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gerrit-public.fairphone.software / platform / external / python / google-api-python-client / c30d2b5d4478b230246dcaaa9f1c533ca3304387 / . / docs / dyn / genomics_v1.variantsets.html
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Takashi Matsuo06694102015-09-11 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 Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]79<p class="firstline">Creates a new variant set.</p>
Takashi Matsuo06694102015-09-11 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 Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]82<p class="firstline">Deletes a variant set including all variants, call sets, and calls within.</p>
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]83<p class="toc_element">
Sai Cheemalapatic30d2b52017-03-13 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 Matsuo06694102015-09-11 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 Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]88<p class="firstline">Gets a variant set by ID.</p>
Takashi Matsuo06694102015-09-11 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 Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]91<p class="firstline">Updates a variant set using patch semantics.</p>
Takashi Matsuo06694102015-09-11 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 Cheemalapatic30d2b52017-03-13 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 Matsuo06694102015-09-11 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 Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]101 <pre>Creates a new variant set.
102
103For the definitions of variant sets and other genomics resources, see
104[Fundamentals of Google
105Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
106
107The provided variant set must have a valid `datasetId` set - all other
108fields are optional. Note that the `id` field will be ignored, as this is
109assigned by the server.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]110
111Args:
112 body: object, The request body. (required)
113 The object takes the form of:
114
Sai Cheemalapatic30d2b52017-03-13 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 Parrott0a471d32016-05-19 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 Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]122 "metadata": [ # The metadata associated with this variant set.
Sai Cheemalapatic30d2b52017-03-13 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 Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]129 "a_key": [
130 "",
131 ],
132 },
133 "description": "A String", # A textual description of this metadata.
Sai Cheemalapatic30d2b52017-03-13 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 Matsuo06694102015-09-11 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 Cheemalapatic30d2b52017-03-13 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 Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]164 },
165 ],
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]166}
167
168 x__xgafv: string, V1 error format.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]169 Allowed values
170 1 - v1 error format
171 2 - v2 error format
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]172
173Returns:
174 An object of the form:
175
Sai Cheemalapatic30d2b52017-03-13 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 Parrott0a471d32016-05-19 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 Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]183 "metadata": [ # The metadata associated with this variant set.
Sai Cheemalapatic30d2b52017-03-13 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 Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]190 "a_key": [
191 "",
192 ],
193 },
194 "description": "A String", # A textual description of this metadata.
Sai Cheemalapatic30d2b52017-03-13 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 Matsuo06694102015-09-11 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 Cheemalapatic30d2b52017-03-13 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 Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]225 },
226 ],
Takashi Matsuo06694102015-09-11 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 Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]232 <pre>Deletes a variant set including all variants, call sets, and calls within.
233This is not reversible.
234
235For the definitions of variant sets and other genomics resources, see
236[Fundamentals of Google
237Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]238
239Args:
240 variantSetId: string, The ID of the variant set to be deleted. (required)
241 x__xgafv: string, V1 error format.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]242 Allowed values
243 1 - v1 error format
244 2 - v2 error format
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]245
246Returns:
247 An object of the form:
248
Sai Cheemalapatic30d2b52017-03-13 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 Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]258 }</pre>
259</div>
260
261<div class="method">
Sai Cheemalapatic30d2b52017-03-13 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
265For the definitions of variant sets and other genomics resources, see
266[Fundamentals of Google
267Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]268
269Args:
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]270 variantSetId: string, Required. The ID of the variant set that contains variant data which
271should be exported. The caller must have READ access to this variant set. (required)
Takashi Matsuo06694102015-09-11 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 Cheemalapatic30d2b52017-03-13 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 Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]283 "A String",
284 ],
Sai Cheemalapatic30d2b52017-03-13 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 Matsuo06694102015-09-11 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 Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]292 Allowed values
293 1 - v1 error format
294 2 - v2 error format
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]295
296Returns:
297 An object of the form:
298
Sai Cheemalapatic30d2b52017-03-13 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 Parrott7d5badb2016-08-16 12:44:29 -0700[diff] [blame]302 "a_key": "", # Properties of the object. Contains field @type with type URL.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]303 },
Sai Cheemalapatic30d2b52017-03-13 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&#58; `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 Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]366 "code": 42, # The status code, which should be an enum value of google.rpc.Code.
Sai Cheemalapatic30d2b52017-03-13 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 Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]369 {
Jon Wayne Parrott7d5badb2016-08-16 12:44:29 -0700[diff] [blame]370 "a_key": "", # Properties of the object. Contains field @type with type URL.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]371 },
372 ],
373 },
Takashi Matsuo06694102015-09-11 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 Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]379 <pre>Gets a variant set by ID.
380
381For the definitions of variant sets and other genomics resources, see
382[Fundamentals of Google
383Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]384
385Args:
386 variantSetId: string, Required. The ID of the variant set. (required)
387 x__xgafv: string, V1 error format.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]388 Allowed values
389 1 - v1 error format
390 2 - v2 error format
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]391
392Returns:
393 An object of the form:
394
Sai Cheemalapatic30d2b52017-03-13 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 Parrott0a471d32016-05-19 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 Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]402 "metadata": [ # The metadata associated with this variant set.
Sai Cheemalapatic30d2b52017-03-13 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 Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]409 "a_key": [
410 "",
411 ],
412 },
413 "description": "A String", # A textual description of this metadata.
Sai Cheemalapatic30d2b52017-03-13 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 Matsuo06694102015-09-11 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 Cheemalapatic30d2b52017-03-13 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 Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]444 },
445 ],
Takashi Matsuo06694102015-09-11 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 Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]451 <pre>Updates a variant set using patch semantics.
452
453For the definitions of variant sets and other genomics resources, see
454[Fundamentals of Google
455Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]456
457Args:
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 Cheemalapatic30d2b52017-03-13 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 Parrott0a471d32016-05-19 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 Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]469 "metadata": [ # The metadata associated with this variant set.
Sai Cheemalapatic30d2b52017-03-13 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 Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]476 "a_key": [
477 "",
478 ],
479 },
480 "description": "A String", # A textual description of this metadata.
Sai Cheemalapatic30d2b52017-03-13 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 Matsuo06694102015-09-11 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 Cheemalapatic30d2b52017-03-13 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 Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]511 },
512 ],
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]513}
514
Sai Cheemalapatic30d2b52017-03-13 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
521Leaving `updateMask` unset is equivalent to specifying all mutable
522fields.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]523 x__xgafv: string, V1 error format.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]524 Allowed values
525 1 - v1 error format
526 2 - v2 error format
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]527
528Returns:
529 An object of the form:
530
Sai Cheemalapatic30d2b52017-03-13 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 Parrott0a471d32016-05-19 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 Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]538 "metadata": [ # The metadata associated with this variant set.
Sai Cheemalapatic30d2b52017-03-13 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 Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]545 "a_key": [
546 "",
547 ],
548 },
549 "description": "A String", # A textual description of this metadata.
Sai Cheemalapatic30d2b52017-03-13 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 Matsuo06694102015-09-11 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 Cheemalapatic30d2b52017-03-13 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 Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]580 },
581 ],
Takashi Matsuo06694102015-09-11 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 Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]587 <pre>Returns a list of all variant sets matching search criteria.
588
589For the definitions of variant sets and other genomics resources, see
590[Fundamentals of Google
591Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
592
593Implements
594[GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L49).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]595
596Args:
597 body: object, The request body. (required)
598 The object takes the form of:
599
600{ # The search variant sets request.
Sai Cheemalapatic30d2b52017-03-13 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 Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]606 "A String",
607 ],
Sai Cheemalapatic30d2b52017-03-13 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 Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]610 }
611
612 x__xgafv: string, V1 error format.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]613 Allowed values
614 1 - v1 error format
615 2 - v2 error format
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]616
617Returns:
618 An object of the form:
619
620 { # The search variant sets response.
Sai Cheemalapatic30d2b52017-03-13 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 Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]624 "variantSets": [ # The variant sets belonging to the requested dataset.
Sai Cheemalapatic30d2b52017-03-13 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 Parrott0a471d32016-05-19 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 Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]632 "metadata": [ # The metadata associated with this variant set.
Sai Cheemalapatic30d2b52017-03-13 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 Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]639 "a_key": [
640 "",
641 ],
642 },
643 "description": "A String", # A textual description of this metadata.
Sai Cheemalapatic30d2b52017-03-13 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 Matsuo06694102015-09-11 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 Cheemalapatic30d2b52017-03-13 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 Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]674 },
675 ],
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]676 },
677 ],
678 }</pre>
679</div>
680
Sai Cheemalapatic30d2b52017-03-13 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
685Args:
686 previous_request: The request for the previous page. (required)
687 previous_response: The response from the request for the previous page. (required)
688
689Returns:
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 Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]695</body></html>