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75<h1><a href="genomics_v1beta2.html">Genomics API</a> . <a href="genomics_v1beta2.readgroupsets.html">readgroupsets</a></h1>
76<h2>Instance Methods</h2>
77<p class="toc_element">
78 <code><a href="genomics_v1beta2.readgroupsets.coveragebuckets.html">coveragebuckets()</a></code>
79</p>
80<p class="firstline">Returns the coveragebuckets Resource.</p>
81
82<p class="toc_element">
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]83 <code><a href="#delete">delete(readGroupSetId)</a></code></p>
84<p class="firstline">Deletes a read group set.</p>
85<p class="toc_element">
86 <code><a href="#export">export(body)</a></code></p>
87<p class="firstline">Exports read group sets to a BAM file in Google Cloud Storage.</p>
88<p class="toc_element">
89 <code><a href="#get">get(readGroupSetId)</a></code></p>
90<p class="firstline">Gets a read group set by ID.</p>
91<p class="toc_element">
92 <code><a href="#import_">import_(body)</a></code></p>
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]93<p class="firstline">Creates read group sets by asynchronously importing the provided information. The caller must have WRITE permissions to the dataset.</p>
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]94<p class="toc_element">
95 <code><a href="#patch">patch(readGroupSetId, body)</a></code></p>
96<p class="firstline">Updates a read group set. This method supports patch semantics.</p>
97<p class="toc_element">
98 <code><a href="#search">search(body)</a></code></p>
99<p class="firstline">Searches for read group sets matching the criteria.</p>
100<p class="toc_element">
101 <code><a href="#update">update(readGroupSetId, body)</a></code></p>
102<p class="firstline">Updates a read group set.</p>
103<h3>Method Details</h3>
104<div class="method">
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]105 <code class="details" id="delete">delete(readGroupSetId)</code>
106 <pre>Deletes a read group set.
107
108Args:
109 readGroupSetId: string, The ID of the read group set to be deleted. The caller must have WRITE permissions to the dataset associated with this read group set. (required)
110</pre>
111</div>
112
113<div class="method">
114 <code class="details" id="export">export(body)</code>
115 <pre>Exports read group sets to a BAM file in Google Cloud Storage.
116
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]117Note that currently there may be some differences between exported BAM files and the original BAM file at the time of import. See ImportReadGroupSets for details.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]118
119Args:
120 body: object, The request body. (required)
121 The object takes the form of:
122
123{ # The read group set export request.
Nathaniel Manista4f877e52015-06-15 16:44:50 +0000[diff] [blame]124 "exportUri": "A String", # Required. A Google Cloud Storage URI for the exported BAM file. The currently authenticated user must have write access to the new file. An error will be returned if the URI already contains data.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]125 "referenceNames": [ # The reference names to export. If this is not specified, all reference sequences, including unmapped reads, are exported. Use * to export only unmapped reads.
126 "A String",
127 ],
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]128 "readGroupSetIds": [ # Required. The IDs of the read group sets to export. The caller must have READ access to these read group sets.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]129 "A String",
130 ],
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]131 "projectNumber": "A String", # Required. The Google Developers Console project number that owns this export. The caller must have WRITE access to this project.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]132 }
133
134
135Returns:
136 An object of the form:
137
138 { # The read group set export response.
139 "jobId": "A String", # A job ID that can be used to get status information.
140 }</pre>
141</div>
142
143<div class="method">
144 <code class="details" id="get">get(readGroupSetId)</code>
145 <pre>Gets a read group set by ID.
146
147Args:
148 readGroupSetId: string, The ID of the read group set. (required)
149
150Returns:
151 An object of the form:
152
153 { # A read group set is a logical collection of read groups, which are collections of reads produced by a sequencer. A read group set typically models reads corresponding to one sample, sequenced one way, and aligned one way.
154 # - A read group set belongs to one dataset.
155 # - A read group belongs to one read group set.
156 # - A read belongs to one read group.
Nathaniel Manista4f877e52015-06-15 16:44:50 +0000[diff] [blame]157 "info": { # A string which maps to an array of values.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]158 "a_key": [ # A string which maps to an array of values.
159 "A String",
160 ],
161 },
162 "name": "A String", # The read group set name. By default this will be initialized to the sample name of the sequenced data contained in this set.
163 "readGroups": [ # The read groups in this set. There are typically 1-10 read groups in a read group set.
164 { # A read group is all the data that's processed the same way by the sequencer.
Nathaniel Manista4f877e52015-06-15 16:44:50 +0000[diff] [blame]165 "info": { # A string which maps to an array of values.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]166 "a_key": [ # A string which maps to an array of values.
167 "A String",
168 ],
169 },
170 "predictedInsertSize": 42, # The predicted insert size of this read group. The insert size is the length the sequenced DNA fragment from end-to-end, not including the adapters.
171 "name": "A String", # The read group name. This corresponds to the @RG ID field in the SAM spec.
172 "programs": [ # The programs used to generate this read group. Programs are always identical for all read groups within a read group set. For this reason, only the first read group in a returned set will have this field populated.
173 {
174 "commandLine": "A String", # The command line used to run this program.
175 "prevProgramId": "A String", # The ID of the program run before this one.
176 "id": "A String", # The user specified locally unique ID of the program. Used along with prevProgramId to define an ordering between programs.
177 "version": "A String", # The version of the program run.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]178 "name": "A String", # The display name of the program. This is typically the colloquial name of the tool used, for example 'bwa' or 'picard'.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]179 },
180 ],
181 "sampleId": "A String", # The sample this read group's data was generated from. Note: This is not an actual ID within this repository, but rather an identifier for a sample which may be meaningful to some external system.
182 "experiment": { # The experiment used to generate this read group.
183 "sequencingCenter": "A String", # The sequencing center used as part of this experiment.
184 "libraryId": "A String", # The library used as part of this experiment. Note: This is not an actual ID within this repository, but rather an identifier for a library which may be meaningful to some external system.
185 "instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to sequencing technology in BAM.
186 "platformUnit": "A String", # The platform unit used as part of this experiment e.g. flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
187 },
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]188 "referenceSetId": "A String", # The reference set to which the reads in this read group are aligned.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]189 "id": "A String", # The generated unique read group ID. Note: This is different than the @RG ID field in the SAM spec. For that value, see the name field.
190 "datasetId": "A String", # The ID of the dataset this read group belongs to.
191 "description": "A String", # A free-form text description of this read group.
192 },
193 ],
194 "filename": "A String", # The filename of the original source file for this read group set, if any.
195 "referenceSetId": "A String", # The reference set the reads in this read group set are aligned to.
196 "id": "A String", # The read group set ID.
197 "datasetId": "A String", # The dataset ID.
198 }</pre>
199</div>
200
201<div class="method">
202 <code class="details" id="import_">import_(body)</code>
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]203 <pre>Creates read group sets by asynchronously importing the provided information. The caller must have WRITE permissions to the dataset.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]204
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]205Notes on BAM import:
206- Tags will be converted to strings - tag types are not preserved
207- Comments (@CO) in the input file header are not imported
208- Original order of reference headers is not preserved
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]209- Any reverse stranded unmapped reads will be reverse complemented, and their qualities (also the "BQ" and "OQ" tags, if any) will be reversed
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]210- Unmapped reads will be stripped of positional information (referenceName and position)
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]211
212Args:
213 body: object, The request body. (required)
214 The object takes the form of:
215
216{ # The read group set import request.
217 "referenceSetId": "A String", # The reference set to which the imported read group sets are aligned to, if any. The reference names of this reference set must be a superset of those found in the imported file headers. If no reference set id is provided, a best effort is made to associate with a matching reference set.
218 "sourceUris": [ # A list of URIs pointing at BAM files in Google Cloud Storage.
219 "A String",
220 ],
221 "partitionStrategy": "A String", # The partition strategy describes how read groups are partitioned into read group sets.
222 "datasetId": "A String", # Required. The ID of the dataset these read group sets will belong to. The caller must have WRITE permissions to this dataset.
223 }
224
225
226Returns:
227 An object of the form:
228
229 { # The read group set import response.
230 "jobId": "A String", # A job ID that can be used to get status information.
231 }</pre>
232</div>
233
234<div class="method">
235 <code class="details" id="patch">patch(readGroupSetId, body)</code>
236 <pre>Updates a read group set. This method supports patch semantics.
237
238Args:
239 readGroupSetId: string, The ID of the read group set to be updated. The caller must have WRITE permissions to the dataset associated with this read group set. (required)
240 body: object, The request body. (required)
241 The object takes the form of:
242
243{ # A read group set is a logical collection of read groups, which are collections of reads produced by a sequencer. A read group set typically models reads corresponding to one sample, sequenced one way, and aligned one way.
244 # - A read group set belongs to one dataset.
245 # - A read group belongs to one read group set.
246 # - A read belongs to one read group.
Nathaniel Manista4f877e52015-06-15 16:44:50 +0000[diff] [blame]247 "info": { # A string which maps to an array of values.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]248 "a_key": [ # A string which maps to an array of values.
249 "A String",
250 ],
251 },
252 "name": "A String", # The read group set name. By default this will be initialized to the sample name of the sequenced data contained in this set.
253 "readGroups": [ # The read groups in this set. There are typically 1-10 read groups in a read group set.
254 { # A read group is all the data that's processed the same way by the sequencer.
Nathaniel Manista4f877e52015-06-15 16:44:50 +0000[diff] [blame]255 "info": { # A string which maps to an array of values.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]256 "a_key": [ # A string which maps to an array of values.
257 "A String",
258 ],
259 },
260 "predictedInsertSize": 42, # The predicted insert size of this read group. The insert size is the length the sequenced DNA fragment from end-to-end, not including the adapters.
261 "name": "A String", # The read group name. This corresponds to the @RG ID field in the SAM spec.
262 "programs": [ # The programs used to generate this read group. Programs are always identical for all read groups within a read group set. For this reason, only the first read group in a returned set will have this field populated.
263 {
264 "commandLine": "A String", # The command line used to run this program.
265 "prevProgramId": "A String", # The ID of the program run before this one.
266 "id": "A String", # The user specified locally unique ID of the program. Used along with prevProgramId to define an ordering between programs.
267 "version": "A String", # The version of the program run.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]268 "name": "A String", # The display name of the program. This is typically the colloquial name of the tool used, for example 'bwa' or 'picard'.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]269 },
270 ],
271 "sampleId": "A String", # The sample this read group's data was generated from. Note: This is not an actual ID within this repository, but rather an identifier for a sample which may be meaningful to some external system.
272 "experiment": { # The experiment used to generate this read group.
273 "sequencingCenter": "A String", # The sequencing center used as part of this experiment.
274 "libraryId": "A String", # The library used as part of this experiment. Note: This is not an actual ID within this repository, but rather an identifier for a library which may be meaningful to some external system.
275 "instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to sequencing technology in BAM.
276 "platformUnit": "A String", # The platform unit used as part of this experiment e.g. flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
277 },
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]278 "referenceSetId": "A String", # The reference set to which the reads in this read group are aligned.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]279 "id": "A String", # The generated unique read group ID. Note: This is different than the @RG ID field in the SAM spec. For that value, see the name field.
280 "datasetId": "A String", # The ID of the dataset this read group belongs to.
281 "description": "A String", # A free-form text description of this read group.
282 },
283 ],
284 "filename": "A String", # The filename of the original source file for this read group set, if any.
285 "referenceSetId": "A String", # The reference set the reads in this read group set are aligned to.
286 "id": "A String", # The read group set ID.
287 "datasetId": "A String", # The dataset ID.
288}
289
290
291Returns:
292 An object of the form:
293
294 { # A read group set is a logical collection of read groups, which are collections of reads produced by a sequencer. A read group set typically models reads corresponding to one sample, sequenced one way, and aligned one way.
295 # - A read group set belongs to one dataset.
296 # - A read group belongs to one read group set.
297 # - A read belongs to one read group.
Nathaniel Manista4f877e52015-06-15 16:44:50 +0000[diff] [blame]298 "info": { # A string which maps to an array of values.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]299 "a_key": [ # A string which maps to an array of values.
300 "A String",
301 ],
302 },
303 "name": "A String", # The read group set name. By default this will be initialized to the sample name of the sequenced data contained in this set.
304 "readGroups": [ # The read groups in this set. There are typically 1-10 read groups in a read group set.
305 { # A read group is all the data that's processed the same way by the sequencer.
Nathaniel Manista4f877e52015-06-15 16:44:50 +0000[diff] [blame]306 "info": { # A string which maps to an array of values.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]307 "a_key": [ # A string which maps to an array of values.
308 "A String",
309 ],
310 },
311 "predictedInsertSize": 42, # The predicted insert size of this read group. The insert size is the length the sequenced DNA fragment from end-to-end, not including the adapters.
312 "name": "A String", # The read group name. This corresponds to the @RG ID field in the SAM spec.
313 "programs": [ # The programs used to generate this read group. Programs are always identical for all read groups within a read group set. For this reason, only the first read group in a returned set will have this field populated.
314 {
315 "commandLine": "A String", # The command line used to run this program.
316 "prevProgramId": "A String", # The ID of the program run before this one.
317 "id": "A String", # The user specified locally unique ID of the program. Used along with prevProgramId to define an ordering between programs.
318 "version": "A String", # The version of the program run.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]319 "name": "A String", # The display name of the program. This is typically the colloquial name of the tool used, for example 'bwa' or 'picard'.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]320 },
321 ],
322 "sampleId": "A String", # The sample this read group's data was generated from. Note: This is not an actual ID within this repository, but rather an identifier for a sample which may be meaningful to some external system.
323 "experiment": { # The experiment used to generate this read group.
324 "sequencingCenter": "A String", # The sequencing center used as part of this experiment.
325 "libraryId": "A String", # The library used as part of this experiment. Note: This is not an actual ID within this repository, but rather an identifier for a library which may be meaningful to some external system.
326 "instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to sequencing technology in BAM.
327 "platformUnit": "A String", # The platform unit used as part of this experiment e.g. flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
328 },
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]329 "referenceSetId": "A String", # The reference set to which the reads in this read group are aligned.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]330 "id": "A String", # The generated unique read group ID. Note: This is different than the @RG ID field in the SAM spec. For that value, see the name field.
331 "datasetId": "A String", # The ID of the dataset this read group belongs to.
332 "description": "A String", # A free-form text description of this read group.
333 },
334 ],
335 "filename": "A String", # The filename of the original source file for this read group set, if any.
336 "referenceSetId": "A String", # The reference set the reads in this read group set are aligned to.
337 "id": "A String", # The read group set ID.
338 "datasetId": "A String", # The dataset ID.
339 }</pre>
340</div>
341
342<div class="method">
343 <code class="details" id="search">search(body)</code>
344 <pre>Searches for read group sets matching the criteria.
345
346Implements GlobalAllianceApi.searchReadGroupSets.
347
348Args:
349 body: object, The request body. (required)
350 The object takes the form of:
351
352{ # The read group set search request.
353 "pageToken": "A String", # The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of nextPageToken from the previous response.
354 "datasetIds": [ # Restricts this query to read group sets within the given datasets. At least one ID must be provided.
355 "A String",
356 ],
357 "name": "A String", # Only return read group sets for which a substring of the name matches this string.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]358 "pageSize": 42, # The maximum number of results to return in a single page. If unspecified, defaults to 256. The maximum value is 1024.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]359 }
360
361
362Returns:
363 An object of the form:
364
365 { # The read group set search response.
366 "nextPageToken": "A String", # The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there aren't any additional results.
367 "readGroupSets": [ # The list of matching read group sets.
368 { # A read group set is a logical collection of read groups, which are collections of reads produced by a sequencer. A read group set typically models reads corresponding to one sample, sequenced one way, and aligned one way.
369 # - A read group set belongs to one dataset.
370 # - A read group belongs to one read group set.
371 # - A read belongs to one read group.
Nathaniel Manista4f877e52015-06-15 16:44:50 +0000[diff] [blame]372 "info": { # A string which maps to an array of values.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]373 "a_key": [ # A string which maps to an array of values.
374 "A String",
375 ],
376 },
377 "name": "A String", # The read group set name. By default this will be initialized to the sample name of the sequenced data contained in this set.
378 "readGroups": [ # The read groups in this set. There are typically 1-10 read groups in a read group set.
379 { # A read group is all the data that's processed the same way by the sequencer.
Nathaniel Manista4f877e52015-06-15 16:44:50 +0000[diff] [blame]380 "info": { # A string which maps to an array of values.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]381 "a_key": [ # A string which maps to an array of values.
382 "A String",
383 ],
384 },
385 "predictedInsertSize": 42, # The predicted insert size of this read group. The insert size is the length the sequenced DNA fragment from end-to-end, not including the adapters.
386 "name": "A String", # The read group name. This corresponds to the @RG ID field in the SAM spec.
387 "programs": [ # The programs used to generate this read group. Programs are always identical for all read groups within a read group set. For this reason, only the first read group in a returned set will have this field populated.
388 {
389 "commandLine": "A String", # The command line used to run this program.
390 "prevProgramId": "A String", # The ID of the program run before this one.
391 "id": "A String", # The user specified locally unique ID of the program. Used along with prevProgramId to define an ordering between programs.
392 "version": "A String", # The version of the program run.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]393 "name": "A String", # The display name of the program. This is typically the colloquial name of the tool used, for example 'bwa' or 'picard'.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]394 },
395 ],
396 "sampleId": "A String", # The sample this read group's data was generated from. Note: This is not an actual ID within this repository, but rather an identifier for a sample which may be meaningful to some external system.
397 "experiment": { # The experiment used to generate this read group.
398 "sequencingCenter": "A String", # The sequencing center used as part of this experiment.
399 "libraryId": "A String", # The library used as part of this experiment. Note: This is not an actual ID within this repository, but rather an identifier for a library which may be meaningful to some external system.
400 "instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to sequencing technology in BAM.
401 "platformUnit": "A String", # The platform unit used as part of this experiment e.g. flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
402 },
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]403 "referenceSetId": "A String", # The reference set to which the reads in this read group are aligned.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]404 "id": "A String", # The generated unique read group ID. Note: This is different than the @RG ID field in the SAM spec. For that value, see the name field.
405 "datasetId": "A String", # The ID of the dataset this read group belongs to.
406 "description": "A String", # A free-form text description of this read group.
407 },
408 ],
409 "filename": "A String", # The filename of the original source file for this read group set, if any.
410 "referenceSetId": "A String", # The reference set the reads in this read group set are aligned to.
411 "id": "A String", # The read group set ID.
412 "datasetId": "A String", # The dataset ID.
413 },
414 ],
415 }</pre>
416</div>
417
418<div class="method">
419 <code class="details" id="update">update(readGroupSetId, body)</code>
420 <pre>Updates a read group set.
421
422Args:
423 readGroupSetId: string, The ID of the read group set to be updated. The caller must have WRITE permissions to the dataset associated with this read group set. (required)
424 body: object, The request body. (required)
425 The object takes the form of:
426
427{ # A read group set is a logical collection of read groups, which are collections of reads produced by a sequencer. A read group set typically models reads corresponding to one sample, sequenced one way, and aligned one way.
428 # - A read group set belongs to one dataset.
429 # - A read group belongs to one read group set.
430 # - A read belongs to one read group.
Nathaniel Manista4f877e52015-06-15 16:44:50 +0000[diff] [blame]431 "info": { # A string which maps to an array of values.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]432 "a_key": [ # A string which maps to an array of values.
433 "A String",
434 ],
435 },
436 "name": "A String", # The read group set name. By default this will be initialized to the sample name of the sequenced data contained in this set.
437 "readGroups": [ # The read groups in this set. There are typically 1-10 read groups in a read group set.
438 { # A read group is all the data that's processed the same way by the sequencer.
Nathaniel Manista4f877e52015-06-15 16:44:50 +0000[diff] [blame]439 "info": { # A string which maps to an array of values.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]440 "a_key": [ # A string which maps to an array of values.
441 "A String",
442 ],
443 },
444 "predictedInsertSize": 42, # The predicted insert size of this read group. The insert size is the length the sequenced DNA fragment from end-to-end, not including the adapters.
445 "name": "A String", # The read group name. This corresponds to the @RG ID field in the SAM spec.
446 "programs": [ # The programs used to generate this read group. Programs are always identical for all read groups within a read group set. For this reason, only the first read group in a returned set will have this field populated.
447 {
448 "commandLine": "A String", # The command line used to run this program.
449 "prevProgramId": "A String", # The ID of the program run before this one.
450 "id": "A String", # The user specified locally unique ID of the program. Used along with prevProgramId to define an ordering between programs.
451 "version": "A String", # The version of the program run.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]452 "name": "A String", # The display name of the program. This is typically the colloquial name of the tool used, for example 'bwa' or 'picard'.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]453 },
454 ],
455 "sampleId": "A String", # The sample this read group's data was generated from. Note: This is not an actual ID within this repository, but rather an identifier for a sample which may be meaningful to some external system.
456 "experiment": { # The experiment used to generate this read group.
457 "sequencingCenter": "A String", # The sequencing center used as part of this experiment.
458 "libraryId": "A String", # The library used as part of this experiment. Note: This is not an actual ID within this repository, but rather an identifier for a library which may be meaningful to some external system.
459 "instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to sequencing technology in BAM.
460 "platformUnit": "A String", # The platform unit used as part of this experiment e.g. flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
461 },
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]462 "referenceSetId": "A String", # The reference set to which the reads in this read group are aligned.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]463 "id": "A String", # The generated unique read group ID. Note: This is different than the @RG ID field in the SAM spec. For that value, see the name field.
464 "datasetId": "A String", # The ID of the dataset this read group belongs to.
465 "description": "A String", # A free-form text description of this read group.
466 },
467 ],
468 "filename": "A String", # The filename of the original source file for this read group set, if any.
469 "referenceSetId": "A String", # The reference set the reads in this read group set are aligned to.
470 "id": "A String", # The read group set ID.
471 "datasetId": "A String", # The dataset ID.
472}
473
474
475Returns:
476 An object of the form:
477
478 { # A read group set is a logical collection of read groups, which are collections of reads produced by a sequencer. A read group set typically models reads corresponding to one sample, sequenced one way, and aligned one way.
479 # - A read group set belongs to one dataset.
480 # - A read group belongs to one read group set.
481 # - A read belongs to one read group.
Nathaniel Manista4f877e52015-06-15 16:44:50 +0000[diff] [blame]482 "info": { # A string which maps to an array of values.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]483 "a_key": [ # A string which maps to an array of values.
484 "A String",
485 ],
486 },
487 "name": "A String", # The read group set name. By default this will be initialized to the sample name of the sequenced data contained in this set.
488 "readGroups": [ # The read groups in this set. There are typically 1-10 read groups in a read group set.
489 { # A read group is all the data that's processed the same way by the sequencer.
Nathaniel Manista4f877e52015-06-15 16:44:50 +0000[diff] [blame]490 "info": { # A string which maps to an array of values.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]491 "a_key": [ # A string which maps to an array of values.
492 "A String",
493 ],
494 },
495 "predictedInsertSize": 42, # The predicted insert size of this read group. The insert size is the length the sequenced DNA fragment from end-to-end, not including the adapters.
496 "name": "A String", # The read group name. This corresponds to the @RG ID field in the SAM spec.
497 "programs": [ # The programs used to generate this read group. Programs are always identical for all read groups within a read group set. For this reason, only the first read group in a returned set will have this field populated.
498 {
499 "commandLine": "A String", # The command line used to run this program.
500 "prevProgramId": "A String", # The ID of the program run before this one.
501 "id": "A String", # The user specified locally unique ID of the program. Used along with prevProgramId to define an ordering between programs.
502 "version": "A String", # The version of the program run.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]503 "name": "A String", # The display name of the program. This is typically the colloquial name of the tool used, for example 'bwa' or 'picard'.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]504 },
505 ],
506 "sampleId": "A String", # The sample this read group's data was generated from. Note: This is not an actual ID within this repository, but rather an identifier for a sample which may be meaningful to some external system.
507 "experiment": { # The experiment used to generate this read group.
508 "sequencingCenter": "A String", # The sequencing center used as part of this experiment.
509 "libraryId": "A String", # The library used as part of this experiment. Note: This is not an actual ID within this repository, but rather an identifier for a library which may be meaningful to some external system.
510 "instrumentModel": "A String", # The instrument model used as part of this experiment. This maps to sequencing technology in BAM.
511 "platformUnit": "A String", # The platform unit used as part of this experiment e.g. flowcell-barcode.lane for Illumina or slide for SOLiD. Corresponds to the
512 },
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]513 "referenceSetId": "A String", # The reference set to which the reads in this read group are aligned.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]514 "id": "A String", # The generated unique read group ID. Note: This is different than the @RG ID field in the SAM spec. For that value, see the name field.
515 "datasetId": "A String", # The ID of the dataset this read group belongs to.
516 "description": "A String", # A free-form text description of this read group.
517 },
518 ],
519 "filename": "A String", # The filename of the original source file for this read group set, if any.
520 "referenceSetId": "A String", # The reference set the reads in this read group set are aligned to.
521 "id": "A String", # The read group set ID.
522 "datasetId": "A String", # The dataset ID.
523 }</pre>
524</div>
525
526</body></html>