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<h1><a href="genomics_v1.html">Genomics API</a> . <a href="genomics_v1.variantsets.html">variantsets</a></h1>
<h2>Instance Methods</h2>
<p class="toc_element">
<code><a href="#create">create(body, x__xgafv=None)</a></code></p>
<p class="firstline">Creates a new variant set. 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 provided variant set must have a valid `datasetId` set - all other fields are optional. Note that the `id` field will be ignored, as this is assigned by the server.</p>
<p class="toc_element">
<code><a href="#delete">delete(variantSetId, x__xgafv=None)</a></code></p>
<p class="firstline">Deletes a variant set including all variants, call sets, and calls within. This is not reversible. For the definitions of variant sets 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="#export">export(variantSetId, body, x__xgafv=None)</a></code></p>
<p class="firstline">Exports variant set data to an external destination. For the definitions of variant sets 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="#get">get(variantSetId, x__xgafv=None)</a></code></p>
<p class="firstline">Gets a variant set by ID. For the definitions of variant sets 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="#patch">patch(variantSetId, body, updateMask=None, x__xgafv=None)</a></code></p>
<p class="firstline">Updates a variant set using patch semantics. For the definitions of variant sets 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="#search">search(body, x__xgafv=None)</a></code></p>
<p class="firstline">Returns a list of all variant sets matching search criteria. For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) Implements [GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L49).</p>
<h3>Method Details</h3>
<div class="method">
<code class="details" id="create">create(body, x__xgafv=None)</code>
<pre>Creates a new variant set. 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 provided variant set must have a valid `datasetId` set - all other fields are optional. Note that the `id` field will be ignored, as this is assigned by the server.
Args:
body: object, The request body. (required)
The object takes the form of:
{ # A variant set is a collection of call sets and variants. It contains summary statistics of those contents. A variant set belongs to a dataset. For more genomics resource definitions, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
"name": "A String", # User-specified, mutable name.
"description": "A String", # A textual description of this variant set.
"referenceBounds": [ # A list of all references used by the variants in a variant set with associated coordinate upper bounds for each one.
{ # ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
"upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any variant in the reference sequence.
"referenceName": "A String", # The name of the reference associated with this reference bound.
},
],
"referenceSetId": "A String", # The reference set to which the variant set is mapped. The reference set describes the alignment provenance of the variant set, while the `referenceBounds` describe the shape of the actual variant data. The reference set's reference names are a superset of those found in the `referenceBounds`. For example, given a variant set that is mapped to the GRCh38 reference set and contains a single variant on reference 'X', `referenceBounds` would contain only an entry for 'X', while the associated reference set enumerates all possible references: '1', '2', 'X', 'Y', 'MT', etc.
"id": "A String", # The server-generated variant set ID, unique across all variant sets.
"datasetId": "A String", # The dataset to which this variant set belongs.
"metadata": [ # The metadata associated with this variant set.
{ # 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.
"info": { # Remaining structured metadata key-value pairs. This must be of the form map (string key mapping to a list of string values).
"a_key": [
"",
],
},
"description": "A String", # A textual description of this metadata.
"number": "A String", # The number of values that can be included in a field described by this metadata.
"value": "A String", # The value field for simple metadata
"key": "A String", # The top-level key.
"type": "A String", # The type of data. Possible types include: Integer, Float, Flag, Character, and String.
"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.
},
],
}
x__xgafv: string, V1 error format.
Returns:
An object of the form:
{ # A variant set is a collection of call sets and variants. It contains summary statistics of those contents. A variant set belongs to a dataset. For more genomics resource definitions, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
"name": "A String", # User-specified, mutable name.
"description": "A String", # A textual description of this variant set.
"referenceBounds": [ # A list of all references used by the variants in a variant set with associated coordinate upper bounds for each one.
{ # ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
"upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any variant in the reference sequence.
"referenceName": "A String", # The name of the reference associated with this reference bound.
},
],
"referenceSetId": "A String", # The reference set to which the variant set is mapped. The reference set describes the alignment provenance of the variant set, while the `referenceBounds` describe the shape of the actual variant data. The reference set's reference names are a superset of those found in the `referenceBounds`. For example, given a variant set that is mapped to the GRCh38 reference set and contains a single variant on reference 'X', `referenceBounds` would contain only an entry for 'X', while the associated reference set enumerates all possible references: '1', '2', 'X', 'Y', 'MT', etc.
"id": "A String", # The server-generated variant set ID, unique across all variant sets.
"datasetId": "A String", # The dataset to which this variant set belongs.
"metadata": [ # The metadata associated with this variant set.
{ # 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.
"info": { # Remaining structured metadata key-value pairs. This must be of the form map (string key mapping to a list of string values).
"a_key": [
"",
],
},
"description": "A String", # A textual description of this metadata.
"number": "A String", # The number of values that can be included in a field described by this metadata.
"value": "A String", # The value field for simple metadata
"key": "A String", # The top-level key.
"type": "A String", # The type of data. Possible types include: Integer, Float, Flag, Character, and String.
"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.
},
],
}</pre>
</div>
<div class="method">
<code class="details" id="delete">delete(variantSetId, x__xgafv=None)</code>
<pre>Deletes a variant set including all variants, call sets, and calls within. This is not reversible. For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Args:
variantSetId: string, The ID of the variant set to be deleted. (required)
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="export">export(variantSetId, body, x__xgafv=None)</code>
<pre>Exports variant set data to an external destination. For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Args:
variantSetId: string, Required. The ID of the variant set that contains variant data which should be exported. The caller must have READ access to this variant set. (required)
body: object, The request body. (required)
The object takes the form of:
{ # The variant data export request.
"projectId": "A String", # Required. The Google Cloud project ID that owns the destination BigQuery dataset. The caller must have WRITE access to this project. This project will also own the resulting export job.
"bigqueryTable": "A String", # Required. The BigQuery table to export data to. If the table doesn't exist, it will be created. If it already exists, it will be overwritten.
"bigqueryDataset": "A String", # Required. The BigQuery dataset to export data to. This dataset must already exist. Note that this is distinct from the Genomics concept of "dataset".
"callSetIds": [ # If provided, only variant call information from the specified call sets will be exported. By default all variant calls are exported.
"A String",
],
"format": "A String", # The format for the exported data.
}
x__xgafv: string, V1 error format.
Returns:
An object of the form:
{ # This resource represents a long-running operation that is the result of a network API call.
"response": { # If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If importing Variants, an ImportVariantsResponse is returned. For exports, an empty response is returned.
"a_key": "", # Properties of the object. Contains field @ype with type URL.
},
"error": { # The `Status` type defines a logical error model that is suitable for different programming environments, including REST APIs and RPC APIs. It is used by [gRPC](https://github.com/grpc). The error model is designed to be: - Simple to use and understand for most users - Flexible enough to meet unexpected needs # Overview The `Status` message contains three pieces of data: error code, error message, and error details. The error code should be an enum value of google.rpc.Code, but it may accept additional error codes if needed. The error message should be a developer-facing English message that helps developers *understand* and *resolve* the error. If a localized user-facing error message is needed, put the localized message in the error details or localize it in the client. The optional error details may contain arbitrary information about the error. There is a predefined set of error detail types in the package `google.rpc` which can be used for common error conditions. # Language mapping The `Status` message is the logical representation of the error model, but it is not necessarily the actual wire format. When the `Status` message is exposed in different client libraries and different wire protocols, it can be mapped differently. For example, it will likely be mapped to some exceptions in Java, but more likely mapped to some error codes in C. # Other uses The error model and the `Status` message can be used in a variety of environments, either with or without APIs, to provide a consistent developer experience across different environments. Example uses of this error model include: - Partial errors. If a service needs to return partial errors to the client, it may embed the `Status` in the normal response to indicate the partial errors. - Workflow errors. A typical workflow has multiple steps. Each step may have a `Status` message for error reporting purpose. - Batch operations. If a client uses batch request and batch response, the `Status` message should be used directly inside batch response, one for each error sub-response. - Asynchronous operations. If an API call embeds asynchronous operation results in its response, the status of those operations should be represented directly using the `Status` message. - Logging. If some API errors are stored in logs, the message `Status` could be used directly after any stripping needed for security/privacy reasons. # The error result of the operation in case of failure.
"message": "A String", # A developer-facing error message, which should be in English. Any user-facing error message should be localized and sent in the google.rpc.Status.details field, or localized by the client.
"code": 42, # The status code, which should be an enum value of google.rpc.Code.
"details": [ # A list of messages that carry the error details. There will be a common set of message types for APIs to use.
{
"a_key": "", # Properties of the object. Contains field @ype with type URL.
},
],
},
"done": True or False, # If the value is `false`, it means the operation is still in progress. If true, the operation is completed, and either `error` or `response` is available.
"name": "A String", # The server-assigned name, which is only unique within the same service that originally returns it. For example: `operations/CJHU7Oi_ChDrveSpBRjfuL-qzoWAgEw`
"metadata": { # An OperationMetadata object. This will always be returned with the Operation.
"a_key": "", # Properties of the object. Contains field @ype with type URL.
},
}</pre>
</div>
<div class="method">
<code class="details" id="get">get(variantSetId, x__xgafv=None)</code>
<pre>Gets a variant set by ID. For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Args:
variantSetId: string, Required. The ID of the variant set. (required)
x__xgafv: string, V1 error format.
Returns:
An object of the form:
{ # A variant set is a collection of call sets and variants. It contains summary statistics of those contents. A variant set belongs to a dataset. For more genomics resource definitions, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
"name": "A String", # User-specified, mutable name.
"description": "A String", # A textual description of this variant set.
"referenceBounds": [ # A list of all references used by the variants in a variant set with associated coordinate upper bounds for each one.
{ # ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
"upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any variant in the reference sequence.
"referenceName": "A String", # The name of the reference associated with this reference bound.
},
],
"referenceSetId": "A String", # The reference set to which the variant set is mapped. The reference set describes the alignment provenance of the variant set, while the `referenceBounds` describe the shape of the actual variant data. The reference set's reference names are a superset of those found in the `referenceBounds`. For example, given a variant set that is mapped to the GRCh38 reference set and contains a single variant on reference 'X', `referenceBounds` would contain only an entry for 'X', while the associated reference set enumerates all possible references: '1', '2', 'X', 'Y', 'MT', etc.
"id": "A String", # The server-generated variant set ID, unique across all variant sets.
"datasetId": "A String", # The dataset to which this variant set belongs.
"metadata": [ # The metadata associated with this variant set.
{ # 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.
"info": { # Remaining structured metadata key-value pairs. This must be of the form map (string key mapping to a list of string values).
"a_key": [
"",
],
},
"description": "A String", # A textual description of this metadata.
"number": "A String", # The number of values that can be included in a field described by this metadata.
"value": "A String", # The value field for simple metadata
"key": "A String", # The top-level key.
"type": "A String", # The type of data. Possible types include: Integer, Float, Flag, Character, and String.
"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.
},
],
}</pre>
</div>
<div class="method">
<code class="details" id="patch">patch(variantSetId, body, updateMask=None, x__xgafv=None)</code>
<pre>Updates a variant set using patch semantics. For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Args:
variantSetId: string, The ID of the variant to be updated (must already exist). (required)
body: object, The request body. (required)
The object takes the form of:
{ # A variant set is a collection of call sets and variants. It contains summary statistics of those contents. A variant set belongs to a dataset. For more genomics resource definitions, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
"name": "A String", # User-specified, mutable name.
"description": "A String", # A textual description of this variant set.
"referenceBounds": [ # A list of all references used by the variants in a variant set with associated coordinate upper bounds for each one.
{ # ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
"upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any variant in the reference sequence.
"referenceName": "A String", # The name of the reference associated with this reference bound.
},
],
"referenceSetId": "A String", # The reference set to which the variant set is mapped. The reference set describes the alignment provenance of the variant set, while the `referenceBounds` describe the shape of the actual variant data. The reference set's reference names are a superset of those found in the `referenceBounds`. For example, given a variant set that is mapped to the GRCh38 reference set and contains a single variant on reference 'X', `referenceBounds` would contain only an entry for 'X', while the associated reference set enumerates all possible references: '1', '2', 'X', 'Y', 'MT', etc.
"id": "A String", # The server-generated variant set ID, unique across all variant sets.
"datasetId": "A String", # The dataset to which this variant set belongs.
"metadata": [ # The metadata associated with this variant set.
{ # 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.
"info": { # Remaining structured metadata key-value pairs. This must be of the form map (string key mapping to a list of string values).
"a_key": [
"",
],
},
"description": "A String", # A textual description of this metadata.
"number": "A String", # The number of values that can be included in a field described by this metadata.
"value": "A String", # The value field for simple metadata
"key": "A String", # The top-level key.
"type": "A String", # The type of data. Possible types include: Integer, Float, Flag, Character, and String.
"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.
},
],
}
updateMask: string, An optional mask specifying which fields to update. Supported fields: * metadata. * name. * description. Leaving `updateMask` unset is equivalent to specifying all mutable fields.
x__xgafv: string, V1 error format.
Returns:
An object of the form:
{ # A variant set is a collection of call sets and variants. It contains summary statistics of those contents. A variant set belongs to a dataset. For more genomics resource definitions, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
"name": "A String", # User-specified, mutable name.
"description": "A String", # A textual description of this variant set.
"referenceBounds": [ # A list of all references used by the variants in a variant set with associated coordinate upper bounds for each one.
{ # ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
"upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any variant in the reference sequence.
"referenceName": "A String", # The name of the reference associated with this reference bound.
},
],
"referenceSetId": "A String", # The reference set to which the variant set is mapped. The reference set describes the alignment provenance of the variant set, while the `referenceBounds` describe the shape of the actual variant data. The reference set's reference names are a superset of those found in the `referenceBounds`. For example, given a variant set that is mapped to the GRCh38 reference set and contains a single variant on reference 'X', `referenceBounds` would contain only an entry for 'X', while the associated reference set enumerates all possible references: '1', '2', 'X', 'Y', 'MT', etc.
"id": "A String", # The server-generated variant set ID, unique across all variant sets.
"datasetId": "A String", # The dataset to which this variant set belongs.
"metadata": [ # The metadata associated with this variant set.
{ # 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.
"info": { # Remaining structured metadata key-value pairs. This must be of the form map (string key mapping to a list of string values).
"a_key": [
"",
],
},
"description": "A String", # A textual description of this metadata.
"number": "A String", # The number of values that can be included in a field described by this metadata.
"value": "A String", # The value field for simple metadata
"key": "A String", # The top-level key.
"type": "A String", # The type of data. Possible types include: Integer, Float, Flag, Character, and String.
"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.
},
],
}</pre>
</div>
<div class="method">
<code class="details" id="search">search(body, x__xgafv=None)</code>
<pre>Returns a list of all variant sets matching search criteria. For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) Implements [GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L49).
Args:
body: object, The request body. (required)
The object takes the form of:
{ # The search variant sets request.
"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.
"datasetIds": [ # Exactly one dataset ID must be provided here. Only variant sets which belong to this dataset will be returned.
"A String",
],
"pageSize": 42, # The maximum number of results to return in a single page. If unspecified, defaults to 1024.
}
x__xgafv: string, V1 error format.
Returns:
An object of the form:
{ # The search variant sets response.
"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.
"variantSets": [ # The variant sets belonging to the requested dataset.
{ # A variant set is a collection of call sets and variants. It contains summary statistics of those contents. A variant set belongs to a dataset. For more genomics resource definitions, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
"name": "A String", # User-specified, mutable name.
"description": "A String", # A textual description of this variant set.
"referenceBounds": [ # A list of all references used by the variants in a variant set with associated coordinate upper bounds for each one.
{ # ReferenceBound records an upper bound for the starting coordinate of variants in a particular reference.
"upperBound": "A String", # An upper bound (inclusive) on the starting coordinate of any variant in the reference sequence.
"referenceName": "A String", # The name of the reference associated with this reference bound.
},
],
"referenceSetId": "A String", # The reference set to which the variant set is mapped. The reference set describes the alignment provenance of the variant set, while the `referenceBounds` describe the shape of the actual variant data. The reference set's reference names are a superset of those found in the `referenceBounds`. For example, given a variant set that is mapped to the GRCh38 reference set and contains a single variant on reference 'X', `referenceBounds` would contain only an entry for 'X', while the associated reference set enumerates all possible references: '1', '2', 'X', 'Y', 'MT', etc.
"id": "A String", # The server-generated variant set ID, unique across all variant sets.
"datasetId": "A String", # The dataset to which this variant set belongs.
"metadata": [ # The metadata associated with this variant set.
{ # 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.
"info": { # Remaining structured metadata key-value pairs. This must be of the form map (string key mapping to a list of string values).
"a_key": [
"",
],
},
"description": "A String", # A textual description of this metadata.
"number": "A String", # The number of values that can be included in a field described by this metadata.
"value": "A String", # The value field for simple metadata
"key": "A String", # The top-level key.
"type": "A String", # The type of data. Possible types include: Integer, Float, Flag, Character, and String.
"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.
},
],
},
],
}</pre>
</div>
</body></html>