google-api-client 0.9.pre1 → 0.9.pre2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/CHANGELOG.md +5 -0
- data/README.md +4 -3
- data/api_names.yaml +42 -0
- data/api_names_out.yaml +977 -651
- data/generated/google/apis/adexchangebuyer_v1_3.rb +1 -1
- data/generated/google/apis/adexchangeseller_v2_0.rb +1 -1
- data/generated/google/apis/adsense_v1_4.rb +1 -1
- data/generated/google/apis/adsensehost_v4_1.rb +1 -1
- data/generated/google/apis/androidenterprise_v1/classes.rb +31 -24
- data/generated/google/apis/androidenterprise_v1/service.rb +11 -6
- data/generated/google/apis/androidenterprise_v1.rb +2 -1
- data/generated/google/apis/appstate_v1.rb +1 -1
- data/generated/google/apis/autoscaler_v1beta2.rb +1 -1
- data/generated/google/apis/bigquery_v2/classes.rb +34 -0
- data/generated/google/apis/bigquery_v2/representations.rb +14 -0
- data/generated/google/apis/bigquery_v2/service.rb +2 -2
- data/generated/google/apis/bigquery_v2.rb +1 -1
- data/generated/google/apis/calendar_v3/classes.rb +8 -0
- data/generated/google/apis/calendar_v3/representations.rb +1 -0
- data/generated/google/apis/calendar_v3.rb +1 -1
- data/generated/google/apis/civicinfo_v2/classes.rb +61 -0
- data/generated/google/apis/civicinfo_v2/representations.rb +8 -0
- data/generated/google/apis/civicinfo_v2.rb +1 -1
- data/generated/google/apis/classroom_v1beta1/classes.rb +447 -0
- data/generated/google/apis/classroom_v1beta1/representations.rb +190 -0
- data/generated/google/apis/classroom_v1beta1/service.rb +791 -0
- data/generated/google/apis/classroom_v1beta1.rb +49 -0
- data/generated/google/apis/cloudmonitoring_v2beta2.rb +4 -1
- data/generated/google/apis/cloudresourcemanager_v1beta1/classes.rb +20 -19
- data/generated/google/apis/cloudresourcemanager_v1beta1/service.rb +34 -34
- data/generated/google/apis/cloudresourcemanager_v1beta1.rb +2 -5
- data/generated/google/apis/compute_v1/classes.rb +2638 -1136
- data/generated/google/apis/compute_v1/representations.rb +580 -0
- data/generated/google/apis/compute_v1/service.rb +2448 -305
- data/generated/google/apis/compute_v1.rb +1 -1
- data/generated/google/apis/container_v1/classes.rb +438 -0
- data/generated/google/apis/container_v1/representations.rb +163 -0
- data/generated/google/apis/container_v1/service.rb +346 -0
- data/generated/google/apis/container_v1.rb +35 -0
- data/generated/google/apis/container_v1beta1.rb +1 -1
- data/generated/google/apis/content_v2/service.rb +48 -12
- data/generated/google/apis/content_v2.rb +1 -1
- data/generated/google/apis/deploymentmanager_v2beta2/classes.rb +13 -9
- data/generated/google/apis/deploymentmanager_v2beta2/service.rb +110 -15
- data/generated/google/apis/deploymentmanager_v2beta2.rb +1 -1
- data/generated/google/apis/discovery_v1/classes.rb +7 -0
- data/generated/google/apis/discovery_v1/representations.rb +1 -0
- data/generated/google/apis/dns_v1/service.rb +4 -1
- data/generated/google/apis/dns_v1.rb +1 -1
- data/generated/google/apis/doubleclicksearch_v2.rb +1 -1
- data/generated/google/apis/drive_v2.rb +1 -1
- data/generated/google/apis/fitness_v1/classes.rb +65 -2
- data/generated/google/apis/fitness_v1/representations.rb +27 -0
- data/generated/google/apis/fitness_v1.rb +1 -1
- data/generated/google/apis/games_configuration_v1configuration.rb +1 -1
- data/generated/google/apis/games_v1.rb +1 -1
- data/generated/google/apis/genomics_v1/classes.rb +2287 -0
- data/generated/google/apis/genomics_v1/representations.rb +796 -0
- data/generated/google/apis/genomics_v1/service.rb +1520 -0
- data/generated/google/apis/genomics_v1.rb +47 -0
- data/generated/google/apis/genomics_v1beta2/service.rb +36 -0
- data/generated/google/apis/genomics_v1beta2.rb +1 -1
- data/generated/google/apis/identitytoolkit_v3.rb +1 -1
- data/generated/google/apis/mapsengine_v1.rb +1 -1
- data/generated/google/apis/oauth2_v2.rb +1 -1
- data/generated/google/apis/plus_domains_v1.rb +1 -1
- data/generated/google/apis/plus_v1.rb +1 -1
- data/generated/google/apis/prediction_v1_6/classes.rb +1 -1
- data/generated/google/apis/pubsub_v1beta2/classes.rb +42 -42
- data/generated/google/apis/pubsub_v1beta2/service.rb +26 -22
- data/generated/google/apis/pubsub_v1beta2.rb +1 -1
- data/generated/google/apis/replicapool_v1beta2/classes.rb +10 -0
- data/generated/google/apis/replicapool_v1beta2/representations.rb +1 -0
- data/generated/google/apis/replicapool_v1beta2.rb +1 -1
- data/generated/google/apis/resourceviews_v1beta2.rb +1 -1
- data/generated/google/apis/storage_v1/classes.rb +4 -2
- data/generated/google/apis/storage_v1.rb +1 -1
- data/generated/google/apis/youtube_analytics_v1.rb +1 -1
- data/generated/google/apis/youtube_v3/classes.rb +3 -3
- data/generated/google/apis/youtube_v3/representations.rb +1 -1
- data/generated/google/apis/youtube_v3/service.rb +78 -0
- data/generated/google/apis/youtube_v3.rb +1 -1
- data/google-api-client.gemspec +0 -1
- data/lib/google/api_client/auth/installed_app.rb +6 -4
- data/lib/google/api_client/auth/key_utils.rb +93 -0
- data/lib/google/apis/core/api_command.rb +12 -5
- data/lib/google/apis/core/http_command.rb +17 -7
- data/lib/google/apis/core/json_representation.rb +6 -2
- data/lib/google/apis/errors.rb +9 -2
- data/lib/google/apis/version.rb +1 -1
- data/script/generate +4 -3
- data/spec/google/apis/core/http_command_spec.rb +20 -0
- data/spec/google/apis/core/json_representation_spec.rb +1 -1
- metadata +15 -16
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# @see https://developers.google.com/fit/rest/
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module FitnessV1
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VERSION = 'V1'
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# View your activity information in Google Fit
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AUTH_FITNESS_ACTIVITY_READ = 'https://www.googleapis.com/auth/fitness.activity.read'
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# @see https://developers.google.com/games/services
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module GamesConfigurationV1configuration
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VERSION = 'V1configuration'
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REVISION = '20150713'
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# View and manage your Google Play Developer account
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AUTH_ANDROIDPUBLISHER = 'https://www.googleapis.com/auth/androidpublisher'
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# @see https://developers.google.com/games/services/
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module GamesV1
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VERSION = 'V1'
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# View and manage its own configuration data in your Google Drive
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AUTH_DRIVE_APPDATA = 'https://www.googleapis.com/auth/drive.appdata'
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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] unless args[:datasets].nil?
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@next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
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end
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end
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# A Dataset is a collection of genomic data.
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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] unless args[:id].nil?
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@project_id = args[:project_id] unless args[:project_id].nil?
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@name = args[:name] unless args[:name].nil?
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@create_time = args[:create_time] unless args[:create_time].nil?
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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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# 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][google.genomics.v1.OperationMetadata] object. This will
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# always be returned with the [Operation][google.longrunning.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 the `result` 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` 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 3 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][google.rpc.Code], but it may accept additional error codes if needed.
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# The error message should be a developer-facing English message that helps
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# developers *understand* and *resolve* the error. If a localized user-facing
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# error message is needed, it can be sent in the error details or localized by
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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 -
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# either with or without APIs - to provide consistent developer experience
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# across different environments. Example uses of this error model include: -
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# Partial errors. If a service needs to return partial errors to the client, it
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# may embed the `Status` in the normal response to indicate the partial errors. -
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# Workflow errors. A typical workflow has multiple steps. Each step may have a `
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# Status` message for error reporting purpose. - Batch operations. If a client
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# uses batch request and batch response, the `Status` message should be used
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# directly inside batch response, one for each error sub-response. -
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# Asynchronous operations. If an API call embeds asynchronous operation results
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# in its response, the status of those operations should be represented directly
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# using the `Status` message. - Logging. If some API errors are stored in logs,
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# the message `Status` could be used directly after any stripping needed for
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# security/privacy reasons.
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# Corresponds to the JSON property `error`
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# @return [Google::Apis::GenomicsV1::Status]
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attr_accessor :error
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# If importing [ReadGroupSets][google.genomics.v1.ReadGroupSet], an [
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# ImportReadGroupSetsResponse][google.genomics.v1.ImportReadGroupSetsResponse]
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# is returned. If importing [Variants][google.genomics.v1.Variant], an [
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# ImportVariantsResponse][google.genomics.v1.ImportVariantsResponse] is returned.
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# For exports, an empty response is returned.
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# Corresponds to the JSON property `response`
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# @return [Hash<String,Object>]
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attr_accessor :response
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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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@name = args[:name] unless args[:name].nil?
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@metadata = args[:metadata] unless args[:metadata].nil?
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@done = args[:done] unless args[:done].nil?
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@error = args[:error] unless args[:error].nil?
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@response = args[:response] unless args[:response].nil?
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end
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end
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# The `Status` 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 3 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][google.rpc.Code], but it may accept additional error codes if needed.
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# The error message should be a developer-facing English message that helps
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# developers *understand* and *resolve* the error. If a localized user-facing
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# error message is needed, it can be sent in the error details or localized by
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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 -
|
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# either with or without APIs - to provide consistent developer experience
|
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# across different environments. Example uses of this error model include: -
|
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# Partial errors. If a service needs to return partial errors to the client, it
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# may embed the `Status` in the normal response to indicate the partial errors. -
|
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# Workflow errors. A typical workflow has multiple steps. Each step may have a `
|
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# Status` message for error reporting purpose. - Batch operations. If a client
|
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# uses batch request and batch response, the `Status` message should be used
|
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# directly inside batch response, one for each error sub-response. -
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# Asynchronous operations. If an API call embeds asynchronous operation results
|
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# in its response, the status of those operations should be represented directly
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# using the `Status` message. - Logging. If some API errors are stored in logs,
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# the message `Status` could be used directly after any stripping needed for
|
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# security/privacy reasons.
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class Status
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include Google::Apis::Core::Hashable
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+
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# The status code, which should be an enum value of [google.rpc.Code][google.rpc.
|
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# Code].
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# Corresponds to the JSON property `code`
|
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# @return [Fixnum]
|
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attr_accessor :code
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|
+
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|
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# A developer-facing error message, which should be in English. Any user-facing
|
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|
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# error message should be localized and sent in the [google.rpc.Status.details][
|
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|
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# google.rpc.Status.details] field, or localized by the client.
|
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|
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# Corresponds to the JSON property `message`
|
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|
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# @return [String]
|
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|
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attr_accessor :message
|
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|
+
|
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|
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# A list of messages that carry the error details. There will be a common set of
|
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|
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# message types for APIs to use.
|
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|
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# Corresponds to the JSON property `details`
|
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|
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# @return [Array<Hash<String,Object>>]
|
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|
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attr_accessor :details
|
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|
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|
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|
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def initialize(**args)
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|
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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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@code = args[:code] unless args[:code].nil?
|
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|
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@message = args[:message] unless args[:message].nil?
|
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@details = args[:details] unless args[:details].nil?
|
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|
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end
|
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|
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end
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|
+
|
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|
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# The response message for [Operations.ListOperations][google.longrunning.
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|
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# Operations.ListOperations].
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class ListOperationsResponse
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include Google::Apis::Core::Hashable
|
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+
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# A list of operations that matches the specified filter in the request.
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# Corresponds to the JSON property `operations`
|
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|
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# @return [Array<Google::Apis::GenomicsV1::Operation>]
|
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|
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attr_accessor :operations
|
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|
+
|
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|
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# The standard List next-page token.
|
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# Corresponds to the JSON property `nextPageToken`
|
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|
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# @return [String]
|
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|
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attr_accessor :next_page_token
|
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|
+
|
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|
+
def initialize(**args)
|
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|
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update!(**args)
|
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|
+
end
|
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|
+
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|
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# Update properties of this object
|
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|
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def update!(**args)
|
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|
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@operations = args[:operations] unless args[:operations].nil?
|
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|
+
@next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
|
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|
+
end
|
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|
+
end
|
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294
|
+
|
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|
+
# The request message for [Operations.CancelOperation][google.longrunning.
|
|
296
|
+
# Operations.CancelOperation].
|
|
297
|
+
class CancelOperationRequest
|
|
298
|
+
include Google::Apis::Core::Hashable
|
|
299
|
+
|
|
300
|
+
def initialize(**args)
|
|
301
|
+
update!(**args)
|
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|
+
end
|
|
303
|
+
|
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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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307
|
+
end
|
|
308
|
+
|
|
309
|
+
# The read group set import request.
|
|
310
|
+
class ImportReadGroupSetsRequest
|
|
311
|
+
include Google::Apis::Core::Hashable
|
|
312
|
+
|
|
313
|
+
# Required. The ID of the dataset these read group sets will belong to. The
|
|
314
|
+
# caller must have WRITE permissions to this dataset.
|
|
315
|
+
# Corresponds to the JSON property `datasetId`
|
|
316
|
+
# @return [String]
|
|
317
|
+
attr_accessor :dataset_id
|
|
318
|
+
|
|
319
|
+
# The reference set to which the imported read group sets are aligned to, if any.
|
|
320
|
+
# The reference names of this reference set must be a superset of those found
|
|
321
|
+
# in the imported file headers. If no reference set id is provided, a best
|
|
322
|
+
# effort is made to associate with a matching reference set.
|
|
323
|
+
# Corresponds to the JSON property `referenceSetId`
|
|
324
|
+
# @return [String]
|
|
325
|
+
attr_accessor :reference_set_id
|
|
326
|
+
|
|
327
|
+
# A list of URIs pointing at BAM files in Google Cloud Storage.
|
|
328
|
+
# Corresponds to the JSON property `sourceUris`
|
|
329
|
+
# @return [Array<String>]
|
|
330
|
+
attr_accessor :source_uris
|
|
331
|
+
|
|
332
|
+
# The partition strategy describes how read groups are partitioned into read
|
|
333
|
+
# group sets.
|
|
334
|
+
# Corresponds to the JSON property `partitionStrategy`
|
|
335
|
+
# @return [String]
|
|
336
|
+
attr_accessor :partition_strategy
|
|
337
|
+
|
|
338
|
+
def initialize(**args)
|
|
339
|
+
update!(**args)
|
|
340
|
+
end
|
|
341
|
+
|
|
342
|
+
# Update properties of this object
|
|
343
|
+
def update!(**args)
|
|
344
|
+
@dataset_id = args[:dataset_id] unless args[:dataset_id].nil?
|
|
345
|
+
@reference_set_id = args[:reference_set_id] unless args[:reference_set_id].nil?
|
|
346
|
+
@source_uris = args[:source_uris] unless args[:source_uris].nil?
|
|
347
|
+
@partition_strategy = args[:partition_strategy] unless args[:partition_strategy].nil?
|
|
348
|
+
end
|
|
349
|
+
end
|
|
350
|
+
|
|
351
|
+
# The read group set export request.
|
|
352
|
+
class ExportReadGroupSetRequest
|
|
353
|
+
include Google::Apis::Core::Hashable
|
|
354
|
+
|
|
355
|
+
# Required. The Google Developers Console project ID that owns this export.
|
|
356
|
+
# Corresponds to the JSON property `projectId`
|
|
357
|
+
# @return [String]
|
|
358
|
+
attr_accessor :project_id
|
|
359
|
+
|
|
360
|
+
# Required. A Google Cloud Storage URI for the exported BAM file. The currently
|
|
361
|
+
# authenticated user must have write access to the new file. An error will be
|
|
362
|
+
# returned if the URI already contains data.
|
|
363
|
+
# Corresponds to the JSON property `exportUri`
|
|
364
|
+
# @return [String]
|
|
365
|
+
attr_accessor :export_uri
|
|
366
|
+
|
|
367
|
+
# The reference names to export. If this is not specified, all reference
|
|
368
|
+
# sequences, including unmapped reads, are exported. Use `*` to export only
|
|
369
|
+
# unmapped reads.
|
|
370
|
+
# Corresponds to the JSON property `referenceNames`
|
|
371
|
+
# @return [Array<String>]
|
|
372
|
+
attr_accessor :reference_names
|
|
373
|
+
|
|
374
|
+
def initialize(**args)
|
|
375
|
+
update!(**args)
|
|
376
|
+
end
|
|
377
|
+
|
|
378
|
+
# Update properties of this object
|
|
379
|
+
def update!(**args)
|
|
380
|
+
@project_id = args[:project_id] unless args[:project_id].nil?
|
|
381
|
+
@export_uri = args[:export_uri] unless args[:export_uri].nil?
|
|
382
|
+
@reference_names = args[:reference_names] unless args[:reference_names].nil?
|
|
383
|
+
end
|
|
384
|
+
end
|
|
385
|
+
|
|
386
|
+
# The read group set search request.
|
|
387
|
+
class SearchReadGroupSetsRequest
|
|
388
|
+
include Google::Apis::Core::Hashable
|
|
389
|
+
|
|
390
|
+
# Restricts this query to read group sets within the given datasets. At least
|
|
391
|
+
# one ID must be provided.
|
|
392
|
+
# Corresponds to the JSON property `datasetIds`
|
|
393
|
+
# @return [Array<String>]
|
|
394
|
+
attr_accessor :dataset_ids
|
|
395
|
+
|
|
396
|
+
# Only return read group sets for which a substring of the name matches this
|
|
397
|
+
# string.
|
|
398
|
+
# Corresponds to the JSON property `name`
|
|
399
|
+
# @return [String]
|
|
400
|
+
attr_accessor :name
|
|
401
|
+
|
|
402
|
+
# The continuation token, which is used to page through large result sets. To
|
|
403
|
+
# get the next page of results, set this parameter to the value of `
|
|
404
|
+
# nextPageToken` from the previous response.
|
|
405
|
+
# Corresponds to the JSON property `pageToken`
|
|
406
|
+
# @return [String]
|
|
407
|
+
attr_accessor :page_token
|
|
408
|
+
|
|
409
|
+
# Specifies number of results to return in a single page. If unspecified, it
|
|
410
|
+
# will default to 256. The maximum value is 1024.
|
|
411
|
+
# Corresponds to the JSON property `pageSize`
|
|
412
|
+
# @return [Fixnum]
|
|
413
|
+
attr_accessor :page_size
|
|
414
|
+
|
|
415
|
+
def initialize(**args)
|
|
416
|
+
update!(**args)
|
|
417
|
+
end
|
|
418
|
+
|
|
419
|
+
# Update properties of this object
|
|
420
|
+
def update!(**args)
|
|
421
|
+
@dataset_ids = args[:dataset_ids] unless args[:dataset_ids].nil?
|
|
422
|
+
@name = args[:name] unless args[:name].nil?
|
|
423
|
+
@page_token = args[:page_token] unless args[:page_token].nil?
|
|
424
|
+
@page_size = args[:page_size] unless args[:page_size].nil?
|
|
425
|
+
end
|
|
426
|
+
end
|
|
427
|
+
|
|
428
|
+
# The read group set search response.
|
|
429
|
+
class SearchReadGroupSetsResponse
|
|
430
|
+
include Google::Apis::Core::Hashable
|
|
431
|
+
|
|
432
|
+
# The list of matching read group sets.
|
|
433
|
+
# Corresponds to the JSON property `readGroupSets`
|
|
434
|
+
# @return [Array<Google::Apis::GenomicsV1::ReadGroupSet>]
|
|
435
|
+
attr_accessor :read_group_sets
|
|
436
|
+
|
|
437
|
+
# The continuation token, which is used to page through large result sets.
|
|
438
|
+
# Provide this value in a subsequent request to return the next page of results.
|
|
439
|
+
# This field will be empty if there aren't any additional results.
|
|
440
|
+
# Corresponds to the JSON property `nextPageToken`
|
|
441
|
+
# @return [String]
|
|
442
|
+
attr_accessor :next_page_token
|
|
443
|
+
|
|
444
|
+
def initialize(**args)
|
|
445
|
+
update!(**args)
|
|
446
|
+
end
|
|
447
|
+
|
|
448
|
+
# Update properties of this object
|
|
449
|
+
def update!(**args)
|
|
450
|
+
@read_group_sets = args[:read_group_sets] unless args[:read_group_sets].nil?
|
|
451
|
+
@next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
|
|
452
|
+
end
|
|
453
|
+
end
|
|
454
|
+
|
|
455
|
+
# A read group set is a logical collection of read groups, which are collections
|
|
456
|
+
# of reads produced by a sequencer. A read group set typically models reads
|
|
457
|
+
# corresponding to one sample, sequenced one way, and aligned one way. * A read
|
|
458
|
+
# group set belongs to one dataset. * A read group belongs to one read group set.
|
|
459
|
+
# * A read belongs to one read group.
|
|
460
|
+
class ReadGroupSet
|
|
461
|
+
include Google::Apis::Core::Hashable
|
|
462
|
+
|
|
463
|
+
# The server-generated read group set ID, unique for all read group sets.
|
|
464
|
+
# Corresponds to the JSON property `id`
|
|
465
|
+
# @return [String]
|
|
466
|
+
attr_accessor :id
|
|
467
|
+
|
|
468
|
+
# The dataset ID.
|
|
469
|
+
# Corresponds to the JSON property `datasetId`
|
|
470
|
+
# @return [String]
|
|
471
|
+
attr_accessor :dataset_id
|
|
472
|
+
|
|
473
|
+
# The reference set the reads in this read group set are aligned to.
|
|
474
|
+
# Corresponds to the JSON property `referenceSetId`
|
|
475
|
+
# @return [String]
|
|
476
|
+
attr_accessor :reference_set_id
|
|
477
|
+
|
|
478
|
+
# The read group set name. By default this will be initialized to the sample
|
|
479
|
+
# name of the sequenced data contained in this set.
|
|
480
|
+
# Corresponds to the JSON property `name`
|
|
481
|
+
# @return [String]
|
|
482
|
+
attr_accessor :name
|
|
483
|
+
|
|
484
|
+
# The filename of the original source file for this read group set, if any.
|
|
485
|
+
# Corresponds to the JSON property `filename`
|
|
486
|
+
# @return [String]
|
|
487
|
+
attr_accessor :filename
|
|
488
|
+
|
|
489
|
+
# The read groups in this set. There are typically 1-10 read groups in a read
|
|
490
|
+
# group set.
|
|
491
|
+
# Corresponds to the JSON property `readGroups`
|
|
492
|
+
# @return [Array<Google::Apis::GenomicsV1::ReadGroup>]
|
|
493
|
+
attr_accessor :read_groups
|
|
494
|
+
|
|
495
|
+
# A map of additional read group set information.
|
|
496
|
+
# Corresponds to the JSON property `info`
|
|
497
|
+
# @return [Hash<String,Array<Object>>]
|
|
498
|
+
attr_accessor :info
|
|
499
|
+
|
|
500
|
+
def initialize(**args)
|
|
501
|
+
update!(**args)
|
|
502
|
+
end
|
|
503
|
+
|
|
504
|
+
# Update properties of this object
|
|
505
|
+
def update!(**args)
|
|
506
|
+
@id = args[:id] unless args[:id].nil?
|
|
507
|
+
@dataset_id = args[:dataset_id] unless args[:dataset_id].nil?
|
|
508
|
+
@reference_set_id = args[:reference_set_id] unless args[:reference_set_id].nil?
|
|
509
|
+
@name = args[:name] unless args[:name].nil?
|
|
510
|
+
@filename = args[:filename] unless args[:filename].nil?
|
|
511
|
+
@read_groups = args[:read_groups] unless args[:read_groups].nil?
|
|
512
|
+
@info = args[:info] unless args[:info].nil?
|
|
513
|
+
end
|
|
514
|
+
end
|
|
515
|
+
|
|
516
|
+
# A read group is all the data that's processed the same way by the sequencer.
|
|
517
|
+
class ReadGroup
|
|
518
|
+
include Google::Apis::Core::Hashable
|
|
519
|
+
|
|
520
|
+
# The server-generated read group ID, unique for all read groups. Note: This is
|
|
521
|
+
# different than the `@RG ID` field in the SAM spec. For that value, see the `
|
|
522
|
+
# name` field.
|
|
523
|
+
# Corresponds to the JSON property `id`
|
|
524
|
+
# @return [String]
|
|
525
|
+
attr_accessor :id
|
|
526
|
+
|
|
527
|
+
# The ID of the dataset this read group belongs to.
|
|
528
|
+
# Corresponds to the JSON property `datasetId`
|
|
529
|
+
# @return [String]
|
|
530
|
+
attr_accessor :dataset_id
|
|
531
|
+
|
|
532
|
+
# The read group name. This corresponds to the @RG ID field in the SAM spec.
|
|
533
|
+
# Corresponds to the JSON property `name`
|
|
534
|
+
# @return [String]
|
|
535
|
+
attr_accessor :name
|
|
536
|
+
|
|
537
|
+
# A free-form text description of this read group.
|
|
538
|
+
# Corresponds to the JSON property `description`
|
|
539
|
+
# @return [String]
|
|
540
|
+
attr_accessor :description
|
|
541
|
+
|
|
542
|
+
# The sample this read group's data was generated from. Note: This is not an
|
|
543
|
+
# actual ID within this repository, but rather an identifier for a sample which
|
|
544
|
+
# may be meaningful to some external system.
|
|
545
|
+
# Corresponds to the JSON property `sampleId`
|
|
546
|
+
# @return [String]
|
|
547
|
+
attr_accessor :sample_id
|
|
548
|
+
|
|
549
|
+
# The experiment used to generate this read group.
|
|
550
|
+
# Corresponds to the JSON property `experiment`
|
|
551
|
+
# @return [Google::Apis::GenomicsV1::Experiment]
|
|
552
|
+
attr_accessor :experiment
|
|
553
|
+
|
|
554
|
+
# The predicted insert size of this read group. The insert size is the length
|
|
555
|
+
# the sequenced DNA fragment from end-to-end, not including the adapters.
|
|
556
|
+
# Corresponds to the JSON property `predictedInsertSize`
|
|
557
|
+
# @return [Fixnum]
|
|
558
|
+
attr_accessor :predicted_insert_size
|
|
559
|
+
|
|
560
|
+
# The programs used to generate this read group. Programs are always identical
|
|
561
|
+
# for all read groups within a read group set. For this reason, only the first
|
|
562
|
+
# read group in a returned set will have this field populated.
|
|
563
|
+
# Corresponds to the JSON property `programs`
|
|
564
|
+
# @return [Array<Google::Apis::GenomicsV1::Program>]
|
|
565
|
+
attr_accessor :programs
|
|
566
|
+
|
|
567
|
+
# The reference set the reads in this read group are aligned to. Required if
|
|
568
|
+
# there are any read alignments.
|
|
569
|
+
# Corresponds to the JSON property `referenceSetId`
|
|
570
|
+
# @return [String]
|
|
571
|
+
attr_accessor :reference_set_id
|
|
572
|
+
|
|
573
|
+
# A map of additional read group information. This must be of the form map (
|
|
574
|
+
# string key mapping to a list of string values).
|
|
575
|
+
# Corresponds to the JSON property `info`
|
|
576
|
+
# @return [Hash<String,Array<Object>>]
|
|
577
|
+
attr_accessor :info
|
|
578
|
+
|
|
579
|
+
def initialize(**args)
|
|
580
|
+
update!(**args)
|
|
581
|
+
end
|
|
582
|
+
|
|
583
|
+
# Update properties of this object
|
|
584
|
+
def update!(**args)
|
|
585
|
+
@id = args[:id] unless args[:id].nil?
|
|
586
|
+
@dataset_id = args[:dataset_id] unless args[:dataset_id].nil?
|
|
587
|
+
@name = args[:name] unless args[:name].nil?
|
|
588
|
+
@description = args[:description] unless args[:description].nil?
|
|
589
|
+
@sample_id = args[:sample_id] unless args[:sample_id].nil?
|
|
590
|
+
@experiment = args[:experiment] unless args[:experiment].nil?
|
|
591
|
+
@predicted_insert_size = args[:predicted_insert_size] unless args[:predicted_insert_size].nil?
|
|
592
|
+
@programs = args[:programs] unless args[:programs].nil?
|
|
593
|
+
@reference_set_id = args[:reference_set_id] unless args[:reference_set_id].nil?
|
|
594
|
+
@info = args[:info] unless args[:info].nil?
|
|
595
|
+
end
|
|
596
|
+
end
|
|
597
|
+
|
|
598
|
+
#
|
|
599
|
+
class Experiment
|
|
600
|
+
include Google::Apis::Core::Hashable
|
|
601
|
+
|
|
602
|
+
# The library used as part of this experiment. Note: This is not an actual ID
|
|
603
|
+
# within this repository, but rather an identifier for a library which may be
|
|
604
|
+
# meaningful to some external system.
|
|
605
|
+
# Corresponds to the JSON property `libraryId`
|
|
606
|
+
# @return [String]
|
|
607
|
+
attr_accessor :library_id
|
|
608
|
+
|
|
609
|
+
# The platform unit used as part of this experiment e.g. flowcell-barcode.lane
|
|
610
|
+
# for Illumina or slide for SOLiD. Corresponds to the @RG PU field in the SAM
|
|
611
|
+
# spec.
|
|
612
|
+
# Corresponds to the JSON property `platformUnit`
|
|
613
|
+
# @return [String]
|
|
614
|
+
attr_accessor :platform_unit
|
|
615
|
+
|
|
616
|
+
# The sequencing center used as part of this experiment.
|
|
617
|
+
# Corresponds to the JSON property `sequencingCenter`
|
|
618
|
+
# @return [String]
|
|
619
|
+
attr_accessor :sequencing_center
|
|
620
|
+
|
|
621
|
+
# The instrument model used as part of this experiment. This maps to sequencing
|
|
622
|
+
# technology in BAM.
|
|
623
|
+
# Corresponds to the JSON property `instrumentModel`
|
|
624
|
+
# @return [String]
|
|
625
|
+
attr_accessor :instrument_model
|
|
626
|
+
|
|
627
|
+
def initialize(**args)
|
|
628
|
+
update!(**args)
|
|
629
|
+
end
|
|
630
|
+
|
|
631
|
+
# Update properties of this object
|
|
632
|
+
def update!(**args)
|
|
633
|
+
@library_id = args[:library_id] unless args[:library_id].nil?
|
|
634
|
+
@platform_unit = args[:platform_unit] unless args[:platform_unit].nil?
|
|
635
|
+
@sequencing_center = args[:sequencing_center] unless args[:sequencing_center].nil?
|
|
636
|
+
@instrument_model = args[:instrument_model] unless args[:instrument_model].nil?
|
|
637
|
+
end
|
|
638
|
+
end
|
|
639
|
+
|
|
640
|
+
#
|
|
641
|
+
class Program
|
|
642
|
+
include Google::Apis::Core::Hashable
|
|
643
|
+
|
|
644
|
+
# The command line used to run this program.
|
|
645
|
+
# Corresponds to the JSON property `commandLine`
|
|
646
|
+
# @return [String]
|
|
647
|
+
attr_accessor :command_line
|
|
648
|
+
|
|
649
|
+
# The user specified locally unique ID of the program. Used along with `
|
|
650
|
+
# prevProgramId` to define an ordering between programs.
|
|
651
|
+
# Corresponds to the JSON property `id`
|
|
652
|
+
# @return [String]
|
|
653
|
+
attr_accessor :id
|
|
654
|
+
|
|
655
|
+
# The name of the program.
|
|
656
|
+
# Corresponds to the JSON property `name`
|
|
657
|
+
# @return [String]
|
|
658
|
+
attr_accessor :name
|
|
659
|
+
|
|
660
|
+
# The ID of the program run before this one.
|
|
661
|
+
# Corresponds to the JSON property `prevProgramId`
|
|
662
|
+
# @return [String]
|
|
663
|
+
attr_accessor :prev_program_id
|
|
664
|
+
|
|
665
|
+
# The version of the program run.
|
|
666
|
+
# Corresponds to the JSON property `version`
|
|
667
|
+
# @return [String]
|
|
668
|
+
attr_accessor :version
|
|
669
|
+
|
|
670
|
+
def initialize(**args)
|
|
671
|
+
update!(**args)
|
|
672
|
+
end
|
|
673
|
+
|
|
674
|
+
# Update properties of this object
|
|
675
|
+
def update!(**args)
|
|
676
|
+
@command_line = args[:command_line] unless args[:command_line].nil?
|
|
677
|
+
@id = args[:id] unless args[:id].nil?
|
|
678
|
+
@name = args[:name] unless args[:name].nil?
|
|
679
|
+
@prev_program_id = args[:prev_program_id] unless args[:prev_program_id].nil?
|
|
680
|
+
@version = args[:version] unless args[:version].nil?
|
|
681
|
+
end
|
|
682
|
+
end
|
|
683
|
+
|
|
684
|
+
#
|
|
685
|
+
class ListCoverageBucketsResponse
|
|
686
|
+
include Google::Apis::Core::Hashable
|
|
687
|
+
|
|
688
|
+
# The length of each coverage bucket in base pairs. Note that buckets at the end
|
|
689
|
+
# of a reference sequence may be shorter. This value is omitted if the bucket
|
|
690
|
+
# width is infinity (the default behaviour, with no range or `targetBucketWidth`)
|
|
691
|
+
# .
|
|
692
|
+
# Corresponds to the JSON property `bucketWidth`
|
|
693
|
+
# @return [String]
|
|
694
|
+
attr_accessor :bucket_width
|
|
695
|
+
|
|
696
|
+
# The coverage buckets. The list of buckets is sparse; a bucket with 0
|
|
697
|
+
# overlapping reads is not returned. A bucket never crosses more than one
|
|
698
|
+
# reference sequence. Each bucket has width `bucketWidth`, unless its end is the
|
|
699
|
+
# end of the reference sequence.
|
|
700
|
+
# Corresponds to the JSON property `coverageBuckets`
|
|
701
|
+
# @return [Array<Google::Apis::GenomicsV1::CoverageBucket>]
|
|
702
|
+
attr_accessor :coverage_buckets
|
|
703
|
+
|
|
704
|
+
# The continuation token, which is used to page through large result sets.
|
|
705
|
+
# Provide this value in a subsequent request to return the next page of results.
|
|
706
|
+
# This field will be empty if there aren't any additional results.
|
|
707
|
+
# Corresponds to the JSON property `nextPageToken`
|
|
708
|
+
# @return [String]
|
|
709
|
+
attr_accessor :next_page_token
|
|
710
|
+
|
|
711
|
+
def initialize(**args)
|
|
712
|
+
update!(**args)
|
|
713
|
+
end
|
|
714
|
+
|
|
715
|
+
# Update properties of this object
|
|
716
|
+
def update!(**args)
|
|
717
|
+
@bucket_width = args[:bucket_width] unless args[:bucket_width].nil?
|
|
718
|
+
@coverage_buckets = args[:coverage_buckets] unless args[:coverage_buckets].nil?
|
|
719
|
+
@next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
|
|
720
|
+
end
|
|
721
|
+
end
|
|
722
|
+
|
|
723
|
+
# A bucket over which read coverage has been precomputed. A bucket corresponds
|
|
724
|
+
# to a specific range of the reference sequence.
|
|
725
|
+
class CoverageBucket
|
|
726
|
+
include Google::Apis::Core::Hashable
|
|
727
|
+
|
|
728
|
+
# A 0-based half-open genomic coordinate range for search requests.
|
|
729
|
+
# Corresponds to the JSON property `range`
|
|
730
|
+
# @return [Google::Apis::GenomicsV1::Range]
|
|
731
|
+
attr_accessor :range
|
|
732
|
+
|
|
733
|
+
# The average number of reads which are aligned to each individual reference
|
|
734
|
+
# base in this bucket.
|
|
735
|
+
# Corresponds to the JSON property `meanCoverage`
|
|
736
|
+
# @return [Float]
|
|
737
|
+
attr_accessor :mean_coverage
|
|
738
|
+
|
|
739
|
+
def initialize(**args)
|
|
740
|
+
update!(**args)
|
|
741
|
+
end
|
|
742
|
+
|
|
743
|
+
# Update properties of this object
|
|
744
|
+
def update!(**args)
|
|
745
|
+
@range = args[:range] unless args[:range].nil?
|
|
746
|
+
@mean_coverage = args[:mean_coverage] unless args[:mean_coverage].nil?
|
|
747
|
+
end
|
|
748
|
+
end
|
|
749
|
+
|
|
750
|
+
# A 0-based half-open genomic coordinate range for search requests.
|
|
751
|
+
class Range
|
|
752
|
+
include Google::Apis::Core::Hashable
|
|
753
|
+
|
|
754
|
+
# The reference sequence name, for example `chr1`, `1`, or `chrX`.
|
|
755
|
+
# Corresponds to the JSON property `referenceName`
|
|
756
|
+
# @return [String]
|
|
757
|
+
attr_accessor :reference_name
|
|
758
|
+
|
|
759
|
+
# The start position of the range on the reference, 0-based inclusive.
|
|
760
|
+
# Corresponds to the JSON property `start`
|
|
761
|
+
# @return [String]
|
|
762
|
+
attr_accessor :start
|
|
763
|
+
|
|
764
|
+
# The end position of the range on the reference, 0-based exclusive.
|
|
765
|
+
# Corresponds to the JSON property `end`
|
|
766
|
+
# @return [String]
|
|
767
|
+
attr_accessor :end
|
|
768
|
+
|
|
769
|
+
def initialize(**args)
|
|
770
|
+
update!(**args)
|
|
771
|
+
end
|
|
772
|
+
|
|
773
|
+
# Update properties of this object
|
|
774
|
+
def update!(**args)
|
|
775
|
+
@reference_name = args[:reference_name] unless args[:reference_name].nil?
|
|
776
|
+
@start = args[:start] unless args[:start].nil?
|
|
777
|
+
@end = args[:end] unless args[:end].nil?
|
|
778
|
+
end
|
|
779
|
+
end
|
|
780
|
+
|
|
781
|
+
# The read search request.
|
|
782
|
+
class SearchReadsRequest
|
|
783
|
+
include Google::Apis::Core::Hashable
|
|
784
|
+
|
|
785
|
+
# The IDs of the read groups sets within which to search for reads. All
|
|
786
|
+
# specified read group sets must be aligned against a common set of reference
|
|
787
|
+
# sequences; this defines the genomic coordinates for the query. Must specify
|
|
788
|
+
# one of `readGroupSetIds` or `readGroupIds`.
|
|
789
|
+
# Corresponds to the JSON property `readGroupSetIds`
|
|
790
|
+
# @return [Array<String>]
|
|
791
|
+
attr_accessor :read_group_set_ids
|
|
792
|
+
|
|
793
|
+
# The IDs of the read groups within which to search for reads. All specified
|
|
794
|
+
# read groups must belong to the same read group sets. Must specify one of `
|
|
795
|
+
# readGroupSetIds` or `readGroupIds`.
|
|
796
|
+
# Corresponds to the JSON property `readGroupIds`
|
|
797
|
+
# @return [Array<String>]
|
|
798
|
+
attr_accessor :read_group_ids
|
|
799
|
+
|
|
800
|
+
# The reference sequence name, for example `chr1`, `1`, or `chrX`. If set to *,
|
|
801
|
+
# only unmapped reads are returned.
|
|
802
|
+
# Corresponds to the JSON property `referenceName`
|
|
803
|
+
# @return [String]
|
|
804
|
+
attr_accessor :reference_name
|
|
805
|
+
|
|
806
|
+
# The start position of the range on the reference, 0-based inclusive. If
|
|
807
|
+
# specified, `referenceName` must also be specified.
|
|
808
|
+
# Corresponds to the JSON property `start`
|
|
809
|
+
# @return [String]
|
|
810
|
+
attr_accessor :start
|
|
811
|
+
|
|
812
|
+
# The end position of the range on the reference, 0-based exclusive. If
|
|
813
|
+
# specified, `referenceName` must also be specified.
|
|
814
|
+
# Corresponds to the JSON property `end`
|
|
815
|
+
# @return [String]
|
|
816
|
+
attr_accessor :end
|
|
817
|
+
|
|
818
|
+
# The continuation token, which is used to page through large result sets. To
|
|
819
|
+
# get the next page of results, set this parameter to the value of `
|
|
820
|
+
# nextPageToken` from the previous response.
|
|
821
|
+
# Corresponds to the JSON property `pageToken`
|
|
822
|
+
# @return [String]
|
|
823
|
+
attr_accessor :page_token
|
|
824
|
+
|
|
825
|
+
# Specifies number of results to return in a single page. If unspecified, it
|
|
826
|
+
# will default to 256. The maximum value is 2048.
|
|
827
|
+
# Corresponds to the JSON property `pageSize`
|
|
828
|
+
# @return [Fixnum]
|
|
829
|
+
attr_accessor :page_size
|
|
830
|
+
|
|
831
|
+
def initialize(**args)
|
|
832
|
+
update!(**args)
|
|
833
|
+
end
|
|
834
|
+
|
|
835
|
+
# Update properties of this object
|
|
836
|
+
def update!(**args)
|
|
837
|
+
@read_group_set_ids = args[:read_group_set_ids] unless args[:read_group_set_ids].nil?
|
|
838
|
+
@read_group_ids = args[:read_group_ids] unless args[:read_group_ids].nil?
|
|
839
|
+
@reference_name = args[:reference_name] unless args[:reference_name].nil?
|
|
840
|
+
@start = args[:start] unless args[:start].nil?
|
|
841
|
+
@end = args[:end] unless args[:end].nil?
|
|
842
|
+
@page_token = args[:page_token] unless args[:page_token].nil?
|
|
843
|
+
@page_size = args[:page_size] unless args[:page_size].nil?
|
|
844
|
+
end
|
|
845
|
+
end
|
|
846
|
+
|
|
847
|
+
# The read search response.
|
|
848
|
+
class SearchReadsResponse
|
|
849
|
+
include Google::Apis::Core::Hashable
|
|
850
|
+
|
|
851
|
+
# The list of matching alignments sorted by mapped genomic coordinate, if any,
|
|
852
|
+
# ascending in position within the same reference. Unmapped reads, which have no
|
|
853
|
+
# position, are returned last and are further sorted in ascending lexicographic
|
|
854
|
+
# order by fragment name.
|
|
855
|
+
# Corresponds to the JSON property `alignments`
|
|
856
|
+
# @return [Array<Google::Apis::GenomicsV1::Read>]
|
|
857
|
+
attr_accessor :alignments
|
|
858
|
+
|
|
859
|
+
# The continuation token, which is used to page through large result sets.
|
|
860
|
+
# Provide this value in a subsequent request to return the next page of results.
|
|
861
|
+
# This field will be empty if there aren't any additional results.
|
|
862
|
+
# Corresponds to the JSON property `nextPageToken`
|
|
863
|
+
# @return [String]
|
|
864
|
+
attr_accessor :next_page_token
|
|
865
|
+
|
|
866
|
+
def initialize(**args)
|
|
867
|
+
update!(**args)
|
|
868
|
+
end
|
|
869
|
+
|
|
870
|
+
# Update properties of this object
|
|
871
|
+
def update!(**args)
|
|
872
|
+
@alignments = args[:alignments] unless args[:alignments].nil?
|
|
873
|
+
@next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
|
|
874
|
+
end
|
|
875
|
+
end
|
|
876
|
+
|
|
877
|
+
# A read alignment describes a linear alignment of a string of DNA to a [
|
|
878
|
+
# reference sequence][google.genomics.v1.Reference], in addition to metadata
|
|
879
|
+
# about the fragment (the molecule of DNA sequenced) and the read (the bases
|
|
880
|
+
# which were read by the sequencer). A read is equivalent to a line in a SAM
|
|
881
|
+
# file. A read belongs to exactly one read group and exactly one [read group set]
|
|
882
|
+
# [google.genomics.v1.ReadGroupSet]. ### Generating a reference-aligned sequence
|
|
883
|
+
# string When interacting with mapped reads, it's often useful to produce a
|
|
884
|
+
# string representing the local alignment of the read to reference. The
|
|
885
|
+
# following pseudocode demonstrates one way of doing this: out = "" offset = 0
|
|
886
|
+
# for c in read.alignment.cigar ` switch c.operation ` case "ALIGNMENT_MATCH", "
|
|
887
|
+
# SEQUENCE_MATCH", "SEQUENCE_MISMATCH": out += read.alignedSequence[offset:
|
|
888
|
+
# offset+c.operationLength] offset += c.operationLength break case "CLIP_SOFT", "
|
|
889
|
+
# INSERT": offset += c.operationLength break case "PAD": out += repeat("*", c.
|
|
890
|
+
# operationLength) break case "DELETE": out += repeat("-", c.operationLength)
|
|
891
|
+
# break case "SKIP": out += repeat(" ", c.operationLength) break case "CLIP_HARD"
|
|
892
|
+
# : break ` ` return out ### Converting to SAM's CIGAR string The following
|
|
893
|
+
# pseudocode generates a SAM CIGAR string from the `cigar` field. Note that this
|
|
894
|
+
# is a lossy conversion (`cigar.referenceSequence` is lost). cigarMap = ` "
|
|
895
|
+
# ALIGNMENT_MATCH": "M", "INSERT": "I", "DELETE": "D", "SKIP": "N", "CLIP_SOFT":
|
|
896
|
+
# "S", "CLIP_HARD": "H", "PAD": "P", "SEQUENCE_MATCH": "=", "SEQUENCE_MISMATCH":
|
|
897
|
+
# "X", ` cigarStr = "" for c in read.alignment.cigar ` cigarStr += c.
|
|
898
|
+
# operationLength + cigarMap[c.operation] ` return cigarStr
|
|
899
|
+
class Read
|
|
900
|
+
include Google::Apis::Core::Hashable
|
|
901
|
+
|
|
902
|
+
# The server-generated read ID, unique across all reads. This is different from
|
|
903
|
+
# the `fragmentName`.
|
|
904
|
+
# Corresponds to the JSON property `id`
|
|
905
|
+
# @return [String]
|
|
906
|
+
attr_accessor :id
|
|
907
|
+
|
|
908
|
+
# The ID of the read group this read belongs to. (Every read must belong to
|
|
909
|
+
# exactly one read group.)
|
|
910
|
+
# Corresponds to the JSON property `readGroupId`
|
|
911
|
+
# @return [String]
|
|
912
|
+
attr_accessor :read_group_id
|
|
913
|
+
|
|
914
|
+
# The ID of the read group set this read belongs to. (Every read must belong to
|
|
915
|
+
# exactly one read group set.)
|
|
916
|
+
# Corresponds to the JSON property `readGroupSetId`
|
|
917
|
+
# @return [String]
|
|
918
|
+
attr_accessor :read_group_set_id
|
|
919
|
+
|
|
920
|
+
# The fragment name. Equivalent to QNAME (query template name) in SAM.
|
|
921
|
+
# Corresponds to the JSON property `fragmentName`
|
|
922
|
+
# @return [String]
|
|
923
|
+
attr_accessor :fragment_name
|
|
924
|
+
|
|
925
|
+
# The orientation and the distance between reads from the fragment are
|
|
926
|
+
# consistent with the sequencing protocol (SAM flag 0x2)
|
|
927
|
+
# Corresponds to the JSON property `properPlacement`
|
|
928
|
+
# @return [Boolean]
|
|
929
|
+
attr_accessor :proper_placement
|
|
930
|
+
alias_method :proper_placement?, :proper_placement
|
|
931
|
+
|
|
932
|
+
# The fragment is a PCR or optical duplicate (SAM flag 0x400)
|
|
933
|
+
# Corresponds to the JSON property `duplicateFragment`
|
|
934
|
+
# @return [Boolean]
|
|
935
|
+
attr_accessor :duplicate_fragment
|
|
936
|
+
alias_method :duplicate_fragment?, :duplicate_fragment
|
|
937
|
+
|
|
938
|
+
# The observed length of the fragment, equivalent to TLEN in SAM.
|
|
939
|
+
# Corresponds to the JSON property `fragmentLength`
|
|
940
|
+
# @return [Fixnum]
|
|
941
|
+
attr_accessor :fragment_length
|
|
942
|
+
|
|
943
|
+
# The read number in sequencing. 0-based and less than numberReads. This field
|
|
944
|
+
# replaces SAM flag 0x40 and 0x80.
|
|
945
|
+
# Corresponds to the JSON property `readNumber`
|
|
946
|
+
# @return [Fixnum]
|
|
947
|
+
attr_accessor :read_number
|
|
948
|
+
|
|
949
|
+
# The number of reads in the fragment (extension to SAM flag 0x1).
|
|
950
|
+
# Corresponds to the JSON property `numberReads`
|
|
951
|
+
# @return [Fixnum]
|
|
952
|
+
attr_accessor :number_reads
|
|
953
|
+
|
|
954
|
+
# SAM flag 0x200
|
|
955
|
+
# Corresponds to the JSON property `failedVendorQualityChecks`
|
|
956
|
+
# @return [Boolean]
|
|
957
|
+
attr_accessor :failed_vendor_quality_checks
|
|
958
|
+
alias_method :failed_vendor_quality_checks?, :failed_vendor_quality_checks
|
|
959
|
+
|
|
960
|
+
# A linear alignment can be represented by one CIGAR string. Describes the
|
|
961
|
+
# mapped position and local alignment of the read to the reference.
|
|
962
|
+
# Corresponds to the JSON property `alignment`
|
|
963
|
+
# @return [Google::Apis::GenomicsV1::LinearAlignment]
|
|
964
|
+
attr_accessor :alignment
|
|
965
|
+
|
|
966
|
+
# Whether this alignment is secondary. Equivalent to SAM flag 0x100. A secondary
|
|
967
|
+
# alignment represents an alternative to the primary alignment for this read.
|
|
968
|
+
# Aligners may return secondary alignments if a read can map ambiguously to
|
|
969
|
+
# multiple coordinates in the genome. By convention, each read has one and only
|
|
970
|
+
# one alignment where both `secondaryAlignment` and `supplementaryAlignment` are
|
|
971
|
+
# false.
|
|
972
|
+
# Corresponds to the JSON property `secondaryAlignment`
|
|
973
|
+
# @return [Boolean]
|
|
974
|
+
attr_accessor :secondary_alignment
|
|
975
|
+
alias_method :secondary_alignment?, :secondary_alignment
|
|
976
|
+
|
|
977
|
+
# Whether this alignment is supplementary. Equivalent to SAM flag 0x800.
|
|
978
|
+
# Supplementary alignments are used in the representation of a chimeric
|
|
979
|
+
# alignment. In a chimeric alignment, a read is split into multiple linear
|
|
980
|
+
# alignments that map to different reference contigs. The first linear alignment
|
|
981
|
+
# in the read will be designated as the representative alignment; the remaining
|
|
982
|
+
# linear alignments will be designated as supplementary alignments. These
|
|
983
|
+
# alignments may have different mapping quality scores. In each linear alignment
|
|
984
|
+
# in a chimeric alignment, the read will be hard clipped. The `alignedSequence`
|
|
985
|
+
# and `alignedQuality` fields in the alignment record will only represent the
|
|
986
|
+
# bases for its respective linear alignment.
|
|
987
|
+
# Corresponds to the JSON property `supplementaryAlignment`
|
|
988
|
+
# @return [Boolean]
|
|
989
|
+
attr_accessor :supplementary_alignment
|
|
990
|
+
alias_method :supplementary_alignment?, :supplementary_alignment
|
|
991
|
+
|
|
992
|
+
# The bases of the read sequence contained in this alignment record, *without
|
|
993
|
+
# CIGAR operations applied*. `alignedSequence` and `alignedQuality` may be
|
|
994
|
+
# shorter than the full read sequence and quality. This will occur if the
|
|
995
|
+
# alignment is part of a chimeric alignment, or if the read was trimmed. When
|
|
996
|
+
# this occurs, the CIGAR for this read will begin/end with a hard clip operator
|
|
997
|
+
# that will indicate the length of the excised sequence.
|
|
998
|
+
# Corresponds to the JSON property `alignedSequence`
|
|
999
|
+
# @return [String]
|
|
1000
|
+
attr_accessor :aligned_sequence
|
|
1001
|
+
|
|
1002
|
+
# The quality of the read sequence contained in this alignment record. `
|
|
1003
|
+
# alignedSequence` and `alignedQuality` may be shorter than the full read
|
|
1004
|
+
# sequence and quality. This will occur if the alignment is part of a chimeric
|
|
1005
|
+
# alignment, or if the read was trimmed. When this occurs, the CIGAR for this
|
|
1006
|
+
# read will begin/end with a hard clip operator that will indicate the length of
|
|
1007
|
+
# the excised sequence.
|
|
1008
|
+
# Corresponds to the JSON property `alignedQuality`
|
|
1009
|
+
# @return [Array<Fixnum>]
|
|
1010
|
+
attr_accessor :aligned_quality
|
|
1011
|
+
|
|
1012
|
+
# An abstraction for referring to a genomic position, in relation to some
|
|
1013
|
+
# already known reference. For now, represents a genomic position as a reference
|
|
1014
|
+
# name, a base number on that reference (0-based), and a determination of
|
|
1015
|
+
# forward or reverse strand.
|
|
1016
|
+
# Corresponds to the JSON property `nextMatePosition`
|
|
1017
|
+
# @return [Google::Apis::GenomicsV1::Position]
|
|
1018
|
+
attr_accessor :next_mate_position
|
|
1019
|
+
|
|
1020
|
+
# A map of additional read alignment information. This must be of the form map (
|
|
1021
|
+
# string key mapping to a list of string values).
|
|
1022
|
+
# Corresponds to the JSON property `info`
|
|
1023
|
+
# @return [Hash<String,Array<Object>>]
|
|
1024
|
+
attr_accessor :info
|
|
1025
|
+
|
|
1026
|
+
def initialize(**args)
|
|
1027
|
+
update!(**args)
|
|
1028
|
+
end
|
|
1029
|
+
|
|
1030
|
+
# Update properties of this object
|
|
1031
|
+
def update!(**args)
|
|
1032
|
+
@id = args[:id] unless args[:id].nil?
|
|
1033
|
+
@read_group_id = args[:read_group_id] unless args[:read_group_id].nil?
|
|
1034
|
+
@read_group_set_id = args[:read_group_set_id] unless args[:read_group_set_id].nil?
|
|
1035
|
+
@fragment_name = args[:fragment_name] unless args[:fragment_name].nil?
|
|
1036
|
+
@proper_placement = args[:proper_placement] unless args[:proper_placement].nil?
|
|
1037
|
+
@duplicate_fragment = args[:duplicate_fragment] unless args[:duplicate_fragment].nil?
|
|
1038
|
+
@fragment_length = args[:fragment_length] unless args[:fragment_length].nil?
|
|
1039
|
+
@read_number = args[:read_number] unless args[:read_number].nil?
|
|
1040
|
+
@number_reads = args[:number_reads] unless args[:number_reads].nil?
|
|
1041
|
+
@failed_vendor_quality_checks = args[:failed_vendor_quality_checks] unless args[:failed_vendor_quality_checks].nil?
|
|
1042
|
+
@alignment = args[:alignment] unless args[:alignment].nil?
|
|
1043
|
+
@secondary_alignment = args[:secondary_alignment] unless args[:secondary_alignment].nil?
|
|
1044
|
+
@supplementary_alignment = args[:supplementary_alignment] unless args[:supplementary_alignment].nil?
|
|
1045
|
+
@aligned_sequence = args[:aligned_sequence] unless args[:aligned_sequence].nil?
|
|
1046
|
+
@aligned_quality = args[:aligned_quality] unless args[:aligned_quality].nil?
|
|
1047
|
+
@next_mate_position = args[:next_mate_position] unless args[:next_mate_position].nil?
|
|
1048
|
+
@info = args[:info] unless args[:info].nil?
|
|
1049
|
+
end
|
|
1050
|
+
end
|
|
1051
|
+
|
|
1052
|
+
# A linear alignment can be represented by one CIGAR string. Describes the
|
|
1053
|
+
# mapped position and local alignment of the read to the reference.
|
|
1054
|
+
class LinearAlignment
|
|
1055
|
+
include Google::Apis::Core::Hashable
|
|
1056
|
+
|
|
1057
|
+
# An abstraction for referring to a genomic position, in relation to some
|
|
1058
|
+
# already known reference. For now, represents a genomic position as a reference
|
|
1059
|
+
# name, a base number on that reference (0-based), and a determination of
|
|
1060
|
+
# forward or reverse strand.
|
|
1061
|
+
# Corresponds to the JSON property `position`
|
|
1062
|
+
# @return [Google::Apis::GenomicsV1::Position]
|
|
1063
|
+
attr_accessor :position
|
|
1064
|
+
|
|
1065
|
+
# The mapping quality of this alignment. Represents how likely the read maps to
|
|
1066
|
+
# this position as opposed to other locations.
|
|
1067
|
+
# Corresponds to the JSON property `mappingQuality`
|
|
1068
|
+
# @return [Fixnum]
|
|
1069
|
+
attr_accessor :mapping_quality
|
|
1070
|
+
|
|
1071
|
+
# Represents the local alignment of this sequence (alignment matches, indels,
|
|
1072
|
+
# etc) against the reference.
|
|
1073
|
+
# Corresponds to the JSON property `cigar`
|
|
1074
|
+
# @return [Array<Google::Apis::GenomicsV1::CigarUnit>]
|
|
1075
|
+
attr_accessor :cigar
|
|
1076
|
+
|
|
1077
|
+
def initialize(**args)
|
|
1078
|
+
update!(**args)
|
|
1079
|
+
end
|
|
1080
|
+
|
|
1081
|
+
# Update properties of this object
|
|
1082
|
+
def update!(**args)
|
|
1083
|
+
@position = args[:position] unless args[:position].nil?
|
|
1084
|
+
@mapping_quality = args[:mapping_quality] unless args[:mapping_quality].nil?
|
|
1085
|
+
@cigar = args[:cigar] unless args[:cigar].nil?
|
|
1086
|
+
end
|
|
1087
|
+
end
|
|
1088
|
+
|
|
1089
|
+
# An abstraction for referring to a genomic position, in relation to some
|
|
1090
|
+
# already known reference. For now, represents a genomic position as a reference
|
|
1091
|
+
# name, a base number on that reference (0-based), and a determination of
|
|
1092
|
+
# forward or reverse strand.
|
|
1093
|
+
class Position
|
|
1094
|
+
include Google::Apis::Core::Hashable
|
|
1095
|
+
|
|
1096
|
+
# The name of the reference in whatever reference set is being used.
|
|
1097
|
+
# Corresponds to the JSON property `referenceName`
|
|
1098
|
+
# @return [String]
|
|
1099
|
+
attr_accessor :reference_name
|
|
1100
|
+
|
|
1101
|
+
# The 0-based offset from the start of the forward strand for that reference.
|
|
1102
|
+
# Corresponds to the JSON property `position`
|
|
1103
|
+
# @return [String]
|
|
1104
|
+
attr_accessor :position
|
|
1105
|
+
|
|
1106
|
+
# Whether this position is on the reverse strand, as opposed to the forward
|
|
1107
|
+
# strand.
|
|
1108
|
+
# Corresponds to the JSON property `reverseStrand`
|
|
1109
|
+
# @return [Boolean]
|
|
1110
|
+
attr_accessor :reverse_strand
|
|
1111
|
+
alias_method :reverse_strand?, :reverse_strand
|
|
1112
|
+
|
|
1113
|
+
def initialize(**args)
|
|
1114
|
+
update!(**args)
|
|
1115
|
+
end
|
|
1116
|
+
|
|
1117
|
+
# Update properties of this object
|
|
1118
|
+
def update!(**args)
|
|
1119
|
+
@reference_name = args[:reference_name] unless args[:reference_name].nil?
|
|
1120
|
+
@position = args[:position] unless args[:position].nil?
|
|
1121
|
+
@reverse_strand = args[:reverse_strand] unless args[:reverse_strand].nil?
|
|
1122
|
+
end
|
|
1123
|
+
end
|
|
1124
|
+
|
|
1125
|
+
# A single CIGAR operation.
|
|
1126
|
+
class CigarUnit
|
|
1127
|
+
include Google::Apis::Core::Hashable
|
|
1128
|
+
|
|
1129
|
+
#
|
|
1130
|
+
# Corresponds to the JSON property `operation`
|
|
1131
|
+
# @return [String]
|
|
1132
|
+
attr_accessor :operation
|
|
1133
|
+
|
|
1134
|
+
# The number of genomic bases that the operation runs for. Required.
|
|
1135
|
+
# Corresponds to the JSON property `operationLength`
|
|
1136
|
+
# @return [String]
|
|
1137
|
+
attr_accessor :operation_length
|
|
1138
|
+
|
|
1139
|
+
# `referenceSequence` is only used at mismatches (`SEQUENCE_MISMATCH`) and
|
|
1140
|
+
# deletions (`DELETE`). Filling this field replaces SAM's MD tag. If the
|
|
1141
|
+
# relevant information is not available, this field is unset.
|
|
1142
|
+
# Corresponds to the JSON property `referenceSequence`
|
|
1143
|
+
# @return [String]
|
|
1144
|
+
attr_accessor :reference_sequence
|
|
1145
|
+
|
|
1146
|
+
def initialize(**args)
|
|
1147
|
+
update!(**args)
|
|
1148
|
+
end
|
|
1149
|
+
|
|
1150
|
+
# Update properties of this object
|
|
1151
|
+
def update!(**args)
|
|
1152
|
+
@operation = args[:operation] unless args[:operation].nil?
|
|
1153
|
+
@operation_length = args[:operation_length] unless args[:operation_length].nil?
|
|
1154
|
+
@reference_sequence = args[:reference_sequence] unless args[:reference_sequence].nil?
|
|
1155
|
+
end
|
|
1156
|
+
end
|
|
1157
|
+
|
|
1158
|
+
#
|
|
1159
|
+
class SearchReferenceSetsRequest
|
|
1160
|
+
include Google::Apis::Core::Hashable
|
|
1161
|
+
|
|
1162
|
+
# If present, return references for which the `md5checksum` matches. See `
|
|
1163
|
+
# ReferenceSet.md5checksum` for details.
|
|
1164
|
+
# Corresponds to the JSON property `md5checksums`
|
|
1165
|
+
# @return [Array<String>]
|
|
1166
|
+
attr_accessor :md5checksums
|
|
1167
|
+
|
|
1168
|
+
# If present, return references for which the accession matches any of these
|
|
1169
|
+
# strings. Best to give a version number, for example `GCF_000001405.26`. If
|
|
1170
|
+
# only the main accession number is given then all records with that main
|
|
1171
|
+
# accession will be returned, whichever version. Note that different versions
|
|
1172
|
+
# will have different sequences.
|
|
1173
|
+
# Corresponds to the JSON property `accessions`
|
|
1174
|
+
# @return [Array<String>]
|
|
1175
|
+
attr_accessor :accessions
|
|
1176
|
+
|
|
1177
|
+
# If present, return reference sets for which a substring of their `assemblyId`
|
|
1178
|
+
# matches this string (case insensitive).
|
|
1179
|
+
# Corresponds to the JSON property `assemblyId`
|
|
1180
|
+
# @return [String]
|
|
1181
|
+
attr_accessor :assembly_id
|
|
1182
|
+
|
|
1183
|
+
# The continuation token, which is used to page through large result sets. To
|
|
1184
|
+
# get the next page of results, set this parameter to the value of `
|
|
1185
|
+
# nextPageToken` from the previous response.
|
|
1186
|
+
# Corresponds to the JSON property `pageToken`
|
|
1187
|
+
# @return [String]
|
|
1188
|
+
attr_accessor :page_token
|
|
1189
|
+
|
|
1190
|
+
# Specifies the maximum number of results to return in a single page.
|
|
1191
|
+
# Corresponds to the JSON property `pageSize`
|
|
1192
|
+
# @return [Fixnum]
|
|
1193
|
+
attr_accessor :page_size
|
|
1194
|
+
|
|
1195
|
+
def initialize(**args)
|
|
1196
|
+
update!(**args)
|
|
1197
|
+
end
|
|
1198
|
+
|
|
1199
|
+
# Update properties of this object
|
|
1200
|
+
def update!(**args)
|
|
1201
|
+
@md5checksums = args[:md5checksums] unless args[:md5checksums].nil?
|
|
1202
|
+
@accessions = args[:accessions] unless args[:accessions].nil?
|
|
1203
|
+
@assembly_id = args[:assembly_id] unless args[:assembly_id].nil?
|
|
1204
|
+
@page_token = args[:page_token] unless args[:page_token].nil?
|
|
1205
|
+
@page_size = args[:page_size] unless args[:page_size].nil?
|
|
1206
|
+
end
|
|
1207
|
+
end
|
|
1208
|
+
|
|
1209
|
+
#
|
|
1210
|
+
class SearchReferenceSetsResponse
|
|
1211
|
+
include Google::Apis::Core::Hashable
|
|
1212
|
+
|
|
1213
|
+
# The matching references sets.
|
|
1214
|
+
# Corresponds to the JSON property `referenceSets`
|
|
1215
|
+
# @return [Array<Google::Apis::GenomicsV1::ReferenceSet>]
|
|
1216
|
+
attr_accessor :reference_sets
|
|
1217
|
+
|
|
1218
|
+
# The continuation token, which is used to page through large result sets.
|
|
1219
|
+
# Provide this value in a subsequent request to return the next page of results.
|
|
1220
|
+
# This field will be empty if there aren't any additional results.
|
|
1221
|
+
# Corresponds to the JSON property `nextPageToken`
|
|
1222
|
+
# @return [String]
|
|
1223
|
+
attr_accessor :next_page_token
|
|
1224
|
+
|
|
1225
|
+
def initialize(**args)
|
|
1226
|
+
update!(**args)
|
|
1227
|
+
end
|
|
1228
|
+
|
|
1229
|
+
# Update properties of this object
|
|
1230
|
+
def update!(**args)
|
|
1231
|
+
@reference_sets = args[:reference_sets] unless args[:reference_sets].nil?
|
|
1232
|
+
@next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
|
|
1233
|
+
end
|
|
1234
|
+
end
|
|
1235
|
+
|
|
1236
|
+
# A reference set is a set of references which typically comprise a reference
|
|
1237
|
+
# assembly for a species, such as `GRCh38` which is representative of the human
|
|
1238
|
+
# genome. A reference set defines a common coordinate space for comparing
|
|
1239
|
+
# reference-aligned experimental data. A reference set contains 1 or more
|
|
1240
|
+
# references.
|
|
1241
|
+
class ReferenceSet
|
|
1242
|
+
include Google::Apis::Core::Hashable
|
|
1243
|
+
|
|
1244
|
+
# The server-generated reference set ID, unique across all reference sets.
|
|
1245
|
+
# Corresponds to the JSON property `id`
|
|
1246
|
+
# @return [String]
|
|
1247
|
+
attr_accessor :id
|
|
1248
|
+
|
|
1249
|
+
# The IDs of the reference objects that are part of this set. `Reference.
|
|
1250
|
+
# md5checksum` must be unique within this set.
|
|
1251
|
+
# Corresponds to the JSON property `referenceIds`
|
|
1252
|
+
# @return [Array<String>]
|
|
1253
|
+
attr_accessor :reference_ids
|
|
1254
|
+
|
|
1255
|
+
# Order-independent MD5 checksum which identifies this reference set. The
|
|
1256
|
+
# checksum is computed by sorting all lower case hexidecimal string `reference.
|
|
1257
|
+
# md5checksum` (for all reference in this set) in ascending lexicographic order,
|
|
1258
|
+
# concatenating, and taking the MD5 of that value. The resulting value is
|
|
1259
|
+
# represented in lower case hexadecimal format.
|
|
1260
|
+
# Corresponds to the JSON property `md5checksum`
|
|
1261
|
+
# @return [String]
|
|
1262
|
+
attr_accessor :md5checksum
|
|
1263
|
+
|
|
1264
|
+
# ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human) indicating the
|
|
1265
|
+
# species which this assembly is intended to model. Note that contained
|
|
1266
|
+
# references may specify a different `ncbiTaxonId`, as assemblies may contain
|
|
1267
|
+
# reference sequences which do not belong to the modeled species, e.g. EBV in a
|
|
1268
|
+
# human reference genome.
|
|
1269
|
+
# Corresponds to the JSON property `ncbiTaxonId`
|
|
1270
|
+
# @return [Fixnum]
|
|
1271
|
+
attr_accessor :ncbi_taxon_id
|
|
1272
|
+
|
|
1273
|
+
# Free text description of this reference set.
|
|
1274
|
+
# Corresponds to the JSON property `description`
|
|
1275
|
+
# @return [String]
|
|
1276
|
+
attr_accessor :description
|
|
1277
|
+
|
|
1278
|
+
# Public id of this reference set, such as `GRCh37`.
|
|
1279
|
+
# Corresponds to the JSON property `assemblyId`
|
|
1280
|
+
# @return [String]
|
|
1281
|
+
attr_accessor :assembly_id
|
|
1282
|
+
|
|
1283
|
+
# The URI from which the references were obtained.
|
|
1284
|
+
# Corresponds to the JSON property `sourceUri`
|
|
1285
|
+
# @return [String]
|
|
1286
|
+
attr_accessor :source_uri
|
|
1287
|
+
|
|
1288
|
+
# All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with
|
|
1289
|
+
# a version number, for example `NC_000001.11`.
|
|
1290
|
+
# Corresponds to the JSON property `sourceAccessions`
|
|
1291
|
+
# @return [Array<String>]
|
|
1292
|
+
attr_accessor :source_accessions
|
|
1293
|
+
|
|
1294
|
+
def initialize(**args)
|
|
1295
|
+
update!(**args)
|
|
1296
|
+
end
|
|
1297
|
+
|
|
1298
|
+
# Update properties of this object
|
|
1299
|
+
def update!(**args)
|
|
1300
|
+
@id = args[:id] unless args[:id].nil?
|
|
1301
|
+
@reference_ids = args[:reference_ids] unless args[:reference_ids].nil?
|
|
1302
|
+
@md5checksum = args[:md5checksum] unless args[:md5checksum].nil?
|
|
1303
|
+
@ncbi_taxon_id = args[:ncbi_taxon_id] unless args[:ncbi_taxon_id].nil?
|
|
1304
|
+
@description = args[:description] unless args[:description].nil?
|
|
1305
|
+
@assembly_id = args[:assembly_id] unless args[:assembly_id].nil?
|
|
1306
|
+
@source_uri = args[:source_uri] unless args[:source_uri].nil?
|
|
1307
|
+
@source_accessions = args[:source_accessions] unless args[:source_accessions].nil?
|
|
1308
|
+
end
|
|
1309
|
+
end
|
|
1310
|
+
|
|
1311
|
+
#
|
|
1312
|
+
class SearchReferencesRequest
|
|
1313
|
+
include Google::Apis::Core::Hashable
|
|
1314
|
+
|
|
1315
|
+
# If present, return references for which the `md5checksum` matches. See `
|
|
1316
|
+
# Reference.md5checksum` for construction details.
|
|
1317
|
+
# Corresponds to the JSON property `md5checksums`
|
|
1318
|
+
# @return [Array<String>]
|
|
1319
|
+
attr_accessor :md5checksums
|
|
1320
|
+
|
|
1321
|
+
# If present, return references for which the accession matches this string.
|
|
1322
|
+
# Best to give a version number, for example `GCF_000001405.26`. If only the
|
|
1323
|
+
# main accession number is given then all records with that main accession will
|
|
1324
|
+
# be returned, whichever version. Note that different versions will have
|
|
1325
|
+
# different sequences.
|
|
1326
|
+
# Corresponds to the JSON property `accessions`
|
|
1327
|
+
# @return [Array<String>]
|
|
1328
|
+
attr_accessor :accessions
|
|
1329
|
+
|
|
1330
|
+
# If present, return only references which belong to this reference set.
|
|
1331
|
+
# Corresponds to the JSON property `referenceSetId`
|
|
1332
|
+
# @return [String]
|
|
1333
|
+
attr_accessor :reference_set_id
|
|
1334
|
+
|
|
1335
|
+
# The continuation token, which is used to page through large result sets. To
|
|
1336
|
+
# get the next page of results, set this parameter to the value of `
|
|
1337
|
+
# nextPageToken` from the previous response.
|
|
1338
|
+
# Corresponds to the JSON property `pageToken`
|
|
1339
|
+
# @return [String]
|
|
1340
|
+
attr_accessor :page_token
|
|
1341
|
+
|
|
1342
|
+
# Specifies the maximum number of results to return in a single page.
|
|
1343
|
+
# Corresponds to the JSON property `pageSize`
|
|
1344
|
+
# @return [Fixnum]
|
|
1345
|
+
attr_accessor :page_size
|
|
1346
|
+
|
|
1347
|
+
def initialize(**args)
|
|
1348
|
+
update!(**args)
|
|
1349
|
+
end
|
|
1350
|
+
|
|
1351
|
+
# Update properties of this object
|
|
1352
|
+
def update!(**args)
|
|
1353
|
+
@md5checksums = args[:md5checksums] unless args[:md5checksums].nil?
|
|
1354
|
+
@accessions = args[:accessions] unless args[:accessions].nil?
|
|
1355
|
+
@reference_set_id = args[:reference_set_id] unless args[:reference_set_id].nil?
|
|
1356
|
+
@page_token = args[:page_token] unless args[:page_token].nil?
|
|
1357
|
+
@page_size = args[:page_size] unless args[:page_size].nil?
|
|
1358
|
+
end
|
|
1359
|
+
end
|
|
1360
|
+
|
|
1361
|
+
#
|
|
1362
|
+
class SearchReferencesResponse
|
|
1363
|
+
include Google::Apis::Core::Hashable
|
|
1364
|
+
|
|
1365
|
+
# The matching references.
|
|
1366
|
+
# Corresponds to the JSON property `references`
|
|
1367
|
+
# @return [Array<Google::Apis::GenomicsV1::Reference>]
|
|
1368
|
+
attr_accessor :references
|
|
1369
|
+
|
|
1370
|
+
# The continuation token, which is used to page through large result sets.
|
|
1371
|
+
# Provide this value in a subsequent request to return the next page of results.
|
|
1372
|
+
# This field will be empty if there aren't any additional results.
|
|
1373
|
+
# Corresponds to the JSON property `nextPageToken`
|
|
1374
|
+
# @return [String]
|
|
1375
|
+
attr_accessor :next_page_token
|
|
1376
|
+
|
|
1377
|
+
def initialize(**args)
|
|
1378
|
+
update!(**args)
|
|
1379
|
+
end
|
|
1380
|
+
|
|
1381
|
+
# Update properties of this object
|
|
1382
|
+
def update!(**args)
|
|
1383
|
+
@references = args[:references] unless args[:references].nil?
|
|
1384
|
+
@next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
|
|
1385
|
+
end
|
|
1386
|
+
end
|
|
1387
|
+
|
|
1388
|
+
# A reference is a canonical assembled DNA sequence, intended to act as a
|
|
1389
|
+
# reference coordinate space for other genomic annotations. A single reference
|
|
1390
|
+
# might represent the human chromosome 1 or mitochandrial DNA, for instance. A
|
|
1391
|
+
# reference belongs to one or more reference sets.
|
|
1392
|
+
class Reference
|
|
1393
|
+
include Google::Apis::Core::Hashable
|
|
1394
|
+
|
|
1395
|
+
# The server-generated reference ID, unique across all references.
|
|
1396
|
+
# Corresponds to the JSON property `id`
|
|
1397
|
+
# @return [String]
|
|
1398
|
+
attr_accessor :id
|
|
1399
|
+
|
|
1400
|
+
# The length of this reference's sequence.
|
|
1401
|
+
# Corresponds to the JSON property `length`
|
|
1402
|
+
# @return [String]
|
|
1403
|
+
attr_accessor :length
|
|
1404
|
+
|
|
1405
|
+
# MD5 of the upper-case sequence excluding all whitespace characters (this is
|
|
1406
|
+
# equivalent to SQ:M5 in SAM). This value is represented in lower case
|
|
1407
|
+
# hexadecimal format.
|
|
1408
|
+
# Corresponds to the JSON property `md5checksum`
|
|
1409
|
+
# @return [String]
|
|
1410
|
+
attr_accessor :md5checksum
|
|
1411
|
+
|
|
1412
|
+
# The name of this reference, for example `22`.
|
|
1413
|
+
# Corresponds to the JSON property `name`
|
|
1414
|
+
# @return [String]
|
|
1415
|
+
attr_accessor :name
|
|
1416
|
+
|
|
1417
|
+
# The URI from which the sequence was obtained. Specifies a FASTA format file/
|
|
1418
|
+
# string with one name, sequence pair.
|
|
1419
|
+
# Corresponds to the JSON property `sourceUri`
|
|
1420
|
+
# @return [String]
|
|
1421
|
+
attr_accessor :source_uri
|
|
1422
|
+
|
|
1423
|
+
# All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with
|
|
1424
|
+
# a version number, for example `GCF_000001405.26`.
|
|
1425
|
+
# Corresponds to the JSON property `sourceAccessions`
|
|
1426
|
+
# @return [Array<String>]
|
|
1427
|
+
attr_accessor :source_accessions
|
|
1428
|
+
|
|
1429
|
+
# ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human) if not
|
|
1430
|
+
# specified by the containing reference set.
|
|
1431
|
+
# Corresponds to the JSON property `ncbiTaxonId`
|
|
1432
|
+
# @return [Fixnum]
|
|
1433
|
+
attr_accessor :ncbi_taxon_id
|
|
1434
|
+
|
|
1435
|
+
def initialize(**args)
|
|
1436
|
+
update!(**args)
|
|
1437
|
+
end
|
|
1438
|
+
|
|
1439
|
+
# Update properties of this object
|
|
1440
|
+
def update!(**args)
|
|
1441
|
+
@id = args[:id] unless args[:id].nil?
|
|
1442
|
+
@length = args[:length] unless args[:length].nil?
|
|
1443
|
+
@md5checksum = args[:md5checksum] unless args[:md5checksum].nil?
|
|
1444
|
+
@name = args[:name] unless args[:name].nil?
|
|
1445
|
+
@source_uri = args[:source_uri] unless args[:source_uri].nil?
|
|
1446
|
+
@source_accessions = args[:source_accessions] unless args[:source_accessions].nil?
|
|
1447
|
+
@ncbi_taxon_id = args[:ncbi_taxon_id] unless args[:ncbi_taxon_id].nil?
|
|
1448
|
+
end
|
|
1449
|
+
end
|
|
1450
|
+
|
|
1451
|
+
#
|
|
1452
|
+
class ListBasesResponse
|
|
1453
|
+
include Google::Apis::Core::Hashable
|
|
1454
|
+
|
|
1455
|
+
# The offset position (0-based) of the given `sequence` from the start of this `
|
|
1456
|
+
# Reference`. This value will differ for each page in a paginated request.
|
|
1457
|
+
# Corresponds to the JSON property `offset`
|
|
1458
|
+
# @return [String]
|
|
1459
|
+
attr_accessor :offset
|
|
1460
|
+
|
|
1461
|
+
# A substring of the bases that make up this reference.
|
|
1462
|
+
# Corresponds to the JSON property `sequence`
|
|
1463
|
+
# @return [String]
|
|
1464
|
+
attr_accessor :sequence
|
|
1465
|
+
|
|
1466
|
+
# The continuation token, which is used to page through large result sets.
|
|
1467
|
+
# Provide this value in a subsequent request to return the next page of results.
|
|
1468
|
+
# This field will be empty if there aren't any additional results.
|
|
1469
|
+
# Corresponds to the JSON property `nextPageToken`
|
|
1470
|
+
# @return [String]
|
|
1471
|
+
attr_accessor :next_page_token
|
|
1472
|
+
|
|
1473
|
+
def initialize(**args)
|
|
1474
|
+
update!(**args)
|
|
1475
|
+
end
|
|
1476
|
+
|
|
1477
|
+
# Update properties of this object
|
|
1478
|
+
def update!(**args)
|
|
1479
|
+
@offset = args[:offset] unless args[:offset].nil?
|
|
1480
|
+
@sequence = args[:sequence] unless args[:sequence].nil?
|
|
1481
|
+
@next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
|
|
1482
|
+
end
|
|
1483
|
+
end
|
|
1484
|
+
|
|
1485
|
+
# The variant data import request.
|
|
1486
|
+
class ImportVariantsRequest
|
|
1487
|
+
include Google::Apis::Core::Hashable
|
|
1488
|
+
|
|
1489
|
+
# Required. The variant set to which variant data should be imported.
|
|
1490
|
+
# Corresponds to the JSON property `variantSetId`
|
|
1491
|
+
# @return [String]
|
|
1492
|
+
attr_accessor :variant_set_id
|
|
1493
|
+
|
|
1494
|
+
# A list of URIs referencing variant files in Google Cloud Storage. URIs can
|
|
1495
|
+
# include wildcards [as described here](https://cloud.google.com/storage/docs/
|
|
1496
|
+
# gsutil/addlhelp/WildcardNames). Note that recursive wildcards ('**') are not
|
|
1497
|
+
# supported.
|
|
1498
|
+
# Corresponds to the JSON property `sourceUris`
|
|
1499
|
+
# @return [Array<String>]
|
|
1500
|
+
attr_accessor :source_uris
|
|
1501
|
+
|
|
1502
|
+
# The format of the variant data being imported. If unspecified, defaults to to `
|
|
1503
|
+
# VCF`.
|
|
1504
|
+
# Corresponds to the JSON property `format`
|
|
1505
|
+
# @return [String]
|
|
1506
|
+
attr_accessor :format
|
|
1507
|
+
|
|
1508
|
+
# Convert reference names to the canonical representation. hg19 haploytypes (
|
|
1509
|
+
# those reference names containing "_hap") are not modified in any way. All
|
|
1510
|
+
# other reference names are modified according to the following rules: The
|
|
1511
|
+
# reference name is capitalized. The "chr" prefix is dropped for all autosomes
|
|
1512
|
+
# and sex chromsomes. For example "chr17" becomes "17" and "chrX" becomes "X".
|
|
1513
|
+
# All mitochondrial chromosomes ("chrM", "chrMT", etc) become "MT".
|
|
1514
|
+
# Corresponds to the JSON property `normalizeReferenceNames`
|
|
1515
|
+
# @return [Boolean]
|
|
1516
|
+
attr_accessor :normalize_reference_names
|
|
1517
|
+
alias_method :normalize_reference_names?, :normalize_reference_names
|
|
1518
|
+
|
|
1519
|
+
def initialize(**args)
|
|
1520
|
+
update!(**args)
|
|
1521
|
+
end
|
|
1522
|
+
|
|
1523
|
+
# Update properties of this object
|
|
1524
|
+
def update!(**args)
|
|
1525
|
+
@variant_set_id = args[:variant_set_id] unless args[:variant_set_id].nil?
|
|
1526
|
+
@source_uris = args[:source_uris] unless args[:source_uris].nil?
|
|
1527
|
+
@format = args[:format] unless args[:format].nil?
|
|
1528
|
+
@normalize_reference_names = args[:normalize_reference_names] unless args[:normalize_reference_names].nil?
|
|
1529
|
+
end
|
|
1530
|
+
end
|
|
1531
|
+
|
|
1532
|
+
# A variant set is a collection of call sets and variants. It contains summary
|
|
1533
|
+
# statistics of those contents. A variant set belongs to a dataset.
|
|
1534
|
+
class VariantSet
|
|
1535
|
+
include Google::Apis::Core::Hashable
|
|
1536
|
+
|
|
1537
|
+
# The dataset to which this variant set belongs.
|
|
1538
|
+
# Corresponds to the JSON property `datasetId`
|
|
1539
|
+
# @return [String]
|
|
1540
|
+
attr_accessor :dataset_id
|
|
1541
|
+
|
|
1542
|
+
# The server-generated variant set ID, unique across all variant sets.
|
|
1543
|
+
# Corresponds to the JSON property `id`
|
|
1544
|
+
# @return [String]
|
|
1545
|
+
attr_accessor :id
|
|
1546
|
+
|
|
1547
|
+
# A list of all references used by the variants in a variant set with associated
|
|
1548
|
+
# coordinate upper bounds for each one.
|
|
1549
|
+
# Corresponds to the JSON property `referenceBounds`
|
|
1550
|
+
# @return [Array<Google::Apis::GenomicsV1::ReferenceBound>]
|
|
1551
|
+
attr_accessor :reference_bounds
|
|
1552
|
+
|
|
1553
|
+
# The metadata associated with this variant set.
|
|
1554
|
+
# Corresponds to the JSON property `metadata`
|
|
1555
|
+
# @return [Array<Google::Apis::GenomicsV1::VariantSetMetadata>]
|
|
1556
|
+
attr_accessor :metadata
|
|
1557
|
+
|
|
1558
|
+
def initialize(**args)
|
|
1559
|
+
update!(**args)
|
|
1560
|
+
end
|
|
1561
|
+
|
|
1562
|
+
# Update properties of this object
|
|
1563
|
+
def update!(**args)
|
|
1564
|
+
@dataset_id = args[:dataset_id] unless args[:dataset_id].nil?
|
|
1565
|
+
@id = args[:id] unless args[:id].nil?
|
|
1566
|
+
@reference_bounds = args[:reference_bounds] unless args[:reference_bounds].nil?
|
|
1567
|
+
@metadata = args[:metadata] unless args[:metadata].nil?
|
|
1568
|
+
end
|
|
1569
|
+
end
|
|
1570
|
+
|
|
1571
|
+
# ReferenceBound records an upper bound for the starting coordinate of variants
|
|
1572
|
+
# in a particular reference.
|
|
1573
|
+
class ReferenceBound
|
|
1574
|
+
include Google::Apis::Core::Hashable
|
|
1575
|
+
|
|
1576
|
+
# The reference the bound is associate with.
|
|
1577
|
+
# Corresponds to the JSON property `referenceName`
|
|
1578
|
+
# @return [String]
|
|
1579
|
+
attr_accessor :reference_name
|
|
1580
|
+
|
|
1581
|
+
# An upper bound (inclusive) on the starting coordinate of any variant in the
|
|
1582
|
+
# reference sequence.
|
|
1583
|
+
# Corresponds to the JSON property `upperBound`
|
|
1584
|
+
# @return [String]
|
|
1585
|
+
attr_accessor :upper_bound
|
|
1586
|
+
|
|
1587
|
+
def initialize(**args)
|
|
1588
|
+
update!(**args)
|
|
1589
|
+
end
|
|
1590
|
+
|
|
1591
|
+
# Update properties of this object
|
|
1592
|
+
def update!(**args)
|
|
1593
|
+
@reference_name = args[:reference_name] unless args[:reference_name].nil?
|
|
1594
|
+
@upper_bound = args[:upper_bound] unless args[:upper_bound].nil?
|
|
1595
|
+
end
|
|
1596
|
+
end
|
|
1597
|
+
|
|
1598
|
+
# Metadata describes a single piece of variant call metadata. These data include
|
|
1599
|
+
# a top level key and either a single value string (value) or a list of key-
|
|
1600
|
+
# value pairs (info.) Value and info are mutually exclusive.
|
|
1601
|
+
class VariantSetMetadata
|
|
1602
|
+
include Google::Apis::Core::Hashable
|
|
1603
|
+
|
|
1604
|
+
# The top-level key.
|
|
1605
|
+
# Corresponds to the JSON property `key`
|
|
1606
|
+
# @return [String]
|
|
1607
|
+
attr_accessor :key
|
|
1608
|
+
|
|
1609
|
+
# The value field for simple metadata
|
|
1610
|
+
# Corresponds to the JSON property `value`
|
|
1611
|
+
# @return [String]
|
|
1612
|
+
attr_accessor :value
|
|
1613
|
+
|
|
1614
|
+
# User-provided ID field, not enforced by this API. Two or more pieces of
|
|
1615
|
+
# structured metadata with identical id and key fields are considered equivalent.
|
|
1616
|
+
# Corresponds to the JSON property `id`
|
|
1617
|
+
# @return [String]
|
|
1618
|
+
attr_accessor :id
|
|
1619
|
+
|
|
1620
|
+
# The type of data. Possible types include: Integer, Float, Flag, Character, and
|
|
1621
|
+
# String.
|
|
1622
|
+
# Corresponds to the JSON property `type`
|
|
1623
|
+
# @return [String]
|
|
1624
|
+
attr_accessor :type
|
|
1625
|
+
|
|
1626
|
+
# The number of values that can be included in a field described by this
|
|
1627
|
+
# metadata.
|
|
1628
|
+
# Corresponds to the JSON property `number`
|
|
1629
|
+
# @return [Fixnum]
|
|
1630
|
+
attr_accessor :number
|
|
1631
|
+
|
|
1632
|
+
# A textual description of this metadata.
|
|
1633
|
+
# Corresponds to the JSON property `description`
|
|
1634
|
+
# @return [String]
|
|
1635
|
+
attr_accessor :description
|
|
1636
|
+
|
|
1637
|
+
# Remaining structured metadata key-value pairs. This must be of the form map (
|
|
1638
|
+
# string key mapping to a list of string values).
|
|
1639
|
+
# Corresponds to the JSON property `info`
|
|
1640
|
+
# @return [Hash<String,Array<Object>>]
|
|
1641
|
+
attr_accessor :info
|
|
1642
|
+
|
|
1643
|
+
def initialize(**args)
|
|
1644
|
+
update!(**args)
|
|
1645
|
+
end
|
|
1646
|
+
|
|
1647
|
+
# Update properties of this object
|
|
1648
|
+
def update!(**args)
|
|
1649
|
+
@key = args[:key] unless args[:key].nil?
|
|
1650
|
+
@value = args[:value] unless args[:value].nil?
|
|
1651
|
+
@id = args[:id] unless args[:id].nil?
|
|
1652
|
+
@type = args[:type] unless args[:type].nil?
|
|
1653
|
+
@number = args[:number] unless args[:number].nil?
|
|
1654
|
+
@description = args[:description] unless args[:description].nil?
|
|
1655
|
+
@info = args[:info] unless args[:info].nil?
|
|
1656
|
+
end
|
|
1657
|
+
end
|
|
1658
|
+
|
|
1659
|
+
# The variant data export request.
|
|
1660
|
+
class ExportVariantSetRequest
|
|
1661
|
+
include Google::Apis::Core::Hashable
|
|
1662
|
+
|
|
1663
|
+
# If provided, only variant call information from the specified call sets will
|
|
1664
|
+
# be exported. By default all variant calls are exported.
|
|
1665
|
+
# Corresponds to the JSON property `callSetIds`
|
|
1666
|
+
# @return [Array<String>]
|
|
1667
|
+
attr_accessor :call_set_ids
|
|
1668
|
+
|
|
1669
|
+
# Required. The Google Cloud project ID that owns the destination BigQuery
|
|
1670
|
+
# dataset. The caller must have WRITE access to this project. This project will
|
|
1671
|
+
# also own the resulting export job.
|
|
1672
|
+
# Corresponds to the JSON property `projectId`
|
|
1673
|
+
# @return [String]
|
|
1674
|
+
attr_accessor :project_id
|
|
1675
|
+
|
|
1676
|
+
# The format for the exported data.
|
|
1677
|
+
# Corresponds to the JSON property `format`
|
|
1678
|
+
# @return [String]
|
|
1679
|
+
attr_accessor :format
|
|
1680
|
+
|
|
1681
|
+
# Required. The BigQuery dataset to export data to. This dataset must already
|
|
1682
|
+
# exist. Note that this is distinct from the Genomics concept of "dataset".
|
|
1683
|
+
# Corresponds to the JSON property `bigqueryDataset`
|
|
1684
|
+
# @return [String]
|
|
1685
|
+
attr_accessor :bigquery_dataset
|
|
1686
|
+
|
|
1687
|
+
# Required. The BigQuery table to export data to. If the table doesn't exist, it
|
|
1688
|
+
# will be created. If it already exists, it will be overwritten.
|
|
1689
|
+
# Corresponds to the JSON property `bigqueryTable`
|
|
1690
|
+
# @return [String]
|
|
1691
|
+
attr_accessor :bigquery_table
|
|
1692
|
+
|
|
1693
|
+
def initialize(**args)
|
|
1694
|
+
update!(**args)
|
|
1695
|
+
end
|
|
1696
|
+
|
|
1697
|
+
# Update properties of this object
|
|
1698
|
+
def update!(**args)
|
|
1699
|
+
@call_set_ids = args[:call_set_ids] unless args[:call_set_ids].nil?
|
|
1700
|
+
@project_id = args[:project_id] unless args[:project_id].nil?
|
|
1701
|
+
@format = args[:format] unless args[:format].nil?
|
|
1702
|
+
@bigquery_dataset = args[:bigquery_dataset] unless args[:bigquery_dataset].nil?
|
|
1703
|
+
@bigquery_table = args[:bigquery_table] unless args[:bigquery_table].nil?
|
|
1704
|
+
end
|
|
1705
|
+
end
|
|
1706
|
+
|
|
1707
|
+
# The search variant sets request.
|
|
1708
|
+
class SearchVariantSetsRequest
|
|
1709
|
+
include Google::Apis::Core::Hashable
|
|
1710
|
+
|
|
1711
|
+
# Exactly one dataset ID must be provided here. Only variant sets which belong
|
|
1712
|
+
# to this dataset will be returned.
|
|
1713
|
+
# Corresponds to the JSON property `datasetIds`
|
|
1714
|
+
# @return [Array<String>]
|
|
1715
|
+
attr_accessor :dataset_ids
|
|
1716
|
+
|
|
1717
|
+
# The continuation token, which is used to page through large result sets. To
|
|
1718
|
+
# get the next page of results, set this parameter to the value of `
|
|
1719
|
+
# nextPageToken` from the previous response.
|
|
1720
|
+
# Corresponds to the JSON property `pageToken`
|
|
1721
|
+
# @return [String]
|
|
1722
|
+
attr_accessor :page_token
|
|
1723
|
+
|
|
1724
|
+
# The maximum number of variant sets to return in a request.
|
|
1725
|
+
# Corresponds to the JSON property `pageSize`
|
|
1726
|
+
# @return [Fixnum]
|
|
1727
|
+
attr_accessor :page_size
|
|
1728
|
+
|
|
1729
|
+
def initialize(**args)
|
|
1730
|
+
update!(**args)
|
|
1731
|
+
end
|
|
1732
|
+
|
|
1733
|
+
# Update properties of this object
|
|
1734
|
+
def update!(**args)
|
|
1735
|
+
@dataset_ids = args[:dataset_ids] unless args[:dataset_ids].nil?
|
|
1736
|
+
@page_token = args[:page_token] unless args[:page_token].nil?
|
|
1737
|
+
@page_size = args[:page_size] unless args[:page_size].nil?
|
|
1738
|
+
end
|
|
1739
|
+
end
|
|
1740
|
+
|
|
1741
|
+
# The search variant sets response.
|
|
1742
|
+
class SearchVariantSetsResponse
|
|
1743
|
+
include Google::Apis::Core::Hashable
|
|
1744
|
+
|
|
1745
|
+
# The variant sets belonging to the requested dataset.
|
|
1746
|
+
# Corresponds to the JSON property `variantSets`
|
|
1747
|
+
# @return [Array<Google::Apis::GenomicsV1::VariantSet>]
|
|
1748
|
+
attr_accessor :variant_sets
|
|
1749
|
+
|
|
1750
|
+
# The continuation token, which is used to page through large result sets.
|
|
1751
|
+
# Provide this value in a subsequent request to return the next page of results.
|
|
1752
|
+
# This field will be empty if there aren't any additional results.
|
|
1753
|
+
# Corresponds to the JSON property `nextPageToken`
|
|
1754
|
+
# @return [String]
|
|
1755
|
+
attr_accessor :next_page_token
|
|
1756
|
+
|
|
1757
|
+
def initialize(**args)
|
|
1758
|
+
update!(**args)
|
|
1759
|
+
end
|
|
1760
|
+
|
|
1761
|
+
# Update properties of this object
|
|
1762
|
+
def update!(**args)
|
|
1763
|
+
@variant_sets = args[:variant_sets] unless args[:variant_sets].nil?
|
|
1764
|
+
@next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
|
|
1765
|
+
end
|
|
1766
|
+
end
|
|
1767
|
+
|
|
1768
|
+
# The variant search request.
|
|
1769
|
+
class SearchVariantsRequest
|
|
1770
|
+
include Google::Apis::Core::Hashable
|
|
1771
|
+
|
|
1772
|
+
# At most one variant set ID must be provided. Only variants from this variant
|
|
1773
|
+
# set will be returned. If omitted, a call set id must be included in the
|
|
1774
|
+
# request.
|
|
1775
|
+
# Corresponds to the JSON property `variantSetIds`
|
|
1776
|
+
# @return [Array<String>]
|
|
1777
|
+
attr_accessor :variant_set_ids
|
|
1778
|
+
|
|
1779
|
+
# Only return variants which have exactly this name.
|
|
1780
|
+
# Corresponds to the JSON property `variantName`
|
|
1781
|
+
# @return [String]
|
|
1782
|
+
attr_accessor :variant_name
|
|
1783
|
+
|
|
1784
|
+
# Only return variant calls which belong to call sets with these ids. Leaving
|
|
1785
|
+
# this blank returns all variant calls. If a variant has no calls belonging to
|
|
1786
|
+
# any of these call sets, it won't be returned at all. Currently, variants with
|
|
1787
|
+
# no calls from any call set will never be returned.
|
|
1788
|
+
# Corresponds to the JSON property `callSetIds`
|
|
1789
|
+
# @return [Array<String>]
|
|
1790
|
+
attr_accessor :call_set_ids
|
|
1791
|
+
|
|
1792
|
+
# Required. Only return variants in this reference sequence.
|
|
1793
|
+
# Corresponds to the JSON property `referenceName`
|
|
1794
|
+
# @return [String]
|
|
1795
|
+
attr_accessor :reference_name
|
|
1796
|
+
|
|
1797
|
+
# The beginning of the window (0-based, inclusive) for which overlapping
|
|
1798
|
+
# variants should be returned. If unspecified, defaults to 0.
|
|
1799
|
+
# Corresponds to the JSON property `start`
|
|
1800
|
+
# @return [String]
|
|
1801
|
+
attr_accessor :start
|
|
1802
|
+
|
|
1803
|
+
# The end of the window, 0-based exclusive. If unspecified or 0, defaults to the
|
|
1804
|
+
# length of the reference.
|
|
1805
|
+
# Corresponds to the JSON property `end`
|
|
1806
|
+
# @return [String]
|
|
1807
|
+
attr_accessor :end
|
|
1808
|
+
|
|
1809
|
+
# The continuation token, which is used to page through large result sets. To
|
|
1810
|
+
# get the next page of results, set this parameter to the value of `
|
|
1811
|
+
# nextPageToken` from the previous response.
|
|
1812
|
+
# Corresponds to the JSON property `pageToken`
|
|
1813
|
+
# @return [String]
|
|
1814
|
+
attr_accessor :page_token
|
|
1815
|
+
|
|
1816
|
+
# The maximum number of variants to return. If unspecified, defaults to 5000.
|
|
1817
|
+
# Corresponds to the JSON property `pageSize`
|
|
1818
|
+
# @return [Fixnum]
|
|
1819
|
+
attr_accessor :page_size
|
|
1820
|
+
|
|
1821
|
+
# The maximum number of calls to return. However, at least one variant will
|
|
1822
|
+
# always be returned, even if it has more calls than this limit. If unspecified,
|
|
1823
|
+
# defaults to 5000.
|
|
1824
|
+
# Corresponds to the JSON property `maxCalls`
|
|
1825
|
+
# @return [Fixnum]
|
|
1826
|
+
attr_accessor :max_calls
|
|
1827
|
+
|
|
1828
|
+
def initialize(**args)
|
|
1829
|
+
update!(**args)
|
|
1830
|
+
end
|
|
1831
|
+
|
|
1832
|
+
# Update properties of this object
|
|
1833
|
+
def update!(**args)
|
|
1834
|
+
@variant_set_ids = args[:variant_set_ids] unless args[:variant_set_ids].nil?
|
|
1835
|
+
@variant_name = args[:variant_name] unless args[:variant_name].nil?
|
|
1836
|
+
@call_set_ids = args[:call_set_ids] unless args[:call_set_ids].nil?
|
|
1837
|
+
@reference_name = args[:reference_name] unless args[:reference_name].nil?
|
|
1838
|
+
@start = args[:start] unless args[:start].nil?
|
|
1839
|
+
@end = args[:end] unless args[:end].nil?
|
|
1840
|
+
@page_token = args[:page_token] unless args[:page_token].nil?
|
|
1841
|
+
@page_size = args[:page_size] unless args[:page_size].nil?
|
|
1842
|
+
@max_calls = args[:max_calls] unless args[:max_calls].nil?
|
|
1843
|
+
end
|
|
1844
|
+
end
|
|
1845
|
+
|
|
1846
|
+
# The variant search response.
|
|
1847
|
+
class SearchVariantsResponse
|
|
1848
|
+
include Google::Apis::Core::Hashable
|
|
1849
|
+
|
|
1850
|
+
# The list of matching Variants.
|
|
1851
|
+
# Corresponds to the JSON property `variants`
|
|
1852
|
+
# @return [Array<Google::Apis::GenomicsV1::Variant>]
|
|
1853
|
+
attr_accessor :variants
|
|
1854
|
+
|
|
1855
|
+
# The continuation token, which is used to page through large result sets.
|
|
1856
|
+
# Provide this value in a subsequent request to return the next page of results.
|
|
1857
|
+
# This field will be empty if there aren't any additional results.
|
|
1858
|
+
# Corresponds to the JSON property `nextPageToken`
|
|
1859
|
+
# @return [String]
|
|
1860
|
+
attr_accessor :next_page_token
|
|
1861
|
+
|
|
1862
|
+
def initialize(**args)
|
|
1863
|
+
update!(**args)
|
|
1864
|
+
end
|
|
1865
|
+
|
|
1866
|
+
# Update properties of this object
|
|
1867
|
+
def update!(**args)
|
|
1868
|
+
@variants = args[:variants] unless args[:variants].nil?
|
|
1869
|
+
@next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
|
|
1870
|
+
end
|
|
1871
|
+
end
|
|
1872
|
+
|
|
1873
|
+
# A variant represents a change in DNA sequence relative to a reference sequence.
|
|
1874
|
+
# For example, a variant could represent a SNP or an insertion. Variants belong
|
|
1875
|
+
# to a variant set. Each of the calls on a variant represent a determination of
|
|
1876
|
+
# genotype with respect to that variant. For example, a call might assign
|
|
1877
|
+
# probability of 0.32 to the occurrence of a SNP named rs1234 in a sample named
|
|
1878
|
+
# NA12345. A call belongs to a call set, which contains related calls typically
|
|
1879
|
+
# from one sample.
|
|
1880
|
+
class Variant
|
|
1881
|
+
include Google::Apis::Core::Hashable
|
|
1882
|
+
|
|
1883
|
+
# The ID of the variant set this variant belongs to.
|
|
1884
|
+
# Corresponds to the JSON property `variantSetId`
|
|
1885
|
+
# @return [String]
|
|
1886
|
+
attr_accessor :variant_set_id
|
|
1887
|
+
|
|
1888
|
+
# The server-generated variant ID, unique across all variants.
|
|
1889
|
+
# Corresponds to the JSON property `id`
|
|
1890
|
+
# @return [String]
|
|
1891
|
+
attr_accessor :id
|
|
1892
|
+
|
|
1893
|
+
# Names for the variant, for example a RefSNP ID.
|
|
1894
|
+
# Corresponds to the JSON property `names`
|
|
1895
|
+
# @return [Array<String>]
|
|
1896
|
+
attr_accessor :names
|
|
1897
|
+
|
|
1898
|
+
# The date this variant was created, in milliseconds from the epoch.
|
|
1899
|
+
# Corresponds to the JSON property `created`
|
|
1900
|
+
# @return [String]
|
|
1901
|
+
attr_accessor :created
|
|
1902
|
+
|
|
1903
|
+
# The reference on which this variant occurs. (such as `chr20` or `X`)
|
|
1904
|
+
# Corresponds to the JSON property `referenceName`
|
|
1905
|
+
# @return [String]
|
|
1906
|
+
attr_accessor :reference_name
|
|
1907
|
+
|
|
1908
|
+
# The position at which this variant occurs (0-based). This corresponds to the
|
|
1909
|
+
# first base of the string of reference bases.
|
|
1910
|
+
# Corresponds to the JSON property `start`
|
|
1911
|
+
# @return [String]
|
|
1912
|
+
attr_accessor :start
|
|
1913
|
+
|
|
1914
|
+
# The end position (0-based) of this variant. This corresponds to the first base
|
|
1915
|
+
# after the last base in the reference allele. So, the length of the reference
|
|
1916
|
+
# allele is (end - start). This is useful for variants that don't explicitly
|
|
1917
|
+
# give alternate bases, for example large deletions.
|
|
1918
|
+
# Corresponds to the JSON property `end`
|
|
1919
|
+
# @return [String]
|
|
1920
|
+
attr_accessor :end
|
|
1921
|
+
|
|
1922
|
+
# The reference bases for this variant. They start at the given position.
|
|
1923
|
+
# Corresponds to the JSON property `referenceBases`
|
|
1924
|
+
# @return [String]
|
|
1925
|
+
attr_accessor :reference_bases
|
|
1926
|
+
|
|
1927
|
+
# The bases that appear instead of the reference bases.
|
|
1928
|
+
# Corresponds to the JSON property `alternateBases`
|
|
1929
|
+
# @return [Array<String>]
|
|
1930
|
+
attr_accessor :alternate_bases
|
|
1931
|
+
|
|
1932
|
+
# A measure of how likely this variant is to be real. A higher value is better.
|
|
1933
|
+
# Corresponds to the JSON property `quality`
|
|
1934
|
+
# @return [Float]
|
|
1935
|
+
attr_accessor :quality
|
|
1936
|
+
|
|
1937
|
+
# A list of filters (normally quality filters) this variant has failed. `PASS`
|
|
1938
|
+
# indicates this variant has passed all filters.
|
|
1939
|
+
# Corresponds to the JSON property `filter`
|
|
1940
|
+
# @return [Array<String>]
|
|
1941
|
+
attr_accessor :filter
|
|
1942
|
+
|
|
1943
|
+
# A map of additional variant information. This must be of the form map (string
|
|
1944
|
+
# key mapping to a list of string values).
|
|
1945
|
+
# Corresponds to the JSON property `info`
|
|
1946
|
+
# @return [Hash<String,Array<Object>>]
|
|
1947
|
+
attr_accessor :info
|
|
1948
|
+
|
|
1949
|
+
# The variant calls for this particular variant. Each one represents the
|
|
1950
|
+
# determination of genotype with respect to this variant.
|
|
1951
|
+
# Corresponds to the JSON property `calls`
|
|
1952
|
+
# @return [Array<Google::Apis::GenomicsV1::VariantCall>]
|
|
1953
|
+
attr_accessor :calls
|
|
1954
|
+
|
|
1955
|
+
def initialize(**args)
|
|
1956
|
+
update!(**args)
|
|
1957
|
+
end
|
|
1958
|
+
|
|
1959
|
+
# Update properties of this object
|
|
1960
|
+
def update!(**args)
|
|
1961
|
+
@variant_set_id = args[:variant_set_id] unless args[:variant_set_id].nil?
|
|
1962
|
+
@id = args[:id] unless args[:id].nil?
|
|
1963
|
+
@names = args[:names] unless args[:names].nil?
|
|
1964
|
+
@created = args[:created] unless args[:created].nil?
|
|
1965
|
+
@reference_name = args[:reference_name] unless args[:reference_name].nil?
|
|
1966
|
+
@start = args[:start] unless args[:start].nil?
|
|
1967
|
+
@end = args[:end] unless args[:end].nil?
|
|
1968
|
+
@reference_bases = args[:reference_bases] unless args[:reference_bases].nil?
|
|
1969
|
+
@alternate_bases = args[:alternate_bases] unless args[:alternate_bases].nil?
|
|
1970
|
+
@quality = args[:quality] unless args[:quality].nil?
|
|
1971
|
+
@filter = args[:filter] unless args[:filter].nil?
|
|
1972
|
+
@info = args[:info] unless args[:info].nil?
|
|
1973
|
+
@calls = args[:calls] unless args[:calls].nil?
|
|
1974
|
+
end
|
|
1975
|
+
end
|
|
1976
|
+
|
|
1977
|
+
# A call represents the determination of genotype with respect to a particular
|
|
1978
|
+
# variant. It may include associated information such as quality and phasing.
|
|
1979
|
+
# For example, a call might assign a probability of 0.32 to the occurrence of a
|
|
1980
|
+
# SNP named rs1234 in a call set with the name NA12345.
|
|
1981
|
+
class VariantCall
|
|
1982
|
+
include Google::Apis::Core::Hashable
|
|
1983
|
+
|
|
1984
|
+
# The ID of the call set this variant call belongs to.
|
|
1985
|
+
# Corresponds to the JSON property `callSetId`
|
|
1986
|
+
# @return [String]
|
|
1987
|
+
attr_accessor :call_set_id
|
|
1988
|
+
|
|
1989
|
+
# The name of the call set this variant call belongs to.
|
|
1990
|
+
# Corresponds to the JSON property `callSetName`
|
|
1991
|
+
# @return [String]
|
|
1992
|
+
attr_accessor :call_set_name
|
|
1993
|
+
|
|
1994
|
+
# The genotype of this variant call. Each value represents either the value of
|
|
1995
|
+
# the `referenceBases` field or a 1-based index into `alternateBases`. If a
|
|
1996
|
+
# variant had a `referenceBases` value of `T` and an `alternateBases` value of `[
|
|
1997
|
+
# "A", "C"]`, and the `genotype` was `[2, 1]`, that would mean the call
|
|
1998
|
+
# represented the heterozygous value `CA` for this variant. If the `genotype`
|
|
1999
|
+
# was instead `[0, 1]`, the represented value would be `TA`. Ordering of the
|
|
2000
|
+
# genotype values is important if the `phaseset` is present. If a genotype is
|
|
2001
|
+
# not called (that is, a `.` is present in the GT string) -1 is returned.
|
|
2002
|
+
# Corresponds to the JSON property `genotype`
|
|
2003
|
+
# @return [Array<Fixnum>]
|
|
2004
|
+
attr_accessor :genotype
|
|
2005
|
+
|
|
2006
|
+
# If this field is present, this variant call's genotype ordering implies the
|
|
2007
|
+
# phase of the bases and is consistent with any other variant calls in the same
|
|
2008
|
+
# reference sequence which have the same phaseset value. When importing data
|
|
2009
|
+
# from VCF, if the genotype data was phased but no phase set was specified this
|
|
2010
|
+
# field will be set to `*`.
|
|
2011
|
+
# Corresponds to the JSON property `phaseset`
|
|
2012
|
+
# @return [String]
|
|
2013
|
+
attr_accessor :phaseset
|
|
2014
|
+
|
|
2015
|
+
# The genotype likelihoods for this variant call. Each array entry represents
|
|
2016
|
+
# how likely a specific genotype is for this call. The value ordering is defined
|
|
2017
|
+
# by the GL tag in the VCF spec. If Phred-scaled genotype likelihood scores (PL)
|
|
2018
|
+
# are available and log10(P) genotype likelihood scores (GL) are not, PL scores
|
|
2019
|
+
# are converted to GL scores. If both are available, PL scores are stored in `
|
|
2020
|
+
# info`.
|
|
2021
|
+
# Corresponds to the JSON property `genotypeLikelihood`
|
|
2022
|
+
# @return [Array<Float>]
|
|
2023
|
+
attr_accessor :genotype_likelihood
|
|
2024
|
+
|
|
2025
|
+
# A map of additional variant call information. This must be of the form map (
|
|
2026
|
+
# string key mapping to a list of string values).
|
|
2027
|
+
# Corresponds to the JSON property `info`
|
|
2028
|
+
# @return [Hash<String,Array<Object>>]
|
|
2029
|
+
attr_accessor :info
|
|
2030
|
+
|
|
2031
|
+
def initialize(**args)
|
|
2032
|
+
update!(**args)
|
|
2033
|
+
end
|
|
2034
|
+
|
|
2035
|
+
# Update properties of this object
|
|
2036
|
+
def update!(**args)
|
|
2037
|
+
@call_set_id = args[:call_set_id] unless args[:call_set_id].nil?
|
|
2038
|
+
@call_set_name = args[:call_set_name] unless args[:call_set_name].nil?
|
|
2039
|
+
@genotype = args[:genotype] unless args[:genotype].nil?
|
|
2040
|
+
@phaseset = args[:phaseset] unless args[:phaseset].nil?
|
|
2041
|
+
@genotype_likelihood = args[:genotype_likelihood] unless args[:genotype_likelihood].nil?
|
|
2042
|
+
@info = args[:info] unless args[:info].nil?
|
|
2043
|
+
end
|
|
2044
|
+
end
|
|
2045
|
+
|
|
2046
|
+
#
|
|
2047
|
+
class MergeVariantsRequest
|
|
2048
|
+
include Google::Apis::Core::Hashable
|
|
2049
|
+
|
|
2050
|
+
# The destination variant set.
|
|
2051
|
+
# Corresponds to the JSON property `variantSetId`
|
|
2052
|
+
# @return [String]
|
|
2053
|
+
attr_accessor :variant_set_id
|
|
2054
|
+
|
|
2055
|
+
# The variants to be merged with existing variants.
|
|
2056
|
+
# Corresponds to the JSON property `variants`
|
|
2057
|
+
# @return [Array<Google::Apis::GenomicsV1::Variant>]
|
|
2058
|
+
attr_accessor :variants
|
|
2059
|
+
|
|
2060
|
+
def initialize(**args)
|
|
2061
|
+
update!(**args)
|
|
2062
|
+
end
|
|
2063
|
+
|
|
2064
|
+
# Update properties of this object
|
|
2065
|
+
def update!(**args)
|
|
2066
|
+
@variant_set_id = args[:variant_set_id] unless args[:variant_set_id].nil?
|
|
2067
|
+
@variants = args[:variants] unless args[:variants].nil?
|
|
2068
|
+
end
|
|
2069
|
+
end
|
|
2070
|
+
|
|
2071
|
+
# The call set search request.
|
|
2072
|
+
class SearchCallSetsRequest
|
|
2073
|
+
include Google::Apis::Core::Hashable
|
|
2074
|
+
|
|
2075
|
+
# Restrict the query to call sets within the given variant sets. At least one ID
|
|
2076
|
+
# must be provided.
|
|
2077
|
+
# Corresponds to the JSON property `variantSetIds`
|
|
2078
|
+
# @return [Array<String>]
|
|
2079
|
+
attr_accessor :variant_set_ids
|
|
2080
|
+
|
|
2081
|
+
# Only return call sets for which a substring of the name matches this string.
|
|
2082
|
+
# Corresponds to the JSON property `name`
|
|
2083
|
+
# @return [String]
|
|
2084
|
+
attr_accessor :name
|
|
2085
|
+
|
|
2086
|
+
# The continuation token, which is used to page through large result sets. To
|
|
2087
|
+
# get the next page of results, set this parameter to the value of `
|
|
2088
|
+
# nextPageToken` from the previous response.
|
|
2089
|
+
# Corresponds to the JSON property `pageToken`
|
|
2090
|
+
# @return [String]
|
|
2091
|
+
attr_accessor :page_token
|
|
2092
|
+
|
|
2093
|
+
# The maximum number of call sets to return. If unspecified, defaults to 1000.
|
|
2094
|
+
# Corresponds to the JSON property `pageSize`
|
|
2095
|
+
# @return [Fixnum]
|
|
2096
|
+
attr_accessor :page_size
|
|
2097
|
+
|
|
2098
|
+
def initialize(**args)
|
|
2099
|
+
update!(**args)
|
|
2100
|
+
end
|
|
2101
|
+
|
|
2102
|
+
# Update properties of this object
|
|
2103
|
+
def update!(**args)
|
|
2104
|
+
@variant_set_ids = args[:variant_set_ids] unless args[:variant_set_ids].nil?
|
|
2105
|
+
@name = args[:name] unless args[:name].nil?
|
|
2106
|
+
@page_token = args[:page_token] unless args[:page_token].nil?
|
|
2107
|
+
@page_size = args[:page_size] unless args[:page_size].nil?
|
|
2108
|
+
end
|
|
2109
|
+
end
|
|
2110
|
+
|
|
2111
|
+
# The call set search response.
|
|
2112
|
+
class SearchCallSetsResponse
|
|
2113
|
+
include Google::Apis::Core::Hashable
|
|
2114
|
+
|
|
2115
|
+
# The list of matching call sets.
|
|
2116
|
+
# Corresponds to the JSON property `callSets`
|
|
2117
|
+
# @return [Array<Google::Apis::GenomicsV1::CallSet>]
|
|
2118
|
+
attr_accessor :call_sets
|
|
2119
|
+
|
|
2120
|
+
# The continuation token, which is used to page through large result sets.
|
|
2121
|
+
# Provide this value in a subsequent request to return the next page of results.
|
|
2122
|
+
# This field will be empty if there aren't any additional results.
|
|
2123
|
+
# Corresponds to the JSON property `nextPageToken`
|
|
2124
|
+
# @return [String]
|
|
2125
|
+
attr_accessor :next_page_token
|
|
2126
|
+
|
|
2127
|
+
def initialize(**args)
|
|
2128
|
+
update!(**args)
|
|
2129
|
+
end
|
|
2130
|
+
|
|
2131
|
+
# Update properties of this object
|
|
2132
|
+
def update!(**args)
|
|
2133
|
+
@call_sets = args[:call_sets] unless args[:call_sets].nil?
|
|
2134
|
+
@next_page_token = args[:next_page_token] unless args[:next_page_token].nil?
|
|
2135
|
+
end
|
|
2136
|
+
end
|
|
2137
|
+
|
|
2138
|
+
# A call set is a collection of variant calls, typically for one sample. It
|
|
2139
|
+
# belongs to a variant set.
|
|
2140
|
+
class CallSet
|
|
2141
|
+
include Google::Apis::Core::Hashable
|
|
2142
|
+
|
|
2143
|
+
# The server-generated call set ID, unique across all call sets.
|
|
2144
|
+
# Corresponds to the JSON property `id`
|
|
2145
|
+
# @return [String]
|
|
2146
|
+
attr_accessor :id
|
|
2147
|
+
|
|
2148
|
+
# The call set name.
|
|
2149
|
+
# Corresponds to the JSON property `name`
|
|
2150
|
+
# @return [String]
|
|
2151
|
+
attr_accessor :name
|
|
2152
|
+
|
|
2153
|
+
# The sample ID this call set corresponds to.
|
|
2154
|
+
# Corresponds to the JSON property `sampleId`
|
|
2155
|
+
# @return [String]
|
|
2156
|
+
attr_accessor :sample_id
|
|
2157
|
+
|
|
2158
|
+
# The IDs of the variant sets this call set belongs to.
|
|
2159
|
+
# Corresponds to the JSON property `variantSetIds`
|
|
2160
|
+
# @return [Array<String>]
|
|
2161
|
+
attr_accessor :variant_set_ids
|
|
2162
|
+
|
|
2163
|
+
# The date this call set was created in milliseconds from the epoch.
|
|
2164
|
+
# Corresponds to the JSON property `created`
|
|
2165
|
+
# @return [String]
|
|
2166
|
+
attr_accessor :created
|
|
2167
|
+
|
|
2168
|
+
# A map of additional call set information. This must be of the form map (string
|
|
2169
|
+
# key mapping to a list of string values).
|
|
2170
|
+
# Corresponds to the JSON property `info`
|
|
2171
|
+
# @return [Hash<String,Array<Object>>]
|
|
2172
|
+
attr_accessor :info
|
|
2173
|
+
|
|
2174
|
+
def initialize(**args)
|
|
2175
|
+
update!(**args)
|
|
2176
|
+
end
|
|
2177
|
+
|
|
2178
|
+
# Update properties of this object
|
|
2179
|
+
def update!(**args)
|
|
2180
|
+
@id = args[:id] unless args[:id].nil?
|
|
2181
|
+
@name = args[:name] unless args[:name].nil?
|
|
2182
|
+
@sample_id = args[:sample_id] unless args[:sample_id].nil?
|
|
2183
|
+
@variant_set_ids = args[:variant_set_ids] unless args[:variant_set_ids].nil?
|
|
2184
|
+
@created = args[:created] unless args[:created].nil?
|
|
2185
|
+
@info = args[:info] unless args[:info].nil?
|
|
2186
|
+
end
|
|
2187
|
+
end
|
|
2188
|
+
|
|
2189
|
+
# The read group set import response.
|
|
2190
|
+
class ImportReadGroupSetsResponse
|
|
2191
|
+
include Google::Apis::Core::Hashable
|
|
2192
|
+
|
|
2193
|
+
# IDs of the read group sets that were created.
|
|
2194
|
+
# Corresponds to the JSON property `readGroupSetIds`
|
|
2195
|
+
# @return [Array<String>]
|
|
2196
|
+
attr_accessor :read_group_set_ids
|
|
2197
|
+
|
|
2198
|
+
def initialize(**args)
|
|
2199
|
+
update!(**args)
|
|
2200
|
+
end
|
|
2201
|
+
|
|
2202
|
+
# Update properties of this object
|
|
2203
|
+
def update!(**args)
|
|
2204
|
+
@read_group_set_ids = args[:read_group_set_ids] unless args[:read_group_set_ids].nil?
|
|
2205
|
+
end
|
|
2206
|
+
end
|
|
2207
|
+
|
|
2208
|
+
# The variant data import response.
|
|
2209
|
+
class ImportVariantsResponse
|
|
2210
|
+
include Google::Apis::Core::Hashable
|
|
2211
|
+
|
|
2212
|
+
# IDs of the call sets that were created.
|
|
2213
|
+
# Corresponds to the JSON property `callSetIds`
|
|
2214
|
+
# @return [Array<String>]
|
|
2215
|
+
attr_accessor :call_set_ids
|
|
2216
|
+
|
|
2217
|
+
def initialize(**args)
|
|
2218
|
+
update!(**args)
|
|
2219
|
+
end
|
|
2220
|
+
|
|
2221
|
+
# Update properties of this object
|
|
2222
|
+
def update!(**args)
|
|
2223
|
+
@call_set_ids = args[:call_set_ids] unless args[:call_set_ids].nil?
|
|
2224
|
+
end
|
|
2225
|
+
end
|
|
2226
|
+
|
|
2227
|
+
# Metadata describing an [Operation][google.longrunning.Operation].
|
|
2228
|
+
class OperationMetadata
|
|
2229
|
+
include Google::Apis::Core::Hashable
|
|
2230
|
+
|
|
2231
|
+
# The Google Cloud Project in which the job is scoped.
|
|
2232
|
+
# Corresponds to the JSON property `projectId`
|
|
2233
|
+
# @return [String]
|
|
2234
|
+
attr_accessor :project_id
|
|
2235
|
+
|
|
2236
|
+
# The time at which the job was submitted to the Genomics service.
|
|
2237
|
+
# Corresponds to the JSON property `createTime`
|
|
2238
|
+
# @return [String]
|
|
2239
|
+
attr_accessor :create_time
|
|
2240
|
+
|
|
2241
|
+
# The original request that started the operation. Note that this will be in
|
|
2242
|
+
# current version of the API. If the operation was started with v1beta2 API and
|
|
2243
|
+
# a GetOperation is performed on v1 API, a v1 request will be returned.
|
|
2244
|
+
# Corresponds to the JSON property `request`
|
|
2245
|
+
# @return [Hash<String,Object>]
|
|
2246
|
+
attr_accessor :request
|
|
2247
|
+
|
|
2248
|
+
# Optional event messages that were generated during the job's execution. This
|
|
2249
|
+
# also contains any warnings that were generated during import or export.
|
|
2250
|
+
# Corresponds to the JSON property `events`
|
|
2251
|
+
# @return [Array<Google::Apis::GenomicsV1::OperationEvent>]
|
|
2252
|
+
attr_accessor :events
|
|
2253
|
+
|
|
2254
|
+
def initialize(**args)
|
|
2255
|
+
update!(**args)
|
|
2256
|
+
end
|
|
2257
|
+
|
|
2258
|
+
# Update properties of this object
|
|
2259
|
+
def update!(**args)
|
|
2260
|
+
@project_id = args[:project_id] unless args[:project_id].nil?
|
|
2261
|
+
@create_time = args[:create_time] unless args[:create_time].nil?
|
|
2262
|
+
@request = args[:request] unless args[:request].nil?
|
|
2263
|
+
@events = args[:events] unless args[:events].nil?
|
|
2264
|
+
end
|
|
2265
|
+
end
|
|
2266
|
+
|
|
2267
|
+
# An event that occurred during an [Operation][google.longrunning.Operation].
|
|
2268
|
+
class OperationEvent
|
|
2269
|
+
include Google::Apis::Core::Hashable
|
|
2270
|
+
|
|
2271
|
+
# Required description of event.
|
|
2272
|
+
# Corresponds to the JSON property `description`
|
|
2273
|
+
# @return [String]
|
|
2274
|
+
attr_accessor :description
|
|
2275
|
+
|
|
2276
|
+
def initialize(**args)
|
|
2277
|
+
update!(**args)
|
|
2278
|
+
end
|
|
2279
|
+
|
|
2280
|
+
# Update properties of this object
|
|
2281
|
+
def update!(**args)
|
|
2282
|
+
@description = args[:description] unless args[:description].nil?
|
|
2283
|
+
end
|
|
2284
|
+
end
|
|
2285
|
+
end
|
|
2286
|
+
end
|
|
2287
|
+
end
|