapis.com/auth/genomics"

372 ]

373 }

374 }

375 },

376 "callsets": {

377 "methods": {

378 "create": {

379 "description": "Creates a new call set.",

380 "httpMethod": "POST",

381 "id": "genomics.callsets.create",

382 "path": "callsets",

383 "request": {

384 "$ref": "CallSet"

385 },

386 "response": {

387 "$ref": "CallSet"

388 },

389 "scopes": [

390 "https://www.googleapis.com/auth/cloud-platform",

391 "https://www.googleapis.com/auth/genomics"	496 "https://www.googleapis.com/auth/genomics"

392 ]	497 ]

393 },	498 },

394 "delete": {	499 "delete": {

395 "description": "Deletes a call set.",	500 "description": "Deletes a read group set.",

396 "httpMethod": "DELETE",	501 "httpMethod": "DELETE",

397 "id": "genomics.callsets.delete",	502 "id": "genomics.readgroupsets.delete",

398 "parameterOrder": [	503 "parameterOrder": [

399 "callSetId"	504 "readGroupSetId"

400 ],	505 ],

401 "parameters": {	506 "parameters": {

402 "callSetId": {	507 "readGroupSetId": {

403 "description": "The ID of the call set to be deleted .",	508 "description": "The ID of the read group set to be d eleted. The caller must have WRITE permissions to the dataset associated with th is read group set.",

404 "location": "path",	509 "location": "path",

405 "required": true,	510 "required": true,

406 "type": "string"	511 "type": "string"

407 }	512 }

408 },	513 },

409 "path": "callsets/{callSetId}",	514 "path": "v1/readgroupsets/{readGroupSetId}",

	515 "response": {

	516 "$ref": "Empty"

	517 },

410 "scopes": [	518 "scopes": [

411 "https://www.googleapis.com/auth/cloud-platform",	519 "https://www.googleapis.com/auth/cloud-platform",

412 "https://www.googleapis.com/auth/genomics"	520 "https://www.googleapis.com/auth/genomics"

413 ]	521 ]

414 },	522 },

415 "get": {	523 "get": {

416 "description": "Gets a call set by ID.",	524 "description": "Gets a read group set by ID.",

417 "httpMethod": "GET",	525 "httpMethod": "GET",

418 "id": "genomics.callsets.get",	526 "id": "genomics.readgroupsets.get",

419 "parameterOrder": [	527 "parameterOrder": [

420 "callSetId"	528 "readGroupSetId"

421 ],	529 ],

422 "parameters": {	530 "parameters": {

423 "callSetId": {	531 "readGroupSetId": {

424 "description": "The ID of the call set.",	532 "description": "The ID of the read group set.",

425 "location": "path",	533 "location": "path",

426 "required": true,	534 "required": true,

427 "type": "string"	535 "type": "string"

428 }	536 }

429 },	537 },

430 "path": "callsets/{callSetId}",	538 "path": "v1/readgroupsets/{readGroupSetId}",

431 "response": {	539 "response": {

432 "$ref": "CallSet"	540 "$ref": "ReadGroupSet"

433 },	541 },

434 "scopes": [	542 "scopes": [

435 "https://www.googleapis.com/auth/cloud-platform",	543 "https://www.googleapis.com/auth/cloud-platform",

436 "https://www.googleapis.com/auth/genomics",	544 "https://www.googleapis.com/auth/genomics",

437 "https://www.googleapis.com/auth/genomics.readonly"	545 "https://www.googleapis.com/auth/genomics.readonly"

438 ]	546 ]

439 },	547 }

440 "patch": {	548 },

441 "description": "Updates a call set. This method supports pat ch semantics.",	549 "resources": {

442 "httpMethod": "PATCH",	550 "coveragebuckets": {

443 "id": "genomics.callsets.patch",	551 "methods": {

444 "parameterOrder": [	552 "list": {

445 "callSetId"	553 "description": "Lists fixed width coverage buckets f or a read group set, each of which correspond to a range of a reference sequence . Each bucket summarizes coverage information across its corresponding genomic r ange. Coverage is defined as the number of reads which are aligned to a given ba se in the reference sequence. Coverage buckets are available at several precompu ted bucket widths, enabling retrieval of various coverage 'zoom levels'. The cal ler must have READ permissions for the target read group set.",

446 ],	554 "httpMethod": "GET",

447 "parameters": {	555 "id": "genomics.readgroupsets.coveragebuckets.list",

448 "callSetId": {	556 "parameterOrder": [

449 "description": "The ID of the call set to be updated .",	557 "readGroupSetId"

450 "location": "path",	558 ],

451 "required": true,	559 "parameters": {

452 "type": "string"	560 "readGroupSetId": {

	561 "description": "Required. The ID of the read group set over which coverage is requested.",

	562 "location": "path",

	563 "required": true,

	564 "type": "string"

	565 },

	566 "referenceName": {

	567 "description": "The name of the reference to query, within the reference set associated with this query. Optional.",

	568 "location": "query",

	569 "type": "string"

	570 },

	571 "start": {

	572 "description": "The start position of the ra nge on the reference, 0-based inclusive. If specified, `referenceName` must also be specified. Defaults to 0.",

	573 "format": "int64",

	574 "location": "query",

	575 "type": "string"

	576 },

	577 "end": {

	578 "description": "The end position of the rang e on the reference, 0-based exclusive. If specified, `referenceName` must also b e specified. If unset or 0, defaults to the length of the reference.",

	579 "format": "int64",

	580 "location": "query",

	581 "type": "string"

	582 },

	583 "targetBucketWidth": {

	584 "description": "The desired width of each re ported coverage bucket in base pairs. This will be rounded down to the nearest p recomputed bucket width; the value of which is returned as `bucketWidth` in the response. Defaults to infinity (each bucket spans an entire reference sequence) or the length of the target range, if specified. The smallest precomputed `bucke tWidth` is currently 2048 base pairs; this is subject to change.",

	585 "format": "int64",

	586 "location": "query",

	587 "type": "string"

	588 },

	589 "pageToken": {

	590 "description": "The continuation token, whic h is used to page through large result sets. To get the next page of results, se t this parameter to the value of `nextPageToken` from the previous response.",

	591 "location": "query",

	592 "type": "string"

	593 },

	594 "pageSize": {

	595 "description": "The maximum number of result s to return in a single page. If unspecified, defaults to 1024. The maximum valu e is 2048.",

	596 "format": "int32",

	597 "location": "query",

	598 "type": "integer"

	599 }

	600 },

	601 "path": "v1/readgroupsets/{readGroupSetId}/coverageb uckets",

	602 "response": {

	603 "$ref": "ListCoverageBucketsResponse"

	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.readon ly"

	609 ]

453 }	610 }

454 },	611 }

455 "path": "callsets/{callSetId}",	612 }

	613 }

	614 },

	615 "reads": {

	616 "methods": {

	617 "search": {

	618 "description": "Gets a list of reads for one or more read gr oup sets. Reads search operates over a genomic coordinate space of reference seq uence & position defined over the reference sequences to which the requested rea d group sets are aligned. If a target positional range is specified, search retu rns all reads whose alignment to the reference genome overlap the range. A query which specifies only read group set IDs yields all reads in those read group se ts, including unmapped reads. All reads returned (including reads on subsequent pages) are ordered by genomic coordinate (reference sequence & position). Reads with equivalent genomic coordinates are returned in a deterministic order. Imple ments [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5 .1/src/main/resources/avro/readmethods.avdl#L85).",

	619 "httpMethod": "POST",

	620 "id": "genomics.reads.search",

	621 "path": "v1/reads/search",

456 "request": {	622 "request": {

457 "$ref": "CallSet"	623 "$ref": "SearchReadsRequest"

458 },	624 },

459 "response": {	625 "response": {

460 "$ref": "CallSet"	626 "$ref": "SearchReadsResponse"

461 },	627 },

462 "scopes": [	628 "scopes": [

463 "https://www.googleapis.com/auth/cloud-platform",	629 "https://www.googleapis.com/auth/cloud-platform",

464 "https://www.googleapis.com/auth/genomics"	630 "https://www.googleapis.com/auth/genomics",

	631 "https://www.googleapis.com/auth/genomics.readonly"

465 ]	632 ]

466 },	633 }

	634 }

	635 },

	636 "referencesets": {

	637 "methods": {

467 "search": {	638 "search": {

468 "description": "Gets a list of call sets matching the criter ia.\n\nImplements GlobalAllianceApi.searchCallSets.",	639 "description": "Searches for reference sets which match the given criteria. Implements [GlobalAllianceApi.searchReferenceSets](http://ga4gh. org/documentation/api/v0.5.1/ga4gh_api.html#/schema/org.ga4gh.searchReferenceSet s).",

469 "httpMethod": "POST",	640 "httpMethod": "POST",

470 "id": "genomics.callsets.search",	641 "id": "genomics.referencesets.search",

471 "path": "callsets/search",	642 "path": "v1/referencesets/search",

472 "request": {	643 "request": {

473 "$ref": "SearchCallSetsRequest"	644 "$ref": "SearchReferenceSetsRequest"

474 },	645 },

475 "response": {	646 "response": {

476 "$ref": "SearchCallSetsResponse"	647 "$ref": "SearchReferenceSetsResponse"

477 },	648 },

478 "scopes": [	649 "scopes": [

479 "https://www.googleapis.com/auth/cloud-platform",	650 "https://www.googleapis.com/auth/cloud-platform",

480 "https://www.googleapis.com/auth/genomics",	651 "https://www.googleapis.com/auth/genomics",

481 "https://www.googleapis.com/auth/genomics.readonly"	652 "https://www.googleapis.com/auth/genomics.readonly"

482 ]	653 ]

483 },	654 },

484 "update": {	655 "get": {

485 "description": "Updates a call set.",	656 "description": "Gets a reference set. Implements [GlobalAlli anceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/r esources/avro/referencemethods.avdl#L83).",

486 "httpMethod": "PUT",	657 "httpMethod": "GET",

487 "id": "genomics.callsets.update",	658 "id": "genomics.referencesets.get",

488 "parameterOrder": [	659 "parameterOrder": [

489 "callSetId"	660 "referenceSetId"

490 ],	661 ],

491 "parameters": {	662 "parameters": {

492 "callSetId": {	663 "referenceSetId": {

493 "description": "The ID of the call set to be updated .",	664 "description": "The ID of the reference set.",

494 "location": "path",	665 "location": "path",

495 "required": true,	666 "required": true,

496 "type": "string"	667 "type": "string"

497 }	668 }

498 },	669 },

499 "path": "callsets/{callSetId}",	670 "path": "v1/referencesets/{referenceSetId}",

500 "request": {

501 "$ref": "CallSet"

502 },

503 "response": {	671 "response": {

504 "$ref": "CallSet"	672 "$ref": "ReferenceSet"

505 },	673 },

506 "scopes": [	674 "scopes": [

507 "https://www.googleapis.com/auth/cloud-platform",	675 "https://www.googleapis.com/auth/cloud-platform",

508 "https://www.googleapis.com/auth/genomics"	676 "https://www.googleapis.com/auth/genomics",

	677 "https://www.googleapis.com/auth/genomics.readonly"

509 ]	678 ]

510 }	679 }

511 }	680 }

512 },	681 },

513 "datasets": {	682 "references": {

514 "methods": {	683 "methods": {

515 "create": {	684 "search": {

516 "description": "Creates a new dataset.",	685 "description": "Searches for references which match the give n criteria. Implements [GlobalAllianceApi.searchReferences](https://github.com/g a4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L146).",

517 "httpMethod": "POST",	686 "httpMethod": "POST",

518 "id": "genomics.datasets.create",	687 "id": "genomics.references.search",

519 "path": "datasets",	688 "path": "v1/references/search",

520 "request": {	689 "request": {

521 "$ref": "Dataset"	690 "$ref": "SearchReferencesRequest"

522 },	691 },

523 "response": {	692 "response": {

524 "$ref": "Dataset"	693 "$ref": "SearchReferencesResponse"

525 },	694 },

526 "scopes": [	695 "scopes": [

527 "https://www.googleapis.com/auth/cloud-platform",	696 "https://www.googleapis.com/auth/cloud-platform",

528 "https://www.googleapis.com/auth/genomics"	697 "https://www.googleapis.com/auth/genomics",

	698 "https://www.googleapis.com/auth/genomics.readonly"

529 ]	699 ]

530 },	700 },

531 "delete": {	701 "get": {

532 "description": "Deletes a dataset.",	702 "description": "Gets a reference. Implements [GlobalAlliance Api.getReference](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resource s/avro/referencemethods.avdl#L158).",

533 "httpMethod": "DELETE",	703 "httpMethod": "GET",

534 "id": "genomics.datasets.delete",	704 "id": "genomics.references.get",

535 "parameterOrder": [	705 "parameterOrder": [

536 "datasetId"	706 "referenceId"

537 ],	707 ],

538 "parameters": {	708 "parameters": {

539 "datasetId": {	709 "referenceId": {

540 "description": "The ID of the dataset to be deleted. ",	710 "description": "The ID of the reference.",

541 "location": "path",	711 "location": "path",

542 "required": true,	712 "required": true,

543 "type": "string"	713 "type": "string"

544 }	714 }

545 },	715 },

546 "path": "datasets/{datasetId}",	716 "path": "v1/references/{referenceId}",

	717 "response": {

	718 "$ref": "Reference"

	719 },

547 "scopes": [	720 "scopes": [

548 "https://www.googleapis.com/auth/cloud-platform",	721 "https://www.googleapis.com/auth/cloud-platform",

	722 "https://www.googleapis.com/auth/genomics",

	723 "https://www.googleapis.com/auth/genomics.readonly"

	724 ]

	725 }

	726 },

	727 "resources": {

	728 "bases": {

	729 "methods": {

	730 "list": {

	731 "description": "Lists the bases in a reference, opti onally restricted to a range. Implements [GlobalAllianceApi.getReferenceBases](h ttps://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemet hods.avdl#L221).",

	732 "httpMethod": "GET",

	733 "id": "genomics.references.bases.list",

	734 "parameterOrder": [

	735 "referenceId"

	736 ],

	737 "parameters": {

	738 "referenceId": {

	739 "description": "The ID of the reference.",

	740 "location": "path",

	741 "required": true,

	742 "type": "string"

	743 },

	744 "start": {

	745 "description": "The start position (0-based) of this query. Defaults to 0.",

	746 "format": "int64",

	747 "location": "query",

	748 "type": "string"

	749 },

	750 "end": {

	751 "description": "The end position (0-based, e xclusive) of this query. Defaults to the length of this reference.",

	752 "format": "int64",

	753 "location": "query",

	754 "type": "string"

	755 },

	756 "pageToken": {

	757 "description": "The continuation token, whic h is used to page through large result sets. To get the next page of results, se t this parameter to the value of `nextPageToken` from the previous response.",

	758 "location": "query",

	759 "type": "string"

	760 },

	761 "pageSize": {

	762 "description": "Specifies the maximum number of bases to return in a single page.",

	763 "format": "int32",

	764 "location": "query",

	765 "type": "integer"

	766 }

	767 },

	768 "path": "v1/references/{referenceId}/bases",

	769 "response": {

	770 "$ref": "ListBasesResponse"

	771 },

	772 "scopes": [

	773 "https://www.googleapis.com/auth/cloud-platform" ,

	774 "https://www.googleapis.com/auth/genomics",

	775 "https://www.googleapis.com/auth/genomics.readon ly"

	776 ]

	777 }

	778 }

	779 }

	780 }

	781 },

	782 "variants": {

	783 "methods": {

	784 "import": {

	785 "description": "Creates variant data by asynchronously impor ting the provided information. The variants for import will be merged with any e xisting data and each other according to the behavior of mergeVariants. In parti cular, this means for merged VCF variants that have conflicting INFO fields, som e data will be arbitrarily discarded. As a special case, for single-sample VCF f iles, QUAL and FILTER fields will be moved to the call level; these are sometime s interpreted in a call-specific context. Imported VCF headers are appended to t he metadata already in a variant set.",

	786 "httpMethod": "POST",

	787 "id": "genomics.variants.import",

	788 "path": "v1/variants:import",

	789 "request": {

	790 "$ref": "ImportVariantsRequest"

	791 },

	792 "response": {

	793 "$ref": "Operation"

	794 },

	795 "scopes": [

	796 "https://www.googleapis.com/auth/cloud-platform",

	797 "https://www.googleapis.com/auth/devstorage.read_write",

549 "https://www.googleapis.com/auth/genomics"	798 "https://www.googleapis.com/auth/genomics"

550 ]	799 ]

551 },	800 },

552 "get": {	801 "search": {

553 "description": "Gets a dataset by ID.",	802 "description": "Gets a list of variants matching the criteri a. Implements [GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schema s/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L126).",

554 "httpMethod": "GET",	803 "httpMethod": "POST",

555 "id": "genomics.datasets.get",	804 "id": "genomics.variants.search",

556 "parameterOrder": [	805 "path": "v1/variants/search",

557 "datasetId"	806 "request": {

558 ],	807 "$ref": "SearchVariantsRequest"

559 "parameters": {

560 "datasetId": {

561 "description": "The ID of the dataset.",

562 "location": "path",

563 "required": true,

564 "type": "string"

565 }

566 },	808 },

567 "path": "datasets/{datasetId}",

568 "response": {	809 "response": {

569 "$ref": "Dataset"	810 "$ref": "SearchVariantsResponse"

570 },	811 },

571 "scopes": [	812 "scopes": [

572 "https://www.googleapis.com/auth/cloud-platform",	813 "https://www.googleapis.com/auth/cloud-platform",

573 "https://www.googleapis.com/auth/genomics",	814 "https://www.googleapis.com/auth/genomics",

574 "https://www.googleapis.com/auth/genomics.readonly"	815 "https://www.googleapis.com/auth/genomics.readonly"

575 ]	816 ]

576 },	817 },

577 "list": {	818 "create": {

578 "description": "Lists datasets within a project.",	819 "description": "Creates a new variant.",

579 "httpMethod": "GET",	820 "httpMethod": "POST",

580 "id": "genomics.datasets.list",	821 "id": "genomics.variants.create",

	822 "path": "v1/variants",

	823 "request": {

	824 "$ref": "Variant"

	825 },

	826 "response": {

	827 "$ref": "Variant"

	828 },

	829 "scopes": [

	830 "https://www.googleapis.com/auth/cloud-platform",

	831 "https://www.googleapis.com/auth/genomics"

	832 ]

	833 },

	834 "patch": {

	835 "description": "Updates a variant. This method supports patc h semantics. Returns the modified variant without its calls.",

	836 "httpMethod": "PATCH",

	837 "id": "genomics.variants.patch",

	838 "parameterOrder": [

	839 "variantId"

	840 ],

581 "parameters": {	841 "parameters": {

582 "pageSize": {	842 "variantId": {

583 "description": "The maximum number of results return ed by this request. If unspecified, defaults to 50.",	843 "description": "The ID of the variant to be updated. ",

584 "format": "int32",	844 "location": "path",

585 "location": "query",	845 "required": true,

586 "type": "integer"

587 },

588 "pageToken": {

589 "description": "The continuation token, which is use d to page through large result sets. To get the next page of results, set this p arameter to the value of nextPageToken from the previous response.",

590 "location": "query",

591 "type": "string"	846 "type": "string"

592 },	847 },

593 "projectNumber": {	848 "updateMask": {

594 "description": "Required. The project to list datase ts for.",	849 "description": "An optional mask specifying which fi elds to update. At this time, mutable fields are [names][google.genomics.v1.Vari ant.names] and [info][google.genomics.v1.Variant.info]. Acceptable values are \" names\" and \"info\". If unspecified, all mutable fields will be updated.",

595 "format": "int64",

596 "location": "query",	850 "location": "query",

597 "type": "string"	851 "type": "string"

598 }	852 }

599 },	853 },

600 "path": "datasets",	854 "path": "v1/variants/{variantId}",

	855 "request": {

	856 "$ref": "Variant"

	857 },

601 "response": {	858 "response": {

602 "$ref": "ListDatasetsResponse"	859 "$ref": "Variant"

	860 },

	861 "scopes": [

	862 "https://www.googleapis.com/auth/cloud-platform",

	863 "https://www.googleapis.com/auth/genomics"

	864 ]

	865 },

	866 "delete": {

	867 "description": "Deletes a variant.",

	868 "httpMethod": "DELETE",

	869 "id": "genomics.variants.delete",

	870 "parameterOrder": [

	871 "variantId"

	872 ],

	873 "parameters": {

	874 "variantId": {

	875 "description": "The ID of the variant to be deleted. ",

	876 "location": "path",

	877 "required": true,

	878 "type": "string"

	879 }

	880 },

	881 "path": "v1/variants/{variantId}",

	882 "response": {

	883 "$ref": "Empty"

	884 },

	885 "scopes": [

	886 "https://www.googleapis.com/auth/cloud-platform",

	887 "https://www.googleapis.com/auth/genomics"

	888 ]

	889 },

	890 "get": {

	891 "description": "Gets a variant by ID.",

	892 "httpMethod": "GET",

	893 "id": "genomics.variants.get",

	894 "parameterOrder": [

	895 "variantId"

	896 ],

	897 "parameters": {

	898 "variantId": {

	899 "description": "The ID of the variant.",

	900 "location": "path",

	901 "required": true,

	902 "type": "string"

	903 }

	904 },

	905 "path": "v1/variants/{variantId}",

	906 "response": {

	907 "$ref": "Variant"

603 },	908 },

604 "scopes": [	909 "scopes": [

605 "https://www.googleapis.com/auth/cloud-platform",	910 "https://www.googleapis.com/auth/cloud-platform",

606 "https://www.googleapis.com/auth/genomics",	911 "https://www.googleapis.com/auth/genomics",

607 "https://www.googleapis.com/auth/genomics.readonly"	912 "https://www.googleapis.com/auth/genomics.readonly"

608 ]	913 ]

609 },	914 }

610 "patch": {	915 }

611 "description": "Updates a dataset. This method supports patc h semantics.",	916 },

612 "httpMethod": "PATCH",	917 "variantsets": {

613 "id": "genomics.datasets.patch",	918 "methods": {

614 "parameterOrder": [	919 "create": {

615 "datasetId"	920 "description": "Creates a new variant set.",

616 ],	921 "httpMethod": "POST",

617 "parameters": {	922 "id": "genomics.variantsets.create",

618 "datasetId": {	923 "path": "v1/variantsets",

619 "description": "The ID of the dataset to be updated. ",

620 "location": "path",

621 "required": true,

622 "type": "string"

623 }

624 },

625 "path": "datasets/{datasetId}",

626 "request": {	924 "request": {

627 "$ref": "Dataset"	925 "$ref": "VariantSet"

628 },	926 },

629 "response": {	927 "response": {

630 "$ref": "Dataset"	928 "$ref": "VariantSet"

631 },	929 },

632 "scopes": [	930 "scopes": [

633 "https://www.googleapis.com/auth/cloud-platform",	931 "https://www.googleapis.com/auth/cloud-platform",

634 "https://www.googleapis.com/auth/genomics"	932 "https://www.googleapis.com/auth/genomics"

635 ]	933 ]

636 },	934 },

637 "undelete": {	935 "export": {

638 "description": "Undeletes a dataset by restoring a dataset w hich was deleted via this API. This operation is only possible for a week after the deletion occurred.",	936 "description": "Exports variant set data to an external dest ination.",

639 "httpMethod": "POST",	937 "httpMethod": "POST",

640 "id": "genomics.datasets.undelete",	938 "id": "genomics.variantsets.export",

641 "parameterOrder": [	939 "parameterOrder": [

642 "datasetId"	940 "variantSetId"

643 ],	941 ],

644 "parameters": {	942 "parameters": {

645 "datasetId": {	943 "variantSetId": {

646 "description": "The ID of the dataset to be undelete d.",	944 "description": "Required. The ID of the variant set that contains variant data which should be exported. The caller must have READ a ccess to this variant set.",

647 "location": "path",	945 "location": "path",

648 "required": true,	946 "required": true,

649 "type": "string"	947 "type": "string"

650 }	948 }

651 },	949 },

652 "path": "datasets/{datasetId}/undelete",	950 "path": "v1/variantsets/{variantSetId}:export",

	951 "request": {

	952 "$ref": "ExportVariantSetRequest"

	953 },

653 "response": {	954 "response": {

654 "$ref": "Dataset"	955 "$ref": "Operation"

655 },	956 },

656 "scopes": [	957 "scopes": [

	958 "https://www.googleapis.com/auth/bigquery",

657 "https://www.googleapis.com/auth/cloud-platform",	959 "https://www.googleapis.com/auth/cloud-platform",

658 "https://www.googleapis.com/auth/genomics"	960 "https://www.googleapis.com/auth/genomics"

659 ]	961 ]

660 },	962 },

661 "update": {	963 "get": {

662 "description": "Updates a dataset.",	964 "description": "Gets a variant set by ID.",

663 "httpMethod": "PUT",	965 "httpMethod": "GET",

664 "id": "genomics.datasets.update",	966 "id": "genomics.variantsets.get",

665 "parameterOrder": [	967 "parameterOrder": [

666 "datasetId"	968 "variantSetId"

667 ],	969 ],

668 "parameters": {	970 "parameters": {

669 "datasetId": {	971 "variantSetId": {

670 "description": "The ID of the dataset to be updated. ",	972 "description": "Required. The ID of the variant set. ",

671 "location": "path",	973 "location": "path",

672 "required": true,	974 "required": true,

673 "type": "string"	975 "type": "string"

674 }	976 }

675 },	977 },

676 "path": "datasets/{datasetId}",	978 "path": "v1/variantsets/{variantSetId}",

677 "request": {

678 "$ref": "Dataset"

679 },

680 "response": {	979 "response": {

681 "$ref": "Dataset"	980 "$ref": "VariantSet"

682 },	981 },

683 "scopes": [	982 "scopes": [

684 "https://www.googleapis.com/auth/cloud-platform",	983 "https://www.googleapis.com/auth/cloud-platform",

685 "https://www.googleapis.com/auth/genomics"

686 ]

687 }

688 }

689 },

690 "experimental": {

691 "resources": {

692 "jobs": {

693 "methods": {

694 "create": {

695 "description": "Creates and asynchronously runs an a d-hoc job. This is an experimental call and may be removed or changed at any tim e.",

696 "httpMethod": "POST",

697 "id": "genomics.experimental.jobs.create",

698 "path": "experimental/jobs/create",

699 "request": {

700 "$ref": "ExperimentalCreateJobRequest"

701 },

702 "response": {

703 "$ref": "ExperimentalCreateJobResponse"

704 },

705 "scopes": [

706 "https://www.googleapis.com/auth/cloud-platform" ,

707 "https://www.googleapis.com/auth/devstorage.read _write",

708 "https://www.googleapis.com/auth/genomics"

709 ]

710 }

711 }

712 }

713 }

714 },

715 "jobs": {

716 "methods": {

717 "cancel": {

718 "description": "Cancels a job by ID. Note that it is possibl e for partial results to be generated and stored for cancelled jobs.",

719 "httpMethod": "POST",

720 "id": "genomics.jobs.cancel",

721 "parameterOrder": [

722 "jobId"

723 ],

724 "parameters": {

725 "jobId": {

726 "description": "Required. The ID of the job.",

727 "location": "path",

728 "required": true,

729 "type": "string"

730 }

731 },

732 "path": "jobs/{jobId}/cancel",

733 "scopes": [

734 "https://www.googleapis.com/auth/cloud-platform",

735 "https://www.googleapis.com/auth/genomics"

736 ]

737 },

738 "get": {

739 "description": "Gets a job by ID.",

740 "httpMethod": "GET",

741 "id": "genomics.jobs.get",

742 "parameterOrder": [

743 "jobId"

744 ],

745 "parameters": {

746 "jobId": {

747 "description": "Required. The ID of the job.",

748 "location": "path",

749 "required": true,

750 "type": "string"

751 }

752 },

753 "path": "jobs/{jobId}",

754 "response": {

755 "$ref": "Job"

756 },

757 "scopes": [

758 "https://www.googleapis.com/auth/cloud-platform",

759 "https://www.googleapis.com/auth/genomics",	984 "https://www.googleapis.com/auth/genomics",

760 "https://www.googleapis.com/auth/genomics.readonly"	985 "https://www.googleapis.com/auth/genomics.readonly"

761 ]	986 ]

762 },	987 },

763 "search": {	988 "search": {

764 "description": "Gets a list of jobs matching the criteria.",	989 "description": "Returns a list of all variant sets matching search criteria. Implements [GlobalAllianceApi.searchVariantSets](https://github .com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L49). ",

765 "httpMethod": "POST",	990 "httpMethod": "POST",

766 "id": "genomics.jobs.search",	991 "id": "genomics.variantsets.search",

767 "path": "jobs/search",	992 "path": "v1/variantsets/search",

768 "request": {	993 "request": {

769 "$ref": "SearchJobsRequest"	994 "$ref": "SearchVariantSetsRequest"

770 },	995 },

771 "response": {	996 "response": {

772 "$ref": "SearchJobsResponse"	997 "$ref": "SearchVariantSetsResponse"

773 },

774 "scopes": [

775 "https://www.googleapis.com/auth/cloud-platform",

776 "https://www.googleapis.com/auth/genomics",

777 "https://www.googleapis.com/auth/genomics.readonly"

778 ]

779 }

780 }

781 },

782 "readgroupsets": {

783 "methods": {

784 "align": {

785 "description": "Aligns read data from existing read group se ts or files from Google Cloud Storage. See the alignment and variant calling do cumentation for more details.",

786 "httpMethod": "POST",

787 "id": "genomics.readgroupsets.align",

788 "path": "readgroupsets/align",

789 "request": {

790 "$ref": "AlignReadGroupSetsRequest"

791 },

792 "response": {

793 "$ref": "AlignReadGroupSetsResponse"

794 },

795 "scopes": [

796 "https://www.googleapis.com/auth/cloud-platform",

797 "https://www.googleapis.com/auth/devstorage.read_write",

798 "https://www.googleapis.com/auth/genomics"

799 ]

800 },

801 "call": {

802 "description": "Calls variants on read data from existing re ad group sets or files from Google Cloud Storage. See the alignment and variant calling documentation for more details.",

803 "httpMethod": "POST",

804 "id": "genomics.readgroupsets.call",

805 "path": "readgroupsets/call",

806 "request": {

807 "$ref": "CallReadGroupSetsRequest"

808 },

809 "response": {

810 "$ref": "CallReadGroupSetsResponse"

811 },

812 "scopes": [

813 "https://www.googleapis.com/auth/cloud-platform",

814 "https://www.googleapis.com/auth/devstorage.read_write",

815 "https://www.googleapis.com/auth/genomics"

816 ]

817 },

818 "delete": {

819 "description": "Deletes a read group set.",

820 "httpMethod": "DELETE",

821 "id": "genomics.readgroupsets.delete",

822 "parameterOrder": [

823 "readGroupSetId"

824 ],

825 "parameters": {

826 "readGroupSetId": {

827 "description": "The ID of the read group set to be d eleted. The caller must have WRITE permissions to the dataset associated with th is read group set.",

828 "location": "path",

829 "required": true,

830 "type": "string"

831 }

832 },

833 "path": "readgroupsets/{readGroupSetId}",

834 "scopes": [

835 "https://www.googleapis.com/auth/cloud-platform",

836 "https://www.googleapis.com/auth/genomics"

837 ]

838 },

839 "export": {

840 "description": "Exports read group sets to a BAM file in Goo gle Cloud Storage.\n\nNote that currently there may be some differences between exported BAM files and the original BAM file at the time of import. In particula r, comments in the input file header will not be preserved, some custom tags wil l be converted to strings, and original reference sequence order is not necessar ily preserved.",

841 "httpMethod": "POST",

842 "id": "genomics.readgroupsets.export",

843 "path": "readgroupsets/export",

844 "request": {

845 "$ref": "ExportReadGroupSetsRequest"

846 },

847 "response": {

848 "$ref": "ExportReadGroupSetsResponse"

849 },

850 "scopes": [

851 "https://www.googleapis.com/auth/cloud-platform",

852 "https://www.googleapis.com/auth/devstorage.read_write",

853 "https://www.googleapis.com/auth/genomics"

854 ]

855 },

856 "get": {

857 "description": "Gets a read group set by ID.",

858 "httpMethod": "GET",

859 "id": "genomics.readgroupsets.get",

860 "parameterOrder": [

861 "readGroupSetId"

862 ],

863 "parameters": {

864 "readGroupSetId": {

865 "description": "The ID of the read group set.",

866 "location": "path",

867 "required": true,

868 "type": "string"

869 }

870 },

871 "path": "readgroupsets/{readGroupSetId}",

872 "response": {

873 "$ref": "ReadGroupSet"

874 },	998 },

875 "scopes": [	999 "scopes": [

876 "https://www.googleapis.com/auth/cloud-platform",	1000 "https://www.googleapis.com/auth/cloud-platform",

877 "https://www.googleapis.com/auth/genomics",	1001 "https://www.googleapis.com/auth/genomics",

878 "https://www.googleapis.com/auth/genomics.readonly"	1002 "https://www.googleapis.com/auth/genomics.readonly"

879 ]	1003 ]

880 },	1004 },

881 "import": {	1005 "delete": {

882 "description": "Creates read group sets by asynchronously im porting the provided information.\n\nNote that currently comments in the input f ile header are not imported and some custom tags will be converted to strings, r ather than preserving tag types. The caller must have WRITE permissions to the d ataset.",	1006 "description": "Deletes the contents of a variant set. The v ariant set object is not deleted.",

883 "httpMethod": "POST",	1007 "httpMethod": "DELETE",

884 "id": "genomics.readgroupsets.import",	1008 "id": "genomics.variantsets.delete",

885 "path": "readgroupsets/import",

886 "request": {

887 "$ref": "ImportReadGroupSetsRequest"

888 },

889 "response": {

890 "$ref": "ImportReadGroupSetsResponse"

891 },

892 "scopes": [

893 "https://www.googleapis.com/auth/cloud-platform",

894 "https://www.googleapis.com/auth/devstorage.read_write",

895 "https://www.googleapis.com/auth/genomics"

896 ]

897 },

898 "patch": {

899 "description": "Updates a read group set. This method suppor ts patch semantics.",

900 "httpMethod": "PATCH",

901 "id": "genomics.readgroupsets.patch",

902 "parameterOrder": [	1009 "parameterOrder": [

903 "readGroupSetId"	1010 "variantSetId"

904 ],	1011 ],

905 "parameters": {	1012 "parameters": {

906 "readGroupSetId": {	1013 "variantSetId": {

907 "description": "The ID of the read group set to be u pdated. The caller must have WRITE permissions to the dataset associated with th is read group set.",	1014 "description": "The ID of the variant set to be dele ted.",

908 "location": "path",	1015 "location": "path",

909 "required": true,	1016 "required": true,

910 "type": "string"	1017 "type": "string"

911 }	1018 }

912 },	1019 },

913 "path": "readgroupsets/{readGroupSetId}",	1020 "path": "v1/variantsets/{variantSetId}",

914 "request": {

915 "$ref": "ReadGroupSet"

916 },

917 "response": {	1021 "response": {

918 "$ref": "ReadGroupSet"	1022 "$ref": "Empty"

919 },	1023 },

920 "scopes": [	1024 "scopes": [

921 "https://www.googleapis.com/auth/cloud-platform",	1025 "https://www.googleapis.com/auth/cloud-platform",

922 "https://www.googleapis.com/auth/genomics"	1026 "https://www.googleapis.com/auth/genomics"

923 ]	1027 ]

924 },	1028 },

925 "search": {	1029 "patch": {

926 "description": "Searches for read group sets matching the cr iteria.\n\nImplements GlobalAllianceApi.searchReadGroupSets.",	1030 "description": "Updates a variant set. This method supports patch semantics.",

927 "httpMethod": "POST",	1031 "httpMethod": "PATCH",

928 "id": "genomics.readgroupsets.search",	1032 "id": "genomics.variantsets.patch",

929 "path": "readgroupsets/search",	1033 "parameterOrder": [

	1034 "variantSetId"

	1035 ],

	1036 "parameters": {

	1037 "variantSetId": {

	1038 "description": "The ID of the variant to be updated (must already exist).",

	1039 "location": "path",

	1040 "required": true,

	1041 "type": "string"

	1042 },

	1043 "updateMask": {

	1044 "description": "An optional mask specifying which fi elds to update. At this time, the only mutable field is [metadata][google.genomi cs.v1.VariantSet.metadata]. The only acceptable value is \"metadata\". If unspec ified, all mutable fields will be updated.",

	1045 "location": "query",

	1046 "type": "string"

	1047 }

	1048 },

	1049 "path": "v1/variantsets/{variantSetId}",

930 "request": {	1050 "request": {

931 "$ref": "SearchReadGroupSetsRequest"	1051 "$ref": "VariantSet"

932 },	1052 },

933 "response": {	1053 "response": {

934 "$ref": "SearchReadGroupSetsResponse"	1054 "$ref": "VariantSet"

	1055 },

	1056 "scopes": [

	1057 "https://www.googleapis.com/auth/cloud-platform",

	1058 "https://www.googleapis.com/auth/genomics"

	1059 ]

	1060 }

	1061 }

	1062 },

	1063 "callsets": {

	1064 "methods": {

	1065 "search": {

	1066 "description": "Gets a list of call sets matching the criter ia. Implements [GlobalAllianceApi.searchCallSets](https://github.com/ga4gh/schem as/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L178).",

	1067 "httpMethod": "POST",

	1068 "id": "genomics.callsets.search",

	1069 "path": "v1/callsets/search",

	1070 "request": {

	1071 "$ref": "SearchCallSetsRequest"

	1072 },

	1073 "response": {

	1074 "$ref": "SearchCallSetsResponse"

935 },	1075 },

936 "scopes": [	1076 "scopes": [

937 "https://www.googleapis.com/auth/cloud-platform",	1077 "https://www.googleapis.com/auth/cloud-platform",

938 "https://www.googleapis.com/auth/genomics",	1078 "https://www.googleapis.com/auth/genomics",

939 "https://www.googleapis.com/auth/genomics.readonly"	1079 "https://www.googleapis.com/auth/genomics.readonly"

940 ]	1080 ]

941 },	1081 },

942 "update": {	1082 "create": {

943 "description": "Updates a read group set.",	1083 "description": "Creates a new call set.",

944 "httpMethod": "PUT",	1084 "httpMethod": "POST",

945 "id": "genomics.readgroupsets.update",	1085 "id": "genomics.callsets.create",

946 "parameterOrder": [	1086 "path": "v1/callsets",

947 "readGroupSetId"

948 ],

949 "parameters": {

950 "readGroupSetId": {

951 "description": "The ID of the read group set to be u pdated. The caller must have WRITE permissions to the dataset associated with th is read group set.",

952 "location": "path",

953 "required": true,

954 "type": "string"

955 }

956 },

957 "path": "readgroupsets/{readGroupSetId}",

958 "request": {	1087 "request": {

959 "$ref": "ReadGroupSet"	1088 "$ref": "CallSet"

960 },	1089 },

961 "response": {	1090 "response": {

962 "$ref": "ReadGroupSet"	1091 "$ref": "CallSet"

963 },	1092 },

964 "scopes": [	1093 "scopes": [

965 "https://www.googleapis.com/auth/cloud-platform",	1094 "https://www.googleapis.com/auth/cloud-platform",

966 "https://www.googleapis.com/auth/genomics"	1095 "https://www.googleapis.com/auth/genomics"

967 ]	1096 ]

968 }	1097 },

969 },	1098 "patch": {

970 "resources": {	1099 "description": "Updates a call set. This method supports pat ch semantics.",

971 "coveragebuckets": {	1100 "httpMethod": "PATCH",

972 "methods": {	1101 "id": "genomics.callsets.patch",

973 "list": {	1102 "parameterOrder": [

974 "description": "Lists fixed width coverage buckets f or a read group set, each of which correspond to a range of a reference sequence . Each bucket summarizes coverage information across its corresponding genomic r ange.\n\nCoverage is defined as the number of reads which are aligned to a given base in the reference sequence. Coverage buckets are available at several preco mputed bucket widths, enabling retrieval of various coverage 'zoom levels'. The caller must have READ permissions for the target read group set.",	1103 "callSetId"

975 "httpMethod": "GET",	1104 ],

976 "id": "genomics.readgroupsets.coveragebuckets.list",	1105 "parameters": {

977 "parameterOrder": [	1106 "callSetId": {

978 "readGroupSetId"	1107 "description": "The ID of the call set to be updated .",

979 ],	1108 "location": "path",

980 "parameters": {	1109 "required": true,

981 "pageSize": {	1110 "type": "string"

982 "description": "The maximum number of result s to return in a single page. If unspecified, defaults to 1024. The maximum valu e is 2048.",	1111 },

983 "format": "int32",	1112 "updateMask": {

984 "location": "query",	1113 "description": "An optional mask specifying which fi elds to update. At this time, the only mutable field is [name][google.genomics.v 1.CallSet.name]. The only acceptable value is \"name\". If unspecified, all muta ble fields will be updated.",

985 "type": "integer"	1114 "location": "query",

986 },	1115 "type": "string"

987 "pageToken": {

988 "description": "The continuation token, whic h is used to page through large result sets. To get the next page of results, se t this parameter to the value of nextPageToken from the previous response.",

989 "location": "query",

990 "type": "string"

991 },

992 "range.end": {

993 "description": "The end position of the rang e on the reference, 0-based exclusive. If specified, referenceName must also be specified.",

994 "format": "int64",

995 "location": "query",

996 "type": "string"

997 },

998 "range.referenceName": {

999 "description": "The reference sequence name, for example chr1, 1, or chrX.",

1000 "location": "query",

1001 "type": "string"

1002 },

1003 "range.start": {

1004 "description": "The start position of the ra nge on the reference, 0-based inclusive. If specified, referenceName must also b e specified.",

1005 "format": "int64",

1006 "location": "query",

1007 "type": "string"

1008 },

1009 "readGroupSetId": {

1010 "description": "Required. The ID of the read group set over which coverage is requested.",

1011 "location": "path",

1012 "required": true,

1013 "type": "string"

1014 },

1015 "targetBucketWidth": {

1016 "description": "The desired width of each re ported coverage bucket in base pairs. This will be rounded down to the nearest p recomputed bucket width; the value of which is returned as bucketWidth in the re sponse. Defaults to infinity (each bucket spans an entire reference sequence) or the length of the target range, if specified. The smallest precomputed bucketWi dth is currently 2048 base pairs; this is subject to change.",

1017 "format": "int64",

1018 "location": "query",

1019 "type": "string"

1020 }

1021 },

1022 "path": "readgroupsets/{readGroupSetId}/coveragebuck ets",

1023 "response": {

1024 "$ref": "ListCoverageBucketsResponse"

1025 },

1026 "scopes": [

1027 "https://www.googleapis.com/auth/cloud-platform" ,

1028 "https://www.googleapis.com/auth/genomics",

1029 "https://www.googleapis.com/auth/genomics.readon ly"

1030 ]

1031 }	1116 }

1032 }	1117 },

1033 }	1118 "path": "v1/callsets/{callSetId}",

1034 }

1035 },

1036 "reads": {

1037 "methods": {

1038 "search": {

1039 "description": "Gets a list of reads for one or more read gr oup sets. Reads search operates over a genomic coordinate space of reference seq uence & position defined over the reference sequences to which the requested rea d group sets are aligned.\n\nIf a target positional range is specified, search r eturns all reads whose alignment to the reference genome overlap the range. A qu ery which specifies only read group set IDs yields all reads in those read group sets, including unmapped reads.\n\nAll reads returned (including reads on subse quent pages) are ordered by genomic coordinate (reference sequence & position). Reads with equivalent genomic coordinates are returned in a deterministic order. \n\nImplements GlobalAllianceApi.searchReads.",

1040 "httpMethod": "POST",

1041 "id": "genomics.reads.search",

1042 "path": "reads/search",

1043 "request": {	1119 "request": {

1044 "$ref": "SearchReadsRequest"	1120 "$ref": "CallSet"

1045 },	1121 },

1046 "response": {	1122 "response": {

1047 "$ref": "SearchReadsResponse"	1123 "$ref": "CallSet"

1048 },	1124 },

1049 "scopes": [	1125 "scopes": [

1050 "https://www.googleapis.com/auth/cloud-platform",	1126 "https://www.googleapis.com/auth/cloud-platform",

1051 "https://www.googleapis.com/auth/genomics",

1052 "https://www.googleapis.com/auth/genomics.readonly"

1053 ]

1054 }

1055 }

1056 },

1057 "references": {

1058 "methods": {

1059 "get": {

1060 "description": "Gets a reference.\n\nImplements GlobalAllian ceApi.getReference.",

1061 "httpMethod": "GET",

1062 "id": "genomics.references.get",

1063 "parameterOrder": [

1064 "referenceId"

1065 ],

1066 "parameters": {

1067 "referenceId": {

1068 "description": "The ID of the reference.",

1069 "location": "path",

1070 "required": true,

1071 "type": "string"

1072 }

1073 },

1074 "path": "references/{referenceId}",

1075 "response": {

1076 "$ref": "Reference"

1077 },

1078 "scopes": [

1079 "https://www.googleapis.com/auth/cloud-platform",

1080 "https://www.googleapis.com/auth/genomics",

1081 "https://www.googleapis.com/auth/genomics.readonly"

1082 ]

1083 },

1084 "search": {

1085 "description": "Searches for references which match the give n criteria.\n\nImplements GlobalAllianceApi.searchReferences.",

1086 "httpMethod": "POST",

1087 "id": "genomics.references.search",

1088 "path": "references/search",

1089 "request": {

1090 "$ref": "SearchReferencesRequest"

1091 },

1092 "response": {

1093 "$ref": "SearchReferencesResponse"

1094 },

1095 "scopes": [

1096 "https://www.googleapis.com/auth/cloud-platform",

1097 "https://www.googleapis.com/auth/genomics",

1098 "https://www.googleapis.com/auth/genomics.readonly"

1099 ]

1100 }

1101 },

1102 "resources": {

1103 "bases": {

1104 "methods": {

1105 "list": {

1106 "description": "Lists the bases in a reference, opti onally restricted to a range.\n\nImplements GlobalAllianceApi.getReferenceBases. ",

1107 "httpMethod": "GET",

1108 "id": "genomics.references.bases.list",

1109 "parameterOrder": [

1110 "referenceId"

1111 ],

1112 "parameters": {

1113 "end": {

1114 "description": "The end position (0-based, e xclusive) of this query. Defaults to the length of this reference.",

1115 "format": "int64",

1116 "location": "query",

1117 "type": "string"

1118 },

1119 "pageSize": {

1120 "description": "Specifies the maximum number of bases to return in a single page.",

1121 "format": "int32",

1122 "location": "query",

1123 "type": "integer"

1124 },

1125 "pageToken": {

1126 "description": "The continuation token, whic h is used to page through large result sets. To get the next page of results, se t this parameter to the value of nextPageToken from the previous response.",

1127 "location": "query",

1128 "type": "string"

1129 },

1130 "referenceId": {

1131 "description": "The ID of the reference.",

1132 "location": "path",

1133 "required": true,

1134 "type": "string"

1135 },

1136 "start": {

1137 "description": "The start position (0-based) of this query. Defaults to 0.",

1138 "format": "int64",

1139 "location": "query",

1140 "type": "string"

1141 }

1142 },

1143 "path": "references/{referenceId}/bases",

1144 "response": {

1145 "$ref": "ListBasesResponse"

1146 },

1147 "scopes": [

1148 "https://www.googleapis.com/auth/cloud-platform" ,

1149 "https://www.googleapis.com/auth/genomics",

1150 "https://www.googleapis.com/auth/genomics.readon ly"

1151 ]

1152 }

1153 }

1154 }

1155 }

1156 },

1157 "referencesets": {

1158 "methods": {

1159 "get": {

1160 "description": "Gets a reference set.\n\nImplements GlobalAl lianceApi.getReferenceSet.",

1161 "httpMethod": "GET",

1162 "id": "genomics.referencesets.get",

1163 "parameterOrder": [

1164 "referenceSetId"

1165 ],

1166 "parameters": {

1167 "referenceSetId": {

1168 "description": "The ID of the reference set.",

1169 "location": "path",

1170 "required": true,

1171 "type": "string"

1172 }

1173 },

1174 "path": "referencesets/{referenceSetId}",

1175 "response": {

1176 "$ref": "ReferenceSet"

1177 },

1178 "scopes": [

1179 "https://www.googleapis.com/auth/cloud-platform",

1180 "https://www.googleapis.com/auth/genomics",

1181 "https://www.googleapis.com/auth/genomics.readonly"

1182 ]

1183 },

1184 "search": {

1185 "description": "Searches for reference sets which match the given criteria.\n\nImplements GlobalAllianceApi.searchReferenceSets.",

1186 "httpMethod": "POST",

1187 "id": "genomics.referencesets.search",

1188 "path": "referencesets/search",

1189 "request": {

1190 "$ref": "SearchReferenceSetsRequest"

1191 },

1192 "response": {

1193 "$ref": "SearchReferenceSetsResponse"

1194 },

1195 "scopes": [

1196 "https://www.googleapis.com/auth/cloud-platform",

1197 "https://www.googleapis.com/auth/genomics",

1198 "https://www.googleapis.com/auth/genomics.readonly"

1199 ]

1200 }

1201 }

1202 },

1203 "variants": {

1204 "methods": {

1205 "create": {

1206 "description": "Creates a new variant.",

1207 "httpMethod": "POST",

1208 "id": "genomics.variants.create",

1209 "path": "variants",

1210 "request": {

1211 "$ref": "Variant"

1212 },

1213 "response": {

1214 "$ref": "Variant"

1215 },

1216 "scopes": [

1217 "https://www.googleapis.com/auth/cloud-platform",

1218 "https://www.googleapis.com/auth/genomics"	1127 "https://www.googleapis.com/auth/genomics"

1219 ]	1128 ]

1220 },	1129 },

1221 "delete": {	1130 "delete": {

1222 "description": "Deletes a variant.",	1131 "description": "Deletes a call set.",

1223 "httpMethod": "DELETE",	1132 "httpMethod": "DELETE",

1224 "id": "genomics.variants.delete",	1133 "id": "genomics.callsets.delete",

1225 "parameterOrder": [	1134 "parameterOrder": [

1226 "variantId"	1135 "callSetId"

1227 ],	1136 ],

1228 "parameters": {	1137 "parameters": {

1229 "variantId": {	1138 "callSetId": {

1230 "description": "The ID of the variant to be deleted. ",	1139 "description": "The ID of the call set to be deleted .",

1231 "location": "path",	1140 "location": "path",

1232 "required": true,	1141 "required": true,

1233 "type": "string"	1142 "type": "string"

1234 }	1143 }

1235 },	1144 },

1236 "path": "variants/{variantId}",	1145 "path": "v1/callsets/{callSetId}",

	1146 "response": {

	1147 "$ref": "Empty"

	1148 },

1237 "scopes": [	1149 "scopes": [

1238 "https://www.googleapis.com/auth/cloud-platform",	1150 "https://www.googleapis.com/auth/cloud-platform",

1239 "https://www.googleapis.com/auth/genomics"	1151 "https://www.googleapis.com/auth/genomics"

1240 ]	1152 ]

1241 },	1153 },

1242 "get": {	1154 "get": {

1243 "description": "Gets a variant by ID.",	1155 "description": "Gets a call set by ID.",

1244 "httpMethod": "GET",	1156 "httpMethod": "GET",

1245 "id": "genomics.variants.get",	1157 "id": "genomics.callsets.get",

1246 "parameterOrder": [	1158 "parameterOrder": [

1247 "variantId"	1159 "callSetId"

1248 ],	1160 ],

1249 "parameters": {	1161 "parameters": {

1250 "variantId": {	1162 "callSetId": {

1251 "description": "The ID of the variant.",	1163 "description": "The ID of the call set.",

1252 "location": "path",	1164 "location": "path",

1253 "required": true,	1165 "required": true,

1254 "type": "string"	1166 "type": "string"

1255 }	1167 }

1256 },	1168 },

1257 "path": "variants/{variantId}",	1169 "path": "v1/callsets/{callSetId}",

1258 "response": {	1170 "response": {

1259 "$ref": "Variant"	1171 "$ref": "CallSet"

1260 },	1172 },

1261 "scopes": [	1173 "scopes": [

1262 "https://www.googleapis.com/auth/cloud-platform",	1174 "https://www.googleapis.com/auth/cloud-platform",

1263 "https://www.googleapis.com/auth/genomics",	1175 "https://www.googleapis.com/auth/genomics",

1264 "https://www.googleapis.com/auth/genomics.readonly"	1176 "https://www.googleapis.com/auth/genomics.readonly"

1265 ]	1177 ]

1266 },

1267 "search": {

1268 "description": "Gets a list of variants matching the criteri a.\n\nImplements GlobalAllianceApi.searchVariants.",

1269 "httpMethod": "POST",

1270 "id": "genomics.variants.search",

1271 "path": "variants/search",

1272 "request": {

1273 "$ref": "SearchVariantsRequest"

1274 },

1275 "response": {

1276 "$ref": "SearchVariantsResponse"

1277 },

1278 "scopes": [

1279 "https://www.googleapis.com/auth/cloud-platform",

1280 "https://www.googleapis.com/auth/genomics",

1281 "https://www.googleapis.com/auth/genomics.readonly"

1282 ]

1283 },

1284 "update": {

1285 "description": "Updates a variant's names and info fields. A ll other modifications are silently ignored. Returns the modified variant withou t its calls.",

1286 "httpMethod": "PUT",

1287 "id": "genomics.variants.update",

1288 "parameterOrder": [

1289 "variantId"

1290 ],

1291 "parameters": {

1292 "variantId": {

1293 "description": "The ID of the variant to be updated. ",

1294 "location": "path",

1295 "required": true,

1296 "type": "string"

1297 }

1298 },

1299 "path": "variants/{variantId}",

1300 "request": {

1301 "$ref": "Variant"

1302 },

1303 "response": {

1304 "$ref": "Variant"

1305 },

1306 "scopes": [

1307 "https://www.googleapis.com/auth/cloud-platform",

1308 "https://www.googleapis.com/auth/genomics"

1309 ]

1310 }

1311 }

1312 },

1313 "variantsets": {

1314 "methods": {

1315 "delete": {

1316 "description": "Deletes the contents of a variant set. The v ariant set object is not deleted.",

1317 "httpMethod": "DELETE",

1318 "id": "genomics.variantsets.delete",

1319 "parameterOrder": [

1320 "variantSetId"

1321 ],

1322 "parameters": {

1323 "variantSetId": {

1324 "description": "The ID of the variant set to be dele ted.",

1325 "location": "path",

1326 "required": true,

1327 "type": "string"

1328 }

1329 },

1330 "path": "variantsets/{variantSetId}",

1331 "scopes": [

1332 "https://www.googleapis.com/auth/cloud-platform",

1333 "https://www.googleapis.com/auth/genomics"

1334 ]

1335 },

1336 "export": {

1337 "description": "Exports variant set data to an external dest ination.",

1338 "httpMethod": "POST",

1339 "id": "genomics.variantsets.export",

1340 "parameterOrder": [

1341 "variantSetId"

1342 ],

1343 "parameters": {

1344 "variantSetId": {

1345 "description": "Required. The ID of the variant set that contains variant data which should be exported. The caller must have READ a ccess to this variant set.",

1346 "location": "path",

1347 "required": true,

1348 "type": "string"

1349 }

1350 },

1351 "path": "variantsets/{variantSetId}/export",

1352 "request": {

1353 "$ref": "ExportVariantSetRequest"

1354 },

1355 "response": {

1356 "$ref": "ExportVariantSetResponse"

1357 },

1358 "scopes": [

1359 "https://www.googleapis.com/auth/bigquery",

1360 "https://www.googleapis.com/auth/cloud-platform",

1361 "https://www.googleapis.com/auth/genomics"

1362 ]

1363 },

1364 "get": {

1365 "description": "Gets a variant set by ID.",

1366 "httpMethod": "GET",

1367 "id": "genomics.variantsets.get",

1368 "parameterOrder": [

1369 "variantSetId"

1370 ],

1371 "parameters": {

1372 "variantSetId": {

1373 "description": "Required. The ID of the variant set. ",

1374 "location": "path",

1375 "required": true,

1376 "type": "string"

1377 }

1378 },

1379 "path": "variantsets/{variantSetId}",

1380 "response": {

1381 "$ref": "VariantSet"

1382 },

1383 "scopes": [

1384 "https://www.googleapis.com/auth/cloud-platform",

1385 "https://www.googleapis.com/auth/genomics",

1386 "https://www.googleapis.com/auth/genomics.readonly"

1387 ]

1388 },

1389 "importVariants": {

1390 "description": "Creates variant data by asynchronously impor ting the provided information.\n\nThe variants for import will be merged with an y existing data and each other according to the behavior of mergeVariants. In pa rticular, this means for merged VCF variants that have conflicting INFO fields, some data will be arbitrarily discarded. As a special case, for single-sample VC F files, QUAL and FILTER fields will be moved to the call level; these are somet imes interpreted in a call-specific context. Imported VCF headers are appended t o the metadata already in a variant set.",

1391 "httpMethod": "POST",

1392 "id": "genomics.variantsets.importVariants",

1393 "parameterOrder": [

1394 "variantSetId"

1395 ],

1396 "parameters": {

1397 "variantSetId": {

1398 "description": "Required. The variant set to which v ariant data should be imported.",

1399 "location": "path",

1400 "required": true,

1401 "type": "string"

1402 }

1403 },

1404 "path": "variantsets/{variantSetId}/importVariants",

1405 "request": {

1406 "$ref": "ImportVariantsRequest"

1407 },

1408 "response": {

1409 "$ref": "ImportVariantsResponse"

1410 },

1411 "scopes": [

1412 "https://www.googleapis.com/auth/cloud-platform",

1413 "https://www.googleapis.com/auth/devstorage.read_write",

1414 "https://www.googleapis.com/auth/genomics"

1415 ]

1416 },

1417 "mergeVariants": {

1418 "description": "Merges the given variants with existing vari ants. Each variant will be merged with an existing variant that matches its refe rence sequence, start, end, reference bases, and alternative bases. If no such v ariant exists, a new one will be created.\n\nWhen variants are merged, the call information from the new variant is added to the existing variant, and other fie lds (such as key/value pairs) are discarded.",

1419 "httpMethod": "POST",

1420 "id": "genomics.variantsets.mergeVariants",

1421 "parameterOrder": [

1422 "variantSetId"

1423 ],

1424 "parameters": {

1425 "variantSetId": {

1426 "description": "The destination variant set.",

1427 "location": "path",

1428 "required": true,

1429 "type": "string"

1430 }

1431 },

1432 "path": "variantsets/{variantSetId}/mergeVariants",

1433 "request": {

1434 "$ref": "MergeVariantsRequest"

1435 },

1436 "scopes": [

1437 "https://www.googleapis.com/auth/cloud-platform",

1438 "https://www.googleapis.com/auth/genomics"

1439 ]

1440 },

1441 "patch": {

1442 "description": "Updates a variant set's metadata. All other modifications are silently ignored. This method supports patch semantics.",

1443 "httpMethod": "PATCH",

1444 "id": "genomics.variantsets.patch",

1445 "parameterOrder": [

1446 "variantSetId"

1447 ],

1448 "parameters": {

1449 "variantSetId": {

1450 "description": "The ID of the variant to be updated (must already exist).",

1451 "location": "path",

1452 "required": true,

1453 "type": "string"

1454 }

1455 },

1456 "path": "variantsets/{variantSetId}",

1457 "request": {

1458 "$ref": "VariantSet"

1459 },

1460 "response": {

1461 "$ref": "VariantSet"

1462 },

1463 "scopes": [

1464 "https://www.googleapis.com/auth/cloud-platform",

1465 "https://www.googleapis.com/auth/genomics"

1466 ]

1467 },

1468 "search": {

1469 "description": "Returns a list of all variant sets matching search criteria.\n\nImplements GlobalAllianceApi.searchVariantSets.",

1470 "httpMethod": "POST",

1471 "id": "genomics.variantsets.search",

1472 "path": "variantsets/search",

1473 "request": {

1474 "$ref": "SearchVariantSetsRequest"

1475 },

1476 "response": {

1477 "$ref": "SearchVariantSetsResponse"

1478 },

1479 "scopes": [

1480 "https://www.googleapis.com/auth/cloud-platform",

1481 "https://www.googleapis.com/auth/genomics",

1482 "https://www.googleapis.com/auth/genomics.readonly"

1483 ]

1484 },

1485 "update": {

1486 "description": "Updates a variant set's metadata. All other modifications are silently ignored.",

1487 "httpMethod": "PUT",

1488 "id": "genomics.variantsets.update",

1489 "parameterOrder": [

1490 "variantSetId"

1491 ],

1492 "parameters": {

1493 "variantSetId": {

1494 "description": "The ID of the variant to be updated (must already exist).",

1495 "location": "path",

1496 "required": true,

1497 "type": "string"

1498 }

1499 },

1500 "path": "variantsets/{variantSetId}",

1501 "request": {

1502 "$ref": "VariantSet"

1503 },

1504 "response": {

1505 "$ref": "VariantSet"

1506 },

1507 "scopes": [

1508 "https://www.googleapis.com/auth/cloud-platform",

1509 "https://www.googleapis.com/auth/genomics"

1510 ]

1511 }	1178 }

1512 }	1179 }

1513 }	1180 }

1514 },	1181 },

1515 "revision": "20150629",	1182 "revision": "20150725",

1516 "rootUrl": "https://www.googleapis.com/",	1183 "rootUrl": "https://genomics.googleapis.com/",

1517 "schemas": {	1184 "schemas": {

1518 "AlignReadGroupSetsRequest": {

1519 "description": "The read group set align request.",

1520 "id": "AlignReadGroupSetsRequest",

1521 "properties": {

1522 "bamSourceUris": {

1523 "description": "The BAM source files for alignment. Exactly one of readGroupSetId, bamSourceUris, interleavedFastqSource or pairedFastqSourc e must be provided. The caller must have READ permissions for these files.",

1524 "items": {

1525 "type": "string"

1526 },

1527 "type": "array"

1528 },

1529 "datasetId": {

1530 "description": "Required. The ID of the dataset the newly al igned read group sets will belong to. The caller must have WRITE permissions to this dataset.",

1531 "type": "string"

1532 },

1533 "interleavedFastqSource": {

1534 "$ref": "InterleavedFastqSource",

1535 "description": "The interleaved FASTQ source files for align ment, where both members of each pair of reads are found on consecutive records within the same FASTQ file. Exactly one of readGroupSetId, bamSourceUris, interl eavedFastqSource or pairedFastqSource must be provided."

1536 },

1537 "pairedFastqSource": {

1538 "$ref": "PairedFastqSource",

1539 "description": "The paired end FASTQ source files for alignm ent, where each member of a pair of reads are found in separate files. Exactly o ne of readGroupSetId, bamSourceUris, interleavedFastqSource or pairedFastqSource must be provided."

1540 },

1541 "readGroupSetId": {

1542 "description": "The ID of the read group set which will be a ligned. A new read group set will be generated to hold the aligned data, the ori ginals will not be modified. The caller must have READ permissions for this read group set. Exactly one of readGroupSetId, bamSourceUris, interleavedFastqSource or pairedFastqSource must be provided.",

1543 "type": "string"

1544 }

1545 },

1546 "type": "object"

1547 },

1548 "AlignReadGroupSetsResponse": {

1549 "description": "The read group set align response.",

1550 "id": "AlignReadGroupSetsResponse",

1551 "properties": {

1552 "jobId": {

1553 "description": "A job ID that can be used to get status info rmation.",

1554 "type": "string"

1555 }

1556 },

1557 "type": "object"

1558 },

1559 "Annotation": {

1560 "description": "An annotation describes a region of reference genome . The value of an annotation may be one of several canonical types, supplemented by arbitrary info tags. A variant annotation is represented by one or more of t hese canonical types. An annotation is not inherently associated with a specific sample or individual (though a client could choose to use annotations in this w ay). Example canonical annotation types are 'Gene' and 'Variant'.",

1561 "id": "Annotation",

1562 "properties": {

1563 "annotationSetId": {

1564 "description": "The ID of the containing annotation set.",

1565 "type": "string"

1566 },

1567 "id": {

1568 "description": "The generated unique ID for this annotation. ",

1569 "type": "string"

1570 },

1571 "info": {

1572 "additionalProperties": {

1573 "description": "A string which maps to an array of value s.",

1574 "items": {

1575 "type": "string"

1576 },

1577 "type": "array"

1578 },

1579 "description": "A string which maps to an array of values.",

1580 "type": "object"

1581 },

1582 "name": {

1583 "description": "The display name of this annotation.",

1584 "type": "string"

1585 },

1586 "position": {

1587 "$ref": "RangePosition",

1588 "description": "The position of this annotation on the refer ence sequence."

1589 },

1590 "transcript": {

1591 "$ref": "Transcript",

1592 "description": "A transcript value represents the assertion that a particular region of the reference genome may be transcribed as RNA. An a lternative splicing pattern would be represented as a separate transcript object . This field is only set for annotations of type TRANSCRIPT."

1593 },

1594 "type": {

1595 "description": "The data type for this annotation. Must matc h the containing annotation set's type.",

1596 "enum": [

1597 "GENE",

1598 "GENERIC",

1599 "TRANSCRIPT",

1600 "VARIANT"

1601 ],

1602 "enumDescriptions": [

1603 "",

1604 "",

1605 "",

1606 ""

1607 ],

1608 "type": "string"

1609 },

1610 "variant": {

1611 "$ref": "VariantAnnotation",

1612 "description": "A variant annotation, which describes the ef fect of a variant on the genome, the coding sequence, and/or higher level conseq uences at the organism level e.g. pathogenicity. This field is only set for anno tations of type VARIANT."

1613 }

1614 },

1615 "type": "object"

1616 },

1617 "AnnotationSet": {

1618 "description": "An annotation set is a logical grouping of annotatio ns that share consistent type information and provenance. Examples of annotation sets include 'all genes from refseq', and 'all variant annotations from ClinVar '.",

1619 "id": "AnnotationSet",

1620 "properties": {

1621 "datasetId": {

1622 "description": "The ID of the containing dataset.",

1623 "type": "string"

1624 },

1625 "id": {

1626 "description": "The generated unique ID for this annotation set.",

1627 "type": "string"

1628 },

1629 "info": {

1630 "additionalProperties": {

1631 "description": "A string which maps to an array of value s.",

1632 "items": {

1633 "type": "string"

1634 },

1635 "type": "array"

1636 },

1637 "description": "A string which maps to an array of values.",

1638 "type": "object"

1639 },

1640 "name": {

1641 "description": "The display name for this annotation set.",

1642 "type": "string"

1643 },

1644 "referenceSetId": {

1645 "description": "The ID of the reference set that defines the coordinate space for this set's annotations.",

1646 "type": "string"

1647 },

1648 "sourceUri": {

1649 "description": "The source URI describing the file from whic h this annotation set was generated, if any.",

1650 "type": "string"

1651 },

1652 "type": {

1653 "description": "The type of annotations contained within thi s set.",

1654 "enum": [

1655 "GENE",

1656 "GENERIC",

1657 "TRANSCRIPT",

1658 "VARIANT"

1659 ],

1660 "enumDescriptions": [

1661 "",

1662 "",

1663 "",

1664 ""

1665 ],

1666 "type": "string"

1667 }

1668 },

1669 "type": "object"

1670 },

1671 "BatchAnnotationsResponse": {

1672 "id": "BatchAnnotationsResponse",

1673 "properties": {

1674 "entries": {

1675 "description": "The resulting per-annotation entries, ordere d consistently with the original request.",

1676 "items": {

1677 "$ref": "BatchAnnotationsResponseEntry"

1678 },

1679 "type": "array"

1680 }

1681 },

1682 "type": "object"

1683 },

1684 "BatchAnnotationsResponseEntry": {

1685 "id": "BatchAnnotationsResponseEntry",

1686 "properties": {

1687 "annotation": {

1688 "$ref": "Annotation",

1689 "description": "The annotation, if any."

1690 },

1691 "status": {

1692 "$ref": "BatchAnnotationsResponseEntryStatus",

1693 "description": "The resulting status for this annotation ope ration."

1694 }

1695 },

1696 "type": "object"

1697 },

1698 "BatchAnnotationsResponseEntryStatus": {

1699 "description": "",

1700 "id": "BatchAnnotationsResponseEntryStatus",

1701 "properties": {

1702 "code": {

1703 "description": "The HTTP status code for this operation.",

1704 "format": "int32",

1705 "type": "integer"

1706 },

1707 "message": {

1708 "description": "Error message for this status, if any.",

1709 "type": "string"

1710 }

1711 },

1712 "type": "object"

1713 },

1714 "BatchCreateAnnotationsRequest": {

1715 "id": "BatchCreateAnnotationsRequest",

1716 "properties": {

1717 "annotations": {

1718 "description": "The annotations to be created. At most 4096 can be specified in a single request.",

1719 "items": {

1720 "$ref": "Annotation"

1721 },

1722 "type": "array"

1723 }

1724 },

1725 "type": "object"

1726 },

1727 "Call": {

1728 "description": "A call represents the determination of genotype with respect to a particular variant. It may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to t he occurrence of a SNP named rs1234 in a call set with the name NA12345.",

1729 "id": "Call",

1730 "properties": {

1731 "callSetId": {

1732 "description": "The ID of the call set this variant call bel ongs to.",

1733 "type": "string"

1734 },

1735 "callSetName": {

1736 "description": "The name of the call set this variant call b elongs to.",

1737 "type": "string"

1738 },

1739 "genotype": {

1740 "description": "The genotype of this variant call. Each valu e represents either the value of the referenceBases field or a 1-based index int o alternateBases. If a variant had a referenceBases value of T and an alternateB ases value of [\"A\", \"C\"], and the genotype was [2, 1], that would mean the c all represented the heterozygous value CA for this variant. If the genotype was instead [0, 1], the represented value would be TA. Ordering of the genotype valu es is important if the phaseset is present. If a genotype is not called (that is , a . is present in the GT string) -1 is returned.",

1741 "items": {

1742 "format": "int32",

1743 "type": "integer"

1744 },

1745 "type": "array"

1746 },

1747 "genotypeLikelihood": {

1748 "description": "The genotype likelihoods for this variant ca ll. Each array entry represents how likely a specific genotype is for this call. The value ordering is defined by the GL tag in the VCF spec. If Phred-scaled ge notype likelihood scores (PL) are available and log10(P) genotype likelihood sco res (GL) are not, PL scores are converted to GL scores. If both are available, P L scores are stored in info.",

1749 "items": {

1750 "format": "double",

1751 "type": "number"

1752 },

1753 "type": "array"

1754 },

1755 "info": {

1756 "additionalProperties": {

1757 "description": "A string which maps to an array of value s.",

1758 "items": {

1759 "type": "string"

1760 },

1761 "type": "array"

1762 },

1763 "description": "A string which maps to an array of values.",

1764 "type": "object"

1765 },

1766 "phaseset": {

1767 "description": "If this field is present, this variant call' s genotype ordering implies the phase of the bases and is consistent with any ot her variant calls in the same reference sequence which have the same phaseset va lue. When importing data from VCF, if the genotype data was phased but no phase set was specified this field will be set to *.",

1768 "type": "string"

1769 }

1770 },

1771 "type": "object"

1772 },

1773 "CallReadGroupSetsRequest": {

1774 "description": "The read group set call request.",

1775 "id": "CallReadGroupSetsRequest",

1776 "properties": {

1777 "datasetId": {

1778 "description": "Required. The ID of the dataset the called v ariants will belong to. The caller must have WRITE permissions to this dataset." ,

1779 "type": "string"

1780 },

1781 "readGroupSetId": {

1782 "description": "The IDs of the read group sets which will be called. The caller must have READ permissions for these read group sets. One of readGroupSetId or sourceUris must be provided.",

1783 "type": "string"

1784 },

1785 "sourceUris": {

1786 "description": "A list of URIs pointing at BAM files in Goog le Cloud Storage which will be called. FASTQ files are not allowed. The caller m ust have READ permissions for these files. One of readGroupSetId or sourceUris m ust be provided.",

1787 "items": {

1788 "type": "string"

1789 },

1790 "type": "array"

1791 }

1792 },

1793 "type": "object"

1794 },

1795 "CallReadGroupSetsResponse": {

1796 "description": "The read group set call response.",

1797 "id": "CallReadGroupSetsResponse",

1798 "properties": {

1799 "jobId": {

1800 "description": "A job ID that can be used to get status info rmation.",

1801 "type": "string"

1802 }

1803 },

1804 "type": "object"

1805 },

1806 "CallSet": {

1807 "description": "A call set is a collection of variant calls, typical ly for one sample. It belongs to a variant set.",

1808 "id": "CallSet",

1809 "properties": {

1810 "created": {

1811 "description": "The date this call set was created in millis econds from the epoch.",

1812 "format": "int64",

1813 "type": "string"

1814 },

1815 "id": {

1816 "description": "The Google generated ID of the call set, imm utable.",

1817 "type": "string"

1818 },

1819 "info": {

1820 "additionalProperties": {

1821 "description": "A string which maps to an array of value s.",

1822 "items": {

1823 "type": "string"

1824 },

1825 "type": "array"

1826 },

1827 "description": "A string which maps to an array of values.",

1828 "type": "object"

1829 },

1830 "name": {

1831 "description": "The call set name.",

1832 "type": "string"

1833 },

1834 "sampleId": {

1835 "description": "The sample ID this call set corresponds to." ,

1836 "type": "string"

1837 },

1838 "variantSetIds": {

1839 "description": "The IDs of the variant sets this call set be longs to.",

1840 "items": {

1841 "type": "string"

1842 },

1843 "type": "array"

1844 }

1845 },

1846 "type": "object"

1847 },

1848 "CigarUnit": {

1849 "description": "A single CIGAR operation.",

1850 "id": "CigarUnit",

1851 "properties": {

1852 "operation": {

1853 "enum": [

1854 "ALIGNMENT_MATCH",

1855 "CLIP_HARD",

1856 "CLIP_SOFT",

1857 "DELETE",

1858 "INSERT",

1859 "OPERATION_UNSPECIFIED",

1860 "PAD",

1861 "SEQUENCE_MATCH",

1862 "SEQUENCE_MISMATCH",

1863 "SKIP"

1864 ],

1865 "enumDescriptions": [

1866 "",

1867 "",

1868 "",

1869 "",

1870 "",

1871 "",

1872 "",

1873 "",

1874 "",

1875 ""

1876 ],

1877 "type": "string"

1878 },

1879 "operationLength": {

1880 "description": "The number of bases that the operation runs for. Required.",

1881 "format": "int64",

1882 "type": "string"

1883 },

1884 "referenceSequence": {

1885 "description": "referenceSequence is only used at mismatches (SEQUENCE_MISMATCH) and deletions (DELETE). Filling this field replaces SAM's M D tag. If the relevant information is not available, this field is unset.",

1886 "type": "string"

1887 }

1888 },

1889 "type": "object"

1890 },

1891 "CoverageBucket": {

1892 "description": "A bucket over which read coverage has been precomput ed. A bucket corresponds to a specific range of the reference sequence.",

1893 "id": "CoverageBucket",

1894 "properties": {

1895 "meanCoverage": {

1896 "description": "The average number of reads which are aligne d to each individual reference base in this bucket.",

1897 "format": "float",

1898 "type": "number"

1899 },

1900 "range": {

1901 "$ref": "Range",

1902 "description": "The genomic coordinate range spanned by this bucket."

1903 }

1904 },

1905 "type": "object"

1906 },

1907 "Dataset": {

1908 "description": "A Dataset is a collection of genomic data.",

1909 "id": "Dataset",

1910 "properties": {

1911 "createTime": {

1912 "description": "The time this dataset was created, in second s from the epoch.",

1913 "format": "int64",

1914 "type": "string"

1915 },

1916 "id": {

1917 "description": "The Google generated ID of the dataset, immu table.",

1918 "type": "string"

1919 },

1920 "isPublic": {

1921 "description": "Flag indicating whether or not a dataset is publicly viewable. If a dataset is not public, it inherits viewing permissions f rom its project.",

1922 "type": "boolean"

1923 },

1924 "name": {

1925 "description": "The dataset name.",

1926 "type": "string"

1927 },

1928 "projectNumber": {

1929 "description": "The Google Developers Console project number that this dataset belongs to.",

1930 "format": "int64",

1931 "type": "string"

1932 }

1933 },

1934 "type": "object"

1935 },

1936 "ExperimentalCreateJobRequest": {

1937 "description": "The job creation request.",

1938 "id": "ExperimentalCreateJobRequest",

1939 "properties": {

1940 "align": {

1941 "description": "Specifies whether or not to run the alignmen t pipeline. Either align or callVariants must be set.",

1942 "type": "boolean"

1943 },

1944 "callVariants": {

1945 "description": "Specifies whether or not to run the variant calling pipeline. Either align or callVariants must be set.",

1946 "type": "boolean"

1947 },

1948 "gcsOutputPath": {

1949 "description": "Specifies where to copy the results of certa in pipelines. This should be in the form of gs://bucket/path.",

1950 "type": "string"

1951 },

1952 "pairedSourceUris": {

1953 "description": "A list of Google Cloud Storage URIs of paire d end .fastq files to operate upon. If specified, this represents the second fil e of each paired .fastq file. The first file of each pair should be specified in sourceUris.",

1954 "items": {

1955 "type": "string"

1956 },

1957 "type": "array"

1958 },

1959 "projectNumber": {

1960 "description": "Required. The Google Cloud Project ID with w hich to associate the request.",

1961 "format": "int64",

1962 "type": "string"

1963 },

1964 "sourceUris": {

1965 "description": "A list of Google Cloud Storage URIs of data files to operate upon. These can be .bam, interleaved .fastq, or paired .fastq. If specifying paired .fastq files, the first of each pair of files should be lis ted here, and the second of each pair should be listed in pairedSourceUris.",

1966 "items": {

1967 "type": "string"

1968 },

1969 "type": "array"

1970 }

1971 },

1972 "type": "object"

1973 },

1974 "ExperimentalCreateJobResponse": {

1975 "description": "The job creation response.",

1976 "id": "ExperimentalCreateJobResponse",

1977 "properties": {

1978 "jobId": {

1979 "description": "A job ID that can be used to get status info rmation.",

1980 "type": "string"

1981 }

1982 },

1983 "type": "object"

1984 },

1985 "ExportReadGroupSetsRequest": {

1986 "description": "The read group set export request.",

1987 "id": "ExportReadGroupSetsRequest",

1988 "properties": {

1989 "exportUri": {

1990 "description": "Required. A Google Cloud Storage URI for the exported BAM file. The currently authenticated user must have write access to t he new file. An error will be returned if the URI already contains data.",

1991 "type": "string"

1992 },

1993 "projectNumber": {

1994 "description": "Required. The Google Developers Console proj ect number that owns this export.",

1995 "format": "int64",

1996 "type": "string"

1997 },

1998 "readGroupSetIds": {

1999 "description": "Required. The IDs of the read group sets to export.",

2000 "items": {

2001 "type": "string"

2002 },

2003 "type": "array"

2004 },

2005 "referenceNames": {

2006 "description": "The reference names to export. If this is no t specified, all reference sequences, including unmapped reads, are exported. Us e * to export only unmapped reads.",

2007 "items": {

2008 "type": "string"

2009 },

2010 "type": "array"

2011 }

2012 },

2013 "type": "object"

2014 },

2015 "ExportReadGroupSetsResponse": {

2016 "description": "The read group set export response.",

2017 "id": "ExportReadGroupSetsResponse",

2018 "properties": {

2019 "jobId": {

2020 "description": "A job ID that can be used to get status info rmation.",

2021 "type": "string"

2022 }

2023 },

2024 "type": "object"

2025 },

2026 "ExportVariantSetRequest": {

2027 "description": "The variant data export request.",

2028 "id": "ExportVariantSetRequest",

2029 "properties": {

2030 "bigqueryDataset": {

2031 "description": "Required. The BigQuery dataset to export dat a to. This dataset must already exist. Note that this is distinct from the Genom ics concept of \"dataset\".",

2032 "type": "string"

2033 },

2034 "bigqueryTable": {

2035 "description": "Required. The BigQuery table to export data to. If the table doesn't exist, it will be created. If it already exists, it wil l be overwritten.",

2036 "type": "string"

2037 },

2038 "callSetIds": {

2039 "description": "If provided, only variant call information f rom the specified call sets will be exported. By default all variant calls are e xported.",

2040 "items": {

2041 "type": "string"

2042 },

2043 "type": "array"

2044 },

2045 "format": {

2046 "description": "The format for the exported data.",

2047 "enum": [

2048 "BIGQUERY"

2049 ],

2050 "enumDescriptions": [

2051 ""

2052 ],

2053 "type": "string"

2054 },

2055 "projectNumber": {

2056 "description": "Required. The Google Cloud project number th at owns the destination BigQuery dataset. The caller must have WRITE access to t his project. This project will also own the resulting export job.",

2057 "format": "int64",

2058 "type": "string"

2059 }

2060 },

2061 "type": "object"

2062 },

2063 "ExportVariantSetResponse": {

2064 "description": "The variant data export response.",

2065 "id": "ExportVariantSetResponse",

2066 "properties": {

2067 "jobId": {

2068 "description": "A job ID that can be used to get status info rmation.",

2069 "type": "string"

2070 }

2071 },

2072 "type": "object"

2073 },

2074 "ExternalId": {

2075 "description": "",

2076 "id": "ExternalId",

2077 "properties": {

2078 "id": {

2079 "description": "The id used by the source of this data.",

2080 "type": "string"

2081 },

2082 "sourceName": {

2083 "description": "The name of the source of this data.",

2084 "type": "string"

2085 }

2086 },

2087 "type": "object"

2088 },

2089 "FastqMetadata": {

2090 "id": "FastqMetadata",

2091 "properties": {

2092 "libraryName": {

2093 "description": "Optionally specifies the library name for al ignment from FASTQ.",

2094 "type": "string"

2095 },

2096 "platformName": {

2097 "description": "Optionally specifies the platform name for a lignment from FASTQ. For example: CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IO NTORRENT, PACBIO.",

2098 "type": "string"

2099 },

2100 "platformUnit": {

2101 "description": "Optionally specifies the platform unit for a lignment from FASTQ. For example: flowcell-barcode.lane for Illumina or slide fo r SOLID.",

2102 "type": "string"

2103 },

2104 "readGroupName": {

2105 "description": "Optionally specifies the read group name for alignment from FASTQ.",

2106 "type": "string"

2107 },

2108 "sampleName": {

2109 "description": "Optionally specifies the sample name for ali gnment from FASTQ.",

2110 "type": "string"

2111 }

2112 },

2113 "type": "object"

2114 },

2115 "ImportReadGroupSetsRequest": {

2116 "description": "The read group set import request.",

2117 "id": "ImportReadGroupSetsRequest",

2118 "properties": {

2119 "datasetId": {

2120 "description": "Required. The ID of the dataset these read g roup sets will belong to. The caller must have WRITE permissions to this dataset .",

2121 "type": "string"

2122 },

2123 "partitionStrategy": {

2124 "description": "The partition strategy describes how read gr oups are partitioned into read group sets.",

2125 "enum": [

2126 "MERGE_ALL",

2127 "PER_FILE_PER_SAMPLE"

2128 ],

2129 "enumDescriptions": [

2130 "",

2131 ""

2132 ],

2133 "type": "string"

2134 },

2135 "referenceSetId": {

2136 "description": "The reference set to which the imported read group sets are aligned to, if any. The reference names of this reference set mu st be a superset of those found in the imported file headers. If no reference se t id is provided, a best effort is made to associate with a matching reference s et.",

2137 "type": "string"

2138 },

2139 "sourceUris": {

2140 "description": "A list of URIs pointing at BAM files in Goog le Cloud Storage.",

2141 "items": {

2142 "type": "string"

2143 },

2144 "type": "array"

2145 }

2146 },

2147 "type": "object"

2148 },

2149 "ImportReadGroupSetsResponse": {

2150 "description": "The read group set import response.",

2151 "id": "ImportReadGroupSetsResponse",

2152 "properties": {

2153 "jobId": {

2154 "description": "A job ID that can be used to get status info rmation.",

2155 "type": "string"

2156 }

2157 },

2158 "type": "object"

2159 },

2160 "ImportVariantsRequest": {

2161 "description": "The variant data import request.",

2162 "id": "ImportVariantsRequest",

2163 "properties": {

2164 "format": {

2165 "description": "The format of the variant data being importe d. If unspecified, defaults to to \"VCF\".",

2166 "enum": [

2167 "COMPLETE_GENOMICS",

2168 "VCF"

2169 ],

2170 "enumDescriptions": [

2171 "",

2172 ""

2173 ],

2174 "type": "string"

2175 },

2176 "normalizeReferenceNames": {

2177 "description": "Convert reference names to the canonical rep resentation. hg19 haploytypes (those reference names containing \"_hap\") are no t modified in any way. All other reference names are modified according to the f ollowing rules: The reference name is capitalized. The \"chr\" prefix is dropped for all autosomes and sex chromsomes. For example \"chr17\" becomes \"17\" and \"chrX\" becomes \"X\". All mitochondrial chromosomes (\"chrM\", \"chrMT\", etc) become \"MT\".",

2178 "type": "boolean"

2179 },

2180 "sourceUris": {

2181 "description": "A list of URIs referencing variant files in Google Cloud Storage. URIs can include wildcards as described here. Note that re cursive wildcards ('**') are not supported.",

2182 "items": {

2183 "type": "string"

2184 },

2185 "type": "array"

2186 }

2187 },

2188 "type": "object"

2189 },

2190 "ImportVariantsResponse": {

2191 "description": "The variant data import response.",

2192 "id": "ImportVariantsResponse",

2193 "properties": {

2194 "jobId": {

2195 "description": "A job ID that can be used to get status info rmation.",

2196 "type": "string"

2197 }

2198 },

2199 "type": "object"

2200 },

2201 "Int32Value": {

2202 "description": "Wrapper message for `int32`.\n\nThe JSON representat ion for `Int32Value` is JSON number.",

2203 "id": "Int32Value",

2204 "properties": {

2205 "value": {

2206 "description": "The int32 value.",

2207 "format": "int32",

2208 "type": "integer"

2209 }

2210 },

2211 "type": "object"

2212 },

2213 "InterleavedFastqSource": {

2214 "description": "Describes an interleaved FASTQ file source for align ment.",

2215 "id": "InterleavedFastqSource",

2216 "properties": {

2217 "metadata": {

2218 "$ref": "FastqMetadata",

2219 "description": "Optionally specifies the metadata to be asso ciated with the final aligned read group set."

2220 },

2221 "sourceUris": {

2222 "description": "A list of URIs pointing at interleaved FASTQ files in Google Cloud Storage which will be aligned. The caller must have READ permissions for these files.",

2223 "items": {

2224 "type": "string"

2225 },

2226 "type": "array"

2227 }

2228 },

2229 "type": "object"

2230 },

2231 "Job": {

2232 "description": "A Job represents an ongoing process that can be moni tored for status information.",

2233 "id": "Job",

2234 "properties": {

2235 "created": {

2236 "description": "The date this job was created, in millisecon ds from the epoch.",

2237 "format": "int64",

2238 "type": "string"

2239 },

2240 "detailedStatus": {

2241 "description": "A more detailed description of this job's cu rrent status.",

2242 "type": "string"

2243 },

2244 "errors": {

2245 "description": "Any errors that occurred during processing." ,

2246 "items": {

2247 "type": "string"

2248 },

2249 "type": "array"

2250 },

2251 "id": {

2252 "description": "The job ID.",

2253 "type": "string"

2254 },

2255 "importedIds": {

2256 "description": "If this Job represents an import, this field will contain the IDs of the objects that were successfully imported.",

2257 "items": {

2258 "type": "string"

2259 },

2260 "type": "array"

2261 },

2262 "projectNumber": {

2263 "description": "The Google Developers Console project number to which this job belongs.",

2264 "format": "int64",

2265 "type": "string"

2266 },

2267 "request": {

2268 "$ref": "JobRequest",

2269 "description": "A summarized representation of the original service request."

2270 },

2271 "status": {

2272 "description": "The status of this job.",

2273 "enum": [

2274 "CANCELED",

2275 "FAILURE",

2276 "NEW",

2277 "PENDING",

2278 "RUNNING",

2279 "SUCCESS",

2280 "UNKNOWN_STATUS"

2281 ],

2282 "enumDescriptions": [

2283 "",

2284 "",

2285 "",

2286 "",

2287 "",

2288 "",

2289 ""

2290 ],

2291 "type": "string"

2292 },

2293 "warnings": {

2294 "description": "Any warnings that occurred during processing .",

2295 "items": {

2296 "type": "string"

2297 },

2298 "type": "array"

2299 }

2300 },

2301 "type": "object"

2302 },

2303 "JobRequest": {

2304 "description": "A summary representation of the service request that spawned the job.",

2305 "id": "JobRequest",

2306 "properties": {

2307 "destination": {

2308 "description": "The data destination of the request, for exa mple, a Google BigQuery Table or Dataset ID.",

2309 "items": {

2310 "type": "string"

2311 },

2312 "type": "array"

2313 },

2314 "source": {

2315 "description": "The data source of the request, for example, a Google Cloud Storage object path or Readset ID.",

2316 "items": {

2317 "type": "string"

2318 },

2319 "type": "array"

2320 },

2321 "type": {

2322 "description": "The original request type.",

2323 "enum": [

2324 "ALIGN_READSETS",

2325 "CALL_READSETS",

2326 "EXPERIMENTAL_CREATE_JOB",

2327 "EXPORT_READSETS",

2328 "EXPORT_VARIANTS",

2329 "IMPORT_READSETS",

2330 "IMPORT_VARIANTS",

2331 "UNKNOWN_TYPE"

2332 ],

2333 "enumDescriptions": [

2334 "",

2335 "",

2336 "",

2337 "",

2338 "",

2339 "",

2340 "",

2341 ""

2342 ],

2343 "type": "string"

2344 }

2345 },

2346 "type": "object"

2347 },

2348 "KeyValue": {

2349 "description": "Used to hold basic key value information.",

2350 "id": "KeyValue",

2351 "properties": {

2352 "key": {

2353 "description": "A string which maps to an array of values.",

2354 "type": "string"

2355 },

2356 "value": {

2357 "description": "The string values.",

2358 "items": {

2359 "type": "string"

2360 },

2361 "type": "array"

2362 }

2363 },

2364 "type": "object"

2365 },

2366 "LinearAlignment": {

2367 "description": "A linear alignment can be represented by one CIGAR s tring. Describes the mapped position and local alignment of the read to the refe rence.",

2368 "id": "LinearAlignment",

2369 "properties": {

2370 "cigar": {

2371 "description": "Represents the local alignment of this seque nce (alignment matches, indels, etc) against the reference.",

2372 "items": {

2373 "$ref": "CigarUnit"

2374 },

2375 "type": "array"

2376 },

2377 "mappingQuality": {

2378 "description": "The mapping quality of this alignment. Repre sents how likely the read maps to this position as opposed to other locations.",

2379 "format": "int32",

2380 "type": "integer"

2381 },

2382 "position": {

2383 "$ref": "Position",

2384 "description": "The position of this alignment."

2385 }

2386 },

2387 "type": "object"

2388 },

2389 "ListBasesResponse": {

2390 "id": "ListBasesResponse",

2391 "properties": {

2392 "nextPageToken": {

2393 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",

2394 "type": "string"

2395 },

2396 "offset": {

2397 "description": "The offset position (0-based) of the given s equence from the start of this Reference. This value will differ for each page i n a paginated request.",

2398 "format": "int64",

2399 "type": "string"

2400 },

2401 "sequence": {

2402 "description": "A substring of the bases that make up this r eference.",

2403 "type": "string"

2404 }

2405 },

2406 "type": "object"

2407 },

2408 "ListCoverageBucketsResponse": {

2409 "id": "ListCoverageBucketsResponse",

2410 "properties": {

2411 "bucketWidth": {

2412 "description": "The length of each coverage bucket in base p airs. Note that buckets at the end of a reference sequence may be shorter. This value is omitted if the bucket width is infinity (the default behaviour, with no range or targetBucketWidth).",

2413 "format": "int64",

2414 "type": "string"

2415 },

2416 "coverageBuckets": {

2417 "description": "The coverage buckets. The list of buckets is sparse; a bucket with 0 overlapping reads is not returned. A bucket never cross es more than one reference sequence. Each bucket has width bucketWidth, unless i ts end is the end of the reference sequence.",

2418 "items": {

2419 "$ref": "CoverageBucket"

2420 },

2421 "type": "array"

2422 },

2423 "nextPageToken": {

2424 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",

2425 "type": "string"

2426 }

2427 },

2428 "type": "object"

2429 },

2430 "ListDatasetsResponse": {	1185 "ListDatasetsResponse": {

2431 "description": "The dataset list response.",	1186 "description": "The dataset list response.",

2432 "id": "ListDatasetsResponse",	1187 "id": "ListDatasetsResponse",

2433 "properties": {	1188 "properties": {

2434 "datasets": {	1189 "datasets": {

2435 "description": "The list of matching Datasets.",	1190 "description": "The list of matching Datasets.",

2436 "items": {	1191 "items": {

2437 "$ref": "Dataset"	1192 "$ref": "Dataset"

2438 },	1193 },

2439 "type": "array"	1194 "type": "array"

2440 },	1195 },

2441 "nextPageToken": {	1196 "nextPageToken": {

2442 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",	1197 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",

2443 "type": "string"	1198 "type": "string"

2444 }	1199 }

2445 },	1200 },

2446 "type": "object"	1201 "type": "object"

2447 },	1202 },

2448 "MergeVariantsRequest": {	1203 "Dataset": {

2449 "id": "MergeVariantsRequest",	1204 "description": "A Dataset is a collection of genomic data.",

2450 "properties": {	1205 "id": "Dataset",

2451 "variants": {	1206 "properties": {

2452 "description": "The variants to be merged with existing vari ants.",

2453 "items": {

2454 "$ref": "Variant"

2455 },

2456 "type": "array"

2457 }

2458 },

2459 "type": "object"

2460 },

2461 "Metadata": {

2462 "description": "Metadata describes a single piece of variant call me tadata. These data include a top level key and either a single value string (val ue) or a list of key-value pairs (info.) Value and info are mutually exclusive." ,

2463 "id": "Metadata",

2464 "properties": {

2465 "description": {

2466 "description": "A textual description of this metadata.",

2467 "type": "string"

2468 },

2469 "id": {	1207 "id": {

2470 "description": "User-provided ID field, not enforced by this API. Two or more pieces of structured metadata with identical id and key fields are considered equivalent.",	1208 "description": "The server-generated dataset ID, unique acro ss all datasets.",

2471 "type": "string"	1209 "type": "string"

	1210 },

	1211 "projectId": {

	1212 "description": "The Google Developers Console project ID tha t this dataset belongs to.",

	1213 "type": "string"

	1214 },

	1215 "name": {

	1216 "description": "The dataset name.",

	1217 "type": "string"

	1218 },

	1219 "createTime": {

	1220 "description": "The time this dataset was created, in second s from the epoch.",

	1221 "type": "string"

	1222 }

	1223 },

	1224 "type": "object"

	1225 },

	1226 "Empty": {

	1227 "description": "A generic empty message that you can re-use to avoid defining duplicated empty messages in your APIs. A typical example is to use it as the request or the response type of an API method. For instance: service Foo { rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty); } The JSON re presentation for `Empty` is empty JSON object `{}`.",

	1228 "id": "Empty",

	1229 "type": "object"

	1230 },

	1231 "UndeleteDatasetRequest": {

	1232 "id": "UndeleteDatasetRequest",

	1233 "type": "object"

	1234 },

	1235 "Operation": {

	1236 "description": "This resource represents a long-running operation th at is the result of a network API call.",

	1237 "id": "Operation",

	1238 "properties": {

	1239 "name": {

	1240 "description": "The server-assigned name, which is only uniq ue within the same service that originally returns it. For example: `operations/ CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw`",

	1241 "type": "string"

	1242 },

	1243 "metadata": {

	1244 "additionalProperties": {

	1245 "description": "Properties of the object. Contains field @ype with type URL.",

	1246 "type": "any"

	1247 },

	1248 "description": "An [OperationMetadata][google.genomics.v1.Op erationMetadata] object. This will always be returned with the [Operation][googl e.longrunning.Operation].",

	1249 "type": "object"

	1250 },

	1251 "done": {

	1252 "description": "If the value is `false`, it means the operat ion is still in progress. If true, the operation is completed and the `result` i s available.",

	1253 "type": "boolean"

	1254 },

	1255 "error": {

	1256 "$ref": "Status",

	1257 "description": "The error result of the operation in case of failure."

	1258 },

	1259 "response": {

	1260 "additionalProperties": {

	1261 "description": "Properties of the object. Contains field @ype with type URL.",

	1262 "type": "any"

	1263 },

	1264 "description": "If importing [ReadGroupSets][google.genomics .v1.ReadGroupSet], an [ImportReadGroupSetsResponse][google.genomics.v1.ImportRea dGroupSetsResponse] is returned. If importing [Variants][google.genomics.v1.Vari ant], an [ImportVariantsResponse][google.genomics.v1.ImportVariantsResponse] is returned. For exports, an empty response is returned.",

	1265 "type": "object"

	1266 }

	1267 },

	1268 "type": "object"

	1269 },

	1270 "Status": {

	1271 "description": "The `Status` type defines a logical error model that is suitable for different programming environments, including REST APIs and RPC APIs. It is used by [gRPC](https://github.com/grpc). The error model is designe d to be: - Simple to use and understand for most users - Flexible enough to meet unexpected needs # Overview The `Status` message contains three pieces of data: error code, error message, and error details. The error code should be an enum value of [google.rpc.Code][google.rpc.Code], but it may accept additional error codes if needed. The error message should be a developer-facing English message that helps developers understand and resolve the error. If a localized user- facing error message is needed, put the localized message in the error details o r localize it in the client. The optional error details may contain arbitrary in formation about the error. There is a predefined set of error detail types in th e package `google.rpc` which can be used for common error conditions. # Language mapping The `Status` message is the logical representation of the error model, but it is not necessarily the actual wire format. When the `Status` message is e xposed in different client libraries and different wire protocols, it can be map ped differently. For example, it will likely be mapped to some exceptions in Jav a, but more likely mapped to some error codes in C. # Other uses The error model and the `Status` message can be used in a variety of environments, either with or without APIs, to provide a consistent developer experience across different e nvironments. Example uses of this error model include: - Partial errors. If a se rvice needs to return partial errors to the client, it may embed the `Status` in the normal response to indicate the partial errors. - Workflow errors. A typica l workflow has multiple steps. Each step may have a `Status` message for error r eporting purpose. - Batch operations. If a client uses batch request and batch r esponse, the `Status` message should be used directly inside batch response, one for each error sub-response. - Asynchronous operations. If an API call embeds a synchronous operation results in its response, the status of those operations sh ould be represented directly using the `Status` message. - Logging. If some API errors are stored in logs, the message `Status` could be used directly after any stripping needed for security/privacy reasons.",

	1272 "id": "Status",

	1273 "properties": {

	1274 "code": {

	1275 "description": "The status code, which should be an enum val ue of [google.rpc.Code][google.rpc.Code].",

	1276 "format": "int32",

	1277 "type": "integer"

	1278 },

	1279 "message": {

	1280 "description": "A developer-facing error message, which shou ld be in English. Any user-facing error message should be localized and sent in the [google.rpc.Status.details][google.rpc.Status.details] field, or localized b y the client.",

	1281 "type": "string"

	1282 },

	1283 "details": {

	1284 "description": "A list of messages that carry the error deta ils. There will be a common set of message types for APIs to use.",

	1285 "items": {

	1286 "additionalProperties": {

	1287 "description": "Properties of the object. Contains f ield @ype with type URL.",

	1288 "type": "any"

	1289 },

	1290 "type": "object"

	1291 },

	1292 "type": "array"

	1293 }

	1294 },

	1295 "type": "object"

	1296 },

	1297 "ListOperationsResponse": {

	1298 "description": "The response message for [Operations.ListOperations] [google.longrunning.Operations.ListOperations].",

	1299 "id": "ListOperationsResponse",

	1300 "properties": {

	1301 "operations": {

	1302 "description": "A list of operations that matches the specif ied filter in the request.",

	1303 "items": {

	1304 "$ref": "Operation"

	1305 },

	1306 "type": "array"

	1307 },

	1308 "nextPageToken": {

	1309 "description": "The standard List next-page token.",

	1310 "type": "string"

	1311 }

	1312 },

	1313 "type": "object"

	1314 },

	1315 "CancelOperationRequest": {

	1316 "description": "The request message for [Operations.CancelOperation] [google.longrunning.Operations.CancelOperation].",

	1317 "id": "CancelOperationRequest",

	1318 "type": "object"

	1319 },

	1320 "ImportReadGroupSetsRequest": {

	1321 "description": "The read group set import request.",

	1322 "id": "ImportReadGroupSetsRequest",

	1323 "properties": {

	1324 "datasetId": {

	1325 "description": "Required. The ID of the dataset these read g roup sets will belong to. The caller must have WRITE permissions to this dataset .",

	1326 "type": "string"

	1327 },

	1328 "referenceSetId": {

	1329 "description": "The reference set to which the imported read group sets are aligned to, if any. The reference names of this reference set mu st be a superset of those found in the imported file headers. If no reference se t id is provided, a best effort is made to associate with a matching reference s et.",

	1330 "type": "string"

	1331 },

	1332 "sourceUris": {

	1333 "description": "A list of URIs pointing at BAM files in Goog le Cloud Storage.",

	1334 "items": {

	1335 "type": "string"

	1336 },

	1337 "type": "array"

	1338 },

	1339 "partitionStrategy": {

	1340 "description": "The partition strategy describes how read gr oups are partitioned into read group sets.",

	1341 "enum": [

	1342 "PARTITION_STRATEGY_UNSPECIFIED",

	1343 "PER_FILE_PER_SAMPLE",

	1344 "MERGE_ALL"

	1345 ],

	1346 "type": "string"

	1347 }

	1348 },

	1349 "type": "object"

	1350 },

	1351 "ExportReadGroupSetRequest": {

	1352 "description": "The read group set export request.",

	1353 "id": "ExportReadGroupSetRequest",

	1354 "properties": {

	1355 "projectId": {

	1356 "description": "Required. The Google Developers Console proj ect ID that owns this export.",

	1357 "type": "string"

	1358 },

	1359 "exportUri": {

	1360 "description": "Required. A Google Cloud Storage URI for the exported BAM file. The currently authenticated user must have write access to t he new file. An error will be returned if the URI already contains data.",

	1361 "type": "string"

	1362 },

	1363 "referenceNames": {

	1364 "description": "The reference names to export. If this is no t specified, all reference sequences, including unmapped reads, are exported. Us e `*` to export only unmapped reads.",

	1365 "items": {

	1366 "type": "string"

	1367 },

	1368 "type": "array"

	1369 }

	1370 },

	1371 "type": "object"

	1372 },

	1373 "SearchReadGroupSetsRequest": {

	1374 "description": "The read group set search request.",

	1375 "id": "SearchReadGroupSetsRequest",

	1376 "properties": {

	1377 "datasetIds": {

	1378 "description": "Restricts this query to read group sets with in the given datasets. At least one ID must be provided.",

	1379 "items": {

	1380 "type": "string"

	1381 },

	1382 "type": "array"

	1383 },

	1384 "name": {

	1385 "description": "Only return read group sets for which a subs tring of the name matches this string.",

	1386 "type": "string"

	1387 },

	1388 "pageToken": {

	1389 "description": "The continuation token, which is used to pag e through large result sets. To get the next page of results, set this parameter to the value of `nextPageToken` from the previous response.",

	1390 "type": "string"

	1391 },

	1392 "pageSize": {

	1393 "description": "Specifies number of results to return in a s ingle page. If unspecified, it will default to 256. The maximum value is 1024.",

	1394 "format": "int32",

	1395 "type": "integer"

	1396 }

	1397 },

	1398 "type": "object"

	1399 },

	1400 "SearchReadGroupSetsResponse": {

	1401 "description": "The read group set search response.",

	1402 "id": "SearchReadGroupSetsResponse",

	1403 "properties": {

	1404 "readGroupSets": {

	1405 "description": "The list of matching read group sets.",

	1406 "items": {

	1407 "$ref": "ReadGroupSet"

	1408 },

	1409 "type": "array"

	1410 },

	1411 "nextPageToken": {

	1412 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",

	1413 "type": "string"

	1414 }

	1415 },

	1416 "type": "object"

	1417 },

	1418 "ReadGroupSet": {

	1419 "description": "A read group set is a logical collection of read gro ups, which are collections of reads produced by a sequencer. A read group set ty pically models reads corresponding to one sample, sequenced one way, and aligned one way. * A read group set belongs to one dataset. * A read group belongs to o ne read group set. * A read belongs to one read group.",

	1420 "id": "ReadGroupSet",

	1421 "properties": {

	1422 "id": {

	1423 "description": "The server-generated read group set ID, uniq ue for all read group sets.",

	1424 "type": "string"

	1425 },

	1426 "datasetId": {

	1427 "description": "The dataset ID.",

	1428 "type": "string"

	1429 },

	1430 "referenceSetId": {

	1431 "description": "The reference set the reads in this read gro up set are aligned to.",

	1432 "type": "string"

	1433 },

	1434 "name": {

	1435 "description": "The read group set name. By default this wil l be initialized to the sample name of the sequenced data contained in this set. ",

	1436 "type": "string"

	1437 },

	1438 "filename": {

	1439 "description": "The filename of the original source file for this read group set, if any.",

	1440 "type": "string"

	1441 },

	1442 "readGroups": {

	1443 "description": "The read groups in this set. There are typic ally 1-10 read groups in a read group set.",

	1444 "items": {

	1445 "$ref": "ReadGroup"

	1446 },

	1447 "type": "array"

2472 },	1448 },

2473 "info": {	1449 "info": {

2474 "additionalProperties": {	1450 "additionalProperties": {

2475 "description": "A string which maps to an array of value s.",

2476 "items": {	1451 "items": {

2477 "type": "string"	1452 "type": "any"

2478 },	1453 },

2479 "type": "array"	1454 "type": "array"

2480 },	1455 },

2481 "description": "A string which maps to an array of values.",	1456 "description": "A map of additional read group set informati on.",

2482 "type": "object"	1457 "type": "object"

2483 },	1458 }

2484 "key": {	1459 },

2485 "description": "The top-level key.",	1460 "type": "object"

2486 "type": "string"

2487 },

2488 "number": {

2489 "description": "The number of values that can be included in a field described by this metadata.",

2490 "type": "string"

2491 },

2492 "type": {

2493 "description": "The type of data. Possible types include: In teger, Float, Flag, Character, and String.",

2494 "enum": [

2495 "CHARACTER",

2496 "FLAG",

2497 "FLOAT",

2498 "INTEGER",

2499 "STRING",

2500 "UNKNOWN_TYPE"

2501 ],

2502 "enumDescriptions": [

2503 "",

2504 "",

2505 "",

2506 "",

2507 "",

2508 ""

2509 ],

2510 "type": "string"

2511 },

2512 "value": {

2513 "description": "The value field for simple metadata",

2514 "type": "string"

2515 }

2516 },

2517 "type": "object"

2518 },

2519 "PairedFastqSource": {

2520 "description": "Describes a paired-end FASTQ file source for alignme nt.",

2521 "id": "PairedFastqSource",

2522 "properties": {

2523 "firstSourceUris": {

2524 "description": "A list of URIs pointing at paired end FASTQ files in Google Cloud Storage which will be aligned. The first of each paired fi le should be specified here, in an order that matches the second of each paired file specified in secondSourceUris. For example: firstSourceUris: [file1_1.fq, f ile2_1.fq], secondSourceUris: [file1_2.fq, file2_2.fq]. The caller must have REA D permissions for these files.",

2525 "items": {

2526 "type": "string"

2527 },

2528 "type": "array"

2529 },

2530 "metadata": {

2531 "$ref": "FastqMetadata",

2532 "description": "Optionally specifies the metadata to be asso ciated with the final aligned read group set."

2533 },

2534 "secondSourceUris": {

2535 "description": "A list of URIs pointing at paired end FASTQ files in Google Cloud Storage which will be aligned. The second of each paired f ile should be specified here, in an order that matches the first of each paired file specified in firstSourceUris. For example: firstSourceUris: [file1_1.fq, fi le2_1.fq], secondSourceUris: [file1_2.fq, file2_2.fq]. The caller must have READ permissions for these files.",

2536 "items": {

2537 "type": "string"

2538 },

2539 "type": "array"

2540 }

2541 },

2542 "type": "object"

2543 },

2544 "Position": {

2545 "description": "An abstraction for referring to a genomic position, in relation to some already known reference. For now, represents a genomic posit ion as a reference name, a base number on that reference (0-based), and a determ ination of forward or reverse strand.",

2546 "id": "Position",

2547 "properties": {

2548 "position": {

2549 "description": "The 0-based offset from the start of the for ward strand for that reference.",

2550 "format": "int64",

2551 "type": "string"

2552 },

2553 "referenceName": {

2554 "description": "The name of the reference in whatever refere nce set is being used.",

2555 "type": "string"

2556 },

2557 "reverseStrand": {

2558 "description": "Whether this position is on the reverse stra nd, as opposed to the forward strand.",

2559 "type": "boolean"

2560 }

2561 },

2562 "type": "object"

2563 },

2564 "QueryRange": {

2565 "description": "A 0-based half-open genomic coordinate range for sea rch requests.",

2566 "id": "QueryRange",

2567 "properties": {

2568 "end": {

2569 "description": "The end position of the range on the referen ce, 0-based exclusive. If specified, referenceId or referenceName must also be s pecified. If unset or 0, defaults to the length of the reference.",

2570 "format": "int64",

2571 "type": "string"

2572 },

2573 "referenceId": {

2574 "description": "The ID of the reference to query. At most on e of referenceId and referenceName should be specified.",

2575 "type": "string"

2576 },

2577 "referenceName": {

2578 "description": "The name of the reference to query, within t he reference set associated with this query. At most one of referenceId and refe renceName pshould be specified.",

2579 "type": "string"

2580 },

2581 "start": {

2582 "description": "The start position of the range on the refer ence, 0-based inclusive. If specified, referenceId or referenceName must also be specified. Defaults to 0.",

2583 "format": "int64",

2584 "type": "string"

2585 }

2586 },

2587 "type": "object"

2588 },

2589 "Range": {

2590 "description": "A 0-based half-open genomic coordinate range over a reference sequence.",

2591 "id": "Range",

2592 "properties": {

2593 "end": {

2594 "description": "The end position of the range on the referen ce, 0-based exclusive. If specified, referenceName must also be specified.",

2595 "format": "int64",

2596 "type": "string"

2597 },

2598 "referenceName": {

2599 "description": "The reference sequence name, for example chr 1, 1, or chrX.",

2600 "type": "string"

2601 },

2602 "start": {

2603 "description": "The start position of the range on the refer ence, 0-based inclusive. If specified, referenceName must also be specified.",

2604 "format": "int64",

2605 "type": "string"

2606 }

2607 },

2608 "type": "object"

2609 },

2610 "RangePosition": {

2611 "description": "A 0-based half-open genomic coordinate range over a reference sequence, for representing the position of a genomic resource.",

2612 "id": "RangePosition",

2613 "properties": {

2614 "end": {

2615 "description": "The end position of the range on the referen ce, 0-based exclusive.",

2616 "format": "int64",

2617 "type": "string"

2618 },

2619 "referenceId": {

2620 "description": "The ID of the Google Genomics reference asso ciated with this range.",

2621 "type": "string"

2622 },

2623 "referenceName": {

2624 "description": "The display name corresponding to the refere nce specified by referenceId, for example chr1, 1, or chrX.",

2625 "type": "string"

2626 },

2627 "reverseStrand": {

2628 "description": "Whether this range refers to the reverse str and, as opposed to the forward strand. Note that regardless of this field, the s tart/end position of the range always refer to the forward strand.",

2629 "type": "boolean"

2630 },

2631 "start": {

2632 "description": "The start position of the range on the refer ence, 0-based inclusive.",

2633 "format": "int64",

2634 "type": "string"

2635 }

2636 },

2637 "type": "object"

2638 },

2639 "Read": {

2640 "description": "A read alignment describes a linear alignment of a s tring of DNA to a reference sequence, in addition to metadata about the fragment (the molecule of DNA sequenced) and the read (the bases which were read by the sequencer). A read is equivalent to a line in a SAM file. A read belongs to exac tly one read group and exactly one read group set. Generating a reference-aligne d sequence string When interacting with mapped reads, it's often useful to produ ce a string representing the local alignment of the read to reference. The follo wing pseudocode demonstrates one way of doing this:\nout = \"\" offset = 0 for c in read.alignment.cigar { switch c.operation { case \"ALIGNMENT_MATCH\", \"SEQU ENCE_MATCH\", \"SEQUENCE_MISMATCH\": out += read.alignedSequence[offset:offset+c .operationLength] offset += c.operationLength break case \"CLIP_SOFT\", \"INSERT \": offset += c.operationLength break case \"PAD\": out += repeat(\"*\", c.opera tionLength) break case \"DELETE\": out += repeat(\"-\", c.operationLength) break case \"SKIP\": out += repeat(\" \", c.operationLength) break case \"CLIP_HARD\" : break } } return out\nConverting to SAM's CIGAR string The following pseudocod e generates a SAM CIGAR string from the cigar field. Note that this is a lossy c onversion (cigar.referenceSequence is lost).\ncigarMap = { \"ALIGNMENT_MATCH\": \"M\", \"INSERT\": \"I\", \"DELETE\": \"D\", \"SKIP\": \"N\", \"CLIP_SOFT\": \"S \", \"CLIP_HARD\": \"H\", \"PAD\": \"P\", \"SEQUENCE_MATCH\": \"=\", \"SEQUENCE_ MISMATCH\": \"X\", } cigarStr = \"\" for c in read.alignment.cigar { cigarStr += c.operationLength + cigarMap[c.operation] } return cigarStr",

2641 "id": "Read",

2642 "properties": {

2643 "alignedQuality": {

2644 "description": "The quality of the read sequence contained i n this alignment record. alignedSequence and alignedQuality may be shorter than the full read sequence and quality. This will occur if the alignment is part of a chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR fo r this read will begin/end with a hard clip operator that will indicate the leng th of the excised sequence.",

2645 "items": {

2646 "format": "int32",

2647 "type": "integer"

2648 },

2649 "type": "array"

2650 },

2651 "alignedSequence": {

2652 "description": "The bases of the read sequence contained in this alignment record, without CIGAR operations applied. alignedSequence and ali gnedQuality may be shorter than the full read sequence and quality. This will oc cur if the alignment is part of a chimeric alignment, or if the read was trimmed . When this occurs, the CIGAR for this read will begin/end with a hard clip oper ator that will indicate the length of the excised sequence.",

2653 "type": "string"

2654 },

2655 "alignment": {

2656 "$ref": "LinearAlignment",

2657 "description": "The linear alignment for this alignment reco rd. This field will be unset if the read is unmapped."

2658 },

2659 "duplicateFragment": {

2660 "description": "The fragment is a PCR or optical duplicate ( SAM flag 0x400)",

2661 "type": "boolean"

2662 },

2663 "failedVendorQualityChecks": {

2664 "description": "SAM flag 0x200",

2665 "type": "boolean"

2666 },

2667 "fragmentLength": {

2668 "description": "The observed length of the fragment, equival ent to TLEN in SAM.",

2669 "format": "int32",

2670 "type": "integer"

2671 },

2672 "fragmentName": {

2673 "description": "The fragment name. Equivalent to QNAME (quer y template name) in SAM.",

2674 "type": "string"

2675 },

2676 "id": {

2677 "description": "The unique ID for this read. This is a gener ated unique ID, not to be confused with fragmentName.",

2678 "type": "string"

2679 },

2680 "info": {

2681 "additionalProperties": {

2682 "description": "A string which maps to an array of value s.",

2683 "items": {

2684 "type": "string"

2685 },

2686 "type": "array"

2687 },

2688 "description": "A string which maps to an array of values.",

2689 "type": "object"

2690 },

2691 "nextMatePosition": {

2692 "$ref": "Position",

2693 "description": "The position of the primary alignment of the (readNumber+1)%numberReads read in the fragment. It replaces mate position and mate strand in SAM. This field will be unset if that read is unmapped or if the fragment only has a single read."

2694 },

2695 "numberReads": {

2696 "description": "The number of reads in the fragment (extensi on to SAM flag 0x1).",

2697 "format": "int32",

2698 "type": "integer"

2699 },

2700 "properPlacement": {

2701 "description": "The orientation and the distance between rea ds from the fragment are consistent with the sequencing protocol (SAM flag 0x2)" ,

2702 "type": "boolean"

2703 },

2704 "readGroupId": {

2705 "description": "The ID of the read group this read belongs t o. (Every read must belong to exactly one read group.)",

2706 "type": "string"

2707 },

2708 "readGroupSetId": {

2709 "description": "The ID of the read group set this read belon gs to. (Every read must belong to exactly one read group set.)",

2710 "type": "string"

2711 },

2712 "readNumber": {

2713 "description": "The read number in sequencing. 0-based and l ess than numberReads. This field replaces SAM flag 0x40 and 0x80.",

2714 "format": "int32",

2715 "type": "integer"

2716 },

2717 "secondaryAlignment": {

2718 "description": "Whether this alignment is secondary. Equival ent to SAM flag 0x100. A secondary alignment represents an alternative to the pr imary alignment for this read. Aligners may return secondary alignments if a rea d can map ambiguously to multiple coordinates in the genome. By convention, each read has one and only one alignment where both secondaryAlignment and supplemen taryAlignment are false.",

2719 "type": "boolean"

2720 },

2721 "supplementaryAlignment": {

2722 "description": "Whether this alignment is supplementary. Equ ivalent to SAM flag 0x800. Supplementary alignments are used in the representati on of a chimeric alignment. In a chimeric alignment, a read is split into multip le linear alignments that map to different reference contigs. The first linear a lignment in the read will be designated as the representative alignment; the rem aining linear alignments will be designated as supplementary alignments. These a lignments may have different mapping quality scores. In each linear alignment in a chimeric alignment, the read will be hard clipped. The alignedSequence and al ignedQuality fields in the alignment record will only represent the bases for it s respective linear alignment.",

2723 "type": "boolean"

2724 }

2725 },

2726 "type": "object"

2727 },	1461 },

2728 "ReadGroup": {	1462 "ReadGroup": {

2729 "description": "A read group is all the data that's processed the sa me way by the sequencer.",	1463 "description": "A read group is all the data that's processed the sa me way by the sequencer.",

2730 "id": "ReadGroup",	1464 "id": "ReadGroup",

2731 "properties": {	1465 "properties": {

	1466 "id": {

	1467 "description": "The server-generated read group ID, unique f or all read groups. Note: This is different than the `@RG ID` field in the SAM s pec. For that value, see the `name` field.",

	1468 "type": "string"

	1469 },

2732 "datasetId": {	1470 "datasetId": {

2733 "description": "The ID of the dataset this read group belong s to.",	1471 "description": "The ID of the dataset this read group belong s to.",

2734 "type": "string"	1472 "type": "string"

2735 },	1473 },

	1474 "name": {

	1475 "description": "The read group name. This corresponds to the @RG ID field in the SAM spec.",

	1476 "type": "string"

	1477 },

2736 "description": {	1478 "description": {

2737 "description": "A free-form text description of this read gr oup.",	1479 "description": "A free-form text description of this read gr oup.",

2738 "type": "string"	1480 "type": "string"

2739 },	1481 },

2740 "experiment": {	1482 "sampleId": {

2741 "$ref": "ReadGroupExperiment",	1483 "description": "The sample this read group's data was genera ted from. Note: This is not an actual ID within this repository, but rather an i dentifier for a sample which may be meaningful to some external system.",

2742 "description": "The experiment used to generate this read gr oup."

2743 },

2744 "id": {

2745 "description": "The generated unique read group ID. Note: Th is is different than the @RG ID field in the SAM spec. For that value, see the n ame field.",

2746 "type": "string"	1484 "type": "string"

2747 },	1485 },

2748 "info": {	1486 "experiment": {

2749 "additionalProperties": {	1487 "$ref": "Experiment",

2750 "description": "A string which maps to an array of value s.",	1488 "description": "The experiment used to generate this read gr oup."

2751 "items": {

2752 "type": "string"

2753 },

2754 "type": "array"

2755 },

2756 "description": "A string which maps to an array of values.",

2757 "type": "object"

2758 },

2759 "name": {

2760 "description": "The read group name. This corresponds to the @RG ID field in the SAM spec.",

2761 "type": "string"

2762 },	1489 },

2763 "predictedInsertSize": {	1490 "predictedInsertSize": {

2764 "description": "The predicted insert size of this read group . The insert size is the length the sequenced DNA fragment from end-to-end, not including the adapters.",	1491 "description": "The predicted insert size of this read group . The insert size is the length the sequenced DNA fragment from end-to-end, not including the adapters.",

2765 "format": "int32",	1492 "format": "int32",

2766 "type": "integer"	1493 "type": "integer"

2767 },	1494 },

2768 "programs": {	1495 "programs": {

2769 "description": "The programs used to generate this read grou p. Programs are always identical for all read groups within a read group set. Fo r this reason, only the first read group in a returned set will have this field populated.",	1496 "description": "The programs used to generate this read grou p. Programs are always identical for all read groups within a read group set. Fo r this reason, only the first read group in a returned set will have this field populated.",

2770 "items": {	1497 "items": {

2771 "$ref": "ReadGroupProgram"	1498 "$ref": "Program"

2772 },	1499 },

2773 "type": "array"	1500 "type": "array"

2774 },	1501 },

2775 "referenceSetId": {	1502 "referenceSetId": {

2776 "description": "The reference set the reads in this read gro up are aligned to. Required if there are any read alignments.",	1503 "description": "The reference set the reads in this read gro up are aligned to. Required if there are any read alignments.",

2777 "type": "string"	1504 "type": "string"

2778 },	1505 },

2779 "sampleId": {	1506 "info": {

2780 "description": "The sample this read group's data was genera ted from. Note: This is not an actual ID within this repository, but rather an i dentifier for a sample which may be meaningful to some external system.",	1507 "additionalProperties": {

	1508 "items": {

	1509 "type": "any"

	1510 },

	1511 "type": "array"

	1512 },

	1513 "description": "A map of additional read group information. This must be of the form map (string key mapping to a list of string values).",

	1514 "type": "object"

	1515 }

	1516 },

	1517 "type": "object"

	1518 },

	1519 "Experiment": {

	1520 "id": "Experiment",

	1521 "properties": {

	1522 "libraryId": {

	1523 "description": "The library used as part of this experiment. Note: This is not an actual ID within this repository, but rather an identifier for a library which may be meaningful to some external system.",

	1524 "type": "string"

	1525 },

	1526 "platformUnit": {

	1527 "description": "The platform unit used as part of this exper iment e.g. flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the @RG PU field in the SAM spec.",

	1528 "type": "string"

	1529 },

	1530 "sequencingCenter": {

	1531 "description": "The sequencing center used as part of this e xperiment.",

	1532 "type": "string"

	1533 },

	1534 "instrumentModel": {

	1535 "description": "The instrument model used as part of this ex periment. This maps to sequencing technology in BAM.",

2781 "type": "string"	1536 "type": "string"

2782 }	1537 }

2783 },	1538 },

2784 "type": "object"	1539 "type": "object"

2785 },	1540 },

2786 "ReadGroupExperiment": {	1541 "Program": {

2787 "id": "ReadGroupExperiment",	1542 "id": "Program",

2788 "properties": {

2789 "instrumentModel": {

2790 "description": "The instrument model used as part of this ex periment. This maps to sequencing technology in BAM.",

2791 "type": "string"

2792 },

2793 "libraryId": {

2794 "description": "The library used as part of this experiment. Note: This is not an actual ID within this repository, but rather an identifier for a library which may be meaningful to some external system.",

2795 "type": "string"

2796 },

2797 "platformUnit": {

2798 "description": "The platform unit used as part of this exper iment e.g. flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the",

2799 "type": "string"

2800 },

2801 "sequencingCenter": {

2802 "description": "The sequencing center used as part of this e xperiment.",

2803 "type": "string"

2804 }

2805 },

2806 "type": "object"

2807 },

2808 "ReadGroupProgram": {

2809 "id": "ReadGroupProgram",

2810 "properties": {	1543 "properties": {

2811 "commandLine": {	1544 "commandLine": {

2812 "description": "The command line used to run this program.",	1545 "description": "The command line used to run this program.",

2813 "type": "string"	1546 "type": "string"

2814 },	1547 },

2815 "id": {	1548 "id": {

2816 "description": "The user specified locally unique ID of the program. Used along with prevProgramId to define an ordering between programs.",	1549 "description": "The user specified locally unique ID of the program. Used along with `prevProgramId` to define an ordering between programs. ",

2817 "type": "string"	1550 "type": "string"

2818 },	1551 },

2819 "name": {	1552 "name": {

2820 "description": "The name of the program.",	1553 "description": "The name of the program.",

2821 "type": "string"	1554 "type": "string"

2822 },	1555 },

2823 "prevProgramId": {	1556 "prevProgramId": {

2824 "description": "The ID of the program run before this one.",	1557 "description": "The ID of the program run before this one.",

2825 "type": "string"	1558 "type": "string"

2826 },	1559 },

2827 "version": {	1560 "version": {

2828 "description": "The version of the program run.",	1561 "description": "The version of the program run.",

2829 "type": "string"	1562 "type": "string"

2830 }	1563 }

2831 },	1564 },

2832 "type": "object"	1565 "type": "object"

2833 },	1566 },

2834 "ReadGroupSet": {	1567 "ListCoverageBucketsResponse": {

2835 "description": "A read group set is a logical collection of read gro ups, which are collections of reads produced by a sequencer. A read group set ty pically models reads corresponding to one sample, sequenced one way, and aligned one way. \n- A read group set belongs to one dataset.\n- A read group belongs to one read group set.\n- A read belongs to one read group.",	1568 "id": "ListCoverageBucketsResponse",

2836 "id": "ReadGroupSet",

2837 "properties": {	1569 "properties": {

2838 "datasetId": {	1570 "bucketWidth": {

2839 "description": "The dataset ID.",	1571 "description": "The length of each coverage bucket in base p airs. Note that buckets at the end of a reference sequence may be shorter. This value is omitted if the bucket width is infinity (the default behaviour, with no range or `targetBucketWidth`).",

2840 "type": "string"

2841 },

2842 "filename": {

2843 "description": "The filename of the original source file for this read group set, if any.",

2844 "type": "string"

2845 },

2846 "id": {

2847 "description": "The read group set ID.",

2848 "type": "string"

2849 },

2850 "info": {

2851 "additionalProperties": {

2852 "description": "A string which maps to an array of value s.",

2853 "items": {

2854 "type": "string"

2855 },

2856 "type": "array"

2857 },

2858 "description": "A string which maps to an array of values.",

2859 "type": "object"

2860 },

2861 "name": {

2862 "description": "The read group set name. By default this wil l be initialized to the sample name of the sequenced data contained in this set. ",

2863 "type": "string"

2864 },

2865 "readGroups": {

2866 "description": "The read groups in this set. There are typic ally 1-10 read groups in a read group set.",

2867 "items": {

2868 "$ref": "ReadGroup"

2869 },

2870 "type": "array"

2871 },

2872 "referenceSetId": {

2873 "description": "The reference set the reads in this read gro up set are aligned to.",

2874 "type": "string"

2875 }

2876 },

2877 "type": "object"

2878 },

2879 "Reference": {

2880 "description": "A reference is a canonical assembled DNA sequence, i ntended to act as a reference coordinate space for other genomic annotations. A single reference might represent the human chromosome 1 or mitochandrial DNA, fo r instance. A reference belongs to one or more reference sets.",

2881 "id": "Reference",

2882 "properties": {

2883 "id": {

2884 "description": "The Google generated immutable ID of the ref erence.",

2885 "type": "string"

2886 },

2887 "length": {

2888 "description": "The length of this reference's sequence.",

2889 "format": "int64",	1572 "format": "int64",

2890 "type": "string"	1573 "type": "string"

2891 },	1574 },

2892 "md5checksum": {	1575 "coverageBuckets": {

2893 "description": "MD5 of the upper-case sequence excluding all whitespace characters (this is equivalent to SQ:M5 in SAM). This value is repre sented in lower case hexadecimal format.",	1576 "description": "The coverage buckets. The list of buckets is sparse; a bucket with 0 overlapping reads is not returned. A bucket never cross es more than one reference sequence. Each bucket has width `bucketWidth`, unless its end is the end of the reference sequence.",

2894 "type": "string"

2895 },

2896 "name": {

2897 "description": "The name of this reference, for example 22." ,

2898 "type": "string"

2899 },

2900 "ncbiTaxonId": {

2901 "description": "ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human) if not specified by the containing reference set.",

2902 "format": "int32",

2903 "type": "integer"

2904 },

2905 "sourceAccessions": {

2906 "description": "All known corresponding accession IDs in INS DC (GenBank/ENA/DDBJ) ideally with a version number, for example GCF_000001405.2 6.",

2907 "items": {	1577 "items": {

2908 "type": "string"	1578 "$ref": "CoverageBucket"

2909 },

2910 "type": "array"

2911 },

2912 "sourceURI": {

2913 "description": "The URI from which the sequence was obtained . Specifies a FASTA format file/string with one name, sequence pair.",

2914 "type": "string"

2915 }

2916 },

2917 "type": "object"

2918 },

2919 "ReferenceBound": {

2920 "description": "ReferenceBound records an upper bound for the starti ng coordinate of variants in a particular reference.",

2921 "id": "ReferenceBound",

2922 "properties": {

2923 "referenceName": {

2924 "description": "The reference the bound is associate with.",

2925 "type": "string"

2926 },

2927 "upperBound": {

2928 "description": "An upper bound (inclusive) on the starting c oordinate of any variant in the reference sequence.",

2929 "format": "int64",

2930 "type": "string"

2931 }

2932 },

2933 "type": "object"

2934 },

2935 "ReferenceSet": {

2936 "description": "A reference set is a set of references which typical ly comprise a reference assembly for a species, such as GRCh38 which is represen tative of the human genome. A reference set defines a common coordinate space fo r comparing reference-aligned experimental data. A reference set contains 1 or m ore references.",

2937 "id": "ReferenceSet",

2938 "properties": {

2939 "assemblyId": {

2940 "description": "Public id of this reference set, such as GRC h37.",

2941 "type": "string"

2942 },

2943 "description": {

2944 "description": "Free text description of this reference set. ",

2945 "type": "string"

2946 },

2947 "id": {

2948 "description": "The Google generated immutable ID of the ref erence set.",

2949 "type": "string"

2950 },

2951 "md5checksum": {

2952 "description": "Order-independent MD5 checksum which identif ies this reference set. The checksum is computed by sorting all lower case hexid ecimal string reference.md5checksum (for all reference in this set) in ascending lexicographic order, concatenating, and taking the MD5 of that value. The resul ting value is represented in lower case hexadecimal format.",

2953 "type": "string"

2954 },

2955 "ncbiTaxonId": {

2956 "description": "ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human) indicating the species which this assembly is intended to mo del. Note that contained references may specify a different ncbiTaxonId, as asse mblies may contain reference sequences which do not belong to the modeled specie s, e.g. EBV in a human reference genome.",

2957 "format": "int32",

2958 "type": "integer"

2959 },

2960 "referenceIds": {

2961 "description": "The IDs of the reference objects that are pa rt of this set. Reference.md5checksum must be unique within this set.",

2962 "items": {

2963 "type": "string"

2964 },

2965 "type": "array"

2966 },

2967 "sourceAccessions": {

2968 "description": "All known corresponding accession IDs in INS DC (GenBank/ENA/DDBJ) ideally with a version number, for example NC_000001.11.",

2969 "items": {

2970 "type": "string"

2971 },

2972 "type": "array"

2973 },

2974 "sourceURI": {

2975 "description": "The URI from which the references were obtai ned.",

2976 "type": "string"

2977 }

2978 },

2979 "type": "object"

2980 },

2981 "SearchAnnotationSetsRequest": {

2982 "id": "SearchAnnotationSetsRequest",

2983 "properties": {

2984 "datasetIds": {

2985 "description": "The dataset IDs to search within. Caller mus t have READ access to these datasets.",

2986 "items": {

2987 "type": "string"

2988 },

2989 "type": "array"

2990 },

2991 "name": {

2992 "description": "Only return annotations sets for which a sub string of the name matches this string (case insensitive).",

2993 "type": "string"

2994 },

2995 "pageSize": {

2996 "description": "Specifies number of results to return in a s ingle page. If unspecified, it will default to 128. The maximum value is 1024.",

2997 "format": "int32",

2998 "type": "integer"

2999 },

3000 "pageToken": {

3001 "description": "The continuation token, which is used to pag e through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.",

3002 "type": "string"

3003 },

3004 "referenceSetId": {

3005 "description": "If specified, only annotation sets associate d with the given reference set are returned.",

3006 "type": "string"

3007 },

3008 "types": {

3009 "description": "If specified, only annotation sets that have any of these types are returned.",

3010 "items": {

3011 "enum": [

3012 "GENE",

3013 "GENERIC",

3014 "TRANSCRIPT",

3015 "VARIANT"

3016 ],

3017 "enumDescriptions": [

3018 "",

3019 "",

3020 "",

3021 ""

3022 ],

3023 "type": "string"

3024 },

3025 "type": "array"

3026 }

3027 },

3028 "type": "object"

3029 },

3030 "SearchAnnotationSetsResponse": {

3031 "id": "SearchAnnotationSetsResponse",

3032 "properties": {

3033 "annotationSets": {

3034 "description": "The matching annotation sets.",

3035 "items": {

3036 "$ref": "AnnotationSet"

3037 },	1579 },

3038 "type": "array"	1580 "type": "array"

3039 },	1581 },

3040 "nextPageToken": {	1582 "nextPageToken": {

3041 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",	1583 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",

3042 "type": "string"	1584 "type": "string"

3043 }	1585 }

3044 },	1586 },

3045 "type": "object"	1587 "type": "object"

3046 },	1588 },

3047 "SearchAnnotationsRequest": {	1589 "CoverageBucket": {

3048 "id": "SearchAnnotationsRequest",	1590 "description": "A bucket over which read coverage has been precomput ed. A bucket corresponds to a specific range of the reference sequence.",

	1591 "id": "CoverageBucket",

3049 "properties": {	1592 "properties": {

3050 "annotationSetIds": {	1593 "range": {

3051 "description": "The annotation sets to search within. The ca ller must have READ access to these annotation sets. Required. All queried annot ation sets must have the same type.",	1594 "$ref": "Range",

	1595 "description": "The genomic coordinate range spanned by this bucket."

	1596 },

	1597 "meanCoverage": {

	1598 "description": "The average number of reads which are aligne d to each individual reference base in this bucket.",

	1599 "format": "float",

	1600 "type": "number"

	1601 }

	1602 },

	1603 "type": "object"

	1604 },

	1605 "Range": {

	1606 "description": "A 0-based half-open genomic coordinate range for sea rch requests.",

	1607 "id": "Range",

	1608 "properties": {

	1609 "referenceName": {

	1610 "description": "The reference sequence name, for example `ch r1`, `1`, or `chrX`.",

	1611 "type": "string"

	1612 },

	1613 "start": {

	1614 "description": "The start position of the range on the refer ence, 0-based inclusive.",

	1615 "format": "int64",

	1616 "type": "string"

	1617 },

	1618 "end": {

	1619 "description": "The end position of the range on the referen ce, 0-based exclusive.",

	1620 "format": "int64",

	1621 "type": "string"

	1622 }

	1623 },

	1624 "type": "object"

	1625 },

	1626 "SearchReadsRequest": {

	1627 "description": "The read search request.",

	1628 "id": "SearchReadsRequest",

	1629 "properties": {

	1630 "readGroupSetIds": {

	1631 "description": "The IDs of the read groups sets within which to search for reads. All specified read group sets must be aligned against a co mmon set of reference sequences; this defines the genomic coordinates for the qu ery. Must specify one of `readGroupSetIds` or `readGroupIds`.",

3052 "items": {	1632 "items": {

3053 "type": "string"	1633 "type": "string"

3054 },	1634 },

3055 "type": "array"	1635 "type": "array"

3056 },	1636 },

	1637 "readGroupIds": {

	1638 "description": "The IDs of the read groups within which to s earch for reads. All specified read groups must belong to the same read group se ts. Must specify one of `readGroupSetIds` or `readGroupIds`.",

	1639 "items": {

	1640 "type": "string"

	1641 },

	1642 "type": "array"

	1643 },

	1644 "referenceName": {

	1645 "description": "The reference sequence name, for example `ch r1`, `1`, or `chrX`. If set to *, only unmapped reads are returned.",

	1646 "type": "string"

	1647 },

	1648 "start": {

	1649 "description": "The start position of the range on the refer ence, 0-based inclusive. If specified, `referenceName` must also be specified.",

	1650 "format": "int64",

	1651 "type": "string"

	1652 },

	1653 "end": {

	1654 "description": "The end position of the range on the referen ce, 0-based exclusive. If specified, `referenceName` must also be specified.",

	1655 "format": "int64",

	1656 "type": "string"

	1657 },

	1658 "pageToken": {

	1659 "description": "The continuation token, which is used to pag e through large result sets. To get the next page of results, set this parameter to the value of `nextPageToken` from the previous response.",

	1660 "type": "string"

	1661 },

3057 "pageSize": {	1662 "pageSize": {

3058 "description": "Specifies number of results to return in a s ingle page. If unspecified, it will default to 256. The maximum value is 2048.",	1663 "description": "Specifies number of results to return in a s ingle page. If unspecified, it will default to 256. The maximum value is 2048.",

3059 "format": "int32",	1664 "format": "int32",

3060 "type": "integer"	1665 "type": "integer"

3061 },

3062 "pageToken": {

3063 "description": "The continuation token, which is used to pag e through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.",

3064 "type": "string"

3065 },

3066 "range": {

3067 "$ref": "QueryRange",

3068 "description": "If specified, this query matches only annota tions that overlap this range."

3069 }	1666 }

3070 },	1667 },

3071 "type": "object"	1668 "type": "object"

3072 },	1669 },

3073 "SearchAnnotationsResponse": {	1670 "SearchReadsResponse": {

3074 "id": "SearchAnnotationsResponse",	1671 "description": "The read search response.",

	1672 "id": "SearchReadsResponse",

3075 "properties": {	1673 "properties": {

3076 "annotations": {	1674 "alignments": {

3077 "description": "The matching annotations.",	1675 "description": "The list of matching alignments sorted by ma pped genomic coordinate, if any, ascending in position within the same reference . Unmapped reads, which have no position, are returned contiguously and are sort ed in ascending lexicographic order by fragment name.",

3078 "items": {	1676 "items": {

3079 "$ref": "Annotation"	1677 "$ref": "Read"

3080 },	1678 },

3081 "type": "array"	1679 "type": "array"

3082 },	1680 },

3083 "nextPageToken": {	1681 "nextPageToken": {

3084 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",	1682 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",

3085 "type": "string"	1683 "type": "string"

3086 }	1684 }

3087 },	1685 },

3088 "type": "object"	1686 "type": "object"

3089 },	1687 },

3090 "SearchCallSetsRequest": {	1688 "Read": {

3091 "description": "The call set search request.",	1689 "description": "A read alignment describes a linear alignment of a s tring of DNA to a [reference sequence][google.genomics.v1.Reference], in additio n to metadata about the fragment (the molecule of DNA sequenced) and the read (t he bases which were read by the sequencer). A read is equivalent to a line in a SAM file. A read belongs to exactly one read group and exactly one [read group s et][google.genomics.v1.ReadGroupSet]. ### Generating a reference-aligned sequenc e string When interacting with mapped reads, it's often useful to produce a stri ng representing the local alignment of the read to reference. The following pseu docode demonstrates one way of doing this: out = \"\" offset = 0 for c in read.a lignment.cigar { switch c.operation { case \"ALIGNMENT_MATCH\", \"SEQUENCE_MATCH \", \"SEQUENCE_MISMATCH\": out += read.alignedSequence[offset:offset+c.operation Length] offset += c.operationLength break case \"CLIP_SOFT\", \"INSERT\": offset += c.operationLength break case \"PAD\": out += repeat(\"*\", c.operationLength ) break case \"DELETE\": out += repeat(\"-\", c.operationLength) break case \"SK IP\": out += repeat(\" \", c.operationLength) break case \"CLIP_HARD\": break } } return out ### Converting to SAM's CIGAR string The following pseudocode gener ates a SAM CIGAR string from the `cigar` field. Note that this is a lossy conver sion (`cigar.referenceSequence` is lost). cigarMap = { \"ALIGNMENT_MATCH\": \"M\ ", \"INSERT\": \"I\", \"DELETE\": \"D\", \"SKIP\": \"N\", \"CLIP_SOFT\": \"S\", \"CLIP_HARD\": \"H\", \"PAD\": \"P\", \"SEQUENCE_MATCH\": \"=\", \"SEQUENCE_MISM ATCH\": \"X\", } cigarStr = \"\" for c in read.alignment.cigar { cigarStr += c.o perationLength + cigarMap[c.operation] } return cigarStr",

3092 "id": "SearchCallSetsRequest",	1690 "id": "Read",

3093 "properties": {	1691 "properties": {

3094 "name": {	1692 "id": {

3095 "description": "Only return call sets for which a substring of the name matches this string.",	1693 "description": "The server-generated read ID, unique across all reads. This is different from the `fragmentName`.",

	1694 "type": "string"

	1695 },

	1696 "readGroupId": {

	1697 "description": "The ID of the read group this read belongs t o. (Every read must belong to exactly one read group.)",

	1698 "type": "string"

	1699 },

	1700 "readGroupSetId": {

	1701 "description": "The ID of the read group set this read belon gs to. (Every read must belong to exactly one read group set.)",

	1702 "type": "string"

	1703 },

	1704 "fragmentName": {

	1705 "description": "The fragment name. Equivalent to QNAME (quer y template name) in SAM.",

	1706 "type": "string"

	1707 },

	1708 "properPlacement": {

	1709 "description": "The orientation and the distance between rea ds from the fragment are consistent with the sequencing protocol (SAM flag 0x2)" ,

	1710 "type": "boolean"

	1711 },

	1712 "duplicateFragment": {

	1713 "description": "The fragment is a PCR or optical duplicate ( SAM flag 0x400)",

	1714 "type": "boolean"

	1715 },

	1716 "fragmentLength": {

	1717 "description": "The observed length of the fragment, equival ent to TLEN in SAM.",

	1718 "format": "int32",

	1719 "type": "integer"

	1720 },

	1721 "readNumber": {

	1722 "description": "The read number in sequencing. 0-based and l ess than numberReads. This field replaces SAM flag 0x40 and 0x80.",

	1723 "format": "int32",

	1724 "type": "integer"

	1725 },

	1726 "numberReads": {

	1727 "description": "The number of reads in the fragment (extensi on to SAM flag 0x1).",

	1728 "format": "int32",

	1729 "type": "integer"

	1730 },

	1731 "failedVendorQualityChecks": {

	1732 "description": "SAM flag 0x200",

	1733 "type": "boolean"

	1734 },

	1735 "alignment": {

	1736 "$ref": "LinearAlignment",

	1737 "description": "The linear alignment for this alignment reco rd. This field will be null if the read is unmapped."

	1738 },

	1739 "secondaryAlignment": {

	1740 "description": "Whether this alignment is secondary. Equival ent to SAM flag 0x100. A secondary alignment represents an alternative to the pr imary alignment for this read. Aligners may return secondary alignments if a rea d can map ambiguously to multiple coordinates in the genome. By convention, each read has one and only one alignment where both `secondaryAlignment` and `supple mentaryAlignment` are false.",

	1741 "type": "boolean"

	1742 },

	1743 "supplementaryAlignment": {

	1744 "description": "Whether this alignment is supplementary. Equ ivalent to SAM flag 0x800. Supplementary alignments are used in the representati on of a chimeric alignment. In a chimeric alignment, a read is split into multip le linear alignments that map to different reference contigs. The first linear a lignment in the read will be designated as the representative alignment; the rem aining linear alignments will be designated as supplementary alignments. These a lignments may have different mapping quality scores. In each linear alignment in a chimeric alignment, the read will be hard clipped. The `alignedSequence` and `alignedQuality` fields in the alignment record will only represent the bases fo r its respective linear alignment.",

	1745 "type": "boolean"

	1746 },

	1747 "alignedSequence": {

	1748 "description": "The bases of the read sequence contained in this alignment record, without CIGAR operations applied. `alignedSequence` and `alignedQuality` may be shorter than the full read sequence and quality. This w ill occur if the alignment is part of a chimeric alignment, or if the read was t rimmed. When this occurs, the CIGAR for this read will begin/end with a hard cli p operator that will indicate the length of the excised sequence.",

	1749 "type": "string"

	1750 },

	1751 "alignedQuality": {

	1752 "description": "The quality of the read sequence contained i n this alignment record. `alignedSequence` and `alignedQuality` may be shorter t han the full read sequence and quality. This will occur if the alignment is part of a chimeric alignment, or if the read was trimmed. When this occurs, the CIGA R for this read will begin/end with a hard clip operator that will indicate the length of the excised sequence.",

	1753 "items": {

	1754 "format": "int32",

	1755 "type": "integer"

	1756 },

	1757 "type": "array"

	1758 },

	1759 "nextMatePosition": {

	1760 "$ref": "Position",

	1761 "description": "The mapping of the primary alignment of the `(readNumber+1)%numberReads` read in the fragment. It replaces mate position and mate strand in SAM."

	1762 },

	1763 "info": {

	1764 "additionalProperties": {

	1765 "items": {

	1766 "type": "any"

	1767 },

	1768 "type": "array"

	1769 },

	1770 "description": "A map of additional read alignment informati on. This must be of the form map (string key mapping to a list of string values) .",

	1771 "type": "object"

	1772 }

	1773 },

	1774 "type": "object"

	1775 },

	1776 "LinearAlignment": {

	1777 "description": "A linear alignment can be represented by one CIGAR s tring. Describes the mapped position and local alignment of the read to the refe rence.",

	1778 "id": "LinearAlignment",

	1779 "properties": {

	1780 "position": {

	1781 "$ref": "Position",

	1782 "description": "The position of this alignment."

	1783 },

	1784 "mappingQuality": {

	1785 "description": "The mapping quality of this alignment. Repre sents how likely the read maps to this position as opposed to other locations.",

	1786 "format": "int32",

	1787 "type": "integer"

	1788 },

	1789 "cigar": {

	1790 "description": "Represents the local alignment of this seque nce (alignment matches, indels, etc) against the reference.",

	1791 "items": {

	1792 "$ref": "CigarUnit"

	1793 },

	1794 "type": "array"

	1795 }

	1796 },

	1797 "type": "object"

	1798 },

	1799 "Position": {

	1800 "description": "An abstraction for referring to a genomic position, in relation to some already known reference. For now, represents a genomic posit ion as a reference name, a base number on that reference (0-based), and a determ ination of forward or reverse strand.",

	1801 "id": "Position",

	1802 "properties": {

	1803 "referenceName": {

	1804 "description": "The name of the reference in whatever refere nce set is being used.",

	1805 "type": "string"

	1806 },

	1807 "position": {

	1808 "description": "The 0-based offset from the start of the for ward strand for that reference.",

	1809 "format": "int64",

	1810 "type": "string"

	1811 },

	1812 "reverseStrand": {

	1813 "description": "Whether this position is on the reverse stra nd, as opposed to the forward strand.",

	1814 "type": "boolean"

	1815 }

	1816 },

	1817 "type": "object"

	1818 },

	1819 "CigarUnit": {

	1820 "description": "A single CIGAR operation.",

	1821 "id": "CigarUnit",

	1822 "properties": {

	1823 "operation": {

	1824 "enum": [

	1825 "OPERATION_UNSPECIFIED",

	1826 "ALIGNMENT_MATCH",

	1827 "INSERT",

	1828 "DELETE",

	1829 "SKIP",

	1830 "CLIP_SOFT",

	1831 "CLIP_HARD",

	1832 "PAD",

	1833 "SEQUENCE_MATCH",

	1834 "SEQUENCE_MISMATCH"

	1835 ],

	1836 "type": "string"

	1837 },

	1838 "operationLength": {

	1839 "description": "The number of genomic bases that the operati on runs for. Required.",

	1840 "format": "int64",

	1841 "type": "string"

	1842 },

	1843 "referenceSequence": {

	1844 "description": "`referenceSequence` is only used at mismatch es (`SEQUENCE_MISMATCH`) and deletions (`DELETE`). Filling this field replaces S AM's MD tag. If the relevant information is not available, this field is unset." ,

	1845 "type": "string"

	1846 }

	1847 },

	1848 "type": "object"

	1849 },

	1850 "SearchReferenceSetsRequest": {

	1851 "id": "SearchReferenceSetsRequest",

	1852 "properties": {

	1853 "md5checksums": {

	1854 "description": "If present, return references for which the `md5checksum` matches. See `ReferenceSet.md5checksum` for details.",

	1855 "items": {

	1856 "type": "string"

	1857 },

	1858 "type": "array"

	1859 },

	1860 "accessions": {

	1861 "description": "If present, return references for which the accession matches any of these strings. Best to give a version number, for examp le `GCF_000001405.26`. If only the main accession number is given then all recor ds with that main accession will be returned, whichever version. Note that diffe rent versions will have different sequences.",

	1862 "items": {

	1863 "type": "string"

	1864 },

	1865 "type": "array"

	1866 },

	1867 "assemblyId": {

	1868 "description": "If present, return reference sets for which a substring of their `assemblyId` matches this string (case insensitive).",

	1869 "type": "string"

	1870 },

	1871 "pageToken": {

	1872 "description": "The continuation token, which is used to pag e through large result sets. To get the next page of results, set this parameter to the value of `nextPageToken` from the previous response.",

3096 "type": "string"	1873 "type": "string"

3097 },	1874 },

3098 "pageSize": {	1875 "pageSize": {

3099 "description": "The maximum number of call sets to return. I f unspecified, defaults to 1000.",	1876 "description": "Specifies the maximum number of results to r eturn in a single page.",

3100 "format": "int32",	1877 "format": "int32",

3101 "type": "integer"	1878 "type": "integer"

3102 },	1879 }

3103 "pageToken": {	1880 },

3104 "description": "The continuation token, which is used to pag e through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.",	1881 "type": "object"

3105 "type": "string"	1882 },

3106 },	1883 "SearchReferenceSetsResponse": {

3107 "variantSetIds": {	1884 "id": "SearchReferenceSetsResponse",

3108 "description": "Restrict the query to call sets within the g iven variant sets. At least one ID must be provided.",	1885 "properties": {

3109 "items": {	1886 "referenceSets": {

3110 "type": "string"	1887 "description": "The matching references sets.",

3111 },	1888 "items": {

3112 "type": "array"	1889 "$ref": "ReferenceSet"

3113 }

3114 },

3115 "type": "object"

3116 },

3117 "SearchCallSetsResponse": {

3118 "description": "The call set search response.",

3119 "id": "SearchCallSetsResponse",

3120 "properties": {

3121 "callSets": {

3122 "description": "The list of matching call sets.",

3123 "items": {

3124 "$ref": "CallSet"

3125 },	1890 },

3126 "type": "array"	1891 "type": "array"

3127 },	1892 },

3128 "nextPageToken": {	1893 "nextPageToken": {

3129 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",	1894 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",

3130 "type": "string"	1895 "type": "string"

3131 }	1896 }

3132 },	1897 },

3133 "type": "object"	1898 "type": "object"

3134 },	1899 },

3135 "SearchJobsRequest": {	1900 "ReferenceSet": {

3136 "description": "The jobs search request.",	1901 "description": "A reference set is a set of references which typical ly comprise a reference assembly for a species, such as `GRCh38` which is repres entative of the human genome. A reference set defines a common coordinate space for comparing reference-aligned experimental data. A reference set contains 1 or more references.",

3137 "id": "SearchJobsRequest",	1902 "id": "ReferenceSet",

3138 "properties": {	1903 "properties": {

3139 "createdAfter": {	1904 "id": {

3140 "description": "If specified, only jobs created on or after this date, given in milliseconds since Unix epoch, will be returned.",	1905 "description": "The server-generated reference set ID, uniqu e across all reference sets.",

3141 "format": "int64",	1906 "type": "string"

3142 "type": "string"	1907 },

3143 },	1908 "referenceIds": {

3144 "createdBefore": {	1909 "description": "The IDs of the reference objects that are pa rt of this set. `Reference.md5checksum` must be unique within this set.",

3145 "description": "If specified, only jobs created prior to thi s date, given in milliseconds since Unix epoch, will be returned.",	1910 "items": {

3146 "format": "int64",	1911 "type": "string"

	1912 },

	1913 "type": "array"

	1914 },

	1915 "md5checksum": {

	1916 "description": "Order-independent MD5 checksum which identif ies this reference set. The checksum is computed by sorting all lower case hexid ecimal string `reference.md5checksum` (for all reference in this set) in ascendi ng lexicographic order, concatenating, and taking the MD5 of that value. The res ulting value is represented in lower case hexadecimal format.",

	1917 "type": "string"

	1918 },

	1919 "ncbiTaxonId": {

	1920 "description": "ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human) indicating the species which this assembly is intended to mo del. Note that contained references may specify a different `ncbiTaxonId`, as as semblies may contain reference sequences which do not belong to the modeled spec ies, e.g. EBV in a human reference genome.",

	1921 "format": "int32",

	1922 "type": "integer"

	1923 },

	1924 "description": {

	1925 "description": "Free text description of this reference set. ",

	1926 "type": "string"

	1927 },

	1928 "assemblyId": {

	1929 "description": "Public id of this reference set, such as `GR Ch37`.",

	1930 "type": "string"

	1931 },

	1932 "sourceUri": {

	1933 "description": "The URI from which the references were obtai ned.",

	1934 "type": "string"

	1935 },

	1936 "sourceAccessions": {

	1937 "description": "All known corresponding accession IDs in INS DC (GenBank/ENA/DDBJ) ideally with a version number, for example `NC_000001.11`. ",

	1938 "items": {

	1939 "type": "string"

	1940 },

	1941 "type": "array"

	1942 }

	1943 },

	1944 "type": "object"

	1945 },

	1946 "SearchReferencesRequest": {

	1947 "id": "SearchReferencesRequest",

	1948 "properties": {

	1949 "md5checksums": {

	1950 "description": "If present, return references for which the `md5checksum` matches. See `Reference.md5checksum` for construction details.",

	1951 "items": {

	1952 "type": "string"

	1953 },

	1954 "type": "array"

	1955 },

	1956 "accessions": {

	1957 "description": "If present, return references for which the accession matches this string. Best to give a version number, for example `GCF_0 00001405.26`. If only the main accession number is given then all records with t hat main accession will be returned, whichever version. Note that different vers ions will have different sequences.",

	1958 "items": {

	1959 "type": "string"

	1960 },

	1961 "type": "array"

	1962 },

	1963 "referenceSetId": {

	1964 "description": "If present, return only references which bel ong to this reference set.",

	1965 "type": "string"

	1966 },

	1967 "pageToken": {

	1968 "description": "The continuation token, which is used to pag e through large result sets. To get the next page of results, set this parameter to the value of `nextPageToken` from the previous response.",

3147 "type": "string"	1969 "type": "string"

3148 },	1970 },

3149 "pageSize": {	1971 "pageSize": {

3150 "description": "Specifies the number of results to return in a single page. Defaults to 128. The maximum value is 256.",	1972 "description": "Specifies the maximum number of results to r eturn in a single page.",

3151 "format": "int32",	1973 "format": "int32",

3152 "type": "integer"	1974 "type": "integer"

3153 },	1975 }

3154 "pageToken": {	1976 },

3155 "description": "The continuation token which is used to page through large result sets. To get the next page of results, set this parameter to the value of the nextPageToken from the previous response.",	1977 "type": "object"

3156 "type": "string"	1978 },

3157 },	1979 "SearchReferencesResponse": {

3158 "projectNumber": {	1980 "id": "SearchReferencesResponse",

3159 "description": "Required. Only return jobs which belong to t his Google Developers Console project.",	1981 "properties": {

3160 "format": "int64",	1982 "references": {

3161 "type": "string"	1983 "description": "The matching references.",

3162 },	1984 "items": {

3163 "status": {	1985 "$ref": "Reference"

3164 "description": "Only return jobs which have a matching statu s.",	1986 },

3165 "items": {	1987 "type": "array"

3166 "enum": [	1988 },

3167 "CANCELED",

3168 "FAILURE",

3169 "NEW",

3170 "PENDING",

3171 "RUNNING",

3172 "SUCCESS",

3173 "UNKNOWN_STATUS"

3174 ],

3175 "enumDescriptions": [

3176 "",

3177 "",

3178 "",

3179 "",

3180 "",

3181 "",

3182 ""

3183 ],

3184 "type": "string"

3185 },

3186 "type": "array"

3187 }

3188 },

3189 "type": "object"

3190 },

3191 "SearchJobsResponse": {

3192 "description": "The job search response.",

3193 "id": "SearchJobsResponse",

3194 "properties": {

3195 "jobs": {

3196 "description": "The list of jobs results, ordered newest to oldest.",

3197 "items": {

3198 "$ref": "Job"

3199 },

3200 "type": "array"

3201 },

3202 "nextPageToken": {

3203 "description": "The continuation token which is used to page through large result sets. Provide this value is a subsequent request to return the next page of results. This field will be empty if there are no more results .",

3204 "type": "string"

3205 }

3206 },

3207 "type": "object"

3208 },

3209 "SearchReadGroupSetsRequest": {

3210 "description": "The read group set search request.",

3211 "id": "SearchReadGroupSetsRequest",

3212 "properties": {

3213 "datasetIds": {

3214 "description": "Restricts this query to read group sets with in the given datasets. At least one ID must be provided.",

3215 "items": {

3216 "type": "string"

3217 },

3218 "type": "array"

3219 },

3220 "name": {

3221 "description": "Only return read group sets for which a subs tring of the name matches this string.",

3222 "type": "string"

3223 },

3224 "pageSize": {

3225 "description": "Specifies number of results to return in a s ingle page. If unspecified, it will default to 256. The maximum value is 1024.",

3226 "format": "int32",

3227 "type": "integer"

3228 },

3229 "pageToken": {

3230 "description": "The continuation token, which is used to pag e through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.",

3231 "type": "string"

3232 }

3233 },

3234 "type": "object"

3235 },

3236 "SearchReadGroupSetsResponse": {

3237 "description": "The read group set search response.",

3238 "id": "SearchReadGroupSetsResponse",

3239 "properties": {

3240 "nextPageToken": {

3241 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",

3242 "type": "string"

3243 },

3244 "readGroupSets": {

3245 "description": "The list of matching read group sets.",

3246 "items": {

3247 "$ref": "ReadGroupSet"

3248 },

3249 "type": "array"

3250 }

3251 },

3252 "type": "object"

3253 },

3254 "SearchReadsRequest": {

3255 "description": "The read search request.",

3256 "id": "SearchReadsRequest",

3257 "properties": {

3258 "end": {

3259 "description": "The end position of the range on the referen ce, 0-based exclusive. If specified, referenceName must also be specified.",

3260 "format": "int64",

3261 "type": "string"

3262 },

3263 "pageSize": {

3264 "description": "Specifies number of results to return in a s ingle page. If unspecified, it will default to 256. The maximum value is 2048.",

3265 "format": "int32",

3266 "type": "integer"

3267 },

3268 "pageToken": {

3269 "description": "The continuation token, which is used to pag e through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.",

3270 "type": "string"

3271 },

3272 "readGroupIds": {

3273 "description": "The IDs of the read groups within which to s earch for reads. All specified read groups must belong to the same read group se ts. Must specify one of readGroupSetIds or readGroupIds.",

3274 "items": {

3275 "type": "string"

3276 },

3277 "type": "array"

3278 },

3279 "readGroupSetIds": {

3280 "description": "The IDs of the read groups sets within which to search for reads. All specified read group sets must be aligned against a co mmon set of reference sequences; this defines the genomic coordinates for the qu ery. Must specify one of readGroupSetIds or readGroupIds.",

3281 "items": {

3282 "type": "string"

3283 },

3284 "type": "array"

3285 },

3286 "referenceName": {

3287 "description": "The reference sequence name, for example chr 1, 1, or chrX. If set to *, only unmapped reads are returned.",

3288 "type": "string"

3289 },

3290 "start": {

3291 "description": "The start position of the range on the refer ence, 0-based inclusive. If specified, referenceName must also be specified.",

3292 "format": "int64",

3293 "type": "string"

3294 }

3295 },

3296 "type": "object"

3297 },

3298 "SearchReadsResponse": {

3299 "description": "The read search response.",

3300 "id": "SearchReadsResponse",

3301 "properties": {

3302 "alignments": {

3303 "description": "The list of matching alignments sorted by ma pped genomic coordinate, if any, ascending in position within the same reference . Unmapped reads, which have no position, are returned last and are further sort ed in ascending lexicographic order by fragment name.",

3304 "items": {

3305 "$ref": "Read"

3306 },

3307 "type": "array"

3308 },

3309 "nextPageToken": {	1989 "nextPageToken": {

3310 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",	1990 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",

3311 "type": "string"	1991 "type": "string"

3312 }	1992 }

3313 },	1993 },

3314 "type": "object"	1994 "type": "object"

3315 },	1995 },

3316 "SearchReferenceSetsRequest": {	1996 "Reference": {

3317 "description": "",	1997 "description": "A reference is a canonical assembled DNA sequence, i ntended to act as a reference coordinate space for other genomic annotations. A single reference might represent the human chromosome 1 or mitochandrial DNA, fo r instance. A reference belongs to one or more reference sets.",

3318 "id": "SearchReferenceSetsRequest",	1998 "id": "Reference",

3319 "properties": {	1999 "properties": {

3320 "accessions": {	2000 "id": {

3321 "description": "If present, return references for which the accession matches any of these strings. Best to give a version number, for examp le GCF_000001405.26. If only the main accession number is given then all records with that main accession will be returned, whichever version. Note that differe nt versions will have different sequences.",	2001 "description": "The server-generated reference ID, unique ac ross all references.",

	2002 "type": "string"

	2003 },

	2004 "length": {

	2005 "description": "The length of this reference's sequence.",

	2006 "format": "int64",

	2007 "type": "string"

	2008 },

	2009 "md5checksum": {

	2010 "description": "MD5 of the upper-case sequence excluding all whitespace characters (this is equivalent to SQ:M5 in SAM). This value is repre sented in lower case hexadecimal format.",

	2011 "type": "string"

	2012 },

	2013 "name": {

	2014 "description": "The name of this reference, for example `22` .",

	2015 "type": "string"

	2016 },

	2017 "sourceUri": {

	2018 "description": "The URI from which the sequence was obtained . Specifies a FASTA format file/string with one name, sequence pair.",

	2019 "type": "string"

	2020 },

	2021 "sourceAccessions": {

	2022 "description": "All known corresponding accession IDs in INS DC (GenBank/ENA/DDBJ) ideally with a version number, for example `GCF_000001405. 26`.",

3322 "items": {	2023 "items": {

3323 "type": "string"	2024 "type": "string"

3324 },	2025 },

3325 "type": "array"	2026 "type": "array"

3326 },	2027 },

3327 "assemblyId": {	2028 "ncbiTaxonId": {

3328 "description": "If present, return reference sets for which a substring of their assemblyId matches this string (case insensitive).",	2029 "description": "ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human) if not specified by the containing reference set.",

3329 "type": "string"

3330 },

3331 "md5checksums": {

3332 "description": "If present, return references for which the md5checksum matches. See ReferenceSet.md5checksum for details.",

3333 "items": {

3334 "type": "string"

3335 },

3336 "type": "array"

3337 },

3338 "pageSize": {

3339 "description": "Specifies the maximum number of results to r eturn in a single page.",

3340 "format": "int32",	2030 "format": "int32",

3341 "type": "integer"	2031 "type": "integer"

3342 },	2032 }

3343 "pageToken": {	2033 },

3344 "description": "The continuation token, which is used to pag e through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.",	2034 "type": "object"

3345 "type": "string"	2035 },

3346 }	2036 "ListBasesResponse": {

3347 },	2037 "id": "ListBasesResponse",

3348 "type": "object"	2038 "properties": {

3349 },	2039 "offset": {

3350 "SearchReferenceSetsResponse": {	2040 "description": "The offset position (0-based) of the given ` sequence` from the start of this `Reference`. This value will differ for each pa ge in a paginated request.",

3351 "id": "SearchReferenceSetsResponse",	2041 "format": "int64",

3352 "properties": {	2042 "type": "string"

	2043 },

	2044 "sequence": {

	2045 "description": "A substring of the bases that make up this r eference.",

	2046 "type": "string"

	2047 },

3353 "nextPageToken": {	2048 "nextPageToken": {

3354 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",	2049 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",

3355 "type": "string"	2050 "type": "string"

3356 },	2051 }

3357 "referenceSets": {	2052 },

3358 "description": "The matching references sets.",	2053 "type": "object"

3359 "items": {	2054 },

3360 "$ref": "ReferenceSet"	2055 "ImportVariantsRequest": {

3361 },	2056 "description": "The variant data import request.",

3362 "type": "array"	2057 "id": "ImportVariantsRequest",

3363 }	2058 "properties": {

3364 },	2059 "variantSetId": {

3365 "type": "object"	2060 "description": "Required. The variant set to which variant d ata should be imported.",

3366 },	2061 "type": "string"

3367 "SearchReferencesRequest": {	2062 },

3368 "description": "",	2063 "sourceUris": {

3369 "id": "SearchReferencesRequest",	2064 "description": "A list of URIs referencing variant files in Google Cloud Storage. URIs can include wildcards [as described here](https://clo ud.google.com/storage/docs/gsutil/addlhelp/WildcardNames). Note that recursive w ildcards ('**') are not supported.",

3370 "properties": {

3371 "accessions": {

3372 "description": "If present, return references for which the accession matches this string. Best to give a version number, for example GCF_00 0001405.26. If only the main accession number is given then all records with tha t main accession will be returned, whichever version. Note that different versio ns will have different sequences.",

3373 "items": {	2065 "items": {

3374 "type": "string"	2066 "type": "string"

3375 },	2067 },

3376 "type": "array"	2068 "type": "array"

3377 },	2069 },

3378 "md5checksums": {	2070 "format": {

3379 "description": "If present, return references for which the md5checksum matches. See Reference.md5checksum for construction details.",	2071 "description": "The format of the variant data being importe d. If unspecified, defaults to to `VCF`.",

	2072 "enum": [

	2073 "FORMAT_UNSPECIFIED",

	2074 "FORMAT_VCF",

	2075 "FORMAT_COMPLETE_GENOMICS"

	2076 ],

	2077 "type": "string"

	2078 },

	2079 "normalizeReferenceNames": {

	2080 "description": "Convert reference names to the canonical rep resentation. hg19 haploytypes (those reference names containing \"_hap\") are no t modified in any way. All other reference names are modified according to the f ollowing rules: The reference name is capitalized. The \"chr\" prefix is dropped for all autosomes and sex chromsomes. For example \"chr17\" becomes \"17\" and \"chrX\" becomes \"X\". All mitochondrial chromosomes (\"chrM\", \"chrMT\", etc) become \"MT\".",

	2081 "type": "boolean"

	2082 }

	2083 },

	2084 "type": "object"

	2085 },

	2086 "VariantSet": {

	2087 "description": "A variant set is a collection of call sets and varia nts. It contains summary statistics of those contents. A variant set belongs to a dataset.",

	2088 "id": "VariantSet",

	2089 "properties": {

	2090 "datasetId": {

	2091 "description": "The dataset to which this variant set belong s.",

	2092 "type": "string"

	2093 },

	2094 "id": {

	2095 "description": "The server-generated variant set ID, unique across all variant sets.",

	2096 "type": "string"

	2097 },

	2098 "referenceBounds": {

	2099 "description": "A list of all references used by the variant s in a variant set with associated coordinate upper bounds for each one.",

	2100 "items": {

	2101 "$ref": "ReferenceBound"

	2102 },

	2103 "type": "array"

	2104 },

	2105 "metadata": {

	2106 "description": "The metadata associated with this variant se t.",

	2107 "items": {

	2108 "$ref": "VariantSetMetadata"

	2109 },

	2110 "type": "array"

	2111 }

	2112 },

	2113 "type": "object"

	2114 },

	2115 "ReferenceBound": {

	2116 "description": "ReferenceBound records an upper bound for the starti ng coordinate of variants in a particular reference.",

	2117 "id": "ReferenceBound",

	2118 "properties": {

	2119 "referenceName": {

	2120 "description": "The reference the bound is associate with.",

	2121 "type": "string"

	2122 },

	2123 "upperBound": {

	2124 "description": "An upper bound (inclusive) on the starting c oordinate of any variant in the reference sequence.",

	2125 "format": "int64",

	2126 "type": "string"

	2127 }

	2128 },

	2129 "type": "object"

	2130 },

	2131 "VariantSetMetadata": {

	2132 "description": "Metadata describes a single piece of variant call me tadata. These data include a top level key and either a single value string (val ue) or a list of key-value pairs (info.) Value and info are mutually exclusive." ,

	2133 "id": "VariantSetMetadata",

	2134 "properties": {

	2135 "key": {

	2136 "description": "The top-level key.",

	2137 "type": "string"

	2138 },

	2139 "value": {

	2140 "description": "The value field for simple metadata",

	2141 "type": "string"

	2142 },

	2143 "id": {

	2144 "description": "User-provided ID field, not enforced by this API. Two or more pieces of structured metadata with identical id and key fields are considered equivalent.",

	2145 "type": "string"

	2146 },

	2147 "type": {

	2148 "description": "The type of data. Possible types include: In teger, Float, Flag, Character, and String.",

	2149 "enum": [

	2150 "TYPE_UNSPECIFIED",

	2151 "INTEGER",

	2152 "FLOAT",

	2153 "FLAG",

	2154 "CHARACTER",

	2155 "STRING"

	2156 ],

	2157 "type": "string"

	2158 },

	2159 "number": {

	2160 "description": "The number of values that can be included in a field described by this metadata.",

	2161 "type": "string"

	2162 },

	2163 "description": {

	2164 "description": "A textual description of this metadata.",

	2165 "type": "string"

	2166 },

	2167 "info": {

	2168 "additionalProperties": {

	2169 "items": {

	2170 "type": "any"

	2171 },

	2172 "type": "array"

	2173 },

	2174 "description": "Remaining structured metadata key-value pair s. This must be of the form map (string key mapping to a list of string values). ",

	2175 "type": "object"

	2176 }

	2177 },

	2178 "type": "object"

	2179 },

	2180 "ExportVariantSetRequest": {

	2181 "description": "The variant data export request.",

	2182 "id": "ExportVariantSetRequest",

	2183 "properties": {

	2184 "callSetIds": {

	2185 "description": "If provided, only variant call information f rom the specified call sets will be exported. By default all variant calls are e xported.",

3380 "items": {	2186 "items": {

3381 "type": "string"	2187 "type": "string"

3382 },	2188 },

3383 "type": "array"	2189 "type": "array"

3384 },	2190 },

3385 "pageSize": {	2191 "projectId": {

3386 "description": "Specifies the maximum number of results to r eturn in a single page.",	2192 "description": "Required. The Google Cloud project ID that o wns the destination BigQuery dataset. The caller must have WRITE access to this project. This project will also own the resulting export job.",

3387 "format": "int32",	2193 "type": "string"

3388 "type": "integer"	2194 },

3389 },	2195 "format": {

3390 "pageToken": {	2196 "description": "The format for the exported data.",

3391 "description": "The continuation token, which is used to pag e through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.",	2197 "enum": [

3392 "type": "string"	2198 "FORMAT_UNSPECIFIED",

3393 },	2199 "FORMAT_BIGQUERY"

3394 "referenceSetId": {	2200 ],

3395 "description": "If present, return only references which bel ong to this reference set.",	2201 "type": "string"

3396 "type": "string"	2202 },

3397 }	2203 "bigqueryDataset": {

3398 },	2204 "description": "Required. The BigQuery dataset to export dat a to. This dataset must already exist. Note that this is distinct from the Genom ics concept of \"dataset\".",

3399 "type": "object"	2205 "type": "string"

3400 },	2206 },

3401 "SearchReferencesResponse": {	2207 "bigqueryTable": {

3402 "id": "SearchReferencesResponse",	2208 "description": "Required. The BigQuery table to export data to. If the table doesn't exist, it will be created. If it already exists, it wil l be overwritten.",

3403 "properties": {	2209 "type": "string"

3404 "nextPageToken": {	2210 }

3405 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",	2211 },

3406 "type": "string"	2212 "type": "object"

3407 },

3408 "references": {

3409 "description": "The matching references.",

3410 "items": {

3411 "$ref": "Reference"

3412 },

3413 "type": "array"

3414 }

3415 },

3416 "type": "object"

3417 },	2213 },

3418 "SearchVariantSetsRequest": {	2214 "SearchVariantSetsRequest": {

3419 "description": "The search variant sets request.",	2215 "description": "The search variant sets request.",

3420 "id": "SearchVariantSetsRequest",	2216 "id": "SearchVariantSetsRequest",

3421 "properties": {	2217 "properties": {

3422 "datasetIds": {	2218 "datasetIds": {

3423 "description": "Exactly one dataset ID must be provided here . Only variant sets which belong to this dataset will be returned.",	2219 "description": "Exactly one dataset ID must be provided here . Only variant sets which belong to this dataset will be returned.",

3424 "items": {	2220 "items": {

3425 "type": "string"	2221 "type": "string"

3426 },	2222 },

3427 "type": "array"	2223 "type": "array"

3428 },	2224 },

	2225 "pageToken": {

	2226 "description": "The continuation token, which is used to pag e through large result sets. To get the next page of results, set this parameter to the value of `nextPageToken` from the previous response.",

	2227 "type": "string"

	2228 },

3429 "pageSize": {	2229 "pageSize": {

3430 "description": "The maximum number of variant sets to return in a request.",	2230 "description": "The maximum number of variant sets to return in a request.",

3431 "format": "int32",	2231 "format": "int32",

3432 "type": "integer"	2232 "type": "integer"

3433 },

3434 "pageToken": {

3435 "description": "The continuation token, which is used to pag e through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.",

3436 "type": "string"

3437 }	2233 }

3438 },	2234 },

3439 "type": "object"	2235 "type": "object"

3440 },	2236 },

3441 "SearchVariantSetsResponse": {	2237 "SearchVariantSetsResponse": {

3442 "description": "The search variant sets response.",	2238 "description": "The search variant sets response.",

3443 "id": "SearchVariantSetsResponse",	2239 "id": "SearchVariantSetsResponse",

3444 "properties": {	2240 "properties": {

3445 "nextPageToken": {

3446 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",

3447 "type": "string"

3448 },

3449 "variantSets": {	2241 "variantSets": {

3450 "description": "The variant sets belonging to the requested dataset.",	2242 "description": "The variant sets belonging to the requested dataset.",

3451 "items": {	2243 "items": {

3452 "$ref": "VariantSet"	2244 "$ref": "VariantSet"

3453 },	2245 },

3454 "type": "array"	2246 "type": "array"

	2247 },

	2248 "nextPageToken": {

	2249 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",

	2250 "type": "string"

3455 }	2251 }

3456 },	2252 },

3457 "type": "object"	2253 "type": "object"

3458 },	2254 },

3459 "SearchVariantsRequest": {	2255 "SearchVariantsRequest": {

3460 "description": "The variant search request.",	2256 "description": "The variant search request.",

3461 "id": "SearchVariantsRequest",	2257 "id": "SearchVariantsRequest",

3462 "properties": {	2258 "properties": {

	2259 "variantSetIds": {

	2260 "description": "At most one variant set ID must be provided. Only variants from this variant set will be returned. If omitted, a call set id must be included in the request.",

	2261 "items": {

	2262 "type": "string"

	2263 },

	2264 "type": "array"

	2265 },

	2266 "variantName": {

	2267 "description": "Only return variants which have exactly this name.",

	2268 "type": "string"

	2269 },

3463 "callSetIds": {	2270 "callSetIds": {

3464 "description": "Only return variant calls which belong to ca ll sets with these ids. Leaving this blank returns all variant calls. If a varia nt has no calls belonging to any of these call sets, it won't be returned at all . Currently, variants with no calls from any call set will never be returned.",	2271 "description": "Only return variant calls which belong to ca ll sets with these ids. Leaving this blank returns all variant calls. If a varia nt has no calls belonging to any of these call sets, it won't be returned at all . Currently, variants with no calls from any call set will never be returned.",

3465 "items": {	2272 "items": {

3466 "type": "string"	2273 "type": "string"

3467 },	2274 },

3468 "type": "array"	2275 "type": "array"

3469 },	2276 },

3470 "end": {

3471 "description": "The end of the window, 0-based exclusive. If unspecified or 0, defaults to the length of the reference.",

3472 "format": "int64",

3473 "type": "string"

3474 },

3475 "maxCalls": {

3476 "description": "The maximum number of calls to return. Howev er, at least one variant will always be returned, even if it has more calls than this limit. If unspecified, defaults to 5000.",

3477 "format": "int32",

3478 "type": "integer"

3479 },

3480 "pageSize": {

3481 "description": "The maximum number of variants to return. If unspecified, defaults to 5000.",

3482 "format": "int32",

3483 "type": "integer"

3484 },

3485 "pageToken": {

3486 "description": "The continuation token, which is used to pag e through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.",

3487 "type": "string"

3488 },

3489 "referenceName": {	2277 "referenceName": {

3490 "description": "Required. Only return variants in this refer ence sequence.",	2278 "description": "Required. Only return variants in this refer ence sequence.",

3491 "type": "string"	2279 "type": "string"

3492 },	2280 },

3493 "start": {	2281 "start": {

3494 "description": "The beginning of the window (0-based, inclus ive) for which overlapping variants should be returned. If unspecified, defaults to 0.",	2282 "description": "The beginning of the window (0-based, inclus ive) for which overlapping variants should be returned. If unspecified, defaults to 0.",

3495 "format": "int64",	2283 "format": "int64",

3496 "type": "string"	2284 "type": "string"

3497 },	2285 },

3498 "variantName": {	2286 "end": {

3499 "description": "Only return variants which have exactly this name.",	2287 "description": "The end of the window, 0-based exclusive. If unspecified or 0, defaults to the length of the reference.",

	2288 "format": "int64",

3500 "type": "string"	2289 "type": "string"

3501 },	2290 },

3502 "variantSetIds": {	2291 "pageToken": {

3503 "description": "At most one variant set ID must be provided. Only variants from this variant set will be returned. If omitted, a call set id must be included in the request.",	2292 "description": "The continuation token, which is used to pag e through large result sets. To get the next page of results, set this parameter to the value of `nextPageToken` from the previous response.",

3504 "items": {	2293 "type": "string"

3505 "type": "string"	2294 },

3506 },	2295 "pageSize": {

3507 "type": "array"	2296 "description": "The maximum number of variants to return. If unspecified, defaults to 5000.",

	2297 "format": "int32",

	2298 "type": "integer"

	2299 },

	2300 "maxCalls": {

	2301 "description": "The maximum number of calls to return. Howev er, at least one variant will always be returned, even if it has more calls than this limit. If unspecified, defaults to 5000.",

	2302 "format": "int32",

	2303 "type": "integer"

3508 }	2304 }

3509 },	2305 },

3510 "type": "object"	2306 "type": "object"

3511 },	2307 },

3512 "SearchVariantsResponse": {	2308 "SearchVariantsResponse": {

3513 "description": "The variant search response.",	2309 "description": "The variant search response.",

3514 "id": "SearchVariantsResponse",	2310 "id": "SearchVariantsResponse",

3515 "properties": {	2311 "properties": {

3516 "nextPageToken": {

3517 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",

3518 "type": "string"

3519 },

3520 "variants": {	2312 "variants": {

3521 "description": "The list of matching Variants.",	2313 "description": "The list of matching Variants.",

3522 "items": {	2314 "items": {

3523 "$ref": "Variant"	2315 "$ref": "Variant"

3524 },	2316 },

3525 "type": "array"	2317 "type": "array"

3526 }

3527 },

3528 "type": "object"

3529 },

3530 "Transcript": {

3531 "description": "A transcript represents the assertion that a particu lar region of the reference genome may be transcribed as RNA.",

3532 "id": "Transcript",

3533 "properties": {

3534 "codingSequence": {

3535 "$ref": "TranscriptCodingSequence",

3536 "description": "The range of the coding sequence for this tr anscript, if any. To determine the exact ranges of coding sequence, intersect th is range with those of the exons, if any. If there are any exons, the codingSequ ence must start and end within them.\n\nNote that in some cases, the reference g enome will not exactly match the observed mRNA transcript e.g. due to variance i n the source genome from reference. In these cases, exon.frame will not necessar ily match the expected reference reading frame and coding exon reference bases c annot necessarily be concatenated to produce the original transcript mRNA."

3537 },	2318 },

3538 "exons": {	2319 "nextPageToken": {

3539 "description": "The exons that compose this transcript. This field should be unset for genomes where transcript splicing does not occur, for example prokaryotes.\n\n\nIntrons are regions of the transcript that are not in cluded in the spliced RNA product. Though not explicitly modeled here, intron ra nges can be deduced; all regions of this transcript that are not exons are intro ns.\n\n\nExonic sequences do not necessarily code for a translational product (a mino acids). Only the regions of exons bounded by the codingSequence correspond to coding DNA sequence.\n\n\nExons are ordered by start position and may not ove rlap.",	2320 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",

3540 "items": {

3541 "$ref": "TranscriptExon"

3542 },

3543 "type": "array"

3544 },

3545 "geneId": {

3546 "description": "The annotation ID of the gene from which thi s transcript is transcribed.",

3547 "type": "string"

3548 }

3549 },

3550 "type": "object"

3551 },

3552 "TranscriptCodingSequence": {

3553 "id": "TranscriptCodingSequence",

3554 "properties": {

3555 "end": {

3556 "description": "The end of the coding sequence on this annot ation's reference sequence, 0-based exclusive. Note that this position is relati ve to the reference start, and not the containing annotation start.",

3557 "format": "int64",

3558 "type": "string"

3559 },

3560 "start": {

3561 "description": "The start of the coding sequence on this ann otation's reference sequence, 0-based inclusive. Note that this position is rela tive to the reference start, and not the containing annotation start.",

3562 "format": "int64",

3563 "type": "string"

3564 }

3565 },

3566 "type": "object"

3567 },

3568 "TranscriptExon": {

3569 "id": "TranscriptExon",

3570 "properties": {

3571 "end": {

3572 "description": "The end position of the exon on this annotat ion's reference sequence, 0-based exclusive. Note that this is relative to the r eference start, and not the containing annotation start.",

3573 "format": "int64",

3574 "type": "string"

3575 },

3576 "frame": {

3577 "$ref": "Int32Value",

3578 "description": "The frame of this exon. Contains a value of 0, 1, or 2, which indicates the offset of the first coding base of the exon with in the reading frame of the coding DNA sequence, if any. This field is dependent on the strandedness of this annotation (see Annotation.position.reverseStrand). For forward stranded annotations, this offset is relative to the exon.start. Fo r reverse strand annotations, this offset is relative to the exon.end-1.\n\nUnse t if this exon does not intersect the coding sequence. Upon creation of a transc ript, the frame must be populated for all or none of the coding exons."

3579 },

3580 "start": {

3581 "description": "The start position of the exon on this annot ation's reference sequence, 0-based inclusive. Note that this is relative to the reference start, and not the containing annotation start.",

3582 "format": "int64",

3583 "type": "string"	2321 "type": "string"

3584 }	2322 }

3585 },	2323 },

3586 "type": "object"	2324 "type": "object"

3587 },	2325 },

3588 "Variant": {	2326 "Variant": {

3589 "description": "A variant represents a change in DNA sequence relati ve to a reference sequence. For example, a variant could represent a SNP or an i nsertion. Variants belong to a variant set. Each of the calls on a variant repre sent a determination of genotype with respect to that variant. For example, a ca ll might assign probability of 0.32 to the occurrence of a SNP named rs1234 in a sample named NA12345. A call belongs to a call set, which contains related call s typically from one sample.",	2327 "description": "A variant represents a change in DNA sequence relati ve to a reference sequence. For example, a variant could represent a SNP or an i nsertion. Variants belong to a variant set. Each of the calls on a variant repre sent a determination of genotype with respect to that variant. For example, a ca ll might assign probability of 0.32 to the occurrence of a SNP named rs1234 in a sample named NA12345. A call belongs to a call set, which contains related call s typically from one sample.",

3590 "id": "Variant",	2328 "id": "Variant",

3591 "properties": {	2329 "properties": {

	2330 "variantSetId": {

	2331 "description": "The ID of the variant set this variant belon gs to.",

	2332 "type": "string"

	2333 },

	2334 "id": {

	2335 "description": "The server-generated variant ID, unique acro ss all variants.",

	2336 "type": "string"

	2337 },

	2338 "names": {

	2339 "description": "Names for the variant, for example a RefSNP ID.",

	2340 "items": {

	2341 "type": "string"

	2342 },

	2343 "type": "array"

	2344 },

	2345 "created": {

	2346 "description": "The date this variant was created, in millis econds from the epoch.",

	2347 "format": "int64",

	2348 "type": "string"

	2349 },

	2350 "referenceName": {

	2351 "description": "The reference on which this variant occurs. (such as `chr20` or `X`)",

	2352 "type": "string"

	2353 },

	2354 "start": {

	2355 "description": "The position at which this variant occurs (0 -based). This corresponds to the first base of the string of reference bases.",

	2356 "format": "int64",

	2357 "type": "string"

	2358 },

	2359 "end": {

	2360 "description": "The end position (0-based) of this variant. This corresponds to the first base after the last base in the reference allele. So, the length of the reference allele is (end - start). This is useful for vari ants that don't explicitly give alternate bases, for example large deletions.",

	2361 "format": "int64",

	2362 "type": "string"

	2363 },

	2364 "referenceBases": {

	2365 "description": "The reference bases for this variant. They s tart at the given position.",

	2366 "type": "string"

	2367 },

3592 "alternateBases": {	2368 "alternateBases": {

3593 "description": "The bases that appear instead of the referen ce bases.",	2369 "description": "The bases that appear instead of the referen ce bases.",

3594 "items": {	2370 "items": {

3595 "type": "string"	2371 "type": "string"

3596 },	2372 },

3597 "type": "array"	2373 "type": "array"

3598 },	2374 },

3599 "calls": {

3600 "description": "The variant calls for this particular varian t. Each one represents the determination of genotype with respect to this varian t.",

3601 "items": {

3602 "$ref": "Call"

3603 },

3604 "type": "array"

3605 },

3606 "created": {

3607 "description": "The date this variant was created, in millis econds from the epoch.",

3608 "format": "int64",

3609 "type": "string"

3610 },

3611 "end": {

3612 "description": "The end position (0-based) of this variant. This corresponds to the first base after the last base in the reference allele. So, the length of the reference allele is (end - start). This is useful for vari ants that don't explicitly give alternate bases, for example large deletions.",

3613 "format": "int64",

3614 "type": "string"

3615 },

3616 "filter": {

3617 "description": "A list of filters (normally quality filters) this variant has failed. PASS indicates this variant has passed all filters.",

3618 "items": {

3619 "type": "string"

3620 },

3621 "type": "array"

3622 },

3623 "id": {

3624 "description": "The Google generated ID of the variant, immu table.",

3625 "type": "string"

3626 },

3627 "info": {

3628 "additionalProperties": {

3629 "description": "A string which maps to an array of value s.",

3630 "items": {

3631 "type": "string"

3632 },

3633 "type": "array"

3634 },

3635 "description": "A string which maps to an array of values.",

3636 "type": "object"

3637 },

3638 "names": {

3639 "description": "Names for the variant, for example a RefSNP ID.",

3640 "items": {

3641 "type": "string"

3642 },

3643 "type": "array"

3644 },

3645 "quality": {	2375 "quality": {

3646 "description": "A measure of how likely this variant is to b e real. A higher value is better.",	2376 "description": "A measure of how likely this variant is to b e real. A higher value is better.",

3647 "format": "double",	2377 "format": "double",

3648 "type": "number"	2378 "type": "number"

3649 },	2379 },

3650 "referenceBases": {	2380 "filter": {

3651 "description": "The reference bases for this variant. They s tart at the given position.",	2381 "description": "A list of filters (normally quality filters) this variant has failed. `PASS` indicates this variant has passed all filters." ,

3652 "type": "string"	2382 "items": {

3653 },	2383 "type": "string"

3654 "referenceName": {	2384 },

3655 "description": "The reference on which this variant occurs. (such as chr20 or X)",	2385 "type": "array"

3656 "type": "string"	2386 },

3657 },	2387 "info": {

3658 "start": {	2388 "additionalProperties": {

3659 "description": "The position at which this variant occurs (0 -based). This corresponds to the first base of the string of reference bases.",	2389 "items": {

	2390 "type": "any"

	2391 },

	2392 "type": "array"

	2393 },

	2394 "description": "A map of additional variant information. Thi s must be of the form map (string key mapping to a list of string values).",

	2395 "type": "object"

	2396 },

	2397 "calls": {

	2398 "description": "The variant calls for this particular varian t. Each one represents the determination of genotype with respect to this varian t.",

	2399 "items": {

	2400 "$ref": "VariantCall"

	2401 },

	2402 "type": "array"

	2403 }

	2404 },

	2405 "type": "object"

	2406 },

	2407 "VariantCall": {

	2408 "description": "A call represents the determination of genotype with respect to a particular variant. It may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to t he occurrence of a SNP named rs1234 in a call set with the name NA12345.",

	2409 "id": "VariantCall",

	2410 "properties": {

	2411 "callSetId": {

	2412 "description": "The ID of the call set this variant call bel ongs to.",

	2413 "type": "string"

	2414 },

	2415 "callSetName": {

	2416 "description": "The name of the call set this variant call b elongs to.",

	2417 "type": "string"

	2418 },

	2419 "genotype": {

	2420 "description": "The genotype of this variant call. Each valu e represents either the value of the `referenceBases` field or a 1-based index i nto `alternateBases`. If a variant had a `referenceBases` value of `T` and an `a lternateBases` value of `[\"A\", \"C\"]`, and the `genotype` was `[2, 1]`, that would mean the call represented the heterozygous value `CA` for this variant. If the `genotype` was instead `[0, 1]`, the represented value would be `TA`. Order ing of the genotype values is important if the `phaseset` is present. If a genot ype is not called (that is, a `.` is present in the GT string) -1 is returned.",

	2421 "items": {

	2422 "format": "int32",

	2423 "type": "integer"

	2424 },

	2425 "type": "array"

	2426 },

	2427 "phaseset": {

	2428 "description": "If this field is present, this variant call' s genotype ordering implies the phase of the bases and is consistent with any ot her variant calls in the same reference sequence which have the same phaseset va lue. When importing data from VCF, if the genotype data was phased but no phase set was specified this field will be set to `*`.",

	2429 "type": "string"

	2430 },

	2431 "genotypeLikelihood": {

	2432 "description": "The genotype likelihoods for this variant ca ll. Each array entry represents how likely a specific genotype is for this call. The value ordering is defined by the GL tag in the VCF spec. If Phred-scaled ge notype likelihood scores (PL) are available and log10(P) genotype likelihood sco res (GL) are not, PL scores are converted to GL scores. If both are available, P L scores are stored in `info`.",

	2433 "items": {

	2434 "format": "double",

	2435 "type": "number"

	2436 },

	2437 "type": "array"

	2438 },

	2439 "info": {

	2440 "additionalProperties": {

	2441 "items": {

	2442 "type": "any"

	2443 },

	2444 "type": "array"

	2445 },

	2446 "description": "A map of additional variant call information . This must be of the form map (string key mapping to a list of string values)." ,

	2447 "type": "object"

	2448 }

	2449 },

	2450 "type": "object"

	2451 },

	2452 "SearchCallSetsRequest": {

	2453 "description": "The call set search request.",

	2454 "id": "SearchCallSetsRequest",

	2455 "properties": {

	2456 "variantSetIds": {

	2457 "description": "Restrict the query to call sets within the g iven variant sets. At least one ID must be provided.",

	2458 "items": {

	2459 "type": "string"

	2460 },

	2461 "type": "array"

	2462 },

	2463 "name": {

	2464 "description": "Only return call sets for which a substring of the name matches this string.",

	2465 "type": "string"

	2466 },

	2467 "pageToken": {

	2468 "description": "The continuation token, which is used to pag e through large result sets. To get the next page of results, set this parameter to the value of `nextPageToken` from the previous response.",

	2469 "type": "string"

	2470 },

	2471 "pageSize": {

	2472 "description": "The maximum number of call sets to return. I f unspecified, defaults to 1000.",

	2473 "format": "int32",

	2474 "type": "integer"

	2475 }

	2476 },

	2477 "type": "object"

	2478 },

	2479 "SearchCallSetsResponse": {

	2480 "description": "The call set search response.",

	2481 "id": "SearchCallSetsResponse",

	2482 "properties": {

	2483 "callSets": {

	2484 "description": "The list of matching call sets.",

	2485 "items": {

	2486 "$ref": "CallSet"

	2487 },

	2488 "type": "array"

	2489 },

	2490 "nextPageToken": {

	2491 "description": "The continuation token, which is used to pag e through large result sets. Provide this value in a subsequent request to retur n the next page of results. This field will be empty if there aren't any additio nal results.",

	2492 "type": "string"

	2493 }

	2494 },

	2495 "type": "object"

	2496 },

	2497 "CallSet": {

	2498 "description": "A call set is a collection of variant calls, typical ly for one sample. It belongs to a variant set.",

	2499 "id": "CallSet",

	2500 "properties": {

	2501 "id": {

	2502 "description": "The server-generated call set ID, unique acr oss all call sets.",

	2503 "type": "string"

	2504 },

	2505 "name": {

	2506 "description": "The call set name.",

	2507 "type": "string"

	2508 },

	2509 "sampleId": {

	2510 "description": "The sample ID this call set corresponds to." ,

	2511 "type": "string"

	2512 },

	2513 "variantSetIds": {

	2514 "description": "The IDs of the variant sets this call set be longs to. This field must have exactly length one, as a call set belongs to a si ngle variant set. This field is repeated for compatibility with the [GA4GH 0.5.1 API](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/varia nts.avdl#L76).",

	2515 "items": {

	2516 "type": "string"

	2517 },

	2518 "type": "array"

	2519 },

	2520 "created": {

	2521 "description": "The date this call set was created in millis econds from the epoch.",

3660 "format": "int64",	2522 "format": "int64",

3661 "type": "string"	2523 "type": "string"

3662 },	2524 },

3663 "variantSetId": {	2525 "info": {

3664 "description": "The ID of the variant set this variant belon gs to.",	2526 "additionalProperties": {

3665 "type": "string"	2527 "items": {

3666 }	2528 "type": "any"

3667 },	2529 },

3668 "type": "object"	2530 "type": "array"

3669 },	2531 },

3670 "VariantAnnotation": {	2532 "description": "A map of additional call set information. Th is must be of the form map (string key mapping to a list of string values).",

3671 "description": "A Variant annotation.",	2533 "type": "object"

3672 "id": "VariantAnnotation",	2534 }

3673 "properties": {	2535 },

3674 "alternateBases": {	2536 "type": "object"

3675 "description": "The alternate allele for this variant. If mu ltiple alternate alleles exist at this location, create a separate variant for e ach one, as they may represent distinct conditions.",	2537 },

3676 "type": "string"	2538 "ImportReadGroupSetsResponse": {

3677 },	2539 "description": "The read group set import response.",

3678 "clinicalSignificance": {	2540 "id": "ImportReadGroupSetsResponse",

3679 "description": "Describes the clinical significance of a var iant. It is adapted from the ClinVar controlled vocabulary for clinical signific ance described at: http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/",	2541 "properties": {

3680 "enum": [	2542 "readGroupSetIds": {

3681 "ASSOCIATION",	2543 "description": "IDs of the read group sets that were created .",

3682 "BENIGN",	2544 "items": {

3683 "CLINICAL_SIGNIFICANCE_UNSPECIFIED",	2545 "type": "string"

3684 "CONFERS_SENSITIVITY",	2546 },

3685 "DRUG_RESPONSE",	2547 "type": "array"

3686 "HISTOCOMPATIBILITY",	2548 }

3687 "LIKELY_BENIGN",	2549 },

3688 "LIKELY_PATHOGENIC",	2550 "type": "object"

3689 "MULTIPLE_REPORTED",	2551 },

3690 "OTHER",	2552 "ImportVariantsResponse": {

3691 "PATHOGENIC",	2553 "description": "The variant data import response.",

3692 "PROTECTIVE",	2554 "id": "ImportVariantsResponse",

3693 "RISK_FACTOR",	2555 "properties": {

3694 "UNCERTAIN"	2556 "callSetIds": {

3695 ],	2557 "description": "IDs of the call sets that were created.",

3696 "enumDescriptions": [	2558 "items": {

3697 "",	2559 "type": "string"

3698 "",	2560 },

3699 "",	2561 "type": "array"

3700 "",	2562 }

3701 "",	2563 },

3702 "",	2564 "type": "object"

3703 "",	2565 },

3704 "",	2566 "OperationMetadata": {

3705 "",	2567 "description": "Metadata describing an [Operation][google.longrunnin g.Operation].",

3706 "",	2568 "id": "OperationMetadata",

3707 "",	2569 "properties": {

3708 "",	2570 "projectId": {

3709 "",	2571 "description": "The Google Cloud Project in which the job is scoped.",

3710 ""	2572 "type": "string"

3711 ],	2573 },

3712 "type": "string"	2574 "createTime": {

3713 },	2575 "description": "The time at which the job was submitted to t he Genomics service.",

3714 "conditions": {	2576 "type": "string"

3715 "description": "The set of conditions associated with this v ariant. A condition describes the way a variant influences human health.",	2577 },

3716 "items": {	2578 "request": {

3717 "$ref": "VariantAnnotationCondition"	2579 "additionalProperties": {

3718 },	2580 "description": "Properties of the object. Contains field @ype with type URL.",

3719 "type": "array"	2581 "type": "any"

3720 },	2582 },

3721 "effect": {	2583 "description": "The original request that started the operat ion. Note that this will be in current version of the API. If the operation was started with v1beta2 API and a GetOperation is performed on v1 API, a v1 request will be returned.",

3722 "description": "Effect of the variant on the coding sequence .",	2584 "type": "object"

3723 "enum": [	2585 },

3724 "EFFECT_UNSPECIFIED",	2586 "events": {

3725 "FRAMESHIFT",	2587 "description": "Optional event messages that were generated during the job's execution. This also contains any warnings that were generated during import or export.",

3726 "FRAME_PRESERVING_INDEL",	2588 "items": {

3727 "NONSYNONYMOUS_SNP",	2589 "$ref": "OperationEvent"

3728 "OTHER",	2590 },

3729 "SPLICE_SITE_DISRUPTION",	2591 "type": "array"

3730 "STOP_GAIN",	2592 }

3731 "STOP_LOSS",	2593 },

3732 "SYNONYMOUS_SNP"	2594 "type": "object"

3733 ],	2595 },

3734 "enumDescriptions": [	2596 "OperationEvent": {

3735 "",	2597 "description": "An event that occurred during an [Operation][google. longrunning.Operation].",

3736 "",	2598 "id": "OperationEvent",

3737 "",	2599 "properties": {

3738 "",	2600 "description": {

3739 "",	2601 "description": "Required description of event.",

3740 "",	2602 "type": "string"

3741 "",

3742 "",

3743 ""

3744 ],

3745 "type": "string"

3746 },

3747 "geneId": {

3748 "description": "Google annotation ID of the gene affected by this variant. This should be provided when the variant is created.",

3749 "type": "string"

3750 },

3751 "transcriptIds": {

3752 "description": "Google annotation IDs of the transcripts aff ected by this variant. These should be provided when the variant is created.",

3753 "items": {

3754 "type": "string"

3755 },

3756 "type": "array"

3757 },

3758 "type": {

3759 "description": "Type has been adapted from ClinVar's list of variant types.",

3760 "enum": [

3761 "CNV",

3762 "DELETION",

3763 "INSERTION",

3764 "OTHER",

3765 "SNP",

3766 "STRUCTURAL",

3767 "SUBSTITUTION",

3768 "TYPE_UNSPECIFIED"

3769 ],

3770 "enumDescriptions": [

3771 "",

3772 "",

3773 "",

3774 "",

3775 "",

3776 "",

3777 "",

3778 ""

3779 ],

3780 "type": "string"

3781 }

3782 },

3783 "type": "object"

3784 },

3785 "VariantAnnotationCondition": {

3786 "description": "",

3787 "id": "VariantAnnotationCondition",

3788 "properties": {

3789 "conceptId": {

3790 "description": "The MedGen concept id associated with this g ene. Search for these IDs at http://www.ncbi.nlm.nih.gov/medgen/",

3791 "type": "string"

3792 },

3793 "externalIds": {

3794 "description": "The set of external IDs for this condition." ,

3795 "items": {

3796 "$ref": "ExternalId"

3797 },

3798 "type": "array"

3799 },

3800 "names": {

3801 "description": "A set of names for the condition.",

3802 "items": {

3803 "type": "string"

3804 },

3805 "type": "array"

3806 },

3807 "omimId": {

3808 "description": "The OMIM id for this condition. Search for t hese IDs at http://omim.org/",

3809 "type": "string"

3810 }

3811 },

3812 "type": "object"

3813 },

3814 "VariantSet": {

3815 "description": "A variant set is a collection of call sets and varia nts. It contains summary statistics of those contents. A variant set belongs to a dataset.",

3816 "id": "VariantSet",

3817 "properties": {

3818 "datasetId": {

3819 "description": "The dataset to which this variant set belong s. Immutable.",

3820 "type": "string"

3821 },

3822 "id": {

3823 "description": "The Google-generated ID of the variant set. Immutable.",

3824 "type": "string"

3825 },

3826 "metadata": {

3827 "description": "The metadata associated with this variant se t.",

3828 "items": {

3829 "$ref": "Metadata"

3830 },

3831 "type": "array"

3832 },

3833 "referenceBounds": {

3834 "description": "A list of all references used by the variant s in a variant set with associated coordinate upper bounds for each one.",

3835 "items": {

3836 "$ref": "ReferenceBound"

3837 },

3838 "type": "array"

3839 }	2603 }

3840 },	2604 },

3841 "type": "object"	2605 "type": "object"

3842 }	2606 }

3843 },	2607 },

3844 "servicePath": "genomics/v1beta2/",	2608 "servicePath": "",

3845 "title": "Genomics API",	2609 "title": "Genomics API",

3846 "version": "v1beta2"	2610 "version": "v1"

3847 }	2611 }

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