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75<h1><a href="genomics_v1beta.html">Genomics API</a> . <a href="genomics_v1beta.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="#get">get(variantSetId)</a></code></p>
82<p class="firstline">Gets a variant set by ID.</p>
83<p class="toc_element">
84 <code><a href="#mergeVariants">mergeVariants(variantSetId, body)</a></code></p>
85<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>
86<p class="toc_element">
87 <code><a href="#patch">patch(variantSetId, body)</a></code></p>
88<p class="firstline">Updates a variant set's metadata. All other modifications are silently ignored. Returns the modified variant set. This method supports patch semantics.</p>
89<p class="toc_element">
90 <code><a href="#search">search(body)</a></code></p>
91<p class="firstline">Returns a list of all variant sets matching search criteria.</p>
92<p class="toc_element">
93 <code><a href="#update">update(variantSetId, body)</a></code></p>
94<p class="firstline">Updates a variant set's metadata. All other modifications are silently ignored. Returns the modified variant set.</p>
95<h3>Method Details</h3>
96<div class="method">
97 <code class="details" id="delete">delete(variantSetId)</code>
98 <pre>Deletes the contents of a variant set. The variant set object is not deleted.
99
100Args:
101 variantSetId: string, The ID of the variant set to be deleted. (required)
102</pre>
103</div>
104
105<div class="method">
106 <code class="details" id="get">get(variantSetId)</code>
107 <pre>Gets a variant set by ID.
108
109Args:
110 variantSetId: string, Required. The ID of the variant set. (required)
111
112Returns:
113 An object of the form:
114
115 { # A VariantSet represents a collection of Variants and their summary statistics.
116 "referenceBounds": [ # A list of all references used by the variants in a variant set with associated coordinate upper bounds for each one.
117 { # ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
118 "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any variant in the reference sequence.
119 "referenceName": "A String", # The reference the bound is associate with.
120 },
121 ],
122 "id": "A String", # The Google-generated ID of the variant set. Immutable.
123 "datasetId": "A String", # The dataset to which this variant set belongs. Immutable.
124 "metadata": [ # The metadata associated with this variant set.
125 { # 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.
126 "info": { # Remaining structured metadata key-value pairs.
127 "a_key": [ # A string which maps to an array of values.
128 "A String",
129 ],
130 },
131 "description": "A String", # A textual description of this metadata.
132 "number": "A String", # The number of values that can be included in a field described by this metadata.
133 "value": "A String", # The value field for simple metadata
134 "key": "A String", # The top-level key.
135 "type": "A String", # The type of data. Possible types include: Integer, Float, Flag, Character, and String.
136 "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.
137 },
138 ],
139 }</pre>
140</div>
141
142<div class="method">
143 <code class="details" id="mergeVariants">mergeVariants(variantSetId, body)</code>
144 <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.
145
146When 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.
147
148Args:
149 variantSetId: string, The destination variant set. (required)
150 body: object, The request body. (required)
151 The object takes the form of:
152
153{
154 "variants": [ # The variants to be merged with existing variants.
155 { # A Variant represents a change in DNA sequence relative to some reference. For example, a Variant could represent a SNP or an insertion. Variants belong to a variant set.
156 "info": { # A map of additional variant information.
157 "a_key": [ # A string which maps to an array of values.
158 "A String",
159 ],
160 },
161 "variantSetId": "A String", # The ID of the variant set this variant belongs to.
162 "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.
163 "calls": [ # The variant calls for this particular variant. Each one represents the determination of genotype with respect to this variant.
164 { # 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.
165 "info": { # A map of additional variant call information.
166 "a_key": [ # A string which maps to an array of values.
167 "A String",
168 ],
169 },
170 "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.
171 42,
172 ],
173 "callSetId": "A String", # The ID of the call set this variant call belongs to.
174 "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 *.
175 "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.
176 3.14,
177 ],
178 "callSetName": "A String", # The name of the call set this variant call belongs to.
179 },
180 ],
181 "created": "A String", # The date this variant was created, in milliseconds from the epoch.
182 "referenceBases": "A String", # The reference bases for this variant. They start at the given position.
183 "filter": [ # A list of filters (normally quality filters) this variant has failed. PASS indicates this variant has passed all filters.
184 "A String",
185 ],
186 "start": "A String", # The position at which this variant occurs (0-based). This corresponds to the first base of the string of reference bases.
187 "names": [ # Names for the variant, for example a RefSNP ID.
188 "A String",
189 ],
190 "alternateBases": [ # The bases that appear instead of the reference bases.
191 "A String",
192 ],
193 "referenceName": "A String", # The reference on which this variant occurs. (such as chr20 or X)
194 "quality": 3.14, # A measure of how likely this variant is to be real. A higher value is better.
195 "id": "A String", # The Google generated ID of the variant, immutable.
196 },
197 ],
198 }
199
200</pre>
201</div>
202
203<div class="method">
204 <code class="details" id="patch">patch(variantSetId, body)</code>
205 <pre>Updates a variant set's metadata. All other modifications are silently ignored. Returns the modified variant set. This method supports patch semantics.
206
207Args:
208 variantSetId: string, The ID of the variant to be updated. (required)
209 body: object, The request body. (required)
210 The object takes the form of:
211
212{ # A VariantSet represents a collection of Variants and their summary statistics.
213 "referenceBounds": [ # A list of all references used by the variants in a variant set with associated coordinate upper bounds for each one.
214 { # ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
215 "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any variant in the reference sequence.
216 "referenceName": "A String", # The reference the bound is associate with.
217 },
218 ],
219 "id": "A String", # The Google-generated ID of the variant set. Immutable.
220 "datasetId": "A String", # The dataset to which this variant set belongs. Immutable.
221 "metadata": [ # The metadata associated with this variant set.
222 { # 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.
223 "info": { # Remaining structured metadata key-value pairs.
224 "a_key": [ # A string which maps to an array of values.
225 "A String",
226 ],
227 },
228 "description": "A String", # A textual description of this metadata.
229 "number": "A String", # The number of values that can be included in a field described by this metadata.
230 "value": "A String", # The value field for simple metadata
231 "key": "A String", # The top-level key.
232 "type": "A String", # The type of data. Possible types include: Integer, Float, Flag, Character, and String.
233 "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.
234 },
235 ],
236}
237
238
239Returns:
240 An object of the form:
241
242 { # A VariantSet represents a collection of Variants and their summary statistics.
243 "referenceBounds": [ # A list of all references used by the variants in a variant set with associated coordinate upper bounds for each one.
244 { # ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
245 "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any variant in the reference sequence.
246 "referenceName": "A String", # The reference the bound is associate with.
247 },
248 ],
249 "id": "A String", # The Google-generated ID of the variant set. Immutable.
250 "datasetId": "A String", # The dataset to which this variant set belongs. Immutable.
251 "metadata": [ # The metadata associated with this variant set.
252 { # 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.
253 "info": { # Remaining structured metadata key-value pairs.
254 "a_key": [ # A string which maps to an array of values.
255 "A String",
256 ],
257 },
258 "description": "A String", # A textual description of this metadata.
259 "number": "A String", # The number of values that can be included in a field described by this metadata.
260 "value": "A String", # The value field for simple metadata
261 "key": "A String", # The top-level key.
262 "type": "A String", # The type of data. Possible types include: Integer, Float, Flag, Character, and String.
263 "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.
264 },
265 ],
266 }</pre>
267</div>
268
269<div class="method">
270 <code class="details" id="search">search(body)</code>
271 <pre>Returns a list of all variant sets matching search criteria.
272
273Args:
274 body: object, The request body. (required)
275 The object takes the form of:
276
277{ # The search variant sets request.
278 "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.
279 "datasetIds": [ # Exactly one dataset ID must be provided here. Only variant sets which belong to this dataset will be returned.
280 "A String",
281 ],
282 "pageSize": 42, # The maximum number of variant sets to return in a request.
283 }
284
285
286Returns:
287 An object of the form:
288
289 { # The search variant sets response.
290 "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.
291 "variantSets": [ # The variant sets belonging to the requested dataset.
292 { # A VariantSet represents a collection of Variants and their summary statistics.
293 "referenceBounds": [ # A list of all references used by the variants in a variant set with associated coordinate upper bounds for each one.
294 { # ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
295 "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any variant in the reference sequence.
296 "referenceName": "A String", # The reference the bound is associate with.
297 },
298 ],
299 "id": "A String", # The Google-generated ID of the variant set. Immutable.
300 "datasetId": "A String", # The dataset to which this variant set belongs. Immutable.
301 "metadata": [ # The metadata associated with this variant set.
302 { # 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.
303 "info": { # Remaining structured metadata key-value pairs.
304 "a_key": [ # A string which maps to an array of values.
305 "A String",
306 ],
307 },
308 "description": "A String", # A textual description of this metadata.
309 "number": "A String", # The number of values that can be included in a field described by this metadata.
310 "value": "A String", # The value field for simple metadata
311 "key": "A String", # The top-level key.
312 "type": "A String", # The type of data. Possible types include: Integer, Float, Flag, Character, and String.
313 "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.
314 },
315 ],
316 },
317 ],
318 }</pre>
319</div>
320
321<div class="method">
322 <code class="details" id="update">update(variantSetId, body)</code>
323 <pre>Updates a variant set's metadata. All other modifications are silently ignored. Returns the modified variant set.
324
325Args:
326 variantSetId: string, The ID of the variant to be updated. (required)
327 body: object, The request body. (required)
328 The object takes the form of:
329
330{ # A VariantSet represents a collection of Variants and their summary statistics.
331 "referenceBounds": [ # A list of all references used by the variants in a variant set with associated coordinate upper bounds for each one.
332 { # ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
333 "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any variant in the reference sequence.
334 "referenceName": "A String", # The reference the bound is associate with.
335 },
336 ],
337 "id": "A String", # The Google-generated ID of the variant set. Immutable.
338 "datasetId": "A String", # The dataset to which this variant set belongs. Immutable.
339 "metadata": [ # The metadata associated with this variant set.
340 { # 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.
341 "info": { # Remaining structured metadata key-value pairs.
342 "a_key": [ # A string which maps to an array of values.
343 "A String",
344 ],
345 },
346 "description": "A String", # A textual description of this metadata.
347 "number": "A String", # The number of values that can be included in a field described by this metadata.
348 "value": "A String", # The value field for simple metadata
349 "key": "A String", # The top-level key.
350 "type": "A String", # The type of data. Possible types include: Integer, Float, Flag, Character, and String.
351 "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.
352 },
353 ],
354}
355
356
357Returns:
358 An object of the form:
359
360 { # A VariantSet represents a collection of Variants and their summary statistics.
361 "referenceBounds": [ # A list of all references used by the variants in a variant set with associated coordinate upper bounds for each one.
362 { # ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
363 "upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any variant in the reference sequence.
364 "referenceName": "A String", # The reference the bound is associate with.
365 },
366 ],
367 "id": "A String", # The Google-generated ID of the variant set. Immutable.
368 "datasetId": "A String", # The dataset to which this variant set belongs. Immutable.
369 "metadata": [ # The metadata associated with this variant set.
370 { # 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.
371 "info": { # Remaining structured metadata key-value pairs.
372 "a_key": [ # A string which maps to an array of values.
373 "A String",
374 ],
375 },
376 "description": "A String", # A textual description of this metadata.
377 "number": "A String", # The number of values that can be included in a field described by this metadata.
378 "value": "A String", # The value field for simple metadata
379 "key": "A String", # The top-level key.
380 "type": "A String", # The type of data. Possible types include: Integer, Float, Flag, Character, and String.
381 "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.
382 },
383 ],
384 }</pre>
385</div>
386
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