Gitiles
Code Review Sign In
gerrit-public.fairphone.software / platform / external / python / google-api-python-client / 4f877e562986034f25ea4246ad1256eabd339526 / . / docs / dyn / genomics_v1beta2.variantsets.html
blob: 82029038c039dc729b350ff460b530053eb9c2b0 [file] [log] [blame]
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]1<html><body>
2<style>
3
4body, h1, h2, h3, div, span, p, pre, a {
5 margin: 0;
6 padding: 0;
7 border: 0;
8 font-weight: inherit;
9 font-style: inherit;
10 font-size: 100%;
11 font-family: inherit;
12 vertical-align: baseline;
13}
14
15body {
16 font-size: 13px;
17 padding: 1em;
18}
19
20h1 {
21 font-size: 26px;
22 margin-bottom: 1em;
23}
24
25h2 {
26 font-size: 24px;
27 margin-bottom: 1em;
28}
29
30h3 {
31 font-size: 20px;
32 margin-bottom: 1em;
33 margin-top: 1em;
34}
35
36pre, code {
37 line-height: 1.5;
38 font-family: Monaco, 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', 'Lucida Console', monospace;
39}
40
41pre {
42 margin-top: 0.5em;
43}
44
45h1, h2, h3, p {
46 font-family: Arial, sans serif;
47}
48
49h1, h2, h3 {
50 border-bottom: solid #CCC 1px;
51}
52
53.toc_element {
54 margin-top: 0.5em;
55}
56
57.firstline {
58 margin-left: 2 em;
59}
60
61.method {
62 margin-top: 1em;
63 border: solid 1px #CCC;
64 padding: 1em;
65 background: #EEE;
66}
67
68.details {
69 font-weight: bold;
70 font-size: 14px;
71}
72
73</style>
74
75<h1><a href="genomics_v1beta2.html">Genomics API</a> . <a href="genomics_v1beta2.variantsets.html">variantsets</a></h1>
76<h2>Instance Methods</h2>
77<p class="toc_element">
78 <code><a href="#delete">delete(variantSetId)</a></code></p>
79<p class="firstline">Deletes the contents of a variant set. The variant set object is not deleted.</p>
80<p class="toc_element">
81 <code><a href="#export">export(variantSetId, body)</a></code></p>
82<p class="firstline">Exports variant set data to an external destination.</p>
83<p class="toc_element">
84 <code><a href="#get">get(variantSetId)</a></code></p>
85<p class="firstline">Gets a variant set by ID.</p>
86<p class="toc_element">
87 <code><a href="#importVariants">importVariants(variantSetId, body)</a></code></p>
88<p class="firstline">Creates variant data by asynchronously importing the provided information.</p>
89<p class="toc_element">
90 <code><a href="#mergeVariants">mergeVariants(variantSetId, body)</a></code></p>
91<p class="firstline">Merges the given variants with existing variants. Each variant will be merged with an existing variant that matches its reference sequence, start, end, reference bases, and alternative bases. If no such variant exists, a new one will be created.</p>
92<p class="toc_element">
93 <code><a href="#patch">patch(variantSetId, body)</a></code></p>
94<p class="firstline">Updates a variant set's metadata. All other modifications are silently ignored. This method supports patch semantics.</p>
95<p class="toc_element">
96 <code><a href="#search">search(body)</a></code></p>
97<p class="firstline">Returns a list of all variant sets matching search criteria.</p>
98<p class="toc_element">
99 <code><a href="#update">update(variantSetId, body)</a></code></p>
100<p class="firstline">Updates a variant set's metadata. All other modifications are silently ignored.</p>
101<h3>Method Details</h3>
102<div class="method">
103 <code class="details" id="delete">delete(variantSetId)</code>
104 <pre>Deletes the contents of a variant set. The variant set object is not deleted.
105
106Args:
107 variantSetId: string, The ID of the variant set to be deleted. (required)
108</pre>
109</div>
110
111<div class="method">
112 <code class="details" id="export">export(variantSetId, body)</code>
113 <pre>Exports variant set data to an external destination.
114
115Args:
116 variantSetId: string, Required. The ID of the variant set that contains variant data which should be exported. The caller must have READ access to this variant set. (required)
117 body: object, The request body. (required)
118 The object takes the form of:
119
120{ # The variant data export request.
Nathaniel Manista4f877e52015-06-15 16:44:50 +0000[diff] [blame^]121 "bigqueryDataset": "A String", # Required. The BigQuery dataset to export data to. This dataset must already exist. Note that this is distinct from the Genomics concept of "dataset".
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]122 "format": "A String", # The format for the exported data.
123 "callSetIds": [ # If provided, only variant call information from the specified call sets will be exported. By default all variant calls are exported.
124 "A String",
125 ],
Nathaniel Manista4f877e52015-06-15 16:44:50 +0000[diff] [blame^]126 "projectNumber": "A String", # Required. The Google Cloud project number that owns the destination BigQuery dataset. The caller must have WRITE access to this project. This project will also own the resulting export job.
127 "bigqueryTable": "A String", # Required. The BigQuery table to export data to. If the table doesn't exist, it will be created. If it already exists, it will be overwritten.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]128 }
129
130
131Returns:
132 An object of the form:
133
134 { # The variant data export response.
135 "jobId": "A String", # A job ID that can be used to get status information.
136 }</pre>
137</div>
138
139<div class="method">
140 <code class="details" id="get">get(variantSetId)</code>
141 <pre>Gets a variant set by ID.
142
143Args:
144 variantSetId: string, Required. The ID of the variant set. (required)
145
146Returns:
147 An object of the form:
148
149 { # A variant set is a collection of call sets and variants. It contains summary statistics of those contents. A variant set belongs to a dataset.
150 "referenceBounds": [ # A list of all references used by the variants in a variant set with associated coordinate upper bounds for each one.
151 { # ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
152 "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any variant in the reference sequence.
153 "referenceName": "A String", # The reference the bound is associate with.
154 },
155 ],
156 "id": "A String", # The Google-generated ID of the variant set. Immutable.
157 "datasetId": "A String", # The dataset to which this variant set belongs. Immutable.
158 "metadata": [ # The metadata associated with this variant set.
159 { # Metadata describes a single piece of variant call metadata. These data include a top level key and either a single value string (value) or a list of key-value pairs (info.) Value and info are mutually exclusive.
Nathaniel Manista4f877e52015-06-15 16:44:50 +0000[diff] [blame^]160 "info": { # A string which maps to an array of values.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]161 "a_key": [ # A string which maps to an array of values.
162 "A String",
163 ],
164 },
165 "description": "A String", # A textual description of this metadata.
166 "number": "A String", # The number of values that can be included in a field described by this metadata.
167 "value": "A String", # The value field for simple metadata
168 "key": "A String", # The top-level key.
169 "type": "A String", # The type of data. Possible types include: Integer, Float, Flag, Character, and String.
170 "id": "A String", # User-provided ID field, not enforced by this API. Two or more pieces of structured metadata with identical id and key fields are considered equivalent.
171 },
172 ],
173 }</pre>
174</div>
175
176<div class="method">
177 <code class="details" id="importVariants">importVariants(variantSetId, body)</code>
178 <pre>Creates variant data by asynchronously importing the provided information.
179
180The variants for import will be merged with any existing data and each other according to the behavior of mergeVariants. In particular, this means for merged VCF variants that have conflicting INFO fields, some data will be arbitrarily discarded. As a special case, for single-sample VCF files, QUAL and FILTER fields will be moved to the call level; these are sometimes interpreted in a call-specific context. Imported VCF headers are appended to the metadata already in a variant set.
181
182Args:
183 variantSetId: string, Required. The variant set to which variant data should be imported. (required)
184 body: object, The request body. (required)
185 The object takes the form of:
186
187{ # The variant data import request.
Nathaniel Manista4f877e52015-06-15 16:44:50 +0000[diff] [blame^]188 "normalizeReferenceNames": True or False, # Convert reference names to the canonical representation. hg19 haploytypes (those reference names containing "_hap") are not modified in any way. All other reference names are modified according to the following rules: The reference name is capitalized. The "chr" prefix is dropped for all autosomes and sex chromsomes. For example "chr17" becomes "17" and "chrX" becomes "X". All mitochondrial chromosomes ("chrM", "chrMT", etc) become "MT".
189 "sourceUris": [ # A list of URIs referencing variant files in Google Cloud Storage. URIs can include wildcards as described here. Note that recursive wildcards ('**') are not supported.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]190 "A String",
191 ],
Nathaniel Manista4f877e52015-06-15 16:44:50 +0000[diff] [blame^]192 "format": "A String", # The format of the variant data being imported. If unspecified, defaults to to "VCF".
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]193 }
194
195
196Returns:
197 An object of the form:
198
199 { # The variant data import response.
200 "jobId": "A String", # A job ID that can be used to get status information.
201 }</pre>
202</div>
203
204<div class="method">
205 <code class="details" id="mergeVariants">mergeVariants(variantSetId, body)</code>
206 <pre>Merges the given variants with existing variants. Each variant will be merged with an existing variant that matches its reference sequence, start, end, reference bases, and alternative bases. If no such variant exists, a new one will be created.
207
208When variants are merged, the call information from the new variant is added to the existing variant, and other fields (such as key/value pairs) are discarded.
209
210Args:
211 variantSetId: string, The destination variant set. (required)
212 body: object, The request body. (required)
213 The object takes the form of:
214
215{
216 "variants": [ # The variants to be merged with existing variants.
217 { # A variant represents a change in DNA sequence relative to a reference sequence. For example, a variant could represent a SNP or an insertion. Variants belong to a variant set. Each of the calls on a variant represent a determination of genotype with respect to that variant. For example, a call might assign probability of 0.32 to the occurrence of a SNP named rs1234 in a sample named NA12345. A call belongs to a call set, which contains related calls typically from one sample.
Nathaniel Manista4f877e52015-06-15 16:44:50 +0000[diff] [blame^]218 "info": { # A string which maps to an array of values.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]219 "a_key": [ # A string which maps to an array of values.
220 "A String",
221 ],
222 },
223 "variantSetId": "A String", # The ID of the variant set this variant belongs to.
224 "end": "A String", # The end position (0-based) of this variant. This corresponds to the first base after the last base in the reference allele. So, the length of the reference allele is (end - start). This is useful for variants that don't explicitly give alternate bases, for example large deletions.
225 "calls": [ # The variant calls for this particular variant. Each one represents the determination of genotype with respect to this variant.
226 { # A call represents the determination of genotype with respect to a particular variant. It may include associated information such as quality and phasing. For example, a call might assign a probability of 0.32 to the occurrence of a SNP named rs1234 in a call set with the name NA12345.
Nathaniel Manista4f877e52015-06-15 16:44:50 +0000[diff] [blame^]227 "info": { # A string which maps to an array of values.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]228 "a_key": [ # A string which maps to an array of values.
229 "A String",
230 ],
231 },
232 "genotype": [ # The genotype of this variant call. Each value represents either the value of the referenceBases field or a 1-based index into alternateBases. If a variant had a referenceBases value of T and an alternateBases value of ["A", "C"], and the genotype was [2, 1], that would mean the call represented the heterozygous value CA for this variant. If the genotype was instead [0, 1], the represented value would be TA. Ordering of the genotype values is important if the phaseset is present. If a genotype is not called (that is, a . is present in the GT string) -1 is returned.
233 42,
234 ],
235 "callSetId": "A String", # The ID of the call set this variant call belongs to.
236 "phaseset": "A String", # If this field is present, this variant call's genotype ordering implies the phase of the bases and is consistent with any other variant calls in the same reference sequence which have the same phaseset value. When importing data from VCF, if the genotype data was phased but no phase set was specified this field will be set to *.
237 "genotypeLikelihood": [ # The genotype likelihoods for this variant call. Each array entry represents how likely a specific genotype is for this call. The value ordering is defined by the GL tag in the VCF spec. If Phred-scaled genotype likelihood scores (PL) are available and log10(P) genotype likelihood scores (GL) are not, PL scores are converted to GL scores. If both are available, PL scores are stored in info.
238 3.14,
239 ],
240 "callSetName": "A String", # The name of the call set this variant call belongs to.
241 },
242 ],
243 "created": "A String", # The date this variant was created, in milliseconds from the epoch.
244 "referenceBases": "A String", # The reference bases for this variant. They start at the given position.
245 "filter": [ # A list of filters (normally quality filters) this variant has failed. PASS indicates this variant has passed all filters.
246 "A String",
247 ],
248 "start": "A String", # The position at which this variant occurs (0-based). This corresponds to the first base of the string of reference bases.
249 "names": [ # Names for the variant, for example a RefSNP ID.
250 "A String",
251 ],
252 "alternateBases": [ # The bases that appear instead of the reference bases.
253 "A String",
254 ],
255 "referenceName": "A String", # The reference on which this variant occurs. (such as chr20 or X)
256 "quality": 3.14, # A measure of how likely this variant is to be real. A higher value is better.
257 "id": "A String", # The Google generated ID of the variant, immutable.
258 },
259 ],
260 }
261
262</pre>
263</div>
264
265<div class="method">
266 <code class="details" id="patch">patch(variantSetId, body)</code>
267 <pre>Updates a variant set's metadata. All other modifications are silently ignored. This method supports patch semantics.
268
269Args:
Nathaniel Manista4f877e52015-06-15 16:44:50 +0000[diff] [blame^]270 variantSetId: string, The ID of the variant to be updated (must already exist). (required)
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]271 body: object, The request body. (required)
272 The object takes the form of:
273
274{ # A variant set is a collection of call sets and variants. It contains summary statistics of those contents. A variant set belongs to a dataset.
275 "referenceBounds": [ # A list of all references used by the variants in a variant set with associated coordinate upper bounds for each one.
276 { # ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
277 "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any variant in the reference sequence.
278 "referenceName": "A String", # The reference the bound is associate with.
279 },
280 ],
281 "id": "A String", # The Google-generated ID of the variant set. Immutable.
282 "datasetId": "A String", # The dataset to which this variant set belongs. Immutable.
283 "metadata": [ # The metadata associated with this variant set.
284 { # Metadata describes a single piece of variant call metadata. These data include a top level key and either a single value string (value) or a list of key-value pairs (info.) Value and info are mutually exclusive.
Nathaniel Manista4f877e52015-06-15 16:44:50 +0000[diff] [blame^]285 "info": { # A string which maps to an array of values.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]286 "a_key": [ # A string which maps to an array of values.
287 "A String",
288 ],
289 },
290 "description": "A String", # A textual description of this metadata.
291 "number": "A String", # The number of values that can be included in a field described by this metadata.
292 "value": "A String", # The value field for simple metadata
293 "key": "A String", # The top-level key.
294 "type": "A String", # The type of data. Possible types include: Integer, Float, Flag, Character, and String.
295 "id": "A String", # User-provided ID field, not enforced by this API. Two or more pieces of structured metadata with identical id and key fields are considered equivalent.
296 },
297 ],
298}
299
300
301Returns:
302 An object of the form:
303
304 { # A variant set is a collection of call sets and variants. It contains summary statistics of those contents. A variant set belongs to a dataset.
305 "referenceBounds": [ # A list of all references used by the variants in a variant set with associated coordinate upper bounds for each one.
306 { # ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
307 "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any variant in the reference sequence.
308 "referenceName": "A String", # The reference the bound is associate with.
309 },
310 ],
311 "id": "A String", # The Google-generated ID of the variant set. Immutable.
312 "datasetId": "A String", # The dataset to which this variant set belongs. Immutable.
313 "metadata": [ # The metadata associated with this variant set.
314 { # Metadata describes a single piece of variant call metadata. These data include a top level key and either a single value string (value) or a list of key-value pairs (info.) Value and info are mutually exclusive.
Nathaniel Manista4f877e52015-06-15 16:44:50 +0000[diff] [blame^]315 "info": { # A string which maps to an array of values.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]316 "a_key": [ # A string which maps to an array of values.
317 "A String",
318 ],
319 },
320 "description": "A String", # A textual description of this metadata.
321 "number": "A String", # The number of values that can be included in a field described by this metadata.
322 "value": "A String", # The value field for simple metadata
323 "key": "A String", # The top-level key.
324 "type": "A String", # The type of data. Possible types include: Integer, Float, Flag, Character, and String.
325 "id": "A String", # User-provided ID field, not enforced by this API. Two or more pieces of structured metadata with identical id and key fields are considered equivalent.
326 },
327 ],
328 }</pre>
329</div>
330
331<div class="method">
332 <code class="details" id="search">search(body)</code>
333 <pre>Returns a list of all variant sets matching search criteria.
334
335Implements GlobalAllianceApi.searchVariantSets.
336
337Args:
338 body: object, The request body. (required)
339 The object takes the form of:
340
341{ # The search variant sets request.
342 "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.
343 "datasetIds": [ # Exactly one dataset ID must be provided here. Only variant sets which belong to this dataset will be returned.
344 "A String",
345 ],
346 "pageSize": 42, # The maximum number of variant sets to return in a request.
347 }
348
349
350Returns:
351 An object of the form:
352
353 { # The search variant sets response.
354 "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.
355 "variantSets": [ # The variant sets belonging to the requested dataset.
356 { # A variant set is a collection of call sets and variants. It contains summary statistics of those contents. A variant set belongs to a dataset.
357 "referenceBounds": [ # A list of all references used by the variants in a variant set with associated coordinate upper bounds for each one.
358 { # ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
359 "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any variant in the reference sequence.
360 "referenceName": "A String", # The reference the bound is associate with.
361 },
362 ],
363 "id": "A String", # The Google-generated ID of the variant set. Immutable.
364 "datasetId": "A String", # The dataset to which this variant set belongs. Immutable.
365 "metadata": [ # The metadata associated with this variant set.
366 { # Metadata describes a single piece of variant call metadata. These data include a top level key and either a single value string (value) or a list of key-value pairs (info.) Value and info are mutually exclusive.
Nathaniel Manista4f877e52015-06-15 16:44:50 +0000[diff] [blame^]367 "info": { # A string which maps to an array of values.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]368 "a_key": [ # A string which maps to an array of values.
369 "A String",
370 ],
371 },
372 "description": "A String", # A textual description of this metadata.
373 "number": "A String", # The number of values that can be included in a field described by this metadata.
374 "value": "A String", # The value field for simple metadata
375 "key": "A String", # The top-level key.
376 "type": "A String", # The type of data. Possible types include: Integer, Float, Flag, Character, and String.
377 "id": "A String", # User-provided ID field, not enforced by this API. Two or more pieces of structured metadata with identical id and key fields are considered equivalent.
378 },
379 ],
380 },
381 ],
382 }</pre>
383</div>
384
385<div class="method">
386 <code class="details" id="update">update(variantSetId, body)</code>
387 <pre>Updates a variant set's metadata. All other modifications are silently ignored.
388
389Args:
Nathaniel Manista4f877e52015-06-15 16:44:50 +0000[diff] [blame^]390 variantSetId: string, The ID of the variant to be updated (must already exist). (required)
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]391 body: object, The request body. (required)
392 The object takes the form of:
393
394{ # A variant set is a collection of call sets and variants. It contains summary statistics of those contents. A variant set belongs to a dataset.
395 "referenceBounds": [ # A list of all references used by the variants in a variant set with associated coordinate upper bounds for each one.
396 { # ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
397 "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any variant in the reference sequence.
398 "referenceName": "A String", # The reference the bound is associate with.
399 },
400 ],
401 "id": "A String", # The Google-generated ID of the variant set. Immutable.
402 "datasetId": "A String", # The dataset to which this variant set belongs. Immutable.
403 "metadata": [ # The metadata associated with this variant set.
404 { # Metadata describes a single piece of variant call metadata. These data include a top level key and either a single value string (value) or a list of key-value pairs (info.) Value and info are mutually exclusive.
Nathaniel Manista4f877e52015-06-15 16:44:50 +0000[diff] [blame^]405 "info": { # A string which maps to an array of values.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]406 "a_key": [ # A string which maps to an array of values.
407 "A String",
408 ],
409 },
410 "description": "A String", # A textual description of this metadata.
411 "number": "A String", # The number of values that can be included in a field described by this metadata.
412 "value": "A String", # The value field for simple metadata
413 "key": "A String", # The top-level key.
414 "type": "A String", # The type of data. Possible types include: Integer, Float, Flag, Character, and String.
415 "id": "A String", # User-provided ID field, not enforced by this API. Two or more pieces of structured metadata with identical id and key fields are considered equivalent.
416 },
417 ],
418}
419
420
421Returns:
422 An object of the form:
423
424 { # A variant set is a collection of call sets and variants. It contains summary statistics of those contents. A variant set belongs to a dataset.
425 "referenceBounds": [ # A list of all references used by the variants in a variant set with associated coordinate upper bounds for each one.
426 { # ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
427 "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any variant in the reference sequence.
428 "referenceName": "A String", # The reference the bound is associate with.
429 },
430 ],
431 "id": "A String", # The Google-generated ID of the variant set. Immutable.
432 "datasetId": "A String", # The dataset to which this variant set belongs. Immutable.
433 "metadata": [ # The metadata associated with this variant set.
434 { # Metadata describes a single piece of variant call metadata. These data include a top level key and either a single value string (value) or a list of key-value pairs (info.) Value and info are mutually exclusive.
Nathaniel Manista4f877e52015-06-15 16:44:50 +0000[diff] [blame^]435 "info": { # A string which maps to an array of values.
Craig Citroe633be12015-03-02 13:40:36 -0800[diff] [blame]436 "a_key": [ # A string which maps to an array of values.
437 "A String",
438 ],
439 },
440 "description": "A String", # A textual description of this metadata.
441 "number": "A String", # The number of values that can be included in a field described by this metadata.
442 "value": "A String", # The value field for simple metadata
443 "key": "A String", # The top-level key.
444 "type": "A String", # The type of data. Possible types include: Integer, Float, Flag, Character, and String.
445 "id": "A String", # User-provided ID field, not enforced by this API. Two or more pieces of structured metadata with identical id and key fields are considered equivalent.
446 },
447 ],
448 }</pre>
449</div>
450
451</body></html>