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gerrit-public.fairphone.software / platform / external / python / google-api-python-client / e833b79ffee531ae64e11175718bb2fffc504950 / . / 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.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]121 "metadata": [ # The metadata associated with this variant set.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]122 { # Metadata describes a single piece of variant call metadata.
123 # These data include a top level key and either a single value string (value)
124 # or a list of key-value pairs (info.)
125 # Value and info are mutually exclusive.
126 "info": { # Remaining structured metadata key-value pairs. This must be of the form
127 # map<string, string[]> (string key mapping to a list of string values).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]128 "a_key": [
129 "",
130 ],
131 },
132 "description": "A String", # A textual description of this metadata.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]133 "number": "A String", # The number of values that can be included in a field described by this
134 # metadata.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]135 "value": "A String", # The value field for simple metadata
136 "key": "A String", # The top-level key.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]137 "type": "A String", # The type of data. Possible types include: Integer, Float,
138 # Flag, Character, and String.
139 "id": "A String", # User-provided ID field, not enforced by this API.
140 # Two or more pieces of structured metadata with identical
141 # id and key fields are considered equivalent.
142 },
143 ],
Sai Cheemalapatie833b792017-03-24 15:06:46 -0700[diff] [blame^]144 "referenceBounds": [ # A list of all references used by the variants in a variant set
145 # with associated coordinate upper bounds for each one.
146 { # ReferenceBound records an upper bound for the starting coordinate of
147 # variants in a particular reference.
148 "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any
149 # variant in the reference sequence.
150 "referenceName": "A String", # The name of the reference associated with this reference bound.
151 },
152 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]153 "referenceSetId": "A String", # The reference set to which the variant set is mapped. The reference set
154 # describes the alignment provenance of the variant set, while the
155 # `referenceBounds` describe the shape of the actual variant data. The
156 # reference set's reference names are a superset of those found in the
157 # `referenceBounds`.
158 #
159 # For example, given a variant set that is mapped to the GRCh38 reference set
160 # and contains a single variant on reference 'X', `referenceBounds` would
161 # contain only an entry for 'X', while the associated reference set
162 # enumerates all possible references: '1', '2', 'X', 'Y', 'MT', etc.
163 "id": "A String", # The server-generated variant set ID, unique across all variant sets.
164 "datasetId": "A String", # The dataset to which this variant set belongs.
Sai Cheemalapatie833b792017-03-24 15:06:46 -0700[diff] [blame^]165 "description": "A String", # A textual description of this variant set.
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.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]182 "metadata": [ # The metadata associated with this variant set.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]183 { # Metadata describes a single piece of variant call metadata.
184 # These data include a top level key and either a single value string (value)
185 # or a list of key-value pairs (info.)
186 # Value and info are mutually exclusive.
187 "info": { # Remaining structured metadata key-value pairs. This must be of the form
188 # map<string, string[]> (string key mapping to a list of string values).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]189 "a_key": [
190 "",
191 ],
192 },
193 "description": "A String", # A textual description of this metadata.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]194 "number": "A String", # The number of values that can be included in a field described by this
195 # metadata.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]196 "value": "A String", # The value field for simple metadata
197 "key": "A String", # The top-level key.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]198 "type": "A String", # The type of data. Possible types include: Integer, Float,
199 # Flag, Character, and String.
200 "id": "A String", # User-provided ID field, not enforced by this API.
201 # Two or more pieces of structured metadata with identical
202 # id and key fields are considered equivalent.
203 },
204 ],
Sai Cheemalapatie833b792017-03-24 15:06:46 -0700[diff] [blame^]205 "referenceBounds": [ # A list of all references used by the variants in a variant set
206 # with associated coordinate upper bounds for each one.
207 { # ReferenceBound records an upper bound for the starting coordinate of
208 # variants in a particular reference.
209 "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any
210 # variant in the reference sequence.
211 "referenceName": "A String", # The name of the reference associated with this reference bound.
212 },
213 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]214 "referenceSetId": "A String", # The reference set to which the variant set is mapped. The reference set
215 # describes the alignment provenance of the variant set, while the
216 # `referenceBounds` describe the shape of the actual variant data. The
217 # reference set's reference names are a superset of those found in the
218 # `referenceBounds`.
219 #
220 # For example, given a variant set that is mapped to the GRCh38 reference set
221 # and contains a single variant on reference 'X', `referenceBounds` would
222 # contain only an entry for 'X', while the associated reference set
223 # enumerates all possible references: '1', '2', 'X', 'Y', 'MT', etc.
224 "id": "A String", # The server-generated variant set ID, unique across all variant sets.
225 "datasetId": "A String", # The dataset to which this variant set belongs.
Sai Cheemalapatie833b792017-03-24 15:06:46 -0700[diff] [blame^]226 "description": "A String", # A textual description of this variant set.
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.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]301 "metadata": { # An OperationMetadata object. This will always be returned with the Operation.
302 "a_key": "", # Properties of the object. Contains field @type with type URL.
303 },
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]304 "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.
305 # programming environments, including REST APIs and RPC APIs. It is used by
306 # [gRPC](https://github.com/grpc). The error model is designed to be:
307 #
308 # - Simple to use and understand for most users
309 # - Flexible enough to meet unexpected needs
310 #
311 # # Overview
312 #
313 # The `Status` message contains three pieces of data: error code, error message,
314 # and error details. The error code should be an enum value of
315 # google.rpc.Code, but it may accept additional error codes if needed. The
316 # error message should be a developer-facing English message that helps
317 # developers *understand* and *resolve* the error. If a localized user-facing
318 # error message is needed, put the localized message in the error details or
319 # localize it in the client. The optional error details may contain arbitrary
320 # information about the error. There is a predefined set of error detail types
321 # in the package `google.rpc` which can be used for common error conditions.
322 #
323 # # Language mapping
324 #
325 # The `Status` message is the logical representation of the error model, but it
326 # is not necessarily the actual wire format. When the `Status` message is
327 # exposed in different client libraries and different wire protocols, it can be
328 # mapped differently. For example, it will likely be mapped to some exceptions
329 # in Java, but more likely mapped to some error codes in C.
330 #
331 # # Other uses
332 #
333 # The error model and the `Status` message can be used in a variety of
334 # environments, either with or without APIs, to provide a
335 # consistent developer experience across different environments.
336 #
337 # Example uses of this error model include:
338 #
339 # - Partial errors. If a service needs to return partial errors to the client,
340 # it may embed the `Status` in the normal response to indicate the partial
341 # errors.
342 #
343 # - Workflow errors. A typical workflow has multiple steps. Each step may
344 # have a `Status` message for error reporting purpose.
345 #
346 # - Batch operations. If a client uses batch request and batch response, the
347 # `Status` message should be used directly inside batch response, one for
348 # each error sub-response.
349 #
350 # - Asynchronous operations. If an API call embeds asynchronous operation
351 # results in its response, the status of those operations should be
352 # represented directly using the `Status` message.
353 #
354 # - Logging. If some API errors are stored in logs, the message `Status` could
355 # be used directly after any stripping needed for security/privacy reasons.
356 "message": "A String", # A developer-facing error message, which should be in English. Any
357 # user-facing error message should be localized and sent in the
358 # google.rpc.Status.details field, or localized by the client.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]359 "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]360 "details": [ # A list of messages that carry the error details. There will be a
361 # common set of message types for APIs to use.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]362 {
Jon Wayne Parrott7d5badb2016-08-16 12:44:29 -0700[diff] [blame]363 "a_key": "", # Properties of the object. Contains field @type with type URL.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]364 },
365 ],
366 },
Sai Cheemalapatie833b792017-03-24 15:06:46 -0700[diff] [blame^]367 "done": True or False, # If the value is `false`, it means the operation is still in progress.
368 # If true, the operation is completed, and either `error` or `response` is
369 # available.
370 "response": { # If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If importing Variants, an ImportVariantsResponse is returned. For pipelines and exports, an empty response is returned.
371 "a_key": "", # Properties of the object. Contains field @type with type URL.
372 },
373 "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`
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.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]401 "metadata": [ # The metadata associated with this variant set.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]402 { # Metadata describes a single piece of variant call metadata.
403 # These data include a top level key and either a single value string (value)
404 # or a list of key-value pairs (info.)
405 # Value and info are mutually exclusive.
406 "info": { # Remaining structured metadata key-value pairs. This must be of the form
407 # map<string, string[]> (string key mapping to a list of string values).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]408 "a_key": [
409 "",
410 ],
411 },
412 "description": "A String", # A textual description of this metadata.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]413 "number": "A String", # The number of values that can be included in a field described by this
414 # metadata.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]415 "value": "A String", # The value field for simple metadata
416 "key": "A String", # The top-level key.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]417 "type": "A String", # The type of data. Possible types include: Integer, Float,
418 # Flag, Character, and String.
419 "id": "A String", # User-provided ID field, not enforced by this API.
420 # Two or more pieces of structured metadata with identical
421 # id and key fields are considered equivalent.
422 },
423 ],
Sai Cheemalapatie833b792017-03-24 15:06:46 -0700[diff] [blame^]424 "referenceBounds": [ # A list of all references used by the variants in a variant set
425 # with associated coordinate upper bounds for each one.
426 { # ReferenceBound records an upper bound for the starting coordinate of
427 # variants in a particular reference.
428 "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any
429 # variant in the reference sequence.
430 "referenceName": "A String", # The name of the reference associated with this reference bound.
431 },
432 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]433 "referenceSetId": "A String", # The reference set to which the variant set is mapped. The reference set
434 # describes the alignment provenance of the variant set, while the
435 # `referenceBounds` describe the shape of the actual variant data. The
436 # reference set's reference names are a superset of those found in the
437 # `referenceBounds`.
438 #
439 # For example, given a variant set that is mapped to the GRCh38 reference set
440 # and contains a single variant on reference 'X', `referenceBounds` would
441 # contain only an entry for 'X', while the associated reference set
442 # enumerates all possible references: '1', '2', 'X', 'Y', 'MT', etc.
443 "id": "A String", # The server-generated variant set ID, unique across all variant sets.
444 "datasetId": "A String", # The dataset to which this variant set belongs.
Sai Cheemalapatie833b792017-03-24 15:06:46 -0700[diff] [blame^]445 "description": "A String", # A textual description of this variant set.
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.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]468 "metadata": [ # The metadata associated with this variant set.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]469 { # Metadata describes a single piece of variant call metadata.
470 # These data include a top level key and either a single value string (value)
471 # or a list of key-value pairs (info.)
472 # Value and info are mutually exclusive.
473 "info": { # Remaining structured metadata key-value pairs. This must be of the form
474 # map<string, string[]> (string key mapping to a list of string values).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]475 "a_key": [
476 "",
477 ],
478 },
479 "description": "A String", # A textual description of this metadata.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]480 "number": "A String", # The number of values that can be included in a field described by this
481 # metadata.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]482 "value": "A String", # The value field for simple metadata
483 "key": "A String", # The top-level key.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]484 "type": "A String", # The type of data. Possible types include: Integer, Float,
485 # Flag, Character, and String.
486 "id": "A String", # User-provided ID field, not enforced by this API.
487 # Two or more pieces of structured metadata with identical
488 # id and key fields are considered equivalent.
489 },
490 ],
Sai Cheemalapatie833b792017-03-24 15:06:46 -0700[diff] [blame^]491 "referenceBounds": [ # A list of all references used by the variants in a variant set
492 # with associated coordinate upper bounds for each one.
493 { # ReferenceBound records an upper bound for the starting coordinate of
494 # variants in a particular reference.
495 "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any
496 # variant in the reference sequence.
497 "referenceName": "A String", # The name of the reference associated with this reference bound.
498 },
499 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]500 "referenceSetId": "A String", # The reference set to which the variant set is mapped. The reference set
501 # describes the alignment provenance of the variant set, while the
502 # `referenceBounds` describe the shape of the actual variant data. The
503 # reference set's reference names are a superset of those found in the
504 # `referenceBounds`.
505 #
506 # For example, given a variant set that is mapped to the GRCh38 reference set
507 # and contains a single variant on reference 'X', `referenceBounds` would
508 # contain only an entry for 'X', while the associated reference set
509 # enumerates all possible references: '1', '2', 'X', 'Y', 'MT', etc.
510 "id": "A String", # The server-generated variant set ID, unique across all variant sets.
511 "datasetId": "A String", # The dataset to which this variant set belongs.
Sai Cheemalapatie833b792017-03-24 15:06:46 -0700[diff] [blame^]512 "description": "A String", # A textual description of this variant set.
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.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]537 "metadata": [ # The metadata associated with this variant set.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]538 { # Metadata describes a single piece of variant call metadata.
539 # These data include a top level key and either a single value string (value)
540 # or a list of key-value pairs (info.)
541 # Value and info are mutually exclusive.
542 "info": { # Remaining structured metadata key-value pairs. This must be of the form
543 # map<string, string[]> (string key mapping to a list of string values).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]544 "a_key": [
545 "",
546 ],
547 },
548 "description": "A String", # A textual description of this metadata.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]549 "number": "A String", # The number of values that can be included in a field described by this
550 # metadata.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]551 "value": "A String", # The value field for simple metadata
552 "key": "A String", # The top-level key.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]553 "type": "A String", # The type of data. Possible types include: Integer, Float,
554 # Flag, Character, and String.
555 "id": "A String", # User-provided ID field, not enforced by this API.
556 # Two or more pieces of structured metadata with identical
557 # id and key fields are considered equivalent.
558 },
559 ],
Sai Cheemalapatie833b792017-03-24 15:06:46 -0700[diff] [blame^]560 "referenceBounds": [ # A list of all references used by the variants in a variant set
561 # with associated coordinate upper bounds for each one.
562 { # ReferenceBound records an upper bound for the starting coordinate of
563 # variants in a particular reference.
564 "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any
565 # variant in the reference sequence.
566 "referenceName": "A String", # The name of the reference associated with this reference bound.
567 },
568 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]569 "referenceSetId": "A String", # The reference set to which the variant set is mapped. The reference set
570 # describes the alignment provenance of the variant set, while the
571 # `referenceBounds` describe the shape of the actual variant data. The
572 # reference set's reference names are a superset of those found in the
573 # `referenceBounds`.
574 #
575 # For example, given a variant set that is mapped to the GRCh38 reference set
576 # and contains a single variant on reference 'X', `referenceBounds` would
577 # contain only an entry for 'X', while the associated reference set
578 # enumerates all possible references: '1', '2', 'X', 'Y', 'MT', etc.
579 "id": "A String", # The server-generated variant set ID, unique across all variant sets.
580 "datasetId": "A String", # The dataset to which this variant set belongs.
Sai Cheemalapatie833b792017-03-24 15:06:46 -0700[diff] [blame^]581 "description": "A String", # A textual description of this variant set.
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.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]631 "metadata": [ # The metadata associated with this variant set.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]632 { # Metadata describes a single piece of variant call metadata.
633 # These data include a top level key and either a single value string (value)
634 # or a list of key-value pairs (info.)
635 # Value and info are mutually exclusive.
636 "info": { # Remaining structured metadata key-value pairs. This must be of the form
637 # map<string, string[]> (string key mapping to a list of string values).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]638 "a_key": [
639 "",
640 ],
641 },
642 "description": "A String", # A textual description of this metadata.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]643 "number": "A String", # The number of values that can be included in a field described by this
644 # metadata.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]645 "value": "A String", # The value field for simple metadata
646 "key": "A String", # The top-level key.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]647 "type": "A String", # The type of data. Possible types include: Integer, Float,
648 # Flag, Character, and String.
649 "id": "A String", # User-provided ID field, not enforced by this API.
650 # Two or more pieces of structured metadata with identical
651 # id and key fields are considered equivalent.
652 },
653 ],
Sai Cheemalapatie833b792017-03-24 15:06:46 -0700[diff] [blame^]654 "referenceBounds": [ # A list of all references used by the variants in a variant set
655 # with associated coordinate upper bounds for each one.
656 { # ReferenceBound records an upper bound for the starting coordinate of
657 # variants in a particular reference.
658 "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any
659 # variant in the reference sequence.
660 "referenceName": "A String", # The name of the reference associated with this reference bound.
661 },
662 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]663 "referenceSetId": "A String", # The reference set to which the variant set is mapped. The reference set
664 # describes the alignment provenance of the variant set, while the
665 # `referenceBounds` describe the shape of the actual variant data. The
666 # reference set's reference names are a superset of those found in the
667 # `referenceBounds`.
668 #
669 # For example, given a variant set that is mapped to the GRCh38 reference set
670 # and contains a single variant on reference 'X', `referenceBounds` would
671 # contain only an entry for 'X', while the associated reference set
672 # enumerates all possible references: '1', '2', 'X', 'Y', 'MT', etc.
673 "id": "A String", # The server-generated variant set ID, unique across all variant sets.
674 "datasetId": "A String", # The dataset to which this variant set belongs.
Sai Cheemalapatie833b792017-03-24 15:06:46 -0700[diff] [blame^]675 "description": "A String", # A textual description of this variant set.
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>