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# Copyright 2015 Google Inc.
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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require 'date'
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require 'google/apis/core/base_service'
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require 'google/apis/core/json_representation'
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require 'google/apis/core/hashable'
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require 'google/apis/errors'
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module Google
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module Apis
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module GenomicsV1
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# The dataset list response.
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class ListDatasetsResponse
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include Google::Apis::Core::Hashable
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# The list of matching Datasets.
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# Corresponds to the JSON property `datasets`
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# @return [Array<Google::Apis::GenomicsV1::Dataset>]
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attr_accessor :datasets
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# The continuation token, which is used to page through large result sets.
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# Provide this value in a subsequent request to return the next page of results.
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# This field will be empty if there aren't any additional results.
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# Corresponds to the JSON property `nextPageToken`
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# @return [String]
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attr_accessor :next_page_token
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@datasets = args[:datasets] if args.key?(:datasets)
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@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
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end
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end
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2015-12-03 01:10:07 +00:00
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# A Dataset is a collection of genomic data. For more genomics resource
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# definitions, see [Fundamentals of Google Genomics](https://cloud.google.com/
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# genomics/fundamentals-of-google-genomics)
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class Dataset
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include Google::Apis::Core::Hashable
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# The server-generated dataset ID, unique across all datasets.
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# Corresponds to the JSON property `id`
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# @return [String]
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attr_accessor :id
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# The Google Developers Console project ID that this dataset belongs to.
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# Corresponds to the JSON property `projectId`
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# @return [String]
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attr_accessor :project_id
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# The dataset name.
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# Corresponds to the JSON property `name`
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# @return [String]
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attr_accessor :name
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# The time this dataset was created, in seconds from the epoch.
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# Corresponds to the JSON property `createTime`
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# @return [String]
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attr_accessor :create_time
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@id = args[:id] if args.key?(:id)
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@project_id = args[:project_id] if args.key?(:project_id)
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@name = args[:name] if args.key?(:name)
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@create_time = args[:create_time] if args.key?(:create_time)
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end
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end
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# A generic empty message that you can re-use to avoid defining duplicated empty
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# messages in your APIs. A typical example is to use it as the request or the
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# response type of an API method. For instance: service Foo ` rpc Bar(google.
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# protobuf.Empty) returns (google.protobuf.Empty); ` The JSON representation for
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# `Empty` is empty JSON object ````.
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class Empty
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include Google::Apis::Core::Hashable
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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end
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end
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#
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class UndeleteDatasetRequest
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include Google::Apis::Core::Hashable
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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end
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end
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# Request message for `SetIamPolicy` method.
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class SetIamPolicyRequest
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include Google::Apis::Core::Hashable
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# Defines an Identity and Access Management (IAM) policy. It is used to specify
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# access control policies for Cloud Platform resources. A `Policy` consists of a
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# list of `bindings`. A `Binding` binds a list of `members` to a `role`, where
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# the members can be user accounts, Google groups, Google domains, and service
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# accounts. A `role` is a named list of permissions defined by IAM. **Example** `
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# "bindings": [ ` "role": "roles/owner", "members": [ "user:mike@example.com", "
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# group:admins@example.com", "domain:google.com", "serviceAccount:my-other-app@
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# appspot.gserviceaccount.com"] `, ` "role": "roles/viewer", "members": ["user:
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# sean@example.com"] ` ] ` For a description of IAM and its features, see the [
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# IAM developer's guide](https://cloud.google.com/iam).
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# Corresponds to the JSON property `policy`
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# @return [Google::Apis::GenomicsV1::Policy]
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attr_accessor :policy
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@policy = args[:policy] if args.key?(:policy)
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end
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end
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# Defines an Identity and Access Management (IAM) policy. It is used to specify
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# access control policies for Cloud Platform resources. A `Policy` consists of a
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# list of `bindings`. A `Binding` binds a list of `members` to a `role`, where
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# the members can be user accounts, Google groups, Google domains, and service
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# accounts. A `role` is a named list of permissions defined by IAM. **Example** `
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# "bindings": [ ` "role": "roles/owner", "members": [ "user:mike@example.com", "
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# group:admins@example.com", "domain:google.com", "serviceAccount:my-other-app@
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# appspot.gserviceaccount.com"] `, ` "role": "roles/viewer", "members": ["user:
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# sean@example.com"] ` ] ` For a description of IAM and its features, see the [
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# IAM developer's guide](https://cloud.google.com/iam).
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class Policy
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include Google::Apis::Core::Hashable
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# Version of the `Policy`. The default version is 0.
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# Corresponds to the JSON property `version`
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# @return [Fixnum]
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attr_accessor :version
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# Associates a list of `members` to a `role`. Multiple `bindings` must not be
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# specified for the same `role`. `bindings` with no members will result in an
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# error.
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# Corresponds to the JSON property `bindings`
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# @return [Array<Google::Apis::GenomicsV1::Binding>]
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attr_accessor :bindings
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# `etag` is used for optimistic concurrency control as a way to help prevent
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# simultaneous updates of a policy from overwriting each other. It is strongly
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# suggested that systems make use of the `etag` in the read-modify-write cycle
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# to perform policy updates in order to avoid race conditions: An `etag` is
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# returned in the response to `getIamPolicy`, and systems are expected to put
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# that etag in the request to `setIamPolicy` to ensure that their change will be
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# applied to the same version of the policy. If no `etag` is provided in the
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# call to `setIamPolicy`, then the existing policy is overwritten blindly.
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# Corresponds to the JSON property `etag`
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# @return [String]
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attr_accessor :etag
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@version = args[:version] if args.key?(:version)
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@bindings = args[:bindings] if args.key?(:bindings)
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@etag = args[:etag] if args.key?(:etag)
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end
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end
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# Associates `members` with a `role`.
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class Binding
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include Google::Apis::Core::Hashable
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# Role that is assigned to `members`. For example, `roles/viewer`, `roles/editor`
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# , or `roles/owner`. Required
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# Corresponds to the JSON property `role`
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# @return [String]
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attr_accessor :role
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# Specifies the identities requesting access for a Cloud Platform resource. `
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# members` can have the following values: * `allUsers`: A special identifier
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# that represents anyone who is on the internet; with or without a Google
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# account. * `allAuthenticatedUsers`: A special identifier that represents
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# anyone who is authenticated with a Google account or a service account. * `
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# user:`emailid``: An email address that represents a specific Google account.
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# For example, `alice@gmail.com` or `joe@example.com`. * `serviceAccount:`
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# emailid``: An email address that represents a service account. For example, `
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# my-other-app@appspot.gserviceaccount.com`. * `group:`emailid``: An email
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# address that represents a Google group. For example, `admins@example.com`. * `
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# domain:`domain``: A Google Apps domain name that represents all the users of
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# that domain. For example, `google.com` or `example.com`.
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# Corresponds to the JSON property `members`
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# @return [Array<String>]
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attr_accessor :members
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@role = args[:role] if args.key?(:role)
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@members = args[:members] if args.key?(:members)
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end
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end
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# Request message for `GetIamPolicy` method.
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class GetIamPolicyRequest
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include Google::Apis::Core::Hashable
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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end
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end
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# Request message for `TestIamPermissions` method.
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class TestIamPermissionsRequest
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include Google::Apis::Core::Hashable
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# REQUIRED: The set of permissions to check for the 'resource'. Permissions with
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# wildcards (such as '*' or 'storage.*') are not allowed. Allowed permissions
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# are: * `genomics.datasets.create` * `genomics.datasets.delete` * `genomics.
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# datasets.get` * `genomics.datasets.list` * `genomics.datasets.update` * `
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# genomics.datasets.getIamPolicy` * `genomics.datasets.setIamPolicy`
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# Corresponds to the JSON property `permissions`
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# @return [Array<String>]
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attr_accessor :permissions
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@permissions = args[:permissions] if args.key?(:permissions)
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end
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end
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# Response message for `TestIamPermissions` method.
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class TestIamPermissionsResponse
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include Google::Apis::Core::Hashable
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# A subset of `TestPermissionsRequest.permissions` that the caller is allowed.
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# Corresponds to the JSON property `permissions`
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# @return [Array<String>]
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attr_accessor :permissions
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def initialize(**args)
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update!(**args)
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end
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# Update properties of this object
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def update!(**args)
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@permissions = args[:permissions] if args.key?(:permissions)
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end
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end
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# This resource represents a long-running operation that is the result of a
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# network API call.
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class Operation
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include Google::Apis::Core::Hashable
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# The server-assigned name, which is only unique within the same service that
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# originally returns it. For example: `operations/CJHU7Oi_ChDrveSpBRjfuL-
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# qzoWAgEw`
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# Corresponds to the JSON property `name`
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# @return [String]
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attr_accessor :name
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# An OperationMetadata object. This will always be returned with the Operation.
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# Corresponds to the JSON property `metadata`
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# @return [Hash<String,Object>]
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attr_accessor :metadata
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# If the value is `false`, it means the operation is still in progress. If true,
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# the operation is completed, and either `error` or `response` is available.
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# Corresponds to the JSON property `done`
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# @return [Boolean]
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attr_accessor :done
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alias_method :done?, :done
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# The `Status` type defines a logical error model that is suitable for different
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# programming environments, including REST APIs and RPC APIs. It is used by [
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# gRPC](https://github.com/grpc). The error model is designed to be: - Simple to
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# use and understand for most users - Flexible enough to meet unexpected needs #
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# Overview The `Status` message contains three pieces of data: error code, error
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# message, and error details. The error code should be an enum value of google.
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# rpc.Code, but it may accept additional error codes if needed. The error
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# message should be a developer-facing English message that helps developers *
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# understand* and *resolve* the error. If a localized user-facing error message
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# is needed, put the localized message in the error details or localize it in
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# the client. The optional error details may contain arbitrary information about
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# the error. There is a predefined set of error detail types in the package `
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# google.rpc` which can be used for common error conditions. # Language mapping
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# The `Status` message is the logical representation of the error model, but it
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# is not necessarily the actual wire format. When the `Status` message is
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# exposed in different client libraries and different wire protocols, it can be
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# mapped differently. For example, it will likely be mapped to some exceptions
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# in Java, but more likely mapped to some error codes in C. # Other uses The
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# 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.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `error`
|
|
|
|
# @return [Google::Apis::GenomicsV1::Status]
|
|
|
|
attr_accessor :error
|
|
|
|
|
2015-12-03 01:10:07 +00:00
|
|
|
# If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If
|
|
|
|
# importing Variants, an ImportVariantsResponse is returned. For exports, an
|
|
|
|
# empty response is returned.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `response`
|
|
|
|
# @return [Hash<String,Object>]
|
|
|
|
attr_accessor :response
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@name = args[:name] if args.key?(:name)
|
|
|
|
@metadata = args[:metadata] if args.key?(:metadata)
|
|
|
|
@done = args[:done] if args.key?(:done)
|
|
|
|
@error = args[:error] if args.key?(:error)
|
|
|
|
@response = args[:response] if args.key?(:response)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
2015-07-31 00:05:47 +00:00
|
|
|
# The `Status` type defines a logical error model that is suitable for different
|
2015-07-20 21:49:34 +00:00
|
|
|
# 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
|
2015-07-31 00:05:47 +00:00
|
|
|
# use and understand for most users - Flexible enough to meet unexpected needs #
|
|
|
|
# Overview The `Status` message contains three pieces of data: error code, error
|
2015-12-03 01:10:07 +00:00
|
|
|
# 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.
|
2015-07-20 21:49:34 +00:00
|
|
|
class Status
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
2015-12-03 01:10:07 +00:00
|
|
|
# The status code, which should be an enum value of google.rpc.Code.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `code`
|
|
|
|
# @return [Fixnum]
|
|
|
|
attr_accessor :code
|
|
|
|
|
|
|
|
# A developer-facing error message, which should be in English. Any user-facing
|
2015-12-03 01:10:07 +00:00
|
|
|
# error message should be localized and sent in the google.rpc.Status.details
|
|
|
|
# field, or localized by the client.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `message`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :message
|
|
|
|
|
|
|
|
# A list of messages that carry the error details. There will be a common set of
|
|
|
|
# message types for APIs to use.
|
|
|
|
# Corresponds to the JSON property `details`
|
|
|
|
# @return [Array<Hash<String,Object>>]
|
|
|
|
attr_accessor :details
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@code = args[:code] if args.key?(:code)
|
|
|
|
@message = args[:message] if args.key?(:message)
|
|
|
|
@details = args[:details] if args.key?(:details)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
2015-12-03 01:10:07 +00:00
|
|
|
# The response message for Operations.ListOperations.
|
2015-07-20 21:49:34 +00:00
|
|
|
class ListOperationsResponse
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# A list of operations that matches the specified filter in the request.
|
|
|
|
# Corresponds to the JSON property `operations`
|
|
|
|
# @return [Array<Google::Apis::GenomicsV1::Operation>]
|
|
|
|
attr_accessor :operations
|
|
|
|
|
|
|
|
# The standard List next-page token.
|
|
|
|
# Corresponds to the JSON property `nextPageToken`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :next_page_token
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@operations = args[:operations] if args.key?(:operations)
|
|
|
|
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
2015-12-03 01:10:07 +00:00
|
|
|
# The request message for Operations.CancelOperation.
|
2015-07-20 21:49:34 +00:00
|
|
|
class CancelOperationRequest
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# The read group set import request.
|
|
|
|
class ImportReadGroupSetsRequest
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# Required. The ID of the dataset these read group sets will belong to. The
|
|
|
|
# caller must have WRITE permissions to this dataset.
|
|
|
|
# Corresponds to the JSON property `datasetId`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :dataset_id
|
|
|
|
|
|
|
|
# The reference set to which the imported read group sets are aligned to, if any.
|
|
|
|
# The reference names of this reference set must be a superset of those found
|
|
|
|
# in the imported file headers. If no reference set id is provided, a best
|
|
|
|
# effort is made to associate with a matching reference set.
|
|
|
|
# Corresponds to the JSON property `referenceSetId`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :reference_set_id
|
|
|
|
|
2015-12-03 01:10:07 +00:00
|
|
|
# A list of URIs pointing at [BAM files](https://samtools.github.io/hts-specs/
|
|
|
|
# SAMv1.pdf) in Google Cloud Storage.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `sourceUris`
|
|
|
|
# @return [Array<String>]
|
|
|
|
attr_accessor :source_uris
|
|
|
|
|
|
|
|
# The partition strategy describes how read groups are partitioned into read
|
|
|
|
# group sets.
|
|
|
|
# Corresponds to the JSON property `partitionStrategy`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :partition_strategy
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@dataset_id = args[:dataset_id] if args.key?(:dataset_id)
|
|
|
|
@reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
|
|
|
|
@source_uris = args[:source_uris] if args.key?(:source_uris)
|
|
|
|
@partition_strategy = args[:partition_strategy] if args.key?(:partition_strategy)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# The read group set export request.
|
|
|
|
class ExportReadGroupSetRequest
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# Required. The Google Developers Console project ID that owns this export. The
|
|
|
|
# caller must have WRITE access to this project.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `projectId`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :project_id
|
|
|
|
|
|
|
|
# Required. A Google Cloud Storage URI for the exported BAM file. The currently
|
|
|
|
# authenticated user must have write access to the new file. An error will be
|
|
|
|
# returned if the URI already contains data.
|
|
|
|
# Corresponds to the JSON property `exportUri`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :export_uri
|
|
|
|
|
|
|
|
# The reference names to export. If this is not specified, all reference
|
|
|
|
# sequences, including unmapped reads, are exported. Use `*` to export only
|
|
|
|
# unmapped reads.
|
|
|
|
# Corresponds to the JSON property `referenceNames`
|
|
|
|
# @return [Array<String>]
|
|
|
|
attr_accessor :reference_names
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@project_id = args[:project_id] if args.key?(:project_id)
|
|
|
|
@export_uri = args[:export_uri] if args.key?(:export_uri)
|
|
|
|
@reference_names = args[:reference_names] if args.key?(:reference_names)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# The read group set search request.
|
|
|
|
class SearchReadGroupSetsRequest
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# Restricts this query to read group sets within the given datasets. At least
|
|
|
|
# one ID must be provided.
|
|
|
|
# Corresponds to the JSON property `datasetIds`
|
|
|
|
# @return [Array<String>]
|
|
|
|
attr_accessor :dataset_ids
|
|
|
|
|
|
|
|
# Only return read group sets for which a substring of the name matches this
|
|
|
|
# string.
|
|
|
|
# Corresponds to the JSON property `name`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :name
|
|
|
|
|
|
|
|
# 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.
|
|
|
|
# Corresponds to the JSON property `pageToken`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :page_token
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# The maximum number of results to return in a single page. If unspecified,
|
|
|
|
# defaults to 256. The maximum value is 1024.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `pageSize`
|
|
|
|
# @return [Fixnum]
|
|
|
|
attr_accessor :page_size
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@dataset_ids = args[:dataset_ids] if args.key?(:dataset_ids)
|
|
|
|
@name = args[:name] if args.key?(:name)
|
|
|
|
@page_token = args[:page_token] if args.key?(:page_token)
|
|
|
|
@page_size = args[:page_size] if args.key?(:page_size)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# The read group set search response.
|
|
|
|
class SearchReadGroupSetsResponse
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# The list of matching read group sets.
|
|
|
|
# Corresponds to the JSON property `readGroupSets`
|
|
|
|
# @return [Array<Google::Apis::GenomicsV1::ReadGroupSet>]
|
|
|
|
attr_accessor :read_group_sets
|
|
|
|
|
|
|
|
# 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.
|
|
|
|
# Corresponds to the JSON property `nextPageToken`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :next_page_token
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@read_group_sets = args[:read_group_sets] if args.key?(:read_group_sets)
|
|
|
|
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# A read group set is a logical collection of read groups, which are collections
|
|
|
|
# of reads produced by a sequencer. A read group set typically models reads
|
|
|
|
# corresponding to one sample, sequenced one way, and aligned one way. * A read
|
|
|
|
# group set belongs to one dataset. * A read group belongs to one read group set.
|
2015-12-03 01:10:07 +00:00
|
|
|
# * A read belongs to one read group. For more genomics resource definitions,
|
|
|
|
# see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/
|
|
|
|
# fundamentals-of-google-genomics)
|
2015-07-20 21:49:34 +00:00
|
|
|
class ReadGroupSet
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# The server-generated read group set ID, unique for all read group sets.
|
|
|
|
# Corresponds to the JSON property `id`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :id
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# The dataset to which this read group set belongs.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `datasetId`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :dataset_id
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# The reference set to which the reads in this read group set are aligned.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `referenceSetId`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :reference_set_id
|
|
|
|
|
|
|
|
# The read group set name. By default this will be initialized to the sample
|
|
|
|
# name of the sequenced data contained in this set.
|
|
|
|
# Corresponds to the JSON property `name`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :name
|
|
|
|
|
|
|
|
# The filename of the original source file for this read group set, if any.
|
|
|
|
# Corresponds to the JSON property `filename`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :filename
|
|
|
|
|
|
|
|
# The read groups in this set. There are typically 1-10 read groups in a read
|
|
|
|
# group set.
|
|
|
|
# Corresponds to the JSON property `readGroups`
|
|
|
|
# @return [Array<Google::Apis::GenomicsV1::ReadGroup>]
|
|
|
|
attr_accessor :read_groups
|
|
|
|
|
|
|
|
# A map of additional read group set information.
|
|
|
|
# Corresponds to the JSON property `info`
|
|
|
|
# @return [Hash<String,Array<Object>>]
|
|
|
|
attr_accessor :info
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@id = args[:id] if args.key?(:id)
|
|
|
|
@dataset_id = args[:dataset_id] if args.key?(:dataset_id)
|
|
|
|
@reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
|
|
|
|
@name = args[:name] if args.key?(:name)
|
|
|
|
@filename = args[:filename] if args.key?(:filename)
|
|
|
|
@read_groups = args[:read_groups] if args.key?(:read_groups)
|
|
|
|
@info = args[:info] if args.key?(:info)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# A read group is all the data that's processed the same way by the sequencer.
|
|
|
|
class ReadGroup
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# The server-generated read group ID, unique for all read groups. Note: This is
|
2015-12-14 22:27:57 +00:00
|
|
|
# different than the @RG ID field in the SAM spec. For that value, see name.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `id`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :id
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# The dataset to which this read group belongs.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `datasetId`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :dataset_id
|
|
|
|
|
|
|
|
# The read group name. This corresponds to the @RG ID field in the SAM spec.
|
|
|
|
# Corresponds to the JSON property `name`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :name
|
|
|
|
|
|
|
|
# A free-form text description of this read group.
|
|
|
|
# Corresponds to the JSON property `description`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :description
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# A client-supplied sample identifier for the reads in this read group.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `sampleId`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :sample_id
|
|
|
|
|
|
|
|
# The experiment used to generate this read group.
|
|
|
|
# Corresponds to the JSON property `experiment`
|
|
|
|
# @return [Google::Apis::GenomicsV1::Experiment]
|
|
|
|
attr_accessor :experiment
|
|
|
|
|
|
|
|
# The predicted insert size of this read group. The insert size is the length
|
|
|
|
# the sequenced DNA fragment from end-to-end, not including the adapters.
|
|
|
|
# Corresponds to the JSON property `predictedInsertSize`
|
|
|
|
# @return [Fixnum]
|
|
|
|
attr_accessor :predicted_insert_size
|
|
|
|
|
|
|
|
# The programs used to generate this read group. Programs are always identical
|
|
|
|
# for all read groups within a read group set. For this reason, only the first
|
|
|
|
# read group in a returned set will have this field populated.
|
|
|
|
# Corresponds to the JSON property `programs`
|
|
|
|
# @return [Array<Google::Apis::GenomicsV1::Program>]
|
|
|
|
attr_accessor :programs
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# The reference set the reads in this read group are aligned to.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `referenceSetId`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :reference_set_id
|
|
|
|
|
|
|
|
# A map of additional read group information. This must be of the form map (
|
|
|
|
# string key mapping to a list of string values).
|
|
|
|
# Corresponds to the JSON property `info`
|
|
|
|
# @return [Hash<String,Array<Object>>]
|
|
|
|
attr_accessor :info
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@id = args[:id] if args.key?(:id)
|
|
|
|
@dataset_id = args[:dataset_id] if args.key?(:dataset_id)
|
|
|
|
@name = args[:name] if args.key?(:name)
|
|
|
|
@description = args[:description] if args.key?(:description)
|
|
|
|
@sample_id = args[:sample_id] if args.key?(:sample_id)
|
|
|
|
@experiment = args[:experiment] if args.key?(:experiment)
|
|
|
|
@predicted_insert_size = args[:predicted_insert_size] if args.key?(:predicted_insert_size)
|
|
|
|
@programs = args[:programs] if args.key?(:programs)
|
|
|
|
@reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
|
|
|
|
@info = args[:info] if args.key?(:info)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
#
|
|
|
|
class Experiment
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# A client-supplied library identifier; a library is a collection of DNA
|
|
|
|
# fragments which have been prepared for sequencing from a sample. This field is
|
|
|
|
# important for quality control as error or bias can be introduced during sample
|
|
|
|
# preparation.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `libraryId`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :library_id
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# The platform unit used as part of this experiment, for example flowcell-
|
|
|
|
# barcode.lane for Illumina or slide for SOLiD. Corresponds to the @RG PU field
|
|
|
|
# in the SAM spec.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `platformUnit`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :platform_unit
|
|
|
|
|
|
|
|
# The sequencing center used as part of this experiment.
|
|
|
|
# Corresponds to the JSON property `sequencingCenter`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :sequencing_center
|
|
|
|
|
|
|
|
# The instrument model used as part of this experiment. This maps to sequencing
|
2015-12-14 22:27:57 +00:00
|
|
|
# technology in the SAM spec.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `instrumentModel`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :instrument_model
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@library_id = args[:library_id] if args.key?(:library_id)
|
|
|
|
@platform_unit = args[:platform_unit] if args.key?(:platform_unit)
|
|
|
|
@sequencing_center = args[:sequencing_center] if args.key?(:sequencing_center)
|
|
|
|
@instrument_model = args[:instrument_model] if args.key?(:instrument_model)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
#
|
|
|
|
class Program
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# The command line used to run this program.
|
|
|
|
# Corresponds to the JSON property `commandLine`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :command_line
|
|
|
|
|
|
|
|
# The user specified locally unique ID of the program. Used along with `
|
|
|
|
# prevProgramId` to define an ordering between programs.
|
|
|
|
# Corresponds to the JSON property `id`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :id
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# The display name of the program. This is typically the colloquial name of the
|
|
|
|
# tool used, for example 'bwa' or 'picard'.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `name`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :name
|
|
|
|
|
|
|
|
# The ID of the program run before this one.
|
|
|
|
# Corresponds to the JSON property `prevProgramId`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :prev_program_id
|
|
|
|
|
|
|
|
# The version of the program run.
|
|
|
|
# Corresponds to the JSON property `version`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :version
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@command_line = args[:command_line] if args.key?(:command_line)
|
|
|
|
@id = args[:id] if args.key?(:id)
|
|
|
|
@name = args[:name] if args.key?(:name)
|
|
|
|
@prev_program_id = args[:prev_program_id] if args.key?(:prev_program_id)
|
|
|
|
@version = args[:version] if args.key?(:version)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
#
|
|
|
|
class ListCoverageBucketsResponse
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# The length of each coverage bucket in base pairs. Note that buckets at the end
|
|
|
|
# of a reference sequence may be shorter. This value is omitted if the bucket
|
|
|
|
# width is infinity (the default behaviour, with no range or `targetBucketWidth`)
|
|
|
|
# .
|
|
|
|
# Corresponds to the JSON property `bucketWidth`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :bucket_width
|
|
|
|
|
|
|
|
# The coverage buckets. The list of buckets is sparse; a bucket with 0
|
|
|
|
# overlapping reads is not returned. A bucket never crosses more than one
|
|
|
|
# reference sequence. Each bucket has width `bucketWidth`, unless its end is the
|
|
|
|
# end of the reference sequence.
|
|
|
|
# Corresponds to the JSON property `coverageBuckets`
|
|
|
|
# @return [Array<Google::Apis::GenomicsV1::CoverageBucket>]
|
|
|
|
attr_accessor :coverage_buckets
|
|
|
|
|
|
|
|
# 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.
|
|
|
|
# Corresponds to the JSON property `nextPageToken`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :next_page_token
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@bucket_width = args[:bucket_width] if args.key?(:bucket_width)
|
|
|
|
@coverage_buckets = args[:coverage_buckets] if args.key?(:coverage_buckets)
|
|
|
|
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# A bucket over which read coverage has been precomputed. A bucket corresponds
|
|
|
|
# to a specific range of the reference sequence.
|
|
|
|
class CoverageBucket
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# A 0-based half-open genomic coordinate range for search requests.
|
|
|
|
# Corresponds to the JSON property `range`
|
|
|
|
# @return [Google::Apis::GenomicsV1::Range]
|
|
|
|
attr_accessor :range
|
|
|
|
|
|
|
|
# The average number of reads which are aligned to each individual reference
|
|
|
|
# base in this bucket.
|
|
|
|
# Corresponds to the JSON property `meanCoverage`
|
|
|
|
# @return [Float]
|
|
|
|
attr_accessor :mean_coverage
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@range = args[:range] if args.key?(:range)
|
|
|
|
@mean_coverage = args[:mean_coverage] if args.key?(:mean_coverage)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# A 0-based half-open genomic coordinate range for search requests.
|
|
|
|
class Range
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# The reference sequence name, for example `chr1`, `1`, or `chrX`.
|
|
|
|
# Corresponds to the JSON property `referenceName`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :reference_name
|
|
|
|
|
|
|
|
# The start position of the range on the reference, 0-based inclusive.
|
|
|
|
# Corresponds to the JSON property `start`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :start
|
|
|
|
|
|
|
|
# The end position of the range on the reference, 0-based exclusive.
|
|
|
|
# Corresponds to the JSON property `end`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :end
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
|
|
|
@start = args[:start] if args.key?(:start)
|
|
|
|
@end = args[:end] if args.key?(:end)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# The read search request.
|
|
|
|
class SearchReadsRequest
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# The IDs of the read groups sets within which to search for reads. All
|
|
|
|
# specified read group sets must be aligned against a common set of reference
|
|
|
|
# sequences; this defines the genomic coordinates for the query. Must specify
|
|
|
|
# one of `readGroupSetIds` or `readGroupIds`.
|
|
|
|
# Corresponds to the JSON property `readGroupSetIds`
|
|
|
|
# @return [Array<String>]
|
|
|
|
attr_accessor :read_group_set_ids
|
|
|
|
|
|
|
|
# The IDs of the read groups within which to search for reads. All specified
|
|
|
|
# read groups must belong to the same read group sets. Must specify one of `
|
|
|
|
# readGroupSetIds` or `readGroupIds`.
|
|
|
|
# Corresponds to the JSON property `readGroupIds`
|
|
|
|
# @return [Array<String>]
|
|
|
|
attr_accessor :read_group_ids
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# The reference sequence name, for example `chr1`, `1`, or `chrX`. If set to `*`,
|
|
|
|
# only unmapped reads are returned. If unspecified, all reads (mapped and
|
|
|
|
# unmapped) are returned.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `referenceName`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :reference_name
|
|
|
|
|
|
|
|
# The start position of the range on the reference, 0-based inclusive. If
|
|
|
|
# specified, `referenceName` must also be specified.
|
|
|
|
# Corresponds to the JSON property `start`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :start
|
|
|
|
|
|
|
|
# The end position of the range on the reference, 0-based exclusive. If
|
|
|
|
# specified, `referenceName` must also be specified.
|
|
|
|
# Corresponds to the JSON property `end`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :end
|
|
|
|
|
|
|
|
# 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.
|
|
|
|
# Corresponds to the JSON property `pageToken`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :page_token
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# The maximum number of results to return in a single page. If unspecified,
|
|
|
|
# defaults to 256. The maximum value is 2048.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `pageSize`
|
|
|
|
# @return [Fixnum]
|
|
|
|
attr_accessor :page_size
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@read_group_set_ids = args[:read_group_set_ids] if args.key?(:read_group_set_ids)
|
|
|
|
@read_group_ids = args[:read_group_ids] if args.key?(:read_group_ids)
|
|
|
|
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
|
|
|
@start = args[:start] if args.key?(:start)
|
|
|
|
@end = args[:end] if args.key?(:end)
|
|
|
|
@page_token = args[:page_token] if args.key?(:page_token)
|
|
|
|
@page_size = args[:page_size] if args.key?(:page_size)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# The read search response.
|
|
|
|
class SearchReadsResponse
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# The list of matching alignments sorted by mapped genomic coordinate, if any,
|
|
|
|
# ascending in position within the same reference. Unmapped reads, which have no
|
2015-12-03 01:10:07 +00:00
|
|
|
# position, are returned contiguously and are sorted in ascending lexicographic
|
2015-07-20 21:49:34 +00:00
|
|
|
# order by fragment name.
|
|
|
|
# Corresponds to the JSON property `alignments`
|
|
|
|
# @return [Array<Google::Apis::GenomicsV1::Read>]
|
|
|
|
attr_accessor :alignments
|
|
|
|
|
|
|
|
# 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.
|
|
|
|
# Corresponds to the JSON property `nextPageToken`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :next_page_token
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@alignments = args[:alignments] if args.key?(:alignments)
|
|
|
|
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
2015-12-03 01:10:07 +00:00
|
|
|
# A read alignment describes a linear alignment of a string of DNA to a
|
|
|
|
# reference sequence, in addition to metadata about the fragment (the molecule
|
|
|
|
# of DNA sequenced) and the read (the bases which were read by the sequencer). A
|
|
|
|
# read is equivalent to a line in a SAM file. A read belongs to exactly one read
|
|
|
|
# group and exactly one read group set. For more genomics resource definitions,
|
|
|
|
# see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/
|
2015-12-14 22:27:57 +00:00
|
|
|
# fundamentals-of-google-genomics) ### Reverse-stranded reads Mapped reads (
|
|
|
|
# reads having a non-null `alignment`) can be aligned to either the forward or
|
|
|
|
# the reverse strand of their associated reference. Strandedness of a mapped
|
|
|
|
# read is encoded by `alignment.position.reverseStrand`. If we consider the
|
|
|
|
# reference to be a forward-stranded coordinate space of `[0, reference.length)`
|
|
|
|
# with `0` as the left-most position and `reference.length` as the right-most
|
|
|
|
# position, reads are always aligned left to right. That is, `alignment.position.
|
|
|
|
# position` always refers to the left-most reference coordinate and `alignment.
|
|
|
|
# cigar` describes the alignment of this read to the reference from left to
|
|
|
|
# right. All per-base fields such as `alignedSequence` and `alignedQuality`
|
|
|
|
# share this same left-to-right orientation; this is true of reads which are
|
|
|
|
# aligned to either strand. For reverse-stranded reads, this means that `
|
|
|
|
# alignedSequence` is the reverse complement of the bases that were originally
|
|
|
|
# reported by the sequencing machine. ### Generating a reference-aligned
|
|
|
|
# sequence string When interacting with mapped reads, it's often useful to
|
|
|
|
# produce a string representing the local alignment of the read to reference.
|
|
|
|
# The following pseudocode demonstrates one way of doing this: out = "" offset =
|
|
|
|
# 0 for c in read.alignment.cigar ` switch c.operation ` case "ALIGNMENT_MATCH",
|
|
|
|
# "SEQUENCE_MATCH", "SEQUENCE_MISMATCH": out += read.alignedSequence[offset:
|
2015-07-20 21:49:34 +00:00
|
|
|
# offset+c.operationLength] offset += c.operationLength break case "CLIP_SOFT", "
|
|
|
|
# INSERT": offset += c.operationLength break case "PAD": out += repeat("*", c.
|
|
|
|
# operationLength) break case "DELETE": out += repeat("-", c.operationLength)
|
|
|
|
# break case "SKIP": out += repeat(" ", c.operationLength) break case "CLIP_HARD"
|
|
|
|
# : break ` ` return out ### Converting to SAM's CIGAR string The following
|
|
|
|
# pseudocode generates a SAM CIGAR string from the `cigar` field. Note that this
|
|
|
|
# is a lossy conversion (`cigar.referenceSequence` is lost). cigarMap = ` "
|
|
|
|
# ALIGNMENT_MATCH": "M", "INSERT": "I", "DELETE": "D", "SKIP": "N", "CLIP_SOFT":
|
|
|
|
# "S", "CLIP_HARD": "H", "PAD": "P", "SEQUENCE_MATCH": "=", "SEQUENCE_MISMATCH":
|
|
|
|
# "X", ` cigarStr = "" for c in read.alignment.cigar ` cigarStr += c.
|
|
|
|
# operationLength + cigarMap[c.operation] ` return cigarStr
|
|
|
|
class Read
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# The server-generated read ID, unique across all reads. This is different from
|
|
|
|
# the `fragmentName`.
|
|
|
|
# Corresponds to the JSON property `id`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :id
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# The ID of the read group this read belongs to. A read belongs to exactly one
|
|
|
|
# read group. This is a server-generated ID which is distinct from SAM's RG tag (
|
|
|
|
# for that value, see ReadGroup.name).
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `readGroupId`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :read_group_id
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# The ID of the read group set this read belongs to. A read belongs to exactly
|
|
|
|
# one read group set.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `readGroupSetId`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :read_group_set_id
|
|
|
|
|
|
|
|
# The fragment name. Equivalent to QNAME (query template name) in SAM.
|
|
|
|
# Corresponds to the JSON property `fragmentName`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :fragment_name
|
|
|
|
|
|
|
|
# The orientation and the distance between reads from the fragment are
|
2015-12-14 22:27:57 +00:00
|
|
|
# consistent with the sequencing protocol (SAM flag 0x2).
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `properPlacement`
|
|
|
|
# @return [Boolean]
|
|
|
|
attr_accessor :proper_placement
|
|
|
|
alias_method :proper_placement?, :proper_placement
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# The fragment is a PCR or optical duplicate (SAM flag 0x400).
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `duplicateFragment`
|
|
|
|
# @return [Boolean]
|
|
|
|
attr_accessor :duplicate_fragment
|
|
|
|
alias_method :duplicate_fragment?, :duplicate_fragment
|
|
|
|
|
|
|
|
# The observed length of the fragment, equivalent to TLEN in SAM.
|
|
|
|
# Corresponds to the JSON property `fragmentLength`
|
|
|
|
# @return [Fixnum]
|
|
|
|
attr_accessor :fragment_length
|
|
|
|
|
|
|
|
# The read number in sequencing. 0-based and less than numberReads. This field
|
|
|
|
# replaces SAM flag 0x40 and 0x80.
|
|
|
|
# Corresponds to the JSON property `readNumber`
|
|
|
|
# @return [Fixnum]
|
|
|
|
attr_accessor :read_number
|
|
|
|
|
|
|
|
# The number of reads in the fragment (extension to SAM flag 0x1).
|
|
|
|
# Corresponds to the JSON property `numberReads`
|
|
|
|
# @return [Fixnum]
|
|
|
|
attr_accessor :number_reads
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# Whether this read did not pass filters, such as platform or vendor quality
|
|
|
|
# controls (SAM flag 0x200).
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `failedVendorQualityChecks`
|
|
|
|
# @return [Boolean]
|
|
|
|
attr_accessor :failed_vendor_quality_checks
|
|
|
|
alias_method :failed_vendor_quality_checks?, :failed_vendor_quality_checks
|
|
|
|
|
|
|
|
# A linear alignment can be represented by one CIGAR string. Describes the
|
|
|
|
# mapped position and local alignment of the read to the reference.
|
|
|
|
# Corresponds to the JSON property `alignment`
|
|
|
|
# @return [Google::Apis::GenomicsV1::LinearAlignment]
|
|
|
|
attr_accessor :alignment
|
|
|
|
|
|
|
|
# Whether this alignment is secondary. Equivalent to SAM flag 0x100. A secondary
|
|
|
|
# alignment represents an alternative to the primary alignment for this read.
|
|
|
|
# Aligners may return secondary alignments if a read can map ambiguously to
|
|
|
|
# multiple coordinates in the genome. By convention, each read has one and only
|
|
|
|
# one alignment where both `secondaryAlignment` and `supplementaryAlignment` are
|
|
|
|
# false.
|
|
|
|
# Corresponds to the JSON property `secondaryAlignment`
|
|
|
|
# @return [Boolean]
|
|
|
|
attr_accessor :secondary_alignment
|
|
|
|
alias_method :secondary_alignment?, :secondary_alignment
|
|
|
|
|
|
|
|
# Whether this alignment is supplementary. Equivalent to SAM flag 0x800.
|
|
|
|
# Supplementary alignments are used in the representation of a chimeric
|
|
|
|
# alignment. In a chimeric alignment, a read is split into multiple linear
|
|
|
|
# alignments that map to different reference contigs. The first linear alignment
|
|
|
|
# in the read will be designated as the representative alignment; the remaining
|
|
|
|
# linear alignments will be designated as supplementary alignments. These
|
|
|
|
# alignments may have different mapping quality scores. In each linear alignment
|
|
|
|
# in a chimeric alignment, the read will be hard clipped. The `alignedSequence`
|
|
|
|
# and `alignedQuality` fields in the alignment record will only represent the
|
|
|
|
# bases for its respective linear alignment.
|
|
|
|
# Corresponds to the JSON property `supplementaryAlignment`
|
|
|
|
# @return [Boolean]
|
|
|
|
attr_accessor :supplementary_alignment
|
|
|
|
alias_method :supplementary_alignment?, :supplementary_alignment
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# The bases of the read sequence contained in this alignment record, **without
|
|
|
|
# CIGAR operations applied** (equivalent to SEQ in SAM). `alignedSequence` and `
|
|
|
|
# alignedQuality` may be shorter than the full read sequence and quality. This
|
|
|
|
# will occur if the alignment is part of a chimeric alignment, or if the read
|
|
|
|
# was trimmed. When this occurs, the CIGAR for this read will begin/end with a
|
|
|
|
# hard clip operator that will indicate the length of the excised sequence.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `alignedSequence`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :aligned_sequence
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# The quality of the read sequence contained in this alignment record (
|
|
|
|
# equivalent to QUAL in SAM). `alignedSequence` and `alignedQuality` may be
|
|
|
|
# shorter than the full read sequence and quality. This will occur if the
|
|
|
|
# alignment is part of a chimeric alignment, or if the read was trimmed. When
|
|
|
|
# this occurs, the CIGAR for this read will begin/end with a hard clip operator
|
|
|
|
# that will indicate the length of the excised sequence.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `alignedQuality`
|
|
|
|
# @return [Array<Fixnum>]
|
|
|
|
attr_accessor :aligned_quality
|
|
|
|
|
|
|
|
# An abstraction for referring to a genomic position, in relation to some
|
|
|
|
# already known reference. For now, represents a genomic position as a reference
|
|
|
|
# name, a base number on that reference (0-based), and a determination of
|
|
|
|
# forward or reverse strand.
|
|
|
|
# Corresponds to the JSON property `nextMatePosition`
|
|
|
|
# @return [Google::Apis::GenomicsV1::Position]
|
|
|
|
attr_accessor :next_mate_position
|
|
|
|
|
|
|
|
# A map of additional read alignment information. This must be of the form map (
|
|
|
|
# string key mapping to a list of string values).
|
|
|
|
# Corresponds to the JSON property `info`
|
|
|
|
# @return [Hash<String,Array<Object>>]
|
|
|
|
attr_accessor :info
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@id = args[:id] if args.key?(:id)
|
|
|
|
@read_group_id = args[:read_group_id] if args.key?(:read_group_id)
|
|
|
|
@read_group_set_id = args[:read_group_set_id] if args.key?(:read_group_set_id)
|
|
|
|
@fragment_name = args[:fragment_name] if args.key?(:fragment_name)
|
|
|
|
@proper_placement = args[:proper_placement] if args.key?(:proper_placement)
|
|
|
|
@duplicate_fragment = args[:duplicate_fragment] if args.key?(:duplicate_fragment)
|
|
|
|
@fragment_length = args[:fragment_length] if args.key?(:fragment_length)
|
|
|
|
@read_number = args[:read_number] if args.key?(:read_number)
|
|
|
|
@number_reads = args[:number_reads] if args.key?(:number_reads)
|
|
|
|
@failed_vendor_quality_checks = args[:failed_vendor_quality_checks] if args.key?(:failed_vendor_quality_checks)
|
|
|
|
@alignment = args[:alignment] if args.key?(:alignment)
|
|
|
|
@secondary_alignment = args[:secondary_alignment] if args.key?(:secondary_alignment)
|
|
|
|
@supplementary_alignment = args[:supplementary_alignment] if args.key?(:supplementary_alignment)
|
|
|
|
@aligned_sequence = args[:aligned_sequence] if args.key?(:aligned_sequence)
|
|
|
|
@aligned_quality = args[:aligned_quality] if args.key?(:aligned_quality)
|
|
|
|
@next_mate_position = args[:next_mate_position] if args.key?(:next_mate_position)
|
|
|
|
@info = args[:info] if args.key?(:info)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# A linear alignment can be represented by one CIGAR string. Describes the
|
|
|
|
# mapped position and local alignment of the read to the reference.
|
|
|
|
class LinearAlignment
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# An abstraction for referring to a genomic position, in relation to some
|
|
|
|
# already known reference. For now, represents a genomic position as a reference
|
|
|
|
# name, a base number on that reference (0-based), and a determination of
|
|
|
|
# forward or reverse strand.
|
|
|
|
# Corresponds to the JSON property `position`
|
|
|
|
# @return [Google::Apis::GenomicsV1::Position]
|
|
|
|
attr_accessor :position
|
|
|
|
|
|
|
|
# The mapping quality of this alignment. Represents how likely the read maps to
|
2015-12-14 22:27:57 +00:00
|
|
|
# this position as opposed to other locations. Specifically, this is -10 log10
|
|
|
|
# Pr(mapping position is wrong), rounded to the nearest integer.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `mappingQuality`
|
|
|
|
# @return [Fixnum]
|
|
|
|
attr_accessor :mapping_quality
|
|
|
|
|
|
|
|
# Represents the local alignment of this sequence (alignment matches, indels,
|
|
|
|
# etc) against the reference.
|
|
|
|
# Corresponds to the JSON property `cigar`
|
|
|
|
# @return [Array<Google::Apis::GenomicsV1::CigarUnit>]
|
|
|
|
attr_accessor :cigar
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@position = args[:position] if args.key?(:position)
|
|
|
|
@mapping_quality = args[:mapping_quality] if args.key?(:mapping_quality)
|
|
|
|
@cigar = args[:cigar] if args.key?(:cigar)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# An abstraction for referring to a genomic position, in relation to some
|
|
|
|
# already known reference. For now, represents a genomic position as a reference
|
|
|
|
# name, a base number on that reference (0-based), and a determination of
|
|
|
|
# forward or reverse strand.
|
|
|
|
class Position
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# The name of the reference in whatever reference set is being used.
|
|
|
|
# Corresponds to the JSON property `referenceName`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :reference_name
|
|
|
|
|
|
|
|
# The 0-based offset from the start of the forward strand for that reference.
|
|
|
|
# Corresponds to the JSON property `position`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :position
|
|
|
|
|
|
|
|
# Whether this position is on the reverse strand, as opposed to the forward
|
|
|
|
# strand.
|
|
|
|
# Corresponds to the JSON property `reverseStrand`
|
|
|
|
# @return [Boolean]
|
|
|
|
attr_accessor :reverse_strand
|
|
|
|
alias_method :reverse_strand?, :reverse_strand
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
|
|
|
@position = args[:position] if args.key?(:position)
|
|
|
|
@reverse_strand = args[:reverse_strand] if args.key?(:reverse_strand)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# A single CIGAR operation.
|
|
|
|
class CigarUnit
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
#
|
|
|
|
# Corresponds to the JSON property `operation`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :operation
|
|
|
|
|
|
|
|
# The number of genomic bases that the operation runs for. Required.
|
|
|
|
# Corresponds to the JSON property `operationLength`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :operation_length
|
|
|
|
|
|
|
|
# `referenceSequence` is only used at mismatches (`SEQUENCE_MISMATCH`) and
|
|
|
|
# deletions (`DELETE`). Filling this field replaces SAM's MD tag. If the
|
|
|
|
# relevant information is not available, this field is unset.
|
|
|
|
# Corresponds to the JSON property `referenceSequence`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :reference_sequence
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@operation = args[:operation] if args.key?(:operation)
|
|
|
|
@operation_length = args[:operation_length] if args.key?(:operation_length)
|
|
|
|
@reference_sequence = args[:reference_sequence] if args.key?(:reference_sequence)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# The stream reads request.
|
|
|
|
class StreamReadsRequest
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# The Google Developers Console project ID or number which will be billed for
|
|
|
|
# this access. The caller must have WRITE access to this project. Required.
|
|
|
|
# Corresponds to the JSON property `projectId`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :project_id
|
|
|
|
|
|
|
|
# The ID of the read group set from which to stream reads.
|
|
|
|
# Corresponds to the JSON property `readGroupSetId`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :read_group_set_id
|
|
|
|
|
|
|
|
# The reference sequence name, for example `chr1`, `1`, or `chrX`. If set to *,
|
|
|
|
# only unmapped reads are returned.
|
|
|
|
# Corresponds to the JSON property `referenceName`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :reference_name
|
|
|
|
|
|
|
|
# The start position of the range on the reference, 0-based inclusive. If
|
|
|
|
# specified, `referenceName` must also be specified.
|
|
|
|
# Corresponds to the JSON property `start`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :start
|
|
|
|
|
|
|
|
# The end position of the range on the reference, 0-based exclusive. If
|
|
|
|
# specified, `referenceName` must also be specified.
|
|
|
|
# Corresponds to the JSON property `end`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :end
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@project_id = args[:project_id] if args.key?(:project_id)
|
|
|
|
@read_group_set_id = args[:read_group_set_id] if args.key?(:read_group_set_id)
|
|
|
|
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
|
|
|
@start = args[:start] if args.key?(:start)
|
|
|
|
@end = args[:end] if args.key?(:end)
|
2015-12-14 22:27:57 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
#
|
|
|
|
class StreamReadsResponse
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
#
|
|
|
|
# Corresponds to the JSON property `alignments`
|
|
|
|
# @return [Array<Google::Apis::GenomicsV1::Read>]
|
|
|
|
attr_accessor :alignments
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@alignments = args[:alignments] if args.key?(:alignments)
|
2015-12-14 22:27:57 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
2015-07-20 21:49:34 +00:00
|
|
|
#
|
|
|
|
class SearchReferenceSetsRequest
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# If present, return reference sets for which the md5checksum matches exactly.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `md5checksums`
|
|
|
|
# @return [Array<String>]
|
|
|
|
attr_accessor :md5checksums
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# If present, return reference sets for which a prefix of any of
|
|
|
|
# sourceAccessions match any of these strings. Accession numbers typically have
|
|
|
|
# a main number and a version, for example `NC_000001.11`.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `accessions`
|
|
|
|
# @return [Array<String>]
|
|
|
|
attr_accessor :accessions
|
|
|
|
|
|
|
|
# If present, return reference sets for which a substring of their `assemblyId`
|
|
|
|
# matches this string (case insensitive).
|
|
|
|
# Corresponds to the JSON property `assemblyId`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :assembly_id
|
|
|
|
|
|
|
|
# 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.
|
|
|
|
# Corresponds to the JSON property `pageToken`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :page_token
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# The maximum number of results to return in a single page. If unspecified,
|
|
|
|
# defaults to 1024. The maximum value is 4096.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `pageSize`
|
|
|
|
# @return [Fixnum]
|
|
|
|
attr_accessor :page_size
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@md5checksums = args[:md5checksums] if args.key?(:md5checksums)
|
|
|
|
@accessions = args[:accessions] if args.key?(:accessions)
|
|
|
|
@assembly_id = args[:assembly_id] if args.key?(:assembly_id)
|
|
|
|
@page_token = args[:page_token] if args.key?(:page_token)
|
|
|
|
@page_size = args[:page_size] if args.key?(:page_size)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
#
|
|
|
|
class SearchReferenceSetsResponse
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# The matching references sets.
|
|
|
|
# Corresponds to the JSON property `referenceSets`
|
|
|
|
# @return [Array<Google::Apis::GenomicsV1::ReferenceSet>]
|
|
|
|
attr_accessor :reference_sets
|
|
|
|
|
|
|
|
# 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.
|
|
|
|
# Corresponds to the JSON property `nextPageToken`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :next_page_token
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@reference_sets = args[:reference_sets] if args.key?(:reference_sets)
|
|
|
|
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# A reference set is a set of references which typically comprise a reference
|
|
|
|
# assembly for a species, such as `GRCh38` which is representative of the human
|
|
|
|
# genome. A reference set defines a common coordinate space for comparing
|
|
|
|
# reference-aligned experimental data. A reference set contains 1 or more
|
2015-12-03 01:10:07 +00:00
|
|
|
# references. For more genomics resource definitions, see [Fundamentals of
|
|
|
|
# Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-
|
|
|
|
# genomics)
|
2015-07-20 21:49:34 +00:00
|
|
|
class ReferenceSet
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# The server-generated reference set ID, unique across all reference sets.
|
|
|
|
# Corresponds to the JSON property `id`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :id
|
|
|
|
|
|
|
|
# The IDs of the reference objects that are part of this set. `Reference.
|
|
|
|
# md5checksum` must be unique within this set.
|
|
|
|
# Corresponds to the JSON property `referenceIds`
|
|
|
|
# @return [Array<String>]
|
|
|
|
attr_accessor :reference_ids
|
|
|
|
|
|
|
|
# Order-independent MD5 checksum which identifies this reference set. The
|
|
|
|
# checksum is computed by sorting all lower case hexidecimal string `reference.
|
|
|
|
# md5checksum` (for all reference in this set) in ascending lexicographic order,
|
|
|
|
# concatenating, and taking the MD5 of that value. The resulting value is
|
|
|
|
# represented in lower case hexadecimal format.
|
|
|
|
# Corresponds to the JSON property `md5checksum`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :md5checksum
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# ID from http://www.ncbi.nlm.nih.gov/taxonomy (for example, 9606 for human)
|
|
|
|
# indicating the species which this reference set is intended to model. Note
|
|
|
|
# that contained references may specify a different `ncbiTaxonId`, as assemblies
|
|
|
|
# may contain reference sequences which do not belong to the modeled species,
|
|
|
|
# for example EBV in a human reference genome.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `ncbiTaxonId`
|
|
|
|
# @return [Fixnum]
|
|
|
|
attr_accessor :ncbi_taxon_id
|
|
|
|
|
|
|
|
# Free text description of this reference set.
|
|
|
|
# Corresponds to the JSON property `description`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :description
|
|
|
|
|
|
|
|
# Public id of this reference set, such as `GRCh37`.
|
|
|
|
# Corresponds to the JSON property `assemblyId`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :assembly_id
|
|
|
|
|
|
|
|
# The URI from which the references were obtained.
|
|
|
|
# Corresponds to the JSON property `sourceUri`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :source_uri
|
|
|
|
|
|
|
|
# All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with
|
|
|
|
# a version number, for example `NC_000001.11`.
|
|
|
|
# Corresponds to the JSON property `sourceAccessions`
|
|
|
|
# @return [Array<String>]
|
|
|
|
attr_accessor :source_accessions
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@id = args[:id] if args.key?(:id)
|
|
|
|
@reference_ids = args[:reference_ids] if args.key?(:reference_ids)
|
|
|
|
@md5checksum = args[:md5checksum] if args.key?(:md5checksum)
|
|
|
|
@ncbi_taxon_id = args[:ncbi_taxon_id] if args.key?(:ncbi_taxon_id)
|
|
|
|
@description = args[:description] if args.key?(:description)
|
|
|
|
@assembly_id = args[:assembly_id] if args.key?(:assembly_id)
|
|
|
|
@source_uri = args[:source_uri] if args.key?(:source_uri)
|
|
|
|
@source_accessions = args[:source_accessions] if args.key?(:source_accessions)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
#
|
|
|
|
class SearchReferencesRequest
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# If present, return references for which the md5checksum matches exactly.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `md5checksums`
|
|
|
|
# @return [Array<String>]
|
|
|
|
attr_accessor :md5checksums
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# If present, return references for which a prefix of any of sourceAccessions
|
|
|
|
# match any of these strings. Accession numbers typically have a main number and
|
|
|
|
# a version, for example `GCF_000001405.26`.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `accessions`
|
|
|
|
# @return [Array<String>]
|
|
|
|
attr_accessor :accessions
|
|
|
|
|
|
|
|
# If present, return only references which belong to this reference set.
|
|
|
|
# Corresponds to the JSON property `referenceSetId`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :reference_set_id
|
|
|
|
|
|
|
|
# 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.
|
|
|
|
# Corresponds to the JSON property `pageToken`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :page_token
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# The maximum number of results to return in a single page. If unspecified,
|
|
|
|
# defaults to 1024. The maximum value is 4096.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `pageSize`
|
|
|
|
# @return [Fixnum]
|
|
|
|
attr_accessor :page_size
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@md5checksums = args[:md5checksums] if args.key?(:md5checksums)
|
|
|
|
@accessions = args[:accessions] if args.key?(:accessions)
|
|
|
|
@reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
|
|
|
|
@page_token = args[:page_token] if args.key?(:page_token)
|
|
|
|
@page_size = args[:page_size] if args.key?(:page_size)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
#
|
|
|
|
class SearchReferencesResponse
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# The matching references.
|
|
|
|
# Corresponds to the JSON property `references`
|
|
|
|
# @return [Array<Google::Apis::GenomicsV1::Reference>]
|
|
|
|
attr_accessor :references
|
|
|
|
|
|
|
|
# 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.
|
|
|
|
# Corresponds to the JSON property `nextPageToken`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :next_page_token
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@references = args[:references] if args.key?(:references)
|
|
|
|
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# A reference is a canonical assembled DNA sequence, intended to act as a
|
|
|
|
# reference coordinate space for other genomic annotations. A single reference
|
|
|
|
# might represent the human chromosome 1 or mitochandrial DNA, for instance. A
|
2015-12-03 01:10:07 +00:00
|
|
|
# reference belongs to one or more reference sets. For more genomics resource
|
|
|
|
# definitions, see [Fundamentals of Google Genomics](https://cloud.google.com/
|
|
|
|
# genomics/fundamentals-of-google-genomics)
|
2015-07-20 21:49:34 +00:00
|
|
|
class Reference
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# The server-generated reference ID, unique across all references.
|
|
|
|
# Corresponds to the JSON property `id`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :id
|
|
|
|
|
|
|
|
# The length of this reference's sequence.
|
|
|
|
# Corresponds to the JSON property `length`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :length
|
|
|
|
|
|
|
|
# MD5 of the upper-case sequence excluding all whitespace characters (this is
|
|
|
|
# equivalent to SQ:M5 in SAM). This value is represented in lower case
|
|
|
|
# hexadecimal format.
|
|
|
|
# Corresponds to the JSON property `md5checksum`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :md5checksum
|
|
|
|
|
|
|
|
# The name of this reference, for example `22`.
|
|
|
|
# Corresponds to the JSON property `name`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :name
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# The URI from which the sequence was obtained. Typically specifies a FASTA
|
|
|
|
# format file.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `sourceUri`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :source_uri
|
|
|
|
|
|
|
|
# All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with
|
|
|
|
# a version number, for example `GCF_000001405.26`.
|
|
|
|
# Corresponds to the JSON property `sourceAccessions`
|
|
|
|
# @return [Array<String>]
|
|
|
|
attr_accessor :source_accessions
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# ID from http://www.ncbi.nlm.nih.gov/taxonomy. For example, 9606 for human.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `ncbiTaxonId`
|
|
|
|
# @return [Fixnum]
|
|
|
|
attr_accessor :ncbi_taxon_id
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@id = args[:id] if args.key?(:id)
|
|
|
|
@length = args[:length] if args.key?(:length)
|
|
|
|
@md5checksum = args[:md5checksum] if args.key?(:md5checksum)
|
|
|
|
@name = args[:name] if args.key?(:name)
|
|
|
|
@source_uri = args[:source_uri] if args.key?(:source_uri)
|
|
|
|
@source_accessions = args[:source_accessions] if args.key?(:source_accessions)
|
|
|
|
@ncbi_taxon_id = args[:ncbi_taxon_id] if args.key?(:ncbi_taxon_id)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
#
|
|
|
|
class ListBasesResponse
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# The offset position (0-based) of the given `sequence` from the start of this `
|
|
|
|
# Reference`. This value will differ for each page in a paginated request.
|
|
|
|
# Corresponds to the JSON property `offset`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :offset
|
|
|
|
|
|
|
|
# A substring of the bases that make up this reference.
|
|
|
|
# Corresponds to the JSON property `sequence`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :sequence
|
|
|
|
|
|
|
|
# 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.
|
|
|
|
# Corresponds to the JSON property `nextPageToken`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :next_page_token
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@offset = args[:offset] if args.key?(:offset)
|
|
|
|
@sequence = args[:sequence] if args.key?(:sequence)
|
|
|
|
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# The variant data import request.
|
|
|
|
class ImportVariantsRequest
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# Required. The variant set to which variant data should be imported.
|
|
|
|
# Corresponds to the JSON property `variantSetId`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :variant_set_id
|
|
|
|
|
|
|
|
# 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.
|
|
|
|
# Corresponds to the JSON property `sourceUris`
|
|
|
|
# @return [Array<String>]
|
|
|
|
attr_accessor :source_uris
|
|
|
|
|
|
|
|
# The format of the variant data being imported. If unspecified, defaults to to `
|
|
|
|
# VCF`.
|
|
|
|
# Corresponds to the JSON property `format`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :format
|
|
|
|
|
|
|
|
# Convert reference names to the canonical representation. hg19 haploytypes (
|
|
|
|
# those reference names containing "_hap") are not modified in any way. All
|
|
|
|
# other reference names are modified according to the following rules: The
|
|
|
|
# reference name is capitalized. The "chr" prefix is dropped for all autosomes
|
|
|
|
# and sex chromsomes. For example "chr17" becomes "17" and "chrX" becomes "X".
|
|
|
|
# All mitochondrial chromosomes ("chrM", "chrMT", etc) become "MT".
|
|
|
|
# Corresponds to the JSON property `normalizeReferenceNames`
|
|
|
|
# @return [Boolean]
|
|
|
|
attr_accessor :normalize_reference_names
|
|
|
|
alias_method :normalize_reference_names?, :normalize_reference_names
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@variant_set_id = args[:variant_set_id] if args.key?(:variant_set_id)
|
|
|
|
@source_uris = args[:source_uris] if args.key?(:source_uris)
|
|
|
|
@format = args[:format] if args.key?(:format)
|
|
|
|
@normalize_reference_names = args[:normalize_reference_names] if args.key?(:normalize_reference_names)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# A variant set is a collection of call sets and variants. It contains summary
|
2015-12-03 01:10:07 +00:00
|
|
|
# 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)
|
2015-07-20 21:49:34 +00:00
|
|
|
class VariantSet
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# The dataset to which this variant set belongs.
|
|
|
|
# Corresponds to the JSON property `datasetId`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :dataset_id
|
|
|
|
|
|
|
|
# The server-generated variant set ID, unique across all variant sets.
|
|
|
|
# Corresponds to the JSON property `id`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :id
|
|
|
|
|
2015-12-03 01:10:07 +00:00
|
|
|
# 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.
|
|
|
|
# Corresponds to the JSON property `referenceSetId`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :reference_set_id
|
|
|
|
|
2015-07-20 21:49:34 +00:00
|
|
|
# A list of all references used by the variants in a variant set with associated
|
|
|
|
# coordinate upper bounds for each one.
|
|
|
|
# Corresponds to the JSON property `referenceBounds`
|
|
|
|
# @return [Array<Google::Apis::GenomicsV1::ReferenceBound>]
|
|
|
|
attr_accessor :reference_bounds
|
|
|
|
|
|
|
|
# The metadata associated with this variant set.
|
|
|
|
# Corresponds to the JSON property `metadata`
|
|
|
|
# @return [Array<Google::Apis::GenomicsV1::VariantSetMetadata>]
|
|
|
|
attr_accessor :metadata
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@dataset_id = args[:dataset_id] if args.key?(:dataset_id)
|
|
|
|
@id = args[:id] if args.key?(:id)
|
|
|
|
@reference_set_id = args[:reference_set_id] if args.key?(:reference_set_id)
|
|
|
|
@reference_bounds = args[:reference_bounds] if args.key?(:reference_bounds)
|
|
|
|
@metadata = args[:metadata] if args.key?(:metadata)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# ReferenceBound records an upper bound for the starting coordinate of variants
|
|
|
|
# in a particular reference.
|
|
|
|
class ReferenceBound
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# The name of the reference associated with this ReferenceBound.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `referenceName`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :reference_name
|
|
|
|
|
|
|
|
# An upper bound (inclusive) on the starting coordinate of any variant in the
|
|
|
|
# reference sequence.
|
|
|
|
# Corresponds to the JSON property `upperBound`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :upper_bound
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
|
|
|
@upper_bound = args[:upper_bound] if args.key?(:upper_bound)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# 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.
|
|
|
|
class VariantSetMetadata
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# The top-level key.
|
|
|
|
# Corresponds to the JSON property `key`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :key
|
|
|
|
|
|
|
|
# The value field for simple metadata
|
|
|
|
# Corresponds to the JSON property `value`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :value
|
|
|
|
|
|
|
|
# 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.
|
|
|
|
# Corresponds to the JSON property `id`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :id
|
|
|
|
|
|
|
|
# The type of data. Possible types include: Integer, Float, Flag, Character, and
|
|
|
|
# String.
|
|
|
|
# Corresponds to the JSON property `type`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :type
|
|
|
|
|
|
|
|
# The number of values that can be included in a field described by this
|
|
|
|
# metadata.
|
|
|
|
# Corresponds to the JSON property `number`
|
2015-12-03 01:10:07 +00:00
|
|
|
# @return [String]
|
2015-07-20 21:49:34 +00:00
|
|
|
attr_accessor :number
|
|
|
|
|
|
|
|
# A textual description of this metadata.
|
|
|
|
# Corresponds to the JSON property `description`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :description
|
|
|
|
|
|
|
|
# Remaining structured metadata key-value pairs. This must be of the form map (
|
|
|
|
# string key mapping to a list of string values).
|
|
|
|
# Corresponds to the JSON property `info`
|
|
|
|
# @return [Hash<String,Array<Object>>]
|
|
|
|
attr_accessor :info
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@key = args[:key] if args.key?(:key)
|
|
|
|
@value = args[:value] if args.key?(:value)
|
|
|
|
@id = args[:id] if args.key?(:id)
|
|
|
|
@type = args[:type] if args.key?(:type)
|
|
|
|
@number = args[:number] if args.key?(:number)
|
|
|
|
@description = args[:description] if args.key?(:description)
|
|
|
|
@info = args[:info] if args.key?(:info)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# The variant data export request.
|
|
|
|
class ExportVariantSetRequest
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# If provided, only variant call information from the specified call sets will
|
|
|
|
# be exported. By default all variant calls are exported.
|
|
|
|
# Corresponds to the JSON property `callSetIds`
|
|
|
|
# @return [Array<String>]
|
|
|
|
attr_accessor :call_set_ids
|
|
|
|
|
|
|
|
# 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.
|
|
|
|
# Corresponds to the JSON property `projectId`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :project_id
|
|
|
|
|
|
|
|
# The format for the exported data.
|
|
|
|
# Corresponds to the JSON property `format`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :format
|
|
|
|
|
|
|
|
# Required. The BigQuery dataset to export data to. This dataset must already
|
|
|
|
# exist. Note that this is distinct from the Genomics concept of "dataset".
|
|
|
|
# Corresponds to the JSON property `bigqueryDataset`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :bigquery_dataset
|
|
|
|
|
|
|
|
# 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.
|
|
|
|
# Corresponds to the JSON property `bigqueryTable`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :bigquery_table
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@call_set_ids = args[:call_set_ids] if args.key?(:call_set_ids)
|
|
|
|
@project_id = args[:project_id] if args.key?(:project_id)
|
|
|
|
@format = args[:format] if args.key?(:format)
|
|
|
|
@bigquery_dataset = args[:bigquery_dataset] if args.key?(:bigquery_dataset)
|
|
|
|
@bigquery_table = args[:bigquery_table] if args.key?(:bigquery_table)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# The search variant sets request.
|
|
|
|
class SearchVariantSetsRequest
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# Exactly one dataset ID must be provided here. Only variant sets which belong
|
|
|
|
# to this dataset will be returned.
|
|
|
|
# Corresponds to the JSON property `datasetIds`
|
|
|
|
# @return [Array<String>]
|
|
|
|
attr_accessor :dataset_ids
|
|
|
|
|
|
|
|
# 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.
|
|
|
|
# Corresponds to the JSON property `pageToken`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :page_token
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# The maximum number of results to return in a single page. If unspecified,
|
|
|
|
# defaults to 1024.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `pageSize`
|
|
|
|
# @return [Fixnum]
|
|
|
|
attr_accessor :page_size
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@dataset_ids = args[:dataset_ids] if args.key?(:dataset_ids)
|
|
|
|
@page_token = args[:page_token] if args.key?(:page_token)
|
|
|
|
@page_size = args[:page_size] if args.key?(:page_size)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# The search variant sets response.
|
|
|
|
class SearchVariantSetsResponse
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# The variant sets belonging to the requested dataset.
|
|
|
|
# Corresponds to the JSON property `variantSets`
|
|
|
|
# @return [Array<Google::Apis::GenomicsV1::VariantSet>]
|
|
|
|
attr_accessor :variant_sets
|
|
|
|
|
|
|
|
# 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.
|
|
|
|
# Corresponds to the JSON property `nextPageToken`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :next_page_token
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@variant_sets = args[:variant_sets] if args.key?(:variant_sets)
|
|
|
|
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# The variant search request.
|
|
|
|
class SearchVariantsRequest
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# At most one variant set ID must be provided. Only variants from this variant
|
|
|
|
# set will be returned. If omitted, a call set id must be included in the
|
|
|
|
# request.
|
|
|
|
# Corresponds to the JSON property `variantSetIds`
|
|
|
|
# @return [Array<String>]
|
|
|
|
attr_accessor :variant_set_ids
|
|
|
|
|
|
|
|
# Only return variants which have exactly this name.
|
|
|
|
# Corresponds to the JSON property `variantName`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :variant_name
|
|
|
|
|
|
|
|
# Only return variant calls which belong to call sets with these ids. Leaving
|
|
|
|
# this blank returns all variant calls. If a variant has no calls belonging to
|
|
|
|
# any of these call sets, it won't be returned at all. Currently, variants with
|
|
|
|
# no calls from any call set will never be returned.
|
|
|
|
# Corresponds to the JSON property `callSetIds`
|
|
|
|
# @return [Array<String>]
|
|
|
|
attr_accessor :call_set_ids
|
|
|
|
|
|
|
|
# Required. Only return variants in this reference sequence.
|
|
|
|
# Corresponds to the JSON property `referenceName`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :reference_name
|
|
|
|
|
|
|
|
# The beginning of the window (0-based, inclusive) for which overlapping
|
|
|
|
# variants should be returned. If unspecified, defaults to 0.
|
|
|
|
# Corresponds to the JSON property `start`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :start
|
|
|
|
|
|
|
|
# The end of the window, 0-based exclusive. If unspecified or 0, defaults to the
|
|
|
|
# length of the reference.
|
|
|
|
# Corresponds to the JSON property `end`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :end
|
|
|
|
|
|
|
|
# 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.
|
|
|
|
# Corresponds to the JSON property `pageToken`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :page_token
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# The maximum number of variants to return in a single page. If unspecified,
|
|
|
|
# defaults to 5000. The maximum value is 10000.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `pageSize`
|
|
|
|
# @return [Fixnum]
|
|
|
|
attr_accessor :page_size
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# The maximum number of calls to return in a single page. Note that this limit
|
|
|
|
# may be exceeded; at least one variant is always returned per page, even if it
|
|
|
|
# has more calls than this limit. If unspecified, defaults to 5000. The maximum
|
|
|
|
# value is 10000.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `maxCalls`
|
|
|
|
# @return [Fixnum]
|
|
|
|
attr_accessor :max_calls
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@variant_set_ids = args[:variant_set_ids] if args.key?(:variant_set_ids)
|
|
|
|
@variant_name = args[:variant_name] if args.key?(:variant_name)
|
|
|
|
@call_set_ids = args[:call_set_ids] if args.key?(:call_set_ids)
|
|
|
|
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
|
|
|
@start = args[:start] if args.key?(:start)
|
|
|
|
@end = args[:end] if args.key?(:end)
|
|
|
|
@page_token = args[:page_token] if args.key?(:page_token)
|
|
|
|
@page_size = args[:page_size] if args.key?(:page_size)
|
|
|
|
@max_calls = args[:max_calls] if args.key?(:max_calls)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# The variant search response.
|
|
|
|
class SearchVariantsResponse
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# The list of matching Variants.
|
|
|
|
# Corresponds to the JSON property `variants`
|
|
|
|
# @return [Array<Google::Apis::GenomicsV1::Variant>]
|
|
|
|
attr_accessor :variants
|
|
|
|
|
|
|
|
# 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.
|
|
|
|
# Corresponds to the JSON property `nextPageToken`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :next_page_token
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@variants = args[:variants] if args.key?(:variants)
|
|
|
|
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# 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
|
2015-12-03 01:10:07 +00:00
|
|
|
# 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.
|
2015-07-20 21:49:34 +00:00
|
|
|
class Variant
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# The ID of the variant set this variant belongs to.
|
|
|
|
# Corresponds to the JSON property `variantSetId`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :variant_set_id
|
|
|
|
|
|
|
|
# The server-generated variant ID, unique across all variants.
|
|
|
|
# Corresponds to the JSON property `id`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :id
|
|
|
|
|
|
|
|
# Names for the variant, for example a RefSNP ID.
|
|
|
|
# Corresponds to the JSON property `names`
|
|
|
|
# @return [Array<String>]
|
|
|
|
attr_accessor :names
|
|
|
|
|
|
|
|
# The date this variant was created, in milliseconds from the epoch.
|
|
|
|
# Corresponds to the JSON property `created`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :created
|
|
|
|
|
|
|
|
# The reference on which this variant occurs. (such as `chr20` or `X`)
|
|
|
|
# Corresponds to the JSON property `referenceName`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :reference_name
|
|
|
|
|
|
|
|
# The position at which this variant occurs (0-based). This corresponds to the
|
|
|
|
# first base of the string of reference bases.
|
|
|
|
# Corresponds to the JSON property `start`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :start
|
|
|
|
|
|
|
|
# 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.
|
|
|
|
# Corresponds to the JSON property `end`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :end
|
|
|
|
|
|
|
|
# The reference bases for this variant. They start at the given position.
|
|
|
|
# Corresponds to the JSON property `referenceBases`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :reference_bases
|
|
|
|
|
|
|
|
# The bases that appear instead of the reference bases.
|
|
|
|
# Corresponds to the JSON property `alternateBases`
|
|
|
|
# @return [Array<String>]
|
|
|
|
attr_accessor :alternate_bases
|
|
|
|
|
|
|
|
# A measure of how likely this variant is to be real. A higher value is better.
|
|
|
|
# Corresponds to the JSON property `quality`
|
|
|
|
# @return [Float]
|
|
|
|
attr_accessor :quality
|
|
|
|
|
|
|
|
# A list of filters (normally quality filters) this variant has failed. `PASS`
|
|
|
|
# indicates this variant has passed all filters.
|
|
|
|
# Corresponds to the JSON property `filter`
|
|
|
|
# @return [Array<String>]
|
|
|
|
attr_accessor :filter
|
|
|
|
|
|
|
|
# A map of additional variant information. This must be of the form map (string
|
|
|
|
# key mapping to a list of string values).
|
|
|
|
# Corresponds to the JSON property `info`
|
|
|
|
# @return [Hash<String,Array<Object>>]
|
|
|
|
attr_accessor :info
|
|
|
|
|
|
|
|
# The variant calls for this particular variant. Each one represents the
|
|
|
|
# determination of genotype with respect to this variant.
|
|
|
|
# Corresponds to the JSON property `calls`
|
|
|
|
# @return [Array<Google::Apis::GenomicsV1::VariantCall>]
|
|
|
|
attr_accessor :calls
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@variant_set_id = args[:variant_set_id] if args.key?(:variant_set_id)
|
|
|
|
@id = args[:id] if args.key?(:id)
|
|
|
|
@names = args[:names] if args.key?(:names)
|
|
|
|
@created = args[:created] if args.key?(:created)
|
|
|
|
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
|
|
|
@start = args[:start] if args.key?(:start)
|
|
|
|
@end = args[:end] if args.key?(:end)
|
|
|
|
@reference_bases = args[:reference_bases] if args.key?(:reference_bases)
|
|
|
|
@alternate_bases = args[:alternate_bases] if args.key?(:alternate_bases)
|
|
|
|
@quality = args[:quality] if args.key?(:quality)
|
|
|
|
@filter = args[:filter] if args.key?(:filter)
|
|
|
|
@info = args[:info] if args.key?(:info)
|
|
|
|
@calls = args[:calls] if args.key?(:calls)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# 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.
|
|
|
|
class VariantCall
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# The ID of the call set this variant call belongs to.
|
|
|
|
# Corresponds to the JSON property `callSetId`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :call_set_id
|
|
|
|
|
|
|
|
# The name of the call set this variant call belongs to.
|
|
|
|
# Corresponds to the JSON property `callSetName`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :call_set_name
|
|
|
|
|
|
|
|
# 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.
|
|
|
|
# Corresponds to the JSON property `genotype`
|
|
|
|
# @return [Array<Fixnum>]
|
|
|
|
attr_accessor :genotype
|
|
|
|
|
|
|
|
# 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 `*`.
|
|
|
|
# Corresponds to the JSON property `phaseset`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :phaseset
|
|
|
|
|
|
|
|
# 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`.
|
|
|
|
# Corresponds to the JSON property `genotypeLikelihood`
|
|
|
|
# @return [Array<Float>]
|
|
|
|
attr_accessor :genotype_likelihood
|
|
|
|
|
|
|
|
# A map of additional variant call information. This must be of the form map (
|
|
|
|
# string key mapping to a list of string values).
|
|
|
|
# Corresponds to the JSON property `info`
|
|
|
|
# @return [Hash<String,Array<Object>>]
|
|
|
|
attr_accessor :info
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@call_set_id = args[:call_set_id] if args.key?(:call_set_id)
|
|
|
|
@call_set_name = args[:call_set_name] if args.key?(:call_set_name)
|
|
|
|
@genotype = args[:genotype] if args.key?(:genotype)
|
|
|
|
@phaseset = args[:phaseset] if args.key?(:phaseset)
|
|
|
|
@genotype_likelihood = args[:genotype_likelihood] if args.key?(:genotype_likelihood)
|
|
|
|
@info = args[:info] if args.key?(:info)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# The call set search request.
|
|
|
|
class SearchCallSetsRequest
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# Restrict the query to call sets within the given variant sets. At least one ID
|
|
|
|
# must be provided.
|
|
|
|
# Corresponds to the JSON property `variantSetIds`
|
|
|
|
# @return [Array<String>]
|
|
|
|
attr_accessor :variant_set_ids
|
|
|
|
|
|
|
|
# Only return call sets for which a substring of the name matches this string.
|
|
|
|
# Corresponds to the JSON property `name`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :name
|
|
|
|
|
|
|
|
# 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.
|
|
|
|
# Corresponds to the JSON property `pageToken`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :page_token
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# The maximum number of results to return in a single page. If unspecified,
|
|
|
|
# defaults to 1024.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `pageSize`
|
|
|
|
# @return [Fixnum]
|
|
|
|
attr_accessor :page_size
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@variant_set_ids = args[:variant_set_ids] if args.key?(:variant_set_ids)
|
|
|
|
@name = args[:name] if args.key?(:name)
|
|
|
|
@page_token = args[:page_token] if args.key?(:page_token)
|
|
|
|
@page_size = args[:page_size] if args.key?(:page_size)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# The call set search response.
|
|
|
|
class SearchCallSetsResponse
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# The list of matching call sets.
|
|
|
|
# Corresponds to the JSON property `callSets`
|
|
|
|
# @return [Array<Google::Apis::GenomicsV1::CallSet>]
|
|
|
|
attr_accessor :call_sets
|
|
|
|
|
|
|
|
# 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.
|
|
|
|
# Corresponds to the JSON property `nextPageToken`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :next_page_token
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@call_sets = args[:call_sets] if args.key?(:call_sets)
|
|
|
|
@next_page_token = args[:next_page_token] if args.key?(:next_page_token)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# A call set is a collection of variant calls, typically for one sample. It
|
2015-12-03 01:10:07 +00:00
|
|
|
# belongs to a variant set. For more genomics resource definitions, see [
|
|
|
|
# Fundamentals of Google Genomics](https://cloud.google.com/genomics/
|
|
|
|
# fundamentals-of-google-genomics)
|
2015-07-20 21:49:34 +00:00
|
|
|
class CallSet
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# The server-generated call set ID, unique across all call sets.
|
|
|
|
# Corresponds to the JSON property `id`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :id
|
|
|
|
|
|
|
|
# The call set name.
|
|
|
|
# Corresponds to the JSON property `name`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :name
|
|
|
|
|
|
|
|
# The sample ID this call set corresponds to.
|
|
|
|
# Corresponds to the JSON property `sampleId`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :sample_id
|
|
|
|
|
2015-07-31 00:05:47 +00:00
|
|
|
# The IDs of the variant sets this call set belongs to. This field must have
|
|
|
|
# exactly length one, as a call set belongs to a single variant set. This field
|
|
|
|
# is repeated for compatibility with the [GA4GH 0.5.1 API](https://github.com/
|
|
|
|
# ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variants.avdl#L76).
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `variantSetIds`
|
|
|
|
# @return [Array<String>]
|
|
|
|
attr_accessor :variant_set_ids
|
|
|
|
|
|
|
|
# The date this call set was created in milliseconds from the epoch.
|
|
|
|
# Corresponds to the JSON property `created`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :created
|
|
|
|
|
|
|
|
# A map of additional call set information. This must be of the form map (string
|
|
|
|
# key mapping to a list of string values).
|
|
|
|
# Corresponds to the JSON property `info`
|
|
|
|
# @return [Hash<String,Array<Object>>]
|
|
|
|
attr_accessor :info
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@id = args[:id] if args.key?(:id)
|
|
|
|
@name = args[:name] if args.key?(:name)
|
|
|
|
@sample_id = args[:sample_id] if args.key?(:sample_id)
|
|
|
|
@variant_set_ids = args[:variant_set_ids] if args.key?(:variant_set_ids)
|
|
|
|
@created = args[:created] if args.key?(:created)
|
|
|
|
@info = args[:info] if args.key?(:info)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# The stream variants request.
|
|
|
|
class StreamVariantsRequest
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# The Google Developers Console project ID or number which will be billed for
|
|
|
|
# this access. The caller must have WRITE access to this project. Required.
|
|
|
|
# Corresponds to the JSON property `projectId`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :project_id
|
|
|
|
|
|
|
|
# The variant set ID from which to stream variants.
|
|
|
|
# Corresponds to the JSON property `variantSetId`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :variant_set_id
|
|
|
|
|
|
|
|
# Only return variant calls which belong to call sets with these IDs. Leaving
|
|
|
|
# this blank returns all variant calls.
|
|
|
|
# Corresponds to the JSON property `callSetIds`
|
|
|
|
# @return [Array<String>]
|
|
|
|
attr_accessor :call_set_ids
|
|
|
|
|
|
|
|
# Required. Only return variants in this reference sequence.
|
|
|
|
# Corresponds to the JSON property `referenceName`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :reference_name
|
|
|
|
|
|
|
|
# The beginning of the window (0-based, inclusive) for which overlapping
|
|
|
|
# variants should be returned.
|
|
|
|
# Corresponds to the JSON property `start`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :start
|
|
|
|
|
|
|
|
# The end of the window (0-based, exclusive) for which overlapping variants
|
|
|
|
# should be returned.
|
|
|
|
# Corresponds to the JSON property `end`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :end
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@project_id = args[:project_id] if args.key?(:project_id)
|
|
|
|
@variant_set_id = args[:variant_set_id] if args.key?(:variant_set_id)
|
|
|
|
@call_set_ids = args[:call_set_ids] if args.key?(:call_set_ids)
|
|
|
|
@reference_name = args[:reference_name] if args.key?(:reference_name)
|
|
|
|
@start = args[:start] if args.key?(:start)
|
|
|
|
@end = args[:end] if args.key?(:end)
|
2015-12-14 22:27:57 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
#
|
|
|
|
class StreamVariantsResponse
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
#
|
|
|
|
# Corresponds to the JSON property `variants`
|
|
|
|
# @return [Array<Google::Apis::GenomicsV1::Variant>]
|
|
|
|
attr_accessor :variants
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@variants = args[:variants] if args.key?(:variants)
|
2015-12-14 22:27:57 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
2015-07-20 21:49:34 +00:00
|
|
|
# The read group set import response.
|
|
|
|
class ImportReadGroupSetsResponse
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# IDs of the read group sets that were created.
|
|
|
|
# Corresponds to the JSON property `readGroupSetIds`
|
|
|
|
# @return [Array<String>]
|
|
|
|
attr_accessor :read_group_set_ids
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@read_group_set_ids = args[:read_group_set_ids] if args.key?(:read_group_set_ids)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
|
|
|
# The variant data import response.
|
|
|
|
class ImportVariantsResponse
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
2015-12-14 22:27:57 +00:00
|
|
|
# IDs of the call sets created during the import.
|
2015-07-20 21:49:34 +00:00
|
|
|
# Corresponds to the JSON property `callSetIds`
|
|
|
|
# @return [Array<String>]
|
|
|
|
attr_accessor :call_set_ids
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@call_set_ids = args[:call_set_ids] if args.key?(:call_set_ids)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
2015-12-03 01:10:07 +00:00
|
|
|
# Metadata describing an Operation.
|
2015-07-20 21:49:34 +00:00
|
|
|
class OperationMetadata
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# The Google Cloud Project in which the job is scoped.
|
|
|
|
# Corresponds to the JSON property `projectId`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :project_id
|
|
|
|
|
|
|
|
# The time at which the job was submitted to the Genomics service.
|
|
|
|
# Corresponds to the JSON property `createTime`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :create_time
|
|
|
|
|
|
|
|
# The original request that started the operation. Note that this will be in
|
|
|
|
# current version of the API. If the operation was started with v1beta2 API and
|
|
|
|
# a GetOperation is performed on v1 API, a v1 request will be returned.
|
|
|
|
# Corresponds to the JSON property `request`
|
|
|
|
# @return [Hash<String,Object>]
|
|
|
|
attr_accessor :request
|
|
|
|
|
|
|
|
# Optional event messages that were generated during the job's execution. This
|
|
|
|
# also contains any warnings that were generated during import or export.
|
|
|
|
# Corresponds to the JSON property `events`
|
|
|
|
# @return [Array<Google::Apis::GenomicsV1::OperationEvent>]
|
|
|
|
attr_accessor :events
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@project_id = args[:project_id] if args.key?(:project_id)
|
|
|
|
@create_time = args[:create_time] if args.key?(:create_time)
|
|
|
|
@request = args[:request] if args.key?(:request)
|
|
|
|
@events = args[:events] if args.key?(:events)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
|
2015-12-03 01:10:07 +00:00
|
|
|
# An event that occurred during an Operation.
|
2015-07-20 21:49:34 +00:00
|
|
|
class OperationEvent
|
|
|
|
include Google::Apis::Core::Hashable
|
|
|
|
|
|
|
|
# Required description of event.
|
|
|
|
# Corresponds to the JSON property `description`
|
|
|
|
# @return [String]
|
|
|
|
attr_accessor :description
|
|
|
|
|
|
|
|
def initialize(**args)
|
|
|
|
update!(**args)
|
|
|
|
end
|
|
|
|
|
|
|
|
# Update properties of this object
|
|
|
|
def update!(**args)
|
2016-01-29 22:32:46 +00:00
|
|
|
@description = args[:description] if args.key?(:description)
|
2015-07-20 21:49:34 +00:00
|
|
|
end
|
|
|
|
end
|
|
|
|
end
|
|
|
|
end
|
|
|
|
end
|