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gerrit-public.fairphone.software / platform / external / python / google-api-python-client / 0669410c6b2c48884ae31671b9d710a9ff6346c6 / . / docs / dyn / genomics_v1.variantsets.html
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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>
79<p class="firstline">Creates a new variant set. The provided variant set must have a valid `datasetId` set - all other fields are optional. Note that the `id` field will be ignored, as this is assigned by the server.</p>
80<p class="toc_element">
81 <code><a href="#delete">delete(variantSetId, x__xgafv=None)</a></code></p>
82<p class="firstline">Deletes the contents of a variant set. The variant set object is not deleted.</p>
83<p class="toc_element">
84 <code><a href="#export">export(variantSetId, body, x__xgafv=None)</a></code></p>
85<p class="firstline">Exports variant set data to an external destination.</p>
86<p class="toc_element">
87 <code><a href="#get">get(variantSetId, x__xgafv=None)</a></code></p>
88<p class="firstline">Gets a variant set by ID.</p>
89<p class="toc_element">
90 <code><a href="#patch">patch(variantSetId, body, updateMask=None, x__xgafv=None)</a></code></p>
91<p class="firstline">Updates a variant set. This method supports patch semantics.</p>
92<p class="toc_element">
93 <code><a href="#search">search(body, x__xgafv=None)</a></code></p>
94<p class="firstline">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).</p>
95<h3>Method Details</h3>
96<div class="method">
97 <code class="details" id="create">create(body, x__xgafv=None)</code>
98 <pre>Creates a new variant set. The provided variant set must have a valid `datasetId` set - all other fields are optional. Note that the `id` field will be ignored, as this is assigned by the server.
99
100Args:
101 body: object, The request body. (required)
102 The object takes the form of:
103
104{ # A variant set is a collection of call sets and variants. It contains summary statistics of those contents. A variant set belongs to a dataset.
105 "metadata": [ # The metadata associated with this variant set.
106 { # Metadata describes a single piece of variant call metadata. These data include a top level key and either a single value string (value) or a list of key-value pairs (info.) Value and info are mutually exclusive.
107 "info": { # Remaining structured metadata key-value pairs. This must be of the form map (string key mapping to a list of string values).
108 "a_key": [
109 "",
110 ],
111 },
112 "description": "A String", # A textual description of this metadata.
113 "number": "A String", # The number of values that can be included in a field described by this metadata.
114 "value": "A String", # The value field for simple metadata
115 "key": "A String", # The top-level key.
116 "type": "A String", # The type of data. Possible types include: Integer, Float, Flag, Character, and String.
117 "id": "A String", # 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.
118 },
119 ],
120 "id": "A String", # The server-generated variant set ID, unique across all variant sets.
121 "datasetId": "A String", # The dataset to which this variant set belongs.
122 "referenceBounds": [ # A list of all references used by the variants in a variant set with associated coordinate upper bounds for each one.
123 { # ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
124 "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any variant in the reference sequence.
125 "referenceName": "A String", # The reference the bound is associate with.
126 },
127 ],
128}
129
130 x__xgafv: string, V1 error format.
131
132Returns:
133 An object of the form:
134
135 { # A variant set is a collection of call sets and variants. It contains summary statistics of those contents. A variant set belongs to a dataset.
136 "metadata": [ # The metadata associated with this variant set.
137 { # Metadata describes a single piece of variant call metadata. These data include a top level key and either a single value string (value) or a list of key-value pairs (info.) Value and info are mutually exclusive.
138 "info": { # Remaining structured metadata key-value pairs. This must be of the form map (string key mapping to a list of string values).
139 "a_key": [
140 "",
141 ],
142 },
143 "description": "A String", # A textual description of this metadata.
144 "number": "A String", # The number of values that can be included in a field described by this metadata.
145 "value": "A String", # The value field for simple metadata
146 "key": "A String", # The top-level key.
147 "type": "A String", # The type of data. Possible types include: Integer, Float, Flag, Character, and String.
148 "id": "A String", # 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.
149 },
150 ],
151 "id": "A String", # The server-generated variant set ID, unique across all variant sets.
152 "datasetId": "A String", # The dataset to which this variant set belongs.
153 "referenceBounds": [ # A list of all references used by the variants in a variant set with associated coordinate upper bounds for each one.
154 { # ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
155 "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any variant in the reference sequence.
156 "referenceName": "A String", # The reference the bound is associate with.
157 },
158 ],
159 }</pre>
160</div>
161
162<div class="method">
163 <code class="details" id="delete">delete(variantSetId, x__xgafv=None)</code>
164 <pre>Deletes the contents of a variant set. The variant set object is not deleted.
165
166Args:
167 variantSetId: string, The ID of the variant set to be deleted. (required)
168 x__xgafv: string, V1 error format.
169
170Returns:
171 An object of the form:
172
173 { # 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 representation for `Empty` is empty JSON object `{}`.
174 }</pre>
175</div>
176
177<div class="method">
178 <code class="details" id="export">export(variantSetId, body, x__xgafv=None)</code>
179 <pre>Exports variant set data to an external destination.
180
181Args:
182 variantSetId: string, Required. The ID of the variant set that contains variant data which should be exported. The caller must have READ access to this variant set. (required)
183 body: object, The request body. (required)
184 The object takes the form of:
185
186{ # The variant data export request.
187 "projectId": "A String", # Required. The Google Cloud project ID that owns the destination BigQuery dataset. The caller must have WRITE access to this project. This project will also own the resulting export job.
188 "bigqueryTable": "A String", # Required. The BigQuery table to export data to. If the table doesn't exist, it will be created. If it already exists, it will be overwritten.
189 "bigqueryDataset": "A String", # Required. The BigQuery dataset to export data to. This dataset must already exist. Note that this is distinct from the Genomics concept of "dataset".
190 "callSetIds": [ # If provided, only variant call information from the specified call sets will be exported. By default all variant calls are exported.
191 "A String",
192 ],
193 "format": "A String", # The format for the exported data.
194 }
195
196 x__xgafv: string, V1 error format.
197
198Returns:
199 An object of the form:
200
201 { # This resource represents a long-running operation that is the result of a network API call.
202 "response": { # If importing [ReadGroupSets][google.genomics.v1.ReadGroupSet], an [ImportReadGroupSetsResponse][google.genomics.v1.ImportReadGroupSetsResponse] is returned. If importing [Variants][google.genomics.v1.Variant], an [ImportVariantsResponse][google.genomics.v1.ImportVariantsResponse] is returned. For exports, an empty response is returned.
203 "a_key": "", # Properties of the object. Contains field @ype with type URL.
204 },
205 "error": { # 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 designed 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 or localize it in the client. The optional error details may contain arbitrary information about the error. There is a predefined set of error detail types in the 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 exposed in different client libraries and different wire protocols, it can be mapped differently. For example, it will likely be mapped to some exceptions in Java, 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 environments. Example uses of this error model include: - Partial errors. If a service 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 typical workflow has multiple steps. Each step may have a `Status` message for error reporting purpose. - Batch operations. If a client uses batch request and batch response, the `Status` message should be used directly inside batch response, one for each error sub-response. - Asynchronous operations. If an API call embeds asynchronous operation results in its response, the status of those operations should 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. # The error result of the operation in case of failure.
206 "message": "A String", # A developer-facing error message, which should 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 by the client.
207 "code": 42, # The status code, which should be an enum value of [google.rpc.Code][google.rpc.Code].
208 "details": [ # A list of messages that carry the error details. There will be a common set of message types for APIs to use.
209 {
210 "a_key": "", # Properties of the object. Contains field @ype with type URL.
211 },
212 ],
213 },
214 "done": True or False, # If the value is `false`, it means the operation is still in progress. If true, the operation is completed, and either `error` or `response` is available.
215 "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`
216 "metadata": { # An [OperationMetadata][google.genomics.v1.OperationMetadata] object. This will always be returned with the [Operation][google.longrunning.Operation].
217 "a_key": "", # Properties of the object. Contains field @ype with type URL.
218 },
219 }</pre>
220</div>
221
222<div class="method">
223 <code class="details" id="get">get(variantSetId, x__xgafv=None)</code>
224 <pre>Gets a variant set by ID.
225
226Args:
227 variantSetId: string, Required. The ID of the variant set. (required)
228 x__xgafv: string, V1 error format.
229
230Returns:
231 An object of the form:
232
233 { # A variant set is a collection of call sets and variants. It contains summary statistics of those contents. A variant set belongs to a dataset.
234 "metadata": [ # The metadata associated with this variant set.
235 { # Metadata describes a single piece of variant call metadata. These data include a top level key and either a single value string (value) or a list of key-value pairs (info.) Value and info are mutually exclusive.
236 "info": { # Remaining structured metadata key-value pairs. This must be of the form map (string key mapping to a list of string values).
237 "a_key": [
238 "",
239 ],
240 },
241 "description": "A String", # A textual description of this metadata.
242 "number": "A String", # The number of values that can be included in a field described by this metadata.
243 "value": "A String", # The value field for simple metadata
244 "key": "A String", # The top-level key.
245 "type": "A String", # The type of data. Possible types include: Integer, Float, Flag, Character, and String.
246 "id": "A String", # 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.
247 },
248 ],
249 "id": "A String", # The server-generated variant set ID, unique across all variant sets.
250 "datasetId": "A String", # The dataset to which this variant set belongs.
251 "referenceBounds": [ # A list of all references used by the variants in a variant set with associated coordinate upper bounds for each one.
252 { # ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
253 "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any variant in the reference sequence.
254 "referenceName": "A String", # The reference the bound is associate with.
255 },
256 ],
257 }</pre>
258</div>
259
260<div class="method">
261 <code class="details" id="patch">patch(variantSetId, body, updateMask=None, x__xgafv=None)</code>
262 <pre>Updates a variant set. This method supports patch semantics.
263
264Args:
265 variantSetId: string, The ID of the variant to be updated (must already exist). (required)
266 body: object, The request body. (required)
267 The object takes the form of:
268
269{ # A variant set is a collection of call sets and variants. It contains summary statistics of those contents. A variant set belongs to a dataset.
270 "metadata": [ # The metadata associated with this variant set.
271 { # Metadata describes a single piece of variant call metadata. These data include a top level key and either a single value string (value) or a list of key-value pairs (info.) Value and info are mutually exclusive.
272 "info": { # Remaining structured metadata key-value pairs. This must be of the form map (string key mapping to a list of string values).
273 "a_key": [
274 "",
275 ],
276 },
277 "description": "A String", # A textual description of this metadata.
278 "number": "A String", # The number of values that can be included in a field described by this metadata.
279 "value": "A String", # The value field for simple metadata
280 "key": "A String", # The top-level key.
281 "type": "A String", # The type of data. Possible types include: Integer, Float, Flag, Character, and String.
282 "id": "A String", # 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.
283 },
284 ],
285 "id": "A String", # The server-generated variant set ID, unique across all variant sets.
286 "datasetId": "A String", # The dataset to which this variant set belongs.
287 "referenceBounds": [ # A list of all references used by the variants in a variant set with associated coordinate upper bounds for each one.
288 { # ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
289 "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any variant in the reference sequence.
290 "referenceName": "A String", # The reference the bound is associate with.
291 },
292 ],
293}
294
295 updateMask: string, An optional mask specifying which fields to update. At this time, the only mutable field is [metadata][google.genomics.v1.VariantSet.metadata]. The only acceptable value is "metadata". If unspecified, all mutable fields will be updated.
296 x__xgafv: string, V1 error format.
297
298Returns:
299 An object of the form:
300
301 { # A variant set is a collection of call sets and variants. It contains summary statistics of those contents. A variant set belongs to a dataset.
302 "metadata": [ # The metadata associated with this variant set.
303 { # Metadata describes a single piece of variant call metadata. These data include a top level key and either a single value string (value) or a list of key-value pairs (info.) Value and info are mutually exclusive.
304 "info": { # Remaining structured metadata key-value pairs. This must be of the form map (string key mapping to a list of string values).
305 "a_key": [
306 "",
307 ],
308 },
309 "description": "A String", # A textual description of this metadata.
310 "number": "A String", # The number of values that can be included in a field described by this metadata.
311 "value": "A String", # The value field for simple metadata
312 "key": "A String", # The top-level key.
313 "type": "A String", # The type of data. Possible types include: Integer, Float, Flag, Character, and String.
314 "id": "A String", # 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.
315 },
316 ],
317 "id": "A String", # The server-generated variant set ID, unique across all variant sets.
318 "datasetId": "A String", # The dataset to which this variant set belongs.
319 "referenceBounds": [ # A list of all references used by the variants in a variant set with associated coordinate upper bounds for each one.
320 { # ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
321 "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any variant in the reference sequence.
322 "referenceName": "A String", # The reference the bound is associate with.
323 },
324 ],
325 }</pre>
326</div>
327
328<div class="method">
329 <code class="details" id="search">search(body, x__xgafv=None)</code>
330 <pre>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).
331
332Args:
333 body: object, The request body. (required)
334 The object takes the form of:
335
336{ # The search variant sets request.
337 "pageToken": "A String", # 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 `nextPageToken` from the previous response.
338 "datasetIds": [ # Exactly one dataset ID must be provided here. Only variant sets which belong to this dataset will be returned.
339 "A String",
340 ],
341 "pageSize": 42, # The maximum number of variant sets to return in a request.
342 }
343
344 x__xgafv: string, V1 error format.
345
346Returns:
347 An object of the form:
348
349 { # The search variant sets response.
350 "nextPageToken": "A String", # The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there aren't any additional results.
351 "variantSets": [ # The variant sets belonging to the requested dataset.
352 { # A variant set is a collection of call sets and variants. It contains summary statistics of those contents. A variant set belongs to a dataset.
353 "metadata": [ # The metadata associated with this variant set.
354 { # Metadata describes a single piece of variant call metadata. These data include a top level key and either a single value string (value) or a list of key-value pairs (info.) Value and info are mutually exclusive.
355 "info": { # Remaining structured metadata key-value pairs. This must be of the form map (string key mapping to a list of string values).
356 "a_key": [
357 "",
358 ],
359 },
360 "description": "A String", # A textual description of this metadata.
361 "number": "A String", # The number of values that can be included in a field described by this metadata.
362 "value": "A String", # The value field for simple metadata
363 "key": "A String", # The top-level key.
364 "type": "A String", # The type of data. Possible types include: Integer, Float, Flag, Character, and String.
365 "id": "A String", # 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.
366 },
367 ],
368 "id": "A String", # The server-generated variant set ID, unique across all variant sets.
369 "datasetId": "A String", # The dataset to which this variant set belongs.
370 "referenceBounds": [ # A list of all references used by the variants in a variant set with associated coordinate upper bounds for each one.
371 { # ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
372 "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any variant in the reference sequence.
373 "referenceName": "A String", # The reference the bound is associate with.
374 },
375 ],
376 },
377 ],
378 }</pre>
379</div>
380
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