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gerrit-public.fairphone.software / platform / external / python / google-api-python-client / 4ba8c235185d73c50911d3e1ef511904b474fee2 / . / docs / dyn / genomics_v1.readgroupsets.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.readgroupsets.html">readgroupsets</a></h1>
76<h2>Instance Methods</h2>
77<p class="toc_element">
78 <code><a href="genomics_v1.readgroupsets.coveragebuckets.html">coveragebuckets()</a></code>
79</p>
80<p class="firstline">Returns the coveragebuckets Resource.</p>
81
82<p class="toc_element">
Thomas Coffee2f245372017-03-27 10:39:26 -0700[diff] [blame]83 <code><a href="#delete">delete(readGroupSetId, x__xgafv=None)</a></code></p>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]84<p class="firstline">Deletes a read group set.</p>
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]85<p class="toc_element">
Thomas Coffee2f245372017-03-27 10:39:26 -0700[diff] [blame]86 <code><a href="#export">export(readGroupSetId, body, x__xgafv=None)</a></code></p>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]87<p class="firstline">Exports a read group set to a BAM file in Google Cloud Storage.</p>
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]88<p class="toc_element">
89 <code><a href="#get">get(readGroupSetId, x__xgafv=None)</a></code></p>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]90<p class="firstline">Gets a read group set by ID.</p>
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]91<p class="toc_element">
92 <code><a href="#import_">import_(body, x__xgafv=None)</a></code></p>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]93<p class="firstline">Creates read group sets by asynchronously importing the provided</p>
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]94<p class="toc_element">
Thomas Coffee2f245372017-03-27 10:39:26 -0700[diff] [blame]95 <code><a href="#patch">patch(readGroupSetId, body, updateMask=None, x__xgafv=None)</a></code></p>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]96<p class="firstline">Updates a read group set.</p>
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]97<p class="toc_element">
98 <code><a href="#search">search(body, x__xgafv=None)</a></code></p>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]99<p class="firstline">Searches for read group sets matching the criteria.</p>
100<p class="toc_element">
101 <code><a href="#search_next">search_next(previous_request, previous_response)</a></code></p>
102<p class="firstline">Retrieves the next page of results.</p>
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]103<h3>Method Details</h3>
104<div class="method">
Thomas Coffee2f245372017-03-27 10:39:26 -0700[diff] [blame]105 <code class="details" id="delete">delete(readGroupSetId, x__xgafv=None)</code>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]106 <pre>Deletes a read group set.
107
108For the definitions of read group sets and other genomics resources, see
109[Fundamentals of Google
110Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]111
112Args:
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]113 readGroupSetId: string, The ID of the read group set to be deleted. The caller must have WRITE
114permissions to the dataset associated with this read group set. (required)
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]115 x__xgafv: string, V1 error format.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]116 Allowed values
117 1 - v1 error format
118 2 - v2 error format
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]119
120Returns:
121 An object of the form:
122
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]123 { # A generic empty message that you can re-use to avoid defining duplicated
124 # empty messages in your APIs. A typical example is to use it as the request
125 # or the response type of an API method. For instance:
126 #
127 # service Foo {
128 # rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty);
129 # }
130 #
131 # The JSON representation for `Empty` is empty JSON object `{}`.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]132 }</pre>
133</div>
134
135<div class="method">
Thomas Coffee2f245372017-03-27 10:39:26 -0700[diff] [blame]136 <code class="details" id="export">export(readGroupSetId, body, x__xgafv=None)</code>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]137 <pre>Exports a read group set to a BAM file in Google Cloud Storage.
138
139For the definitions of read group sets and other genomics resources, see
140[Fundamentals of Google
141Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
142
143Note that currently there may be some differences between exported BAM
144files and the original BAM file at the time of import. See
145ImportReadGroupSets
146for caveats.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]147
148Args:
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]149 readGroupSetId: string, Required. The ID of the read group set to export. The caller must have
150READ access to this read group set. (required)
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]151 body: object, The request body. (required)
152 The object takes the form of:
153
154{ # The read group set export request.
Sai Cheemalapati4ba8c232017-06-06 18:46:08 -0400[diff] [blame^]155 "projectId": "A String", # Required. The Google Cloud project ID that owns this
156 # export. The caller must have WRITE access to this project.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]157 "referenceNames": [ # The reference names to export. If this is not specified, all reference
158 # sequences, including unmapped reads, are exported.
159 # Use `*` to export only unmapped reads.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]160 "A String",
161 ],
Sai Cheemalapati4ba8c232017-06-06 18:46:08 -0400[diff] [blame^]162 "exportUri": "A String", # Required. A Google Cloud Storage URI for the exported BAM file.
163 # The currently authenticated user must have write access to the new file.
164 # An error will be returned if the URI already contains data.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]165 }
166
167 x__xgafv: string, V1 error format.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]168 Allowed values
169 1 - v1 error format
170 2 - v2 error format
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]171
172Returns:
173 An object of the form:
174
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]175 { # This resource represents a long-running operation that is the result of a
176 # network API call.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]177 "metadata": { # An OperationMetadata object. This will always be returned with the Operation.
178 "a_key": "", # Properties of the object. Contains field @type with type URL.
179 },
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]180 "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.
181 # programming environments, including REST APIs and RPC APIs. It is used by
182 # [gRPC](https://github.com/grpc). The error model is designed to be:
183 #
184 # - Simple to use and understand for most users
185 # - Flexible enough to meet unexpected needs
186 #
187 # # Overview
188 #
189 # The `Status` message contains three pieces of data: error code, error message,
190 # and error details. The error code should be an enum value of
191 # google.rpc.Code, but it may accept additional error codes if needed. The
192 # error message should be a developer-facing English message that helps
193 # developers *understand* and *resolve* the error. If a localized user-facing
194 # error message is needed, put the localized message in the error details or
195 # localize it in the client. The optional error details may contain arbitrary
196 # information about the error. There is a predefined set of error detail types
Sai Cheemalapati4ba8c232017-06-06 18:46:08 -0400[diff] [blame^]197 # in the package `google.rpc` that can be used for common error conditions.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]198 #
199 # # Language mapping
200 #
201 # The `Status` message is the logical representation of the error model, but it
202 # is not necessarily the actual wire format. When the `Status` message is
203 # exposed in different client libraries and different wire protocols, it can be
204 # mapped differently. For example, it will likely be mapped to some exceptions
205 # in Java, but more likely mapped to some error codes in C.
206 #
207 # # Other uses
208 #
209 # The error model and the `Status` message can be used in a variety of
210 # environments, either with or without APIs, to provide a
211 # consistent developer experience across different environments.
212 #
213 # Example uses of this error model include:
214 #
215 # - Partial errors. If a service needs to return partial errors to the client,
216 # it may embed the `Status` in the normal response to indicate the partial
217 # errors.
218 #
219 # - Workflow errors. A typical workflow has multiple steps. Each step may
Sai Cheemalapati4ba8c232017-06-06 18:46:08 -0400[diff] [blame^]220 # have a `Status` message for error reporting.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]221 #
222 # - Batch operations. If a client uses batch request and batch response, the
223 # `Status` message should be used directly inside batch response, one for
224 # each error sub-response.
225 #
226 # - Asynchronous operations. If an API call embeds asynchronous operation
227 # results in its response, the status of those operations should be
228 # represented directly using the `Status` message.
229 #
230 # - Logging. If some API errors are stored in logs, the message `Status` could
231 # be used directly after any stripping needed for security/privacy reasons.
232 "message": "A String", # A developer-facing error message, which should be in English. Any
233 # user-facing error message should be localized and sent in the
234 # google.rpc.Status.details field, or localized by the client.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]235 "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]236 "details": [ # A list of messages that carry the error details. There will be a
237 # common set of message types for APIs to use.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]238 {
Jon Wayne Parrott7d5badb2016-08-16 12:44:29 -0700[diff] [blame]239 "a_key": "", # Properties of the object. Contains field @type with type URL.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]240 },
241 ],
242 },
Sai Cheemalapatie833b792017-03-24 15:06:46 -0700[diff] [blame]243 "done": True or False, # If the value is `false`, it means the operation is still in progress.
244 # If true, the operation is completed, and either `error` or `response` is
245 # available.
246 "response": { # If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If importing Variants, an ImportVariantsResponse is returned. For pipelines and exports, an empty response is returned.
247 "a_key": "", # Properties of the object. Contains field @type with type URL.
248 },
249 "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]250 }</pre>
251</div>
252
253<div class="method">
254 <code class="details" id="get">get(readGroupSetId, x__xgafv=None)</code>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]255 <pre>Gets a read group set by ID.
256
257For the definitions of read group sets and other genomics resources, see
258[Fundamentals of Google
259Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]260
261Args:
262 readGroupSetId: string, The ID of the read group set. (required)
263 x__xgafv: string, V1 error format.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]264 Allowed values
265 1 - v1 error format
266 2 - v2 error format
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]267
268Returns:
269 An object of the form:
270
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]271 { # A read group set is a logical collection of read groups, which are
272 # collections of reads produced by a sequencer. A read group set typically
273 # models reads corresponding to one sample, sequenced one way, and aligned one
274 # way.
275 #
276 # * A read group set belongs to one dataset.
277 # * A read group belongs to one read group set.
278 # * A read belongs to one read group.
279 #
280 # For more genomics resource definitions, see [Fundamentals of Google
281 # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]282 "info": { # A map of additional read group set information.
283 "a_key": [
284 "",
285 ],
286 },
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]287 "name": "A String", # The read group set name. By default this will be initialized to the sample
288 # name of the sequenced data contained in this set.
289 "readGroups": [ # The read groups in this set. There are typically 1-10 read groups in a read
290 # group set.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]291 { # A read group is all the data that's processed the same way by the sequencer.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]292 "info": { # A map of additional read group information. This must be of the form
293 # map<string, string[]> (string key mapping to a list of string values).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]294 "a_key": [
295 "",
296 ],
297 },
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]298 "predictedInsertSize": 42, # The predicted insert size of this read group. The insert size is the length
299 # the sequenced DNA fragment from end-to-end, not including the adapters.
300 "name": "A String", # The read group name. This corresponds to the @RG ID field in the SAM spec.
301 "programs": [ # The programs used to generate this read group. Programs are always
302 # identical for all read groups within a read group set. For this reason,
303 # only the first read group in a returned set will have this field
304 # populated.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]305 {
Sai Cheemalapati4ba8c232017-06-06 18:46:08 -0400[diff] [blame^]306 "prevProgramId": "A String", # The ID of the program run before this one.
Sai Cheemalapatie833b792017-03-24 15:06:46 -0700[diff] [blame]307 "commandLine": "A String", # The command line used to run this program.
308 "version": "A String", # The version of the program run.
Thomas Coffee2f245372017-03-27 10:39:26 -0700[diff] [blame]309 "id": "A String", # The user specified locally unique ID of the program. Used along with
310 # `prevProgramId` to define an ordering between programs.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]311 "name": "A String", # The display name of the program. This is typically the colloquial name of
312 # the tool used, for example 'bwa' or 'picard'.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]313 },
314 ],
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]315 "sampleId": "A String", # A client-supplied sample identifier for the reads in this read group.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]316 "experiment": { # The experiment used to generate this read group.
317 "sequencingCenter": "A String", # The sequencing center used as part of this experiment.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]318 "libraryId": "A String", # A client-supplied library identifier; a library is a collection of DNA
319 # fragments which have been prepared for sequencing from a sample. This
320 # field is important for quality control as error or bias can be introduced
321 # during sample preparation.
322 "instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to
323 # sequencing technology in the SAM spec.
324 "platformUnit": "A String", # The platform unit used as part of this experiment, for example
325 # flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
326 # @RG PU field in the SAM spec.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]327 },
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]328 "referenceSetId": "A String", # The reference set the reads in this read group are aligned to.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]329 "id": "A String", # The server-generated read group ID, unique for all read groups.
330 # Note: This is different than the @RG ID field in the SAM spec. For that
331 # value, see name.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]332 "datasetId": "A String", # The dataset to which this read group belongs.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]333 "description": "A String", # A free-form text description of this read group.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]334 },
335 ],
336 "filename": "A String", # The filename of the original source file for this read group set, if any.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]337 "referenceSetId": "A String", # The reference set to which the reads in this read group set are aligned.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]338 "id": "A String", # The server-generated read group set ID, unique for all read group sets.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]339 "datasetId": "A String", # The dataset to which this read group set belongs.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]340 }</pre>
341</div>
342
343<div class="method">
344 <code class="details" id="import_">import_(body, x__xgafv=None)</code>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]345 <pre>Creates read group sets by asynchronously importing the provided
346information.
347
348For the definitions of read group sets and other genomics resources, see
349[Fundamentals of Google
350Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
351
352The caller must have WRITE permissions to the dataset.
353
354## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import
355
356- Tags will be converted to strings - tag types are not preserved
357- Comments (`@CO`) in the input file header will not be preserved
358- Original header order of references (`@SQ`) will not be preserved
359- Any reverse stranded unmapped reads will be reverse complemented, and
360their qualities (also the "BQ" and "OQ" tags, if any) will be reversed
361- Unmapped reads will be stripped of positional information (reference name
362and position)
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]363
364Args:
365 body: object, The request body. (required)
366 The object takes the form of:
367
368{ # The read group set import request.
Sai Cheemalapati4ba8c232017-06-06 18:46:08 -0400[diff] [blame^]369 "partitionStrategy": "A String", # The partition strategy describes how read groups are partitioned into read
370 # group sets.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]371 "sourceUris": [ # A list of URIs pointing at [BAM
372 # files](https://samtools.github.io/hts-specs/SAMv1.pdf)
373 # in Google Cloud Storage.
374 # Those URIs can include wildcards (*), but do not add or remove
375 # matching files before import has completed.
376 #
377 # Note that Google Cloud Storage object listing is only eventually
378 # consistent: files added may be not be immediately visible to
379 # everyone. Thus, if using a wildcard it is preferable not to start
380 # the import immediately after the files are created.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]381 "A String",
382 ],
Sai Cheemalapati4ba8c232017-06-06 18:46:08 -0400[diff] [blame^]383 "referenceSetId": "A String", # The reference set to which the imported read group sets are aligned to, if
384 # any. The reference names of this reference set must be a superset of those
385 # found in the imported file headers. If no reference set id is provided, a
386 # best effort is made to associate with a matching reference set.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]387 "datasetId": "A String", # Required. The ID of the dataset these read group sets will belong to. The
388 # caller must have WRITE permissions to this dataset.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]389 }
390
391 x__xgafv: string, V1 error format.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]392 Allowed values
393 1 - v1 error format
394 2 - v2 error format
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]395
396Returns:
397 An object of the form:
398
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]399 { # This resource represents a long-running operation that is the result of a
400 # network API call.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]401 "metadata": { # An OperationMetadata object. This will always be returned with the Operation.
402 "a_key": "", # Properties of the object. Contains field @type with type URL.
403 },
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]404 "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.
405 # programming environments, including REST APIs and RPC APIs. It is used by
406 # [gRPC](https://github.com/grpc). The error model is designed to be:
407 #
408 # - Simple to use and understand for most users
409 # - Flexible enough to meet unexpected needs
410 #
411 # # Overview
412 #
413 # The `Status` message contains three pieces of data: error code, error message,
414 # and error details. The error code should be an enum value of
415 # google.rpc.Code, but it may accept additional error codes if needed. The
416 # error message should be a developer-facing English message that helps
417 # developers *understand* and *resolve* the error. If a localized user-facing
418 # error message is needed, put the localized message in the error details or
419 # localize it in the client. The optional error details may contain arbitrary
420 # information about the error. There is a predefined set of error detail types
Sai Cheemalapati4ba8c232017-06-06 18:46:08 -0400[diff] [blame^]421 # in the package `google.rpc` that can be used for common error conditions.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]422 #
423 # # Language mapping
424 #
425 # The `Status` message is the logical representation of the error model, but it
426 # is not necessarily the actual wire format. When the `Status` message is
427 # exposed in different client libraries and different wire protocols, it can be
428 # mapped differently. For example, it will likely be mapped to some exceptions
429 # in Java, but more likely mapped to some error codes in C.
430 #
431 # # Other uses
432 #
433 # The error model and the `Status` message can be used in a variety of
434 # environments, either with or without APIs, to provide a
435 # consistent developer experience across different environments.
436 #
437 # Example uses of this error model include:
438 #
439 # - Partial errors. If a service needs to return partial errors to the client,
440 # it may embed the `Status` in the normal response to indicate the partial
441 # errors.
442 #
443 # - Workflow errors. A typical workflow has multiple steps. Each step may
Sai Cheemalapati4ba8c232017-06-06 18:46:08 -0400[diff] [blame^]444 # have a `Status` message for error reporting.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]445 #
446 # - Batch operations. If a client uses batch request and batch response, the
447 # `Status` message should be used directly inside batch response, one for
448 # each error sub-response.
449 #
450 # - Asynchronous operations. If an API call embeds asynchronous operation
451 # results in its response, the status of those operations should be
452 # represented directly using the `Status` message.
453 #
454 # - Logging. If some API errors are stored in logs, the message `Status` could
455 # be used directly after any stripping needed for security/privacy reasons.
456 "message": "A String", # A developer-facing error message, which should be in English. Any
457 # user-facing error message should be localized and sent in the
458 # google.rpc.Status.details field, or localized by the client.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]459 "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]460 "details": [ # A list of messages that carry the error details. There will be a
461 # common set of message types for APIs to use.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]462 {
Jon Wayne Parrott7d5badb2016-08-16 12:44:29 -0700[diff] [blame]463 "a_key": "", # Properties of the object. Contains field @type with type URL.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]464 },
465 ],
466 },
Sai Cheemalapatie833b792017-03-24 15:06:46 -0700[diff] [blame]467 "done": True or False, # If the value is `false`, it means the operation is still in progress.
468 # If true, the operation is completed, and either `error` or `response` is
469 # available.
470 "response": { # If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If importing Variants, an ImportVariantsResponse is returned. For pipelines and exports, an empty response is returned.
471 "a_key": "", # Properties of the object. Contains field @type with type URL.
472 },
473 "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]474 }</pre>
475</div>
476
477<div class="method">
Thomas Coffee2f245372017-03-27 10:39:26 -0700[diff] [blame]478 <code class="details" id="patch">patch(readGroupSetId, body, updateMask=None, x__xgafv=None)</code>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]479 <pre>Updates a read group set.
480
481For the definitions of read group sets and other genomics resources, see
482[Fundamentals of Google
483Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
484
485This method supports patch semantics.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]486
487Args:
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]488 readGroupSetId: string, The ID of the read group set to be updated. The caller must have WRITE
489permissions to the dataset associated with this read group set. (required)
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]490 body: object, The request body. (required)
491 The object takes the form of:
492
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]493{ # A read group set is a logical collection of read groups, which are
494 # collections of reads produced by a sequencer. A read group set typically
495 # models reads corresponding to one sample, sequenced one way, and aligned one
496 # way.
497 #
498 # * A read group set belongs to one dataset.
499 # * A read group belongs to one read group set.
500 # * A read belongs to one read group.
501 #
502 # For more genomics resource definitions, see [Fundamentals of Google
503 # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]504 "info": { # A map of additional read group set information.
505 "a_key": [
506 "",
507 ],
508 },
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]509 "name": "A String", # The read group set name. By default this will be initialized to the sample
510 # name of the sequenced data contained in this set.
511 "readGroups": [ # The read groups in this set. There are typically 1-10 read groups in a read
512 # group set.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]513 { # A read group is all the data that's processed the same way by the sequencer.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]514 "info": { # A map of additional read group information. This must be of the form
515 # map<string, string[]> (string key mapping to a list of string values).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]516 "a_key": [
517 "",
518 ],
519 },
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]520 "predictedInsertSize": 42, # The predicted insert size of this read group. The insert size is the length
521 # the sequenced DNA fragment from end-to-end, not including the adapters.
522 "name": "A String", # The read group name. This corresponds to the @RG ID field in the SAM spec.
523 "programs": [ # The programs used to generate this read group. Programs are always
524 # identical for all read groups within a read group set. For this reason,
525 # only the first read group in a returned set will have this field
526 # populated.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]527 {
Sai Cheemalapati4ba8c232017-06-06 18:46:08 -0400[diff] [blame^]528 "prevProgramId": "A String", # The ID of the program run before this one.
Sai Cheemalapatie833b792017-03-24 15:06:46 -0700[diff] [blame]529 "commandLine": "A String", # The command line used to run this program.
530 "version": "A String", # The version of the program run.
Thomas Coffee2f245372017-03-27 10:39:26 -0700[diff] [blame]531 "id": "A String", # The user specified locally unique ID of the program. Used along with
532 # `prevProgramId` to define an ordering between programs.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]533 "name": "A String", # The display name of the program. This is typically the colloquial name of
534 # the tool used, for example 'bwa' or 'picard'.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]535 },
536 ],
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]537 "sampleId": "A String", # A client-supplied sample identifier for the reads in this read group.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]538 "experiment": { # The experiment used to generate this read group.
539 "sequencingCenter": "A String", # The sequencing center used as part of this experiment.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]540 "libraryId": "A String", # A client-supplied library identifier; a library is a collection of DNA
541 # fragments which have been prepared for sequencing from a sample. This
542 # field is important for quality control as error or bias can be introduced
543 # during sample preparation.
544 "instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to
545 # sequencing technology in the SAM spec.
546 "platformUnit": "A String", # The platform unit used as part of this experiment, for example
547 # flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
548 # @RG PU field in the SAM spec.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]549 },
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]550 "referenceSetId": "A String", # The reference set the reads in this read group are aligned to.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]551 "id": "A String", # The server-generated read group ID, unique for all read groups.
552 # Note: This is different than the @RG ID field in the SAM spec. For that
553 # value, see name.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]554 "datasetId": "A String", # The dataset to which this read group belongs.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]555 "description": "A String", # A free-form text description of this read group.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]556 },
557 ],
558 "filename": "A String", # The filename of the original source file for this read group set, if any.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]559 "referenceSetId": "A String", # The reference set to which the reads in this read group set are aligned.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]560 "id": "A String", # The server-generated read group set ID, unique for all read group sets.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]561 "datasetId": "A String", # The dataset to which this read group set belongs.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]562}
563
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]564 updateMask: string, An optional mask specifying which fields to update. Supported fields:
565
566* name.
567* referenceSetId.
568
569Leaving `updateMask` unset is equivalent to specifying all mutable
570fields.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]571 x__xgafv: string, V1 error format.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]572 Allowed values
573 1 - v1 error format
574 2 - v2 error format
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]575
576Returns:
577 An object of the form:
578
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]579 { # A read group set is a logical collection of read groups, which are
580 # collections of reads produced by a sequencer. A read group set typically
581 # models reads corresponding to one sample, sequenced one way, and aligned one
582 # way.
583 #
584 # * A read group set belongs to one dataset.
585 # * A read group belongs to one read group set.
586 # * A read belongs to one read group.
587 #
588 # For more genomics resource definitions, see [Fundamentals of Google
589 # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]590 "info": { # A map of additional read group set information.
591 "a_key": [
592 "",
593 ],
594 },
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]595 "name": "A String", # The read group set name. By default this will be initialized to the sample
596 # name of the sequenced data contained in this set.
597 "readGroups": [ # The read groups in this set. There are typically 1-10 read groups in a read
598 # group set.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]599 { # A read group is all the data that's processed the same way by the sequencer.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]600 "info": { # A map of additional read group information. This must be of the form
601 # map<string, string[]> (string key mapping to a list of string values).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]602 "a_key": [
603 "",
604 ],
605 },
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]606 "predictedInsertSize": 42, # The predicted insert size of this read group. The insert size is the length
607 # the sequenced DNA fragment from end-to-end, not including the adapters.
608 "name": "A String", # The read group name. This corresponds to the @RG ID field in the SAM spec.
609 "programs": [ # The programs used to generate this read group. Programs are always
610 # identical for all read groups within a read group set. For this reason,
611 # only the first read group in a returned set will have this field
612 # populated.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]613 {
Sai Cheemalapati4ba8c232017-06-06 18:46:08 -0400[diff] [blame^]614 "prevProgramId": "A String", # The ID of the program run before this one.
Sai Cheemalapatie833b792017-03-24 15:06:46 -0700[diff] [blame]615 "commandLine": "A String", # The command line used to run this program.
616 "version": "A String", # The version of the program run.
Thomas Coffee2f245372017-03-27 10:39:26 -0700[diff] [blame]617 "id": "A String", # The user specified locally unique ID of the program. Used along with
618 # `prevProgramId` to define an ordering between programs.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]619 "name": "A String", # The display name of the program. This is typically the colloquial name of
620 # the tool used, for example 'bwa' or 'picard'.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]621 },
622 ],
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]623 "sampleId": "A String", # A client-supplied sample identifier for the reads in this read group.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]624 "experiment": { # The experiment used to generate this read group.
625 "sequencingCenter": "A String", # The sequencing center used as part of this experiment.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]626 "libraryId": "A String", # A client-supplied library identifier; a library is a collection of DNA
627 # fragments which have been prepared for sequencing from a sample. This
628 # field is important for quality control as error or bias can be introduced
629 # during sample preparation.
630 "instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to
631 # sequencing technology in the SAM spec.
632 "platformUnit": "A String", # The platform unit used as part of this experiment, for example
633 # flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
634 # @RG PU field in the SAM spec.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]635 },
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]636 "referenceSetId": "A String", # The reference set the reads in this read group are aligned to.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]637 "id": "A String", # The server-generated read group ID, unique for all read groups.
638 # Note: This is different than the @RG ID field in the SAM spec. For that
639 # value, see name.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]640 "datasetId": "A String", # The dataset to which this read group belongs.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]641 "description": "A String", # A free-form text description of this read group.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]642 },
643 ],
644 "filename": "A String", # The filename of the original source file for this read group set, if any.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]645 "referenceSetId": "A String", # The reference set to which the reads in this read group set are aligned.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]646 "id": "A String", # The server-generated read group set ID, unique for all read group sets.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]647 "datasetId": "A String", # The dataset to which this read group set belongs.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]648 }</pre>
649</div>
650
651<div class="method">
652 <code class="details" id="search">search(body, x__xgafv=None)</code>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]653 <pre>Searches for read group sets matching the criteria.
654
655For the definitions of read group sets and other genomics resources, see
656[Fundamentals of Google
657Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
658
659Implements
660[GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]661
662Args:
663 body: object, The request body. (required)
664 The object takes the form of:
665
666{ # The read group set search request.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]667 "pageToken": "A String", # The continuation token, which is used to page through large result sets.
668 # To get the next page of results, set this parameter to the value of
669 # `nextPageToken` from the previous response.
670 "datasetIds": [ # Restricts this query to read group sets within the given datasets. At least
671 # one ID must be provided.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]672 "A String",
673 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]674 "name": "A String", # Only return read group sets for which a substring of the name matches this
675 # string.
676 "pageSize": 42, # The maximum number of results to return in a single page. If unspecified,
677 # defaults to 256. The maximum value is 1024.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]678 }
679
680 x__xgafv: string, V1 error format.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]681 Allowed values
682 1 - v1 error format
683 2 - v2 error format
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]684
685Returns:
686 An object of the form:
687
688 { # The read group set search response.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]689 "nextPageToken": "A String", # The continuation token, which is used to page through large result sets.
690 # Provide this value in a subsequent request to return the next page of
691 # results. This field will be empty if there aren't any additional results.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]692 "readGroupSets": [ # The list of matching read group sets.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]693 { # A read group set is a logical collection of read groups, which are
694 # collections of reads produced by a sequencer. A read group set typically
695 # models reads corresponding to one sample, sequenced one way, and aligned one
696 # way.
697 #
698 # * A read group set belongs to one dataset.
699 # * A read group belongs to one read group set.
700 # * A read belongs to one read group.
701 #
702 # For more genomics resource definitions, see [Fundamentals of Google
703 # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]704 "info": { # A map of additional read group set information.
705 "a_key": [
706 "",
707 ],
708 },
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]709 "name": "A String", # The read group set name. By default this will be initialized to the sample
710 # name of the sequenced data contained in this set.
711 "readGroups": [ # The read groups in this set. There are typically 1-10 read groups in a read
712 # group set.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]713 { # A read group is all the data that's processed the same way by the sequencer.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]714 "info": { # A map of additional read group information. This must be of the form
715 # map<string, string[]> (string key mapping to a list of string values).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]716 "a_key": [
717 "",
718 ],
719 },
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]720 "predictedInsertSize": 42, # The predicted insert size of this read group. The insert size is the length
721 # the sequenced DNA fragment from end-to-end, not including the adapters.
722 "name": "A String", # The read group name. This corresponds to the @RG ID field in the SAM spec.
723 "programs": [ # The programs used to generate this read group. Programs are always
724 # identical for all read groups within a read group set. For this reason,
725 # only the first read group in a returned set will have this field
726 # populated.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]727 {
Sai Cheemalapati4ba8c232017-06-06 18:46:08 -0400[diff] [blame^]728 "prevProgramId": "A String", # The ID of the program run before this one.
Sai Cheemalapatie833b792017-03-24 15:06:46 -0700[diff] [blame]729 "commandLine": "A String", # The command line used to run this program.
730 "version": "A String", # The version of the program run.
Thomas Coffee2f245372017-03-27 10:39:26 -0700[diff] [blame]731 "id": "A String", # The user specified locally unique ID of the program. Used along with
732 # `prevProgramId` to define an ordering between programs.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]733 "name": "A String", # The display name of the program. This is typically the colloquial name of
734 # the tool used, for example 'bwa' or 'picard'.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]735 },
736 ],
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]737 "sampleId": "A String", # A client-supplied sample identifier for the reads in this read group.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]738 "experiment": { # The experiment used to generate this read group.
739 "sequencingCenter": "A String", # The sequencing center used as part of this experiment.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]740 "libraryId": "A String", # A client-supplied library identifier; a library is a collection of DNA
741 # fragments which have been prepared for sequencing from a sample. This
742 # field is important for quality control as error or bias can be introduced
743 # during sample preparation.
744 "instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to
745 # sequencing technology in the SAM spec.
746 "platformUnit": "A String", # The platform unit used as part of this experiment, for example
747 # flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
748 # @RG PU field in the SAM spec.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]749 },
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]750 "referenceSetId": "A String", # The reference set the reads in this read group are aligned to.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]751 "id": "A String", # The server-generated read group ID, unique for all read groups.
752 # Note: This is different than the @RG ID field in the SAM spec. For that
753 # value, see name.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]754 "datasetId": "A String", # The dataset to which this read group belongs.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]755 "description": "A String", # A free-form text description of this read group.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]756 },
757 ],
758 "filename": "A String", # The filename of the original source file for this read group set, if any.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]759 "referenceSetId": "A String", # The reference set to which the reads in this read group set are aligned.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]760 "id": "A String", # The server-generated read group set ID, unique for all read group sets.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]761 "datasetId": "A String", # The dataset to which this read group set belongs.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]762 },
763 ],
764 }</pre>
765</div>
766
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]767<div class="method">
768 <code class="details" id="search_next">search_next(previous_request, previous_response)</code>
769 <pre>Retrieves the next page of results.
770
771Args:
772 previous_request: The request for the previous page. (required)
773 previous_response: The response from the request for the previous page. (required)
774
775Returns:
776 A request object that you can call 'execute()' on to request the next
777 page. Returns None if there are no more items in the collection.
778 </pre>
779</div>
780
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]781</body></html>