Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 1 | <html><body> |
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| 74 | |
| 75 | <h1><a href="genomics_v1.html">Genomics API</a> . <a href="genomics_v1.variantsets.html">variantsets</a></h1> |
| 76 | <h2>Instance Methods</h2> |
| 77 | <p class="toc_element"> |
| 78 | <code><a href="#create">create(body, x__xgafv=None)</a></code></p> |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 79 | <p class="firstline">Creates a new variant set.</p> |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 80 | <p class="toc_element"> |
| 81 | <code><a href="#delete">delete(variantSetId, x__xgafv=None)</a></code></p> |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 82 | <p class="firstline">Deletes a variant set including all variants, call sets, and calls within.</p> |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 83 | <p class="toc_element"> |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 84 | <code><a href="#export">export(variantSetId=None, body, x__xgafv=None)</a></code></p> |
| 85 | <p class="firstline">Exports variant set data to an external destination.</p> |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 86 | <p class="toc_element"> |
| 87 | <code><a href="#get">get(variantSetId, x__xgafv=None)</a></code></p> |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 88 | <p class="firstline">Gets a variant set by ID.</p> |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 89 | <p class="toc_element"> |
| 90 | <code><a href="#patch">patch(variantSetId, body, updateMask=None, x__xgafv=None)</a></code></p> |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 91 | <p class="firstline">Updates a variant set using patch semantics.</p> |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 92 | <p class="toc_element"> |
| 93 | <code><a href="#search">search(body, x__xgafv=None)</a></code></p> |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 94 | <p class="firstline">Returns a list of all variant sets matching search criteria.</p> |
| 95 | <p class="toc_element"> |
| 96 | <code><a href="#search_next">search_next(previous_request, previous_response)</a></code></p> |
| 97 | <p class="firstline">Retrieves the next page of results.</p> |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 98 | <h3>Method Details</h3> |
| 99 | <div class="method"> |
| 100 | <code class="details" id="create">create(body, x__xgafv=None)</code> |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 101 | <pre>Creates a new variant set. |
| 102 | |
| 103 | For the definitions of variant sets and other genomics resources, see |
| 104 | [Fundamentals of Google |
| 105 | Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
| 106 | |
| 107 | The provided variant set must have a valid `datasetId` set - all other |
| 108 | fields are optional. Note that the `id` field will be ignored, as this is |
| 109 | assigned by the server. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 110 | |
| 111 | Args: |
| 112 | body: object, The request body. (required) |
| 113 | The object takes the form of: |
| 114 | |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 115 | { # A variant set is a collection of call sets and variants. It contains summary |
| 116 | # statistics of those contents. A variant set belongs to a dataset. |
| 117 | # |
| 118 | # For more genomics resource definitions, see [Fundamentals of Google |
| 119 | # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
Jon Wayne Parrott | 0a471d3 | 2016-05-19 10:54:38 -0700 | [diff] [blame] | 120 | "name": "A String", # User-specified, mutable name. |
| 121 | "description": "A String", # A textual description of this variant set. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 122 | "metadata": [ # The metadata associated with this variant set. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 123 | { # Metadata describes a single piece of variant call metadata. |
| 124 | # These data include a top level key and either a single value string (value) |
| 125 | # or a list of key-value pairs (info.) |
| 126 | # Value and info are mutually exclusive. |
| 127 | "info": { # Remaining structured metadata key-value pairs. This must be of the form |
| 128 | # map<string, string[]> (string key mapping to a list of string values). |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 129 | "a_key": [ |
| 130 | "", |
| 131 | ], |
| 132 | }, |
| 133 | "description": "A String", # A textual description of this metadata. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 134 | "number": "A String", # The number of values that can be included in a field described by this |
| 135 | # metadata. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 136 | "value": "A String", # The value field for simple metadata |
| 137 | "key": "A String", # The top-level key. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 138 | "type": "A String", # The type of data. Possible types include: Integer, Float, |
| 139 | # Flag, Character, and String. |
| 140 | "id": "A String", # User-provided ID field, not enforced by this API. |
| 141 | # Two or more pieces of structured metadata with identical |
| 142 | # id and key fields are considered equivalent. |
| 143 | }, |
| 144 | ], |
| 145 | "referenceSetId": "A String", # The reference set to which the variant set is mapped. The reference set |
| 146 | # describes the alignment provenance of the variant set, while the |
| 147 | # `referenceBounds` describe the shape of the actual variant data. The |
| 148 | # reference set's reference names are a superset of those found in the |
| 149 | # `referenceBounds`. |
| 150 | # |
| 151 | # For example, given a variant set that is mapped to the GRCh38 reference set |
| 152 | # and contains a single variant on reference 'X', `referenceBounds` would |
| 153 | # contain only an entry for 'X', while the associated reference set |
| 154 | # enumerates all possible references: '1', '2', 'X', 'Y', 'MT', etc. |
| 155 | "id": "A String", # The server-generated variant set ID, unique across all variant sets. |
| 156 | "datasetId": "A String", # The dataset to which this variant set belongs. |
| 157 | "referenceBounds": [ # A list of all references used by the variants in a variant set |
| 158 | # with associated coordinate upper bounds for each one. |
| 159 | { # ReferenceBound records an upper bound for the starting coordinate of |
| 160 | # variants in a particular reference. |
| 161 | "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any |
| 162 | # variant in the reference sequence. |
| 163 | "referenceName": "A String", # The name of the reference associated with this reference bound. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 164 | }, |
| 165 | ], |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 166 | } |
| 167 | |
| 168 | x__xgafv: string, V1 error format. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 169 | Allowed values |
| 170 | 1 - v1 error format |
| 171 | 2 - v2 error format |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 172 | |
| 173 | Returns: |
| 174 | An object of the form: |
| 175 | |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 176 | { # A variant set is a collection of call sets and variants. It contains summary |
| 177 | # statistics of those contents. A variant set belongs to a dataset. |
| 178 | # |
| 179 | # For more genomics resource definitions, see [Fundamentals of Google |
| 180 | # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
Jon Wayne Parrott | 0a471d3 | 2016-05-19 10:54:38 -0700 | [diff] [blame] | 181 | "name": "A String", # User-specified, mutable name. |
| 182 | "description": "A String", # A textual description of this variant set. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 183 | "metadata": [ # The metadata associated with this variant set. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 184 | { # Metadata describes a single piece of variant call metadata. |
| 185 | # These data include a top level key and either a single value string (value) |
| 186 | # or a list of key-value pairs (info.) |
| 187 | # Value and info are mutually exclusive. |
| 188 | "info": { # Remaining structured metadata key-value pairs. This must be of the form |
| 189 | # map<string, string[]> (string key mapping to a list of string values). |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 190 | "a_key": [ |
| 191 | "", |
| 192 | ], |
| 193 | }, |
| 194 | "description": "A String", # A textual description of this metadata. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 195 | "number": "A String", # The number of values that can be included in a field described by this |
| 196 | # metadata. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 197 | "value": "A String", # The value field for simple metadata |
| 198 | "key": "A String", # The top-level key. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 199 | "type": "A String", # The type of data. Possible types include: Integer, Float, |
| 200 | # Flag, Character, and String. |
| 201 | "id": "A String", # User-provided ID field, not enforced by this API. |
| 202 | # Two or more pieces of structured metadata with identical |
| 203 | # id and key fields are considered equivalent. |
| 204 | }, |
| 205 | ], |
| 206 | "referenceSetId": "A String", # The reference set to which the variant set is mapped. The reference set |
| 207 | # describes the alignment provenance of the variant set, while the |
| 208 | # `referenceBounds` describe the shape of the actual variant data. The |
| 209 | # reference set's reference names are a superset of those found in the |
| 210 | # `referenceBounds`. |
| 211 | # |
| 212 | # For example, given a variant set that is mapped to the GRCh38 reference set |
| 213 | # and contains a single variant on reference 'X', `referenceBounds` would |
| 214 | # contain only an entry for 'X', while the associated reference set |
| 215 | # enumerates all possible references: '1', '2', 'X', 'Y', 'MT', etc. |
| 216 | "id": "A String", # The server-generated variant set ID, unique across all variant sets. |
| 217 | "datasetId": "A String", # The dataset to which this variant set belongs. |
| 218 | "referenceBounds": [ # A list of all references used by the variants in a variant set |
| 219 | # with associated coordinate upper bounds for each one. |
| 220 | { # ReferenceBound records an upper bound for the starting coordinate of |
| 221 | # variants in a particular reference. |
| 222 | "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any |
| 223 | # variant in the reference sequence. |
| 224 | "referenceName": "A String", # The name of the reference associated with this reference bound. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 225 | }, |
| 226 | ], |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 227 | }</pre> |
| 228 | </div> |
| 229 | |
| 230 | <div class="method"> |
| 231 | <code class="details" id="delete">delete(variantSetId, x__xgafv=None)</code> |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 232 | <pre>Deletes a variant set including all variants, call sets, and calls within. |
| 233 | This is not reversible. |
| 234 | |
| 235 | For the definitions of variant sets and other genomics resources, see |
| 236 | [Fundamentals of Google |
| 237 | Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 238 | |
| 239 | Args: |
| 240 | variantSetId: string, The ID of the variant set to be deleted. (required) |
| 241 | x__xgafv: string, V1 error format. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 242 | Allowed values |
| 243 | 1 - v1 error format |
| 244 | 2 - v2 error format |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 245 | |
| 246 | Returns: |
| 247 | An object of the form: |
| 248 | |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 249 | { # A generic empty message that you can re-use to avoid defining duplicated |
| 250 | # empty messages in your APIs. A typical example is to use it as the request |
| 251 | # or the response type of an API method. For instance: |
| 252 | # |
| 253 | # service Foo { |
| 254 | # rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty); |
| 255 | # } |
| 256 | # |
| 257 | # The JSON representation for `Empty` is empty JSON object `{}`. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 258 | }</pre> |
| 259 | </div> |
| 260 | |
| 261 | <div class="method"> |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 262 | <code class="details" id="export">export(variantSetId=None, body, x__xgafv=None)</code> |
| 263 | <pre>Exports variant set data to an external destination. |
| 264 | |
| 265 | For the definitions of variant sets and other genomics resources, see |
| 266 | [Fundamentals of Google |
| 267 | Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 268 | |
| 269 | Args: |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 270 | variantSetId: string, Required. The ID of the variant set that contains variant data which |
| 271 | should be exported. The caller must have READ access to this variant set. (required) |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 272 | body: object, The request body. (required) |
| 273 | The object takes the form of: |
| 274 | |
| 275 | { # The variant data export request. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 276 | "bigqueryDataset": "A String", # Required. The BigQuery dataset to export data to. This dataset must already |
| 277 | # exist. Note that this is distinct from the Genomics concept of "dataset". |
| 278 | "bigqueryTable": "A String", # Required. The BigQuery table to export data to. |
| 279 | # If the table doesn't exist, it will be created. If it already exists, it |
| 280 | # will be overwritten. |
| 281 | "callSetIds": [ # If provided, only variant call information from the specified call sets |
| 282 | # will be exported. By default all variant calls are exported. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 283 | "A String", |
| 284 | ], |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 285 | "projectId": "A String", # Required. The Google Cloud project ID that owns the destination |
| 286 | # BigQuery dataset. The caller must have WRITE access to this project. This |
| 287 | # project will also own the resulting export job. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 288 | "format": "A String", # The format for the exported data. |
| 289 | } |
| 290 | |
| 291 | x__xgafv: string, V1 error format. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 292 | Allowed values |
| 293 | 1 - v1 error format |
| 294 | 2 - v2 error format |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 295 | |
| 296 | Returns: |
| 297 | An object of the form: |
| 298 | |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 299 | { # This resource represents a long-running operation that is the result of a |
| 300 | # network API call. |
| 301 | "response": { # If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If importing Variants, an ImportVariantsResponse is returned. For pipelines and exports, an empty response is returned. |
Jon Wayne Parrott | 7d5badb | 2016-08-16 12:44:29 -0700 | [diff] [blame] | 302 | "a_key": "", # Properties of the object. Contains field @type with type URL. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 303 | }, |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 304 | "metadata": { # An OperationMetadata object. This will always be returned with the Operation. |
| 305 | "a_key": "", # Properties of the object. Contains field @type with type URL. |
| 306 | }, |
| 307 | "done": True or False, # If the value is `false`, it means the operation is still in progress. |
| 308 | # If true, the operation is completed, and either `error` or `response` is |
| 309 | # available. |
| 310 | "name": "A String", # The server-assigned name, which is only unique within the same service that originally returns it. For example: `operations/CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw` |
| 311 | "error": { # The `Status` type defines a logical error model that is suitable for different # The error result of the operation in case of failure or cancellation. |
| 312 | # programming environments, including REST APIs and RPC APIs. It is used by |
| 313 | # [gRPC](https://github.com/grpc). The error model is designed to be: |
| 314 | # |
| 315 | # - Simple to use and understand for most users |
| 316 | # - Flexible enough to meet unexpected needs |
| 317 | # |
| 318 | # # Overview |
| 319 | # |
| 320 | # The `Status` message contains three pieces of data: error code, error message, |
| 321 | # and error details. The error code should be an enum value of |
| 322 | # google.rpc.Code, but it may accept additional error codes if needed. The |
| 323 | # error message should be a developer-facing English message that helps |
| 324 | # developers *understand* and *resolve* the error. If a localized user-facing |
| 325 | # error message is needed, put the localized message in the error details or |
| 326 | # localize it in the client. The optional error details may contain arbitrary |
| 327 | # information about the error. There is a predefined set of error detail types |
| 328 | # in the package `google.rpc` which can be used for common error conditions. |
| 329 | # |
| 330 | # # Language mapping |
| 331 | # |
| 332 | # The `Status` message is the logical representation of the error model, but it |
| 333 | # is not necessarily the actual wire format. When the `Status` message is |
| 334 | # exposed in different client libraries and different wire protocols, it can be |
| 335 | # mapped differently. For example, it will likely be mapped to some exceptions |
| 336 | # in Java, but more likely mapped to some error codes in C. |
| 337 | # |
| 338 | # # Other uses |
| 339 | # |
| 340 | # The error model and the `Status` message can be used in a variety of |
| 341 | # environments, either with or without APIs, to provide a |
| 342 | # consistent developer experience across different environments. |
| 343 | # |
| 344 | # Example uses of this error model include: |
| 345 | # |
| 346 | # - Partial errors. If a service needs to return partial errors to the client, |
| 347 | # it may embed the `Status` in the normal response to indicate the partial |
| 348 | # errors. |
| 349 | # |
| 350 | # - Workflow errors. A typical workflow has multiple steps. Each step may |
| 351 | # have a `Status` message for error reporting purpose. |
| 352 | # |
| 353 | # - Batch operations. If a client uses batch request and batch response, the |
| 354 | # `Status` message should be used directly inside batch response, one for |
| 355 | # each error sub-response. |
| 356 | # |
| 357 | # - Asynchronous operations. If an API call embeds asynchronous operation |
| 358 | # results in its response, the status of those operations should be |
| 359 | # represented directly using the `Status` message. |
| 360 | # |
| 361 | # - Logging. If some API errors are stored in logs, the message `Status` could |
| 362 | # be used directly after any stripping needed for security/privacy reasons. |
| 363 | "message": "A String", # A developer-facing error message, which should be in English. Any |
| 364 | # user-facing error message should be localized and sent in the |
| 365 | # google.rpc.Status.details field, or localized by the client. |
Jon Wayne Parrott | 36e41bc | 2016-02-19 16:02:29 -0800 | [diff] [blame] | 366 | "code": 42, # The status code, which should be an enum value of google.rpc.Code. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 367 | "details": [ # A list of messages that carry the error details. There will be a |
| 368 | # common set of message types for APIs to use. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 369 | { |
Jon Wayne Parrott | 7d5badb | 2016-08-16 12:44:29 -0700 | [diff] [blame] | 370 | "a_key": "", # Properties of the object. Contains field @type with type URL. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 371 | }, |
| 372 | ], |
| 373 | }, |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 374 | }</pre> |
| 375 | </div> |
| 376 | |
| 377 | <div class="method"> |
| 378 | <code class="details" id="get">get(variantSetId, x__xgafv=None)</code> |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 379 | <pre>Gets a variant set by ID. |
| 380 | |
| 381 | For the definitions of variant sets and other genomics resources, see |
| 382 | [Fundamentals of Google |
| 383 | Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 384 | |
| 385 | Args: |
| 386 | variantSetId: string, Required. The ID of the variant set. (required) |
| 387 | x__xgafv: string, V1 error format. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 388 | Allowed values |
| 389 | 1 - v1 error format |
| 390 | 2 - v2 error format |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 391 | |
| 392 | Returns: |
| 393 | An object of the form: |
| 394 | |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 395 | { # A variant set is a collection of call sets and variants. It contains summary |
| 396 | # statistics of those contents. A variant set belongs to a dataset. |
| 397 | # |
| 398 | # For more genomics resource definitions, see [Fundamentals of Google |
| 399 | # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
Jon Wayne Parrott | 0a471d3 | 2016-05-19 10:54:38 -0700 | [diff] [blame] | 400 | "name": "A String", # User-specified, mutable name. |
| 401 | "description": "A String", # A textual description of this variant set. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 402 | "metadata": [ # The metadata associated with this variant set. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 403 | { # Metadata describes a single piece of variant call metadata. |
| 404 | # These data include a top level key and either a single value string (value) |
| 405 | # or a list of key-value pairs (info.) |
| 406 | # Value and info are mutually exclusive. |
| 407 | "info": { # Remaining structured metadata key-value pairs. This must be of the form |
| 408 | # map<string, string[]> (string key mapping to a list of string values). |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 409 | "a_key": [ |
| 410 | "", |
| 411 | ], |
| 412 | }, |
| 413 | "description": "A String", # A textual description of this metadata. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 414 | "number": "A String", # The number of values that can be included in a field described by this |
| 415 | # metadata. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 416 | "value": "A String", # The value field for simple metadata |
| 417 | "key": "A String", # The top-level key. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 418 | "type": "A String", # The type of data. Possible types include: Integer, Float, |
| 419 | # Flag, Character, and String. |
| 420 | "id": "A String", # User-provided ID field, not enforced by this API. |
| 421 | # Two or more pieces of structured metadata with identical |
| 422 | # id and key fields are considered equivalent. |
| 423 | }, |
| 424 | ], |
| 425 | "referenceSetId": "A String", # The reference set to which the variant set is mapped. The reference set |
| 426 | # describes the alignment provenance of the variant set, while the |
| 427 | # `referenceBounds` describe the shape of the actual variant data. The |
| 428 | # reference set's reference names are a superset of those found in the |
| 429 | # `referenceBounds`. |
| 430 | # |
| 431 | # For example, given a variant set that is mapped to the GRCh38 reference set |
| 432 | # and contains a single variant on reference 'X', `referenceBounds` would |
| 433 | # contain only an entry for 'X', while the associated reference set |
| 434 | # enumerates all possible references: '1', '2', 'X', 'Y', 'MT', etc. |
| 435 | "id": "A String", # The server-generated variant set ID, unique across all variant sets. |
| 436 | "datasetId": "A String", # The dataset to which this variant set belongs. |
| 437 | "referenceBounds": [ # A list of all references used by the variants in a variant set |
| 438 | # with associated coordinate upper bounds for each one. |
| 439 | { # ReferenceBound records an upper bound for the starting coordinate of |
| 440 | # variants in a particular reference. |
| 441 | "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any |
| 442 | # variant in the reference sequence. |
| 443 | "referenceName": "A String", # The name of the reference associated with this reference bound. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 444 | }, |
| 445 | ], |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 446 | }</pre> |
| 447 | </div> |
| 448 | |
| 449 | <div class="method"> |
| 450 | <code class="details" id="patch">patch(variantSetId, body, updateMask=None, x__xgafv=None)</code> |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 451 | <pre>Updates a variant set using patch semantics. |
| 452 | |
| 453 | For the definitions of variant sets and other genomics resources, see |
| 454 | [Fundamentals of Google |
| 455 | Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 456 | |
| 457 | Args: |
| 458 | variantSetId: string, The ID of the variant to be updated (must already exist). (required) |
| 459 | body: object, The request body. (required) |
| 460 | The object takes the form of: |
| 461 | |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 462 | { # A variant set is a collection of call sets and variants. It contains summary |
| 463 | # statistics of those contents. A variant set belongs to a dataset. |
| 464 | # |
| 465 | # For more genomics resource definitions, see [Fundamentals of Google |
| 466 | # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
Jon Wayne Parrott | 0a471d3 | 2016-05-19 10:54:38 -0700 | [diff] [blame] | 467 | "name": "A String", # User-specified, mutable name. |
| 468 | "description": "A String", # A textual description of this variant set. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 469 | "metadata": [ # The metadata associated with this variant set. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 470 | { # Metadata describes a single piece of variant call metadata. |
| 471 | # These data include a top level key and either a single value string (value) |
| 472 | # or a list of key-value pairs (info.) |
| 473 | # Value and info are mutually exclusive. |
| 474 | "info": { # Remaining structured metadata key-value pairs. This must be of the form |
| 475 | # map<string, string[]> (string key mapping to a list of string values). |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 476 | "a_key": [ |
| 477 | "", |
| 478 | ], |
| 479 | }, |
| 480 | "description": "A String", # A textual description of this metadata. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 481 | "number": "A String", # The number of values that can be included in a field described by this |
| 482 | # metadata. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 483 | "value": "A String", # The value field for simple metadata |
| 484 | "key": "A String", # The top-level key. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 485 | "type": "A String", # The type of data. Possible types include: Integer, Float, |
| 486 | # Flag, Character, and String. |
| 487 | "id": "A String", # User-provided ID field, not enforced by this API. |
| 488 | # Two or more pieces of structured metadata with identical |
| 489 | # id and key fields are considered equivalent. |
| 490 | }, |
| 491 | ], |
| 492 | "referenceSetId": "A String", # The reference set to which the variant set is mapped. The reference set |
| 493 | # describes the alignment provenance of the variant set, while the |
| 494 | # `referenceBounds` describe the shape of the actual variant data. The |
| 495 | # reference set's reference names are a superset of those found in the |
| 496 | # `referenceBounds`. |
| 497 | # |
| 498 | # For example, given a variant set that is mapped to the GRCh38 reference set |
| 499 | # and contains a single variant on reference 'X', `referenceBounds` would |
| 500 | # contain only an entry for 'X', while the associated reference set |
| 501 | # enumerates all possible references: '1', '2', 'X', 'Y', 'MT', etc. |
| 502 | "id": "A String", # The server-generated variant set ID, unique across all variant sets. |
| 503 | "datasetId": "A String", # The dataset to which this variant set belongs. |
| 504 | "referenceBounds": [ # A list of all references used by the variants in a variant set |
| 505 | # with associated coordinate upper bounds for each one. |
| 506 | { # ReferenceBound records an upper bound for the starting coordinate of |
| 507 | # variants in a particular reference. |
| 508 | "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any |
| 509 | # variant in the reference sequence. |
| 510 | "referenceName": "A String", # The name of the reference associated with this reference bound. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 511 | }, |
| 512 | ], |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 513 | } |
| 514 | |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 515 | updateMask: string, An optional mask specifying which fields to update. Supported fields: |
| 516 | |
| 517 | * metadata. |
| 518 | * name. |
| 519 | * description. |
| 520 | |
| 521 | Leaving `updateMask` unset is equivalent to specifying all mutable |
| 522 | fields. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 523 | x__xgafv: string, V1 error format. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 524 | Allowed values |
| 525 | 1 - v1 error format |
| 526 | 2 - v2 error format |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 527 | |
| 528 | Returns: |
| 529 | An object of the form: |
| 530 | |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 531 | { # A variant set is a collection of call sets and variants. It contains summary |
| 532 | # statistics of those contents. A variant set belongs to a dataset. |
| 533 | # |
| 534 | # For more genomics resource definitions, see [Fundamentals of Google |
| 535 | # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
Jon Wayne Parrott | 0a471d3 | 2016-05-19 10:54:38 -0700 | [diff] [blame] | 536 | "name": "A String", # User-specified, mutable name. |
| 537 | "description": "A String", # A textual description of this variant set. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 538 | "metadata": [ # The metadata associated with this variant set. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 539 | { # Metadata describes a single piece of variant call metadata. |
| 540 | # These data include a top level key and either a single value string (value) |
| 541 | # or a list of key-value pairs (info.) |
| 542 | # Value and info are mutually exclusive. |
| 543 | "info": { # Remaining structured metadata key-value pairs. This must be of the form |
| 544 | # map<string, string[]> (string key mapping to a list of string values). |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 545 | "a_key": [ |
| 546 | "", |
| 547 | ], |
| 548 | }, |
| 549 | "description": "A String", # A textual description of this metadata. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 550 | "number": "A String", # The number of values that can be included in a field described by this |
| 551 | # metadata. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 552 | "value": "A String", # The value field for simple metadata |
| 553 | "key": "A String", # The top-level key. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 554 | "type": "A String", # The type of data. Possible types include: Integer, Float, |
| 555 | # Flag, Character, and String. |
| 556 | "id": "A String", # User-provided ID field, not enforced by this API. |
| 557 | # Two or more pieces of structured metadata with identical |
| 558 | # id and key fields are considered equivalent. |
| 559 | }, |
| 560 | ], |
| 561 | "referenceSetId": "A String", # The reference set to which the variant set is mapped. The reference set |
| 562 | # describes the alignment provenance of the variant set, while the |
| 563 | # `referenceBounds` describe the shape of the actual variant data. The |
| 564 | # reference set's reference names are a superset of those found in the |
| 565 | # `referenceBounds`. |
| 566 | # |
| 567 | # For example, given a variant set that is mapped to the GRCh38 reference set |
| 568 | # and contains a single variant on reference 'X', `referenceBounds` would |
| 569 | # contain only an entry for 'X', while the associated reference set |
| 570 | # enumerates all possible references: '1', '2', 'X', 'Y', 'MT', etc. |
| 571 | "id": "A String", # The server-generated variant set ID, unique across all variant sets. |
| 572 | "datasetId": "A String", # The dataset to which this variant set belongs. |
| 573 | "referenceBounds": [ # A list of all references used by the variants in a variant set |
| 574 | # with associated coordinate upper bounds for each one. |
| 575 | { # ReferenceBound records an upper bound for the starting coordinate of |
| 576 | # variants in a particular reference. |
| 577 | "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any |
| 578 | # variant in the reference sequence. |
| 579 | "referenceName": "A String", # The name of the reference associated with this reference bound. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 580 | }, |
| 581 | ], |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 582 | }</pre> |
| 583 | </div> |
| 584 | |
| 585 | <div class="method"> |
| 586 | <code class="details" id="search">search(body, x__xgafv=None)</code> |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 587 | <pre>Returns a list of all variant sets matching search criteria. |
| 588 | |
| 589 | For the definitions of variant sets and other genomics resources, see |
| 590 | [Fundamentals of Google |
| 591 | Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
| 592 | |
| 593 | Implements |
| 594 | [GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L49). |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 595 | |
| 596 | Args: |
| 597 | body: object, The request body. (required) |
| 598 | The object takes the form of: |
| 599 | |
| 600 | { # The search variant sets request. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 601 | "pageToken": "A String", # The continuation token, which is used to page through large result sets. |
| 602 | # To get the next page of results, set this parameter to the value of |
| 603 | # `nextPageToken` from the previous response. |
| 604 | "datasetIds": [ # Exactly one dataset ID must be provided here. Only variant sets which |
| 605 | # belong to this dataset will be returned. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 606 | "A String", |
| 607 | ], |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 608 | "pageSize": 42, # The maximum number of results to return in a single page. If unspecified, |
| 609 | # defaults to 1024. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 610 | } |
| 611 | |
| 612 | x__xgafv: string, V1 error format. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 613 | Allowed values |
| 614 | 1 - v1 error format |
| 615 | 2 - v2 error format |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 616 | |
| 617 | Returns: |
| 618 | An object of the form: |
| 619 | |
| 620 | { # The search variant sets response. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 621 | "nextPageToken": "A String", # The continuation token, which is used to page through large result sets. |
| 622 | # Provide this value in a subsequent request to return the next page of |
| 623 | # results. This field will be empty if there aren't any additional results. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 624 | "variantSets": [ # The variant sets belonging to the requested dataset. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 625 | { # A variant set is a collection of call sets and variants. It contains summary |
| 626 | # statistics of those contents. A variant set belongs to a dataset. |
| 627 | # |
| 628 | # For more genomics resource definitions, see [Fundamentals of Google |
| 629 | # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
Jon Wayne Parrott | 0a471d3 | 2016-05-19 10:54:38 -0700 | [diff] [blame] | 630 | "name": "A String", # User-specified, mutable name. |
| 631 | "description": "A String", # A textual description of this variant set. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 632 | "metadata": [ # The metadata associated with this variant set. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 633 | { # Metadata describes a single piece of variant call metadata. |
| 634 | # These data include a top level key and either a single value string (value) |
| 635 | # or a list of key-value pairs (info.) |
| 636 | # Value and info are mutually exclusive. |
| 637 | "info": { # Remaining structured metadata key-value pairs. This must be of the form |
| 638 | # map<string, string[]> (string key mapping to a list of string values). |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 639 | "a_key": [ |
| 640 | "", |
| 641 | ], |
| 642 | }, |
| 643 | "description": "A String", # A textual description of this metadata. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 644 | "number": "A String", # The number of values that can be included in a field described by this |
| 645 | # metadata. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 646 | "value": "A String", # The value field for simple metadata |
| 647 | "key": "A String", # The top-level key. |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 648 | "type": "A String", # The type of data. Possible types include: Integer, Float, |
| 649 | # Flag, Character, and String. |
| 650 | "id": "A String", # User-provided ID field, not enforced by this API. |
| 651 | # Two or more pieces of structured metadata with identical |
| 652 | # id and key fields are considered equivalent. |
| 653 | }, |
| 654 | ], |
| 655 | "referenceSetId": "A String", # The reference set to which the variant set is mapped. The reference set |
| 656 | # describes the alignment provenance of the variant set, while the |
| 657 | # `referenceBounds` describe the shape of the actual variant data. The |
| 658 | # reference set's reference names are a superset of those found in the |
| 659 | # `referenceBounds`. |
| 660 | # |
| 661 | # For example, given a variant set that is mapped to the GRCh38 reference set |
| 662 | # and contains a single variant on reference 'X', `referenceBounds` would |
| 663 | # contain only an entry for 'X', while the associated reference set |
| 664 | # enumerates all possible references: '1', '2', 'X', 'Y', 'MT', etc. |
| 665 | "id": "A String", # The server-generated variant set ID, unique across all variant sets. |
| 666 | "datasetId": "A String", # The dataset to which this variant set belongs. |
| 667 | "referenceBounds": [ # A list of all references used by the variants in a variant set |
| 668 | # with associated coordinate upper bounds for each one. |
| 669 | { # ReferenceBound records an upper bound for the starting coordinate of |
| 670 | # variants in a particular reference. |
| 671 | "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any |
| 672 | # variant in the reference sequence. |
| 673 | "referenceName": "A String", # The name of the reference associated with this reference bound. |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 674 | }, |
| 675 | ], |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 676 | }, |
| 677 | ], |
| 678 | }</pre> |
| 679 | </div> |
| 680 | |
Sai Cheemalapati | c30d2b5 | 2017-03-13 12:12:03 -0400 | [diff] [blame^] | 681 | <div class="method"> |
| 682 | <code class="details" id="search_next">search_next(previous_request, previous_response)</code> |
| 683 | <pre>Retrieves the next page of results. |
| 684 | |
| 685 | Args: |
| 686 | previous_request: The request for the previous page. (required) |
| 687 | previous_response: The response from the request for the previous page. (required) |
| 688 | |
| 689 | Returns: |
| 690 | A request object that you can call 'execute()' on to request the next |
| 691 | page. Returns None if there are no more items in the collection. |
| 692 | </pre> |
| 693 | </div> |
| 694 | |
Takashi Matsuo | 0669410 | 2015-09-11 13:55:40 -0700 | [diff] [blame] | 695 | </body></html> |