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gerrit-public.fairphone.software / platform / external / python / google-api-python-client / c30d2b5d4478b230246dcaaa9f1c533ca3304387 / . / docs / dyn / genomics_v1.variants.html
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74
75<h1><a href="genomics_v1.html">Genomics API</a> . <a href="genomics_v1.variants.html">variants</a></h1>
76<h2>Instance Methods</h2>
77<p class="toc_element">
78 <code><a href="#create">create(body, x__xgafv=None)</a></code></p>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]79<p class="firstline">Creates a new variant.</p>
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]80<p class="toc_element">
81 <code><a href="#delete">delete(variantId, x__xgafv=None)</a></code></p>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]82<p class="firstline">Deletes a variant.</p>
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]83<p class="toc_element">
84 <code><a href="#get">get(variantId, x__xgafv=None)</a></code></p>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]85<p class="firstline">Gets a variant by ID.</p>
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]86<p class="toc_element">
87 <code><a href="#import_">import_(body, x__xgafv=None)</a></code></p>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]88<p class="firstline">Creates variant data by asynchronously importing the provided information.</p>
Jon Wayne Parrott0a471d32016-05-19 10:54:38 -0700[diff] [blame]89<p class="toc_element">
90 <code><a href="#merge">merge(body, x__xgafv=None)</a></code></p>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]91<p class="firstline">Merges the given variants with existing variants.</p>
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]92<p class="toc_element">
93 <code><a href="#patch">patch(variantId, body, x__xgafv=None, updateMask=None)</a></code></p>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]94<p class="firstline">Updates a variant.</p>
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]95<p class="toc_element">
96 <code><a href="#search">search(body, x__xgafv=None)</a></code></p>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]97<p class="firstline">Gets a list of variants matching the criteria.</p>
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]98<p class="toc_element">
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]99 <code><a href="#search_next">search_next(previous_request, previous_response)</a></code></p>
100<p class="firstline">Retrieves the next page of results.</p>
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]101<h3>Method Details</h3>
102<div class="method">
103 <code class="details" id="create">create(body, x__xgafv=None)</code>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]104 <pre>Creates a new variant.
105
106For the definitions of variants and other genomics resources, see
107[Fundamentals of Google
108Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]109
110Args:
111 body: object, The request body. (required)
112 The object takes the form of:
113
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]114{ # A variant represents a change in DNA sequence relative to a reference
115 # sequence. For example, a variant could represent a SNP or an insertion.
116 # Variants belong to a variant set.
117 #
118 # For more genomics resource definitions, see [Fundamentals of Google
119 # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
120 #
121 # Each of the calls on a variant represent a determination of genotype with
122 # respect to that variant. For example, a call might assign probability of 0.32
123 # to the occurrence of a SNP named rs1234 in a sample named NA12345. A call
124 # belongs to a call set, which contains related calls typically from one
125 # sample.
126 "info": { # A map of additional variant information. This must be of the form
127 # map<string, string[]> (string key mapping to a list of string values).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]128 "a_key": [
129 "",
130 ],
131 },
132 "variantSetId": "A String", # The ID of the variant set this variant belongs to.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]133 "end": "A String", # The end position (0-based) of this variant. This corresponds to the first
134 # base after the last base in the reference allele. So, the length of
135 # the reference allele is (end - start). This is useful for variants
136 # that don't explicitly give alternate bases, for example large deletions.
137 "calls": [ # The variant calls for this particular variant. Each one represents the
138 # determination of genotype with respect to this variant.
139 { # A call represents the determination of genotype with respect to a particular
140 # variant. It may include associated information such as quality and phasing.
141 # For example, a call might assign a probability of 0.32 to the occurrence of
142 # a SNP named rs1234 in a call set with the name NA12345.
143 "info": { # A map of additional variant call information. This must be of the form
144 # map<string, string[]> (string key mapping to a list of string values).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]145 "a_key": [
146 "",
147 ],
148 },
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]149 "genotype": [ # The genotype of this variant call. Each value represents either the value
150 # of the `referenceBases` field or a 1-based index into
151 # `alternateBases`. If a variant had a `referenceBases`
152 # value of `T` and an `alternateBases`
153 # value of `["A", "C"]`, and the `genotype` was
154 # `[2, 1]`, that would mean the call
155 # represented the heterozygous value `CA` for this variant.
156 # If the `genotype` was instead `[0, 1]`, the
157 # represented value would be `TA`. Ordering of the
158 # genotype values is important if the `phaseset` is present.
159 # If a genotype is not called (that is, a `.` is present in the
160 # GT string) -1 is returned.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]161 42,
162 ],
163 "callSetId": "A String", # The ID of the call set this variant call belongs to.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]164 "phaseset": "A String", # If this field is present, this variant call's genotype ordering implies
165 # the phase of the bases and is consistent with any other variant calls in
166 # the same reference sequence which have the same phaseset value.
167 # When importing data from VCF, if the genotype data was phased but no
168 # phase set was specified this field will be set to `*`.
169 "genotypeLikelihood": [ # The genotype likelihoods for this variant call. Each array entry
170 # represents how likely a specific genotype is for this call. The value
171 # ordering is defined by the GL tag in the VCF spec.
172 # If Phred-scaled genotype likelihood scores (PL) are available and
173 # log10(P) genotype likelihood scores (GL) are not, PL scores are converted
174 # to GL scores. If both are available, PL scores are stored in `info`.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]175 3.14,
176 ],
177 "callSetName": "A String", # The name of the call set this variant call belongs to.
178 },
179 ],
180 "created": "A String", # The date this variant was created, in milliseconds from the epoch.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]181 "referenceBases": "A String", # The reference bases for this variant. They start at the given
182 # position.
183 "filter": [ # A list of filters (normally quality filters) this variant has failed.
184 # `PASS` indicates this variant has passed all filters.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]185 "A String",
186 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]187 "start": "A String", # The position at which this variant occurs (0-based).
188 # This corresponds to the first base of the string of reference bases.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]189 "names": [ # Names for the variant, for example a RefSNP ID.
190 "A String",
191 ],
192 "alternateBases": [ # The bases that appear instead of the reference bases.
193 "A String",
194 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]195 "referenceName": "A String", # The reference on which this variant occurs.
196 # (such as `chr20` or `X`)
197 "quality": 3.14, # A measure of how likely this variant is to be real.
198 # A higher value is better.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]199 "id": "A String", # The server-generated variant ID, unique across all variants.
200}
201
202 x__xgafv: string, V1 error format.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]203 Allowed values
204 1 - v1 error format
205 2 - v2 error format
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]206
207Returns:
208 An object of the form:
209
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]210 { # A variant represents a change in DNA sequence relative to a reference
211 # sequence. For example, a variant could represent a SNP or an insertion.
212 # Variants belong to a variant set.
213 #
214 # For more genomics resource definitions, see [Fundamentals of Google
215 # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
216 #
217 # Each of the calls on a variant represent a determination of genotype with
218 # respect to that variant. For example, a call might assign probability of 0.32
219 # to the occurrence of a SNP named rs1234 in a sample named NA12345. A call
220 # belongs to a call set, which contains related calls typically from one
221 # sample.
222 "info": { # A map of additional variant information. This must be of the form
223 # map<string, string[]> (string key mapping to a list of string values).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]224 "a_key": [
225 "",
226 ],
227 },
228 "variantSetId": "A String", # The ID of the variant set this variant belongs to.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]229 "end": "A String", # The end position (0-based) of this variant. This corresponds to the first
230 # base after the last base in the reference allele. So, the length of
231 # the reference allele is (end - start). This is useful for variants
232 # that don't explicitly give alternate bases, for example large deletions.
233 "calls": [ # The variant calls for this particular variant. Each one represents the
234 # determination of genotype with respect to this variant.
235 { # A call represents the determination of genotype with respect to a particular
236 # variant. It may include associated information such as quality and phasing.
237 # For example, a call might assign a probability of 0.32 to the occurrence of
238 # a SNP named rs1234 in a call set with the name NA12345.
239 "info": { # A map of additional variant call information. This must be of the form
240 # map<string, string[]> (string key mapping to a list of string values).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]241 "a_key": [
242 "",
243 ],
244 },
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]245 "genotype": [ # The genotype of this variant call. Each value represents either the value
246 # of the `referenceBases` field or a 1-based index into
247 # `alternateBases`. If a variant had a `referenceBases`
248 # value of `T` and an `alternateBases`
249 # value of `["A", "C"]`, and the `genotype` was
250 # `[2, 1]`, that would mean the call
251 # represented the heterozygous value `CA` for this variant.
252 # If the `genotype` was instead `[0, 1]`, the
253 # represented value would be `TA`. Ordering of the
254 # genotype values is important if the `phaseset` is present.
255 # If a genotype is not called (that is, a `.` is present in the
256 # GT string) -1 is returned.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]257 42,
258 ],
259 "callSetId": "A String", # The ID of the call set this variant call belongs to.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]260 "phaseset": "A String", # If this field is present, this variant call's genotype ordering implies
261 # the phase of the bases and is consistent with any other variant calls in
262 # the same reference sequence which have the same phaseset value.
263 # When importing data from VCF, if the genotype data was phased but no
264 # phase set was specified this field will be set to `*`.
265 "genotypeLikelihood": [ # The genotype likelihoods for this variant call. Each array entry
266 # represents how likely a specific genotype is for this call. The value
267 # ordering is defined by the GL tag in the VCF spec.
268 # If Phred-scaled genotype likelihood scores (PL) are available and
269 # log10(P) genotype likelihood scores (GL) are not, PL scores are converted
270 # to GL scores. If both are available, PL scores are stored in `info`.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]271 3.14,
272 ],
273 "callSetName": "A String", # The name of the call set this variant call belongs to.
274 },
275 ],
276 "created": "A String", # The date this variant was created, in milliseconds from the epoch.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]277 "referenceBases": "A String", # The reference bases for this variant. They start at the given
278 # position.
279 "filter": [ # A list of filters (normally quality filters) this variant has failed.
280 # `PASS` indicates this variant has passed all filters.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]281 "A String",
282 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]283 "start": "A String", # The position at which this variant occurs (0-based).
284 # This corresponds to the first base of the string of reference bases.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]285 "names": [ # Names for the variant, for example a RefSNP ID.
286 "A String",
287 ],
288 "alternateBases": [ # The bases that appear instead of the reference bases.
289 "A String",
290 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]291 "referenceName": "A String", # The reference on which this variant occurs.
292 # (such as `chr20` or `X`)
293 "quality": 3.14, # A measure of how likely this variant is to be real.
294 # A higher value is better.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]295 "id": "A String", # The server-generated variant ID, unique across all variants.
296 }</pre>
297</div>
298
299<div class="method">
300 <code class="details" id="delete">delete(variantId, x__xgafv=None)</code>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]301 <pre>Deletes a variant.
302
303For the definitions of variants and other genomics resources, see
304[Fundamentals of Google
305Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]306
307Args:
308 variantId: string, The ID of the variant to be deleted. (required)
309 x__xgafv: string, V1 error format.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]310 Allowed values
311 1 - v1 error format
312 2 - v2 error format
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]313
314Returns:
315 An object of the form:
316
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]317 { # A generic empty message that you can re-use to avoid defining duplicated
318 # empty messages in your APIs. A typical example is to use it as the request
319 # or the response type of an API method. For instance:
320 #
321 # service Foo {
322 # rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty);
323 # }
324 #
325 # The JSON representation for `Empty` is empty JSON object `{}`.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]326 }</pre>
327</div>
328
329<div class="method">
330 <code class="details" id="get">get(variantId, x__xgafv=None)</code>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]331 <pre>Gets a variant by ID.
332
333For the definitions of variants and other genomics resources, see
334[Fundamentals of Google
335Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]336
337Args:
338 variantId: string, The ID of the variant. (required)
339 x__xgafv: string, V1 error format.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]340 Allowed values
341 1 - v1 error format
342 2 - v2 error format
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]343
344Returns:
345 An object of the form:
346
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]347 { # A variant represents a change in DNA sequence relative to a reference
348 # sequence. For example, a variant could represent a SNP or an insertion.
349 # Variants belong to a variant set.
350 #
351 # For more genomics resource definitions, see [Fundamentals of Google
352 # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
353 #
354 # Each of the calls on a variant represent a determination of genotype with
355 # respect to that variant. For example, a call might assign probability of 0.32
356 # to the occurrence of a SNP named rs1234 in a sample named NA12345. A call
357 # belongs to a call set, which contains related calls typically from one
358 # sample.
359 "info": { # A map of additional variant information. This must be of the form
360 # map<string, string[]> (string key mapping to a list of string values).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]361 "a_key": [
362 "",
363 ],
364 },
365 "variantSetId": "A String", # The ID of the variant set this variant belongs to.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]366 "end": "A String", # The end position (0-based) of this variant. This corresponds to the first
367 # base after the last base in the reference allele. So, the length of
368 # the reference allele is (end - start). This is useful for variants
369 # that don't explicitly give alternate bases, for example large deletions.
370 "calls": [ # The variant calls for this particular variant. Each one represents the
371 # determination of genotype with respect to this variant.
372 { # A call represents the determination of genotype with respect to a particular
373 # variant. It may include associated information such as quality and phasing.
374 # For example, a call might assign a probability of 0.32 to the occurrence of
375 # a SNP named rs1234 in a call set with the name NA12345.
376 "info": { # A map of additional variant call information. This must be of the form
377 # map<string, string[]> (string key mapping to a list of string values).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]378 "a_key": [
379 "",
380 ],
381 },
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]382 "genotype": [ # The genotype of this variant call. Each value represents either the value
383 # of the `referenceBases` field or a 1-based index into
384 # `alternateBases`. If a variant had a `referenceBases`
385 # value of `T` and an `alternateBases`
386 # value of `["A", "C"]`, and the `genotype` was
387 # `[2, 1]`, that would mean the call
388 # represented the heterozygous value `CA` for this variant.
389 # If the `genotype` was instead `[0, 1]`, the
390 # represented value would be `TA`. Ordering of the
391 # genotype values is important if the `phaseset` is present.
392 # If a genotype is not called (that is, a `.` is present in the
393 # GT string) -1 is returned.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]394 42,
395 ],
396 "callSetId": "A String", # The ID of the call set this variant call belongs to.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]397 "phaseset": "A String", # If this field is present, this variant call's genotype ordering implies
398 # the phase of the bases and is consistent with any other variant calls in
399 # the same reference sequence which have the same phaseset value.
400 # When importing data from VCF, if the genotype data was phased but no
401 # phase set was specified this field will be set to `*`.
402 "genotypeLikelihood": [ # The genotype likelihoods for this variant call. Each array entry
403 # represents how likely a specific genotype is for this call. The value
404 # ordering is defined by the GL tag in the VCF spec.
405 # If Phred-scaled genotype likelihood scores (PL) are available and
406 # log10(P) genotype likelihood scores (GL) are not, PL scores are converted
407 # to GL scores. If both are available, PL scores are stored in `info`.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]408 3.14,
409 ],
410 "callSetName": "A String", # The name of the call set this variant call belongs to.
411 },
412 ],
413 "created": "A String", # The date this variant was created, in milliseconds from the epoch.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]414 "referenceBases": "A String", # The reference bases for this variant. They start at the given
415 # position.
416 "filter": [ # A list of filters (normally quality filters) this variant has failed.
417 # `PASS` indicates this variant has passed all filters.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]418 "A String",
419 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]420 "start": "A String", # The position at which this variant occurs (0-based).
421 # This corresponds to the first base of the string of reference bases.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]422 "names": [ # Names for the variant, for example a RefSNP ID.
423 "A String",
424 ],
425 "alternateBases": [ # The bases that appear instead of the reference bases.
426 "A String",
427 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]428 "referenceName": "A String", # The reference on which this variant occurs.
429 # (such as `chr20` or `X`)
430 "quality": 3.14, # A measure of how likely this variant is to be real.
431 # A higher value is better.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]432 "id": "A String", # The server-generated variant ID, unique across all variants.
433 }</pre>
434</div>
435
436<div class="method">
437 <code class="details" id="import_">import_(body, x__xgafv=None)</code>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]438 <pre>Creates variant data by asynchronously importing the provided information.
439
440For the definitions of variant sets and other genomics resources, see
441[Fundamentals of Google
442Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
443
444The variants for import will be merged with any existing variant that
445matches its reference sequence, start, end, reference bases, and
446alternative bases. If no such variant exists, a new one will be created.
447
448When variants are merged, the call information from the new variant
449is added to the existing variant, and Variant info fields are merged
450as specified in
451infoMergeConfig.
452As a special case, for single-sample VCF files, QUAL and FILTER fields will
453be moved to the call level; these are sometimes interpreted in a
454call-specific context.
455Imported VCF headers are appended to the metadata already in a variant set.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]456
457Args:
458 body: object, The request body. (required)
459 The object takes the form of:
460
461{ # The variant data import request.
462 "variantSetId": "A String", # Required. The variant set to which variant data should be imported.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]463 "normalizeReferenceNames": True or False, # Convert reference names to the canonical representation.
464 # hg19 haploytypes (those reference names containing "_hap")
465 # are not modified in any way.
466 # All other reference names are modified according to the following rules:
467 # The reference name is capitalized.
468 # The "chr" prefix is dropped for all autosomes and sex chromsomes.
469 # For example "chr17" becomes "17" and "chrX" becomes "X".
470 # All mitochondrial chromosomes ("chrM", "chrMT", etc) become "MT".
471 "sourceUris": [ # A list of URIs referencing variant files in Google Cloud Storage. URIs can
472 # include wildcards [as described
473 # here](https://cloud.google.com/storage/docs/gsutil/addlhelp/WildcardNames).
474 # Note that recursive wildcards ('**') are not supported.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]475 "A String",
476 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]477 "infoMergeConfig": { # A mapping between info field keys and the InfoMergeOperations to
478 # be performed on them. This is plumbed down to the MergeVariantRequests
479 # generated by the resulting import job.
Jon Wayne Parrott0a471d32016-05-19 10:54:38 -0700[diff] [blame]480 "a_key": "A String",
481 },
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]482 "format": "A String", # The format of the variant data being imported. If unspecified, defaults to
483 # to `VCF`.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]484 }
485
486 x__xgafv: string, V1 error format.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]487 Allowed values
488 1 - v1 error format
489 2 - v2 error format
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]490
491Returns:
492 An object of the form:
493
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]494 { # This resource represents a long-running operation that is the result of a
495 # network API call.
496 "response": { # If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If importing Variants, an ImportVariantsResponse is returned. For pipelines and exports, an empty response is returned.
Jon Wayne Parrott7d5badb2016-08-16 12:44:29 -0700[diff] [blame]497 "a_key": "", # Properties of the object. Contains field @type with type URL.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]498 },
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]499 "metadata": { # An OperationMetadata object. This will always be returned with the Operation.
500 "a_key": "", # Properties of the object. Contains field @type with type URL.
501 },
502 "done": True or False, # If the value is `false`, it means the operation is still in progress.
503 # If true, the operation is completed, and either `error` or `response` is
504 # available.
505 "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`
506 "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.
507 # programming environments, including REST APIs and RPC APIs. It is used by
508 # [gRPC](https://github.com/grpc). The error model is designed to be:
509 #
510 # - Simple to use and understand for most users
511 # - Flexible enough to meet unexpected needs
512 #
513 # # Overview
514 #
515 # The `Status` message contains three pieces of data: error code, error message,
516 # and error details. The error code should be an enum value of
517 # google.rpc.Code, but it may accept additional error codes if needed. The
518 # error message should be a developer-facing English message that helps
519 # developers *understand* and *resolve* the error. If a localized user-facing
520 # error message is needed, put the localized message in the error details or
521 # localize it in the client. The optional error details may contain arbitrary
522 # information about the error. There is a predefined set of error detail types
523 # in the package `google.rpc` which can be used for common error conditions.
524 #
525 # # Language mapping
526 #
527 # The `Status` message is the logical representation of the error model, but it
528 # is not necessarily the actual wire format. When the `Status` message is
529 # exposed in different client libraries and different wire protocols, it can be
530 # mapped differently. For example, it will likely be mapped to some exceptions
531 # in Java, but more likely mapped to some error codes in C.
532 #
533 # # Other uses
534 #
535 # The error model and the `Status` message can be used in a variety of
536 # environments, either with or without APIs, to provide a
537 # consistent developer experience across different environments.
538 #
539 # Example uses of this error model include:
540 #
541 # - Partial errors. If a service needs to return partial errors to the client,
542 # it may embed the `Status` in the normal response to indicate the partial
543 # errors.
544 #
545 # - Workflow errors. A typical workflow has multiple steps. Each step may
546 # have a `Status` message for error reporting purpose.
547 #
548 # - Batch operations. If a client uses batch request and batch response, the
549 # `Status` message should be used directly inside batch response, one for
550 # each error sub-response.
551 #
552 # - Asynchronous operations. If an API call embeds asynchronous operation
553 # results in its response, the status of those operations should be
554 # represented directly using the `Status` message.
555 #
556 # - Logging. If some API errors are stored in logs, the message `Status` could
557 # be used directly after any stripping needed for security/privacy reasons.
558 "message": "A String", # A developer-facing error message, which should be in English. Any
559 # user-facing error message should be localized and sent in the
560 # google.rpc.Status.details field, or localized by the client.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]561 "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^]562 "details": [ # A list of messages that carry the error details. There will be a
563 # common set of message types for APIs to use.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]564 {
Jon Wayne Parrott7d5badb2016-08-16 12:44:29 -0700[diff] [blame]565 "a_key": "", # Properties of the object. Contains field @type with type URL.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]566 },
567 ],
568 },
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]569 }</pre>
570</div>
571
572<div class="method">
Jon Wayne Parrott0a471d32016-05-19 10:54:38 -0700[diff] [blame]573 <code class="details" id="merge">merge(body, x__xgafv=None)</code>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]574 <pre>Merges the given variants with existing variants.
575
576For the definitions of variants and other genomics resources, see
577[Fundamentals of Google
578Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
579
580Each variant will be
581merged with an existing variant that matches its reference sequence,
582start, end, reference bases, and alternative bases. If no such variant
583exists, a new one will be created.
584
585When variants are merged, the call information from the new variant
586is added to the existing variant. Variant info fields are merged as
587specified in the
588infoMergeConfig
589field of the MergeVariantsRequest.
590
591Please exercise caution when using this method! It is easy to introduce
592mistakes in existing variants and difficult to back out of them. For
593example,
594suppose you were trying to merge a new variant with an existing one and
595both
596variants contain calls that belong to callsets with the same callset ID.
597
598 // Existing variant - irrelevant fields trimmed for clarity
599 {
600 "variantSetId": "10473108253681171589",
601 "referenceName": "1",
602 "start": "10582",
603 "referenceBases": "G",
604 "alternateBases": [
605 "A"
606 ],
607 "calls": [
608 {
609 "callSetId": "10473108253681171589-0",
610 "callSetName": "CALLSET0",
611 "genotype": [
612 0,
613 1
614 ],
615 }
616 ]
617 }
618
619 // New variant with conflicting call information
620 {
621 "variantSetId": "10473108253681171589",
622 "referenceName": "1",
623 "start": "10582",
624 "referenceBases": "G",
625 "alternateBases": [
626 "A"
627 ],
628 "calls": [
629 {
630 "callSetId": "10473108253681171589-0",
631 "callSetName": "CALLSET0",
632 "genotype": [
633 1,
634 1
635 ],
636 }
637 ]
638 }
639
640The resulting merged variant would overwrite the existing calls with those
641from the new variant:
642
643 {
644 "variantSetId": "10473108253681171589",
645 "referenceName": "1",
646 "start": "10582",
647 "referenceBases": "G",
648 "alternateBases": [
649 "A"
650 ],
651 "calls": [
652 {
653 "callSetId": "10473108253681171589-0",
654 "callSetName": "CALLSET0",
655 "genotype": [
656 1,
657 1
658 ],
659 }
660 ]
661 }
662
663This may be the desired outcome, but it is up to the user to determine if
664if that is indeed the case.
Jon Wayne Parrott0a471d32016-05-19 10:54:38 -0700[diff] [blame]665
666Args:
667 body: object, The request body. (required)
668 The object takes the form of:
669
670{
671 "variantSetId": "A String", # The destination variant set.
672 "variants": [ # The variants to be merged with existing variants.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]673 { # A variant represents a change in DNA sequence relative to a reference
674 # sequence. For example, a variant could represent a SNP or an insertion.
675 # Variants belong to a variant set.
676 #
677 # For more genomics resource definitions, see [Fundamentals of Google
678 # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
679 #
680 # Each of the calls on a variant represent a determination of genotype with
681 # respect to that variant. For example, a call might assign probability of 0.32
682 # to the occurrence of a SNP named rs1234 in a sample named NA12345. A call
683 # belongs to a call set, which contains related calls typically from one
684 # sample.
685 "info": { # A map of additional variant information. This must be of the form
686 # map<string, string[]> (string key mapping to a list of string values).
Jon Wayne Parrott0a471d32016-05-19 10:54:38 -0700[diff] [blame]687 "a_key": [
688 "",
689 ],
690 },
691 "variantSetId": "A String", # The ID of the variant set this variant belongs to.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]692 "end": "A String", # The end position (0-based) of this variant. This corresponds to the first
693 # base after the last base in the reference allele. So, the length of
694 # the reference allele is (end - start). This is useful for variants
695 # that don't explicitly give alternate bases, for example large deletions.
696 "calls": [ # The variant calls for this particular variant. Each one represents the
697 # determination of genotype with respect to this variant.
698 { # A call represents the determination of genotype with respect to a particular
699 # variant. It may include associated information such as quality and phasing.
700 # For example, a call might assign a probability of 0.32 to the occurrence of
701 # a SNP named rs1234 in a call set with the name NA12345.
702 "info": { # A map of additional variant call information. This must be of the form
703 # map<string, string[]> (string key mapping to a list of string values).
Jon Wayne Parrott0a471d32016-05-19 10:54:38 -0700[diff] [blame]704 "a_key": [
705 "",
706 ],
707 },
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]708 "genotype": [ # The genotype of this variant call. Each value represents either the value
709 # of the `referenceBases` field or a 1-based index into
710 # `alternateBases`. If a variant had a `referenceBases`
711 # value of `T` and an `alternateBases`
712 # value of `["A", "C"]`, and the `genotype` was
713 # `[2, 1]`, that would mean the call
714 # represented the heterozygous value `CA` for this variant.
715 # If the `genotype` was instead `[0, 1]`, the
716 # represented value would be `TA`. Ordering of the
717 # genotype values is important if the `phaseset` is present.
718 # If a genotype is not called (that is, a `.` is present in the
719 # GT string) -1 is returned.
Jon Wayne Parrott0a471d32016-05-19 10:54:38 -0700[diff] [blame]720 42,
721 ],
722 "callSetId": "A String", # The ID of the call set this variant call belongs to.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]723 "phaseset": "A String", # If this field is present, this variant call's genotype ordering implies
724 # the phase of the bases and is consistent with any other variant calls in
725 # the same reference sequence which have the same phaseset value.
726 # When importing data from VCF, if the genotype data was phased but no
727 # phase set was specified this field will be set to `*`.
728 "genotypeLikelihood": [ # The genotype likelihoods for this variant call. Each array entry
729 # represents how likely a specific genotype is for this call. The value
730 # ordering is defined by the GL tag in the VCF spec.
731 # If Phred-scaled genotype likelihood scores (PL) are available and
732 # log10(P) genotype likelihood scores (GL) are not, PL scores are converted
733 # to GL scores. If both are available, PL scores are stored in `info`.
Jon Wayne Parrott0a471d32016-05-19 10:54:38 -0700[diff] [blame]734 3.14,
735 ],
736 "callSetName": "A String", # The name of the call set this variant call belongs to.
737 },
738 ],
739 "created": "A String", # The date this variant was created, in milliseconds from the epoch.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]740 "referenceBases": "A String", # The reference bases for this variant. They start at the given
741 # position.
742 "filter": [ # A list of filters (normally quality filters) this variant has failed.
743 # `PASS` indicates this variant has passed all filters.
Jon Wayne Parrott0a471d32016-05-19 10:54:38 -0700[diff] [blame]744 "A String",
745 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]746 "start": "A String", # The position at which this variant occurs (0-based).
747 # This corresponds to the first base of the string of reference bases.
Jon Wayne Parrott0a471d32016-05-19 10:54:38 -0700[diff] [blame]748 "names": [ # Names for the variant, for example a RefSNP ID.
749 "A String",
750 ],
751 "alternateBases": [ # The bases that appear instead of the reference bases.
752 "A String",
753 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]754 "referenceName": "A String", # The reference on which this variant occurs.
755 # (such as `chr20` or `X`)
756 "quality": 3.14, # A measure of how likely this variant is to be real.
757 # A higher value is better.
Jon Wayne Parrott0a471d32016-05-19 10:54:38 -0700[diff] [blame]758 "id": "A String", # The server-generated variant ID, unique across all variants.
759 },
760 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]761 "infoMergeConfig": { # A mapping between info field keys and the InfoMergeOperations to
762 # be performed on them.
Jon Wayne Parrott0a471d32016-05-19 10:54:38 -0700[diff] [blame]763 "a_key": "A String",
764 },
765 }
766
767 x__xgafv: string, V1 error format.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]768 Allowed values
769 1 - v1 error format
770 2 - v2 error format
Jon Wayne Parrott0a471d32016-05-19 10:54:38 -0700[diff] [blame]771
772Returns:
773 An object of the form:
774
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]775 { # A generic empty message that you can re-use to avoid defining duplicated
776 # empty messages in your APIs. A typical example is to use it as the request
777 # or the response type of an API method. For instance:
778 #
779 # service Foo {
780 # rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty);
781 # }
782 #
783 # The JSON representation for `Empty` is empty JSON object `{}`.
Jon Wayne Parrott0a471d32016-05-19 10:54:38 -0700[diff] [blame]784 }</pre>
785</div>
786
787<div class="method">
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]788 <code class="details" id="patch">patch(variantId, body, x__xgafv=None, updateMask=None)</code>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]789 <pre>Updates a variant.
790
791For the definitions of variants and other genomics resources, see
792[Fundamentals of Google
793Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
794
795This method supports patch semantics. Returns the modified variant without
796its calls.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]797
798Args:
799 variantId: string, The ID of the variant to be updated. (required)
800 body: object, The request body. (required)
801 The object takes the form of:
802
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]803{ # A variant represents a change in DNA sequence relative to a reference
804 # sequence. For example, a variant could represent a SNP or an insertion.
805 # Variants belong to a variant set.
806 #
807 # For more genomics resource definitions, see [Fundamentals of Google
808 # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
809 #
810 # Each of the calls on a variant represent a determination of genotype with
811 # respect to that variant. For example, a call might assign probability of 0.32
812 # to the occurrence of a SNP named rs1234 in a sample named NA12345. A call
813 # belongs to a call set, which contains related calls typically from one
814 # sample.
815 "info": { # A map of additional variant information. This must be of the form
816 # map<string, string[]> (string key mapping to a list of string values).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]817 "a_key": [
818 "",
819 ],
820 },
821 "variantSetId": "A String", # The ID of the variant set this variant belongs to.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]822 "end": "A String", # The end position (0-based) of this variant. This corresponds to the first
823 # base after the last base in the reference allele. So, the length of
824 # the reference allele is (end - start). This is useful for variants
825 # that don't explicitly give alternate bases, for example large deletions.
826 "calls": [ # The variant calls for this particular variant. Each one represents the
827 # determination of genotype with respect to this variant.
828 { # A call represents the determination of genotype with respect to a particular
829 # variant. It may include associated information such as quality and phasing.
830 # For example, a call might assign a probability of 0.32 to the occurrence of
831 # a SNP named rs1234 in a call set with the name NA12345.
832 "info": { # A map of additional variant call information. This must be of the form
833 # map<string, string[]> (string key mapping to a list of string values).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]834 "a_key": [
835 "",
836 ],
837 },
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]838 "genotype": [ # The genotype of this variant call. Each value represents either the value
839 # of the `referenceBases` field or a 1-based index into
840 # `alternateBases`. If a variant had a `referenceBases`
841 # value of `T` and an `alternateBases`
842 # value of `["A", "C"]`, and the `genotype` was
843 # `[2, 1]`, that would mean the call
844 # represented the heterozygous value `CA` for this variant.
845 # If the `genotype` was instead `[0, 1]`, the
846 # represented value would be `TA`. Ordering of the
847 # genotype values is important if the `phaseset` is present.
848 # If a genotype is not called (that is, a `.` is present in the
849 # GT string) -1 is returned.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]850 42,
851 ],
852 "callSetId": "A String", # The ID of the call set this variant call belongs to.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]853 "phaseset": "A String", # If this field is present, this variant call's genotype ordering implies
854 # the phase of the bases and is consistent with any other variant calls in
855 # the same reference sequence which have the same phaseset value.
856 # When importing data from VCF, if the genotype data was phased but no
857 # phase set was specified this field will be set to `*`.
858 "genotypeLikelihood": [ # The genotype likelihoods for this variant call. Each array entry
859 # represents how likely a specific genotype is for this call. The value
860 # ordering is defined by the GL tag in the VCF spec.
861 # If Phred-scaled genotype likelihood scores (PL) are available and
862 # log10(P) genotype likelihood scores (GL) are not, PL scores are converted
863 # to GL scores. If both are available, PL scores are stored in `info`.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]864 3.14,
865 ],
866 "callSetName": "A String", # The name of the call set this variant call belongs to.
867 },
868 ],
869 "created": "A String", # The date this variant was created, in milliseconds from the epoch.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]870 "referenceBases": "A String", # The reference bases for this variant. They start at the given
871 # position.
872 "filter": [ # A list of filters (normally quality filters) this variant has failed.
873 # `PASS` indicates this variant has passed all filters.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]874 "A String",
875 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]876 "start": "A String", # The position at which this variant occurs (0-based).
877 # This corresponds to the first base of the string of reference bases.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]878 "names": [ # Names for the variant, for example a RefSNP ID.
879 "A String",
880 ],
881 "alternateBases": [ # The bases that appear instead of the reference bases.
882 "A String",
883 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]884 "referenceName": "A String", # The reference on which this variant occurs.
885 # (such as `chr20` or `X`)
886 "quality": 3.14, # A measure of how likely this variant is to be real.
887 # A higher value is better.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]888 "id": "A String", # The server-generated variant ID, unique across all variants.
889}
890
891 x__xgafv: string, V1 error format.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]892 Allowed values
893 1 - v1 error format
894 2 - v2 error format
895 updateMask: string, An optional mask specifying which fields to update. At this time, mutable
896fields are names and
897info. Acceptable values are "names" and
898"info". If unspecified, all mutable fields will be updated.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]899
900Returns:
901 An object of the form:
902
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]903 { # A variant represents a change in DNA sequence relative to a reference
904 # sequence. For example, a variant could represent a SNP or an insertion.
905 # Variants belong to a variant set.
906 #
907 # For more genomics resource definitions, see [Fundamentals of Google
908 # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
909 #
910 # Each of the calls on a variant represent a determination of genotype with
911 # respect to that variant. For example, a call might assign probability of 0.32
912 # to the occurrence of a SNP named rs1234 in a sample named NA12345. A call
913 # belongs to a call set, which contains related calls typically from one
914 # sample.
915 "info": { # A map of additional variant information. This must be of the form
916 # map<string, string[]> (string key mapping to a list of string values).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]917 "a_key": [
918 "",
919 ],
920 },
921 "variantSetId": "A String", # The ID of the variant set this variant belongs to.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]922 "end": "A String", # The end position (0-based) of this variant. This corresponds to the first
923 # base after the last base in the reference allele. So, the length of
924 # the reference allele is (end - start). This is useful for variants
925 # that don't explicitly give alternate bases, for example large deletions.
926 "calls": [ # The variant calls for this particular variant. Each one represents the
927 # determination of genotype with respect to this variant.
928 { # A call represents the determination of genotype with respect to a particular
929 # variant. It may include associated information such as quality and phasing.
930 # For example, a call might assign a probability of 0.32 to the occurrence of
931 # a SNP named rs1234 in a call set with the name NA12345.
932 "info": { # A map of additional variant call information. This must be of the form
933 # map<string, string[]> (string key mapping to a list of string values).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]934 "a_key": [
935 "",
936 ],
937 },
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]938 "genotype": [ # The genotype of this variant call. Each value represents either the value
939 # of the `referenceBases` field or a 1-based index into
940 # `alternateBases`. If a variant had a `referenceBases`
941 # value of `T` and an `alternateBases`
942 # value of `["A", "C"]`, and the `genotype` was
943 # `[2, 1]`, that would mean the call
944 # represented the heterozygous value `CA` for this variant.
945 # If the `genotype` was instead `[0, 1]`, the
946 # represented value would be `TA`. Ordering of the
947 # genotype values is important if the `phaseset` is present.
948 # If a genotype is not called (that is, a `.` is present in the
949 # GT string) -1 is returned.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]950 42,
951 ],
952 "callSetId": "A String", # The ID of the call set this variant call belongs to.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]953 "phaseset": "A String", # If this field is present, this variant call's genotype ordering implies
954 # the phase of the bases and is consistent with any other variant calls in
955 # the same reference sequence which have the same phaseset value.
956 # When importing data from VCF, if the genotype data was phased but no
957 # phase set was specified this field will be set to `*`.
958 "genotypeLikelihood": [ # The genotype likelihoods for this variant call. Each array entry
959 # represents how likely a specific genotype is for this call. The value
960 # ordering is defined by the GL tag in the VCF spec.
961 # If Phred-scaled genotype likelihood scores (PL) are available and
962 # log10(P) genotype likelihood scores (GL) are not, PL scores are converted
963 # to GL scores. If both are available, PL scores are stored in `info`.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]964 3.14,
965 ],
966 "callSetName": "A String", # The name of the call set this variant call belongs to.
967 },
968 ],
969 "created": "A String", # The date this variant was created, in milliseconds from the epoch.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]970 "referenceBases": "A String", # The reference bases for this variant. They start at the given
971 # position.
972 "filter": [ # A list of filters (normally quality filters) this variant has failed.
973 # `PASS` indicates this variant has passed all filters.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]974 "A String",
975 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]976 "start": "A String", # The position at which this variant occurs (0-based).
977 # This corresponds to the first base of the string of reference bases.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]978 "names": [ # Names for the variant, for example a RefSNP ID.
979 "A String",
980 ],
981 "alternateBases": [ # The bases that appear instead of the reference bases.
982 "A String",
983 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]984 "referenceName": "A String", # The reference on which this variant occurs.
985 # (such as `chr20` or `X`)
986 "quality": 3.14, # A measure of how likely this variant is to be real.
987 # A higher value is better.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]988 "id": "A String", # The server-generated variant ID, unique across all variants.
989 }</pre>
990</div>
991
992<div class="method">
993 <code class="details" id="search">search(body, x__xgafv=None)</code>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]994 <pre>Gets a list of variants matching the criteria.
995
996For the definitions of variants and other genomics resources, see
997[Fundamentals of Google
998Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
999
1000Implements
1001[GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L126).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]1002
1003Args:
1004 body: object, The request body. (required)
1005 The object takes the form of:
1006
1007{ # The variant search request.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]1008 "end": "A String", # The end of the window, 0-based exclusive. If unspecified or 0, defaults to
1009 # the length of the reference.
1010 "pageSize": 42, # The maximum number of variants to return in a single page. If unspecified,
1011 # defaults to 5000. The maximum value is 10000.
1012 "pageToken": "A String", # The continuation token, which is used to page through large result sets.
1013 # To get the next page of results, set this parameter to the value of
1014 # `nextPageToken` from the previous response.
1015 "maxCalls": 42, # The maximum number of calls to return in a single page. Note that this
1016 # limit may be exceeded in the event that a matching variant contains more
1017 # calls than the requested maximum. If unspecified, defaults to 5000. The
1018 # maximum value is 10000.
1019 "start": "A String", # The beginning of the window (0-based, inclusive) for which
1020 # overlapping variants should be returned. If unspecified, defaults to 0.
1021 "callSetIds": [ # Only return variant calls which belong to call sets with these ids.
1022 # Leaving this blank returns all variant calls. If a variant has no
1023 # calls belonging to any of these call sets, it won't be returned at all.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]1024 "A String",
1025 ],
1026 "variantName": "A String", # Only return variants which have exactly this name.
1027 "referenceName": "A String", # Required. Only return variants in this reference sequence.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]1028 "variantSetIds": [ # At most one variant set ID must be provided. Only variants from this
1029 # variant set will be returned. If omitted, a call set id must be included in
1030 # the request.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]1031 "A String",
1032 ],
1033 }
1034
1035 x__xgafv: string, V1 error format.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]1036 Allowed values
1037 1 - v1 error format
1038 2 - v2 error format
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]1039
1040Returns:
1041 An object of the form:
1042
1043 { # The variant search response.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]1044 "nextPageToken": "A String", # The continuation token, which is used to page through large result sets.
1045 # Provide this value in a subsequent request to return the next page of
1046 # results. This field will be empty if there aren't any additional results.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]1047 "variants": [ # The list of matching Variants.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]1048 { # A variant represents a change in DNA sequence relative to a reference
1049 # sequence. For example, a variant could represent a SNP or an insertion.
1050 # Variants belong to a variant set.
1051 #
1052 # For more genomics resource definitions, see [Fundamentals of Google
1053 # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
1054 #
1055 # Each of the calls on a variant represent a determination of genotype with
1056 # respect to that variant. For example, a call might assign probability of 0.32
1057 # to the occurrence of a SNP named rs1234 in a sample named NA12345. A call
1058 # belongs to a call set, which contains related calls typically from one
1059 # sample.
1060 "info": { # A map of additional variant information. This must be of the form
1061 # map<string, string[]> (string key mapping to a list of string values).
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]1062 "a_key": [
1063 "",
1064 ],
1065 },
1066 "variantSetId": "A String", # The ID of the variant set this variant belongs to.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]1067 "end": "A String", # The end position (0-based) of this variant. This corresponds to the first
1068 # base after the last base in the reference allele. So, the length of
1069 # the reference allele is (end - start). This is useful for variants
1070 # that don't explicitly give alternate bases, for example large deletions.
1071 "calls": [ # The variant calls for this particular variant. Each one represents the
1072 # determination of genotype with respect to this variant.
1073 { # A call represents the determination of genotype with respect to a particular
1074 # variant. It may include associated information such as quality and phasing.
1075 # For example, a call might assign a probability of 0.32 to the occurrence of
1076 # a SNP named rs1234 in a call set with the name NA12345.
1077 "info": { # A map of additional variant call information. This must be of the form
1078 # map<string, string[]> (string key mapping to a list of string values).
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]1079 "a_key": [
1080 "",
1081 ],
1082 },
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]1083 "genotype": [ # The genotype of this variant call. Each value represents either the value
1084 # of the `referenceBases` field or a 1-based index into
1085 # `alternateBases`. If a variant had a `referenceBases`
1086 # value of `T` and an `alternateBases`
1087 # value of `["A", "C"]`, and the `genotype` was
1088 # `[2, 1]`, that would mean the call
1089 # represented the heterozygous value `CA` for this variant.
1090 # If the `genotype` was instead `[0, 1]`, the
1091 # represented value would be `TA`. Ordering of the
1092 # genotype values is important if the `phaseset` is present.
1093 # If a genotype is not called (that is, a `.` is present in the
1094 # GT string) -1 is returned.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]1095 42,
1096 ],
1097 "callSetId": "A String", # The ID of the call set this variant call belongs to.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]1098 "phaseset": "A String", # If this field is present, this variant call's genotype ordering implies
1099 # the phase of the bases and is consistent with any other variant calls in
1100 # the same reference sequence which have the same phaseset value.
1101 # When importing data from VCF, if the genotype data was phased but no
1102 # phase set was specified this field will be set to `*`.
1103 "genotypeLikelihood": [ # The genotype likelihoods for this variant call. Each array entry
1104 # represents how likely a specific genotype is for this call. The value
1105 # ordering is defined by the GL tag in the VCF spec.
1106 # If Phred-scaled genotype likelihood scores (PL) are available and
1107 # log10(P) genotype likelihood scores (GL) are not, PL scores are converted
1108 # to GL scores. If both are available, PL scores are stored in `info`.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]1109 3.14,
1110 ],
1111 "callSetName": "A String", # The name of the call set this variant call belongs to.
1112 },
1113 ],
1114 "created": "A String", # The date this variant was created, in milliseconds from the epoch.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]1115 "referenceBases": "A String", # The reference bases for this variant. They start at the given
1116 # position.
1117 "filter": [ # A list of filters (normally quality filters) this variant has failed.
1118 # `PASS` indicates this variant has passed all filters.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]1119 "A String",
1120 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]1121 "start": "A String", # The position at which this variant occurs (0-based).
1122 # This corresponds to the first base of the string of reference bases.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]1123 "names": [ # Names for the variant, for example a RefSNP ID.
1124 "A String",
1125 ],
1126 "alternateBases": [ # The bases that appear instead of the reference bases.
1127 "A String",
1128 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]1129 "referenceName": "A String", # The reference on which this variant occurs.
1130 # (such as `chr20` or `X`)
1131 "quality": 3.14, # A measure of how likely this variant is to be real.
1132 # A higher value is better.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]1133 "id": "A String", # The server-generated variant ID, unique across all variants.
1134 },
1135 ],
1136 }</pre>
1137</div>
1138
1139<div class="method">
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]1140 <code class="details" id="search_next">search_next(previous_request, previous_response)</code>
1141 <pre>Retrieves the next page of results.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]1142
1143Args:
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]1144 previous_request: The request for the previous page. (required)
1145 previous_response: The response from the request for the previous page. (required)
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]1146
1147Returns:
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]1148 A request object that you can call 'execute()' on to request the next
1149 page. Returns None if there are no more items in the collection.
1150 </pre>
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]1151</div>
1152
1153</body></html>