Creates a new variant set.
delete(variantSetId, x__xgafv=None)
Deletes a variant set including all variants, call sets, and calls within.
export(variantSetId, body, x__xgafv=None)
Exports variant set data to an external destination.
get(variantSetId, x__xgafv=None)
Gets a variant set by ID.
patch(variantSetId, body, updateMask=None, x__xgafv=None)
Updates a variant set using patch semantics.
Returns a list of all variant sets matching search criteria.
search_next(previous_request, previous_response)
Retrieves the next page of results.
create(body, x__xgafv=None)
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)
"description": "A String", # A textual description of this variant set.
"name": "A String", # User-specified, mutable name.
"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.
},
],
"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.
"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.
},
],
}
x__xgafv: string, V1 error format.
Allowed values
1 - v1 error format
2 - v2 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)
"description": "A String", # A textual description of this variant set.
"name": "A String", # User-specified, mutable name.
"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.
},
],
"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.
"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.
},
],
}
delete(variantSetId, x__xgafv=None)
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.
Allowed values
1 - v1 error format
2 - v2 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 `{}`.
}
export(variantSetId, body, x__xgafv=None)
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.
"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".
"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.
"callSetIds": [ # If provided, only variant call information from the specified call sets
# will be exported. By default all variant calls are exported.
"A String",
],
"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.
"format": "A String", # The format for the exported data.
}
x__xgafv: string, V1 error format.
Allowed values
1 - v1 error format
2 - v2 error format
Returns:
An object of the form:
{ # This resource represents a long-running operation that is the result of a
# network API call.
"metadata": { # An OperationMetadata object. This will always be returned with the Operation.
"a_key": "", # Properties of the object. Contains field @type with type URL.
},
"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.
# 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` that 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.
#
# - 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.
"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 @type 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.
"response": { # If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If importing Variants, an ImportVariantsResponse is returned. For pipelines and exports, an empty response is returned.
"a_key": "", # Properties of the object. Contains field @type with type URL.
},
"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`
}
get(variantSetId, x__xgafv=None)
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.
Allowed values
1 - v1 error format
2 - v2 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)
"description": "A String", # A textual description of this variant set.
"name": "A String", # User-specified, mutable name.
"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.
},
],
"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.
"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.
},
],
}
patch(variantSetId, body, updateMask=None, x__xgafv=None)
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)
"description": "A String", # A textual description of this variant set.
"name": "A String", # User-specified, mutable name.
"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.
},
],
"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.
"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.
},
],
}
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.
Allowed values
1 - v1 error format
2 - v2 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)
"description": "A String", # A textual description of this variant set.
"name": "A String", # User-specified, mutable name.
"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.
},
],
"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.
"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.
},
],
}
search(body, x__xgafv=None)
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.
Allowed values
1 - v1 error format
2 - v2 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)
"description": "A String", # A textual description of this variant set.
"name": "A String", # User-specified, mutable name.
"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.
},
],
"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.
"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.
},
],
},
],
}
search_next(previous_request, previous_response)
Retrieves the next page of results.
Args:
previous_request: The request for the previous page. (required)
previous_response: The response from the request for the previous page. (required)
Returns:
A request object that you can call 'execute()' on to request the next
page. Returns None if there are no more items in the collection.