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@@ -85,7 +85,10 @@
<p class="firstline">Gets a variant by ID. For the definitions of variants and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)</p>
<p class="toc_element">
<code><a href="#import_">import_(body, x__xgafv=None)</a></code></p>
-<p class="firstline">Creates variant data by asynchronously importing the provided information. For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) The variants for import will be merged with any 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. When 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. 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.</p>
+<p class="firstline">Creates variant data by asynchronously importing the provided information. For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) The variants for import will be merged with any 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. When variants are merged, the call information from the new variant is added to the existing variant, and Variant info fields are merged as specified in infoMergeConfig. 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.</p>
+<p class="toc_element">
+ <code><a href="#merge">merge(body, x__xgafv=None)</a></code></p>
+<p class="firstline">Merges the given variants with existing variants. For the definitions of variants and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 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. When variants are merged, the call information from the new variant is added to the existing variant. Variant info fields are merged as specified in the infoMergeConfig field of the MergeVariantsRequest. Please exercise caution when using this method! It is easy to introduce mistakes in existing variants and difficult to back out of them. For example, suppose you were trying to merge a new variant with an existing one and both variants contain calls that belong to callsets with the same callset ID. // Existing variant - irrelevant fields trimmed for clarity { "variantSetId": "10473108253681171589", "referenceName": "1", "start": "10582", "referenceBases": "G", "alternateBases": [ "A" ], "calls": [ { "callSetId": "10473108253681171589-0", "callSetName": "CALLSET0", "genotype": [ 0, 1 ], } ] } // New variant with conflicting call information { "variantSetId": "10473108253681171589", "referenceName": "1", "start": "10582", "referenceBases": "G", "alternateBases": [ "A" ], "calls": [ { "callSetId": "10473108253681171589-0", "callSetName": "CALLSET0", "genotype": [ 1, 1 ], } ] } The resulting merged variant would overwrite the existing calls with those from the new variant: { "variantSetId": "10473108253681171589", "referenceName": "1", "start": "10582", "referenceBases": "G", "alternateBases": [ "A" ], "calls": [ { "callSetId": "10473108253681171589-0", "callSetName": "CALLSET0", "genotype": [ 1, 1 ], } ] } This may be the desired outcome, but it is up to the user to determine if if that is indeed the case.</p>
<p class="toc_element">
<code><a href="#patch">patch(variantId, body, x__xgafv=None, updateMask=None)</a></code></p>
<p class="firstline">Updates a variant. For the definitions of variants and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) This method supports patch semantics. Returns the modified variant without its calls.</p>
@@ -268,7 +271,7 @@
<div class="method">
<code class="details" id="import_">import_(body, x__xgafv=None)</code>
- <pre>Creates variant data by asynchronously importing the provided information. For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) The variants for import will be merged with any 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. When 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. 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.
+ <pre>Creates variant data by asynchronously importing the provided information. For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) The variants for import will be merged with any 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. When variants are merged, the call information from the new variant is added to the existing variant, and Variant info fields are merged as specified in infoMergeConfig. 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.
Args:
body: object, The request body. (required)
@@ -280,6 +283,9 @@
"sourceUris": [ # A list of URIs referencing variant files in Google Cloud Storage. URIs can include wildcards [as described here](https://cloud.google.com/storage/docs/gsutil/addlhelp/WildcardNames). Note that recursive wildcards ('**') are not supported.
"A String",
],
+ "infoMergeConfig": { # A mapping between info field keys and the InfoMergeOperations to be performed on them. This is plumbed down to the MergeVariantRequests generated by the resulting import job.
+ "a_key": "A String",
+ },
"format": "A String", # The format of the variant data being imported. If unspecified, defaults to to `VCF`.
}
@@ -310,6 +316,74 @@
</div>
<div class="method">
+ <code class="details" id="merge">merge(body, x__xgafv=None)</code>
+ <pre>Merges the given variants with existing variants. For the definitions of variants and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 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. When variants are merged, the call information from the new variant is added to the existing variant. Variant info fields are merged as specified in the infoMergeConfig field of the MergeVariantsRequest. Please exercise caution when using this method! It is easy to introduce mistakes in existing variants and difficult to back out of them. For example, suppose you were trying to merge a new variant with an existing one and both variants contain calls that belong to callsets with the same callset ID. // Existing variant - irrelevant fields trimmed for clarity { "variantSetId": "10473108253681171589", "referenceName": "1", "start": "10582", "referenceBases": "G", "alternateBases": [ "A" ], "calls": [ { "callSetId": "10473108253681171589-0", "callSetName": "CALLSET0", "genotype": [ 0, 1 ], } ] } // New variant with conflicting call information { "variantSetId": "10473108253681171589", "referenceName": "1", "start": "10582", "referenceBases": "G", "alternateBases": [ "A" ], "calls": [ { "callSetId": "10473108253681171589-0", "callSetName": "CALLSET0", "genotype": [ 1, 1 ], } ] } The resulting merged variant would overwrite the existing calls with those from the new variant: { "variantSetId": "10473108253681171589", "referenceName": "1", "start": "10582", "referenceBases": "G", "alternateBases": [ "A" ], "calls": [ { "callSetId": "10473108253681171589-0", "callSetName": "CALLSET0", "genotype": [ 1, 1 ], } ] } This may be the desired outcome, but it is up to the user to determine if if that is indeed the case.
+
+Args:
+ body: object, The request body. (required)
+ The object takes the form of:
+
+{
+ "variantSetId": "A String", # The destination variant set.
+ "variants": [ # The variants to be merged with existing variants.
+ { # 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. For more genomics resource definitions, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) 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.
+ "info": { # A map of additional variant information. This must be of the form map (string key mapping to a list of string values).
+ "a_key": [
+ "",
+ ],
+ },
+ "variantSetId": "A String", # The ID of the variant set this variant belongs to.
+ "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.
+ "calls": [ # The variant calls for this particular variant. Each one represents the determination of genotype with respect to this variant.
+ { # 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.
+ "info": { # A map of additional variant call information. This must be of the form map (string key mapping to a list of string values).
+ "a_key": [
+ "",
+ ],
+ },
+ "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.
+ 42,
+ ],
+ "callSetId": "A String", # The ID of the call set this variant call belongs to.
+ "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 `*`.
+ "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`.
+ 3.14,
+ ],
+ "callSetName": "A String", # The name of the call set this variant call belongs to.
+ },
+ ],
+ "created": "A String", # The date this variant was created, in milliseconds from the epoch.
+ "referenceBases": "A String", # The reference bases for this variant. They start at the given position.
+ "filter": [ # A list of filters (normally quality filters) this variant has failed. `PASS` indicates this variant has passed all filters.
+ "A String",
+ ],
+ "start": "A String", # The position at which this variant occurs (0-based). This corresponds to the first base of the string of reference bases.
+ "names": [ # Names for the variant, for example a RefSNP ID.
+ "A String",
+ ],
+ "alternateBases": [ # The bases that appear instead of the reference bases.
+ "A String",
+ ],
+ "referenceName": "A String", # The reference on which this variant occurs. (such as `chr20` or `X`)
+ "quality": 3.14, # A measure of how likely this variant is to be real. A higher value is better.
+ "id": "A String", # The server-generated variant ID, unique across all variants.
+ },
+ ],
+ "infoMergeConfig": { # A mapping between info field keys and the InfoMergeOperations to be performed on them.
+ "a_key": "A String",
+ },
+ }
+
+ x__xgafv: string, V1 error format.
+
+Returns:
+ An object of the form:
+
+ { # A generic empty message that you can re-use to avoid defining duplicated empty messages in your APIs. A typical example is to use it as the request or the response type of an API method. For instance: service Foo { rpc Bar(google.protobuf.Empty) returns (google.protobuf.Empty); } The JSON representation for `Empty` is empty JSON object `{}`.
+ }</pre>
+</div>
+
+<div class="method">
<code class="details" id="patch">patch(variantId, body, x__xgafv=None, updateMask=None)</code>
<pre>Updates a variant. For the definitions of variants and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) This method supports patch semantics. Returns the modified variant without its calls.