# Copyright 2015 Google Inc. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. require 'date' require 'google/apis/core/base_service' require 'google/apis/core/json_representation' require 'google/apis/core/hashable' require 'google/apis/errors' module Google module Apis module GenomicsV1 # The dataset list response. class ListDatasetsResponse include Google::Apis::Core::Hashable # The list of matching Datasets. # Corresponds to the JSON property `datasets` # @return [Array] attr_accessor :datasets # The continuation token, which is used to page through large result sets. # Provide this value in a subsequent request to return the next page of results. # This field will be empty if there aren't any additional results. # Corresponds to the JSON property `nextPageToken` # @return [String] attr_accessor :next_page_token def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @datasets = args[:datasets] unless args[:datasets].nil? @next_page_token = args[:next_page_token] unless args[:next_page_token].nil? end end # A Dataset is a collection of genomic data. For more genomics resource # definitions, see [Fundamentals of Google Genomics](https://cloud.google.com/ # genomics/fundamentals-of-google-genomics) class Dataset include Google::Apis::Core::Hashable # The server-generated dataset ID, unique across all datasets. # Corresponds to the JSON property `id` # @return [String] attr_accessor :id # The Google Developers Console project ID that this dataset belongs to. # Corresponds to the JSON property `projectId` # @return [String] attr_accessor :project_id # The dataset name. # Corresponds to the JSON property `name` # @return [String] attr_accessor :name # The time this dataset was created, in seconds from the epoch. # Corresponds to the JSON property `createTime` # @return [String] attr_accessor :create_time def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @id = args[:id] unless args[:id].nil? @project_id = args[:project_id] unless args[:project_id].nil? @name = args[:name] unless args[:name].nil? @create_time = args[:create_time] unless args[:create_time].nil? end end # A generic empty message that you can re-use to avoid defining duplicated empty # messages in your APIs. A typical example is to use it as the request or the # response type of an API method. For instance: service Foo ` rpc Bar(google. # protobuf.Empty) returns (google.protobuf.Empty); ` The JSON representation for # `Empty` is empty JSON object ````. class Empty include Google::Apis::Core::Hashable def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) end end # class UndeleteDatasetRequest include Google::Apis::Core::Hashable def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) end end # Request message for `SetIamPolicy` method. class SetIamPolicyRequest include Google::Apis::Core::Hashable # Defines an Identity and Access Management (IAM) policy. It is used to specify # access control policies for Cloud Platform resources. A `Policy` consists of a # list of `bindings`. A `Binding` binds a list of `members` to a `role`, where # the members can be user accounts, Google groups, Google domains, and service # accounts. A `role` is a named list of permissions defined by IAM. **Example** ` # "bindings": [ ` "role": "roles/owner", "members": [ "user:mike@example.com", " # group:admins@example.com", "domain:google.com", "serviceAccount:my-other-app@ # appspot.gserviceaccount.com"] `, ` "role": "roles/viewer", "members": ["user: # sean@example.com"] ` ] ` For a description of IAM and its features, see the [ # IAM developer's guide](https://cloud.google.com/iam). # Corresponds to the JSON property `policy` # @return [Google::Apis::GenomicsV1::Policy] attr_accessor :policy def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @policy = args[:policy] unless args[:policy].nil? end end # Defines an Identity and Access Management (IAM) policy. It is used to specify # access control policies for Cloud Platform resources. A `Policy` consists of a # list of `bindings`. A `Binding` binds a list of `members` to a `role`, where # the members can be user accounts, Google groups, Google domains, and service # accounts. A `role` is a named list of permissions defined by IAM. **Example** ` # "bindings": [ ` "role": "roles/owner", "members": [ "user:mike@example.com", " # group:admins@example.com", "domain:google.com", "serviceAccount:my-other-app@ # appspot.gserviceaccount.com"] `, ` "role": "roles/viewer", "members": ["user: # sean@example.com"] ` ] ` For a description of IAM and its features, see the [ # IAM developer's guide](https://cloud.google.com/iam). class Policy include Google::Apis::Core::Hashable # Version of the `Policy`. The default version is 0. # Corresponds to the JSON property `version` # @return [Fixnum] attr_accessor :version # Associates a list of `members` to a `role`. Multiple `bindings` must not be # specified for the same `role`. `bindings` with no members will result in an # error. # Corresponds to the JSON property `bindings` # @return [Array] attr_accessor :bindings # `etag` is used for optimistic concurrency control as a way to help prevent # simultaneous updates of a policy from overwriting each other. It is strongly # suggested that systems make use of the `etag` in the read-modify-write cycle # to perform policy updates in order to avoid race conditions: An `etag` is # returned in the response to `getIamPolicy`, and systems are expected to put # that etag in the request to `setIamPolicy` to ensure that their change will be # applied to the same version of the policy. If no `etag` is provided in the # call to `setIamPolicy`, then the existing policy is overwritten blindly. # Corresponds to the JSON property `etag` # @return [String] attr_accessor :etag def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @version = args[:version] unless args[:version].nil? @bindings = args[:bindings] unless args[:bindings].nil? @etag = args[:etag] unless args[:etag].nil? end end # Associates `members` with a `role`. class Binding include Google::Apis::Core::Hashable # Role that is assigned to `members`. For example, `roles/viewer`, `roles/editor` # , or `roles/owner`. Required # Corresponds to the JSON property `role` # @return [String] attr_accessor :role # Specifies the identities requesting access for a Cloud Platform resource. ` # members` can have the following values: * `allUsers`: A special identifier # that represents anyone who is on the internet; with or without a Google # account. * `allAuthenticatedUsers`: A special identifier that represents # anyone who is authenticated with a Google account or a service account. * ` # user:`emailid``: An email address that represents a specific Google account. # For example, `alice@gmail.com` or `joe@example.com`. * `serviceAccount:` # emailid``: An email address that represents a service account. For example, ` # my-other-app@appspot.gserviceaccount.com`. * `group:`emailid``: An email # address that represents a Google group. For example, `admins@example.com`. * ` # domain:`domain``: A Google Apps domain name that represents all the users of # that domain. For example, `google.com` or `example.com`. # Corresponds to the JSON property `members` # @return [Array] attr_accessor :members def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @role = args[:role] unless args[:role].nil? @members = args[:members] unless args[:members].nil? end end # Request message for `GetIamPolicy` method. class GetIamPolicyRequest include Google::Apis::Core::Hashable def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) end end # Request message for `TestIamPermissions` method. class TestIamPermissionsRequest include Google::Apis::Core::Hashable # REQUIRED: The set of permissions to check for the 'resource'. Permissions with # wildcards (such as '*' or 'storage.*') are not allowed. Allowed permissions # are: * `genomics.datasets.create` * `genomics.datasets.delete` * `genomics. # datasets.get` * `genomics.datasets.list` * `genomics.datasets.update` * ` # genomics.datasets.getIamPolicy` * `genomics.datasets.setIamPolicy` # Corresponds to the JSON property `permissions` # @return [Array] attr_accessor :permissions def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @permissions = args[:permissions] unless args[:permissions].nil? end end # Response message for `TestIamPermissions` method. class TestIamPermissionsResponse include Google::Apis::Core::Hashable # A subset of `TestPermissionsRequest.permissions` that the caller is allowed. # Corresponds to the JSON property `permissions` # @return [Array] attr_accessor :permissions def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @permissions = args[:permissions] unless args[:permissions].nil? end end # This resource represents a long-running operation that is the result of a # network API call. class Operation include Google::Apis::Core::Hashable # The server-assigned name, which is only unique within the same service that # originally returns it. For example: `operations/CJHU7Oi_ChDrveSpBRjfuL- # qzoWAgEw` # Corresponds to the JSON property `name` # @return [String] attr_accessor :name # An OperationMetadata object. This will always be returned with the Operation. # Corresponds to the JSON property `metadata` # @return [Hash] attr_accessor :metadata # If the value is `false`, it means the operation is still in progress. If true, # the operation is completed, and either `error` or `response` is available. # Corresponds to the JSON property `done` # @return [Boolean] attr_accessor :done alias_method :done?, :done # The `Status` type defines a logical error model that is suitable for different # programming environments, including REST APIs and RPC APIs. It is used by [ # gRPC](https://github.com/grpc). The error model is designed to be: - Simple to # use and understand for most users - Flexible enough to meet unexpected needs # # Overview The `Status` message contains three pieces of data: error code, error # message, and error details. The error code should be an enum value of google. # rpc.Code, but it may accept additional error codes if needed. The error # message should be a developer-facing English message that helps developers * # understand* and *resolve* the error. If a localized user-facing error message # is needed, put the localized message in the error details or localize it in # the client. The optional error details may contain arbitrary information about # the error. There is a predefined set of error detail types in the package ` # google.rpc` which can be used for common error conditions. # Language mapping # The `Status` message is the logical representation of the error model, but it # is not necessarily the actual wire format. When the `Status` message is # exposed in different client libraries and different wire protocols, it can be # mapped differently. For example, it will likely be mapped to some exceptions # in Java, but more likely mapped to some error codes in C. # Other uses The # error model and the `Status` message can be used in a variety of environments, # either with or without APIs, to provide a consistent developer experience # across different environments. Example uses of this error model include: - # Partial errors. If a service needs to return partial errors to the client, it # may embed the `Status` in the normal response to indicate the partial errors. - # Workflow errors. A typical workflow has multiple steps. Each step may have a ` # Status` message for error reporting purpose. - Batch operations. If a client # uses batch request and batch response, the `Status` message should be used # directly inside batch response, one for each error sub-response. - # Asynchronous operations. If an API call embeds asynchronous operation results # in its response, the status of those operations should be represented directly # using the `Status` message. - Logging. If some API errors are stored in logs, # the message `Status` could be used directly after any stripping needed for # security/privacy reasons. # Corresponds to the JSON property `error` # @return [Google::Apis::GenomicsV1::Status] attr_accessor :error # If importing ReadGroupSets, an ImportReadGroupSetsResponse is returned. If # importing Variants, an ImportVariantsResponse is returned. For exports, an # empty response is returned. # Corresponds to the JSON property `response` # @return [Hash] attr_accessor :response def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @name = args[:name] unless args[:name].nil? @metadata = args[:metadata] unless args[:metadata].nil? @done = args[:done] unless args[:done].nil? @error = args[:error] unless args[:error].nil? @response = args[:response] unless args[:response].nil? end end # The `Status` type defines a logical error model that is suitable for different # programming environments, including REST APIs and RPC APIs. It is used by [ # gRPC](https://github.com/grpc). The error model is designed to be: - Simple to # use and understand for most users - Flexible enough to meet unexpected needs # # Overview The `Status` message contains three pieces of data: error code, error # message, and error details. The error code should be an enum value of google. # rpc.Code, but it may accept additional error codes if needed. The error # message should be a developer-facing English message that helps developers * # understand* and *resolve* the error. If a localized user-facing error message # is needed, put the localized message in the error details or localize it in # the client. The optional error details may contain arbitrary information about # the error. There is a predefined set of error detail types in the package ` # google.rpc` which can be used for common error conditions. # Language mapping # The `Status` message is the logical representation of the error model, but it # is not necessarily the actual wire format. When the `Status` message is # exposed in different client libraries and different wire protocols, it can be # mapped differently. For example, it will likely be mapped to some exceptions # in Java, but more likely mapped to some error codes in C. # Other uses The # error model and the `Status` message can be used in a variety of environments, # either with or without APIs, to provide a consistent developer experience # across different environments. Example uses of this error model include: - # Partial errors. If a service needs to return partial errors to the client, it # may embed the `Status` in the normal response to indicate the partial errors. - # Workflow errors. A typical workflow has multiple steps. Each step may have a ` # Status` message for error reporting purpose. - Batch operations. If a client # uses batch request and batch response, the `Status` message should be used # directly inside batch response, one for each error sub-response. - # Asynchronous operations. If an API call embeds asynchronous operation results # in its response, the status of those operations should be represented directly # using the `Status` message. - Logging. If some API errors are stored in logs, # the message `Status` could be used directly after any stripping needed for # security/privacy reasons. class Status include Google::Apis::Core::Hashable # The status code, which should be an enum value of google.rpc.Code. # Corresponds to the JSON property `code` # @return [Fixnum] attr_accessor :code # A developer-facing error message, which should be in English. Any user-facing # error message should be localized and sent in the google.rpc.Status.details # field, or localized by the client. # Corresponds to the JSON property `message` # @return [String] attr_accessor :message # A list of messages that carry the error details. There will be a common set of # message types for APIs to use. # Corresponds to the JSON property `details` # @return [Array>] attr_accessor :details def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @code = args[:code] unless args[:code].nil? @message = args[:message] unless args[:message].nil? @details = args[:details] unless args[:details].nil? end end # The response message for Operations.ListOperations. class ListOperationsResponse include Google::Apis::Core::Hashable # A list of operations that matches the specified filter in the request. # Corresponds to the JSON property `operations` # @return [Array] attr_accessor :operations # The standard List next-page token. # Corresponds to the JSON property `nextPageToken` # @return [String] attr_accessor :next_page_token def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @operations = args[:operations] unless args[:operations].nil? @next_page_token = args[:next_page_token] unless args[:next_page_token].nil? end end # The request message for Operations.CancelOperation. class CancelOperationRequest include Google::Apis::Core::Hashable def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) end end # The read group set import request. class ImportReadGroupSetsRequest include Google::Apis::Core::Hashable # Required. The ID of the dataset these read group sets will belong to. The # caller must have WRITE permissions to this dataset. # Corresponds to the JSON property `datasetId` # @return [String] attr_accessor :dataset_id # The reference set to which the imported read group sets are aligned to, if any. # The reference names of this reference set must be a superset of those found # in the imported file headers. If no reference set id is provided, a best # effort is made to associate with a matching reference set. # Corresponds to the JSON property `referenceSetId` # @return [String] attr_accessor :reference_set_id # A list of URIs pointing at [BAM files](https://samtools.github.io/hts-specs/ # SAMv1.pdf) in Google Cloud Storage. # Corresponds to the JSON property `sourceUris` # @return [Array] attr_accessor :source_uris # The partition strategy describes how read groups are partitioned into read # group sets. # Corresponds to the JSON property `partitionStrategy` # @return [String] attr_accessor :partition_strategy def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @dataset_id = args[:dataset_id] unless args[:dataset_id].nil? @reference_set_id = args[:reference_set_id] unless args[:reference_set_id].nil? @source_uris = args[:source_uris] unless args[:source_uris].nil? @partition_strategy = args[:partition_strategy] unless args[:partition_strategy].nil? end end # The read group set export request. class ExportReadGroupSetRequest include Google::Apis::Core::Hashable # Required. The Google Developers Console project ID that owns this export. The # caller must have WRITE access to this project. # Corresponds to the JSON property `projectId` # @return [String] attr_accessor :project_id # Required. A Google Cloud Storage URI for the exported BAM file. The currently # authenticated user must have write access to the new file. An error will be # returned if the URI already contains data. # Corresponds to the JSON property `exportUri` # @return [String] attr_accessor :export_uri # The reference names to export. If this is not specified, all reference # sequences, including unmapped reads, are exported. Use `*` to export only # unmapped reads. # Corresponds to the JSON property `referenceNames` # @return [Array] attr_accessor :reference_names def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @project_id = args[:project_id] unless args[:project_id].nil? @export_uri = args[:export_uri] unless args[:export_uri].nil? @reference_names = args[:reference_names] unless args[:reference_names].nil? end end # The read group set search request. class SearchReadGroupSetsRequest include Google::Apis::Core::Hashable # Restricts this query to read group sets within the given datasets. At least # one ID must be provided. # Corresponds to the JSON property `datasetIds` # @return [Array] attr_accessor :dataset_ids # Only return read group sets for which a substring of the name matches this # string. # Corresponds to the JSON property `name` # @return [String] attr_accessor :name # The continuation token, which is used to page through large result sets. To # get the next page of results, set this parameter to the value of ` # nextPageToken` from the previous response. # Corresponds to the JSON property `pageToken` # @return [String] attr_accessor :page_token # The maximum number of results to return in a single page. If unspecified, # defaults to 256. The maximum value is 1024. # Corresponds to the JSON property `pageSize` # @return [Fixnum] attr_accessor :page_size def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @dataset_ids = args[:dataset_ids] unless args[:dataset_ids].nil? @name = args[:name] unless args[:name].nil? @page_token = args[:page_token] unless args[:page_token].nil? @page_size = args[:page_size] unless args[:page_size].nil? end end # The read group set search response. class SearchReadGroupSetsResponse include Google::Apis::Core::Hashable # The list of matching read group sets. # Corresponds to the JSON property `readGroupSets` # @return [Array] attr_accessor :read_group_sets # The continuation token, which is used to page through large result sets. # Provide this value in a subsequent request to return the next page of results. # This field will be empty if there aren't any additional results. # Corresponds to the JSON property `nextPageToken` # @return [String] attr_accessor :next_page_token def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @read_group_sets = args[:read_group_sets] unless args[:read_group_sets].nil? @next_page_token = args[:next_page_token] unless args[:next_page_token].nil? end end # A read group set is a logical collection of read groups, which are collections # of reads produced by a sequencer. A read group set typically models reads # corresponding to one sample, sequenced one way, and aligned one way. * A read # group set belongs to one dataset. * A read group belongs to one read group set. # * A read belongs to one read group. For more genomics resource definitions, # see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/ # fundamentals-of-google-genomics) class ReadGroupSet include Google::Apis::Core::Hashable # The server-generated read group set ID, unique for all read group sets. # Corresponds to the JSON property `id` # @return [String] attr_accessor :id # The dataset to which this read group set belongs. # Corresponds to the JSON property `datasetId` # @return [String] attr_accessor :dataset_id # The reference set to which the reads in this read group set are aligned. # Corresponds to the JSON property `referenceSetId` # @return [String] attr_accessor :reference_set_id # The read group set name. By default this will be initialized to the sample # name of the sequenced data contained in this set. # Corresponds to the JSON property `name` # @return [String] attr_accessor :name # The filename of the original source file for this read group set, if any. # Corresponds to the JSON property `filename` # @return [String] attr_accessor :filename # The read groups in this set. There are typically 1-10 read groups in a read # group set. # Corresponds to the JSON property `readGroups` # @return [Array] attr_accessor :read_groups # A map of additional read group set information. # Corresponds to the JSON property `info` # @return [Hash>] attr_accessor :info def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @id = args[:id] unless args[:id].nil? @dataset_id = args[:dataset_id] unless args[:dataset_id].nil? @reference_set_id = args[:reference_set_id] unless args[:reference_set_id].nil? @name = args[:name] unless args[:name].nil? @filename = args[:filename] unless args[:filename].nil? @read_groups = args[:read_groups] unless args[:read_groups].nil? @info = args[:info] unless args[:info].nil? end end # A read group is all the data that's processed the same way by the sequencer. class ReadGroup include Google::Apis::Core::Hashable # The server-generated read group ID, unique for all read groups. Note: This is # different than the @RG ID field in the SAM spec. For that value, see name. # Corresponds to the JSON property `id` # @return [String] attr_accessor :id # The dataset to which this read group belongs. # Corresponds to the JSON property `datasetId` # @return [String] attr_accessor :dataset_id # The read group name. This corresponds to the @RG ID field in the SAM spec. # Corresponds to the JSON property `name` # @return [String] attr_accessor :name # A free-form text description of this read group. # Corresponds to the JSON property `description` # @return [String] attr_accessor :description # A client-supplied sample identifier for the reads in this read group. # Corresponds to the JSON property `sampleId` # @return [String] attr_accessor :sample_id # The experiment used to generate this read group. # Corresponds to the JSON property `experiment` # @return [Google::Apis::GenomicsV1::Experiment] attr_accessor :experiment # The predicted insert size of this read group. The insert size is the length # the sequenced DNA fragment from end-to-end, not including the adapters. # Corresponds to the JSON property `predictedInsertSize` # @return [Fixnum] attr_accessor :predicted_insert_size # The programs used to generate this read group. Programs are always identical # for all read groups within a read group set. For this reason, only the first # read group in a returned set will have this field populated. # Corresponds to the JSON property `programs` # @return [Array] attr_accessor :programs # The reference set the reads in this read group are aligned to. # Corresponds to the JSON property `referenceSetId` # @return [String] attr_accessor :reference_set_id # A map of additional read group information. This must be of the form map ( # string key mapping to a list of string values). # Corresponds to the JSON property `info` # @return [Hash>] attr_accessor :info def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @id = args[:id] unless args[:id].nil? @dataset_id = args[:dataset_id] unless args[:dataset_id].nil? @name = args[:name] unless args[:name].nil? @description = args[:description] unless args[:description].nil? @sample_id = args[:sample_id] unless args[:sample_id].nil? @experiment = args[:experiment] unless args[:experiment].nil? @predicted_insert_size = args[:predicted_insert_size] unless args[:predicted_insert_size].nil? @programs = args[:programs] unless args[:programs].nil? @reference_set_id = args[:reference_set_id] unless args[:reference_set_id].nil? @info = args[:info] unless args[:info].nil? end end # class Experiment include Google::Apis::Core::Hashable # A client-supplied library identifier; a library is a collection of DNA # fragments which have been prepared for sequencing from a sample. This field is # important for quality control as error or bias can be introduced during sample # preparation. # Corresponds to the JSON property `libraryId` # @return [String] attr_accessor :library_id # The platform unit used as part of this experiment, for example flowcell- # barcode.lane for Illumina or slide for SOLiD. Corresponds to the @RG PU field # in the SAM spec. # Corresponds to the JSON property `platformUnit` # @return [String] attr_accessor :platform_unit # The sequencing center used as part of this experiment. # Corresponds to the JSON property `sequencingCenter` # @return [String] attr_accessor :sequencing_center # The instrument model used as part of this experiment. This maps to sequencing # technology in the SAM spec. # Corresponds to the JSON property `instrumentModel` # @return [String] attr_accessor :instrument_model def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @library_id = args[:library_id] unless args[:library_id].nil? @platform_unit = args[:platform_unit] unless args[:platform_unit].nil? @sequencing_center = args[:sequencing_center] unless args[:sequencing_center].nil? @instrument_model = args[:instrument_model] unless args[:instrument_model].nil? end end # class Program include Google::Apis::Core::Hashable # The command line used to run this program. # Corresponds to the JSON property `commandLine` # @return [String] attr_accessor :command_line # The user specified locally unique ID of the program. Used along with ` # prevProgramId` to define an ordering between programs. # Corresponds to the JSON property `id` # @return [String] attr_accessor :id # The display name of the program. This is typically the colloquial name of the # tool used, for example 'bwa' or 'picard'. # Corresponds to the JSON property `name` # @return [String] attr_accessor :name # The ID of the program run before this one. # Corresponds to the JSON property `prevProgramId` # @return [String] attr_accessor :prev_program_id # The version of the program run. # Corresponds to the JSON property `version` # @return [String] attr_accessor :version def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @command_line = args[:command_line] unless args[:command_line].nil? @id = args[:id] unless args[:id].nil? @name = args[:name] unless args[:name].nil? @prev_program_id = args[:prev_program_id] unless args[:prev_program_id].nil? @version = args[:version] unless args[:version].nil? end end # class ListCoverageBucketsResponse include Google::Apis::Core::Hashable # The length of each coverage bucket in base pairs. Note that buckets at the end # of a reference sequence may be shorter. This value is omitted if the bucket # width is infinity (the default behaviour, with no range or `targetBucketWidth`) # . # Corresponds to the JSON property `bucketWidth` # @return [String] attr_accessor :bucket_width # The coverage buckets. The list of buckets is sparse; a bucket with 0 # overlapping reads is not returned. A bucket never crosses more than one # reference sequence. Each bucket has width `bucketWidth`, unless its end is the # end of the reference sequence. # Corresponds to the JSON property `coverageBuckets` # @return [Array] attr_accessor :coverage_buckets # The continuation token, which is used to page through large result sets. # Provide this value in a subsequent request to return the next page of results. # This field will be empty if there aren't any additional results. # Corresponds to the JSON property `nextPageToken` # @return [String] attr_accessor :next_page_token def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @bucket_width = args[:bucket_width] unless args[:bucket_width].nil? @coverage_buckets = args[:coverage_buckets] unless args[:coverage_buckets].nil? @next_page_token = args[:next_page_token] unless args[:next_page_token].nil? end end # A bucket over which read coverage has been precomputed. A bucket corresponds # to a specific range of the reference sequence. class CoverageBucket include Google::Apis::Core::Hashable # A 0-based half-open genomic coordinate range for search requests. # Corresponds to the JSON property `range` # @return [Google::Apis::GenomicsV1::Range] attr_accessor :range # The average number of reads which are aligned to each individual reference # base in this bucket. # Corresponds to the JSON property `meanCoverage` # @return [Float] attr_accessor :mean_coverage def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @range = args[:range] unless args[:range].nil? @mean_coverage = args[:mean_coverage] unless args[:mean_coverage].nil? end end # A 0-based half-open genomic coordinate range for search requests. class Range include Google::Apis::Core::Hashable # The reference sequence name, for example `chr1`, `1`, or `chrX`. # Corresponds to the JSON property `referenceName` # @return [String] attr_accessor :reference_name # The start position of the range on the reference, 0-based inclusive. # Corresponds to the JSON property `start` # @return [String] attr_accessor :start # The end position of the range on the reference, 0-based exclusive. # Corresponds to the JSON property `end` # @return [String] attr_accessor :end def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @reference_name = args[:reference_name] unless args[:reference_name].nil? @start = args[:start] unless args[:start].nil? @end = args[:end] unless args[:end].nil? end end # The read search request. class SearchReadsRequest include Google::Apis::Core::Hashable # The IDs of the read groups sets within which to search for reads. All # specified read group sets must be aligned against a common set of reference # sequences; this defines the genomic coordinates for the query. Must specify # one of `readGroupSetIds` or `readGroupIds`. # Corresponds to the JSON property `readGroupSetIds` # @return [Array] attr_accessor :read_group_set_ids # The IDs of the read groups within which to search for reads. All specified # read groups must belong to the same read group sets. Must specify one of ` # readGroupSetIds` or `readGroupIds`. # Corresponds to the JSON property `readGroupIds` # @return [Array] attr_accessor :read_group_ids # The reference sequence name, for example `chr1`, `1`, or `chrX`. If set to `*`, # only unmapped reads are returned. If unspecified, all reads (mapped and # unmapped) are returned. # Corresponds to the JSON property `referenceName` # @return [String] attr_accessor :reference_name # The start position of the range on the reference, 0-based inclusive. If # specified, `referenceName` must also be specified. # Corresponds to the JSON property `start` # @return [String] attr_accessor :start # The end position of the range on the reference, 0-based exclusive. If # specified, `referenceName` must also be specified. # Corresponds to the JSON property `end` # @return [String] attr_accessor :end # The continuation token, which is used to page through large result sets. To # get the next page of results, set this parameter to the value of ` # nextPageToken` from the previous response. # Corresponds to the JSON property `pageToken` # @return [String] attr_accessor :page_token # The maximum number of results to return in a single page. If unspecified, # defaults to 256. The maximum value is 2048. # Corresponds to the JSON property `pageSize` # @return [Fixnum] attr_accessor :page_size def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @read_group_set_ids = args[:read_group_set_ids] unless args[:read_group_set_ids].nil? @read_group_ids = args[:read_group_ids] unless args[:read_group_ids].nil? @reference_name = args[:reference_name] unless args[:reference_name].nil? @start = args[:start] unless args[:start].nil? @end = args[:end] unless args[:end].nil? @page_token = args[:page_token] unless args[:page_token].nil? @page_size = args[:page_size] unless args[:page_size].nil? end end # The read search response. class SearchReadsResponse include Google::Apis::Core::Hashable # The list of matching alignments sorted by mapped genomic coordinate, if any, # ascending in position within the same reference. Unmapped reads, which have no # position, are returned contiguously and are sorted in ascending lexicographic # order by fragment name. # Corresponds to the JSON property `alignments` # @return [Array] attr_accessor :alignments # The continuation token, which is used to page through large result sets. # Provide this value in a subsequent request to return the next page of results. # This field will be empty if there aren't any additional results. # Corresponds to the JSON property `nextPageToken` # @return [String] attr_accessor :next_page_token def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @alignments = args[:alignments] unless args[:alignments].nil? @next_page_token = args[:next_page_token] unless args[:next_page_token].nil? end end # A read alignment describes a linear alignment of a string of DNA to a # reference sequence, in addition to metadata about the fragment (the molecule # of DNA sequenced) and the read (the bases which were read by the sequencer). A # read is equivalent to a line in a SAM file. A read belongs to exactly one read # group and exactly one read group set. For more genomics resource definitions, # see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/ # fundamentals-of-google-genomics) ### Reverse-stranded reads Mapped reads ( # reads having a non-null `alignment`) can be aligned to either the forward or # the reverse strand of their associated reference. Strandedness of a mapped # read is encoded by `alignment.position.reverseStrand`. If we consider the # reference to be a forward-stranded coordinate space of `[0, reference.length)` # with `0` as the left-most position and `reference.length` as the right-most # position, reads are always aligned left to right. That is, `alignment.position. # position` always refers to the left-most reference coordinate and `alignment. # cigar` describes the alignment of this read to the reference from left to # right. All per-base fields such as `alignedSequence` and `alignedQuality` # share this same left-to-right orientation; this is true of reads which are # aligned to either strand. For reverse-stranded reads, this means that ` # alignedSequence` is the reverse complement of the bases that were originally # reported by the sequencing machine. ### Generating a reference-aligned # sequence string When interacting with mapped reads, it's often useful to # produce a string representing the local alignment of the read to reference. # The following pseudocode demonstrates one way of doing this: out = "" offset = # 0 for c in read.alignment.cigar ` switch c.operation ` case "ALIGNMENT_MATCH", # "SEQUENCE_MATCH", "SEQUENCE_MISMATCH": out += read.alignedSequence[offset: # offset+c.operationLength] offset += c.operationLength break case "CLIP_SOFT", " # INSERT": offset += c.operationLength break case "PAD": out += repeat("*", c. # operationLength) break case "DELETE": out += repeat("-", c.operationLength) # break case "SKIP": out += repeat(" ", c.operationLength) break case "CLIP_HARD" # : break ` ` return out ### Converting to SAM's CIGAR string The following # pseudocode generates a SAM CIGAR string from the `cigar` field. Note that this # is a lossy conversion (`cigar.referenceSequence` is lost). cigarMap = ` " # ALIGNMENT_MATCH": "M", "INSERT": "I", "DELETE": "D", "SKIP": "N", "CLIP_SOFT": # "S", "CLIP_HARD": "H", "PAD": "P", "SEQUENCE_MATCH": "=", "SEQUENCE_MISMATCH": # "X", ` cigarStr = "" for c in read.alignment.cigar ` cigarStr += c. # operationLength + cigarMap[c.operation] ` return cigarStr class Read include Google::Apis::Core::Hashable # The server-generated read ID, unique across all reads. This is different from # the `fragmentName`. # Corresponds to the JSON property `id` # @return [String] attr_accessor :id # The ID of the read group this read belongs to. A read belongs to exactly one # read group. This is a server-generated ID which is distinct from SAM's RG tag ( # for that value, see ReadGroup.name). # Corresponds to the JSON property `readGroupId` # @return [String] attr_accessor :read_group_id # The ID of the read group set this read belongs to. A read belongs to exactly # one read group set. # Corresponds to the JSON property `readGroupSetId` # @return [String] attr_accessor :read_group_set_id # The fragment name. Equivalent to QNAME (query template name) in SAM. # Corresponds to the JSON property `fragmentName` # @return [String] attr_accessor :fragment_name # The orientation and the distance between reads from the fragment are # consistent with the sequencing protocol (SAM flag 0x2). # Corresponds to the JSON property `properPlacement` # @return [Boolean] attr_accessor :proper_placement alias_method :proper_placement?, :proper_placement # The fragment is a PCR or optical duplicate (SAM flag 0x400). # Corresponds to the JSON property `duplicateFragment` # @return [Boolean] attr_accessor :duplicate_fragment alias_method :duplicate_fragment?, :duplicate_fragment # The observed length of the fragment, equivalent to TLEN in SAM. # Corresponds to the JSON property `fragmentLength` # @return [Fixnum] attr_accessor :fragment_length # The read number in sequencing. 0-based and less than numberReads. This field # replaces SAM flag 0x40 and 0x80. # Corresponds to the JSON property `readNumber` # @return [Fixnum] attr_accessor :read_number # The number of reads in the fragment (extension to SAM flag 0x1). # Corresponds to the JSON property `numberReads` # @return [Fixnum] attr_accessor :number_reads # Whether this read did not pass filters, such as platform or vendor quality # controls (SAM flag 0x200). # Corresponds to the JSON property `failedVendorQualityChecks` # @return [Boolean] attr_accessor :failed_vendor_quality_checks alias_method :failed_vendor_quality_checks?, :failed_vendor_quality_checks # A linear alignment can be represented by one CIGAR string. Describes the # mapped position and local alignment of the read to the reference. # Corresponds to the JSON property `alignment` # @return [Google::Apis::GenomicsV1::LinearAlignment] attr_accessor :alignment # Whether this alignment is secondary. Equivalent to SAM flag 0x100. A secondary # alignment represents an alternative to the primary alignment for this read. # Aligners may return secondary alignments if a read can map ambiguously to # multiple coordinates in the genome. By convention, each read has one and only # one alignment where both `secondaryAlignment` and `supplementaryAlignment` are # false. # Corresponds to the JSON property `secondaryAlignment` # @return [Boolean] attr_accessor :secondary_alignment alias_method :secondary_alignment?, :secondary_alignment # Whether this alignment is supplementary. Equivalent to SAM flag 0x800. # Supplementary alignments are used in the representation of a chimeric # alignment. In a chimeric alignment, a read is split into multiple linear # alignments that map to different reference contigs. The first linear alignment # in the read will be designated as the representative alignment; the remaining # linear alignments will be designated as supplementary alignments. These # alignments may have different mapping quality scores. In each linear alignment # in a chimeric alignment, the read will be hard clipped. The `alignedSequence` # and `alignedQuality` fields in the alignment record will only represent the # bases for its respective linear alignment. # Corresponds to the JSON property `supplementaryAlignment` # @return [Boolean] attr_accessor :supplementary_alignment alias_method :supplementary_alignment?, :supplementary_alignment # The bases of the read sequence contained in this alignment record, **without # CIGAR operations applied** (equivalent to SEQ in SAM). `alignedSequence` and ` # alignedQuality` may be shorter than the full read sequence and quality. This # will occur if the alignment is part of a chimeric alignment, or if the read # was trimmed. When this occurs, the CIGAR for this read will begin/end with a # hard clip operator that will indicate the length of the excised sequence. # Corresponds to the JSON property `alignedSequence` # @return [String] attr_accessor :aligned_sequence # The quality of the read sequence contained in this alignment record ( # equivalent to QUAL in SAM). `alignedSequence` and `alignedQuality` may be # shorter than the full read sequence and quality. This will occur if the # alignment is part of a chimeric alignment, or if the read was trimmed. When # this occurs, the CIGAR for this read will begin/end with a hard clip operator # that will indicate the length of the excised sequence. # Corresponds to the JSON property `alignedQuality` # @return [Array] attr_accessor :aligned_quality # An abstraction for referring to a genomic position, in relation to some # already known reference. For now, represents a genomic position as a reference # name, a base number on that reference (0-based), and a determination of # forward or reverse strand. # Corresponds to the JSON property `nextMatePosition` # @return [Google::Apis::GenomicsV1::Position] attr_accessor :next_mate_position # A map of additional read alignment information. This must be of the form map ( # string key mapping to a list of string values). # Corresponds to the JSON property `info` # @return [Hash>] attr_accessor :info def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @id = args[:id] unless args[:id].nil? @read_group_id = args[:read_group_id] unless args[:read_group_id].nil? @read_group_set_id = args[:read_group_set_id] unless args[:read_group_set_id].nil? @fragment_name = args[:fragment_name] unless args[:fragment_name].nil? @proper_placement = args[:proper_placement] unless args[:proper_placement].nil? @duplicate_fragment = args[:duplicate_fragment] unless args[:duplicate_fragment].nil? @fragment_length = args[:fragment_length] unless args[:fragment_length].nil? @read_number = args[:read_number] unless args[:read_number].nil? @number_reads = args[:number_reads] unless args[:number_reads].nil? @failed_vendor_quality_checks = args[:failed_vendor_quality_checks] unless args[:failed_vendor_quality_checks].nil? @alignment = args[:alignment] unless args[:alignment].nil? @secondary_alignment = args[:secondary_alignment] unless args[:secondary_alignment].nil? @supplementary_alignment = args[:supplementary_alignment] unless args[:supplementary_alignment].nil? @aligned_sequence = args[:aligned_sequence] unless args[:aligned_sequence].nil? @aligned_quality = args[:aligned_quality] unless args[:aligned_quality].nil? @next_mate_position = args[:next_mate_position] unless args[:next_mate_position].nil? @info = args[:info] unless args[:info].nil? end end # A linear alignment can be represented by one CIGAR string. Describes the # mapped position and local alignment of the read to the reference. class LinearAlignment include Google::Apis::Core::Hashable # An abstraction for referring to a genomic position, in relation to some # already known reference. For now, represents a genomic position as a reference # name, a base number on that reference (0-based), and a determination of # forward or reverse strand. # Corresponds to the JSON property `position` # @return [Google::Apis::GenomicsV1::Position] attr_accessor :position # The mapping quality of this alignment. Represents how likely the read maps to # this position as opposed to other locations. Specifically, this is -10 log10 # Pr(mapping position is wrong), rounded to the nearest integer. # Corresponds to the JSON property `mappingQuality` # @return [Fixnum] attr_accessor :mapping_quality # Represents the local alignment of this sequence (alignment matches, indels, # etc) against the reference. # Corresponds to the JSON property `cigar` # @return [Array] attr_accessor :cigar def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @position = args[:position] unless args[:position].nil? @mapping_quality = args[:mapping_quality] unless args[:mapping_quality].nil? @cigar = args[:cigar] unless args[:cigar].nil? end end # An abstraction for referring to a genomic position, in relation to some # already known reference. For now, represents a genomic position as a reference # name, a base number on that reference (0-based), and a determination of # forward or reverse strand. class Position include Google::Apis::Core::Hashable # The name of the reference in whatever reference set is being used. # Corresponds to the JSON property `referenceName` # @return [String] attr_accessor :reference_name # The 0-based offset from the start of the forward strand for that reference. # Corresponds to the JSON property `position` # @return [String] attr_accessor :position # Whether this position is on the reverse strand, as opposed to the forward # strand. # Corresponds to the JSON property `reverseStrand` # @return [Boolean] attr_accessor :reverse_strand alias_method :reverse_strand?, :reverse_strand def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @reference_name = args[:reference_name] unless args[:reference_name].nil? @position = args[:position] unless args[:position].nil? @reverse_strand = args[:reverse_strand] unless args[:reverse_strand].nil? end end # A single CIGAR operation. class CigarUnit include Google::Apis::Core::Hashable # # Corresponds to the JSON property `operation` # @return [String] attr_accessor :operation # The number of genomic bases that the operation runs for. Required. # Corresponds to the JSON property `operationLength` # @return [String] attr_accessor :operation_length # `referenceSequence` is only used at mismatches (`SEQUENCE_MISMATCH`) and # deletions (`DELETE`). Filling this field replaces SAM's MD tag. If the # relevant information is not available, this field is unset. # Corresponds to the JSON property `referenceSequence` # @return [String] attr_accessor :reference_sequence def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @operation = args[:operation] unless args[:operation].nil? @operation_length = args[:operation_length] unless args[:operation_length].nil? @reference_sequence = args[:reference_sequence] unless args[:reference_sequence].nil? end end # The stream reads request. class StreamReadsRequest include Google::Apis::Core::Hashable # The Google Developers Console project ID or number which will be billed for # this access. The caller must have WRITE access to this project. Required. # Corresponds to the JSON property `projectId` # @return [String] attr_accessor :project_id # The ID of the read group set from which to stream reads. # Corresponds to the JSON property `readGroupSetId` # @return [String] attr_accessor :read_group_set_id # The reference sequence name, for example `chr1`, `1`, or `chrX`. If set to *, # only unmapped reads are returned. # Corresponds to the JSON property `referenceName` # @return [String] attr_accessor :reference_name # The start position of the range on the reference, 0-based inclusive. If # specified, `referenceName` must also be specified. # Corresponds to the JSON property `start` # @return [String] attr_accessor :start # The end position of the range on the reference, 0-based exclusive. If # specified, `referenceName` must also be specified. # Corresponds to the JSON property `end` # @return [String] attr_accessor :end def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @project_id = args[:project_id] unless args[:project_id].nil? @read_group_set_id = args[:read_group_set_id] unless args[:read_group_set_id].nil? @reference_name = args[:reference_name] unless args[:reference_name].nil? @start = args[:start] unless args[:start].nil? @end = args[:end] unless args[:end].nil? end end # class StreamReadsResponse include Google::Apis::Core::Hashable # # Corresponds to the JSON property `alignments` # @return [Array] attr_accessor :alignments def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @alignments = args[:alignments] unless args[:alignments].nil? end end # class SearchReferenceSetsRequest include Google::Apis::Core::Hashable # If present, return reference sets for which the md5checksum matches exactly. # Corresponds to the JSON property `md5checksums` # @return [Array] attr_accessor :md5checksums # If present, return reference sets for which a prefix of any of # sourceAccessions match any of these strings. Accession numbers typically have # a main number and a version, for example `NC_000001.11`. # Corresponds to the JSON property `accessions` # @return [Array] attr_accessor :accessions # If present, return reference sets for which a substring of their `assemblyId` # matches this string (case insensitive). # Corresponds to the JSON property `assemblyId` # @return [String] attr_accessor :assembly_id # The continuation token, which is used to page through large result sets. To # get the next page of results, set this parameter to the value of ` # nextPageToken` from the previous response. # Corresponds to the JSON property `pageToken` # @return [String] attr_accessor :page_token # The maximum number of results to return in a single page. If unspecified, # defaults to 1024. The maximum value is 4096. # Corresponds to the JSON property `pageSize` # @return [Fixnum] attr_accessor :page_size def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @md5checksums = args[:md5checksums] unless args[:md5checksums].nil? @accessions = args[:accessions] unless args[:accessions].nil? @assembly_id = args[:assembly_id] unless args[:assembly_id].nil? @page_token = args[:page_token] unless args[:page_token].nil? @page_size = args[:page_size] unless args[:page_size].nil? end end # class SearchReferenceSetsResponse include Google::Apis::Core::Hashable # The matching references sets. # Corresponds to the JSON property `referenceSets` # @return [Array] attr_accessor :reference_sets # The continuation token, which is used to page through large result sets. # Provide this value in a subsequent request to return the next page of results. # This field will be empty if there aren't any additional results. # Corresponds to the JSON property `nextPageToken` # @return [String] attr_accessor :next_page_token def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @reference_sets = args[:reference_sets] unless args[:reference_sets].nil? @next_page_token = args[:next_page_token] unless args[:next_page_token].nil? end end # A reference set is a set of references which typically comprise a reference # assembly for a species, such as `GRCh38` which is representative of the human # genome. A reference set defines a common coordinate space for comparing # reference-aligned experimental data. A reference set contains 1 or more # references. For more genomics resource definitions, see [Fundamentals of # Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google- # genomics) class ReferenceSet include Google::Apis::Core::Hashable # The server-generated reference set ID, unique across all reference sets. # Corresponds to the JSON property `id` # @return [String] attr_accessor :id # The IDs of the reference objects that are part of this set. `Reference. # md5checksum` must be unique within this set. # Corresponds to the JSON property `referenceIds` # @return [Array] attr_accessor :reference_ids # Order-independent MD5 checksum which identifies this reference set. The # checksum is computed by sorting all lower case hexidecimal string `reference. # md5checksum` (for all reference in this set) in ascending lexicographic order, # concatenating, and taking the MD5 of that value. The resulting value is # represented in lower case hexadecimal format. # Corresponds to the JSON property `md5checksum` # @return [String] attr_accessor :md5checksum # ID from http://www.ncbi.nlm.nih.gov/taxonomy (for example, 9606 for human) # indicating the species which this reference set is intended to model. Note # that contained references may specify a different `ncbiTaxonId`, as assemblies # may contain reference sequences which do not belong to the modeled species, # for example EBV in a human reference genome. # Corresponds to the JSON property `ncbiTaxonId` # @return [Fixnum] attr_accessor :ncbi_taxon_id # Free text description of this reference set. # Corresponds to the JSON property `description` # @return [String] attr_accessor :description # Public id of this reference set, such as `GRCh37`. # Corresponds to the JSON property `assemblyId` # @return [String] attr_accessor :assembly_id # The URI from which the references were obtained. # Corresponds to the JSON property `sourceUri` # @return [String] attr_accessor :source_uri # All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with # a version number, for example `NC_000001.11`. # Corresponds to the JSON property `sourceAccessions` # @return [Array] attr_accessor :source_accessions def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @id = args[:id] unless args[:id].nil? @reference_ids = args[:reference_ids] unless args[:reference_ids].nil? @md5checksum = args[:md5checksum] unless args[:md5checksum].nil? @ncbi_taxon_id = args[:ncbi_taxon_id] unless args[:ncbi_taxon_id].nil? @description = args[:description] unless args[:description].nil? @assembly_id = args[:assembly_id] unless args[:assembly_id].nil? @source_uri = args[:source_uri] unless args[:source_uri].nil? @source_accessions = args[:source_accessions] unless args[:source_accessions].nil? end end # class SearchReferencesRequest include Google::Apis::Core::Hashable # If present, return references for which the md5checksum matches exactly. # Corresponds to the JSON property `md5checksums` # @return [Array] attr_accessor :md5checksums # If present, return references for which a prefix of any of sourceAccessions # match any of these strings. Accession numbers typically have a main number and # a version, for example `GCF_000001405.26`. # Corresponds to the JSON property `accessions` # @return [Array] attr_accessor :accessions # If present, return only references which belong to this reference set. # Corresponds to the JSON property `referenceSetId` # @return [String] attr_accessor :reference_set_id # The continuation token, which is used to page through large result sets. To # get the next page of results, set this parameter to the value of ` # nextPageToken` from the previous response. # Corresponds to the JSON property `pageToken` # @return [String] attr_accessor :page_token # The maximum number of results to return in a single page. If unspecified, # defaults to 1024. The maximum value is 4096. # Corresponds to the JSON property `pageSize` # @return [Fixnum] attr_accessor :page_size def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @md5checksums = args[:md5checksums] unless args[:md5checksums].nil? @accessions = args[:accessions] unless args[:accessions].nil? @reference_set_id = args[:reference_set_id] unless args[:reference_set_id].nil? @page_token = args[:page_token] unless args[:page_token].nil? @page_size = args[:page_size] unless args[:page_size].nil? end end # class SearchReferencesResponse include Google::Apis::Core::Hashable # The matching references. # Corresponds to the JSON property `references` # @return [Array] attr_accessor :references # The continuation token, which is used to page through large result sets. # Provide this value in a subsequent request to return the next page of results. # This field will be empty if there aren't any additional results. # Corresponds to the JSON property `nextPageToken` # @return [String] attr_accessor :next_page_token def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @references = args[:references] unless args[:references].nil? @next_page_token = args[:next_page_token] unless args[:next_page_token].nil? end end # A reference is a canonical assembled DNA sequence, intended to act as a # reference coordinate space for other genomic annotations. A single reference # might represent the human chromosome 1 or mitochandrial DNA, for instance. A # reference belongs to one or more reference sets. For more genomics resource # definitions, see [Fundamentals of Google Genomics](https://cloud.google.com/ # genomics/fundamentals-of-google-genomics) class Reference include Google::Apis::Core::Hashable # The server-generated reference ID, unique across all references. # Corresponds to the JSON property `id` # @return [String] attr_accessor :id # The length of this reference's sequence. # Corresponds to the JSON property `length` # @return [String] attr_accessor :length # MD5 of the upper-case sequence excluding all whitespace characters (this is # equivalent to SQ:M5 in SAM). This value is represented in lower case # hexadecimal format. # Corresponds to the JSON property `md5checksum` # @return [String] attr_accessor :md5checksum # The name of this reference, for example `22`. # Corresponds to the JSON property `name` # @return [String] attr_accessor :name # The URI from which the sequence was obtained. Typically specifies a FASTA # format file. # Corresponds to the JSON property `sourceUri` # @return [String] attr_accessor :source_uri # All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with # a version number, for example `GCF_000001405.26`. # Corresponds to the JSON property `sourceAccessions` # @return [Array] attr_accessor :source_accessions # ID from http://www.ncbi.nlm.nih.gov/taxonomy. For example, 9606 for human. # Corresponds to the JSON property `ncbiTaxonId` # @return [Fixnum] attr_accessor :ncbi_taxon_id def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @id = args[:id] unless args[:id].nil? @length = args[:length] unless args[:length].nil? @md5checksum = args[:md5checksum] unless args[:md5checksum].nil? @name = args[:name] unless args[:name].nil? @source_uri = args[:source_uri] unless args[:source_uri].nil? @source_accessions = args[:source_accessions] unless args[:source_accessions].nil? @ncbi_taxon_id = args[:ncbi_taxon_id] unless args[:ncbi_taxon_id].nil? end end # class ListBasesResponse include Google::Apis::Core::Hashable # The offset position (0-based) of the given `sequence` from the start of this ` # Reference`. This value will differ for each page in a paginated request. # Corresponds to the JSON property `offset` # @return [String] attr_accessor :offset # A substring of the bases that make up this reference. # Corresponds to the JSON property `sequence` # @return [String] attr_accessor :sequence # The continuation token, which is used to page through large result sets. # Provide this value in a subsequent request to return the next page of results. # This field will be empty if there aren't any additional results. # Corresponds to the JSON property `nextPageToken` # @return [String] attr_accessor :next_page_token def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @offset = args[:offset] unless args[:offset].nil? @sequence = args[:sequence] unless args[:sequence].nil? @next_page_token = args[:next_page_token] unless args[:next_page_token].nil? end end # The variant data import request. class ImportVariantsRequest include Google::Apis::Core::Hashable # Required. The variant set to which variant data should be imported. # Corresponds to the JSON property `variantSetId` # @return [String] attr_accessor :variant_set_id # A list of URIs referencing variant files in Google Cloud Storage. URIs can # include wildcards [as described here](https://cloud.google.com/storage/docs/ # gsutil/addlhelp/WildcardNames). Note that recursive wildcards ('**') are not # supported. # Corresponds to the JSON property `sourceUris` # @return [Array] attr_accessor :source_uris # The format of the variant data being imported. If unspecified, defaults to to ` # VCF`. # Corresponds to the JSON property `format` # @return [String] attr_accessor :format # Convert reference names to the canonical representation. hg19 haploytypes ( # those reference names containing "_hap") are not modified in any way. All # other reference names are modified according to the following rules: The # reference name is capitalized. The "chr" prefix is dropped for all autosomes # and sex chromsomes. For example "chr17" becomes "17" and "chrX" becomes "X". # All mitochondrial chromosomes ("chrM", "chrMT", etc) become "MT". # Corresponds to the JSON property `normalizeReferenceNames` # @return [Boolean] attr_accessor :normalize_reference_names alias_method :normalize_reference_names?, :normalize_reference_names def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @variant_set_id = args[:variant_set_id] unless args[:variant_set_id].nil? @source_uris = args[:source_uris] unless args[:source_uris].nil? @format = args[:format] unless args[:format].nil? @normalize_reference_names = args[:normalize_reference_names] unless args[:normalize_reference_names].nil? end end # A variant set is a collection of call sets and variants. It contains summary # statistics of those contents. A variant set belongs to a dataset. For more # genomics resource definitions, see [Fundamentals of Google Genomics](https:// # cloud.google.com/genomics/fundamentals-of-google-genomics) class VariantSet include Google::Apis::Core::Hashable # The dataset to which this variant set belongs. # Corresponds to the JSON property `datasetId` # @return [String] attr_accessor :dataset_id # The server-generated variant set ID, unique across all variant sets. # Corresponds to the JSON property `id` # @return [String] attr_accessor :id # The reference set to which the variant set is mapped. The reference set # describes the alignment provenance of the variant set, while the ` # referenceBounds` describe the shape of the actual variant data. The reference # set's reference names are a superset of those found in the `referenceBounds`. # For example, given a variant set that is mapped to the GRCh38 reference set # and contains a single variant on reference 'X', `referenceBounds` would # contain only an entry for 'X', while the associated reference set enumerates # all possible references: '1', '2', 'X', 'Y', 'MT', etc. # Corresponds to the JSON property `referenceSetId` # @return [String] attr_accessor :reference_set_id # A list of all references used by the variants in a variant set with associated # coordinate upper bounds for each one. # Corresponds to the JSON property `referenceBounds` # @return [Array] attr_accessor :reference_bounds # The metadata associated with this variant set. # Corresponds to the JSON property `metadata` # @return [Array] attr_accessor :metadata def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @dataset_id = args[:dataset_id] unless args[:dataset_id].nil? @id = args[:id] unless args[:id].nil? @reference_set_id = args[:reference_set_id] unless args[:reference_set_id].nil? @reference_bounds = args[:reference_bounds] unless args[:reference_bounds].nil? @metadata = args[:metadata] unless args[:metadata].nil? end end # ReferenceBound records an upper bound for the starting coordinate of variants # in a particular reference. class ReferenceBound include Google::Apis::Core::Hashable # The name of the reference associated with this ReferenceBound. # Corresponds to the JSON property `referenceName` # @return [String] attr_accessor :reference_name # An upper bound (inclusive) on the starting coordinate of any variant in the # reference sequence. # Corresponds to the JSON property `upperBound` # @return [String] attr_accessor :upper_bound def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @reference_name = args[:reference_name] unless args[:reference_name].nil? @upper_bound = args[:upper_bound] unless args[:upper_bound].nil? end end # Metadata describes a single piece of variant call metadata. These data include # a top level key and either a single value string (value) or a list of key- # value pairs (info.) Value and info are mutually exclusive. class VariantSetMetadata include Google::Apis::Core::Hashable # The top-level key. # Corresponds to the JSON property `key` # @return [String] attr_accessor :key # The value field for simple metadata # Corresponds to the JSON property `value` # @return [String] attr_accessor :value # User-provided ID field, not enforced by this API. Two or more pieces of # structured metadata with identical id and key fields are considered equivalent. # Corresponds to the JSON property `id` # @return [String] attr_accessor :id # The type of data. Possible types include: Integer, Float, Flag, Character, and # String. # Corresponds to the JSON property `type` # @return [String] attr_accessor :type # The number of values that can be included in a field described by this # metadata. # Corresponds to the JSON property `number` # @return [String] attr_accessor :number # A textual description of this metadata. # Corresponds to the JSON property `description` # @return [String] attr_accessor :description # Remaining structured metadata key-value pairs. This must be of the form map ( # string key mapping to a list of string values). # Corresponds to the JSON property `info` # @return [Hash>] attr_accessor :info def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @key = args[:key] unless args[:key].nil? @value = args[:value] unless args[:value].nil? @id = args[:id] unless args[:id].nil? @type = args[:type] unless args[:type].nil? @number = args[:number] unless args[:number].nil? @description = args[:description] unless args[:description].nil? @info = args[:info] unless args[:info].nil? end end # The variant data export request. class ExportVariantSetRequest include Google::Apis::Core::Hashable # If provided, only variant call information from the specified call sets will # be exported. By default all variant calls are exported. # Corresponds to the JSON property `callSetIds` # @return [Array] attr_accessor :call_set_ids # Required. The Google Cloud project ID that owns the destination BigQuery # dataset. The caller must have WRITE access to this project. This project will # also own the resulting export job. # Corresponds to the JSON property `projectId` # @return [String] attr_accessor :project_id # The format for the exported data. # Corresponds to the JSON property `format` # @return [String] attr_accessor :format # Required. The BigQuery dataset to export data to. This dataset must already # exist. Note that this is distinct from the Genomics concept of "dataset". # Corresponds to the JSON property `bigqueryDataset` # @return [String] attr_accessor :bigquery_dataset # Required. The BigQuery table to export data to. If the table doesn't exist, it # will be created. If it already exists, it will be overwritten. # Corresponds to the JSON property `bigqueryTable` # @return [String] attr_accessor :bigquery_table def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @call_set_ids = args[:call_set_ids] unless args[:call_set_ids].nil? @project_id = args[:project_id] unless args[:project_id].nil? @format = args[:format] unless args[:format].nil? @bigquery_dataset = args[:bigquery_dataset] unless args[:bigquery_dataset].nil? @bigquery_table = args[:bigquery_table] unless args[:bigquery_table].nil? end end # The search variant sets request. class SearchVariantSetsRequest include Google::Apis::Core::Hashable # Exactly one dataset ID must be provided here. Only variant sets which belong # to this dataset will be returned. # Corresponds to the JSON property `datasetIds` # @return [Array] attr_accessor :dataset_ids # The continuation token, which is used to page through large result sets. To # get the next page of results, set this parameter to the value of ` # nextPageToken` from the previous response. # Corresponds to the JSON property `pageToken` # @return [String] attr_accessor :page_token # The maximum number of results to return in a single page. If unspecified, # defaults to 1024. # Corresponds to the JSON property `pageSize` # @return [Fixnum] attr_accessor :page_size def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @dataset_ids = args[:dataset_ids] unless args[:dataset_ids].nil? @page_token = args[:page_token] unless args[:page_token].nil? @page_size = args[:page_size] unless args[:page_size].nil? end end # The search variant sets response. class SearchVariantSetsResponse include Google::Apis::Core::Hashable # The variant sets belonging to the requested dataset. # Corresponds to the JSON property `variantSets` # @return [Array] attr_accessor :variant_sets # The continuation token, which is used to page through large result sets. # Provide this value in a subsequent request to return the next page of results. # This field will be empty if there aren't any additional results. # Corresponds to the JSON property `nextPageToken` # @return [String] attr_accessor :next_page_token def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @variant_sets = args[:variant_sets] unless args[:variant_sets].nil? @next_page_token = args[:next_page_token] unless args[:next_page_token].nil? end end # The variant search request. class SearchVariantsRequest include Google::Apis::Core::Hashable # At most one variant set ID must be provided. Only variants from this variant # set will be returned. If omitted, a call set id must be included in the # request. # Corresponds to the JSON property `variantSetIds` # @return [Array] attr_accessor :variant_set_ids # Only return variants which have exactly this name. # Corresponds to the JSON property `variantName` # @return [String] attr_accessor :variant_name # Only return variant calls which belong to call sets with these ids. Leaving # this blank returns all variant calls. If a variant has no calls belonging to # any of these call sets, it won't be returned at all. Currently, variants with # no calls from any call set will never be returned. # Corresponds to the JSON property `callSetIds` # @return [Array] attr_accessor :call_set_ids # Required. Only return variants in this reference sequence. # Corresponds to the JSON property `referenceName` # @return [String] attr_accessor :reference_name # The beginning of the window (0-based, inclusive) for which overlapping # variants should be returned. If unspecified, defaults to 0. # Corresponds to the JSON property `start` # @return [String] attr_accessor :start # The end of the window, 0-based exclusive. If unspecified or 0, defaults to the # length of the reference. # Corresponds to the JSON property `end` # @return [String] attr_accessor :end # The continuation token, which is used to page through large result sets. To # get the next page of results, set this parameter to the value of ` # nextPageToken` from the previous response. # Corresponds to the JSON property `pageToken` # @return [String] attr_accessor :page_token # The maximum number of variants to return in a single page. If unspecified, # defaults to 5000. The maximum value is 10000. # Corresponds to the JSON property `pageSize` # @return [Fixnum] attr_accessor :page_size # The maximum number of calls to return in a single page. Note that this limit # may be exceeded; at least one variant is always returned per page, even if it # has more calls than this limit. If unspecified, defaults to 5000. The maximum # value is 10000. # Corresponds to the JSON property `maxCalls` # @return [Fixnum] attr_accessor :max_calls def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @variant_set_ids = args[:variant_set_ids] unless args[:variant_set_ids].nil? @variant_name = args[:variant_name] unless args[:variant_name].nil? @call_set_ids = args[:call_set_ids] unless args[:call_set_ids].nil? @reference_name = args[:reference_name] unless args[:reference_name].nil? @start = args[:start] unless args[:start].nil? @end = args[:end] unless args[:end].nil? @page_token = args[:page_token] unless args[:page_token].nil? @page_size = args[:page_size] unless args[:page_size].nil? @max_calls = args[:max_calls] unless args[:max_calls].nil? end end # The variant search response. class SearchVariantsResponse include Google::Apis::Core::Hashable # The list of matching Variants. # Corresponds to the JSON property `variants` # @return [Array] attr_accessor :variants # The continuation token, which is used to page through large result sets. # Provide this value in a subsequent request to return the next page of results. # This field will be empty if there aren't any additional results. # Corresponds to the JSON property `nextPageToken` # @return [String] attr_accessor :next_page_token def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @variants = args[:variants] unless args[:variants].nil? @next_page_token = args[:next_page_token] unless args[:next_page_token].nil? end end # A variant represents a change in DNA sequence relative to a reference sequence. # For example, a variant could represent a SNP or an insertion. Variants belong # to a variant set. For more genomics resource definitions, see [Fundamentals of # Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google- # genomics) Each of the calls on a variant represent a determination of genotype # with respect to that variant. For example, a call might assign probability of # 0.32 to the occurrence of a SNP named rs1234 in a sample named NA12345. A call # belongs to a call set, which contains related calls typically from one sample. class Variant include Google::Apis::Core::Hashable # The ID of the variant set this variant belongs to. # Corresponds to the JSON property `variantSetId` # @return [String] attr_accessor :variant_set_id # The server-generated variant ID, unique across all variants. # Corresponds to the JSON property `id` # @return [String] attr_accessor :id # Names for the variant, for example a RefSNP ID. # Corresponds to the JSON property `names` # @return [Array] attr_accessor :names # The date this variant was created, in milliseconds from the epoch. # Corresponds to the JSON property `created` # @return [String] attr_accessor :created # The reference on which this variant occurs. (such as `chr20` or `X`) # Corresponds to the JSON property `referenceName` # @return [String] attr_accessor :reference_name # The position at which this variant occurs (0-based). This corresponds to the # first base of the string of reference bases. # Corresponds to the JSON property `start` # @return [String] attr_accessor :start # The end position (0-based) of this variant. This corresponds to the first base # after the last base in the reference allele. So, the length of the reference # allele is (end - start). This is useful for variants that don't explicitly # give alternate bases, for example large deletions. # Corresponds to the JSON property `end` # @return [String] attr_accessor :end # The reference bases for this variant. They start at the given position. # Corresponds to the JSON property `referenceBases` # @return [String] attr_accessor :reference_bases # The bases that appear instead of the reference bases. # Corresponds to the JSON property `alternateBases` # @return [Array] attr_accessor :alternate_bases # A measure of how likely this variant is to be real. A higher value is better. # Corresponds to the JSON property `quality` # @return [Float] attr_accessor :quality # A list of filters (normally quality filters) this variant has failed. `PASS` # indicates this variant has passed all filters. # Corresponds to the JSON property `filter` # @return [Array] attr_accessor :filter # A map of additional variant information. This must be of the form map (string # key mapping to a list of string values). # Corresponds to the JSON property `info` # @return [Hash>] attr_accessor :info # The variant calls for this particular variant. Each one represents the # determination of genotype with respect to this variant. # Corresponds to the JSON property `calls` # @return [Array] attr_accessor :calls def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @variant_set_id = args[:variant_set_id] unless args[:variant_set_id].nil? @id = args[:id] unless args[:id].nil? @names = args[:names] unless args[:names].nil? @created = args[:created] unless args[:created].nil? @reference_name = args[:reference_name] unless args[:reference_name].nil? @start = args[:start] unless args[:start].nil? @end = args[:end] unless args[:end].nil? @reference_bases = args[:reference_bases] unless args[:reference_bases].nil? @alternate_bases = args[:alternate_bases] unless args[:alternate_bases].nil? @quality = args[:quality] unless args[:quality].nil? @filter = args[:filter] unless args[:filter].nil? @info = args[:info] unless args[:info].nil? @calls = args[:calls] unless args[:calls].nil? end end # A call represents the determination of genotype with respect to a particular # variant. It may include associated information such as quality and phasing. # For example, a call might assign a probability of 0.32 to the occurrence of a # SNP named rs1234 in a call set with the name NA12345. class VariantCall include Google::Apis::Core::Hashable # The ID of the call set this variant call belongs to. # Corresponds to the JSON property `callSetId` # @return [String] attr_accessor :call_set_id # The name of the call set this variant call belongs to. # Corresponds to the JSON property `callSetName` # @return [String] attr_accessor :call_set_name # The genotype of this variant call. Each value represents either the value of # the `referenceBases` field or a 1-based index into `alternateBases`. If a # variant had a `referenceBases` value of `T` and an `alternateBases` value of `[ # "A", "C"]`, and the `genotype` was `[2, 1]`, that would mean the call # represented the heterozygous value `CA` for this variant. If the `genotype` # was instead `[0, 1]`, the represented value would be `TA`. Ordering of the # genotype values is important if the `phaseset` is present. If a genotype is # not called (that is, a `.` is present in the GT string) -1 is returned. # Corresponds to the JSON property `genotype` # @return [Array] attr_accessor :genotype # If this field is present, this variant call's genotype ordering implies the # phase of the bases and is consistent with any other variant calls in the same # reference sequence which have the same phaseset value. When importing data # from VCF, if the genotype data was phased but no phase set was specified this # field will be set to `*`. # Corresponds to the JSON property `phaseset` # @return [String] attr_accessor :phaseset # The genotype likelihoods for this variant call. Each array entry represents # how likely a specific genotype is for this call. The value ordering is defined # by the GL tag in the VCF spec. If Phred-scaled genotype likelihood scores (PL) # are available and log10(P) genotype likelihood scores (GL) are not, PL scores # are converted to GL scores. If both are available, PL scores are stored in ` # info`. # Corresponds to the JSON property `genotypeLikelihood` # @return [Array] attr_accessor :genotype_likelihood # A map of additional variant call information. This must be of the form map ( # string key mapping to a list of string values). # Corresponds to the JSON property `info` # @return [Hash>] attr_accessor :info def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @call_set_id = args[:call_set_id] unless args[:call_set_id].nil? @call_set_name = args[:call_set_name] unless args[:call_set_name].nil? @genotype = args[:genotype] unless args[:genotype].nil? @phaseset = args[:phaseset] unless args[:phaseset].nil? @genotype_likelihood = args[:genotype_likelihood] unless args[:genotype_likelihood].nil? @info = args[:info] unless args[:info].nil? end end # The call set search request. class SearchCallSetsRequest include Google::Apis::Core::Hashable # Restrict the query to call sets within the given variant sets. At least one ID # must be provided. # Corresponds to the JSON property `variantSetIds` # @return [Array] attr_accessor :variant_set_ids # Only return call sets for which a substring of the name matches this string. # Corresponds to the JSON property `name` # @return [String] attr_accessor :name # The continuation token, which is used to page through large result sets. To # get the next page of results, set this parameter to the value of ` # nextPageToken` from the previous response. # Corresponds to the JSON property `pageToken` # @return [String] attr_accessor :page_token # The maximum number of results to return in a single page. If unspecified, # defaults to 1024. # Corresponds to the JSON property `pageSize` # @return [Fixnum] attr_accessor :page_size def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @variant_set_ids = args[:variant_set_ids] unless args[:variant_set_ids].nil? @name = args[:name] unless args[:name].nil? @page_token = args[:page_token] unless args[:page_token].nil? @page_size = args[:page_size] unless args[:page_size].nil? end end # The call set search response. class SearchCallSetsResponse include Google::Apis::Core::Hashable # The list of matching call sets. # Corresponds to the JSON property `callSets` # @return [Array] attr_accessor :call_sets # The continuation token, which is used to page through large result sets. # Provide this value in a subsequent request to return the next page of results. # This field will be empty if there aren't any additional results. # Corresponds to the JSON property `nextPageToken` # @return [String] attr_accessor :next_page_token def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @call_sets = args[:call_sets] unless args[:call_sets].nil? @next_page_token = args[:next_page_token] unless args[:next_page_token].nil? end end # A call set is a collection of variant calls, typically for one sample. It # belongs to a variant set. For more genomics resource definitions, see [ # Fundamentals of Google Genomics](https://cloud.google.com/genomics/ # fundamentals-of-google-genomics) class CallSet include Google::Apis::Core::Hashable # The server-generated call set ID, unique across all call sets. # Corresponds to the JSON property `id` # @return [String] attr_accessor :id # The call set name. # Corresponds to the JSON property `name` # @return [String] attr_accessor :name # The sample ID this call set corresponds to. # Corresponds to the JSON property `sampleId` # @return [String] attr_accessor :sample_id # The IDs of the variant sets this call set belongs to. This field must have # exactly length one, as a call set belongs to a single variant set. This field # is repeated for compatibility with the [GA4GH 0.5.1 API](https://github.com/ # ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variants.avdl#L76). # Corresponds to the JSON property `variantSetIds` # @return [Array] attr_accessor :variant_set_ids # The date this call set was created in milliseconds from the epoch. # Corresponds to the JSON property `created` # @return [String] attr_accessor :created # A map of additional call set information. This must be of the form map (string # key mapping to a list of string values). # Corresponds to the JSON property `info` # @return [Hash>] attr_accessor :info def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @id = args[:id] unless args[:id].nil? @name = args[:name] unless args[:name].nil? @sample_id = args[:sample_id] unless args[:sample_id].nil? @variant_set_ids = args[:variant_set_ids] unless args[:variant_set_ids].nil? @created = args[:created] unless args[:created].nil? @info = args[:info] unless args[:info].nil? end end # The stream variants request. class StreamVariantsRequest include Google::Apis::Core::Hashable # The Google Developers Console project ID or number which will be billed for # this access. The caller must have WRITE access to this project. Required. # Corresponds to the JSON property `projectId` # @return [String] attr_accessor :project_id # The variant set ID from which to stream variants. # Corresponds to the JSON property `variantSetId` # @return [String] attr_accessor :variant_set_id # Only return variant calls which belong to call sets with these IDs. Leaving # this blank returns all variant calls. # Corresponds to the JSON property `callSetIds` # @return [Array] attr_accessor :call_set_ids # Required. Only return variants in this reference sequence. # Corresponds to the JSON property `referenceName` # @return [String] attr_accessor :reference_name # The beginning of the window (0-based, inclusive) for which overlapping # variants should be returned. # Corresponds to the JSON property `start` # @return [String] attr_accessor :start # The end of the window (0-based, exclusive) for which overlapping variants # should be returned. # Corresponds to the JSON property `end` # @return [String] attr_accessor :end def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @project_id = args[:project_id] unless args[:project_id].nil? @variant_set_id = args[:variant_set_id] unless args[:variant_set_id].nil? @call_set_ids = args[:call_set_ids] unless args[:call_set_ids].nil? @reference_name = args[:reference_name] unless args[:reference_name].nil? @start = args[:start] unless args[:start].nil? @end = args[:end] unless args[:end].nil? end end # class StreamVariantsResponse include Google::Apis::Core::Hashable # # Corresponds to the JSON property `variants` # @return [Array] attr_accessor :variants def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @variants = args[:variants] unless args[:variants].nil? end end # The read group set import response. class ImportReadGroupSetsResponse include Google::Apis::Core::Hashable # IDs of the read group sets that were created. # Corresponds to the JSON property `readGroupSetIds` # @return [Array] attr_accessor :read_group_set_ids def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @read_group_set_ids = args[:read_group_set_ids] unless args[:read_group_set_ids].nil? end end # The variant data import response. class ImportVariantsResponse include Google::Apis::Core::Hashable # IDs of the call sets created during the import. # Corresponds to the JSON property `callSetIds` # @return [Array] attr_accessor :call_set_ids def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @call_set_ids = args[:call_set_ids] unless args[:call_set_ids].nil? end end # Metadata describing an Operation. class OperationMetadata include Google::Apis::Core::Hashable # The Google Cloud Project in which the job is scoped. # Corresponds to the JSON property `projectId` # @return [String] attr_accessor :project_id # The time at which the job was submitted to the Genomics service. # Corresponds to the JSON property `createTime` # @return [String] attr_accessor :create_time # The original request that started the operation. Note that this will be in # current version of the API. If the operation was started with v1beta2 API and # a GetOperation is performed on v1 API, a v1 request will be returned. # Corresponds to the JSON property `request` # @return [Hash] attr_accessor :request # Optional event messages that were generated during the job's execution. This # also contains any warnings that were generated during import or export. # Corresponds to the JSON property `events` # @return [Array] attr_accessor :events def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @project_id = args[:project_id] unless args[:project_id].nil? @create_time = args[:create_time] unless args[:create_time].nil? @request = args[:request] unless args[:request].nil? @events = args[:events] unless args[:events].nil? end end # An event that occurred during an Operation. class OperationEvent include Google::Apis::Core::Hashable # Required description of event. # Corresponds to the JSON property `description` # @return [String] attr_accessor :description def initialize(**args) update!(**args) end # Update properties of this object def update!(**args) @description = args[:description] unless args[:description].nil? end end end end end